Public report of xieguigang/mzkit, published 26 October 2026. It has the same score, grades and number of findings as the full report. The details of security findings (where they are in the code, which known vulnerabilities and which passwords or keys were found) are left out, so nobody can use them against the project.
Public
Executive report Measured under the Code Assurance Index, an open standard for code quality, using its published scoring rules (rubric version 2026.10.5). Watchdog signed this survey and filed it in the standard's public register, where anyone can look it up by its survey ID. Check this survey → Signed and filed in the standard's public register, 26 October 2026, 20:13 UTC · Survey ID cd_c2d988ea76f9430e92db957ca42426e9

xieguigang/mzkit

Measured 26 October 2026, 20:07 UTC, at code version 720f844

Regression: 1 dimension fell since the last survey Code coverage: not measuredTest reliability: not measuredBoundary Type-Coupling: not measured

A regression is a drop of 0.5 points or more in the score, or of 2.5 or more out of 10 in a dimension, since the last survey.

Code coverage is not measured: No coverage collector is wired up.

Test reliability is not measured: No test run produced results.

Boundary Type-Coupling is not measured: Bounded contexts not declared.

CAI score 47out of 100 Weak
CriticalWeakAdequateStrongExemplary
Down 4 since the last survey

The score is built from these lenses. Each lens grades one area of the code, such as how easy it is to change or how well it is protected. The weakest lens counts most, so one weak area pulls the score down instead of being averaged away.

Architecture 98 Exemplary Code Health 79 Adequate Security and Compliance 67 Adequate Maturity 39 Weak Production Readiness 36 Weak

A large codebase: 233,360 lines of product code in 88 projects, tests not counted · Estimated rebuild effort: about 1.3 person-years · Weakest lens: Production Readiness, 36

Findings by how serious they are

121 critical 1247 serious 1135 minor

36 dimensions are left out of the score. For each one, Watchdog either couldn't measure it in this code, or found no evidence of the safeguard it looks for, such as a tested backup restore. They count neither for nor against the score, and Limitations lists each one with its reason.

This survey was produced by

Watchdog
Producer
Canine Development
Analyzer
Watchdog engine 1.0.0
Measured
26 October 2026, 20:07 UTC

A measurement, not a certificate. The Code Assurance Index records a number together with the evidence it was worked out from, so anyone can recalculate it, but it doesn't certify or guarantee the code. The standard was written by Canine Development, which also builds Watchdog. It is open to any tool that implements it, and today Watchdog is the only one that does.

The score is deterministic, which means the same code always gets the same score. Watchdog works it out with tools that follow published rules, and an AI model never decides it, so anyone who applies the same rules to the same code gets the same number. How it is done is explained under Methodology ▸

36of 36 dimensions measured by tools.
2490of 2503 findings point to an exact file and line, so you can open each one in the code. The other 13 concern the repository as a whole, such as missing documentation.
36dimensions across 5 lenses, read from 233,360 lines of product code in 88 projects.
Chapters

Executive summary

xieguigang/mzkit falls short of our standard for production because we found no working pipeline that builds or tests changes to the code and no automated security scanning of the code, its secrets or its dependencies. It scores 47 out of 100 and is rated Weak, and 108 of its 121 critical findings are security problems.

Production Readiness, at 36, is the weakest lens and counts most in the score. The best first step is recording design decisions, worth about 10 points. Adding an automated build and test pipeline would lift Production Readiness itself, worth about 8 points. Raising Production Readiness to 70 would lift the score to about 56.

106 passwords or keys are open to anyone who can read the repository. Two weaknesses in the code could be used by an attacker, and twelve errors are caught and ignored, so failures can go unnoticed. Replacing each exposed password or key, fixing the weaknesses the scanner points to and handling or logging the ignored errors would close these risks.

The product code is 233,360 lines, about €200,000 to rebuild.

Code Health 79 Adequate, capped by Cyclomatic Complexity and Cognitive Complexity Architecture 98 ★ Exemplary Maturity 39 Weak, capped by Knowledge Freshness and Architecture documentation Production Readiness 36 Weak, capped by CI/CD gates and Security & performance tooling Security and Compliance 67 Adequate, capped by Secrets (history)

A lens is capped at Adequate while one of its dimensions scores below 4 out of 10, however well the rest of the lens does. That way a serious problem in one place always shows in the lens's rating.

How the score is built: what each lens counts for The lenses don't count equally. The weakest lens counts most, the next weakest a little less, and so on, so a weak area pulls the score down instead of being averaged away. In the bar below, each part's width shows how much that lens counts and its colour shows its rating. Improving the widest part moves the score most, and as that lens improves, it counts for less, because another lens becomes the weakest.
Production Readiness 36 · counts for 47%Maturity 39 · counts for 26%Security and Compliance 67 · counts for 14%Code Health 79 · counts for 8%Architecture 98 · counts for 4%

If Production Readiness rose from 36 to 70, the lowest score rated Strong, the score would rise from 47 to about 56.

Code composition: what the lines of code are
Product code 92%Tests 8%
New since the last survey: 6 findings

These 6 critical or serious findings weren't in the previous survey, on 12 October 2026.

Watchdog compares every finding with the previous survey's. A finding that has only moved to another line in the same file counts as the same finding, so only new findings appear here. Advisory notes from the AI model are left out, because the model words them afresh in every survey.

Fixed since the last survey: 3 findings

These 3 critical or serious findings were in the previous survey, on 12 October 2026, and are gone from this one.

  • Coupling · Off the main sequence: MetabolomeXchange
  • Coupling · Off the main sequence: ProteoWizard.Interop
  • Secrets (history) · REDACTED: REDACTED visual/LCMS_ms1feature_3D_canvas/index.html
Rebuild cost: about €200,000 · Estimate
Cost to rebuild€65,000 to €330,000, for 1,086 to 3,445 hours of work, about 1.3 person-years for 1 to 3 engineers
Difficulty of the problemLow, judged from the kind of software and how it is built. Code that solves a harder problem, such as payments or medical bookings, costs more per line to write.
Quality factor×0.7 at a score of 47. Better code takes more work to write, so the factor is ×1.0 at a score of 70, lower below it and higher above it.
SizeLarge: 233,360 lines of product code
What it is notNot a quotation: nobody has offered to build it for that. Not a valuation: it says nothing about what the business is worth. Not a certified figure: no professional has signed it as one.

How the estimate is made: Watchdog prices the hours a team would need to write this code again, at €60 to €95 an hour. Declarations and boilerplate are priced at a fast rate and logic at a slower one, and the logic is then multiplied by the difficulty of the problem and by the quality factor. The estimate can be about 30% off either way, and it moves most with the hourly rate and the difficulty. For this code, every line is priced as straight logic, which keeps the estimate on the low side.

Top priorities

The three actions that raise the score most for the work they take. The full ranked list is in the Roadmap.

1
Resolve the 1 No ADRs found finding(s) in ADR Quality.
Raises the score by about 10 points · Low effort · ADR Quality
2
Add a CI workflow that builds and runs the test suite on every push/PR.
Raises the score by about 8 points · Medium effort · CI/CD gates
3
Record your significant design decisions.
Write one short document per decision, giving its date, the situation, the decision and its consequences, and keep them together with your other design documents. A docs/adr folder with each file named by number and title is the easiest place to find them.
Raises the score by about 7 points · Medium effort · Architecture documentation

Diagnosis: what the measurements show together

Each conclusion below combines several dimensions into one point that no single dimension shows, and lists the measurements it rests on.

Where the investment is most exposed · Value at risk
This code would cost about €200,000 to build again, about 1.3 person-years of work. Its weakest lens is Production Readiness, at 36 (Weak). Production Readiness is about whether the product is ready to run in production and to change without breaking. Because the weakest lens counts most in the score, work on Production Readiness also moves the score most.
Based on: the rebuild estimate · the Production Readiness grade · how much each lens counts
What to do: Start with the Production Readiness actions in Top priorities.
If you do one thing first · First action
Resolve the 1 No ADRs found finding(s) in ADR Quality. Of all the actions in this report, it raises the score most for the work it takes: about 10 points for low effort, because it clears the 1 ADR Quality findings. The next survey will show the change in the score.
Based on: the ranked actions in Top priorities, by score gain and effort
What hard-to-read code costs each year · Cost
Four dimensions measure how easy the code is to work in: two measure how tangled its logic is, one how much of it is copied, and one how well each part sticks to a single job. In this codebase they average 6.3 out of 10. Code at that level is slower to change than clean code, and Watchdog estimates the extra work at 4% to 10% on every change. The history of the code shows how much it changes: about 19,652 lines over the last 90 days, which is about 79,700 lines a year. At that pace, the extra work comes to an estimated 8.7 to 52.2 engineer-days a year, and it grows as more code changes.
How this is estimated: The number of changed lines is measured from the history of the code. The rest rests on two assumptions of Watchdog's own: code scoring 8 out of 10 or more adds no extra work, and each point below 8 adds 2.5% to 5.6% to every change, never less than 2% to 5% and never more than 40% to 60% in all; and an engineer changes 150 to 400 lines in a day. The result is a range for planning, not a measurement.
Based on: Cyclomatic Complexity · Cognitive Complexity · Code Duplication · Cohesion (LCOM4) · the code's change history
What to do: Start with the files listed under Churn × Complexity Hotspots, which change often and are hard to read, because that is where the extra work is paid most often.

Architecture — bounded-context dependency graph

Each box is a bounded context (its layer projects grouped, or a project count when large); arrows show dependencies between contexts. A shared kernel is where many arrows converge.

arch CLI_tool CLI_tool ctx:metadb metadb 10 projects CLI_tool->ctx:metadb KEGG_MetaDNA KEGG_MetaDNA mz mz pubchem pubchem ctx:assembly assembly 15 projects ctx:mzmath mzmath 12 projects ctx:assembly->ctx:mzmath ctx:visualize visualize 5 projects ctx:assembly->ctx:visualize ctx:metadb->ctx:assembly ctx:metadb->ctx:mzmath ctx:metadna metadna 2 projects ctx:metadna->ctx:metadb ctx:metadna->ctx:mzmath ctx:mzkit_app mzkit_app 3 projects ctx:mzkit_app->ctx:assembly ctx:mzkit_app->ctx:metadb ctx:mzkit_app->ctx:metadna ctx:mzkit_app->ctx:mzmath ctx:mzkit_app->ctx:visualize ctx:mzplot (Rscript/Library/mzkit_app/src/mzplot) mzplot (Rscript/Library/mzkit_app/src/mzplot) 1 project ctx:mzplot (Rscript/Library/mzkit_app/src/mzplot)->ctx:assembly ctx:mzplot (Rscript/Library/mzkit_app/src/mzplot)->ctx:metadb ctx:mzplot (Rscript/Library/mzkit_app/src/mzplot)->ctx:mzmath ctx:mzplot (Rscript/Library/mzkit_app/src/mzplot)->ctx:visualize ctx:test (src/assembly/ThermoRawFileReader/test) test (src/assembly/ThermoRawFileReader/test) 1 project ctx:test (src/assembly/ThermoRawFileReader/test)->ctx:assembly ctx:test (src/assembly/ThermoRawFileReader/test)->ctx:mzmath ctx:visualize->ctx:metadb ctx:visualize->ctx:mzmath __more__ +3 more contexts

Architecture: which parts of the code depend on which

The code is divided into modules, groups of code that each handle one part of the product, and a module depends on another when it uses code from it. The table lists the modules both down the side and across the top, in an order where each module should only use modules listed above it. A number in a cell means the module on that row uses the module in that column, and it counts the pairs of building blocks (types) that connect them. The one thing to look for is a mark above the diagonal line. It means two or more modules use each other in a loop (a dependency cycle), so none of them can be changed, tested or released on its own.

190 modules, with 451 dependencies between them. 7 loops run through 44 of the modules, marked above the diagonal.

The table shows the 40 modules with the most connections; 150 more are left out to keep it readable.

Which modules use which. The module on each row uses the module in each column, and the number counts the pairs of types that connect them. A cell above the diagonal is part of a loop.
uses →1 BioNovoGene.Analytical.NMRFidTool2 BioNovoGene.Analytical.MassSpectrometry.Assembly.MarkupData.mzXML3 BioNovoGene.Analytical.MassSpectrometry.Math.Chromatogram4 BioNovoGene.Analytical.MassSpectrometry.Math.Ms1.Annotations5 BioNovoGene.Analytical.MassSpectrometry.Math.Ms1.PrecursorType6 BioNovoGene.Analytical.MassSpectrometry.Math.Spectra.SplashID7 BioNovoGene.Analytical.MassSpectrometry.Math.Spectra.Xml8 BioNovoGene.Analytical.MassSpectrometry.Assembly.DataReader9 BioNovoGene.Analytical.MassSpectrometry.Math.LinearQuantitative.Linear10 BioNovoGene.BioDeep.Chemoinformatics.Formula.MS11 BioNovoGene.BioDeep.Chemoinformatics.Metabolite12 BioNovoGene.Analytical.MassSpectrometry.Assembly.mzData.mzWebCache13 BioNovoGene.Analytical.MassSpectrometry.Math.LinearQuantitative14 BioNovoGene.BioDeep.Chemoinformatics.Formula15 BioNovoGene.Analytical.MassSpectrometry.Math.MRM16 BioNovoGene.BioDeep.Chemoinformatics.SMILES17 BioNovoGene.Analytical.MassSpectrometry.Math18 BioNovoGene.Analytical.MassSpectrometry.Assembly.ThermoRawFileReader19 BioNovoGene.Analytical.MassSpectrometry.Math.Spectra20 BioNovoGene.Analytical.MassSpectrometry.Math.Ms121 BioNovoGene.BioDeep.Chemistry22 BioNovoGene.Analytical.MassSpectrometry.Assembly.MarkupData.mzML23 BioNovoGene.Analytical.MassSpectrometry.Math.Insilicon24 BioNovoGene.Analytical.MassSpectrometry.SingleCells.File25 BioNovoGene.BioDeep.MSEngine26 BioNovoGene.BioDeep.MSFinder27 BioNovoGene.Analytical.MassSpectrometry.Assembly.MarkupData.imzML28 BioNovoGene.Analytical.MassSpectrometry.Math.GCMS29 BioNovoGene.Analytical.MassSpectrometry.SingleCells.Deconvolute30 BioNovoGene.Analytical.MassSpectrometry.Visualization31 BioNovoGene.BioDeep.Chemistry.MetaLib32 BioNovoGene.BioDeep.MetaDNA.Infer33 BioNovoGene.Analytical.MassSpectrometry.Assembly34 BioNovoGene.Analytical.MassSpectrometry.Math.GCMS.QuantifyAnalysis35 BioNovoGene.Analytical.MassSpectrometry.MsImaging.Pixel36 BioNovoGene.BioDeep.MetaDNA37 BioNovoGene.Analytical.MassSpectrometry.MsImaging.Reader38 BioNovoGene.Analytical.MassSpectrometry.MsImaging39 BioNovoGene.Analytical.MassSpectrometry.Assembly.Comprehensive.MsImaging40 mzkit
1 BioNovoGene.Analytical.NMRFidTool
2 BioNovoGene.Analytical.MassSpectrometry.Assembly.MarkupData.mzXML3141
3 BioNovoGene.Analytical.MassSpectrometry.Math.Chromatogram311
4 BioNovoGene.Analytical.MassSpectrometry.Math.Ms1.Annotations1
5 BioNovoGene.Analytical.MassSpectrometry.Math.Ms1.PrecursorType1
6 BioNovoGene.Analytical.MassSpectrometry.Math.Spectra.SplashID2
7 BioNovoGene.Analytical.MassSpectrometry.Math.Spectra.Xml23
8 BioNovoGene.Analytical.MassSpectrometry.Assembly.DataReader115811
9 BioNovoGene.Analytical.MassSpectrometry.Math.LinearQuantitative.Linear215
10 BioNovoGene.BioDeep.Chemoinformatics.Formula.MS42
11 BioNovoGene.BioDeep.Chemoinformatics.Metabolite10
12 BioNovoGene.Analytical.MassSpectrometry.Assembly.mzData.mzWebCache2111138932
13 BioNovoGene.Analytical.MassSpectrometry.Math.LinearQuantitative121
14 BioNovoGene.BioDeep.Chemoinformatics.Formula12
15 BioNovoGene.Analytical.MassSpectrometry.Math.MRM22113142
16 BioNovoGene.BioDeep.Chemoinformatics.SMILES4
17 BioNovoGene.Analytical.MassSpectrometry.Math111211114611148
18 BioNovoGene.Analytical.MassSpectrometry.Assembly.ThermoRawFileReader11
19 BioNovoGene.Analytical.MassSpectrometry.Math.Spectra1228716
20 BioNovoGene.Analytical.MassSpectrometry.Math.Ms11
21 BioNovoGene.BioDeep.Chemistry144
22 BioNovoGene.Analytical.MassSpectrometry.Assembly.MarkupData.mzML141
23 BioNovoGene.Analytical.MassSpectrometry.Math.Insilicon31121121
24 BioNovoGene.Analytical.MassSpectrometry.SingleCells.File2125
25 BioNovoGene.BioDeep.MSEngine354462810135
26 BioNovoGene.BioDeep.MSFinder21317175
27 BioNovoGene.Analytical.MassSpectrometry.Assembly.MarkupData.imzML3255
28 BioNovoGene.Analytical.MassSpectrometry.Math.GCMS2521
29 BioNovoGene.Analytical.MassSpectrometry.SingleCells.Deconvolute4641
30 BioNovoGene.Analytical.MassSpectrometry.Visualization2318431
31 BioNovoGene.BioDeep.Chemistry.MetaLib5634
32 BioNovoGene.BioDeep.MetaDNA.Infer111122
33 BioNovoGene.Analytical.MassSpectrometry.Assembly17226437323
34 BioNovoGene.Analytical.MassSpectrometry.Math.GCMS.QuantifyAnalysis43212414
35 BioNovoGene.Analytical.MassSpectrometry.MsImaging.Pixel13762
36 BioNovoGene.BioDeep.MetaDNA32415358
37 BioNovoGene.Analytical.MassSpectrometry.MsImaging.Reader31393
38 BioNovoGene.Analytical.MassSpectrometry.MsImaging1105727494
39 BioNovoGene.Analytical.MassSpectrometry.Assembly.Comprehensive.MsImaging1512211171
40 mzkit416923316619431241238211112824511213171
Uses a module listed above itPart of a loopThe module itself
1 BioNovoGene.Analytical.NMRFidTool2 BioNovoGene.Analytical.MassSpectrometry.Assembly.MarkupData.mzXML3 BioNovoGene.Analytical.MassSpectrometry.Math.Chromatogram4 BioNovoGene.Analytical.MassSpectrometry.Math.Ms1.Annotations5 BioNovoGene.Analytical.MassSpectrometry.Math.Ms1.PrecursorType6 BioNovoGene.Analytical.MassSpectrometry.Math.Spectra.SplashID7 BioNovoGene.Analytical.MassSpectrometry.Math.Spectra.Xml8 BioNovoGene.Analytical.MassSpectrometry.Assembly.DataReader9 BioNovoGene.Analytical.MassSpectrometry.Math.LinearQuantitative.Linear10 BioNovoGene.BioDeep.Chemoinformatics.Formula.MS11 BioNovoGene.BioDeep.Chemoinformatics.Metabolite12 BioNovoGene.Analytical.MassSpectrometry.Assembly.mzData.mzWebCache13 BioNovoGene.Analytical.MassSpectrometry.Math.LinearQuantitative14 BioNovoGene.BioDeep.Chemoinformatics.Formula15 BioNovoGene.Analytical.MassSpectrometry.Math.MRM16 BioNovoGene.BioDeep.Chemoinformatics.SMILES17 BioNovoGene.Analytical.MassSpectrometry.Math18 BioNovoGene.Analytical.MassSpectrometry.Assembly.ThermoRawFileReader19 BioNovoGene.Analytical.MassSpectrometry.Math.Spectra20 BioNovoGene.Analytical.MassSpectrometry.Math.Ms121 BioNovoGene.BioDeep.Chemistry22 BioNovoGene.Analytical.MassSpectrometry.Assembly.MarkupData.mzML23 BioNovoGene.Analytical.MassSpectrometry.Math.Insilicon24 BioNovoGene.Analytical.MassSpectrometry.SingleCells.File25 BioNovoGene.BioDeep.MSEngine26 BioNovoGene.BioDeep.MSFinder27 BioNovoGene.Analytical.MassSpectrometry.Assembly.MarkupData.imzML28 BioNovoGene.Analytical.MassSpectrometry.Math.GCMS29 BioNovoGene.Analytical.MassSpectrometry.SingleCells.Deconvolute30 BioNovoGene.Analytical.MassSpectrometry.Visualization31 BioNovoGene.BioDeep.Chemistry.MetaLib32 BioNovoGene.BioDeep.MetaDNA.Infer33 BioNovoGene.Analytical.MassSpectrometry.Assembly34 BioNovoGene.Analytical.MassSpectrometry.Math.GCMS.QuantifyAnalysis35 BioNovoGene.Analytical.MassSpectrometry.MsImaging.Pixel36 BioNovoGene.BioDeep.MetaDNA37 BioNovoGene.Analytical.MassSpectrometry.MsImaging.Reader38 BioNovoGene.Analytical.MassSpectrometry.MsImaging39 BioNovoGene.Analytical.MassSpectrometry.Assembly.Comprehensive.MsImaging40 mzkitBioNovoGene.Analytical.NMRFidTool1BioNovoGene.Analytical.MassSpectrometry.Assembly.MarkupData.mzXML2BioNovoGene.Analytical.MassSpectrometry.Math.Chromatogram3BioNovoGene.Analytical.MassSpectrometry.Math.Ms1.Annotations4BioNovoGene.Analytical.MassSpectrometry.Math.Ms1.PrecursorType5BioNovoGene.Analytical.MassSpectrometry.Math.Spectra.SplashID6BioNovoGene.Analytical.MassSpectrometry.Math.Spectra.Xml7BioNovoGene.Analytical.MassSpectrometry.Assembly.DataReader8BioNovoGene.Analytical.MassSpectrometry.Math.LinearQuantitative.Linear9BioNovoGene.BioDeep.Chemoinformatics.Formula.MS10BioNovoGene.BioDeep.Chemoinformatics.Metabolite11BioNovoGene.Analytical.MassSpectrometry.Assembly.mzData.mzWebCache12BioNovoGene.Analytical.MassSpectrometry.Math.LinearQuantitative13BioNovoGene.BioDeep.Chemoinformatics.Formula14BioNovoGene.Analytical.MassSpectrometry.Math.MRM15BioNovoGene.BioDeep.Chemoinformatics.SMILES16BioNovoGene.Analytical.MassSpectrometry.Math17BioNovoGene.Analytical.MassSpectrometry.Assembly.ThermoRawFileReader18BioNovoGene.Analytical.MassSpectrometry.Math.Spectra19BioNovoGene.Analytical.MassSpectrometry.Math.Ms120BioNovoGene.BioDeep.Chemistry21BioNovoGene.Analytical.MassSpectrometry.Assembly.MarkupData.mzML22BioNovoGene.Analytical.MassSpectrometry.Math.Insilicon23BioNovoGene.Analytical.MassSpectrometry.SingleCells.File24BioNovoGene.BioDeep.MSEngine25BioNovoGene.BioDeep.MSFinder26BioNovoGene.Analytical.MassSpectrometry.Assembly.MarkupData.imzML27BioNovoGene.Analytical.MassSpectrometry.Math.GCMS28BioNovoGene.Analytical.MassSpectrometry.SingleCells.Deconvolute29BioNovoGene.Analytical.MassSpectrometry.Visualization30BioNovoGene.BioDeep.Chemistry.MetaLib31BioNovoGene.BioDeep.MetaDNA.Infer32BioNovoGene.Analytical.MassSpectrometry.Assembly33BioNovoGene.Analytical.MassSpectrometry.Math.GCMS.QuantifyAnalysis34BioNovoGene.Analytical.MassSpectrometry.MsImaging.Pixel35BioNovoGene.BioDeep.MetaDNA36BioNovoGene.Analytical.MassSpectrometry.MsImaging.Reader37BioNovoGene.Analytical.MassSpectrometry.MsImaging38BioNovoGene.Analytical.MassSpectrometry.Assembly.Comprehensive.MsImaging39mzkit40314131111223115811215421021111389321211222113142411121111461114811122871611441413112112121253544628101352131717532552521464123184315634111122172264373234321241413762324153583139311057274941512211171416923316619431241238211112824511213171+150 more modules (most-connected shown)

At a glance — Code Health · 79% · Adequate · gated by D1, D2 ·

The Good
D3 · .NET / C# God Classes 8.8 D4 · .NET / C# Code Duplication 9.3 D17 · .NET / C# Explicit Debt 9.7 D18 · .NET / C# Solution Shape 8.8 GD1 · Repo Unfinished & placeholder code 10.0 X28 · Repo Index access outside its own emptiness guard 10.0
The Ugly
D1 · .NET / C# Cyclomatic Complexity 3.9 D2 · .NET / C# Cognitive Complexity 2.0

At a glance — Architecture · 98% · Exemplary ·

The Good
D5 · .NET / C# Coupling 9.4 D6 · .NET / C# Cohesion (LCOM4) 9.9 D26 · .NET / C# Project Cohesion 8.7 D35 · .NET / C# Change Coupling 9.9 AX10 · Repo Code composition 9.8 AX3 · Repo Project dependency cycles 10.0 AX4 · Repo Dependency direction 10.0 AX5 · Repo Architecture & structure 10.0 AX6 · Repo Interface segregation 10.0

At a glance — Maturity · 39% · Weak · gated by D34, M2 ·

The Good
D15 · .NET / C# Churn × Complexity Hotspots 10.0 M3 · Repo Folder & project structure 8.0
The Bad
M1 · Repo Documentation (README) 5.3
The Ugly
D20 · .NET / C# ADR Quality 0.0 D24 · .NET / C# Comment Value 4.4 D34 · .NET / C# Knowledge Freshness 1.7 M2 · Repo Architecture documentation 0.0

At a glance — Readiness · 36% · Weak · gated by P1, P3 ·

The Good
D13 · .NET / C# REDACTED Scanning 10.0 D14 · .NET / C# License Compliance 10.0 P6 · Repo Release Hygiene 10.0
The Ugly
P1 · Repo CI/CD gates 0.0 P3 · Repo Security & performance tooling 0.0

At a glance — Security · 67% · Adequate · gated by D28 ·

The Good
D30 · .NET / C# Dependency Vulnerabilities 10.0 D43 · .NET / C# Malicious Dependencies 10.0 S1 · Repo Web-Security Posture 8.0
The Bad
D29 · .NET / C# Static Analysis (SAST) 6.1 D44 · .NET / C# Platform End-of-Life 6.0
The Ugly
D28 · .NET / C# Secrets (history) 0.0 D37 · .NET / C# Vulnerability-disclosure Policy 4.0

Security & Compliance — OWASP Top-10 mapping

Findings mapped to OWASP categories; the specific CVEs/secrets are in the Security dimension cards below and findings.md (redacted only on the public version of this report).

OWASP categoryFindingsSeverity
A07:2025 — Authentication Failures107High / Critical
A05:2025 — Injection10High / Critical
A02:2025 — Security Misconfiguration1Medium

Roadmap

Begin by addressing the 988 orphaned files, prioritizing Extensions.vb, Utils.vb, and Provider.vb, and removing 63 redundant comments in AssemblyInfo.vb, FormulaGenerator.vb, and XcaliburRawFileIO.vb. Establish a CI workflow to build and test on every push or pull request to ensure code stability. Finally, resolve the missing architecture decision records by documenting key design choices in a dedicated folder and fixing the single ADR quality gap.

Ranked by impact ÷ effort. "Helps" is the estimated gain on the 0–100 health score.

Do thisHelpsEffortDimension
Resolve the 1 No ADRs found finding(s) in ADR Quality.+9.8 ptsLowADR Quality
Add a CI workflow that builds and runs the test suite on every push/PR.+7.8 ptsMediumCI/CD gates
Record your significant design decisions. Write one short document per decision, giving its date, the situation, the decision and its consequences, and keep them together with your other design documents. A docs/adr folder with each file named by number and title is the easiest place to find them.+7.3 ptsMediumArchitecture documentation
Resolve the 988 Orphaned file finding(s) in Knowledge Freshness — start with Extensions.vb (22), Utils.vb (4), Provider.vb (3).+9.1 ptsHighKnowledge Freshness
Resolve the 63 redundant comment finding(s) in Comment Value — start with AssemblyInfo.vb (44), FormulaGenerator.vb (4), XcaliburRawFileIO.vb (3).+3.6 ptsMediumComment Value
Resolve the 1 REDACTED finding(s) in Vulnerability-disclosure Policy.+1.6 ptsLowVulnerability-disclosure Policy
Resolve the 1 InvertedNullGuard finding(s) in Explicit Debt — start with IonLibrary.vb.+1.5 ptsLowExplicit Debt
Resolve the 3 OnErrorResumeSwallow finding(s) in Explicit Debt — start with mzPackWriter.vb, mzStream.vb, ChemicalDescriptor.vb.+1.5 ptsLowExplicit Debt

File quality

Per-file score 0–10 — a quality signature. Of 297 files carrying findings, judged against the Production bar: 0% slop · 46% mixed · 54% near-clean.

FileScoreBandWorst signal
src/assembly/ThermoRawFileReader/XcaliburRawFileIO.vb1.0SlopExplicit Debt: EmptyCatchBlock
REDACTED4.4MixedSecrets (history): REDACTED: REDACTED
Rscript/Library/mzkit_app/src/mzquant/mzDeco.vb4.6MixedExplicit Debt: EmptyCatchBlock
src/assembly/mzPack/v2.0/mzStream.vb5.8MixedExplicit Debt: OnErrorResumeSwallow
REDACTED5.8MixedStatic Analysis (SAST): High: REDACTED
src/assembly/NMRFidTool/Math/baseline/GolotvinWilliamsBaselineCorrector.vb6.0MixedExplicit Debt: TodoComment
src/metadb/Chemoinformatics/InChI/Extensions.vb6.0MixedExplicit Debt: BarePragmaDisable
src/mzmath/MSFinder/FormulaGenerator.vb6.1MixedCyclomatic Complexity: FormulaGenerator.getFormulaResults (cyclomatic 58)
src/metadb/Massbank/Public/Massbank/RecordIO.vb6.1MixedExplicit Debt: EmptyCatchBlock
src/metadb/Lipidomics/Annotation/LipidomicsConverter.vb6.5MixedCyclomatic Complexity: LipidomicsConverter.acylChainStringSeparatorVS2 (cyclomatic 25)
src/metadb/Massbank/Public/NCBI/PubChemDescriptorRepo.vb6.5MixedExplicit Debt: TodoComment
Rscript/Library/mzkit_app/src/mzkit/functions/z_assembler.vb6.6MixedExplicit Debt: TodoComment repeated across 17 files
src/assembly/BrukerDataReader/flexImaging/mcf/index_sqlite/IndexParser.vb6.6MixedExplicit Debt: TodoComment repeated across 14 files
src/assembly/SpectrumTree/Query/TreeSearch.vb6.7MixedExplicit Debt: BarePragmaDisable
src/assembly/NMRFidTool/Proc.vb6.7MixedExplicit Debt: TodoComment
src/metadb/Lipidomics/TotalChainVariationGenerator.vb6.7MixedExplicit Debt: TodoComment
src/visualize/MsImaging/Reader/PixelReader.vb6.7MixedExplicit Debt: TodoComment
src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb7.0MixedCyclomatic Complexity: MsScanMatching.GetLipidMoleculerSpeciesLevelAnnotationResultForEIEIO (cyclomatic 193)
src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb7.0MixedCyclomatic Complexity: LipidMsmsCharacterization.JudgeIfCardiolipin (cyclomatic 44)
src/assembly/RamanSpectroscopy/RamanDataProcessor.vb7.0MixedCyclomatic Complexity: PeakAnalyzer.MultiPeakFit (cyclomatic 42)

How the grades work

Every finding carries one of four grades. Three say how serious it is. The fourth says this survey could not settle it — and it is a grade, not a gap.

Critical — 121

A definite problem that already costs you something and drags the score down: a missing authorisation check, a dependency with a known exploit, a build that does not reproduce. Failure here tends to cause failures elsewhere.

Serious — 1247

Likely wrong, but not failing yet. It degrades the codebase over a longer horizon and can cause failures elsewhere — not urgent this week, not something to carry for two years either.

Minor — 1135

Recorded, with no effect on how the codebase functions. Present so the survey is complete, not because it needs doing.

Could not be resolved — 36

Something this survey could not settle from the outside, and which could be critical or serious. Either a control was required and no positive evidence of it exists in the repository — a backup job that nothing shows was ever restored from proves nothing about restores — or our own analysis could not run over that part of the tree. This is not a clean result. These are excluded from the score rather than awarded a pass, so the number on the cover neither rewards nor penalises them: if you act on this survey without resolving them, you carry that risk yourself. Each one is named under Limitations.

Methodology & how to trust this report

Watchdog is a deep, periodic assessment — run each sprint, monthly, or quarterly, taking the time to go wider and deeper than a quick check and surfacing in one coherent report what you'd otherwise piece together from a dozen separate tools. It scores deterministically: the same commit yields the same score, every run. 36 of 36 evaluated dimensions are computed purely by tools and static analysis (confidence 1.0); none rely on LLM judgement. Overall confidence is 0.8 — the weighted average across measured dimensions; it falls as more of the score leans on LLM-assisted judgement and rises when it's fully tool-backed.

Every figure here is one of three kinds, and we label which: ✓ Measured — a deterministic fact (LoC, complexity, coverage); ~ Modeled — an estimate from a stated model (cost, effort, value-at-risk), always a range with its assumptions, never a precise fact; ◐ Advisory — an LLM prose judgement. We never present a modelled estimate as if it were measured. Perfect or absent scores carry their provenance too (ADR-0011): ✓ Tool-verified means the property itself was measured across the surface; ○ Nothing flagged means the probes came back clean — a claim bounded by what a repository can show; ⊘ Not evidenced means a working control (a tested restore, an automated rollback) showed no positive evidence — absence of evidence is not evidence of a control, so it's excluded from the score rather than awarded a spurious 10; ◐ Sampled · advisory marks an LLM verdict over a bounded sample — advisory, never a deterministic measurement.

What we checked — 36 dimensions across the health lenses
D1D2D3D4D5D6D13D14D15D17D18D20D24D26D28D29D30D34D35D37D43D44AX10AX3AX4AX5AX6GD1M1M2M3P1P3P6S1X28

Each chip is a dimension scored from real signals across architecture, testing, dependencies, security & compliance, documentation, git-history and code quality — in one coherent pass. A surface report typically covers a handful.

How to trust any code-health report — three questions
  1. Can you open the finding? Real findings cite a repo-relative file and line you can open at the cited line — never an absolute scratch path. Here, 2490 of 2503 do; the remainder are repo-wide signals — a dimension-level measurement, not a single line. (Every path in this report is repo-relative by construction: paths are normalized at the producer and the report is rejected if any rooted path leaks through.)
  2. Is there a tool behind the number? Every score below names the method that produced it — Roslyn, git, a scanner, or (for a handful of documentation/naming dimensions) an LLM labelled sampled · advisory — not a narrative.
  3. Does re-running give the same result? Run it again on the same commit and the score — and this report, byte for byte — is identical. A report whose numbers move between runs is describing the run, not the code.

This report answers yes to all three. That's the bar to hold any assessment to.

Tools & methods

The actual versions used this run (captured at analysis time) — re-run on the same commit for the identical score.

MethodBacksVersionEvaluator
Roslyn static analysisComplexity, cohesion, coupling, dead code, API surface, layering5.3.0✓ deterministic
Native secret scannerHardcoded secrets / credentials1.0.0✓ deterministic
Watchdog duplication detector (in-process)Code duplication1.0.0✓ deterministic
Coverage (coverlet / dotnet-coverage)Line & branch coverage10.0.400✓ deterministic
NuGet / dotnetOutdated, vulnerable & deprecated dependencies10.0.400✓ deterministic
git / LibGit2SharpChurn hotspots, knowledge concentration, history2.43.0 · 0.31.0✓ deterministic
gitleaks · semgrep · trivySecrets in history, SAST, CVEs, IaC & container, PII / GDPR1.86.0 · 0.69.3✓ deterministic
LLM (sampled · advisory)Documentation quality, ADR conformance, naming — sampled over a bounded sample; advisory, never a deterministic measurement—◐ LLM · sampled · advisory

Every finding is locatable in findings.md. Run 01a179d3-72bd-7806-bc44-2bf2e8e81a85.

The exact command behind every deep-scan dimension — tool, version, invocation and retained raw output — is in Appendix B — Reproduction & audit trail.

Run transparency — what happened this run

What ran differently this time — a tool absent, degraded, or that fell back to an estimate. Named openly, not folded silently into the scores. A degraded run also records its exact cause in diagnostics.md.

  • D11 Test Reliability — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. Test reliability NOT MEASURED: the test run produced no results for any test tier, so no test ever ran and flakiness could not be exercised. The cause could not be attributed, so it is excluded from the score rather than read as an absence of tests.
  • D12 Dependency Hygiene — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. `dotnet list package` did not return usable output (restore or query failed); no outdated/vulnerable/deprecated data to assess. The tool said: /usr/share/dotnet/sdk/10.0.400/NuGet.targets(521,5): error MSB3202: The project file "/tmp/Erica/src/SingleCell/SingleExpression/SingleExpression.vbproj" was not found. [Rscript/Library/mzkit.NET5.slnx].
  • D16 Bus Factor — not measured this run — This is a true statement about the repository that carries nothing for its owner to act on, so it is reported here rather than as a defect in their code. Single-maintainer repository — bus factor is not applicable (6 contributor(s) across 19661 commit(s) sampled, automation and bot accounts excluded). One of them holds 94% of the history; the other 5 hold 1.2% each on average, below the 5% at which there is somebody to hand the work to. That is a single maintainer with drive-by contributors, not a team whose knowledge has concentrated — so the bus factor is not applicable and there is nothing here for the owner to act on.
  • D17 Explicit Debt — measured, with a gap in what it reached — Watchdog measured this, but not all of it. What it did not reach is a gap on our side — a collector, parser or image we have not built yet — so the numbers on that dimension cover less than the repository, and the part left out is not evidence that it would have passed. The C# workspace loaded this repository's projects but reported a load failure, and the dead-code reference search is unreliable over a graph that did not load cleanly, so it was skipped. The other debt markers on this row were read; dead symbols were not, and their absence from the score is not a finding that the code has none. First load diagnostic: Failure: Project file not found: '/tmp/Erica/src/SingleCell/SingleExpression/SingleExpression.vbproj'.
  • D18 Solution Shape — measured, with a gap in what it reached — Watchdog measured this, but not all of it. What it did not reach is a gap on our side — a collector, parser or image we have not built yet — so the numbers on that dimension cover less than the repository, and the part left out is not evidence that it would have passed. The build did not finish within its budget on this run; structural metrics are reported, build/warning status is unknown.
  • D18 Solution Shape — measured, with a gap in what it reached — Watchdog measured this, but not all of it. What it did not reach is a gap on our side — a collector, parser or image we have not built yet — so the numbers on that dimension cover less than the repository, and the part left out is not evidence that it would have passed. A scan loads every live solution in the repository into one workspace. Every score, lens, and finding here reflects the projects of `Rscript/Library/mzkit.NET5.slnx`, `src/visualize/MsPlot.NET5.sln`, `src/metadb/Lipidomics.sln`, `src/assembly/MzPackExtensions.sln`, `src/assembly/Comprehensive/Comprehensive.sln`, `src/mzmath/ms2_simulator.sln`, `src/mzmath/Mummichog.sln`, `src/mzmath/TargetedMetabolomics.sln`, `src/metadb/MoNA.sln`, `src/assembly/vendors.sln`, `src/mzmath/TargetedMetabolomics/TargetedMetabolomics.sln`, `src/mzmath/deconv.NET5.sln`, `src/mzmath/mz_deco.sln`, `src/metadb/PeaksAnnotation.sln`, `src/metadb/Massbank.sln`, `src/assembly/BrukerDataReader.sln`, `src/metadb/PubChem.NET6.sln`, `src/assembly/LoadR.NET5.sln`, `src/metadb/SMILES_struct.sln`, `src/mzmath/Oligonucleotide_MS.sln`, `src/assembly/assembly.sln`, `src/metadna/metaDNA.sln`, `src/metadna/KEGG_MetaDNA.sln`, `src/assembly/Raman-Spectroscopy.sln`, `src/mzmath/mzMath.sln`, `src/assembly/ProteoWizard.d.sln`, `src/metadna/MetaDNA_visual.sln`, `src/metadb/MetabolomeXchange.sln`, `src/metadb/KNApSAcK.sln`, `src/metadb/KEGG.sln`; 2 further solution(s) found in this tree (`src/metadb/KNApSAcK.sln`, `src/metadna/metaDNA.sln`) could not be added to it — their project list could not be read, or none of their projects opened — so their code is not represented in the headline. (This is a count of the solutions discovery found and could not show to be covered by the analyzed ones — not a claim about how many solution files the repository contains.) If one of them is an archived or vendored tree, declaring it — `.gitattributes` (`path/** linguist-vendored`) or `.editorconfig` (`[path/**] generated_code = true`) — excludes it from discovery the same way generated code is. You can widen what we reach: if one of these solutions is live code, check that it opens on its own (`dotnet build <solution>`); if it is archived or vendored, declare it so.
  • D19 Documentation Quality — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This kind did not reach the 95 % precision gate in three adjudicated runs (docs/plans/deterministic-engine/adjudication/D19-sample3-v3.md), so by the pre-registered fallback it publishes no row until a re-measurement shows it does. The candidates are counted here, not reported as findings, and the score does not include them.
  • D21 Naming Consistency — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. D21's deterministic naming rules are gated on C# first (docs/plans/deterministic-engine.md, P5): each other language is switched on only after its own concept suite and A/B gate pass. Until then its declarations carry no naming verdict this run — this says nothing about whether its names are consistent.
  • D22 Internal API Consistency — not measured this run — This is a true statement about the repository that carries nothing for its owner to act on, so it is reported here rather than as a defect in their code. The loaded project set declares no packable project and no `.Contracts` project, so there is no intentionally-exposed surface for API consistency to be judged over.
  • D23 Boundary Type-Coupling — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. Large codebase (233,360 production LoC in the .NET projects) with no declared bounded contexts — cross-boundary type coupling is unassessed Bounded contexts cannot be inferred from a codebase that is not physically organised by them (D-321), so with none declared there are no boundaries for the coupling pass to measure across. You can widen what we reach: name this codebase's bounded contexts (≥2 module groups, e.g. per subsystem) so cross-boundary type coupling can be assessed. Declare them in `.codehealth/config.yaml` at the repository root (create it if absent), mapping each context name to the module-path or namespace prefixes that belong to it — e.g. `architecture:` → `contexts:` → `Billing: ["src/billing", "Acme.Billing"]`, `Catalog: ["src/catalog", "Acme.Catalog"]`.
  • D24 Comment Value — measured, with a gap in what it reached — Watchdog measured this, but not all of it. What it did not reach is a gap on our side — a collector, parser or image we have not built yet — so the numbers on that dimension cover less than the repository, and the part left out is not evidence that it would have passed. D24 compares a comment's words with the identifiers, literals and constructs of the code it annotates, using English function-word and rationale lexicons. Comments in another script or language were left unread rather than counted as clean.
  • D24 Comment Value — measured, with a gap in what it reached — Watchdog measured this, but not all of it. What it did not reach is a gap on our side — a collector, parser or image we have not built yet — so the numbers on that dimension cover less than the repository, and the part left out is not evidence that it would have passed. Each source language's comment syntax, and the code a comment annotates in it, needs its own proof before D24 judges it. Until then those comments are left unread, not counted as clean.
  • D28 Secrets (history) — measured, with a gap in what it reached — Watchdog measured this, but not all of it. What it did not reach is a gap on our side — a collector, parser or image we have not built yet — so the numbers on that dimension cover less than the repository, and the part left out is not evidence that it would have passed. D28's config-credential rule (WD-SECRET-0002) parses each committed `.json` config as a document and reads credential-named values; `Rscript/Library/mzkit_app/man/index.json`, `dist/Rscript/metaDNA/lxy-CID30_infers/meta.json`, `DATA/pubchem/.pubchem/cid/5/56-65-5.json`, `DATA/pubchem/.pubchem/cid/C/Cyanidin.json`, `DATA/pubchem/.pubchem/cid/a/aspirin.json` and 2 more did not parse (JSON5, a template, several concatenated documents), so a credential bound there is UNMEASURED by that rule. gitleaks still scanned the same files as text.
  • D30 Dependency Vulnerabilities — measured, with a gap in what it reached — This is a true statement about the repository that carries nothing for its owner to act on, so it is reported here rather than as a defect in their code. The solution did not restore on the analyzer's .NET SDK (an SDK/target-framework/restore mismatch, common for an older codebase), so there was no restored dependency graph to scan. 1 of 2 declared ecosystem(s) (nuget packages.config) WERE scanned and every vulnerability they reported is included in this result; nuget was not, so this dimension's score covers less than the dependency surface this repository declares, and nothing here is evidence that nuget is free of known-vulnerable dependencies.
  • D32 Data Compliance (PII/GDPR) — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. `Rscript/Library/mzkit_app/@export/ChemicalDraw.d.ts`, `Rscript/Library/mzkit_app/@export/GCMS.d.ts`, `Rscript/Library/mzkit_app/@export/MRMLinear.d.ts`, `Rscript/Library/mzkit_app/@export/MSI.d.ts`, `Rscript/Library/mzkit_app/@export/MoleculeNetworking.d.ts`, … (+11 more) produced a parse error, so every rule in this engine's `gdpr.yml` was absent there. That absence is NOT a clean result: these rules detect personal data crossing a boundary into a log sink, a URL or browser storage, and a file that was never parsed cannot report any of the three. The rest of the tree analysed normally and its rows above stand; only these files are unaccounted for. You can widen what we reach: fix the syntax error (or exclude the file deliberately) and re-scan to cover it.
  • D39 IL Efficiency — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. IL NOT MEASURED: the analyzer's own build of this repository failed for an ENVIRONMENT reason (exit 1) — MSBuild's engine or the CLR gave up, or our image does not carry the SDK band/targeting pack this repository needs. This is OUR limitation, not a defect in the repo, and it is not a statement that this repository fails to build. D18 owns the question of whether this repository builds; it was not answered here.
  • AXB1 Runtime evidence locked — no reproducible boot — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. Subject: 1323 markup document(s) — HTML, Razor, JSX, Vue, Svelte or server templates. The Runtime Evidence tier boots an app only via docker-compose, an Aspire AppHost, a Dockerfile, an npm dev script, a web service's own toolchain entry point (cargo, go, dotnet, Python, Spring Boot), or an Android app's own Gradle wrapper (run on an emulator); an Apple or Flutter app needs a host it lacks. None applied, so no live runtime a11y/egress/header evidence was collected. You can widen what we reach: add a docker-compose.yml (or an Aspire AppHost) that brings the app up with its dependencies. Watchdog then boots it in an isolated sandbox and gathers real runtime evidence — you change nothing in your pipeline (no CI step, no SDK).
  • C1 Data Protection — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. These personal data controls are read from declarative annotations, request middleware, entity/column names and guard methods in a C# source model, and none was loaded on this run, so there was nothing to gather. That is a gap in this analyzer's language reach — not a finding that the repository lacks personal data controls.
  • C2 Access Controls — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. These authorization controls are read from declarative annotations, request middleware, entity/column names and guard methods in a C# source model, and none was loaded on this run, so there was nothing to gather. That is a gap in this analyzer's language reach — not a finding that the repository lacks authorization controls.
  • C3 Audit Trail — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. These audit controls are read from declarative annotations, request middleware, entity/column names and guard methods in a C# source model, and none was loaded on this run, so there was nothing to gather. That is a gap in this analyzer's language reach — not a finding that the repository lacks audit controls.
  • C4 Data Retention — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. These retention controls are read from declarative annotations, request middleware, entity/column names and guard methods in a C# source model, and none was loaded on this run, so there was nothing to gather. That is a gap in this analyzer's language reach — not a finding that the repository lacks retention controls.
  • C5 Data-Subject Rights — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. These data-subject rights controls are read from declarative annotations, request middleware, entity/column names and guard methods in a C# source model, and none was loaded on this run, so there was nothing to gather. That is a gap in this analyzer's language reach — not a finding that the repository lacks data-subject rights controls.
  • IC1 Incompleteness & stubs — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
  • P5 DR & Backup — not measured this run — This is a true statement about the repository that carries nothing for its owner to act on, so it is reported here rather than as a defect in their code. No backup/snapshot/replication config, RTO/RPO or restore-procedure documentation was found — and no production persistence was detected either (no data-access packages, no data-store services, no database resources), so there is nothing in this repository whose loss a DR control would recover. If this system's data lives in a platform or ops repo we can't see, that's where the DR evidence belongs.
  • X1 Async correctness — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
  • X12 Unreachable branch — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
  • X13 Undrained process stream — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
  • X14 Bypassable address classification — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
  • X15 Unvalidated length from an untrusted reader — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
  • X16 Unfloored truncation loop — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
  • X17 Uncapped recursion over a caller-supplied document — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
  • X18 Disposal-pattern correctness — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
  • X19 Unrestored process-global state — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
  • X2 Cancellation propagation — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
  • X20 Mistyped argument guard — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
  • X21 Side-effecting pattern guard — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
  • X22 Contradicted release guard — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
  • X23 Unguarded diagnostic materialisation — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
  • X24 Document value interpolated into markup unescaped — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
  • X25 Inert configuration knob — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
  • X26 Unsynchronised callback handoff — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
  • X27 Collection changed while being enumerated — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
  • X29 Per-element action decided by a fixed element — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
  • X3 Exception handling — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
  • X30 Support guard that admits what it rejects — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
  • X32 Type resolved by simple name across every loaded assembly — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
  • X4 Structured logging — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
  • X5 Nullable reference types — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
  • Package restore incomplete — third-party types were unresolved in part of the solution — NuGet restore did not complete for src/metadb/Lipidomics/test/test.vbproj, src/assembly/BrukerDataReader/test/test.vbproj, src/metadb/Massbank/test/unitTest.vbproj, src/assembly/LoadR.NET5/test/test.vbproj, src/mzmath/Oligonucleotide_MS/test/test.vbproj and 1 more, so those projects were analysed with framework references only: every check keyed on a third-party type saw an error type there and reported nothing. Findings on those projects are a lower bound; run `dotnet restore` on them and rescan.

Repo exclusion declarations (.gitattributes linguist-generated/vendored, .editorconfig generated_code): none declared — every source file was scored.

Limitations & what we did not check

Watchdog assesses the repository exactly as committed, and only the repository. By design it does not reach outside the source tree: the live cloud account, the running CI/CD pipeline, the host's branch-protection and approval rules, the production configuration, or a restore actually exercised against a backup are all out of scope. That boundary is a feature, not a gap — a repo-relative, deterministic scan re-runs identically on any commit and every finding opens at a real file and line, where a live audit can neither be reproduced nor traced. The visible consequence is that controls which leave no in-repo evidence are reported as "not evidenced" and excluded from the score rather than awarded a number a static scan cannot justify.

Per-dimension blind spots

For each dimension that was measured, what a static, repo-only scan structurally cannot see — the honest edge of the measurement, not a failure of it.

  • D1 Cyclomatic Complexity: Cyclomatic complexity counts branches statically — it cannot tell an essential decision tree from accidental tangle, nor see complexity that lives in data or configuration (large switch-case token tables, DSL lexers/parsers, data-as-code rule tables) rather than control flow: a tokenizer's many single-character cases read as high complexity though each branch is trivial.
  • D2 Cognitive Complexity: Cognitive-complexity heuristics approximate how hard code is to follow; genuine domain difficulty and well-named intent that eases reading are not captured.
  • D3 God Classes: "God class" is sized by members and responsibilities visible in the type — a deliberately broad facade over a coherent subsystem can read the same as an accidental grab-bag. For front-end JS the file-length check is cohesion-aware (a single-responsibility module — one class/IIFE — earns a 3× threshold), but cohesion is approximated from top-level declarations, not true dependency structure.
  • D4 Code Duplication: Duplication is token-similarity — an in-process token-stream comparison over sliding windows, with type-aware normalization — so it finds copy-paste, not semantic duplication expressed differently. Committed machine-written code (scaffolded migrations, designer/codegen output, protobuf/OpenAPI stubs, model snapshots) is EXCLUDED — its repetition is the tool's, not the team's — so the score reflects hand-written duplication only.
  • D5 Coupling: Coupling is measured between projects/assemblies — runtime coupling through DI, reflection, messaging or shared databases is invisible to a static reference graph.
  • D6 Cohesion (LCOM4): LCOM4 cohesion is syntactic — it infers connectivity from which methods touch which fields/methods by name, not from real runtime behaviour or intent.
  • D13 REDACTED Scanning: REDACTED detection is signature- and entropy-based on the current tree — a secret that does not match a known pattern, or one already rotated, will not be flagged (a clean scan is "nothing matched", not "no secrets exist").
  • D14 License Compliance: License compatibility is checked against declared package metadata and a policy — mislabelled or missing license metadata, and obligations that depend on how you distribute, are not resolved here.
  • D15 Churn × Complexity Hotspots: Churn hotspots come from git history — a freshly imported or squashed repository has no churn signal, and recent rewrites can mask a historically risky file.
  • D17 Explicit Debt: Acknowledged-debt signals (TODO/FIXME, suppressions, dead code) are textual — undocumented debt that nobody marked, and debt that lives in design rather than annotations, is invisible. Committed machine-written code (scaffolded migrations, designer/codegen output, generated stubs) is excluded — it is never the team's dead code to delete.
  • D18 Solution Shape: Build integrity reflects whether the solution compiled in this environment — a build that needs a private feed, a specific SDK, or a generated file absent from the repo can read as broken when it is merely unreproducible here.
  • D20 ADR Quality: ADR quality is an LLM read of the decision records present — it cannot know about decisions made and never recorded, and its verdict is sampled and advisory.
  • D24 Comment Value: Comment value is measured as redundancy only: a comment that repeats its code's words is found, but a paraphrase in other words, a vague comment, or one the code contradicts is not, and whether a comment is valuable is not claimed. Comments in other scripts or languages, and outside C#, are not judged.
  • D26 Project Cohesion: Project focus is sized from members/namespaces per project — a project that is broad by deliberate design reads the same as one that has sprawled.
  • D28 Secrets (history): Secret-history scanning sweeps the git log for known patterns — a secret that predates the available history, or never matched a signature, is not found (clean means "nothing matched in the history we can see").
  • D29 Static Analysis (SAST): SAST findings are pattern-based (semgrep) — it finds classes of bug it has rules for; logic flaws, auth/authorization gaps and issues needing runtime context are out of reach (and clean means "no rule matched").
  • D30 Dependency Vulnerabilities: CVE matching depends on accurate package/version metadata and on the advisory databases — a vulnerability with no published advisory, or in code not declared as a dependency, is not seen. Coverage needs a RESOLVED graph: an unpinned requirements.txt, or a pom without a resolved build, yields partial coverage rather than a clean verdict. An ecosystem the analyzer cannot scan is reported as unmeasured, never as clean.
  • D34 Knowledge Freshness: Freshness is decayed commit RECENCY, not comprehension — code read often but rarely committed reads as orphaned, and stable code that genuinely needs no changes is penalised the same as forgotten code; bot/squash commits distort it like the bus factor.
  • D35 Change Coupling: Change coupling is co-change in COMMITS — files split across separate commits, or coupled only through a shared config/build step, read as uncoupled, and a sweeping commit (rename/format) is excluded so it doesn't couple everything. It shows that files change together, not WHY: a high coupling can be a healthy cohesive pair as readily as a hidden leak.
  • D43 Malicious Dependencies: Only packages some vulnerability database has already NAMED as malicious are seen — a compromise published in the last hours, or never reported at all, is invisible here, and this dimension reading 10 is not evidence that a dependency is trustworthy. There is no typosquat or dependency-confusion analysis: a package nobody has reported is simply absent from the feeds. Coverage is the dependency scan's: an ecosystem that could not be scanned is disclosed as unmeasured, never as clean.
  • D44 Platform End-of-Life: The support table is FROZEN, so it goes out of date by losing RECALL: a release that ended support after the table was written is missed until the table is refreshed, and this dimension reading 10 is not evidence that a platform is current. Only platforms the repository DECLARES in a place this pass reads are seen — a runtime named only in a Dockerfile (D31's subject), in a CI workflow (D29's), or in a file this pass does not parse (go.mod, a Gemfile ruby directive) is invisible here, which is why a repository declaring none of them abstains rather than scoring. Only frameworks with a PUBLISHED support policy are tracked: React, Flask and Express publish none, so their age cannot be judged and their absence from a report is not a statement that they are supported.
  • AX10 Code composition: Role is inferred from namespace/folder convention, not semantics — a domain concept living in a folder named "Services" reads as application, and the split is lines-of-code, not business value. The business-logic-share score is a SOFT, FLOORED signal: it contributes to the Architecture lens but is floored at the Critical gate, so an infrastructure-heavy design (a gateway, an ETL, a driver) is legitimately low without being nuked to zero.
  • P6 Release Hygiene: Rollback/observability controls are inferred from repo artefacts (pipelines, dashboards-as-code) — controls configured in external tooling, with no in-repo trace, cannot be credited.

Dimensions

D1 · Cyclomatic Complexity3.9 / 10Weak✓ Tool-verified

What it measures: How tangled the control flow is — methods with many branches are hard to test and change.

Method: Cyclomatic complexity per method (1 + decision points), computed exhaustively across production source; test projects separated by convention. Deterministic.

Maturity: Documented → Verified → Prevented · effective 3.9 / 10 · rule-coverage 100% · ceiling Prevented

234 method(s) exceeded the cyclomatic complexity threshold of 15; the worst was LipoqualityRest.getLqUrl at 313. A further 14 method(s) were over the threshold but excluded as flat dispatchers (a long switch/match over independent cases: many branches, almost no nesting), the largest being LipidomicsConverter.ConvertMsdialClassDefinitionToSuperClassVS2 at 237 — they are counted neither in the figure above nor in this dimension's score. 6 files carry no cyclomatic complexity row at all for this reason — every one of their over-threshold methods was excluded, so the exclusion is disclosed nowhere in the file itself: src/metadb/Lipidomics/Annotation/LipidMassLibraryGenerator.vb (LipidMassLibraryGenerator.GetIons at 106), src/metadb/Lipidomics/LipoqualityDatabaseManagerUtility.vb (LipoqualityDatabaseManagerUtility.ConvertMsdialClassDefinitionToTraditionalClassDefinition at 81), src/metadb/Massbank/Concentration/Concentration.vb (Concentration.ConvertTo at 48), src/mzmath/MSEngine/Proteomics/ModificationContainer.vb (ModificationContainer.IsEmptyOrNull at 22), src/mzmath/mz_deco/Preprocessing/Normalization.vb (Normalization.Normalize at 19), and 1 more not listed here. They are named here because the per-file figures other dimensions report are taken BEFORE this exclusion, so such a file can show a high maximum complexity elsewhere in this report and nothing here, with nothing to reconcile the two.

LipoqualityRest.getLqUrl (cyclomatic 313)src/metadb/Lipidomics/LipoqualityRest.vb:93
LipidAnnotation.Characterize (cyclomatic 198)src/metadb/Lipidomics/Annotation/Lipidomics.vb:148
MsScanMatching.GetLipidMoleculerSpeciesLevelAnnotationResultForEIEIO (cyclomatic 193)src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:289
MsScanMatching.GetLipidMoleculeAnnotationResult (cyclomatic 193)src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:871
DSPPhaseCorrection.dspPhaseCorrection (cyclomatic 71)src/assembly/NMRFidTool/Math/phasing/DSPPhaseCorrection.vb:77

+ 229 more group(s) — more in Appendix A; the complete list is findings.md.

What to do

  1. Bring the 5 bodies over 60 down to 60 or less in Cyclomatic Complexity — start with LipoqualityRest.getLqUrl (cyclomatic 313), LipidAnnotation.Characterize (cyclomatic 198), MsScanMatching.GetLipidMoleculerSpeciesLevelAnnotationResultForEIEIO (cyclomatic 193). — This score is capped by its worst body, so a finding fixed alone moves it by almost nothing — the next one down takes its place. Refactoring these 5 together lifts Cyclomatic Complexity from 3.9 to about 6.1/10, projected with the scoring formula itself and assuming each lands exactly at 60; a cleaner split scores higher.
  2. Stand up a CI pipeline, then gate Cyclomatic Complexity in it to reach Verified (currently Documented). — This repository has no CI pipeline, so there is nothing to add a gate to yet — the pipeline comes first. Hardens enforcement from Documented toward Prevented — provenance only; does not change the score.

Detailed fixes: d1_recommendation.md · top locations in Appendix A, every location in findings.md.

D2 · Cognitive Complexity2.0 / 10Critical✓ Tool-verified

What it measures: How hard the code is for a person to follow, beyond raw branching.

Method: Cognitive complexity per method (Sonar-style nesting-penalized score), computed exhaustively over production code, excluding test projects. Deterministic.

Maturity: Documented → Verified → Prevented · effective 2.0 / 10 · rule-coverage 100% · ceiling Prevented

404 method(s) exceeded the cognitive complexity threshold of 15; the worst was LipoqualityRest.getLqUrl at 356.

LipoqualityRest.getLqUrl (cognitive 356)src/metadb/Lipidomics/LipoqualityRest.vb:93
FormulaGenerator.getFormulaResults (cognitive 318)src/mzmath/MSFinder/FormulaGenerator.vb:326
FragmentAssigner.getValenceCheckedFragmentFormulaList (cognitive 233)src/mzmath/MSFinder/FragmentAssigner.vb:602
LipidMsmsCharacterization.JudgeIfCardiolipin (cognitive 219)src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7147
IsotopeCalculator.getNominalIsotopeElementPropertyForTenIsotopomerElement (cognitive 144)src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1283

+ 399 more group(s) — more in Appendix A; the complete list is findings.md.

What to do

  1. Bring the 7 bodies over 120 down to 120 or less in Cognitive Complexity — start with LipoqualityRest.getLqUrl (cognitive 356), FormulaGenerator.getFormulaResults (cognitive 318), FragmentAssigner.getValenceCheckedFragmentFormulaList (cognitive 233). — This score is capped by its worst body, so a finding fixed alone moves it by almost nothing — the next one down takes its place. Refactoring these 7 together lifts Cognitive Complexity from 2.0 to about 3.1/10, projected with the scoring formula itself and assuming each lands exactly at 120; a cleaner split scores higher.
  2. Stand up a CI pipeline, then gate Cognitive Complexity in it to reach Verified (currently Documented). — This repository has no CI pipeline, so there is nothing to add a gate to yet — the pipeline comes first. Hardens enforcement from Documented toward Prevented — provenance only; does not change the score.

Detailed fixes: d2_recommendation.md · top locations in Appendix A, every location in findings.md.

D3 · God Classes8.8 / 10Strong✓ Tool-verified

What it measures: Over-large classes that try to do too much ("god classes").

Method: God-class detection by line and method-count thresholds per logical type (partial classes unified), filtered for generated code and registration/contract false positives. Deterministic.

Maturity: Documented → Verified → Prevented · effective 8.8 / 10 · rule-coverage 100% · ceiling Prevented

164 god class(es) detected.

MethodTooLong: LipidomicsConverter.ConvertMsdialClassDefinitionToSuperClassVS2 · ×97src/metadb/Lipidomics/Annotation/LipidomicsConverter.vb:5042
FileTooLong: MsCharacterization/MsmsCharacterization.vb · ×30src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb
ClassTooLong: LipidomicsConverter · ×21src/metadb/Lipidomics/Annotation/LipidomicsConverter.vb
TooManyMethods: LipidMsmsCharacterization · ×16src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb

What to do

  1. Resolve the 97 MethodTooLong finding(s) in God Classes — start with MsmsCharacterization.vb (30), LipidEieioMsmsCharacterization.vb (10), IsotopeCalc.vb (6). — One of this dimension's main actionable groups (97 warning-level).
  2. Resolve the 30 FileTooLong finding(s) in God Classes — start with MsScanMatching.vb (2), MsmsCharacterization.vb, LipidEieioMsmsCharacterization.vb. — One of this dimension's main actionable groups (30 warning-level).
  3. Resolve the 21 ClassTooLong finding(s) in God Classes — start with RamanDataProcessor.vb (2), LipidomicsConverter.vb, MsScanMatching.vb. — One of this dimension's main actionable groups (21 warning-level).
  4. Stand up a CI pipeline, then gate God Classes in it to reach Verified (currently Documented). — This repository has no CI pipeline, so there is nothing to add a gate to yet — the pipeline comes first. Hardens enforcement from Documented toward Prevented — provenance only; does not change the score.

Detailed fixes: d3_recommendation.md · top locations in Appendix A, every location in findings.md.

D4 · Code Duplication9.3 / 10Stronggated by 355 serious findings✓ Tool-verified

What it measures: Copy-pasted code that should be shared instead.

Method: Code duplication via token-stream sliding windows with type-aware normalization (locals masked, type names preserved), density-scored per KLoC of production code. Deterministic.

Maturity: Documented → Verified → Prevented · effective 9.3 / 10 · rule-coverage 100% · ceiling Verified

329 duplicated block group(s) detected. A further 26 rows report members as variants of one another; they aggregate block groups already counted above and are not themselves counted.

Duplicated block (5 lines × 2) · ×18Rscript/Library/mzkit_app/src/mzkit/annotations/Massbank.vb:295
Duplicated block (6 lines × 2) · ×17src/mzmath/mz_deco/PeakAlignment.vb:237
Duplicated block (8 lines × 2) · ×16src/mzmath/MSEngine/Search/MsScanMatching.vb:417
Duplicated block (10 lines × 2) · ×14src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14846
Duplicated block (9 lines × 2) · ×14src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:321

+ 163 more group(s) — more in Appendix A; the complete list is findings.md.

What to do

  1. Resolve the 18 Duplicated block (5 lines × 2) finding(s) in Code Duplication — start with MsmsCharacterization.vb (4), Massbank.vb, TrafApodizator.vb. — One of this dimension's main actionable groups (18 warning-level).
  2. Resolve the 17 Duplicated block (6 lines × 2) finding(s) in Code Duplication — start with LipoqualityRest.vb (2), PeakAlignment.vb, MsmsCharacterization.vb. — One of this dimension's main actionable groups (17 warning-level).
  3. Resolve the 16 Duplicated block (8 lines × 2) finding(s) in Code Duplication — start with LipidEieioMsmsCharacterization.vb (2), MsmsCharacterization.vb (2), MsScanMatching.vb. — One of this dimension's main actionable groups (16 warning-level).
  4. Stand up a CI pipeline, then gate Code Duplication in it to reach Verified (currently Documented). — This repository has no CI pipeline, so there is nothing to add a gate to yet — the pipeline comes first. Hardens enforcement from Documented toward Verified — provenance only; does not change the score.

Detailed fixes: d4_recommendation.md · top locations in Appendix A, every location in findings.md.

D5 · Coupling9.4 / 10Stronggated by 6 serious findings✓ Tool-verified

What it measures: Whether volatile projects sit underneath others that depend on them (so their churn ripples upward), and whether project dependencies form cycles. A widely-depended-on but stable shared/kernel project is healthy, not penalised.

Method: Dependency cycles via elementary-DFS over real .csproj references, plus Martin instability (afferent/efferent) per project. Exhaustive over the reference graph, deterministic.

Coverage: Exhaustive · type-level: afferent/efferent coupling + cycles computed over every production type — the population is all types, not a name convention.

Maturity: Documented → Verified → Prevented · effective 9.4 / 10 · rule-coverage 100% · ceiling Prevented

88 projects, 0 dependency cycle(s), 1 unstable depended-on project(s).

Off the main sequence: TissueMorphology · ×5src/visualize/TissueMorphology/TissueMorphology.vbproj:1
Unstable project Targetted.NET5src/mzmath/TargetedMetabolomics/Targetted.NET5.vbproj:1

What to do

  1. Resolve the 5 Off the main sequence finding(s) in Coupling — start with TissueMorphology.vbproj, deconv.NET5.vbproj, chemoinformatics-netcore5.vbproj. — One of this dimension's main actionable groups (5 warning-level).
  2. Resolve the 1 Unstable project Targetted.NET5 finding(s) in Coupling — start with Targetted.NET5.vbproj. — One of this dimension's main actionable groups (1 warning-level).
  3. Stand up a CI pipeline, then gate Coupling in it to reach Verified (currently Documented). — This repository has no CI pipeline, so there is nothing to add a gate to yet — the pipeline comes first. Hardens enforcement from Documented toward Prevented — provenance only; does not change the score.

Detailed fixes: d5_recommendation.md · top locations in Appendix A, every location in findings.md.

D6 · Cohesion (LCOM4)9.9 / 10Stronggated by 5 serious findings✓ Tool-verified

What it measures: Whether a class's methods are focused on a single responsibility.

Method: LCOM4 cohesion per production class with at least two methods: connected components of methods sharing state or calls, computed syntactically. Deterministic, not a proxy.

Coverage: Exhaustive · type-level: LCOM4 cohesion computed over every production class — the population is all types, not a name convention.

Maturity: Documented → Verified → Prevented · effective 9.9 / 10 · rule-coverage 100% · ceiling Verified

6 of 501 classes have LCOM4 above 3.

Low cohesion: MSScan (LCOM4 4) · ×5src/assembly/assembly/mzPack/Stream/MSScan.vb:74

What to do

  1. Resolve the 5 Low cohesion finding(s) in Cohesion (LCOM4) — start with MSScan.vb, PixelReader.vb, PositionLevelChains.vb. — One of this dimension's main actionable groups (5 warning-level).
  2. Stand up a CI pipeline, then gate Cohesion (LCOM4) in it to reach Verified (currently Documented). — This repository has no CI pipeline, so there is nothing to add a gate to yet — the pipeline comes first. Hardens enforcement from Documented toward Verified — provenance only; does not change the score.

Detailed fixes: d6_recommendation.md · top locations in Appendix A, every location in findings.md.

D13 · REDACTED Scanning10.0 / 10Exemplary○ Nothing flagged

What it measures: Whether any secrets (keys, tokens, passwords) have leaked into the code.

Method: In-process native secret scanner (entropy plus signature patterns) across all tracked files; no external tool. A clean result is a measured 10, not no-data zero. Deterministic.

Maturity: Documented → Verified → Prevented · effective 10.0 / 10 · rule-coverage 100% · ceiling Prevented

REDACTED scan ran and found no leaked secrets.

✓ On the Gold path — maintain.

Detailed fixes: d13_recommendation.md.

D14 · License Compliance10.0 / 10Exemplary○ Nothing flagged

What it measures: Whether the licenses of third-party packages are compatible with your policy.

Method: Third-party package licenses resolved from declared package metadata and checked against the configured policy (allow/deny/copyleft). Deterministic; clean = no incompatible license found at metadata depth.

Maturity: Documented → Verified → Prevented · effective 10.0 / 10 · rule-coverage 100% · ceiling Verified

0 of 30 packages use a banned license. ★ DEPTH: this repository's MSBuild projects declare 2 direct `PackageReference`(s), and 14 further package(s) were reached beyond them by closing the graph over nuget.org's own nuspec dependency graph — so a banned licence pulled in only by a dependency's OWN dependencies is inside this verdict. A package whose licence nuget.org could not be asked for is not graded, and version ranges are taken at their lower bound, so this is the closure as that graph states it rather than a restored consumer's exact resolution.

✓ On the Gold path — maintain.

Detailed fixes: d14_recommendation.md.

D15 · Churn × Complexity Hotspots10.0 / 10Stronggated by 2 serious findings✓ Tool-verified

What it measures: Files that change often and are also complex — the riskiest hotspots.

Method: Per production file churn times cyclomatic complexity over a rolling window, computed from git and Roslyn/JS/Razor analysis. Exhaustive, deterministic per commit date.

Maturity: Documented → Verified → Prevented · effective 10.0 / 10 · rule-coverage 100% · ceiling Documented

Top hotspots: src/visualize/plot/ChromatogramPlot/TICplot.vb (2×21=42) Repeated repair below the complexity floor: Rscript/Library/mzkit_app/src/mzplot/src/Visual.vb (3 of 3 changes were fixes)

Hotspot: src/visualize/plot/ChromatogramPlot/TICplot.vbsrc/visualize/plot/ChromatogramPlot/TICplot.vb:200
Repeated repair: Rscript/Library/mzkit_app/src/mzplot/src/Visual.vbRscript/Library/mzkit_app/src/mzplot/src/Visual.vb:727

What to do

  1. Resolve the 1 Hotspot finding(s) in Churn × Complexity Hotspots — start with TICplot.vb. — One of this dimension's main actionable groups (1 warning-level).
  2. Resolve the 1 Repeated repair finding(s) in Churn × Complexity Hotspots — start with Visual.vb. — One of this dimension's main actionable groups (1 warning-level).

Detailed fixes: d15_recommendation.md · top locations in Appendix A, every location in findings.md.

D17 · Explicit Debt9.7 / 10Adequategated by 13 critical findings✓ Tool-verified

What it measures: Acknowledged debt left in the code — TODOs, dead code, suppressed warnings.

Method: Roslyn syntactic debt markers (suppressions/TODO/FIXME/HACK/empty-catch/commented-code/Obsolete) plus SymbolFinder dead-code analysis; weighted-debt-per-KLoC density deducted 2.0x per unit. Deterministic, exhaustive.

Maturity: Documented → Verified → Prevented · effective 9.7 / 10 · rule-coverage 100% · ceiling Prevented

171 deducted debt markers + unmeasured dead symbols across 233360 LoC in the .NET projects (0.1/KLoC) → score 9.7. Dead code not measured: the solution did not load cleanly, so the reference search was skipped.

EmptyCatchBlock · ×9Rscript/Library/mzkit_app/src/mzquant/mzDeco.vb:193
OnErrorResumeSwallow · ×3src/assembly/assembly/MarkupData/imzML/Writer/mzPackWriter.vb:381
InvertedNullGuardsrc/mzmath/TargetedMetabolomics/MRM/IonLibrary.vb:102
TodoComment · ×23src/assembly/BrukerDataReader/Raw/DataReader.vb:72
BarePragmaDisable · ×6src/assembly/SpectrumTree/Query/TreeSearch.vb:121

+ 5 more group(s) — more in Appendix A; the complete list is findings.md.

What to do

  1. Resolve the 9 EmptyCatchBlock finding(s) in Explicit Debt — start with XcaliburRawFileIO.vb (4), mzDeco.vb, BrukerSettingsFileReader.vb. — One of this dimension's main actionable groups (9 issue-level).
  2. Resolve the 3 OnErrorResumeSwallow finding(s) in Explicit Debt — start with mzPackWriter.vb, mzStream.vb, ChemicalDescriptor.vb. — One of this dimension's main actionable groups (3 issue-level).
  3. Resolve the 1 InvertedNullGuard finding(s) in Explicit Debt — start with IonLibrary.vb. — One of this dimension's main actionable groups (1 issue-level).
  4. Stand up a CI pipeline, then gate Explicit Debt in it to reach Verified (currently Documented). — This repository has no CI pipeline, so there is nothing to add a gate to yet — the pipeline comes first. Hardens enforcement from Documented toward Prevented — provenance only; does not change the score.

Detailed fixes: d17_recommendation.md · top locations in Appendix A, every location in findings.md.

D18 · Solution Shape8.8 / 10Strong✓ Tool-verified

What it measures: Whether the solution is laid out in a sensible, conventional structure.

Method: Solution structure: project count, decomposition, shell-project detection, build success (confirmed failures cap the score); traced to actual .sln files and binaries. Deterministic.

Maturity: Documented → Verified → Prevented · effective 8.8 / 10 · rule-coverage 100% · ceiling Documented

88 projects, 1642 source files, 254169 hand-written lines of code (233360 production / 20809 test — the split is derived per file: test is what its project, its own path, or a compile-guarded region marks as test, and a file carrying no test signal counts as production), plus 3872 generated (machine-written code — designer, scaffolded and tool-emitted files — excluded from quality), 293 inter-project edges (build status unknown — did not finish). Measured across 30 solutions loaded as one workspace: `Rscript/Library/mzkit.NET5.slnx`, `src/visualize/MsPlot.NET5.sln`, `src/metadb/Lipidomics.sln`, `src/assembly/MzPackExtensions.sln`, `src/assembly/Comprehensive/Comprehensive.sln`, `src/mzmath/ms2_simulator.sln`, `src/mzmath/Mummichog.sln`, `src/mzmath/TargetedMetabolomics.sln`, `src/metadb/MoNA.sln`, `src/assembly/vendors.sln`, `src/mzmath/TargetedMetabolomics/TargetedMetabolomics.sln`, `src/mzmath/deconv.NET5.sln`, `src/mzmath/mz_deco.sln`, `src/metadb/PeaksAnnotation.sln`, `src/metadb/Massbank.sln`, `src/assembly/BrukerDataReader.sln`, `src/metadb/PubChem.NET6.sln`, `src/assembly/LoadR.NET5.sln`, `src/metadb/SMILES_struct.sln`, `src/mzmath/Oligonucleotide_MS.sln`, `src/assembly/assembly.sln`, `src/metadna/metaDNA.sln`, `src/metadna/KEGG_MetaDNA.sln`, `src/assembly/Raman-Spectroscopy.sln`, `src/mzmath/mzMath.sln`, `src/assembly/ProteoWizard.d.sln`, `src/metadna/MetaDNA_visual.sln`, `src/metadb/MetabolomeXchange.sln`, `src/metadb/KNApSAcK.sln`, `src/metadb/KEGG.sln`.

Solution references 7 projects that do not exist · ×5src/metadb/Lipidomics.sln
Solution references 4 projects that do not exist · ×4src/metadb/SMILES_struct.sln
Solution references 3 projects that do not exist · ×3src/assembly/assembly.sln
Solution references 13 projects that do not exist · ×2src/assembly/MzPackExtensions.sln
Solution references 9 projects that do not exist · ×2src/mzmath/TargetedMetabolomics.sln

+ 14 more group(s) — more in Appendix A; the complete list is findings.md.

What to do

  1. Resolve the 5 Solution references 7 projects that do not exist finding(s) in Solution Shape — start with Lipidomics.sln, deconv.NET5.sln, PeaksAnnotation.sln. — One of this dimension's main actionable groups (5 warning-level).
  2. Resolve the 4 Solution references 4 projects that do not exist finding(s) in Solution Shape — start with SMILES_struct.sln, Oligonucleotide_MS.sln, Raman-Spectroscopy.sln. — One of this dimension's main actionable groups (4 warning-level).
  3. Resolve the 3 Solution references 3 projects that do not exist finding(s) in Solution Shape — start with assembly.sln, MetabolomeXchange.sln, KEGG.sln. — One of this dimension's main actionable groups (3 warning-level).

Detailed fixes: d18_recommendation.md · top locations in Appendix A, every location in findings.md.

D20 · ADR Quality0.0 / 10Critical✓ Tool-verified

What it measures: Whether architecture decisions are recorded well (context, decision, consequences).

Method: Per-ADR judgment by language model at low temperature with two-pass stability; confidence is share of ADRs evaluated; enforcement-field presence detected deterministically. Advisory.

Maturity: Documented → Verified → Prevented · effective 0.0 / 10 · rule-coverage 100% · ceiling Documented

No architecture decision records were found.

No ADRs found

What to do

  1. Resolve the 1 No ADRs found finding(s) in ADR Quality. — One of this dimension's main actionable groups (1 recommendation-level).

Detailed fixes: d20_recommendation.md · top locations in Appendix A, every location in findings.md.

D24 · Comment Value6.2 4.4 / 10Weak✓ Tool-verified

What it measures: Whether comments are worth it — explaining WHY (valuable) rather than WHAT (redundant).

Method: Every inline C# comment compared word by word with the identifiers, literals and constructs of the code it annotates (taken from the syntax); a comment whose words that code already contains is redundant, as are closing-brace labels and generator template text. Comments giving a reason or a reference are kept; other scripts and languages are not judged. Deterministic, exhaustive, advisory.

Maturity: Documented → Verified → Prevented · effective 4.4 / 10 · rule-coverage 72% · ceiling Documented

90 of 2349 judged comments only repeat the code they sit on (3.8 %). 2083 comment(s) in another language or script were not judged.

redundant comment · ×63src/assembly/ProteoWizard.Interop/My Project/AssemblyInfo.vb:60
doc comments repeat the names · ×47src/assembly/BrukerDataReader/Raw/DataReader.vb:85

What to do

  1. Resolve the 63 redundant comment finding(s) in Comment Value — start with AssemblyInfo.vb (44), FormulaGenerator.vb (4), XcaliburRawFileIO.vb (3). — One of this dimension's main actionable groups (63 recommendation-level).

Detailed fixes: d24_recommendation.md · top locations in Appendix A, every location in findings.md.

D26 · Project Cohesion8.7 / 10Strong✓ Tool-verified

What it measures: Whether each project is a focused, coherent unit rather than an oversized grab-bag.

Method: Project size overshoot penalties (LoC / public-type count / namespace count, 2-of-3 flag) weighted by log magnitude. Exhaustive across projects, deterministic, LLM-independent.

Maturity: Documented → Verified → Prevented · effective 8.7 / 10 · rule-coverage 100% · ceiling Documented

5 of 75 projects flagged as possibly oversized/incoherent.

Projects may be oversized for their cohesion

What to do

  1. Resolve the 1 Projects may be oversized for their cohesion finding(s) in Project Cohesion. — One of this dimension's main actionable groups (1 recommendation-level).

Detailed fixes: d26_recommendation.md · top locations in Appendix A, every location in findings.md.

D28 · Secrets (history)0.0 / 10Critical✓ Tool-verified

What it measures: Whether any secrets were ever committed — scanned across the full git history, not just now.

Method: REDACTED scan via TWO gitleaks detect passes in an isolated checkout — the full git history, then a second --no-git pass over the working tree as it stands — merged and de-duplicated by (rule, file, line); each match flagged High. Both invocations are recorded in the audit trail. Exhaustive; when the tool is absent, or when its output cannot be parsed into the expected shape, the dimension is WITHHELD as an explicit measurement gap on our side — unscored and excluded from the lens, never a hedged middling score.

Maturity: Documented → Verified → Prevented · effective 0.0 / 10 · rule-coverage 100% · ceiling Documented

106 finding(s): 0 critical, 106 high, 0 medium, 0 low. Remediation for historically-committed secrets is credential rotation — they remain in history regardless of later deletion.

REDACTED
REDACTED
REDACTED

What to do

  1. Resolve the 104 REDACTED finding(s) in Secrets (history) — start with REDACTED (102), REDACTED, REDACTED. — One of this dimension's main actionable groups (104 issue-level).
  2. Resolve the 2 High secret finding(s) in Secrets (history) — start with REDACTED (2). — One of this dimension's main actionable groups (2 issue-level).
  3. Resolve the 1 Rotate the exposed credentials finding(s) in Secrets (history). — One of this dimension's main actionable groups (1 recommendation-level).

Detailed fixes: d28_recommendation.md · top locations in Appendix A, every location in findings.md.

D29 · Static Analysis (SAST)6.1 / 10Adequate✓ Tool-verified

What it measures: Real static-analysis (SAST) findings — likely security bugs in the code, any language.

Method: Polyglot static analysis via semgrep across the repo using the pinned, image-baked p/security-audit + p/owasp-top-ten rulesets (no scan-time registry fetch); severity rules (ERROR/WARNING/INFO) map to a full-band severity-weighted score. Exhaustive, deterministic; degrades on parse failure.

Coverage: semgrep pattern rules over all files — exhaustive for the rule set, blind to classes of bug without a rule (clean = no rule matched).

Maturity: Documented → Verified → Prevented · effective 6.1 / 10 · rule-coverage 100% · ceiling Documented

10 finding(s): 0 critical, 2 high, 1 medium, 7 low. semgrep hit a parse error in 32 file(s) — `Rscript/Library/mzkit_app/@export/ChemicalDraw.d.ts` (line 14), `Rscript/Library/mzkit_app/@export/GCMS.d.ts` (lines 16–17, line 21, line 116), `Rscript/Library/mzkit_app/@export/MRMLinear.d.ts` (line 24), `Rscript/Library/mzkit_app/@export/MSI.d.ts` (line 44), `Rscript/Library/mzkit_app/@export/MoleculeNetworking.d.ts` (line 46), … (+27 more) — so no absence of findings in the named regions is evidence of anything; rows reported elsewhere in those files are real. Fix the syntax error (or exclude the file deliberately) and re-scan to cover them.

REDACTED
REDACTED
REDACTED

What to do

  1. Resolve the 7 REDACTED finding(s) in Static Analysis (SAST) — start with REDACTED (2), REDACTED (2), REDACTED. — One of this dimension's main actionable groups (7 recommendation-level).
  2. Resolve the 2 REDACTED finding(s) in Static Analysis (SAST) — start with REDACTED (2). — One of this dimension's main actionable groups (2 issue-level).
  3. Resolve the 1 REDACTED finding(s) in Static Analysis (SAST) — start with REDACTED. — One of this dimension's main actionable groups (1 warning-level).

Detailed fixes: d29_recommendation.md · top locations in Appendix A, every location in findings.md.

D30 · Dependency Vulnerabilities10.0 / 10Exemplary○ Nothing flagged

What it measures: Whether any dependency has a known published vulnerability (CVE), direct or transitive, in ANY ecosystem the repository declares — Dart pub, Elixir and Erlang via Hex, Go modules, Java and Kotlin via Maven/Gradle, JavaScript/npm, .NET/NuGet, PHP/Composer, Python/PyPI, RubyGems, Rust/Cargo and Swift.

Method: Dependency-CVE scan across every ecosystem the repository declares, scored ONCE. Three sources are unioned and deduplicated by advisory identity (rule id + alias closure, CVE<->GHSA) scoped to package+version, keeping the worst severity: `osv-scanner --recursive` over osv.dev for Dart pub, Elixir/Hex (and Erlang, whose `rebar.lock` syft first converts to a CycloneDX SBOM the scanner reads, with rows attributed back to the lock), Go, Java and Kotlin via Maven/Gradle (and Scala, whose sbt build's pinned direct declarations are written into a CycloneDX SBOM the scanner reads, with rows attributed back to the build file), npm, PHP/Composer, Python/PyPI, RubyGems, Rust/Cargo and Swift; `trivy fs --scanners vuln` for npm lockfiles; and `dotnet list package --vulnerable --include-transitive` for NuGet (with per-advisory collapse of the project x target-framework fan-out), plus a DECLARED-dependency arm that resolves a published gem's gemspec against rubygems.org where no Gemfile.lock is committed. `SeverityScore(c,h,m,l, normalizer 8.0)`. NotApplicable only when NO ecosystem is readable; if any applicable ecosystem could not be scanned the findings are REPORTED and the score is withheld. Supersedes the npm and OSV arms, retired 2026-09-05.

Maturity: Documented → Verified → Prevented · effective 10.0 / 10 · rule-coverage 100% · ceiling Documented

No known-vulnerable dependencies in the 1 ecosystem(s) that were scanned (nuget packages.config). Partial dependency scan: 1 of 2 declared ecosystem(s) were scanned (nuget packages.config), and the findings above are real and complete for them. nuget was not scanned (nuget: the solution did not restore on the analyzer's .NET SDK (an SDK/target-framework/restore mismatch, common for an older codebase), so there was no restored dependency graph to scan), so this is not the whole dependency surface and the result is reported at reduced confidence.

✓ On the Gold path — maintain.

Detailed fixes: d30_recommendation.md.

D34 · Knowledge Freshness1.7 / 10Critical✓ Tool-verified

What it measures: Whether anyone still has living knowledge of each file, or it has been orphaned — last understood long ago by someone now gone quiet. The sibling of the bus factor: D16 asks who owns it, D34 asks whether anyone still knows it.

Method: File orphaning as total living-knowledge decay below one focused-commit's worth within a year, computed per-file from the D16 decay model. Exhaustive, deterministic over fixed history.

Maturity: Documented → Verified → Prevented · effective 1.7 / 10 · rule-coverage 100% · ceiling Documented

991 of 1188 significant source file(s) are orphaned — their living knowledge has decayed to nothing, so no one currently understands them. The largest is src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb. Counted over 1188 of the 1306 production source files in this repository: the rest are under the ~2,400-byte size floor this dimension measures over.

Orphaned file · ×988src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1
Most significant orphaned file · ×3src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:1
Concentrated knowledge decay

What to do

  1. Resolve the 988 Orphaned file finding(s) in Knowledge Freshness — start with Extensions.vb (22), Utils.vb (4), Provider.vb (3). — One of this dimension's main actionable groups (988 recommendation-level).
  2. Resolve the 3 Most significant orphaned file finding(s) in Knowledge Freshness — start with MsmsCharacterization.vb, LipidEieioMsmsCharacterization.vb, LipidomicsConverter.vb. — One of this dimension's main actionable groups (3 recommendation-level).
  3. Resolve the 1 Concentrated knowledge decay finding(s) in Knowledge Freshness. — One of this dimension's main actionable groups (1 recommendation-level).

Detailed fixes: d34_recommendation.md · top locations in Appendix A, every location in findings.md.

D35 · Change Coupling9.9 / 10Stronggated by 2 serious findings✓ Tool-verified

What it measures: Whether files that change together actually belong together — pairs that repeatedly co-change in git history despite having no explicit code dependency, surfacing the hidden/logical coupling (and boundaries in the wrong place) a static scan can't see.

Method: Pairwise co-occurrence over the per-commit file sets in git history (production source only — tests and generated dropped): Degree-of-Coupling = shared ÷ min individual revisions, reported above noise floors (each file ≥10 revisions, ≥5 shared commits, ≥50% strength); sweeping commits excluded. Deterministic over fixed history.

Coverage: Population: PRODUCTION source files only — test and generated files are dropped before pairing, so a class co-changing with its own test (trivially ~100%) can't drown the real production↔production coupling. Pairs ranked by Degree-of-Coupling. A non-source file is never a coupling PARTICIPANT either: documentation, schemas, config and data files are dropped with the rest, so a code↔docs pair — a command and the reference page that restates it — is not reported however strongly the two co-change; nor is coupling that runs THROUGH a build step or config file.

Maturity: Documented → Verified → Prevented · effective 9.9 / 10 · rule-coverage 100% · ceiling Documented

Strongest change-coupling: GCxGCTIC2DPlot.vb↔GCxGCTIC3DPeaks.vb 55%; ChromatogramPeakPlot.vb↔PeakTablePlot.vb 50%; TICplot.vb↔PeakTablePlot.vb 50%

Change coupling: GCxGCTIC2DPlot.vb ↔ GCxGCTIC3DPeaks.vbsrc/visualize/ComprehensiveMsPlot/GCxGC/GCxGCTIC2DPlot.vb:1
Change-coupling hub: PeakTablePlot.vb → GCxGCTIC2DPlot.vb, ChromatogramPeakPlot.vb, TICplot.vb, PeakAssign.vb, RawScatterPlot.vbsrc/visualize/plot/PeakTablePlot.vb

What to do

  1. Resolve the 1 Change coupling finding(s) in Change Coupling — start with GCxGCTIC2DPlot.vb. — One of this dimension's main actionable groups (1 warning-level).
  2. Resolve the 1 Change-coupling hub finding(s) in Change Coupling — start with PeakTablePlot.vb. — One of this dimension's main actionable groups (1 warning-level).

Detailed fixes: d35_recommendation.md · top locations in Appendix A, every location in findings.md.

D37 · Vulnerability-disclosure Policy4.0 / 10Weak✓ Tool-verified

What it measures: Whether the repository publishes a coordinated-vulnerability-disclosure policy (SECURITY.md or security.txt) with a reporting contact, so finders know how to report a vulnerability. Presence of a policy file with a contact, not whether the policy is adequate or honoured.

Method: Vulnerability-disclosure policy read deterministically from the repo: a SECURITY.md (root/.github/docs) or .well-known/security.txt / security.txt, regex-checked for a reporting contact (email / URL / mailto). Present + contact → 10; present without a contact → 4; NotApplicable when no policy file exists (it may live off-repo). Detects the policy file's presence + contact, not its adequacy.

Maturity: Documented → Verified → Prevented · effective 4.0 / 10 · rule-coverage 100% · ceiling Documented

A vulnerability-disclosure policy (SECURITY.md) is present but lists no reporting contact.

REDACTED

What to do

  1. Resolve the 1 REDACTED finding(s) in Vulnerability-disclosure Policy. — One of this dimension's main actionable groups (1 recommendation-level).

Detailed fixes: d37_recommendation.md · top locations in Appendix A, every location in findings.md.

D43 · Malicious Dependencies10.0 / 10Exemplary✓ Tool-verified

What it measures: Whether any dependency the repository declares is published as MALICIOUS rather than merely vulnerable — a package that is an attacker's work, in any ecosystem osv-scanner reads. Scored apart from D30 because the answer is binary: there is no safe version to upgrade to, and the fix is to remove the package and rotate every credential it could have read.

Method: The same dependency scan D30 reads, partitioned on the scanner's own classification rather than rescanned: a row is MALICIOUS when its id is in the `MAL-` space (the ossf/malicious-packages feed) OR its `database_specific.cwe_ids` carries `CWE-506` ("Embedded Malicious Code"). Both channels are structural; the summary text is deliberately NOT read, because a malicious-package record whose summary says only "Critical severity vulnerability" is a real shape ([GHSA redacted]) and a text matcher misses it. Scored BINARY: any surviving row is 0, whatever its severity and however many CVEs sit beside it — a hostile dependency is not a quantity. Applicability and degradation are D30's: NotApplicable only when no ecosystem is readable, and an unscannable ecosystem degrades rather than reading clean. SCORED, not informational.

Maturity: Documented → Verified → Prevented · effective 10.0 / 10 · rule-coverage 100% · ceiling Documented

No dependency in any ecosystem this repository declares is published as malicious.

✓ On the Gold path — maintain.

Detailed fixes: d43_recommendation.md.

D44 · Platform End-of-Life6.0 / 10Adequate✓ Tool-verified

What it measures: Whether anyone still ships security patches for the platform this repository RUNS ON — the runtime it pins and the framework majors its own constraints hold it to. Separate from D12 because the question differs: a current Django on an end-of-life Python is perfectly up to date and completely unsupported, and the fix is a migration rather than a version bump. What the repository says it merely SUPPORTS is never charged.

Method: End-of-life PLATFORM read from the repository's own declarations and graded against a FROZEN, dated table of vendor support dates — no network, no feed, no API, so this dimension answers identically inside a closed scan fence. Two subjects: a RUNTIME the project pins (a single or all-end-of-life TargetFramework, a .nvmrc or .python-version, a requires-python CAP) and a FRAMEWORK major a dependency constraint cannot move off (a caret, tilde or exact version; `vue@^2.7.16` pins Vue 2). A FLOOR is deliberately never charged — `requires-python = ">=3.8"` states what a package SUPPORTS, not what it runs on — and a multi-target project is charged only when EVERY target is out of support. Runtime 4.0/product capped 8.0, framework 1.5 capped 4.5. The table is safe to freeze because a statement about support that ended in the past cannot become false: it loses recall as it ages, never precision, and a test asserts every entry predates the freeze date. Disjoint from D31 (a container image's OS layer) and D29 (the toolchain a CI workflow installs). Abstains when the repository declares no platform this pass reads — never scores it clean.

Maturity: Documented → Verified → Prevented · effective 6.0 / 10 · rule-coverage 100% · ceiling Documented

1 end-of-life runtime(s) and 0 end-of-life framework(s), read from 56 platform declaration(s) and 0 dependency declaration(s). This dimension reads what the repository says about ITSELF — a pinned target framework, a version file, a capped requires-python, a Rust toolchain pin, a framework major a constraint cannot move off. A FLOOR is deliberately never charged: `requires-python = ">=3.8"` states what the package SUPPORTS, not what it runs on, and a well-maintained library declares exactly that while running its own CI on a current release. The end-of-life facts are FROZEN and dated, so this dimension needs no network and answers identically inside a closed scan fence; as the table ages it loses recall and never precision, because a statement about support that ended in the past cannot become false. The OS layer of a container image is D31's question and the toolchain a CI workflow installs is D29's; this row is neither.

End-of-life runtime: .NET net6.0src/mzmath/Oligonucleotide_MS/test/test.vbproj:6

What to do

  1. Resolve the 1 End-of-life runtime finding(s) in Platform End-of-Life — start with test.vbproj. — One of this dimension's main actionable groups (1 warning-level).

Detailed fixes: d44_recommendation.md · top locations in Appendix A, every location in findings.md.

Frontend & cross-cutting dimensions

R = React/JS · M = Maturity · P = Readiness.

AX10 · Code composition9.8 / 10Exemplary✓ Tool-verified

Other · Architecture — How the codebase splits by code ROLE — domain, application, infrastructure, test, generated. The significance map behind the knowledge/coupling weighting, and a DDD signal in its own right: a thin domain core under fat infrastructure is the anemic-domain smell, quantified. How each file's role is decided, because the split is only as good as that: a generated name or a build-output tree makes it Generated, a test project makes it Test, and otherwise the file's NAMESPACE and PATH words are matched against fixed vocabularies in a fixed ORDER — domain, then infrastructure, then application — so a file whose words hit two layers is counted under the earlier one. A production file matching none of them counts as application, so that share reads 'application or unclassified' rather than a measured application layer. Roles come from naming convention, never from what the code does. On this repository the split was taken from the source tree on disk rather than from a loaded .NET workspace, so a file's role is decided by its PATH segments alone — no declared namespace was available to add to the evidence — and generated output is excluded from the census entirely rather than counted as a generated share.

Method: Roslyn line-count by code ROLE: every source file classified Domain/Application/Infrastructure/Test/Generated by namespace + path convention (the shared CodeRoleClassifier), then significant lines summed per role. Deterministic; the advisory score is the business-logic (domain+application) share of production code.

Coverage: Population: ALL source files, each bucketed into ONE of five roles (Domain/Application/Infrastructure/Test/Generated) by namespace + path convention — a file whose layer isn't named in the convention falls to Application (the neutral default), and the split is line-count, not semantic depth or business value.

What to do

  • The domain core is a small share of production code, but most of the rest matched no layer vocabulary at all — so this is not yet an anemic-domain finding. The namespace/path convention could not place that code, which makes the composition above a statement about the naming, not about the design. Name the layers (or check that the repository's conventions differ from the ones this check knows) before reading a thin domain into it.
AX3 · Project dependency cycles10.0 / 10Exemplary✓ Tool-verified

Other · Architecture — Whether the project-reference graph is acyclic (cycles block independent build/deploy and signal eroding boundaries).

Method: Project reference cycles via elementary-DFS over real .csproj references, using the engine shared with D5/D7; cyclic versus acyclic. Exhaustive, deterministic.

AX4 · Dependency direction10.0 / 10Exemplary✓ Tool-verified

Other · Architecture — Whether dependencies point inward (Domain ← Application ← Infrastructure/Web) — the clean-architecture dependency rule, checked across the project graph.

Method: Layer violations by name-segment inference (Domain/Core to Application to Infrastructure/Web) over the project-reference graph. Exhaustive over all projects, deterministic.

AX5 · Architecture & structure10.0 / 10Exemplary✓ Tool-verified

Other · Architecture — Whether the codebase has a recognisable, scale-appropriate structure (a named architectural style, or modular enough for its size) rather than being an ad-hoc ball of mud.

Method: Roslyn plus csproj analysis: architecture style detection (DDD, clean, vertical-slice, CQRS) and structure fitness for repo size. Deterministic.

AX6 · Interface segregation10.0 / 10Exemplary✓ Tool-verified

Other · Architecture — Whether interfaces stay focused rather than fat — the Interface-Segregation principle (SOLID 'I').

Method: Roslyn scan: public interface declared-member counts (accessors fold into their property/event); fat-interface threshold (over 15 declared members) flagged per type. Each finding also reports the distinct-OPERATION count — members counted by name, so an overload group counts once — which decides whether it states the caller-side ISP harm or the implementer-side burden of an overload set. TypeScript: exported interfaces that declare behaviour, counted over their REQUIRED operations (method signatures and function-typed properties with no `?`, once per signature) — data-shape interfaces and ambient .d.ts declarations are outside the population; JavaScript declares no interfaces and is not applicable. Deterministic, type-level.

  • `ICrossReference` declares 20 members: `chebi`, `KEGG`, `KEGGdrug`, `pubchem`, `HMDB`, `metlin`, `DrugBank`, `ChEMBL`, `Wikipedia`, `lipidmaps`, `MeSH`, `ChemIDplus`, `MetaCyc`, `KNApSAcK`, `foodb`, `chemspider`, `CAS`, `InChIkey`, `InChI`, `SMILES`. Counted as the author wrote them — a property is ONE member and its get/set accessors are not counted separately, and an event counts once. A wide interface forces every implementer and caller to depend on methods they don't use (the Interface-Segregation 'I' in SOLID). Split it into focused role-interfaces. — src/metadb/Chemoinformatics/Metabolite/CrossReference/CrossReference.vb:67

What to do

  • Split fat interfaces into focused role-interfaces so clients depend only on what they use.
GD1 · Unfinished & placeholder code10.0 / 10Exemplary○ Nothing flagged

Other · Code Health — Unreviewed-generation residue: shipped members still throwing NotImplementedException, and placeholder string literals left in non-test, non-generated code. Scored as a quality signature, never as a claim about authorship.

Method: Roslyn syntax scan: NotImplementedException throws and placeholder string literals in non-test, non-generated shipped code. Deterministic, code-shape signature.

M1 · Documentation (README)5.3 / 10Adequate✓ Tool-verified

Maturity · Maturity — Whether the repo and its projects have a README, and whether it's substantive and current.

Method: Filesystem scan: README presence, word count, and headings for depth; git history for staleness. Exhaustive across root and project dirs, deterministic.

  • 220 code files changed in the last 6 months but the README was not touched — it may no longer reflect the system.

What to do

  • Explain in the README how to run the tests. Add a section called Testing to the README in the repository's top folder, saying how to run the test suite.
  • Add an 'Architecture' / 'How it works' section to the root README — the high-level shape.
  • Add a README to the 66 of 71 project(s) that lack one — worth up to 1.9 pts.
  • Review the README against recent changes; refresh the parts that drifted.
M2 · Architecture documentation0.0 / 10Critical✓ Tool-verified

Maturity · Maturity — Whether key decisions (ADRs) and the high-level shape (C4/diagrams) are written down.

Method: Filesystem scan: ADR folder/naming conventions or content, plus Mermaid/PlantUML/C4/architecture.md discovery. Exhaustive, deterministic.

  • No Architecture Decision Records found — no conventional ADR directory, no numbered `NNNN-title` documents in any markup this check reads, and nothing ADR-shaped by content. Design rationale recorded elsewhere (a design-notes tree, a mailing list, pull-request discussion) is not visible to this check and is not re-findable per decision, so a future maintainer cannot ask why one choice was made and get an answer.
  • No C4/Structurizr/PlantUML/Mermaid/Graphviz/D2 diagram, no drawn diagram named for the architecture, no file named `architecture` or `design` in any markup this check reads, and nothing in the README, docs or contributor guides that announces the shape — no `## Architecture` heading, no "architecture overview"/"high-level design" phrasing, no "the architecture is …" introduction, no guided code tour. A shape laid out in prose that never names itself as the architecture is not visible to this check, and neither is one kept outside the repository, so this row reports the absence of a re-findable shape document — not evidence that nobody wrote the shape down.

What to do

  • Record your significant design decisions. Write one short document per decision, giving its date, the situation, the decision and its consequences, and keep them together with your other design documents. A docs/adr folder with each file named by number and title is the easiest place to find them.
  • Add a C4 context/container diagram (Structurizr, PlantUML or Mermaid) or an architecture.md overview.
M3 · Folder & project structure8.0 / 10Strong✓ Tool-verified

Maturity · Maturity — Whether the repo is organised deliberately — src/test separation and consistent project naming.

Method: Filesystem scan: src/test folder separation and namespace-prefix consistency (majority RootNamespace agreement). Exhaustive across projects, deterministic.

  • Only 40/75 projects share a common root namespace — the code's module identity is inconsistent.

What to do

  • Adopt a consistent root-namespace convention (a shared prefix, e.g. Acme.*); short project-file/directory names are fine as long as the RootNamespace is uniform.
P1 · CI/CD gates0.0 / 10Critical✓ Tool-verified

Readiness · Readiness — Whether an automated pipeline builds and tests every change.

Method: Filesystem scan: CI workflow files (.github/workflows, .gitlab-ci.yml, etc.) for build and test stages. Exhaustive, deterministic.

  • No CI workflow found (.github/workflows, azure-pipelines.yml, .gitlab-ci.yml, …) — changes aren't gated by an automated build/test.

What to do

  • Add a CI workflow that builds and runs the test suite on every push/PR.
P3 · Security & performance tooling0.0 / 10Critical✓ Tool-verified

Readiness · Readiness — Whether SAST, secret/dependency scanning and performance benchmarking are wired in (presence, not runtime).

Method: Filesystem scan: SAST configuration, dependency-update automation, secret scanning, and a benchmark harness or benchmark step — in this repository's own ecosystem. Exhaustive, deterministic.

  • No static application security testing detected. For this repository's stack, add a Roslyn security analyzer package referenced from the project (the analyzer packages do analyse VB.NET), plus gitleaks for committed secrets — CodeQL has no VB.NET extractor, so its csharp pack would extract nothing from this tree and then report it clean — this repository has no CI pipeline yet, so run it locally to clear the existing findings, then make it a step of the first workflow you add so a regression fails the build. What was searched, so you can tell an absence from a miss: the 0 CI workflow file(s) in this repository, and the scanner and linter configuration checked in beside them. A scan that runs outside CI, one configured in your forge's web UI rather than in a committed file, or a tool whose name is none of those this check carries, is not seen — if that is your case the row is wrong, and saying so is more useful than adding a second scanner.

What to do

  • Run what this repository's stack ships: a Roslyn security analyzer package referenced from the project (the analyzer packages do analyse VB.NET), plus gitleaks for committed secrets — CodeQL has no VB.NET extractor, so its csharp pack would extract nothing from this tree and then report it clean — locally for now, since there is no CI pipeline here yet, and as a step of the first workflow you add so a security regression fails the build instead of landing.
  • Enable Dependabot/Renovate or a dependency-review gate.
  • Add gitleaks/trufflehog in CI to block PRs that introduce committed secrets.
P6 · Release Hygiene10.0 / 10Exemplary✓ Tool-verified

Readiness · Readiness — Whether releases are traceable — a maintained changelog and explicit version stamping.

Method: Filesystem scan: changelog file presence and version tags in csproj or git tags. Exhaustive, deterministic.

S1 · Web-Security Posture8.0 / 10Strong✓ Tool-verified

Other · Security — Only what this repository's own non-C# files could be read for was assessed — markup this repository SHIPS is scored for third-party script integrity whether or not the repository serves it itself, since a page handed to a consumer runs in that consumer’s origin. Nothing else in this dimension was assessed: the transport, cookie, input-validation and crypto controls are read from a source model that was not loaded for this repository’s language, so their absence here is not a finding about this repository.

Method: Roslyn plus filesystem scan: HSTS/security headers, secure cookies, input validation, middleware order, weak crypto (MD5/SHA1/DES); HTTPS-metadata context-aware. On a repository with no .NET source it reads JavaScript/TypeScript, Dart, Ruby, Scala, Rust or Elixir source itself (test, vendored, generated and minified paths not) for the arms that hold whether or not the code serves HTTP: a weak hash or cipher, key material fixed in the source, a TLS client that accepts any certificate, and (JavaScript/TypeScript, Ruby, Scala, Rust and Elixir) an obsolete TLS version; the server controls are not assessed there, and a Dart, Ruby, Scala, Rust or Elixir repository that serves no HTTP of its own is N/A on them. Deterministic.

  • `https://query.biodeep.cn/resources/vendor/jquery-3.7.1.min.js` is executed by this page with no Subresource Integrity. Whoever can answer that request — the CDN, anyone who compromises it, anyone on the network path — runs arbitrary script in this page's origin, with its session. The URL also names no version, so it resolves to whatever that origin serves at fetch time — the executed bytes can change with nobody touching this repository. 2536 such include(s) across the repository's markup. — Rscript/Library/mzkit_app/data/MRM/linears.html:15

What to do

  • Pin third-party scripts and verify them: name an exact version in the URL and add an `integrity="sha384-…"` hash alongside `crossorigin="anonymous"` (both are required — an integrity hash on a cross-origin script without `crossorigin` is not evaluated, it blocks the script). Where the vendor ships a continuously-updated loader and publishes no stable hash (tag managers, analytics, chat widgets), Subresource Integrity is not available: constrain it instead with a `Content-Security-Policy` that names the exact origins allowed to execute, and drop the script from the pages that do not need it. Where the page is shipped inside a package that others host, prefer vendoring the asset and serving it from the app’s own origin, so no consumer inherits a third-party dependency they did not choose.
X28 · Index access outside its own emptiness guard10.0 / 10Exemplary○ Nothing flagged

Other · Code Health — Whether a condition that tests a value for emptiness indexes that same value only where the test holds — an `||` written one parenthesis too far to the left leaves an index access outside the guard beside it, so the empty case the guard exists to anticipate reaches the index and throws.

Method: Roslyn syntax only, no semantic model: the OUTERMOST `&&`/`||` of every boolean condition, read for a symbol the condition tests for emptiness (`string.IsNullOrEmpty`/`IsNullOrWhiteSpace`, a `Length`/`Count` comparison against a literal, `Any()`, a `Length`/`Count` pattern, or a comparison against `""`) and ALSO indexes. Each `symbol[...]` access is placed by a boolean-reachability walk from the access up to the outermost connective: an access is COVERED when some enclosing step has it in the right operand and the left operand, under the truth value that step forces, proves the symbol non-empty — a recursion over `&&`/`||` whose true- and false-directions are asymmetric. A finding needs BOTH an uncovered access and a covered one on the same symbol in the same condition, which is the agreeing twin that separates a misplaced parenthesis from an unrelated length test. Bare index accesses with no emptiness test in the condition are neither counted nor reported; a non-identifier receiver and a lambda nested inside the condition are outside the population. Deterministic, provable per finding. Advisory.

Reference — by lens

The score is the rank-weighted fold of these lenses (worst-heaviest), each including its meta-dimensions; a lens with a Critical contributor is capped at Fair (its band reads "gated by …") and is never the strongest area however high its average.

LensScoreRatingImpact
Code Health79%Adequate — gated by D1, D2Capped at Fair by a Critical contributor — resolve it before relying on this lens.
Architecture98%ExemplaryStrongest area.
Maturity39%Weak — gated by D34, M2Capped at Fair by a Critical contributor — resolve it before relying on this lens.
Readiness36%Weak — gated by P1, P3Capped at Fair by a Critical contributor — resolve it before relying on this lens.
Security67%Adequate — gated by D28Capped at Fair by a Critical contributor — resolve it before relying on this lens.
Unscored — 1 check(s) recorded observations but carry no score

These checks ran and found something, but they do not carry a score — either by design (an advisory check reports evidence rather than grading it) or because they could not be scored here. They are excluded from the score for that reason, not because there was nothing to see.

  • SC1 Supply-chain hygiene — 1 observation(s) recorded · Advisory — this card reports evidence and never carries a score, so there is nothing missing here.
Not evidenced — 5 control(s) we could not find positive evidence for

These checks grade a working control, and the repository shows no evidence of one. That is deliberately not scored as a zero: a repository cannot show an ops runbook, a database TTL or an infrastructure-side audit log, so absence of evidence here is not evidence the control is missing. It is also not a statement that the check is irrelevant to this codebase — the thing it grades applies; we just could not see it. Excluded from the score either way.

  • C3 Audit Trail — Not assessed: these audit controls are read from a source model (declarative annotations, request middleware, entity/column names, guard methods) that was not loaded for this repository — because the repository is written in a language this check does not yet model, or because its projects failed to load. Absence of an idiom this check recognises is NOT evidence that this repository lacks audit controls: it may implement them entirely in its own ecosystem. This is a gap in the analyzer's language coverage, not a finding about this repository.
  • C4 Data Retention — Not assessed: these retention controls are read from a source model (declarative annotations, request middleware, entity/column names, guard methods) that was not loaded for this repository — because the repository is written in a language this check does not yet model, or because its projects failed to load. Absence of an idiom this check recognises is NOT evidence that this repository lacks retention controls: it may implement them entirely in its own ecosystem. This is a gap in the analyzer's language coverage, not a finding about this repository.
  • C5 Data-Subject Rights — Not assessed: these data-subject rights controls are read from a source model (declarative annotations, request middleware, entity/column names, guard methods) that was not loaded for this repository — because the repository is written in a language this check does not yet model, or because its projects failed to load. Absence of an idiom this check recognises is NOT evidence that this repository lacks data-subject rights controls: it may implement them entirely in its own ecosystem. This is a gap in the analyzer's language coverage, not a finding about this repository.
  • P4 Deployment & Rollback — not evidenced — no deploy/rollback/approval signal in the repo; absence of evidence is not evidence of a manual release
  • P5 DR & Backup — not evidenced — repo shows no backup/RTO/RPO controls; absence of evidence is not evidence of a working control
Not included — 77 check(s) not relevant to this codebase

These checks had nothing to measure here (no tests, no git history, the codebase is small, or the architecture style doesn't apply), so they're omitted above rather than scored low.

  • AC1 Text alternatives — No user-facing web UI (the repo is a library/CLI/worker/headless service) — accessibility is not applicable.
  • AC2 Forms & labels — No user-facing web UI (the repo is a library/CLI/worker/headless service) — accessibility is not applicable.
  • AC3 Page structure — No user-facing web UI (the repo is a library/CLI/worker/headless service) — accessibility is not applicable.
  • AC4 Keyboard semantics — No user-facing web UI (the repo is a library/CLI/worker/headless service) — accessibility is not applicable.
  • AC5 ARIA correctness — No user-facing web UI (the repo is a library/CLI/worker/headless service) — accessibility is not applicable.
  • AC6 Visual & motion safety — No user-facing web UI (the repo is a library/CLI/worker/headless service) — accessibility is not applicable.
  • AC7 A11y enforcement — No user-facing web UI (the repo is a library/CLI/worker/headless service) — accessibility is not applicable.
  • AX1 Captive dependencies — no DI registrations detected
  • AX2 Stateful singletons — no singleton implementations detected
  • AX7 Slice cohesion — not applicable — not a vertical-slice architecture
  • AX8 Test isolation — no test/production split to check
  • AX9 CQS / query purity — no CQRS query handlers detected — query purity is not applicable to this codebase
  • AXB1 Runtime evidence locked — no reproducible boot — Advisory — this card reports evidence and never carries a score, so there is nothing missing here.
  • C1 Data Protection — Not assessed: these personal data controls are read from a source model (declarative annotations, request middleware, entity/column names, guard methods) that was not loaded for this repository — because the repository is written in a language this check does not yet model, or because its projects failed to load. Absence of an idiom this check recognises is NOT evidence that this repository lacks personal data controls: it may implement them entirely in its own ecosystem. This is a gap in the analyzer's language coverage, not a finding about this repository.
  • C2 Access Controls — Not assessed: these authorization controls are read from a source model (declarative annotations, request middleware, entity/column names, guard methods) that was not loaded for this repository — because the repository is written in a language this check does not yet model, or because its projects failed to load. Absence of an idiom this check recognises is NOT evidence that this repository lacks authorization controls: it may implement them entirely in its own ecosystem. This is a gap in the analyzer's language coverage, not a finding about this repository.
  • D10 Test Quality — ~21459 lines of test source are present (.vb) but no test cases reached the test census for this repository — no test root we could resolve declared them, or the files we read declare no cases in a test framework we recognise — so skipped/assertion-free tests couldn't be counted. Not scored — this is a gap in the analyzer, not a finding about this repository.
  • D11 Test Reliability — Test reliability not measured — no test run produced results
  • D12 Dependency Hygiene — Dependency hygiene not measured
  • D16 Bus Factor — single-maintainer repository — bus factor is not applicable
  • D19 Documentation Quality — D19 withholds "Documentation: empty section": 5 candidate(s) were measured and not published.
  • D21 Naming Consistency — Naming consistency is measured on C# only; JavaScript, Python, Visual Basic, html not measured.
  • D22 Internal API Consistency — No intentionally-exposed public API to evaluate for consistency.
  • D23 Boundary Type-Coupling — Cross-context type coupling could not be assessed — this codebase's bounded contexts are neither declared nor inferable.
  • D25 ADR Conformance — no ADRs to check
  • D27 Navigability — symbol resolution incomplete — navigability not assessed
  • D31 IaC & Container Security — No Infrastructure-as-Code or container manifests found (Dockerfile, Docker Compose, Terraform, Kubernetes/Helm, CloudFormation, ARM, Bicep, Ansible); nothing to scan.
  • D32 Data Compliance (PII/GDPR) — 16 file(s) were not parsed by semgrep — the PII/GDPR ruleset never ran over them
  • D36 Supply-chain Provenance & Signing — No CI/build pipeline found (.github/.forgejo/.gitea workflows, .circleci, .buildkite, .woodpecker, .teamcity, .gitlab-ci.yml, .travis.yml, bitbucket-pipelines.yml, .drone.yml, .cirrus.yml, .woodpecker.yml, appveyor.yml, azure-pipelines*.yml, .pipelines/, .vsts-ci/, .azuredevops/, Jenkinsfile); there is no build to attest provenance for.
  • D39 IL Efficiency — IL not measured — the analyzer's build of the target did not succeed
  • D40 Network Egress Confinement — No Kubernetes/orchestration workloads found in the repository manifests; network egress policy is a cluster-native control that may live at the platform/firewall layer, so there is nothing to assess here.
  • D41 Kernel & Syscall Confinement — No Kubernetes/orchestration workloads found in the repository manifests; seccomp/AppArmor/SELinux confinement is a workload-level control, so there is nothing to assess here.
  • D42 Runtime Threat Enforcement — No Kubernetes/orchestration workloads found in the repository manifests; runtime threat-detection and admission-control policy are cluster-level controls, so there is nothing to assess here.
  • D7 Architectural Integrity — no checkable ADRs and no dependency cycles — architectural integrity not assessed
  • D8 Code Coverage — Coverage NOT MEASURED: `--collect:"XPlat Code Coverage"` names a data collector that ships in the `coverlet.collector` package, and this repository wires up none — no test project references it and no runsettings declares one. The absence of coverage here is therefore not evidence about the suite or about our analyzer environment: without a collector, `--collect` produces nothing even from a suite that builds and passes. Add a `coverlet.collector` PackageReference to the test project(s) (or commit the Cobertura/OpenCover/lcov report your CI produces) and real coverage will be measured. It is excluded from the score rather than counted as a near-zero defect.
  • D9 Test Distribution — Test source is present (.vb) but no test cases reached the test census for this repository — no test root we could resolve declared them, or the files we read declare no cases in a test framework we recognise — so its unit/integration/BDD/E2E split couldn't be counted. Not scored — this is a gap in the analyzer, not a finding about this repository.
  • DM1 Domain Modelling — not scored — this repository shows none of the 3 signals this lens looks for
  • ED1 Event-Driven — not scored — this repository shows none of the 3 signals this lens looks for
  • ED5 Idempotency — no mutating command handlers or message consumers detected — idempotency check not applicable
  • ES1 Event Sourcing — not scored — this repository shows none of the 3 signals this lens looks for
  • IC1 Incompleteness & stubs — not analysed — these correctness checks read a source model that was not loaded for this repository, because the repository is written in a language this check does not yet model, or because its projects failed to load. This is a gap in the analyzer, not a finding about this repository
  • M4 Documentation accuracy — Not applicable: the 25 current-state document(s) make no claim of a kind M4 checks. 3 claim(s) of kinds M4 does not check were not checked (path 3); M4 checks only links and versions.
  • P12 CI test-gate honesty — no CI workflow found
  • P2 Observability — This repo is a library, not a deployed service — it has no process to operate, so production observability (structured logging, tracing/metrics, health checks) is N/A. A library may log via an injected ILogger, but the absence of operational telemetry is not a defect here. If it grows a host (web API, worker), the dimension reactivates.
  • P7 Outbound HTTP resilience — not applicable — this isn't a service/API/worker
  • P8 Schema migrations — no EF Core usage detected
  • P9 Domain vs controller coverage — no coverage report found on disk — produce a coverage report in a standard format (Cobertura — `dotnet test --collect:"XPlat Code Coverage"` with a `coverlet.collector` PackageReference) and commit it — a hosted scan measures a clone of the repository, so a report that exists only in a working tree, a CI runner's or your own, never reaches it; the artefact is commonly gitignored, so `git add -f` that one file (or un-ignore its path) and commit it alongside the code it measures, or wire coverage collection into CI, to enable this cross-layer check
  • PF1 Benchmark discipline — Not applicable: no benchmark suite was found. This check searched for a BenchmarkDotNet reference in an .fsproj or .vbproj, and for a `*benchmark*` script that this repository's CI runs. Benchmarks are credited as a bonus, so their absence is neither scored nor deducted.
  • PF2 Allocation hygiene — Not applicable: allocation awareness is rated where code engineers for it — at least 400 production lines that ship benchmarks or already use allocation-aware idioms (8 or more). This repository's Visual Basic code has 275,326 production line(s), 0 such use(s) and no benchmarks, so there is no allocation work to rate. The card is reward-only: its absence costs nothing.
  • PF3 Async & latency hygiene — Not applicable: this repository declares no async functions, so there is no asynchronous code for a blocking call to stall.
  • X1 Async correctness — not analysed — these correctness checks read a source model that was not loaded for this repository, because the repository is written in a language this check does not yet model, or because its projects failed to load. This is a gap in the analyzer, not a finding about this repository
  • X10 Duplicated predicate — Advisory — this card reports evidence and never carries a score, so there is nothing missing here.
  • X12 Unreachable branch — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
  • X13 Undrained process stream — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
  • X14 Bypassable address classification — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
  • X15 Unvalidated length from an untrusted reader — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
  • X16 Unfloored truncation loop — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
  • X17 Uncapped recursion over a caller-supplied document — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
  • X18 Disposal-pattern correctness — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
  • X19 Unrestored process-global state — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
  • X2 Cancellation propagation — not analysed — these correctness checks read a source model that was not loaded for this repository, because the repository is written in a language this check does not yet model, or because its projects failed to load. This is a gap in the analyzer, not a finding about this repository
  • X20 Mistyped argument guard — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
  • X21 Side-effecting pattern guard — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
  • X22 Contradicted release guard — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
  • X23 Unguarded diagnostic materialisation — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
  • X24 Document value interpolated into markup unescaped — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
  • X25 Inert configuration knob — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
  • X26 Unsynchronised callback handoff — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
  • X27 Collection changed while being enumerated — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
  • X29 Per-element action decided by a fixed element — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
  • X3 Exception handling — not analysed — these correctness checks read a source model that was not loaded for this repository, because the repository is written in a language this check does not yet model, or because its projects failed to load. This is a gap in the analyzer, not a finding about this repository
  • X30 Support guard that admits what it rejects — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
  • X32 Type resolved by simple name across every loaded assembly — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
  • X4 Structured logging — not analysed — these correctness checks read a source model that was not loaded for this repository, because the repository is written in a language this check does not yet model, or because its projects failed to load. This is a gap in the analyzer, not a finding about this repository
  • X5 Nullable reference types — not analysed — these correctness checks read a source model that was not loaded for this repository, because the repository is written in a language this check does not yet model, or because its projects failed to load. This is a gap in the analyzer, not a finding about this repository
  • X6 Hand-rolled structured-format parsing — Advisory — this card reports evidence and never carries a score, so there is nothing missing here.
  • X7 Silent fallback defaults — Advisory — this card reports evidence and never carries a score, so there is nothing missing here.
  • X9 Subsumed condition operand — Advisory — this card reports evidence and never carries a score, so there is nothing missing here.

Appendix A — Findings (grouped)

The findings behind the scores, grouped by severity, then by dimension and kind. The high-severity issues are enumerated in full below; items per group are capped at 25 with any overflow stated explicitly per group, never silently truncated. The complete machine-readable list of every finding (all severities) is the companion findings.md in this report's bundle.

Critical — 121 finding(s)
D28 · Secrets (history) · REDACTED · ×104
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  • + 79 more in this group — see findings.md.
D17 · Explicit Debt · EmptyCatchBlock · ×9
  • EmptyCatchBlock Rscript/Library/mzkit_app/src/mzquant/mzDeco.vb:193 — empty catch block — the error is discarded with nothing recorded, so a failure here leaves no trace anywhere. Record it through whatever this codebase already uses to report problems, or let it propagate. Where swallowing one specific failure really is correct — as it often is on a teardown/dispose path where throwing would mask the original failure — catch exactly that exception type and write down WHY in a comment on the catch. Both are needed: a comment on a catch-all still swallows every failure nobody anticipated, and a note that only restates the swallow ("ignored", "do nothing") is read as no explanation at all.
  • EmptyCatchBlock src/assembly/BrukerDataReader/Raw/BrukerSettingsFileReader.vb:190 — empty catch block — the error is discarded with nothing recorded, so a failure here leaves no trace anywhere. Record it through whatever this codebase already uses to report problems, or let it propagate. Where swallowing one specific failure really is correct — as it often is on a teardown/dispose path where throwing would mask the original failure — catch exactly that exception type and write down WHY in a comment on the catch. Both are needed: a comment on a catch-all still swallows every failure nobody anticipated, and a note that only restates the swallow ("ignored", "do nothing") is read as no explanation at all.
  • EmptyCatchBlock src/assembly/ProteoWizard.Interop/ProteoWizardCLI.vb:339 — empty catch block — the error is discarded with nothing recorded, so a failure here leaves no trace anywhere. Record it through whatever this codebase already uses to report problems, or let it propagate. Where swallowing one specific failure really is correct — as it often is on a teardown/dispose path where throwing would mask the original failure — catch exactly that exception type and write down WHY in a comment on the catch. Both are needed: a comment on a catch-all still swallows every failure nobody anticipated, and a note that only restates the swallow ("ignored", "do nothing") is read as no explanation at all.
  • EmptyCatchBlock src/assembly/SpectrumTree/Pack/Compression.vb:100 — empty catch block — the error is discarded with nothing recorded, so a failure here leaves no trace anywhere. Record it through whatever this codebase already uses to report problems, or let it propagate. Where swallowing one specific failure really is correct — as it often is on a teardown/dispose path where throwing would mask the original failure — catch exactly that exception type and write down WHY in a comment on the catch. Both are needed: a comment on a catch-all still swallows every failure nobody anticipated, and a note that only restates the swallow ("ignored", "do nothing") is read as no explanation at all.
  • EmptyCatchBlock src/assembly/ThermoRawFileReader/XcaliburRawFileIO.vb:374 — empty catch block — the error is discarded with nothing recorded, so a failure here leaves no trace anywhere. Record it through whatever this codebase already uses to report problems, or let it propagate. Where swallowing one specific failure really is correct — as it often is on a teardown/dispose path where throwing would mask the original failure — catch exactly that exception type and write down WHY in a comment on the catch. Both are needed: a comment on a catch-all still swallows every failure nobody anticipated, and a note that only restates the swallow ("ignored", "do nothing") is read as no explanation at all.
  • EmptyCatchBlock src/assembly/ThermoRawFileReader/XcaliburRawFileIO.vb:524 — empty catch block — the error is discarded with nothing recorded, so a failure here leaves no trace anywhere. Record it through whatever this codebase already uses to report problems, or let it propagate. Where swallowing one specific failure really is correct — as it often is on a teardown/dispose path where throwing would mask the original failure — catch exactly that exception type and write down WHY in a comment on the catch. Both are needed: a comment on a catch-all still swallows every failure nobody anticipated, and a note that only restates the swallow ("ignored", "do nothing") is read as no explanation at all.
  • EmptyCatchBlock src/assembly/ThermoRawFileReader/XcaliburRawFileIO.vb:1623 — empty catch block — the error is discarded with nothing recorded, so a failure here leaves no trace anywhere. Record it through whatever this codebase already uses to report problems, or let it propagate. Where swallowing one specific failure really is correct — as it often is on a teardown/dispose path where throwing would mask the original failure — catch exactly that exception type and write down WHY in a comment on the catch. Both are needed: a comment on a catch-all still swallows every failure nobody anticipated, and a note that only restates the swallow ("ignored", "do nothing") is read as no explanation at all.
  • EmptyCatchBlock src/assembly/ThermoRawFileReader/XcaliburRawFileIO.vb:1793 — empty catch block — the error is discarded with nothing recorded, so a failure here leaves no trace anywhere. Record it through whatever this codebase already uses to report problems, or let it propagate. Where swallowing one specific failure really is correct — as it often is on a teardown/dispose path where throwing would mask the original failure — catch exactly that exception type and write down WHY in a comment on the catch. Both are needed: a comment on a catch-all still swallows every failure nobody anticipated, and a note that only restates the swallow ("ignored", "do nothing") is read as no explanation at all.
  • EmptyCatchBlock src/metadb/Massbank/Public/Massbank/RecordIO.vb:122 — empty catch block — the error is discarded with nothing recorded, so a failure here leaves no trace anywhere. Record it through whatever this codebase already uses to report problems, or let it propagate. Where swallowing one specific failure really is correct — as it often is on a teardown/dispose path where throwing would mask the original failure — catch exactly that exception type and write down WHY in a comment on the catch. Both are needed: a comment on a catch-all still swallows every failure nobody anticipated, and a note that only restates the swallow ("ignored", "do nothing") is read as no explanation at all.
D17 · Explicit Debt · OnErrorResumeSwallow · ×3
  • OnErrorResumeSwallow src/assembly/assembly/MarkupData/imzML/Writer/mzPackWriter.vb:381 — On Error Resume Next silently swallows every runtime error until the enclosing method returns — scope it with a paired `On Error GoTo 0` and check `Err.Number`, or convert to a `Try…Catch`.
  • OnErrorResumeSwallow src/assembly/mzPack/v2.0/mzStream.vb:189 — On Error Resume Next silently swallows every runtime error until the enclosing method returns — scope it with a paired `On Error GoTo 0` and check `Err.Number`, or convert to a `Try…Catch`.
  • OnErrorResumeSwallow src/metadb/Chemoinformatics/ChemicalDescriptor.vb:233 — On Error Resume Next silently swallows every runtime error until the enclosing method returns — scope it with a paired `On Error GoTo 0` and check `Err.Number`, or convert to a `Try…Catch`.
D28 · Secrets (history) · High secret · ×2
  • REDACTED
  • REDACTED
D29 · Static Analysis (SAST) · REDACTED
  • REDACTED
  • REDACTED
D17 · Explicit Debt · InvertedNullGuard · ×1
  • InvertedNullGuard src/mzmath/TargetedMetabolomics/MRM/IonLibrary.vb:102 — If ion Is Nothing Then … ion.precursor — the guard has already decided this variable is null on the way into this branch, and nothing here gives it another value, so this dereference cannot run without throwing a NullReferenceException. It survives because the branch is the uncommon one: the code is correct on every input where the variable is set, and crashes on exactly the case the branch was written to handle. Decide which the line meant — if it is reporting the absence, it must not read through the missing value (use the other variable that identifies it, or a literal); if it is meant to work on a value, it belongs in the other branch.
Serious — 1247 finding(s)
D3 · God Classes · MethodTooLong · ×97
  • MethodTooLong: LipidomicsConverter.ConvertMsdialClassDefinitionToSuperClassVS2 src/metadb/Lipidomics/Annotation/LipidomicsConverter.vb:5042 — MethodTooLong — ConvertMsdialClassDefinitionToSuperClassVS2 runs 478 significant lines (blank, comment-only and punctuation-only lines excluded) in one body. The bar is 100 significant lines; this is 378 over it, 4.78× the bar. This is length, not branching: a long straight-line body scores low on complexity and is still read whole to change any part of it, so the complexity numbers beside this row neither confirm nor excuse it. To reduce it, extract each cohesive step of the body — the runs of statements that work on the same values and would earn the same name — into its own named unit, and have this one call them in order.
  • MethodTooLong: LipidomicsConverter.ConvertMsdialClassDefinitionToLbmClassEnumVS2 src/metadb/Lipidomics/Annotation/LipidomicsConverter.vb:4356 — MethodTooLong — ConvertMsdialClassDefinitionToLbmClassEnumVS2 runs 470 significant lines (blank, comment-only and punctuation-only lines excluded) in one body. The bar is 100 significant lines; this is 370 over it, 4.70× the bar. This is length, not branching: a long straight-line body scores low on complexity and is still read whole to change any part of it, so the complexity numbers beside this row neither confirm nor excuse it. To reduce it, extract each cohesive step of the body — the runs of statements that work on the same values and would earn the same name — into its own named unit, and have this one call them in order.
  • MethodTooLong: LipoqualityRest.getLqUrl src/metadb/Lipidomics/LipoqualityRest.vb:93 — MethodTooLong — getLqUrl runs 440 significant lines (blank, comment-only and punctuation-only lines excluded) in one body. The bar is 100 significant lines; this is 340 over it, 4.40× the bar. This is length, not branching: a long straight-line body scores low on complexity and is still read whole to change any part of it, so the complexity numbers beside this row neither confirm nor excuse it. To reduce it, extract each cohesive step of the body — the runs of statements that work on the same values and would earn the same name — into its own named unit, and have this one call them in order.
  • MethodTooLong: MsScanMatching.GetLipidMoleculerSpeciesLevelAnnotationResultForEIEIO src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:289 — MethodTooLong — GetLipidMoleculerSpeciesLevelAnnotationResultForEIEIO runs 431 significant lines (blank, comment-only and punctuation-only lines excluded) in one body. The bar is 100 significant lines; this is 331 over it, 4.31× the bar. This is length, not branching: a long straight-line body scores low on complexity and is still read whole to change any part of it, so the complexity numbers beside this row neither confirm nor excuse it. To reduce it, extract each cohesive step of the body — the runs of statements that work on the same values and would earn the same name — into its own named unit, and have this one call them in order.
  • MethodTooLong: MsScanMatching.GetLipidMoleculeAnnotationResult src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:871 — MethodTooLong — GetLipidMoleculeAnnotationResult runs 431 significant lines (blank, comment-only and punctuation-only lines excluded) in one body. The bar is 100 significant lines; this is 331 over it, 4.31× the bar. This is length, not branching: a long straight-line body scores low on complexity and is still read whole to change any part of it, so the complexity numbers beside this row neither confirm nor excuse it. To reduce it, extract each cohesive step of the body — the runs of statements that work on the same values and would earn the same name — into its own named unit, and have this one call them in order.
  • MethodTooLong: LipidAnnotation.Characterize src/metadb/Lipidomics/Annotation/Lipidomics.vb:148 — MethodTooLong — Characterize runs 415 significant lines (blank, comment-only and punctuation-only lines excluded) in one body. The bar is 100 significant lines; this is 315 over it, 4.15× the bar. This is length, not branching: a long straight-line body scores low on complexity and is still read whole to change any part of it, so the complexity numbers beside this row neither confirm nor excuse it. To reduce it, extract each cohesive step of the body — the runs of statements that work on the same values and would earn the same name — into its own named unit, and have this one call them in order.
  • MethodTooLong: LipidomicsConverter.ConvertLbmClassEnumToMsdialClassDefinitionVS2 src/metadb/Lipidomics/Annotation/LipidomicsConverter.vb:3749 — MethodTooLong — ConvertLbmClassEnumToMsdialClassDefinitionVS2 runs 402 significant lines (blank, comment-only and punctuation-only lines excluded) in one body. The bar is 100 significant lines; this is 302 over it, 4.02× the bar. This is length, not branching: a long straight-line body scores low on complexity and is still read whole to change any part of it, so the complexity numbers beside this row neither confirm nor excuse it. To reduce it, extract each cohesive step of the body — the runs of statements that work on the same values and would earn the same name — into its own named unit, and have this one call them in order.
  • MethodTooLong: Element.MemoryPopulateElements src/metadb/Chemoinformatics/Formula/Models/Element.vb:152 — MethodTooLong — MemoryPopulateElements runs 238 significant lines (blank, comment-only and punctuation-only lines excluded) in one body. The bar is 100 significant lines; this is 138 over it, 2.38× the bar. This is length, not branching: a long straight-line body scores low on complexity and is still read whole to change any part of it, so the complexity numbers beside this row neither confirm nor excuse it. To reduce it, extract each cohesive step of the body — the runs of statements that work on the same values and would earn the same name — into its own named unit, and have this one call them in order.
  • MethodTooLong: MS_Peak_ID.MakeTheoryList src/mzmath/Oligonucleotide_MS/MS_Peak/Oligonucleotide_MS_Peak_ID_Given_Sequence_v8.vb:121 — MethodTooLong — MakeTheoryList runs 229 significant lines (blank, comment-only and punctuation-only lines excluded) in one body. The bar is 100 significant lines; this is 129 over it, 2.29× the bar. This is length, not branching: a long straight-line body scores low on complexity and is still read whole to change any part of it, so the complexity numbers beside this row neither confirm nor excuse it. To reduce it, extract each cohesive step of the body — the runs of statements that work on the same values and would earn the same name — into its own named unit, and have this one call them in order.
  • MethodTooLong: LipidMassLibraryGenerator.GetIons src/metadb/Lipidomics/Annotation/LipidMassLibraryGenerator.vb:95 — MethodTooLong — GetIons runs 226 significant lines (blank, comment-only and punctuation-only lines excluded) in one body. The bar is 100 significant lines; this is 126 over it, 2.26× the bar. This is length, not branching: a long straight-line body scores low on complexity and is still read whole to change any part of it, so the complexity numbers beside this row neither confirm nor excuse it. To reduce it, extract each cohesive step of the body — the runs of statements that work on the same values and would earn the same name — into its own named unit, and have this one call them in order.
  • MethodTooLong: LipidMsmsCharacterization.JudgeIfCardiolipin src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7147 — MethodTooLong — JudgeIfCardiolipin runs 189 significant lines (blank, comment-only and punctuation-only lines excluded) in one body. The bar is 100 significant lines; this is 89 over it, 1.89× the bar. This is length, not branching: a long straight-line body scores low on complexity and is still read whole to change any part of it, so the complexity numbers beside this row neither confirm nor excuse it. To reduce it, extract each cohesive step of the body — the runs of statements that work on the same values and would earn the same name — into its own named unit, and have this one call them in order.
  • MethodTooLong: PeakAssign.PlotInternal src/visualize/plot/PeakAssign.vb:185 — MethodTooLong — PlotInternal runs 170 significant lines (blank, comment-only and punctuation-only lines excluded) in one body. The bar is 100 significant lines; this is 70 over it, 1.70× the bar. This is length, not branching: a long straight-line body scores low on complexity and is still read whole to change any part of it, so the complexity numbers beside this row neither confirm nor excuse it. To reduce it, extract each cohesive step of the body — the runs of statements that work on the same values and would earn the same name — into its own named unit, and have this one call them in order.
  • MethodTooLong: LipoqualityDatabaseManagerUtility.ConvertMsdialClassDefinitionToTraditionalClassDefinition src/metadb/Lipidomics/LipoqualityDatabaseManagerUtility.vb:494 — MethodTooLong — ConvertMsdialClassDefinitionToTraditionalClassDefinition runs 166 significant lines (blank, comment-only and punctuation-only lines excluded) in one body. The bar is 100 significant lines; this is 66 over it, 1.66× the bar. This is length, not branching: a long straight-line body scores low on complexity and is still read whole to change any part of it, so the complexity numbers beside this row neither confirm nor excuse it. To reduce it, extract each cohesive step of the body — the runs of statements that work on the same values and would earn the same name — into its own named unit, and have this one call them in order.
  • MethodTooLong: LipoqualityDatabaseManagerUtility.ConvertMsdialClassDefinitionToSuperClass src/metadb/Lipidomics/LipoqualityDatabaseManagerUtility.vb:678 — MethodTooLong — ConvertMsdialClassDefinitionToSuperClass runs 166 significant lines (blank, comment-only and punctuation-only lines excluded) in one body. The bar is 100 significant lines; this is 66 over it, 1.66× the bar. This is length, not branching: a long straight-line body scores low on complexity and is still read whole to change any part of it, so the complexity numbers beside this row neither confirm nor excuse it. To reduce it, extract each cohesive step of the body — the runs of statements that work on the same values and would earn the same name — into its own named unit, and have this one call them in order.
  • MethodTooLong: SpectrumHandler.EstimateIsotopes src/mzmath/MSEngine/SpectrumHandler.vb:259 — MethodTooLong — EstimateIsotopes runs 164 significant lines (blank, comment-only and punctuation-only lines excluded) in one body. The bar is 100 significant lines; this is 64 over it, 1.64× the bar. This is length, not branching: a long straight-line body scores low on complexity and is still read whole to change any part of it, so the complexity numbers beside this row neither confirm nor excuse it. To reduce it, extract each cohesive step of the body — the runs of statements that work on the same values and would earn the same name — into its own named unit, and have this one call them in order.
  • MethodTooLong: XcaliburRawFileIO.GetScanInfoInternal src/assembly/ThermoRawFileReader/XcaliburRawFileIO.vb:1192 — MethodTooLong — GetScanInfoInternal runs 158 significant lines (blank, comment-only and punctuation-only lines excluded) in one body. The bar is 100 significant lines; this is 58 over it, 1.58× the bar. This is length, not branching: a long straight-line body scores low on complexity and is still read whole to change any part of it, so the complexity numbers beside this row neither confirm nor excuse it. To reduce it, extract each cohesive step of the body — the runs of statements that work on the same values and would earn the same name — into its own named unit, and have this one call them in order.
  • MethodTooLong: DSPPhaseCorrection.dspPhaseCorrection src/assembly/NMRFidTool/Math/phasing/DSPPhaseCorrection.vb:77 — MethodTooLong — dspPhaseCorrection runs 157 significant lines (blank, comment-only and punctuation-only lines excluded) in one body. The bar is 100 significant lines; this is 57 over it, 1.57× the bar. This is length, not branching: a long straight-line body scores low on complexity and is still read whole to change any part of it, so the complexity numbers beside this row neither confirm nor excuse it. To reduce it, extract each cohesive step of the body — the runs of statements that work on the same values and would earn the same name — into its own named unit, and have this one call them in order.
  • MethodTooLong: IsotopeCalculator.getNominalIsotopeElementPropertyForTenIsotopomerElement src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1283 — MethodTooLong — getNominalIsotopeElementPropertyForTenIsotopomerElement runs 155 significant lines (blank, comment-only and punctuation-only lines excluded) in one body. The bar is 100 significant lines; this is 55 over it, 1.55× the bar. This is length, not branching: a long straight-line body scores low on complexity and is still read whole to change any part of it, so the complexity numbers beside this row neither confirm nor excuse it. To reduce it, extract each cohesive step of the body — the runs of statements that work on the same values and would earn the same name — into its own named unit, and have this one call them in order.
  • MethodTooLong: TICplot.RunPlot src/visualize/plot/ChromatogramPlot/TICplot.vb:200 — MethodTooLong — RunPlot runs 151 significant lines (blank, comment-only and punctuation-only lines excluded) in one body. The bar is 100 significant lines; this is 51 over it, 1.51× the bar. This is length, not branching: a long straight-line body scores low on complexity and is still read whole to change any part of it, so the complexity numbers beside this row neither confirm nor excuse it. To reduce it, extract each cohesive step of the body — the runs of statements that work on the same values and would earn the same name — into its own named unit, and have this one call them in order.
  • MethodTooLong: PeakAnalyzer.MultiPeakFit src/assembly/RamanSpectroscopy/RamanDataProcessor.vb:1568 — MethodTooLong — MultiPeakFit runs 150 significant lines (blank, comment-only and punctuation-only lines excluded) in one body. The bar is 100 significant lines; this is 50 over it, 1.50× the bar. This is length, not branching: a long straight-line body scores low on complexity and is still read whole to change any part of it, so the complexity numbers beside this row neither confirm nor excuse it. To reduce it, extract each cohesive step of the body — the runs of statements that work on the same values and would earn the same name — into its own named unit, and have this one call them in order.
  • MethodTooLong: LipidMsmsCharacterization.JudgeIfHexceramideeos src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:10557 — MethodTooLong — JudgeIfHexceramideeos runs 149 significant lines (blank, comment-only and punctuation-only lines excluded) in one body. The bar is 100 significant lines; this is 49 over it, 1.49× the bar. This is length, not branching: a long straight-line body scores low on complexity and is still read whole to change any part of it, so the complexity numbers beside this row neither confirm nor excuse it. To reduce it, extract each cohesive step of the body — the runs of statements that work on the same values and would earn the same name — into its own named unit, and have this one call them in order.
  • MethodTooLong: DensityGroup.DensityGroupAlignment src/mzmath/mz_deco/PeakAlignment/Algorithm/DensityGroup.vb:24 — MethodTooLong — DensityGroupAlignment runs 149 significant lines (blank, comment-only and punctuation-only lines excluded) in one body. The bar is 100 significant lines; this is 49 over it, 1.49× the bar. This is length, not branching: a long straight-line body scores low on complexity and is still read whole to change any part of it, so the complexity numbers beside this row neither confirm nor excuse it. To reduce it, extract each cohesive step of the body — the runs of statements that work on the same values and would earn the same name — into its own named unit, and have this one call them in order.
  • MethodTooLong: LipidMsmsCharacterization.JudgeIfCeramideeos src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:10243 — MethodTooLong — JudgeIfCeramideeos runs 145 significant lines (blank, comment-only and punctuation-only lines excluded) in one body. The bar is 100 significant lines; this is 45 over it, 1.45× the bar. This is length, not branching: a long straight-line body scores low on complexity and is still read whole to change any part of it, so the complexity numbers beside this row neither confirm nor excuse it. To reduce it, extract each cohesive step of the body — the runs of statements that work on the same values and would earn the same name — into its own named unit, and have this one call them in order.
  • MethodTooLong: centWave.DetectByCentWave src/mzmath/mz_deco/Signals/centWave/centWave.vb:26 — MethodTooLong — DetectByCentWave runs 144 significant lines (blank, comment-only and punctuation-only lines excluded) in one body. The bar is 100 significant lines; this is 44 over it, 1.44× the bar. This is length, not branching: a long straight-line body scores low on complexity and is still read whole to change any part of it, so the complexity numbers beside this row neither confirm nor excuse it. To reduce it, extract each cohesive step of the body — the runs of statements that work on the same values and would earn the same name — into its own named unit, and have this one call them in order.
  • MethodTooLong: LipidEieioMsmsCharacterization.JudgeIfPhosphatidylcholine src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:230 — MethodTooLong — JudgeIfPhosphatidylcholine runs 142 significant lines (blank, comment-only and punctuation-only lines excluded) in one body. The bar is 100 significant lines; this is 42 over it, 1.42× the bar. This is length, not branching: a long straight-line body scores low on complexity and is still read whole to change any part of it, so the complexity numbers beside this row neither confirm nor excuse it. To reduce it, extract each cohesive step of the body — the runs of statements that work on the same values and would earn the same name — into its own named unit, and have this one call them in order.
  • + 72 more in this group — see findings.md.
D3 · God Classes · FileTooLong · ×30
  • FileTooLong: MsCharacterization/MsmsCharacterization.vb src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb — FileTooLong — 11810 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 11310 over it, 23.62× the bar. To reduce it, split the file along the responsibilities already in it: move each cohesive group of declarations into its own sibling file in the same module or package, so no one file has to be read whole to change one of them.
  • FileTooLong: MsCharacterization/LipidEieioMsmsCharacterization.vb src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb — FileTooLong — 2719 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 2219 over it, 5.44× the bar. To reduce it, split the file along the responsibilities already in it: move each cohesive group of declarations into its own sibling file in the same module or package, so no one file has to be read whole to change one of them.
  • FileTooLong: Annotation/LipidomicsConverter.vb src/metadb/Lipidomics/Annotation/LipidomicsConverter.vb — FileTooLong — 1787 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 1287 over it, 3.57× the bar. To reduce it, split the file along the responsibilities already in it: move each cohesive group of declarations into its own sibling file in the same module or package, so no one file has to be read whole to change one of them.
  • FileTooLong: Isotopic/IsotopeCalc.vb src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb — FileTooLong — 1685 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 1185 over it, 3.37× the bar. To reduce it, split the file along the responsibilities already in it: move each cohesive group of declarations into its own sibling file in the same module or package, so no one file has to be read whole to change one of them.
  • FileTooLong: RamanSpectroscopy/RamanDataProcessor.vb src/assembly/RamanSpectroscopy/RamanDataProcessor.vb — FileTooLong — 1634 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 1134 over it, 3.27× the bar. To reduce it, split the file along the responsibilities already in it: move each cohesive group of declarations into its own sibling file in the same module or package, so no one file has to be read whole to change one of them.
  • FileTooLong: ThermoRawFileReader/XcaliburRawFileIO.vb src/assembly/ThermoRawFileReader/XcaliburRawFileIO.vb — FileTooLong — 1502 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 1002 over it, 3.00× the bar. To reduce it, split the file along the responsibilities already in it: move each cohesive group of declarations into its own sibling file in the same module or package, so no one file has to be read whole to change one of them.
  • FileTooLong: mzquant/mzDeco.vb Rscript/Library/mzkit_app/src/mzquant/mzDeco.vb — FileTooLong — 1320 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 820 over it, 2.64× the bar. To reduce it, split the file along the responsibilities already in it: move each cohesive group of declarations into its own sibling file in the same module or package, so no one file has to be read whole to change one of them.
  • FileTooLong: Search/MsScanMatching.vb src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb — FileTooLong — 1231 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 731 over it, 2.46× the bar. To reduce it, split the file along the responsibilities already in it: move each cohesive group of declarations into its own sibling file in the same module or package, so no one file has to be read whole to change one of them.
  • FileTooLong: comprehensive/MSI.vb Rscript/Library/mzkit_app/src/mzkit/comprehensive/MSI.vb — FileTooLong — 1198 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 698 over it, 2.40× the bar. To reduce it, split the file along the responsibilities already in it: move each cohesive group of declarations into its own sibling file in the same module or package, so no one file has to be read whole to change one of them.
  • FileTooLong: Annotation/LipidMassLibraryGenerator.vb src/metadb/Lipidomics/Annotation/LipidMassLibraryGenerator.vb — FileTooLong — 1058 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 558 over it, 2.12× the bar. To reduce it, split the file along the responsibilities already in it: move each cohesive group of declarations into its own sibling file in the same module or package, so no one file has to be read whole to change one of them.
  • FileTooLong: Search/MsScanMatching.vb src/mzmath/MSEngine/Search/MsScanMatching.vb — FileTooLong — 936 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 436 over it, 1.87× the bar. To reduce it, split the file along the responsibilities already in it: move each cohesive group of declarations into its own sibling file in the same module or package, so no one file has to be read whole to change one of them.
  • FileTooLong: math/Math.vb Rscript/Library/mzkit_app/src/mzkit/math/Math.vb — FileTooLong — 867 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 367 over it, 1.73× the bar. To reduce it, split the file along the responsibilities already in it: move each cohesive group of declarations into its own sibling file in the same module or package, so no one file has to be read whole to change one of them.
  • FileTooLong: Preprocessing/MathHelpers.vb src/mzmath/mz_deco/Preprocessing/MathHelpers.vb — FileTooLong — 822 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 322 over it, 1.64× the bar. To reduce it, split the file along the responsibilities already in it: move each cohesive group of declarations into its own sibling file in the same module or package, so no one file has to be read whole to change one of them.
  • FileTooLong: annotations/Massbank.vb Rscript/Library/mzkit_app/src/mzkit/annotations/Massbank.vb — FileTooLong — 798 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 298 over it, 1.60× the bar. To reduce it, split the file along the responsibilities already in it: move each cohesive group of declarations into its own sibling file in the same module or package, so no one file has to be read whole to change one of them.
  • FileTooLong: src/MsImaging.vb Rscript/Library/mzkit_app/src/mzplot/src/MsImaging.vb — FileTooLong — 769 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 269 over it, 1.54× the bar. To reduce it, split the file along the responsibilities already in it: move each cohesive group of declarations into its own sibling file in the same module or package, so no one file has to be read whole to change one of them.
  • FileTooLong: src/Visual.vb Rscript/Library/mzkit_app/src/mzplot/src/Visual.vb — FileTooLong — 735 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 235 over it, 1.47× the bar. To reduce it, split the file along the responsibilities already in it: move each cohesive group of declarations into its own sibling file in the same module or package, so no one file has to be read whole to change one of them.
  • FileTooLong: LipidParser/LipidParsers.vb src/metadb/Lipidomics/LipidParser/LipidParsers.vb — FileTooLong — 734 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 234 over it, 1.47× the bar. To reduce it, split the file along the responsibilities already in it: move each cohesive group of declarations into its own sibling file in the same module or package, so no one file has to be read whole to change one of them.
  • FileTooLong: annotations/MetaDbXref.vb Rscript/Library/mzkit_app/src/mzkit/annotations/MetaDbXref.vb — FileTooLong — 720 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 220 over it, 1.44× the bar. To reduce it, split the file along the responsibilities already in it: move each cohesive group of declarations into its own sibling file in the same module or package, so no one file has to be read whole to change one of them.
  • FileTooLong: assembly/MzWeb.vb Rscript/Library/mzkit_app/src/mzkit/assembly/MzWeb.vb — FileTooLong — 708 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 208 over it, 1.42× the bar. To reduce it, split the file along the responsibilities already in it: move each cohesive group of declarations into its own sibling file in the same module or package, so no one file has to be read whole to change one of them.
  • FileTooLong: assembly/data.vb Rscript/Library/mzkit_app/src/mzkit/assembly/data.vb — FileTooLong — 706 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 206 over it, 1.41× the bar. To reduce it, split the file along the responsibilities already in it: move each cohesive group of declarations into its own sibling file in the same module or package, so no one file has to be read whole to change one of them.
  • FileTooLong: MRM/MRMkit.vb Rscript/Library/mzkit_app/src/mzquant/MRM/MRMkit.vb — FileTooLong — 702 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 202 over it, 1.40× the bar. To reduce it, split the file along the responsibilities already in it: move each cohesive group of declarations into its own sibling file in the same module or package, so no one file has to be read whole to change one of them.
  • FileTooLong: Lipidomics/LipoqualityDatabaseManagerUtility.vb src/metadb/Lipidomics/LipoqualityDatabaseManagerUtility.vb — FileTooLong — 624 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 124 over it, 1.25× the bar. To reduce it, split the file along the responsibilities already in it: move each cohesive group of declarations into its own sibling file in the same module or package, so no one file has to be read whole to change one of them.
  • FileTooLong: pipeline/annotation.vb Rscript/Library/mzkit_app/src/mzkit/pipeline/annotation.vb — FileTooLong — 608 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 108 over it, 1.22× the bar. To reduce it, split the file along the responsibilities already in it: move each cohesive group of declarations into its own sibling file in the same module or package, so no one file has to be read whole to change one of them.
  • FileTooLong: MSFinder/FormulaGenerator.vb src/mzmath/MSFinder/FormulaGenerator.vb — FileTooLong — 597 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 97 over it, 1.19× the bar. To reduce it, split the file along the responsibilities already in it: move each cohesive group of declarations into its own sibling file in the same module or package, so no one file has to be read whole to change one of them.
  • FileTooLong: MSFinder/FragmentAssigner.vb src/mzmath/MSFinder/FragmentAssigner.vb — FileTooLong — 592 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 92 over it, 1.18× the bar. To reduce it, split the file along the responsibilities already in it: move each cohesive group of declarations into its own sibling file in the same module or package, so no one file has to be read whole to change one of them.
  • + 5 more in this group — see findings.md.
D17 · Explicit Debt · TodoComment · ×23
  • TodoComment src/assembly/BrukerDataReader/Raw/DataReader.vb:72 — ' TODO: add apodization ability — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `' REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
  • TodoComment src/assembly/BrukerDataReader/Raw/DataReader.vb:73 — ' TODO: remove all dependence on DeconEngine (FFT, apodization, etc). — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `' REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
  • TodoComment src/assembly/NMRFidTool/AbstractFastFourierTransformTool.vb:126 — 'TODO adapt the FFT to the new object Spectrum — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `' REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
  • TodoComment src/assembly/NMRFidTool/Acqu.vb:141 — 'TODO use an enum for parameters that have a limited set of options such as aquisition mode — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `' REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
  • TodoComment src/assembly/NMRFidTool/Math/apodization/ApodizationTool.vb:114 — ' TODO perhaps change this to accept an Acqu object, to make aparent that the acquisition mode has to be defined — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `' REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
  • TodoComment src/assembly/NMRFidTool/Math/apodization/LorentzGausApodizatior.vb:121 — 'TODO check if the equation to calculate the factor is correct — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `' REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
  • TodoComment src/assembly/NMRFidTool/Math/apodization/SineApodizator.vb:96 — 'TODO fix this class — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `' REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
  • TodoComment src/assembly/NMRFidTool/Math/apodization/SineApodizator.vb:101 — ' TODO allow to redifine — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `' REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
  • TodoComment src/assembly/NMRFidTool/Math/apodization/ZeroFillApodizator.vb:93 — 'TODO write down this class — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `' REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
  • TodoComment src/assembly/NMRFidTool/Math/baseline/GolotvinWilliamsBaselineCorrector.vb:191 — ' TODO !!!make sure this is not the first point!!!! but the first point would break this... — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `' REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
  • TodoComment src/assembly/NMRFidTool/Proc.vb:130 — 'TODO consider moving this to the Fourier Transformed class or processing class.... — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `' REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
  • TodoComment src/assembly/NMRFidTool/Reader/SimplePdataReader.vb:119 — 'TODO move to java.nio.file — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `' REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
  • TodoComment src/assembly/assembly/MarkupData/XmlSeek.vb:221 — ' TODO: 释放未托管的资源(未托管的对象)并替代终结器 — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `' REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
  • TodoComment src/assembly/assembly/mzPack/Binary/BinaryStreamReader.vb:399 — ' TODO: 释放未托管的资源(未托管的对象)并替代终结器 — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `' REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
  • TodoComment src/assembly/assembly/mzPack/Binary/BinaryStreamWriter.vb:300 — ' TODO: 释放未托管的资源(未托管的对象)并替代终结器 — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `' REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
  • TodoComment src/visualize/MsImaging/Reader/PixelReader.vb:390 — ' TODO: 释放未托管的资源(未托管的对象)并替代终结器 — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `' REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
  • TodoComment src/metadb/Lipidomics/Annotation/ILipid.vb:108 — ' TODO: Formula class maybe better. — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `' REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
  • TodoComment src/metadb/Lipidomics/TotalChainVariationGenerator.vb:138 — ' TODO: refactoring — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `' REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
  • TodoComment src/metadb/Massbank/Public/NCBI/PubChemDescriptorRepo.vb:249 — ' TODO: dispose managed state (managed objects). — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `' REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
  • TodoComment src/metadb/Massbank/Public/NCBI/PubChemDescriptorRepo.vb:257 — ' TODO: free unmanaged resources (unmanaged objects) and override Finalize() below. — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `' REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
  • TodoComment src/metadb/Massbank/Public/NCBI/PubChemDescriptorRepo.vb:258 — ' TODO: set large fields to null. — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `' REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
  • TodoComment src/metadb/Massbank/Public/NCBI/PubChemDescriptorRepo.vb:263 — ' TODO: override Finalize() only if Dispose(disposing As Boolean) above has code to free unmanaged resources. — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `' REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
  • TodoComment src/metadb/Massbank/Public/NCBI/PubChemDescriptorRepo.vb:274 — ' TODO: uncomment the following line if Finalize() is overridden above. — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `' REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
D3 · God Classes · ClassTooLong · ×21
  • ClassTooLong: LipidomicsConverter src/metadb/Lipidomics/Annotation/LipidomicsConverter.vb — ClassTooLong — 1784 significant lines (blank, comment-only and punctuation-only lines excluded), 22 methods. The bar is 400 significant lines; this is 1384 over it, 4.46× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
  • ClassTooLong: MsScanMatching src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb — ClassTooLong — 1226 significant lines (blank, comment-only and punctuation-only lines excluded), 15 methods. The bar is 400 significant lines; this is 826 over it, 3.07× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
  • ClassTooLong: MetaDbXref Rscript/Library/mzkit_app/src/mzkit/annotations/MetaDbXref.vb — ClassTooLong — 688 significant lines (blank, comment-only and punctuation-only lines excluded), 27 methods. The bar is 400 significant lines; this is 288 over it, 1.72× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
  • ClassTooLong: Visual Rscript/Library/mzkit_app/src/mzplot/src/Visual.vb — ClassTooLong — 688 significant lines (blank, comment-only and punctuation-only lines excluded), 23 methods. The bar is 400 significant lines; this is 288 over it, 1.72× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
  • ClassTooLong: MRMkit Rscript/Library/mzkit_app/src/mzquant/MRM/MRMkit.vb — ClassTooLong — 669 significant lines (blank, comment-only and punctuation-only lines excluded), 29 methods. The bar is 400 significant lines; this is 269 over it, 1.67× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
  • ClassTooLong: MzWeb Rscript/Library/mzkit_app/src/mzkit/assembly/MzWeb.vb — ClassTooLong — 666 significant lines (blank, comment-only and punctuation-only lines excluded), 25 methods. The bar is 400 significant lines; this is 266 over it, 1.67× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
  • ClassTooLong: LipoqualityDatabaseManagerUtility src/metadb/Lipidomics/LipoqualityDatabaseManagerUtility.vb — ClassTooLong — 623 significant lines (blank, comment-only and punctuation-only lines excluded), 9 methods. The bar is 400 significant lines; this is 223 over it, 1.56× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
  • ClassTooLong: FormulaGenerator src/mzmath/MSFinder/FormulaGenerator.vb — ClassTooLong — 590 significant lines (blank, comment-only and punctuation-only lines excluded), 21 methods. The bar is 400 significant lines; this is 190 over it, 1.48× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
  • ClassTooLong: FragmentAssigner src/mzmath/MSFinder/FragmentAssigner.vb — ClassTooLong — 586 significant lines (blank, comment-only and punctuation-only lines excluded), 19 methods. The bar is 400 significant lines; this is 186 over it, 1.47× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
  • ClassTooLong: SpectralPreprocessor src/assembly/RamanSpectroscopy/RamanDataProcessor.vb — ClassTooLong — 578 significant lines (blank, comment-only and punctuation-only lines excluded), 25 methods. The bar is 400 significant lines; this is 178 over it, 1.45× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
  • ClassTooLong: PeakAnalyzer src/assembly/RamanSpectroscopy/RamanDataProcessor.vb — ClassTooLong — 520 significant lines (blank, comment-only and punctuation-only lines excluded), 20 methods. The bar is 400 significant lines; this is 120 over it, 1.30× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
  • ClassTooLong: MummichogAnnotator src/mzmath/Mummichog/MummichogModule.vb — ClassTooLong — 504 significant lines (blank, comment-only and punctuation-only lines excluded), 16 methods. The bar is 400 significant lines; this is 104 over it, 1.26× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
  • ClassTooLong: ReferenceTreePkg Rscript/Library/mzkit_app/src/mzkit/pipeline/ReferenceTree.vb — ClassTooLong — 480 significant lines (blank, comment-only and punctuation-only lines excluded), 21 methods. The bar is 400 significant lines; this is 80 over it, 1.20× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
  • ClassTooLong: FormulaStringParcer src/mzmath/MSFinder/FormulaStringParcer.vb — ClassTooLong — 477 significant lines (blank, comment-only and punctuation-only lines excluded), 11 methods. The bar is 400 significant lines; this is 77 over it, 1.19× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
  • ClassTooLong: TissueMorphology Rscript/Library/mzkit_app/src/mzkit/comprehensive/TissueMorphology.vb — ClassTooLong — 475 significant lines (blank, comment-only and punctuation-only lines excluded), 18 methods. The bar is 400 significant lines; this is 75 over it, 1.19× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
  • ClassTooLong: LipoqualityRest src/metadb/Lipidomics/LipoqualityRest.vb — ClassTooLong — 461 significant lines (blank, comment-only and punctuation-only lines excluded), 3 methods. The bar is 400 significant lines; this is 61 over it, 1.15× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
  • ClassTooLong: metaDNAInfer Rscript/Library/mzkit_app/src/mzDIA/metaDNA.vb — ClassTooLong — 456 significant lines (blank, comment-only and punctuation-only lines excluded), 23 methods. The bar is 400 significant lines; this is 56 over it, 1.14× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
  • ClassTooLong: LipidAnnotation src/metadb/Lipidomics/Annotation/Lipidomics.vb — ClassTooLong — 444 significant lines (blank, comment-only and punctuation-only lines excluded), 4 methods. The bar is 400 significant lines; this is 44 over it, 1.11× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
  • ClassTooLong: MissingValueImputation src/mzmath/mz_deco/Preprocessing/MissingValueImputation.vb — ClassTooLong — 420 significant lines (blank, comment-only and punctuation-only lines excluded), 14 methods. The bar is 400 significant lines; this is 20 over it, 1.05× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
  • ClassTooLong: Assembly Rscript/Library/mzkit_app/src/mzkit/assembly/Assembly.vb — ClassTooLong — 416 significant lines (blank, comment-only and punctuation-only lines excluded), 23 methods. The bar is 400 significant lines; this is 16 over it, 1.04× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
  • ClassTooLong: MS_Peak_ID src/mzmath/Oligonucleotide_MS/MS_Peak/Oligonucleotide_MS_Peak_ID_Given_Sequence_v8.vb — ClassTooLong — 406 significant lines (blank, comment-only and punctuation-only lines excluded), 5 methods. The bar is 400 significant lines; this is 6 over it, 1.02× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
D4 · Code Duplication · Duplicated block (5 lines × 2) · ×18
  • Duplicated block (5 lines × 2) Rscript/Library/mzkit_app/src/mzkit/annotations/Massbank.vb:295 — Rscript/Library/mzkit_app/src/mzkit/annotations/Massbank.vb:295-299 | Rscript/Library/mzkit_app/src/mzquant/mzDeco.vb:180-184 — the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach — a location they all depend on today, or a new shared one if there is none — and call it from each site; until then, every change has to be made twice.
  • Duplicated block (5 lines × 2) src/assembly/NMRFidTool/Math/apodization/TrafApodizator.vb:99 — src/assembly/NMRFidTool/Math/apodization/TrafApodizator.vb:99-103 | src/assembly/NMRFidTool/Math/apodization/TrafsApodizator.vb:98-102 — before extracting anything, compare `src/assembly/NMRFidTool/Math/apodization/TrafApodizator.vb` and `src/assembly/NMRFidTool/Math/apodization/TrafsApodizator.vb` as WHOLE FILES: 84% of the shorter file's lines also appear in the other, so this reads as one file having been copied from the other rather than as a helper waiting to be extracted. The 1 duplicated block(s) this scan matched between them are fragments of that copy, not the extent of it — treat the file pair as the unit. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
  • Duplicated block (5 lines × 2) src/metadb/Massbank/Public/NCBI/PubChem/Web/Graph/WebGraph.vb:130 — src/metadb/Massbank/Public/NCBI/PubChem/Web/Graph/WebGraph.vb:130-134 | src/metadb/Massbank/Public/NCBI/PubChem/Web/Graph/WebGraph.vb:142-146 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (5 lines × 2) src/metadb/Massbank/Public/NCBI/PubChem/Web/Query/QueryPathways.vb:83 — src/metadb/Massbank/Public/NCBI/PubChem/Web/Query/QueryPathways.vb:83-87 | src/metadb/Massbank/Public/NCBI/PubChem/Web/Query/QueryPathways.vb:98-102 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at `src/metadb/Massbank/Public/NCBI/PubChem/Web/Query/QueryPathways.vb:83` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
  • Duplicated block (5 lines × 2) src/visualize/ComprehensiveMsPlot/GCxGC/GCxGCTIC2DPlot.vb:142 — src/visualize/ComprehensiveMsPlot/GCxGC/GCxGCTIC2DPlot.vb:142-146 | src/visualize/plot/ChromatogramPlot/TICplot.vb:228-232 — the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach — a location they all depend on today, or a new shared one if there is none — and call it from each site; until then, every change has to be made twice. Read the line range as the matched WINDOW rather than a finished unit: at `src/visualize/ComprehensiveMsPlot/GCxGC/GCxGCTIC2DPlot.vb:142` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
  • Duplicated block (5 lines × 2) src/metadb/Lipidomics/Annotation/LipidMassLibraryGenerator.vb:916 — src/metadb/Lipidomics/Annotation/LipidMassLibraryGenerator.vb:916-920 | src/metadb/Lipidomics/Annotation/LipidMassLibraryGenerator.vb:1036-1040 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
  • Duplicated block (5 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:694 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:694-698 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:951-955 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
  • Duplicated block (5 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:783 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:783-787 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:996-1000 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
  • Duplicated block (5 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:867 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:867-871 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:908-912 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just before the matched lines, `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:907` calls `If`, `ToString` and `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:865` does not — after which the two agree again for 4 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live.
  • Duplicated block (5 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14235 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14235-14240 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:16877-16881 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
  • Duplicated block (5 lines × 2) src/metadb/Lipidomics/Omega3nChainGenerator.vb:119 — src/metadb/Lipidomics/Omega3nChainGenerator.vb:119-123 | src/metadb/Lipidomics/Omega3nChainGenerator.vb:166-170 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (5 lines × 2) src/metadb/Lipidomics/SpectrumGenerator/BMPEidSpectrumGenerator.vb:208 — src/metadb/Lipidomics/SpectrumGenerator/BMPEidSpectrumGenerator.vb:208-212 | src/metadb/Lipidomics/SpectrumGenerator/TGEidSpectrumGenerator.vb:240-244 — the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach — a file they already depend on, or a new one alongside them — and call it from both call sites, so a change lands once. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
  • Duplicated block (5 lines × 2) src/metadb/Lipidomics/SpectrumGenerator/CESpectrumGenerator.vb:96 — src/metadb/Lipidomics/SpectrumGenerator/CESpectrumGenerator.vb:96-100 | src/metadb/Lipidomics/SpectrumGenerator/CEd7SpectrumGenerator.vb:94-98 — the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach — a file they already depend on, or a new one alongside them — and call it from both call sites, so a change lands once.
  • Duplicated block (5 lines × 2) src/metadb/Lipidomics/SpectrumGenerator/HBMPEidSpectrumGenerator.vb:164 — src/metadb/Lipidomics/SpectrumGenerator/HBMPEidSpectrumGenerator.vb:164-168 | src/metadb/Lipidomics/SpectrumGenerator/HBMPSpectrumGenerator.vb:150-154 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/HBMPEidSpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/HBMPSpectrumGenerator.vb` as WHOLE FILES: this scan already matched 4 separate duplicated blocks between them, totalling at least 47 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
  • Duplicated block (5 lines × 2) src/mzmath/ms2_simulator/MSGNN/Exporters.vb:106 — src/mzmath/ms2_simulator/MSGNN/Exporters.vb:106-112 | src/mzmath/ms2_simulator/MSGNN/Exporters.vb:246-250 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, `src/mzmath/ms2_simulator/MSGNN/Exporters.vb:113` calls `Append` and `src/mzmath/ms2_simulator/MSGNN/Exporters.vb:251` does not — after which the two agree again for 2 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live.
  • Duplicated block (5 lines × 2) src/metadb/Chemoinformatics/Formula/SevenGoldenRulesCheck.vb:153 — src/metadb/Chemoinformatics/Formula/SevenGoldenRulesCheck.vb:153-157 | src/metadb/Chemoinformatics/Formula/SevenGoldenRulesCheck.vb:179-183 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (5 lines × 2) src/metadb/Lipidomics/SpectrumGenerator/LPISpectrumGenerator.vb:209 — src/metadb/Lipidomics/SpectrumGenerator/LPISpectrumGenerator.vb:209-213 | src/metadb/Lipidomics/SpectrumGenerator/LPId5SpectrumGenerator.vb:209-213 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/LPISpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/LPId5SpectrumGenerator.vb` as WHOLE FILES: this scan already matched 4 separate duplicated blocks between them, totalling at least 82 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place. Read the line range as the matched WINDOW rather than a finished unit: at `src/metadb/Lipidomics/SpectrumGenerator/LPISpectrumGenerator.vb:209` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
  • Duplicated block (5 lines × 2) src/metadna/metaDNA/Result/ResultHandler.vb:172 — src/metadna/metaDNA/Result/ResultHandler.vb:172-176 | src/metadna/metaDNA/Result/ResultHandler.vb:190-194 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just before the matched lines, `src/metadna/metaDNA/Result/ResultHandler.vb:172` calls `Select`, `Function`, `Log` and `src/metadna/metaDNA/Result/ResultHandler.vb:190` does not — after which the two agree again for 2 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live.
D4 · Code Duplication · Duplicated block (6 lines × 2) · ×17
  • Duplicated block (6 lines × 2) src/mzmath/mz_deco/PeakAlignment.vb:237 — src/mzmath/mz_deco/PeakAlignment.vb:237-242 | src/mzmath/mz_deco/XcmsTable.vb:99-104 — the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach — a file they already depend on, or a new one alongside them — and call it from both call sites, so a change lands once.
  • Duplicated block (6 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5324 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5324-5329 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5364-5369 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (6 lines × 2) src/metadb/Lipidomics/LipoqualityRest.vb:167 — src/metadb/Lipidomics/LipoqualityRest.vb:167-172 | src/metadb/Lipidomics/LipoqualityRest.vb:241-246 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (6 lines × 2) src/metadb/Lipidomics/LipoqualityRest.vb:259 — src/metadb/Lipidomics/LipoqualityRest.vb:259-264 | src/metadb/Lipidomics/LipoqualityRest.vb:301-306 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (6 lines × 2) src/metadb/Lipidomics/OadSpectrumPeakGenerator.vb:77 — src/metadb/Lipidomics/OadSpectrumPeakGenerator.vb:77-82 | src/metadb/Lipidomics/SpectrumGeneratorUtility.vb:68-73 — the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach — a file they already depend on, or a new one alongside them — and call it from both call sites, so a change lands once.
  • Duplicated block (6 lines × 2) src/mzmath/mz_deco/Preprocessing/Normalization.vb:340 — src/mzmath/mz_deco/Preprocessing/Normalization.vb:340-345 | src/mzmath/mz_deco/Preprocessing/Normalization.vb:362-367 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (6 lines × 2) src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:1561 — src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:1561-1566 | src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:1602-1607 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (6 lines × 2) src/metadb/Lipidomics/MsCharacterization/EieioMsCharacterizationUtility.vb:316 — src/metadb/Lipidomics/MsCharacterization/EieioMsCharacterizationUtility.vb:316-321 | src/metadb/Lipidomics/MsCharacterization/EieioMsCharacterizationUtility.vb:326-331 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (6 lines × 2) src/metadb/Lipidomics/Omega3nChainGenerator.vb:103 — src/metadb/Lipidomics/Omega3nChainGenerator.vb:103-108 | src/metadb/Lipidomics/Omega3nChainGenerator.vb:109-114 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (6 lines × 2) src/visualize/MsImaging/Reader/IndexReader.vb:156 — src/visualize/MsImaging/Reader/IndexReader.vb:156-161 | src/visualize/MsImaging/Reader/ReadRawPack.vb:209-214 — the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach — a file they already depend on, or a new one alongside them — and call it from both call sites, so a change lands once. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just before the matched lines, `src/visualize/MsImaging/Reader/ReadRawPack.vb:207` calls `MethodImpl` and `src/visualize/MsImaging/Reader/IndexReader.vb:153` does not — after which the two agree again for 2 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live.
  • Duplicated block (6 lines × 2) src/metadb/Lipidomics/SpectrumGenerator/BMPEidSpectrumGenerator.vb:86 — src/metadb/Lipidomics/SpectrumGenerator/BMPEidSpectrumGenerator.vb:86-91 | src/metadb/Lipidomics/SpectrumGenerator/BMPSpectrumGenerator.vb:86-91 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/BMPEidSpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/BMPSpectrumGenerator.vb` as WHOLE FILES: this scan already matched 4 separate duplicated blocks between them, totalling at least 55 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
  • Duplicated block (6 lines × 2) src/metadb/Lipidomics/SpectrumGenerator/CLEidSpectrumGenerator.vb:90 — src/metadb/Lipidomics/SpectrumGenerator/CLEidSpectrumGenerator.vb:90-95 | src/metadb/Lipidomics/SpectrumGenerator/CLSpectrumGenerator.vb:90-95 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/CLEidSpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/CLSpectrumGenerator.vb` as WHOLE FILES: this scan already matched 3 separate duplicated blocks between them, totalling at least 38 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
  • Duplicated block (6 lines × 2) src/metadb/Lipidomics/SpectrumGenerator/HBMPEidSpectrumGenerator.vb:91 — src/metadb/Lipidomics/SpectrumGenerator/HBMPEidSpectrumGenerator.vb:91-96 | src/metadb/Lipidomics/SpectrumGenerator/HBMPSpectrumGenerator.vb:91-96 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/HBMPEidSpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/HBMPSpectrumGenerator.vb` as WHOLE FILES: this scan already matched 4 separate duplicated blocks between them, totalling at least 47 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
  • Duplicated block (6 lines × 2) src/metadb/Lipidomics/SpectrumGenerator/LPIEidSpectrumGenerator.vb:92 — src/metadb/Lipidomics/SpectrumGenerator/LPIEidSpectrumGenerator.vb:92-97 | src/metadb/Lipidomics/SpectrumGenerator/LPISpectrumGenerator.vb:92-97 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/LPIEidSpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/LPISpectrumGenerator.vb` as WHOLE FILES: this scan already matched 3 separate duplicated blocks between them, totalling at least 71 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
  • Duplicated block (6 lines × 2) src/metadb/Lipidomics/SpectrumGenerator/MGEidSpectrumGenerator.vb:82 — src/metadb/Lipidomics/SpectrumGenerator/MGEidSpectrumGenerator.vb:82-87 | src/metadb/Lipidomics/SpectrumGenerator/MGSpectrumGenerator.vb:84-89 — the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach — a file they already depend on, or a new one alongside them — and call it from both call sites, so a change lands once.
  • Duplicated block (6 lines × 2) src/metadb/Lipidomics/SpectrumGenerator/PAEidSpectrumGenerator.vb:89 — src/metadb/Lipidomics/SpectrumGenerator/PAEidSpectrumGenerator.vb:89-94 | src/metadb/Lipidomics/SpectrumGenerator/PASpectrumGenerator.vb:90-95 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/PAEidSpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/PASpectrumGenerator.vb` as WHOLE FILES: 90% of the shorter file's lines also appear in the other, so this reads as one file having been copied from the other rather than as a helper waiting to be extracted. The 2 duplicated block(s) this scan matched between them are fragments of that copy, not the extent of it — treat the file pair as the unit. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
  • Duplicated block (6 lines × 2) src/metadb/Massbank/Public/lipidMAPS/LipidClassReader.vb:93 — src/metadb/Massbank/Public/lipidMAPS/LipidClassReader.vb:93-98 | src/metadb/Massbank/Public/lipidMAPS/LipidNameReader.vb:71-76 — the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach — a file they already depend on, or a new one alongside them — and call it from both call sites, so a change lands once.
D3 · God Classes · TooManyMethods · ×16
  • TooManyMethods: LipidMsmsCharacterization src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb — TooManyMethods — 10447 significant lines (blank, comment-only and punctuation-only lines excluded), 181 methods. The bar is 30 methods; this is 151 over it, 6.03× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
  • TooManyMethods: LipidMassLibraryGenerator src/metadb/Lipidomics/Annotation/LipidMassLibraryGenerator.vb — TooManyMethods — 1048 significant lines (blank, comment-only and punctuation-only lines excluded), 125 methods. The bar is 30 methods; this is 95 over it, 4.17× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
  • TooManyMethods: XcaliburRawFileIO src/assembly/ThermoRawFileReader/XcaliburRawFileIO.vb — TooManyMethods — 1487 significant lines (blank, comment-only and punctuation-only lines excluded), 60 methods. The bar is 30 methods; this is 30 over it, 2.00× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
  • TooManyMethods: MSI Rscript/Library/mzkit_app/src/mzkit/comprehensive/MSI.vb — TooManyMethods — 1136 significant lines (blank, comment-only and punctuation-only lines excluded), 52 methods. The bar is 30 methods; this is 22 over it, 1.73× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
  • TooManyMethods: mzDeco Rscript/Library/mzkit_app/src/mzquant/mzDeco.vb — TooManyMethods — 1276 significant lines (blank, comment-only and punctuation-only lines excluded), 48 methods. The bar is 30 methods; this is 18 over it, 1.60× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
  • TooManyMethods: LipidMsmsCharacterizationUtility src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb — TooManyMethods — 1356 significant lines (blank, comment-only and punctuation-only lines excluded), 46 methods. The bar is 30 methods; this is 16 over it, 1.53× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
  • TooManyMethods: Massbank Rscript/Library/mzkit_app/src/mzkit/annotations/Massbank.vb — TooManyMethods — 747 significant lines (blank, comment-only and punctuation-only lines excluded), 46 methods. The bar is 30 methods; this is 16 over it, 1.53× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
  • TooManyMethods: LipidEieioMsmsCharacterization src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb — TooManyMethods — 2714 significant lines (blank, comment-only and punctuation-only lines excluded), 44 methods. The bar is 30 methods; this is 14 over it, 1.47× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
  • TooManyMethods: MathHelpers src/mzmath/mz_deco/Preprocessing/MathHelpers.vb — TooManyMethods — 820 significant lines (blank, comment-only and punctuation-only lines excluded), 42 methods. The bar is 30 methods; this is 12 over it, 1.40× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
  • TooManyMethods: MsScanMatching src/mzmath/MSEngine/Search/MsScanMatching.vb — TooManyMethods — 928 significant lines (blank, comment-only and punctuation-only lines excluded), 38 methods. The bar is 30 methods; this is 8 over it, 1.27× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
  • TooManyMethods: MzMath Rscript/Library/mzkit_app/src/mzkit/math/Math.vb — TooManyMethods — 832 significant lines (blank, comment-only and punctuation-only lines excluded), 38 methods. The bar is 30 methods; this is 8 over it, 1.27× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
  • TooManyMethods: FormulaTools Rscript/Library/mzkit_app/src/mzkit/math/Formula.vb — TooManyMethods — 369 significant lines (blank, comment-only and punctuation-only lines excluded), 36 methods. The bar is 30 methods; this is 6 over it, 1.20× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
  • TooManyMethods: IsotopeCalculator src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb — TooManyMethods — 1680 significant lines (blank, comment-only and punctuation-only lines excluded), 35 methods. The bar is 30 methods; this is 5 over it, 1.17× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
  • TooManyMethods: MsImaging Rscript/Library/mzkit_app/src/mzplot/src/MsImaging.vb — TooManyMethods — 723 significant lines (blank, comment-only and punctuation-only lines excluded), 33 methods. The bar is 30 methods; this is 3 over it, 1.10× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
  • TooManyMethods: data Rscript/Library/mzkit_app/src/mzkit/assembly/data.vb — TooManyMethods — 674 significant lines (blank, comment-only and punctuation-only lines excluded), 32 methods. The bar is 30 methods; this is 2 over it, 1.07× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
  • TooManyMethods: library Rscript/Library/mzkit_app/src/mzkit/pipeline/annotation.vb — TooManyMethods — 574 significant lines (blank, comment-only and punctuation-only lines excluded), 31 methods. The bar is 30 methods; this is 1 over it, 1.03× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
D4 · Code Duplication · Duplicated block (8 lines × 2) · ×16
  • Duplicated block (8 lines × 2) src/mzmath/MSEngine/Search/MsScanMatching.vb:417 — src/mzmath/MSEngine/Search/MsScanMatching.vb:417-424 | src/mzmath/MSEngine/Search/MsScanMatching.vb:433-440 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (8 lines × 2) src/mzmath/mz_deco/Preprocessing/MathHelpers.vb:996 — src/mzmath/mz_deco/Preprocessing/MathHelpers.vb:996-1003 | src/mzmath/mz_deco/Preprocessing/MathHelpers.vb:1020-1027 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (8 lines × 2) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1463 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1463-1470 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3288-3295 — before extracting anything, compare `src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb` and `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb` as WHOLE FILES: this scan already matched 32 separate duplicated blocks between them, totalling at least 530 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
  • Duplicated block (8 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15038 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15038-15045 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15055-15062 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (8 lines × 2) src/mzmath/ms2_simulator/MSGNN/Exporters.vb:59 — src/mzmath/ms2_simulator/MSGNN/Exporters.vb:59-66 | src/mzmath/ms2_simulator/MSGNN/Exporters.vb:87-94 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (8 lines × 2) src/visualize/MsImaging/Blender/Renderer/RenderCMYK.vb:97 — src/visualize/MsImaging/Blender/Renderer/RenderCMYK.vb:97-104 | src/visualize/MsImaging/Blender/Renderer/RenderRGB.vb:80-87 — the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach — a file they already depend on, or a new one alongside them — and call it from both call sites, so a change lands once.
  • Duplicated block (8 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14241 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14241-14248 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14252-14259 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (8 lines × 2) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:275 — src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:275-282 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:299-306 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (8 lines × 2) src/metadb/Lipidomics/MolecularSpeciesLevelChains.vb:111 — src/metadb/Lipidomics/MolecularSpeciesLevelChains.vb:111-119 | src/metadb/Lipidomics/PositionLevelChains.vb:92-99 — the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach — a file they already depend on, or a new one alongside them — and call it from both call sites, so a change lands once.
  • Duplicated block (8 lines × 2) src/metadb/Lipidomics/MsCharacterization/EieioMsCharacterizationUtility.vb:392 — src/metadb/Lipidomics/MsCharacterization/EieioMsCharacterizationUtility.vb:392-399 | src/metadb/Lipidomics/MsCharacterization/EieioMsCharacterizationUtility.vb:406-413 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (8 lines × 2) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:2945 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:2945-2952 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15843-15850 — before extracting anything, compare `src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb` and `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb` as WHOLE FILES: this scan already matched 32 separate duplicated blocks between them, totalling at least 530 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
  • Duplicated block (8 lines × 2) src/mzmath/Oligonucleotide_MS/VBA/MassDefault.vb:111 — src/mzmath/Oligonucleotide_MS/VBA/MassDefault.vb:111-118 | src/mzmath/Oligonucleotide_MS/VBA/MassDefault.vb:122-129 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (8 lines × 2) src/mzmath/mz_deco/PeakAlignment/Algorithm/DensityGroup.vb:26 — src/mzmath/mz_deco/PeakAlignment/Algorithm/DensityGroup.vb:26-33 | src/mzmath/mz_deco/PeakAlignment/Algorithm/DirectMatch.vb:24-32 — the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach — a file they already depend on, or a new one alongside them — and call it from both call sites, so a change lands once. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, `src/mzmath/mz_deco/PeakAlignment/Algorithm/DirectMatch.vb:35` calls `List`, `Tuple` and `src/mzmath/mz_deco/PeakAlignment/Algorithm/DensityGroup.vb:35` does not — after which the two agree again for 3 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live.
  • Duplicated block (8 lines × 2) src/assembly/mz/TIC.vb:80 — src/assembly/mz/TIC.vb:80-87 | src/assembly/mz/TIC.vb:133-140 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at `src/assembly/mz/TIC.vb:80` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just before the matched lines, `src/assembly/mz/TIC.vb:131` calls `args` and `src/assembly/mz/TIC.vb:78` does not — after which the two agree again for 3 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live.
  • Duplicated block (8 lines × 2) src/metadb/Lipidomics/SpectrumGenerator/CESpectrumGenerator.vb:142 — src/metadb/Lipidomics/SpectrumGenerator/CESpectrumGenerator.vb:142-149 | src/metadb/Lipidomics/SpectrumGenerator/CEd7SpectrumGenerator.vb:140-147 — the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach — a file they already depend on, or a new one alongside them — and call it from both call sites, so a change lands once.
  • Duplicated block (8 lines × 2) src/metadb/Lipidomics/SpectrumGenerator/CLEidSpectrumGenerator.vb:233 — src/metadb/Lipidomics/SpectrumGenerator/CLEidSpectrumGenerator.vb:233-240 | src/metadb/Lipidomics/SpectrumGenerator/CLSpectrumGenerator.vb:216-223 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/CLEidSpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/CLSpectrumGenerator.vb` as WHOLE FILES: this scan already matched 3 separate duplicated blocks between them, totalling at least 38 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
D4 · Code Duplication · Duplicated block (10 lines × 2) · ×14
  • Duplicated block (10 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14846 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14846-14855 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14891-14900 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (10 lines × 2) src/mzmath/mz_deco/Preprocessing/MathHelpers.vb:59 — src/mzmath/mz_deco/Preprocessing/MathHelpers.vb:59-68 | src/mzmath/mz_deco/Preprocessing/MathHelpers.vb:76-85 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (10 lines × 2) src/metadb/Lipidomics/ChainGenerator.vb:142 — src/metadb/Lipidomics/ChainGenerator.vb:142-151 | src/metadb/Lipidomics/Omega3nChainGenerator.vb:268-277 — the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach — a file they already depend on, or a new one alongside them — and call it from both call sites, so a change lands once.
  • Duplicated block (10 lines × 2) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:3505 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:3505-3514 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:16518-16527 — before extracting anything, compare `src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb` and `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb` as WHOLE FILES: this scan already matched 32 separate duplicated blocks between them, totalling at least 530 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
  • Duplicated block (10 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7664 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7664-7673 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7707-7716 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (10 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13458 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13458-13467 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13469-13478 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (10 lines × 2) src/mzmath/MoleculeNetworking/SpectrumGrid/SpectrumGrid.vb:195 — src/mzmath/MoleculeNetworking/SpectrumGrid/SpectrumGrid.vb:195-204 | src/mzmath/MoleculeNetworking/SpectrumGrid/SpectrumGrid.vb:224-233 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at `src/mzmath/MoleculeNetworking/SpectrumGrid/SpectrumGrid.vb:195` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
  • Duplicated block (10 lines × 2) src/visualize/MsImaging/Analysis/GridScanner.vb:112 — src/visualize/MsImaging/Analysis/GridScanner.vb:112-121 | src/visualize/MsImaging/Analysis/GridScanner.vb:168-177 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (10 lines × 2) src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:360 — src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:360-369 | src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:943-952 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
  • Duplicated block (10 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:2530 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:2530-2540 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:9070-9079 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
  • Duplicated block (10 lines × 2) src/metadb/Lipidomics/SpectrumGenerator/EtherPCEidSpectrumGenerator.vb:189 — src/metadb/Lipidomics/SpectrumGenerator/EtherPCEidSpectrumGenerator.vb:189-198 | src/metadb/Lipidomics/SpectrumGenerator/EtherPEEidSpectrumGenerator.vb:230-239 — the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach — a file they already depend on, or a new one alongside them — and call it from both call sites, so a change lands once.
  • Duplicated block (10 lines × 2) src/mzmath/MSEngine/Search/MsScanMatching.vb:903 — src/mzmath/MSEngine/Search/MsScanMatching.vb:903-912 | src/mzmath/MSEngine/Search/MsScanMatching.vb:1035-1044 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (10 lines × 2) src/mzmath/mz_deco/Preprocessing/MissingValueImputation.vb:246 — src/mzmath/mz_deco/Preprocessing/MissingValueImputation.vb:246-255 | src/mzmath/mz_deco/Preprocessing/Normalization.vb:554-564 — the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach — a file they already depend on, or a new one alongside them — and call it from both call sites, so a change lands once. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
  • Duplicated block (10 lines × 2) src/metadb/Lipidomics/SpectrumGenerator/HBMPEidSpectrumGenerator.vb:219 — src/metadb/Lipidomics/SpectrumGenerator/HBMPEidSpectrumGenerator.vb:219-228 | src/metadb/Lipidomics/SpectrumGenerator/HBMPSpectrumGenerator.vb:213-222 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/HBMPEidSpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/HBMPSpectrumGenerator.vb` as WHOLE FILES: this scan already matched 4 separate duplicated blocks between them, totalling at least 47 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
D4 · Code Duplication · Duplicated block (9 lines × 2) · ×14
  • Duplicated block (9 lines × 2) src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:321 — src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:321-329 | src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:904-912 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (9 lines × 2) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1172 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1172-1180 | src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:2937-2945 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (9 lines × 2) src/mzmath/MSEngine/Proteomics/PeptideCalc.vb:188 — src/mzmath/MSEngine/Proteomics/PeptideCalc.vb:188-196 | src/mzmath/MSEngine/Proteomics/PeptideCalc.vb:409-417 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (9 lines × 2) src/visualize/plot/ChromatogramPlot/TICplot.vb:261 — src/visualize/plot/ChromatogramPlot/TICplot.vb:261-269 | src/visualize/plot/PlotMassWindowXIC.vb:251-259 — the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach — a location they all depend on today, or a new shared one if there is none — and call it from each site; until then, every change has to be made twice.
  • Duplicated block (9 lines × 2) src/mzmath/TargetedMetabolomics/GCMS/QuantifyAnalysis/SIMMode.vb:111 — src/mzmath/TargetedMetabolomics/GCMS/QuantifyAnalysis/SIMMode.vb:111-119 | src/mzmath/TargetedMetabolomics/GCMS/QuantifyAnalysis/ScanMode.vb:114-122 — the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach — a file they already depend on, or a new one alongside them — and call it from both call sites, so a change lands once. Read the line range as the matched WINDOW rather than a finished unit: at `src/mzmath/TargetedMetabolomics/GCMS/QuantifyAnalysis/SIMMode.vb:111` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
  • Duplicated block (9 lines × 2) Rscript/Library/mzkit_app/src/mzkit/annotations/MetaDbXref.vb:603 — Rscript/Library/mzkit_app/src/mzkit/annotations/MetaDbXref.vb:603-611 | Rscript/Library/mzkit_app/src/mzkit/annotations/MetaDbXref.vb:619-627 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, `Rscript/Library/mzkit_app/src/mzkit/annotations/MetaDbXref.vb:612` calls `uniqueKeys` and `Rscript/Library/mzkit_app/src/mzkit/annotations/MetaDbXref.vb:628` does not — after which the two agree again for 3 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live.
  • Duplicated block (9 lines × 2) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:415 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:415-423 | src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:2053-2061 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (9 lines × 2) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1182 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1182-1190 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3674-3682 — before extracting anything, compare `src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb` and `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb` as WHOLE FILES: this scan already matched 32 separate duplicated blocks between them, totalling at least 530 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
  • Duplicated block (9 lines × 2) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:2938 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:2938-2946 | src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:2958-2971 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (9 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4766 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4766-4775 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12344-12352 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
  • Duplicated block (9 lines × 2) src/metadb/Lipidomics/SpectrumGenerator/PAEidSpectrumGenerator.vb:98 — src/metadb/Lipidomics/SpectrumGenerator/PAEidSpectrumGenerator.vb:98-107 | src/metadb/Lipidomics/SpectrumGenerator/PASpectrumGenerator.vb:99-107 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/PAEidSpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/PASpectrumGenerator.vb` as WHOLE FILES: 90% of the shorter file's lines also appear in the other, so this reads as one file having been copied from the other rather than as a helper waiting to be extracted. The 2 duplicated block(s) this scan matched between them are fragments of that copy, not the extent of it — treat the file pair as the unit. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
  • Duplicated block (9 lines × 2) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:2371 — src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:2371-2379 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:2402-2410 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (9 lines × 2) src/mzmath/mz_deco/Preprocessing/MathHelpers.vb:39 — src/mzmath/mz_deco/Preprocessing/MathHelpers.vb:39-47 | src/mzmath/mz_deco/Preprocessing/MathHelpers.vb:131-139 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (9 lines × 2) src/metadb/Lipidomics/SpectrumGenerator/SMEidSpectrumGenerator.vb:83 — src/metadb/Lipidomics/SpectrumGenerator/SMEidSpectrumGenerator.vb:83-91 | src/metadb/Lipidomics/SpectrumGenerator/SMSpectrumGenerator.vb:86-94 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/SMEidSpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/SMSpectrumGenerator.vb` as WHOLE FILES: this scan already matched 4 separate duplicated blocks between them, totalling at least 66 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
D4 · Code Duplication · Duplicated block (7 lines × 2) · ×11
  • Duplicated block (7 lines × 2) src/mzmath/MSEngine/SpectrumHandler.vb:356 — src/mzmath/MSEngine/SpectrumHandler.vb:356-362 | src/mzmath/MSEngine/SpectrumHandler.vb:375-381 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at `src/mzmath/MSEngine/SpectrumHandler.vb:356` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, `src/mzmath/MSEngine/SpectrumHandler.vb:382` calls `isotopeTemps` and `src/mzmath/MSEngine/SpectrumHandler.vb:363` does not — after which the two agree again for 4 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live.
  • Duplicated block (7 lines × 2) src/mzmath/mz_deco/Preprocessing/MathHelpers.vb:867 — src/mzmath/mz_deco/Preprocessing/MathHelpers.vb:867-873 | src/mzmath/mz_deco/Preprocessing/MathHelpers.vb:884-890 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, `src/mzmath/mz_deco/Preprocessing/MathHelpers.vb:891` calls `loadings` and `src/mzmath/mz_deco/Preprocessing/MathHelpers.vb:874` does not — after which the two agree again for 2 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live.
  • Duplicated block (7 lines × 2) src/visualize/MsImaging/Plot/DualRegionUnionPlot.vb:193 — src/visualize/MsImaging/Plot/DualRegionUnionPlot.vb:193-199 | src/visualize/MsImaging/Plot/MSIPlot.vb:165-171 — the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach — a file they already depend on, or a new one alongside them — and call it from both call sites, so a change lands once. Read the line range as the matched WINDOW rather than a finished unit: at `src/visualize/MsImaging/Plot/DualRegionUnionPlot.vb:193` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
  • Duplicated block (7 lines × 2) src/metadb/Lipidomics/LipoqualityRest.vb:105 — src/metadb/Lipidomics/LipoqualityRest.vb:105-111 | src/metadb/Lipidomics/LipoqualityRest.vb:413-421 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (7 lines × 2) src/metadb/Lipidomics/LipoqualityRest.vb:175 — src/metadb/Lipidomics/LipoqualityRest.vb:175-181 | src/metadb/Lipidomics/LipoqualityRest.vb:249-257 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (7 lines × 2) src/metadb/Lipidomics/LipoqualityRest.vb:267 — src/metadb/Lipidomics/LipoqualityRest.vb:267-273 | src/metadb/Lipidomics/LipoqualityRest.vb:309-317 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (7 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3104 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3104-3111 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4218-4224 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
  • Duplicated block (7 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5316 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5316-5324 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5336-5342 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (7 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7888 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7888-7895 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13644-13650 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (7 lines × 2) src/metadb/Lipidomics/SpectrumGenerator/DMEDFAHFASpectrumGenerator.vb:166 — src/metadb/Lipidomics/SpectrumGenerator/DMEDFAHFASpectrumGenerator.vb:166-187 | src/metadb/Lipidomics/SpectrumGenerator/DMEDFASpectrumGenerator.vb:141-147 — the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach — a file they already depend on, or a new one alongside them — and call it from both call sites, so a change lands once.
  • Duplicated block (7 lines × 2) src/metadna/metaDNA/Models/UnknownSet.vb:147 — src/metadna/metaDNA/Models/UnknownSet.vb:147-153 | src/mzmath/ms2_math-core/Ms1/Tolerance/Tolerance.vb:262-268 — the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach — a location they all depend on today, or a new shared one if there is none — and call it from each site; until then, every change has to be made twice.
D4 · Code Duplication · Duplicated block (11 lines × 2) · ×10
  • Duplicated block (11 lines × 2) Rscript/Library/mzkit_app/src/mzkit/annotations/Massbank.vb:1118 — Rscript/Library/mzkit_app/src/mzkit/annotations/Massbank.vb:1118-1128 | Rscript/Library/mzkit_app/src/mzkit/annotations/Massbank.vb:1137-1147 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (11 lines × 2) src/metadb/Lipidomics/Annotation/LipidomicsConverter.vb:2507 — src/metadb/Lipidomics/Annotation/LipidomicsConverter.vb:2507-2517 | src/metadb/Lipidomics/Annotation/LipidomicsConverter.vb:2523-2533 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (11 lines × 2) src/metadb/Lipidomics/MsCharacterization/EieioMsCharacterizationUtility.vb:307 — src/metadb/Lipidomics/MsCharacterization/EieioMsCharacterizationUtility.vb:307-317 | src/metadb/Lipidomics/MsCharacterization/EieioMsCharacterizationUtility.vb:383-393 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (11 lines × 2) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1181 — src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1181-1191 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:2348-2358 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (11 lines × 2) src/assembly/LoadR.NET5/Ms1Search/SearchList.vb:127 — src/assembly/LoadR.NET5/Ms1Search/SearchList.vb:127-137 | src/assembly/LoadR.NET5/Ms1Search/SearchTable.vb:103-113 — the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach — a file they already depend on, or a new one alongside them — and call it from both call sites, so a change lands once.
  • Duplicated block (11 lines × 2) src/metadb/Lipidomics/ChainParser/AcylChainParser.vb:100 — src/metadb/Lipidomics/ChainParser/AcylChainParser.vb:100-110 | src/metadb/Lipidomics/ChainParser/AlkylChainParser.vb:115-125 — the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach — a file they already depend on, or a new one alongside them — and call it from both call sites, so a change lands once.
  • Duplicated block (11 lines × 2) src/mzmath/MSEngine/Search/MsScanMatching.vb:139 — src/mzmath/MSEngine/Search/MsScanMatching.vb:139-149 | src/mzmath/MSEngine/Search/MsScanMatching.vb:162-172 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (11 lines × 2) src/mzmath/MSFinder/FormulaStringParcer.vb:458 — src/mzmath/MSFinder/FormulaStringParcer.vb:458-468 | src/mzmath/MSFinder/FormulaStringParcer.vb:603-614 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (11 lines × 2) src/mzmath/mz_deco/Preprocessing/Normalization.vb:406 — src/mzmath/mz_deco/Preprocessing/Normalization.vb:406-416 | src/mzmath/mz_deco/Preprocessing/Normalization.vb:486-496 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (11 lines × 2) src/mzmath/mz_deco/Signals/PeakFinding/PeakDetector.vb:598 — src/mzmath/mz_deco/Signals/PeakFinding/PeakDetector.vb:598-608 | src/mzmath/mz_deco/Signals/PeakFinding/PeakProcessor.vb:201-211 — the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach — a file they already depend on, or a new one alongside them — and call it from both call sites, so a change lands once.
D4 · Code Duplication · Duplicated block (12 lines × 2) · ×8
  • Duplicated block (12 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6261 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6261-6272 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6338-6349 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (12 lines × 2) src/mzmath/mz_deco/Preprocessing/Normalization.vb:130 — src/mzmath/mz_deco/Preprocessing/Normalization.vb:130-141 | src/mzmath/mz_deco/Preprocessing/Normalization.vb:175-186 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (12 lines × 2) src/mzmath/MSEngine/Search/MsScanMatching.vb:474 — src/mzmath/MSEngine/Search/MsScanMatching.vb:474-485 | src/mzmath/MSEngine/Search/MsScanMatching.vb:494-505 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (12 lines × 2) Rscript/Library/mzkit_app/src/mzquant/MRM/MRMkit.vb:836 — Rscript/Library/mzkit_app/src/mzquant/MRM/MRMkit.vb:836-847 | Rscript/Library/mzkit_app/src/mzquant/MRM/MRMkit.vb:946-957 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (12 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:2583 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:2583-2594 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15610-15621 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (12 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5589 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5589-5601 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6225-6236 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6225` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
  • Duplicated block (12 lines × 2) src/metadb/Lipidomics/MsCharacterization/PEEadMsCharacterization.vb:68 — src/metadb/Lipidomics/MsCharacterization/PEEadMsCharacterization.vb:68-79 | src/metadb/Lipidomics/MsCharacterization/PSEadMsCharacterization.vb:68-79 — before extracting anything, compare `src/metadb/Lipidomics/MsCharacterization/PEEadMsCharacterization.vb` and `src/metadb/Lipidomics/MsCharacterization/PSEadMsCharacterization.vb` as WHOLE FILES: 92% of the shorter file's lines also appear in the other, so this reads as one file having been copied from the other rather than as a helper waiting to be extracted. The 2 duplicated block(s) this scan matched between them are fragments of that copy, not the extent of it — treat the file pair as the unit. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
  • Duplicated block (12 lines × 2) src/metadb/Lipidomics/MsCharacterization/PGEadMsCharacterization.vb:68 — src/metadb/Lipidomics/MsCharacterization/PGEadMsCharacterization.vb:68-79 | src/metadb/Lipidomics/MsCharacterization/PIEadMsCharacterization.vb:68-79 — before extracting anything, compare `src/metadb/Lipidomics/MsCharacterization/PGEadMsCharacterization.vb` and `src/metadb/Lipidomics/MsCharacterization/PIEadMsCharacterization.vb` as WHOLE FILES: 92% of the shorter file's lines also appear in the other, so this reads as one file having been copied from the other rather than as a helper waiting to be extracted. The 2 duplicated block(s) this scan matched between them are fragments of that copy, not the extent of it — treat the file pair as the unit. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
D4 · Code Duplication · Duplicated block (26 lines × 2) · ×7
  • Duplicated block (26 lines × 2) src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:383 — src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:383-408 | src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:966-991 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (26 lines × 2) src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:843 — src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:843-868 | src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:1423-1448 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (26 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5760 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5760-5785 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15942-15967 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (26 lines × 2) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1260 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1260-1285 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5775-5800 — before extracting anything, compare `src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb` and `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb` as WHOLE FILES: this scan already matched 32 separate duplicated blocks between them, totalling at least 530 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
  • Duplicated block (26 lines × 2) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1298 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1298-1323 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5815-5840 — before extracting anything, compare `src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb` and `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb` as WHOLE FILES: this scan already matched 32 separate duplicated blocks between them, totalling at least 530 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
  • Duplicated block (26 lines × 2) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:3025 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:3025-3050 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15957-15982 — before extracting anything, compare `src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb` and `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb` as WHOLE FILES: this scan already matched 32 separate duplicated blocks between them, totalling at least 530 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
  • Duplicated block (26 lines × 2) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:3063 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:3063-3088 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15997-16022 — before extracting anything, compare `src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb` and `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb` as WHOLE FILES: this scan already matched 32 separate duplicated blocks between them, totalling at least 530 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
D4 · Code Duplication · Duplicated block (15 lines × 2) · ×7
  • Duplicated block (15 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:729 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:729-743 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:982-996 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (15 lines × 2) src/metadb/Lipidomics/Annotation/LipidMassLibraryGenerator.vb:1010 — src/metadb/Lipidomics/Annotation/LipidMassLibraryGenerator.vb:1010-1024 | src/metadb/Lipidomics/Annotation/LipidMassLibraryGenerator.vb:1093-1107 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (15 lines × 2) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1147 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1147-1161 | src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:2914-2928 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (15 lines × 2) src/metadb/Lipidomics/SpectrumGeneratorUtility.vb:79 — src/metadb/Lipidomics/SpectrumGeneratorUtility.vb:79-93 | src/metadb/Lipidomics/SpectrumGeneratorUtility.vb:105-119 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just before the matched lines, `src/metadb/Lipidomics/SpectrumGeneratorUtility.vb:76` calls `diffs` and `src/metadb/Lipidomics/SpectrumGeneratorUtility.vb:102` does not — after which the two agree again for 3 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live.
  • Duplicated block (15 lines × 2) src/mzmath/Oligonucleotide_MS/MS_Peak/Oligonucleotide_MS_Peak_ID_Given_Sequence_v8.vb:261 — src/mzmath/Oligonucleotide_MS/MS_Peak/Oligonucleotide_MS_Peak_ID_Given_Sequence_v8.vb:261-275 | src/mzmath/Oligonucleotide_MS/MS_Peak/Oligonucleotide_MS_Peak_ID_Given_Sequence_v8.vb:284-298 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (15 lines × 2) src/metadb/Lipidomics/SpectrumGenerator/BMPEidSpectrumGenerator.vb:187 — src/metadb/Lipidomics/SpectrumGenerator/BMPEidSpectrumGenerator.vb:187-201 | src/metadb/Lipidomics/SpectrumGenerator/BMPSpectrumGenerator.vb:188-202 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/BMPEidSpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/BMPSpectrumGenerator.vb` as WHOLE FILES: this scan already matched 4 separate duplicated blocks between them, totalling at least 55 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
  • Duplicated block (15 lines × 2) src/mzmath/mz_deco/Preprocessing/Normalization.vb:397 — src/mzmath/mz_deco/Preprocessing/Normalization.vb:397-411 | src/mzmath/mz_deco/Preprocessing/Normalization.vb:436-450 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, `src/mzmath/mz_deco/Preprocessing/Normalization.vb:451` calls `Sqrt` and `src/mzmath/mz_deco/Preprocessing/Normalization.vb:412` does not — after which the two agree again for 4 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live.
D17 · Explicit Debt · BarePragmaDisable · ×6
  • BarePragmaDisable src/assembly/SpectrumTree/Query/TreeSearch.vb:121 — #Disable Warning — the disable is closed again below, so its scope is not the problem; what it records is no reason: there is nothing on the directive line, and no ordinary comment attached to it either side. A suppression is a decision somebody made, and without the reason the next reader cannot tell a considered exception from an unexamined one, so it is never revisited and it outlives the code it was written for. Put the reason on the directive line — what makes this site legitimately different — or fix what the rule is pointing at and delete the pair. A rationale in the member's documentation comment does not clear this row and is not meant to: it explains the member to its callers, and the next person to touch the suppression is not reading it for that.
  • BarePragmaDisable src/assembly/assembly/mzPack/mzXMLWriter.vb:302 — #Disable Warning — the disable is closed again below, so its scope is not the problem; what it records is no reason: there is nothing on the directive line, and no ordinary comment attached to it either side. A suppression is a decision somebody made, and without the reason the next reader cannot tell a considered exception from an unexamined one, so it is never revisited and it outlives the code it was written for. Put the reason on the directive line — what makes this site legitimately different — or fix what the rule is pointing at and delete the pair. A rationale in the member's documentation comment does not clear this row and is not meant to: it explains the member to its callers, and the next person to touch the suppression is not reading it for that.
  • BarePragmaDisable src/assembly/mzPack/v2.0/mzStream.vb:400 — #Disable Warning — the disable is closed again below, so its scope is not the problem; what it records is no reason: there is nothing on the directive line, and no ordinary comment attached to it either side. A suppression is a decision somebody made, and without the reason the next reader cannot tell a considered exception from an unexamined one, so it is never revisited and it outlives the code it was written for. Put the reason on the directive line — what makes this site legitimately different — or fix what the rule is pointing at and delete the pair. A rationale in the member's documentation comment does not clear this row and is not meant to: it explains the member to its callers, and the next person to touch the suppression is not reading it for that.
  • BarePragmaDisable src/metadb/Chemoinformatics/InChI/Extensions.vb:75 — #Disable Warning — the disable is closed again below, so its scope is not the problem; what it records is no reason: there is nothing on the directive line, and no ordinary comment attached to it either side. A suppression is a decision somebody made, and without the reason the next reader cannot tell a considered exception from an unexamined one, so it is never revisited and it outlives the code it was written for. Put the reason on the directive line — what makes this site legitimately different — or fix what the rule is pointing at and delete the pair. A rationale in the member's documentation comment does not clear this row and is not meant to: it explains the member to its callers, and the next person to touch the suppression is not reading it for that.
  • BarePragmaDisable src/visualize/MsImaging/Blender/Ruler.vb:142 — #Disable Warning — the disable is closed again below, so its scope is not the problem; what it records is no reason: there is nothing on the directive line, and no ordinary comment attached to it either side. A suppression is a decision somebody made, and without the reason the next reader cannot tell a considered exception from an unexamined one, so it is never revisited and it outlives the code it was written for. Put the reason on the directive line — what makes this site legitimately different — or fix what the rule is pointing at and delete the pair. A rationale in the member's documentation comment does not clear this row and is not meant to: it explains the member to its callers, and the next person to touch the suppression is not reading it for that.
  • BarePragmaDisable src/visualize/TissueMorphology/Scatter/Extensions.vb:116 — #Disable Warning — the disable is closed again below, so its scope is not the problem; what it records is no reason: there is nothing on the directive line, and no ordinary comment attached to it either side. A suppression is a decision somebody made, and without the reason the next reader cannot tell a considered exception from an unexamined one, so it is never revisited and it outlives the code it was written for. Put the reason on the directive line — what makes this site legitimately different — or fix what the rule is pointing at and delete the pair. A rationale in the member's documentation comment does not clear this row and is not meant to: it explains the member to its callers, and the next person to touch the suppression is not reading it for that.
D4 · Code Duplication · Duplicated block (14 lines × 2) · ×6
  • Duplicated block (14 lines × 2) Rscript/Library/mzkit_app/src/mzkit/assembly/MzWeb.vb:180 — Rscript/Library/mzkit_app/src/mzkit/assembly/MzWeb.vb:180-193 | Rscript/Library/mzkit_app/src/mzkit/assembly/MzWeb.vb:226-239 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at `Rscript/Library/mzkit_app/src/mzkit/assembly/MzWeb.vb:180` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
  • Duplicated block (14 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7822 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7822-7835 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7894-7907 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (14 lines × 2) src/metadb/Lipidomics/SeparatedChains.vb:197 — src/metadb/Lipidomics/SeparatedChains.vb:197-210 | src/metadb/Lipidomics/SeparatedChains.vb:228-241 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (14 lines × 2) Rscript/Library/mzkit_app/src/mzquant/mzDeco.vb:1730 — Rscript/Library/mzkit_app/src/mzquant/mzDeco.vb:1730-1743 | Rscript/Library/mzkit_app/src/mzquant/mzDeco.vb:1789-1802 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (14 lines × 2) src/metadb/Lipidomics/Annotation/LipidMassLibraryGenerator.vb:1161 — src/metadb/Lipidomics/Annotation/LipidMassLibraryGenerator.vb:1161-1174 | src/metadb/Lipidomics/Annotation/LipidMassLibraryGenerator.vb:1207-1220 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (14 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4664 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4664-4678 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4775-4788 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it.
D18 · Solution Shape · Solution references 7 projects that do not exist · ×5
  • Solution references 7 projects that do not exist src/metadb/Lipidomics.sln — `src/metadb/Lipidomics.sln` declares 7 project file(s) that are missing from the tree (`biocore-netcore5.vbproj`, `graph-netcore5.vbproj`, `linear-netcore5.vbproj`, `stats-netcore5.vbproj`, `Math.NET5.vbproj`, `signalprocessing-netcore5.vbproj`, +1 more). A solution-level restore or build fails on a dangling reference, so anyone building the solution rather than an individual project is blocked. Delete the stale entry from the solution, or restore the missing project file.
  • Solution references 7 projects that do not exist src/mzmath/deconv.NET5.sln — `src/mzmath/deconv.NET5.sln` declares 7 project file(s) that are missing from the tree (`binarydata-netcore5.vbproj`, `dataframework-netcore5.vbproj`, `linear-netcore5.vbproj`, `Math.NET5.vbproj`, `signalprocessing-netcore5.vbproj`, `Core.vbproj`, +1 more). A solution-level restore or build fails on a dangling reference, so anyone building the solution rather than an individual project is blocked. Delete the stale entry from the solution, or restore the missing project file.
  • Solution references 7 projects that do not exist src/metadb/PeaksAnnotation.sln — `src/metadb/PeaksAnnotation.sln` declares 7 project file(s) that are missing from the tree (`graph-netcore5.vbproj`, `linear-netcore5.vbproj`, `stats-netcore5.vbproj`, `Math.NET5.vbproj`, `signalprocessing-netcore5.vbproj`, `Core.vbproj`, +1 more). A solution-level restore or build fails on a dangling reference, so anyone building the solution rather than an individual project is blocked. Delete the stale entry from the solution, or restore the missing project file.
  • Solution references 7 projects that do not exist src/assembly/BrukerDataReader.sln — `src/assembly/BrukerDataReader.sln` declares 7 project file(s) that are missing from the tree (`binarydata-netcore5.vbproj`, `datastorage-netcore5.vbproj`, `SQLite3.vbproj`, `dataframework-netcore5.vbproj`, `Math.NET5.vbproj`, `signalprocessing-netcore5.vbproj`, +1 more). A solution-level restore or build fails on a dangling reference, so anyone building the solution rather than an individual project is blocked. Delete the stale entry from the solution, or restore the missing project file.
  • Solution references 7 projects that do not exist src/metadna/KEGG_MetaDNA.sln — `src/metadna/KEGG_MetaDNA.sln` declares 7 project file(s) that are missing from the tree (`Bio.Assembly.vbproj`, `RDotNET.Extensions.VisualBasic.vbproj`, `RDotNET.vbproj`, `47_dotnet_ms-vb_data.framework.vbproj`, `math-core.vbproj`, `47-dotnet_Microsoft.VisualBasic.vbproj`, +1 more). A solution-level restore or build fails on a dangling reference, so anyone building the solution rather than an individual project is blocked. Delete the stale entry from the solution, or restore the missing project file.
D4 · Code Duplication · Duplicated block (22 lines × 2) · ×5
  • Duplicated block (22 lines × 2) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:2023 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:2023-2044 | src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:3498-3519 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (22 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5719 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5719-5740 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15901-15922 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (22 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5804 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5804-5825 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15986-16007 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (22 lines × 2) src/metadb/Lipidomics/SpectrumGenerator/BMPEidSpectrumGenerator.vb:125 — src/metadb/Lipidomics/SpectrumGenerator/BMPEidSpectrumGenerator.vb:125-146 | src/metadb/Lipidomics/SpectrumGenerator/BMPSpectrumGenerator.vb:124-145 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/BMPEidSpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/BMPSpectrumGenerator.vb` as WHOLE FILES: this scan already matched 4 separate duplicated blocks between them, totalling at least 55 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
  • Duplicated block (22 lines × 2) src/metadb/Lipidomics/SpectrumGenerator/PGSpectrumGenerator.vb:174 — src/metadb/Lipidomics/SpectrumGenerator/PGSpectrumGenerator.vb:174-195 | src/metadb/Lipidomics/SpectrumGenerator/PGd5SpectrumGenerator.vb:173-194 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/PGSpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/PGd5SpectrumGenerator.vb` as WHOLE FILES: this scan already matched 3 separate duplicated blocks between them, totalling at least 68 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
D4 · Code Duplication · Duplicated block (16 lines × 2) · ×5
  • Duplicated block (16 lines × 2) src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:339 — src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:339-354 | src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:922-937 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (16 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3715 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3715-3730 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15878-15893 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (16 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13544 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13544-13559 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13581-13596 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (16 lines × 2) src/assembly/Comprehensive/MsImaging/MergeSliders/MergeLinear.vb:111 — src/assembly/Comprehensive/MsImaging/MergeSliders/MergeLinear.vb:111-126 | src/assembly/Comprehensive/MsImaging/MergeSliders/MergeLinear.vb:163-178 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (16 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12310 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12310-12329 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12363-12378 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
D4 · Code Duplication · Duplicated block (12 lines × 3) · ×5
  • Duplicated block (12 lines × 3) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1774 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1774-1785 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12126-12137 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12180-12191 — before extracting anything, compare `src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb` and `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb` as WHOLE FILES: this scan already matched 32 separate duplicated blocks between them, totalling at least 530 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
  • Duplicated block (12 lines × 3) src/metadb/Lipidomics/Annotation/LipidMassLibraryGenerator.vb:980 — src/metadb/Lipidomics/Annotation/LipidMassLibraryGenerator.vb:980-991 | src/metadb/Lipidomics/Annotation/LipidMassLibraryGenerator.vb:1039-1050 | src/metadb/Lipidomics/Annotation/LipidMassLibraryGenerator.vb:1123-1134 — all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited.
  • Duplicated block (12 lines × 3) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5582 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5582-5593 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5648-5664 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7606-7618 — all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5648` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
  • Duplicated block (12 lines × 3) src/metadb/Lipidomics/SpectrumGenerator/LPGEidSpectrumGenerator.vb:99 — src/metadb/Lipidomics/SpectrumGenerator/LPGEidSpectrumGenerator.vb:99-110 | src/metadb/Lipidomics/SpectrumGenerator/LPIEidSpectrumGenerator.vb:103-114 | src/metadb/Lipidomics/SpectrumGenerator/MGSpectrumGenerator.vb:95-109 — the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach — a file they already depend on, or a new one alongside them — and call it from all 3 call sites, so a change lands once.
  • Duplicated block (12 lines × 3) src/metadb/Lipidomics/SpectrumGenerator/CeramidePhytoSphSpectrumGenerator.vb:157 — src/metadb/Lipidomics/SpectrumGenerator/CeramidePhytoSphSpectrumGenerator.vb:157-170 | src/metadb/Lipidomics/SpectrumGenerator/CeramideSpectrumGenerator.vb:160-171 | src/metadb/Lipidomics/SpectrumGenerator/HexCerSpectrumGenerator.vb:173-184 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/CeramidePhytoSphSpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/CeramideSpectrumGenerator.vb` as WHOLE FILES: 88% of the shorter file's lines also appear in the other, so this reads as one file having been copied from the other rather than as a helper waiting to be extracted. The 2 duplicated block(s) this scan matched between them are fragments of that copy, not the extent of it — treat the file pair as the unit. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
D4 · Code Duplication · Duplicated block (10 lines × 6) · ×5
  • Duplicated block (10 lines × 6) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1231 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1231-1240 | src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1272-1281 | src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1310-1319 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5742-5751 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5787-5796 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5827-5836 — before extracting anything, compare `src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb` and `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb` as WHOLE FILES: this scan already matched 32 separate duplicated blocks between them, totalling at least 530 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
  • Duplicated block (10 lines × 6) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:2994 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:2994-3003 | src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:3037-3046 | src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:3075-3084 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15924-15933 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15969-15978 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:16009-16018 — before extracting anything, compare `src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb` and `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb` as WHOLE FILES: this scan already matched 32 separate duplicated blocks between them, totalling at least 530 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
  • Duplicated block (10 lines × 6) src/metadb/Lipidomics/MsCharacterization/BMPEadMsCharacterization.vb:63 — src/metadb/Lipidomics/MsCharacterization/BMPEadMsCharacterization.vb:63-72 | src/metadb/Lipidomics/MsCharacterization/PCEadMsCharacterization.vb:65-74 | src/metadb/Lipidomics/MsCharacterization/PEEadMsCharacterization.vb:64-73 | src/metadb/Lipidomics/MsCharacterization/PGEadMsCharacterization.vb:64-73 | src/metadb/Lipidomics/MsCharacterization/PIEadMsCharacterization.vb:64-73 | src/metadb/Lipidomics/MsCharacterization/PSEadMsCharacterization.vb:64-73 — before extracting anything, compare `src/metadb/Lipidomics/MsCharacterization/BMPEadMsCharacterization.vb` and `src/metadb/Lipidomics/MsCharacterization/PCEadMsCharacterization.vb` as WHOLE FILES: 88% of the shorter file's lines also appear in the other, so this reads as one file having been copied from the other rather than as a helper waiting to be extracted. The 1 duplicated block(s) this scan matched between them are fragments of that copy, not the extent of it — treat the file pair as the unit. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, `src/metadb/Lipidomics/MsCharacterization/PEEadMsCharacterization.vb:74` calls `Equals` and `src/metadb/Lipidomics/MsCharacterization/PCEadMsCharacterization.vb:76` does not — after which the two agree again for 2 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live.
  • Duplicated block (10 lines × 6) src/metadb/Lipidomics/SpectrumGenerator/LPCEidSpectrumGenerator.vb:182 — src/metadb/Lipidomics/SpectrumGenerator/LPCEidSpectrumGenerator.vb:182-191 | src/metadb/Lipidomics/SpectrumGenerator/LPEEidSpectrumGenerator.vb:193-202 | src/metadb/Lipidomics/SpectrumGenerator/LPGEidSpectrumGenerator.vb:205-214 | src/metadb/Lipidomics/SpectrumGenerator/LPIEidSpectrumGenerator.vb:215-224 | src/metadb/Lipidomics/SpectrumGenerator/LPSEidSpectrumGenerator.vb:194-203 | src/metadb/Lipidomics/SpectrumGenerator/PAEidSpectrumGenerator.vb:194-203 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/LPCEidSpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/LPEEidSpectrumGenerator.vb` as WHOLE FILES: this scan already matched 4 separate duplicated blocks between them, totalling at least 66 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
  • Duplicated block (10 lines × 6) src/metadb/Lipidomics/SpectrumGenerator/LPCEidSpectrumGenerator.vb:168 — src/metadb/Lipidomics/SpectrumGenerator/LPCEidSpectrumGenerator.vb:168-179 | src/metadb/Lipidomics/SpectrumGenerator/LPCSpectrumGenerator.vb:173-184 | src/metadb/Lipidomics/SpectrumGenerator/LPCd5SpectrumGenerator.vb:173-184 | src/metadb/Lipidomics/SpectrumGenerator/LPEEidSpectrumGenerator.vb:173-182 | src/metadb/Lipidomics/SpectrumGenerator/LPESpectrumGenerator.vb:177-188 | src/metadb/Lipidomics/SpectrumGenerator/LPEd5SpectrumGenerator.vb:177-188 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/LPCEidSpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/LPCSpectrumGenerator.vb` as WHOLE FILES: this scan already matched 3 separate duplicated blocks between them, totalling at least 37 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
D4 · Code Duplication · Duplicated block (11 lines × 3) · ×5
  • Duplicated block (11 lines × 3) src/mzmath/mz_deco/Preprocessing/MissingValueImputation.vb:206 — src/mzmath/mz_deco/Preprocessing/MissingValueImputation.vb:206-216 | src/mzmath/mz_deco/Preprocessing/MissingValueImputation.vb:256-266 | src/mzmath/mz_deco/Preprocessing/MissingValueImputation.vb:286-296 — all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited.
  • Duplicated block (11 lines × 3) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3094 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3094-3104 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14748-14761 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14817-14828 — all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
  • Duplicated block (11 lines × 3) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5588 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5588-5600 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6224-6234 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7613-7628 — all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
  • Duplicated block (11 lines × 3) src/metadb/Lipidomics/SpectrumGenerator/LPGEidSpectrumGenerator.vb:182 — src/metadb/Lipidomics/SpectrumGenerator/LPGEidSpectrumGenerator.vb:182-192 | src/metadb/Lipidomics/SpectrumGenerator/LPGSpectrumGenerator.vb:194-206 | src/metadb/Lipidomics/SpectrumGenerator/LPGd5SpectrumGenerator.vb:192-204 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/LPGSpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/LPGd5SpectrumGenerator.vb` as WHOLE FILES: this scan already matched 3 separate duplicated blocks between them, totalling at least 79 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
  • Duplicated block (11 lines × 3) src/metadb/Lipidomics/SpectrumGenerator/LPSEidSpectrumGenerator.vb:173 — src/metadb/Lipidomics/SpectrumGenerator/LPSEidSpectrumGenerator.vb:173-183 | src/metadb/Lipidomics/SpectrumGenerator/LPSSpectrumGenerator.vb:177-189 | src/metadb/Lipidomics/SpectrumGenerator/LPSd5SpectrumGenerator.vb:177-189 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/LPSSpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/LPSd5SpectrumGenerator.vb` as WHOLE FILES: 90% of the shorter file's lines also appear in the other, so this reads as one file having been copied from the other rather than as a helper waiting to be extracted. The 2 duplicated block(s) this scan matched between them are fragments of that copy, not the extent of it — treat the file pair as the unit. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
D4 · Code Duplication · Duplicated block (8 lines × 3) · ×5
  • Duplicated block (8 lines × 3) src/metadb/Lipidomics/SpectrumGenerator/CeramideNsD7SpectrumGenerator.vb:196 — src/metadb/Lipidomics/SpectrumGenerator/CeramideNsD7SpectrumGenerator.vb:196-203 | src/metadb/Lipidomics/SpectrumGeneratorUtility.vb:79-86 | src/metadb/Lipidomics/SpectrumGeneratorUtility.vb:105-112 — there are 3 copies across 2 file(s) — more copies than files, so at least one file holds the block twice. Extract it once into a single shared function every call site can reach and call it from all 3 sites; resolving a subset leaves the remainder to drift apart. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just before the matched lines, `src/metadb/Lipidomics/SpectrumGeneratorUtility.vb:76` calls `diffs` and `src/metadb/Lipidomics/SpectrumGeneratorUtility.vb:102` does not — after which the two agree again for 3 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live.
  • Duplicated block (8 lines × 3) src/metadb/Lipidomics/ChainParser/AcylChainParser.vb:89 — src/metadb/Lipidomics/ChainParser/AcylChainParser.vb:89-96 | src/metadb/Lipidomics/ChainParser/AlkylChainParser.vb:104-111 | src/metadb/Lipidomics/ChainParser/SphingoChainParser.vb:92-99 — the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach — a file they already depend on, or a new one alongside them — and call it from all 3 call sites, so a change lands once.
  • Duplicated block (8 lines × 3) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1787 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1787-1794 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12197-12206 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12250-12259 — before extracting anything, compare `src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb` and `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb` as WHOLE FILES: this scan already matched 32 separate duplicated blocks between them, totalling at least 530 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
  • Duplicated block (8 lines × 3) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:425 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:425-433 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:577-584 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:635-642 — all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
  • Duplicated block (8 lines × 3) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12142 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12142-12150 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12196-12203 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12249-12257 — all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it.
D4 · Code Duplication · Duplicated block (5 lines × 3) · ×5
  • Duplicated block (5 lines × 3) src/metadb/Lipidomics/Annotation/LipidMassLibraryGenerator.vb:950 — src/metadb/Lipidomics/Annotation/LipidMassLibraryGenerator.vb:950-954 | src/metadb/Lipidomics/Annotation/LipidMassLibraryGenerator.vb:977-981 | src/metadb/Lipidomics/Annotation/LipidMassLibraryGenerator.vb:1062-1066 — all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
  • Duplicated block (5 lines × 3) src/metadb/Lipidomics/Annotation/LipidMassLibraryGenerator.vb:1009 — src/metadb/Lipidomics/Annotation/LipidMassLibraryGenerator.vb:1009-1013 | src/metadb/Lipidomics/Annotation/LipidMassLibraryGenerator.vb:1092-1096 | src/metadb/Lipidomics/Annotation/LipidMassLibraryGenerator.vb:1119-1123 — all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited.
  • Duplicated block (5 lines × 3) src/metadb/Lipidomics/ChainParser/AcylChainParser.vb:100 — src/metadb/Lipidomics/ChainParser/AcylChainParser.vb:100-104 | src/metadb/Lipidomics/ChainParser/AlkylChainParser.vb:115-119 | src/metadb/Lipidomics/ChainParser/SphingoChainParser.vb:103-107 — the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach — a file they already depend on, or a new one alongside them — and call it from all 3 call sites, so a change lands once.
  • Duplicated block (5 lines × 3) src/metadb/Lipidomics/SpectrumGenerator/TGEidSpectrumGenerator.vb:160 — src/metadb/Lipidomics/SpectrumGenerator/TGEidSpectrumGenerator.vb:160-164 | src/metadb/Lipidomics/SpectrumGenerator/TGSpectrumGenerator.vb:161-165 | src/metadb/Lipidomics/SpectrumGenerator/TGd5SpectrumGenerator.vb:164-168 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/TGEidSpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/TGSpectrumGenerator.vb` as WHOLE FILES: this scan already matched 3 separate duplicated blocks between them, totalling at least 49 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
  • Duplicated block (5 lines × 3) src/metadb/Lipidomics/TotalChainVariationGenerator.vb:174 — src/metadb/Lipidomics/TotalChainVariationGenerator.vb:174-178 | src/metadb/Lipidomics/TotalChainVariationGenerator.vb:188-192 | src/metadb/Lipidomics/TotalChainVariationGenerator.vb:207-211 — all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited.
D5 · Coupling · Off the main sequence · ×5
  • Off the main sequence: TissueMorphology src/visualize/TissueMorphology/TissueMorphology.vbproj:1 — TissueMorphology: abstractness 0.00, instability 0.00, distance 1.00 — zone of pain — concrete and depended on by 4 project(s), so it's rigid to change.
  • Off the main sequence: deconv.NET5 src/mzmath/mz_deco/deconv.NET5.vbproj:1 — deconv.NET5: abstractness 0.02, instability 0.08, distance 0.89 — zone of pain — concrete and depended on by 9 project(s), so it's rigid to change.
  • Off the main sequence: chemoinformatics-netcore5 src/metadb/Chemoinformatics/chemoinformatics-netcore5.vbproj:1 — chemoinformatics-netcore5: abstractness 0.08, instability 0.03, distance 0.89 — zone of pain — concrete and depended on by 21 project(s), so it's rigid to change.
  • Off the main sequence: SMILES.NET5 src/metadb/SMILES/SMILES.NET5.vbproj:1 — SMILES.NET5: abstractness 0.00, instability 0.13, distance 0.88 — zone of pain — concrete and depended on by 6 project(s), so it's rigid to change.
  • Off the main sequence: assembly-netcore5 src/assembly/assembly/assembly-netcore5.vbproj:1 — assembly-netcore5: abstractness 0.10, instability 0.04, distance 0.86 — zone of pain — concrete and depended on by 19 project(s), so it's rigid to change.
D6 · Cohesion (LCOM4) · Low cohesion · ×5
  • Low cohesion: MSScan (LCOM4 4) src/assembly/assembly/mzPack/Stream/MSScan.vb:74 — MSScan's methods fall into 4 groups that share no field and call none of each other, against a bar of more than 3 for this run (LCOM4, configurable — your repository's bar is the one quoted here). Each group is a set of methods reachable from one another through shared fields or direct calls, so 4 groups means the type has that many internally-connected clusters with nothing tying them together. Types whose shape makes a high count expected — and which would otherwise dominate this list — are excluded before this row is raised, so this is a genuine split candidate rather than a metric reading. It is still a shape, not a defect: confirm the groups match responsibilities you can name before splitting.
  • Low cohesion: PixelReader (LCOM4 4) src/visualize/MsImaging/Reader/PixelReader.vb:83 — PixelReader's methods fall into 4 groups that share no field and call none of each other, against a bar of more than 3 for this run (LCOM4, configurable — your repository's bar is the one quoted here). Each group is a set of methods reachable from one another through shared fields or direct calls, so 4 groups means the type has that many internally-connected clusters with nothing tying them together. Types whose shape makes a high count expected — and which would otherwise dominate this list — are excluded before this row is raised, so this is a genuine split candidate rather than a metric reading. It is still a shape, not a defect: confirm the groups match responsibilities you can name before splitting.
  • Low cohesion: PositionLevelChains (LCOM4 4) src/metadb/Lipidomics/PositionLevelChains.vb:59 — PositionLevelChains's methods fall into 4 groups that share no field and call none of each other, against a bar of more than 3 for this run (LCOM4, configurable — your repository's bar is the one quoted here). Each group is a set of methods reachable from one another through shared fields or direct calls, so 4 groups means the type has that many internally-connected clusters with nothing tying them together. Types whose shape makes a high count expected — and which would otherwise dominate this list — are excluded before this row is raised, so this is a genuine split candidate rather than a metric reading. It is still a shape, not a defect: confirm the groups match responsibilities you can name before splitting.
  • Low cohesion: ChemicalFormula (LCOM4 4) src/metadb/SMILES/Graph/ChemicalFormula.vb:70 — ChemicalFormula's methods fall into 4 groups that share no field and call none of each other, against a bar of more than 3 for this run (LCOM4, configurable — your repository's bar is the one quoted here). Each group is a set of methods reachable from one another through shared fields or direct calls, so 4 groups means the type has that many internally-connected clusters with nothing tying them together. Types whose shape makes a high count expected — and which would otherwise dominate this list — are excluded before this row is raised, so this is a genuine split candidate rather than a metric reading. It is still a shape, not a defect: confirm the groups match responsibilities you can name before splitting.
  • Low cohesion: ModificationContainer (LCOM4 4) src/mzmath/MSEngine/Proteomics/ModificationContainer.vb:68 — ModificationContainer's methods fall into 4 groups that share no field and call none of each other, against a bar of more than 3 for this run (LCOM4, configurable — your repository's bar is the one quoted here). Each group is a set of methods reachable from one another through shared fields or direct calls, so 4 groups means the type has that many internally-connected clusters with nothing tying them together. Types whose shape makes a high count expected — and which would otherwise dominate this list — are excluded before this row is raised, so this is a genuine split candidate rather than a metric reading. It is still a shape, not a defect: confirm the groups match responsibilities you can name before splitting.
D17 · Explicit Debt · TodoComment repeated across 14 files · ×4
  • TodoComment repeated across 14 files src/assembly/BrukerDataReader/flexImaging/mcf/index_sqlite/IndexParser.vb:114 — The identical TodoComment appears in 14 files (14 occurrences) — almost certainly one boilerplate line from a single migration or decision, not 14 independent debts. Fix the systemic cause once rather than file-by-file. Text: "' TODO: dispose managed state (managed objects)". Source code is not a task system: track the cleanup where tasks live. (Every occurrence still counts toward the score and metrics.)
  • TodoComment repeated across 14 files src/assembly/BrukerDataReader/flexImaging/mcf/index_sqlite/IndexParser.vb:118 — The identical TodoComment appears in 14 files (14 occurrences) — almost certainly one boilerplate line from a single migration or decision, not 14 independent debts. Fix the systemic cause once rather than file-by-file. Text: "' TODO: free unmanaged resources (unmanaged objects) and override finalizer". Source code is not a task system: track the cleanup where tasks live. (Every occurrence still counts toward the score and metrics.)
  • TodoComment repeated across 14 files src/assembly/BrukerDataReader/flexImaging/mcf/index_sqlite/IndexParser.vb:119 — The identical TodoComment appears in 14 files (14 occurrences) — almost certainly one boilerplate line from a single migration or decision, not 14 independent debts. Fix the systemic cause once rather than file-by-file. Text: "' TODO: set large fields to null". Source code is not a task system: track the cleanup where tasks live. (Every occurrence still counts toward the score and metrics.)
  • TodoComment repeated across 14 files src/assembly/BrukerDataReader/flexImaging/mcf/index_sqlite/IndexParser.vb:124 — The identical TodoComment appears in 14 files (14 occurrences) — almost certainly one boilerplate line from a single migration or decision, not 14 independent debts. Fix the systemic cause once rather than file-by-file. Text: "' ' TODO: override finalizer only if 'Dispose(disposing As Boolean)' has code to free unmanaged resources". Source code is not a task system: track the cleanup where tasks live. (Every occurrence still counts toward the score and metrics.)
D18 · Solution Shape · Solution references 4 projects that do not exist · ×4
  • Solution references 4 projects that do not exist src/metadb/SMILES_struct.sln — `src/metadb/SMILES_struct.sln` declares 4 project file(s) that are missing from the tree (`graph-netcore5.vbproj`, `stats-netcore5.vbproj`, `Math.NET5.vbproj`, `Core.vbproj`). A solution-level restore or build fails on a dangling reference, so anyone building the solution rather than an individual project is blocked. Delete the stale entry from the solution, or restore the missing project file.
  • Solution references 4 projects that do not exist src/mzmath/Oligonucleotide_MS.sln — `src/mzmath/Oligonucleotide_MS.sln` declares 4 project file(s) that are missing from the tree (`biocore-netcore5.vbproj`, `stats-netcore5.vbproj`, `Math.NET5.vbproj`, `Core.vbproj`). A solution-level restore or build fails on a dangling reference, so anyone building the solution rather than an individual project is blocked. Delete the stale entry from the solution, or restore the missing project file.
  • Solution references 4 projects that do not exist src/assembly/Raman-Spectroscopy.sln — `src/assembly/Raman-Spectroscopy.sln` declares 4 project file(s) that are missing from the tree (`linear-netcore5.vbproj`, `Math.NET5.vbproj`, `signalprocessing-netcore5.vbproj`, `Core.vbproj`). A solution-level restore or build fails on a dangling reference, so anyone building the solution rather than an individual project is blocked. Delete the stale entry from the solution, or restore the missing project file.
  • Solution references 4 projects that do not exist src/mzmath/mzMath.sln — `src/mzmath/mzMath.sln` declares 4 project file(s) that are missing from the tree (`dataframework-netcore5.vbproj`, `Math.NET5.vbproj`, `signalprocessing-netcore5.vbproj`, `Core.vbproj`). A solution-level restore or build fails on a dangling reference, so anyone building the solution rather than an individual project is blocked. Delete the stale entry from the solution, or restore the missing project file.
D4 · Code Duplication · Members sharing a duplicated core (8 members, 50+ identical tokens) · ×4
  • Members sharing a duplicated core (8 members, 50+ identical tokens) src/metadb/Lipidomics/Annotation/LipidMassLibraryGenerator.vb:903 — src/metadb/Lipidomics/Annotation/LipidMassLibraryGenerator.vb:903-933 | src/metadb/Lipidomics/Annotation/LipidMassLibraryGenerator.vb:937-965 | src/metadb/Lipidomics/Annotation/LipidMassLibraryGenerator.vb:970-991 | src/metadb/Lipidomics/Annotation/LipidMassLibraryGenerator.vb:997-1024 | src/metadb/Lipidomics/Annotation/LipidMassLibraryGenerator.vb:1029-1050 | src/metadb/Lipidomics/Annotation/LipidMassLibraryGenerator.vb:1055-1076 | src/metadb/Lipidomics/Annotation/LipidMassLibraryGenerator.vb:1080-1107 | src/metadb/Lipidomics/Annotation/LipidMassLibraryGenerator.vb:1112-1134 — These 8 members share a duplicated core: a run of at least 50 identical tokens appears in every one of them. That run is NOT broken out as duplicated-block rows below — it is what admitted this row, and the blocks below cover only the part of it that clears the block floor, so they understate the correspondence. Read the members as one construct written 8 times. The repair is at the members' grain — factor the shared implementation out once and have all of them call it with their differences as parameters or as an injected step, or, where the difference is systematic, generate them from one template. Extracting the individual blocks below is not the same fix: it leaves every body in place and the next edit still has to be made 8 times.
  • Members sharing a duplicated core (8 members, 50+ identical tokens) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:2022 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:2022-2049 | src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:3497-3525 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3341-3376 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13704-13723 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13752-13771 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13775-13794 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13843-13862 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:16511-16538 — These 8 members share a duplicated core: a run of at least 50 identical tokens appears in every one of them. That run is NOT broken out as duplicated-block rows below — it is what admitted this row, and the blocks below cover only the part of it that clears the block floor, so they understate the correspondence. Read the members as one construct written 8 times. The repair is at the members' grain — factor the shared implementation out once and have all of them call it with their differences as parameters or as an injected step, or, where the difference is systematic, generate them from one template. Extracting the individual blocks below is not the same fix: it leaves every body in place and the next edit still has to be made 8 times.
  • Members sharing a duplicated core (8 members, 50+ identical tokens) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11578 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11578-11663 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11667-11730 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11733-11797 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11800-11821 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11824-11845 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11849-11913 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11917-11983 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11987-12053 — These 8 members share a duplicated core: a run of at least 50 identical tokens appears in every one of them. That run is NOT broken out as duplicated-block rows below — it is what admitted this row, and the blocks below cover only the part of it that clears the block floor, so they understate the correspondence. Read the members as one construct written 8 times. The repair is at the members' grain — factor the shared implementation out once and have all of them call it with their differences as parameters or as an injected step, or, where the difference is systematic, generate them from one template. Extracting the individual blocks below is not the same fix: it leaves every body in place and the next edit still has to be made 8 times.
  • Members sharing a duplicated core (8 members, 50+ identical tokens) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12574 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12574-12607 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12611-12644 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12647-12679 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12683-12715 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12719-12751 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12755-12787 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12791-12830 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12834-12866 — These 8 members share a duplicated core: a run of at least 50 identical tokens appears in every one of them. That run is NOT broken out as duplicated-block rows below — it is what admitted this row, and the blocks below cover only the part of it that clears the block floor, so they understate the correspondence. Read the members as one construct written 8 times. The repair is at the members' grain — factor the shared implementation out once and have all of them call it with their differences as parameters or as an injected step, or, where the difference is systematic, generate them from one template. Extracting the individual blocks below is not the same fix: it leaves every body in place and the next edit still has to be made 8 times.
D4 · Code Duplication · Members sharing a duplicated core (6 members, 50+ identical tokens) · ×4
  • Members sharing a duplicated core (6 members, 50+ identical tokens) src/metadb/Lipidomics/MsCharacterization/BMPEadMsCharacterization.vb:62 — src/metadb/Lipidomics/MsCharacterization/BMPEadMsCharacterization.vb:62-75 | src/metadb/Lipidomics/MsCharacterization/PCEadMsCharacterization.vb:64-77 | src/metadb/Lipidomics/MsCharacterization/PEEadMsCharacterization.vb:63-79 | src/metadb/Lipidomics/MsCharacterization/PGEadMsCharacterization.vb:63-79 | src/metadb/Lipidomics/MsCharacterization/PIEadMsCharacterization.vb:63-79 | src/metadb/Lipidomics/MsCharacterization/PSEadMsCharacterization.vb:63-79 — These 6 members share a duplicated core: a run of at least 50 identical tokens appears in every one of them. That run is NOT broken out as duplicated-block rows below — it is what admitted this row, and the blocks below cover only the part of it that clears the block floor, so they understate the correspondence. Read the members as one construct written 6 times. The repair is at the members' grain — factor the shared implementation out once and have all of them call it with their differences as parameters or as an injected step, or, where the difference is systematic, generate them from one template. Extracting the individual blocks below is not the same fix: it leaves every body in place and the next edit still has to be made 6 times.
  • Members sharing a duplicated core (6 members, 50+ identical tokens) src/metadb/Lipidomics/SpectrumGenerator/Hex2CerSpectrumGenerator.vb:92 — src/metadb/Lipidomics/SpectrumGenerator/Hex2CerSpectrumGenerator.vb:92-112 | src/metadb/Lipidomics/SpectrumGenerator/HexCerSpectrumGenerator.vb:92-116 | src/metadb/Lipidomics/SpectrumGenerator/SMEidSpectrumGenerator.vb:95-118 | src/metadb/Lipidomics/SpectrumGenerator/SMOadSpectrumGenerator.vb:98-129 | src/metadb/Lipidomics/SpectrumGenerator/SMSpectrumGenerator.vb:98-118 | src/metadb/Lipidomics/SpectrumGenerator/SMd9SpectrumGenerator.vb:95-115 — These 6 members share a duplicated core: a run of at least 50 identical tokens appears in every one of them. That run is NOT broken out as duplicated-block rows below — it is what admitted this row, and the blocks below cover only the part of it that clears the block floor, so they understate the correspondence. Read the members as one construct written 6 times. The repair is at the members' grain — factor the shared implementation out once and have all of them call it with their differences as parameters or as an injected step, or, where the difference is systematic, generate them from one template. Extracting the individual blocks below is not the same fix: it leaves every body in place and the next edit still has to be made 6 times.
  • Members sharing a duplicated core (6 members, 50+ identical tokens) src/metadb/Lipidomics/SpectrumGenerator/LPCEidSpectrumGenerator.vb:182 — src/metadb/Lipidomics/SpectrumGenerator/LPCEidSpectrumGenerator.vb:182-191 | src/metadb/Lipidomics/SpectrumGenerator/LPEEidSpectrumGenerator.vb:193-202 | src/metadb/Lipidomics/SpectrumGenerator/LPGEidSpectrumGenerator.vb:205-214 | src/metadb/Lipidomics/SpectrumGenerator/LPIEidSpectrumGenerator.vb:215-224 | src/metadb/Lipidomics/SpectrumGenerator/LPSEidSpectrumGenerator.vb:194-203 | src/metadb/Lipidomics/SpectrumGenerator/PAEidSpectrumGenerator.vb:194-203 — These 6 members share a duplicated core: a run of at least 50 identical tokens appears in every one of them. That run is NOT broken out as duplicated-block rows below — it is what admitted this row, and the blocks below cover only the part of it that clears the block floor, so they understate the correspondence. Read the members as one construct written 6 times. The repair is at the members' grain — factor the shared implementation out once and have all of them call it with their differences as parameters or as an injected step, or, where the difference is systematic, generate them from one template. Extracting the individual blocks below is not the same fix: it leaves every body in place and the next edit still has to be made 6 times.
  • Members sharing a duplicated core (6 members, 50+ identical tokens) src/metadb/Lipidomics/SpectrumGenerator/MGEidSpectrumGenerator.vb:184 — src/metadb/Lipidomics/SpectrumGenerator/MGEidSpectrumGenerator.vb:184-196 | src/metadb/Lipidomics/SpectrumGenerator/PCEidSpectrumGenerator.vb:173-190 | src/metadb/Lipidomics/SpectrumGenerator/PGEidSpectrumGenerator.vb:199-211 | src/metadb/Lipidomics/SpectrumGenerator/PIEidSpectrumGenerator.vb:207-219 | src/metadb/Lipidomics/SpectrumGenerator/PSEidSpectrumGenerator.vb:189-201 | src/metadb/Lipidomics/SpectrumGenerator/SMEidSpectrumGenerator.vb:189-201 — These 6 members share a duplicated core: a run of at least 50 identical tokens appears in every one of them. That run is NOT broken out as duplicated-block rows below — it is what admitted this row, and the blocks below cover only the part of it that clears the block floor, so they understate the correspondence. Read the members as one construct written 6 times. The repair is at the members' grain — factor the shared implementation out once and have all of them call it with their differences as parameters or as an injected step, or, where the difference is systematic, generate them from one template. Extracting the individual blocks below is not the same fix: it leaves every body in place and the next edit still has to be made 6 times.
D4 · Code Duplication · Members sharing a duplicated core (4 members, 50+ identical tokens) · ×4
  • Members sharing a duplicated core (4 members, 50+ identical tokens) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:16782 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:16782-16798 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:16801-16817 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:16820-16836 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:16858-16874 — These 4 members share a duplicated core: a run of at least 50 identical tokens appears in every one of them. That run is NOT broken out as duplicated-block rows below — it is what admitted this row, and the blocks below cover only the part of it that clears the block floor, so they understate the correspondence. Read the members as one construct written 4 times. The repair is at the members' grain — factor the shared implementation out once and have all of them call it with their differences as parameters or as an injected step, or, where the difference is systematic, generate them from one template. Extracting the individual blocks below is not the same fix: it leaves every body in place and the next edit still has to be made 4 times.
  • Members sharing a duplicated core (4 members, 50+ identical tokens) src/metadb/Lipidomics/OadSpectrumPeakGenerator.vb:76 — src/metadb/Lipidomics/OadSpectrumPeakGenerator.vb:76-113 | src/metadb/Lipidomics/OadSpectrumPeakGenerator.vb:390-419 | src/metadb/Lipidomics/SpectrumPeakGenerator.vb:66-200 | src/metadb/Lipidomics/SpectrumPeakGenerator.vb:212-303 — These 4 members share a duplicated core: a run of at least 50 identical tokens appears in every one of them. That run is NOT broken out as duplicated-block rows below — it is what admitted this row, and the blocks below cover only the part of it that clears the block floor, so they understate the correspondence. Read the members as one construct written 4 times. The repair is at the members' grain — factor the shared implementation out once and have all of them call it with their differences as parameters or as an injected step, or, where the difference is systematic, generate them from one template. Extracting the individual blocks below is not the same fix: it leaves every body in place and the next edit still has to be made 4 times.
  • Members sharing a duplicated core (4 members, 50+ identical tokens) src/metadb/Lipidomics/SpectrumGenerator/CLSpectrumGenerator.vb:98 — src/metadb/Lipidomics/SpectrumGenerator/CLSpectrumGenerator.vb:98-120 | src/metadb/Lipidomics/SpectrumGenerator/CeramideNsD7SpectrumGenerator.vb:95-111 | src/metadb/Lipidomics/SpectrumGenerator/CeramidePhytoSphSpectrumGenerator.vb:94-110 | src/metadb/Lipidomics/SpectrumGenerator/CeramideSpectrumGenerator.vb:97-113 — These 4 members share a duplicated core: a run of at least 50 identical tokens appears in every one of them. That run is NOT broken out as duplicated-block rows below — it is what admitted this row, and the blocks below cover only the part of it that clears the block floor, so they understate the correspondence. Read the members as one construct written 4 times. The repair is at the members' grain — factor the shared implementation out once and have all of them call it with their differences as parameters or as an injected step, or, where the difference is systematic, generate them from one template. Extracting the individual blocks below is not the same fix: it leaves every body in place and the next edit still has to be made 4 times.
  • Members sharing a duplicated core (4 members, 50+ identical tokens) src/mzmath/ms2_math-core/Chromatogram/ChromXType.vb:130 — src/mzmath/ms2_math-core/Chromatogram/ChromXType.vb:130-141 | src/mzmath/ms2_math-core/Chromatogram/ChromXType.vb:192-203 | src/mzmath/ms2_math-core/Chromatogram/ChromXType.vb:254-265 | src/mzmath/ms2_math-core/Chromatogram/ChromXType.vb:317-328 — These 4 members share a duplicated core: a run of at least 50 identical tokens appears in every one of them. That run is NOT broken out as duplicated-block rows below — it is what admitted this row, and the blocks below cover only the part of it that clears the block floor, so they understate the correspondence. Read the members as one construct written 4 times. The repair is at the members' grain — factor the shared implementation out once and have all of them call it with their differences as parameters or as an injected step, or, where the difference is systematic, generate them from one template. Extracting the individual blocks below is not the same fix: it leaves every body in place and the next edit still has to be made 4 times.
D4 · Code Duplication · Duplicated block (12 lines × 4) · ×4
  • Duplicated block (12 lines × 4) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:16782 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:16782-16793 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:16801-16812 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:16820-16831 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:16858-16869 — all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited.
  • Duplicated block (12 lines × 4) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13705 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13705-13716 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13753-13764 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13776-13787 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13844-13855 — all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited.
  • Duplicated block (12 lines × 4) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:2651 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:2651-2664 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5590-5602 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14092-14103 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15678-15691 — all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:2651` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14103` calls `acylCainMass` and `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:2664` does not — after which the two agree again for 4 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live.
  • Duplicated block (12 lines × 4) src/mzmath/ms2_math-core/Chromatogram/ChromXType.vb:130 — src/mzmath/ms2_math-core/Chromatogram/ChromXType.vb:130-141 | src/mzmath/ms2_math-core/Chromatogram/ChromXType.vb:192-203 | src/mzmath/ms2_math-core/Chromatogram/ChromXType.vb:254-265 | src/mzmath/ms2_math-core/Chromatogram/ChromXType.vb:317-328 — all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited.
D4 · Code Duplication · Duplicated block (10 lines × 4) · ×4
  • Duplicated block (10 lines × 4) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1773 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1773-1782 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12125-12134 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12179-12188 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12232-12241 — before extracting anything, compare `src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb` and `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb` as WHOLE FILES: this scan already matched 32 separate duplicated blocks between them, totalling at least 530 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
  • Duplicated block (10 lines × 4) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1250 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1250-1259 | src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:3014-3024 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5764-5774 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15946-15956 — before extracting anything, compare `src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb` and `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb` as WHOLE FILES: this scan already matched 32 separate duplicated blocks between them, totalling at least 530 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
  • Duplicated block (10 lines × 4) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1290 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1290-1299 | src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:3055-3064 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5807-5816 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15989-15998 — before extracting anything, compare `src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb` and `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb` as WHOLE FILES: this scan already matched 32 separate duplicated blocks between them, totalling at least 530 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
  • Duplicated block (10 lines × 4) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5581 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5581-5590 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5647-5656 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7605-7615 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12290-12300 — all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
D4 · Code Duplication · Duplicated block (8 lines × 5) · ×4
  • Duplicated block (8 lines × 5) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4096 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4096-4103 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4412-4419 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4529-4536 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4650-4657 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4763-4770 — all 5 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited.
  • Duplicated block (8 lines × 5) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:119 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:119-126 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:271-278 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:1127-1134 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:1168-1176 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:1382-1394 — before extracting anything, compare `src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb` and `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb` as WHOLE FILES: this scan already matched 32 separate duplicated blocks between them, totalling at least 530 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
  • Duplicated block (8 lines × 5) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1425 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1425-1432 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14746-14755 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14781-14788 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14815-14823 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14956-14968 — before extracting anything, compare `src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb` and `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb` as WHOLE FILES: this scan already matched 32 separate duplicated blocks between them, totalling at least 530 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14756` calls `isDiagnosticFragmentExist` and `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14824` does not — after which the two agree again for 4 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live.
  • Duplicated block (8 lines × 5) src/metadb/Lipidomics/SpectrumGenerator/CeramideOadSpectrumGenerator.vb:151 — src/metadb/Lipidomics/SpectrumGenerator/CeramideOadSpectrumGenerator.vb:151-160 | src/metadb/Lipidomics/SpectrumGenerator/SHexCerSpectrumGenerator.vb:181-192 | src/metadb/Lipidomics/SpectrumGenerator/SMEidSpectrumGenerator.vb:166-173 | src/metadb/Lipidomics/SpectrumGenerator/SMSpectrumGenerator.vb:169-178 | src/metadb/Lipidomics/SpectrumGenerator/SMd9SpectrumGenerator.vb:160-167 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/SMEidSpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/SMSpectrumGenerator.vb` as WHOLE FILES: this scan already matched 4 separate duplicated blocks between them, totalling at least 66 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
D17 · Explicit Debt · TodoComment repeated across 17 files · ×3
  • TodoComment repeated across 17 files Rscript/Library/mzkit_app/src/mzkit/functions/z_assembler.vb:82 — The identical TodoComment appears in 17 files (17 occurrences) — almost certainly one boilerplate line from a single migration or decision, not 17 independent debts. Fix the systemic cause once rather than file-by-file. Text: "' TODO: 释放托管状态(托管对象)". Source code is not a task system: track the cleanup where tasks live. (Every occurrence still counts toward the score and metrics.)
  • TodoComment repeated across 17 files Rscript/Library/mzkit_app/src/mzkit/functions/z_assembler.vb:87 — The identical TodoComment appears in 17 files (17 occurrences) — almost certainly one boilerplate line from a single migration or decision, not 17 independent debts. Fix the systemic cause once rather than file-by-file. Text: "' TODO: 将大型字段设置为 null". Source code is not a task system: track the cleanup where tasks live. (Every occurrence still counts toward the score and metrics.)
  • TodoComment repeated across 17 files Rscript/Library/mzkit_app/src/mzkit/functions/z_assembler.vb:92 — The identical TodoComment appears in 17 files (17 occurrences) — almost certainly one boilerplate line from a single migration or decision, not 17 independent debts. Fix the systemic cause once rather than file-by-file. Text: "' ' TODO: 仅当“Dispose(disposing As Boolean)”拥有用于释放未托管资源的代码时才替代终结器". Source code is not a task system: track the cleanup where tasks live. (Every occurrence still counts toward the score and metrics.)
D18 · Solution Shape · Solution references 3 projects that do not exist · ×3
  • Solution references 3 projects that do not exist src/assembly/assembly.sln — `src/assembly/assembly.sln` declares 3 project file(s) that are missing from the tree (`binarydata-netcore5.vbproj`, `Math.NET5.vbproj`, `Core.vbproj`). A solution-level restore or build fails on a dangling reference, so anyone building the solution rather than an individual project is blocked. Delete the stale entry from the solution, or restore the missing project file.
  • Solution references 3 projects that do not exist src/metadb/MetabolomeXchange.sln — `src/metadb/MetabolomeXchange.sln` declares 3 project file(s) that are missing from the tree (`47_dotnet_ms-vb_data.framework.vbproj`, `47-dotnet_Microsoft.VisualBasic.vbproj`, `application.json.vbproj`). A solution-level restore or build fails on a dangling reference, so anyone building the solution rather than an individual project is blocked. Delete the stale entry from the solution, or restore the missing project file.
  • Solution references 3 projects that do not exist src/metadb/KEGG.sln — `src/metadb/KEGG.sln` declares 3 project file(s) that are missing from the tree (`Bio.Annotation.vbproj`, `Bio.Assembly.vbproj`, `47-dotnet_Microsoft.VisualBasic.vbproj`). A solution-level restore or build fails on a dangling reference, so anyone building the solution rather than an individual project is blocked. Delete the stale entry from the solution, or restore the missing project file.
D4 · Code Duplication · Members sharing a duplicated core (7 members, 50+ identical tokens) · ×3
  • Members sharing a duplicated core (7 members, 50+ identical tokens) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:149 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:149-174 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:408-448 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:565-590 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:612-648 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:1027-1049 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:1071-1093 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:1328-1353 — These 7 members share a duplicated core: a run of at least 50 identical tokens appears in every one of them. That run is NOT broken out as duplicated-block rows below — it is what admitted this row, and the blocks below cover only the part of it that clears the block floor, so they understate the correspondence. Read the members as one construct written 7 times. The repair is at the members' grain — factor the shared implementation out once and have all of them call it with their differences as parameters or as an injected step, or, where the difference is systematic, generate them from one template. Extracting the individual blocks below is not the same fix: it leaves every body in place and the next edit still has to be made 7 times.
  • Members sharing a duplicated core (7 members, 50+ identical tokens) src/metadb/Lipidomics/SpectrumGenerator/LPCOadSpectrumGenerator.vb:91 — src/metadb/Lipidomics/SpectrumGenerator/LPCOadSpectrumGenerator.vb:91-115 | src/metadb/Lipidomics/SpectrumGenerator/LPEOadSpectrumGenerator.vb:91-116 | src/metadb/Lipidomics/SpectrumGenerator/PCOadSpectrumGenerator.vb:90-122 | src/metadb/Lipidomics/SpectrumGenerator/PEOadSpectrumGenerator.vb:92-130 | src/metadb/Lipidomics/SpectrumGenerator/PGOadSpectrumGenerator.vb:89-129 | src/metadb/Lipidomics/SpectrumGenerator/PIOadSpectrumGenerator.vb:90-126 | src/metadb/Lipidomics/SpectrumGenerator/TGOadSpectrumGenerator.vb:85-107 — These 7 members share a duplicated core: a run of at least 50 identical tokens appears in every one of them. That run is NOT broken out as duplicated-block rows below — it is what admitted this row, and the blocks below cover only the part of it that clears the block floor, so they understate the correspondence. Read the members as one construct written 7 times. The repair is at the members' grain — factor the shared implementation out once and have all of them call it with their differences as parameters or as an injected step, or, where the difference is systematic, generate them from one template. Extracting the individual blocks below is not the same fix: it leaves every body in place and the next edit still has to be made 7 times.
  • Members sharing a duplicated core (7 members, 50+ identical tokens) src/mzmath/mz_deco/Preprocessing/MissingValueImputation.vb:245 — src/mzmath/mz_deco/Preprocessing/MissingValueImputation.vb:245-266 | src/mzmath/mz_deco/Preprocessing/MissingValueImputation.vb:275-296 | src/mzmath/mz_deco/Preprocessing/Normalization.vb:394-416 | src/mzmath/mz_deco/Preprocessing/Normalization.vb:433-456 | src/mzmath/mz_deco/Preprocessing/Normalization.vb:472-496 | src/mzmath/mz_deco/Preprocessing/Normalization.vb:513-537 | src/mzmath/mz_deco/Preprocessing/Normalization.vb:553-573 — These 7 members share a duplicated core: a run of at least 50 identical tokens appears in every one of them. That run is NOT broken out as duplicated-block rows below — it is what admitted this row, and the blocks below cover only the part of it that clears the block floor, so they understate the correspondence. Read the members as one construct written 7 times. The repair is at the members' grain — factor the shared implementation out once and have all of them call it with their differences as parameters or as an injected step, or, where the difference is systematic, generate them from one template. Extracting the individual blocks below is not the same fix: it leaves every body in place and the next edit still has to be made 7 times.
D4 · Code Duplication · Duplicated block (18 lines × 2) · ×3
  • Duplicated block (18 lines × 2) src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:290 — src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:290-307 | src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:873-890 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (18 lines × 2) Rscript/Library/mzkit_app/src/mzkit/assembly/Assembly.vb:625 — Rscript/Library/mzkit_app/src/mzkit/assembly/Assembly.vb:625-643 | Rscript/Library/mzkit_app/src/mzkit/assembly/Assembly.vb:662-679 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (18 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11800 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11800-11817 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11824-11841 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
D4 · Code Duplication · Duplicated block (17 lines × 2) · ×3
  • Duplicated block (17 lines × 2) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1821 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1821-1837 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14795-14811 — before extracting anything, compare `src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb` and `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb` as WHOLE FILES: this scan already matched 32 separate duplicated blocks between them, totalling at least 530 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
  • Duplicated block (17 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12810 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12810-12826 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12846-12862 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (17 lines × 2) src/mzmath/ms2_math-core/Spectra/Centroids.vb:56 — src/mzmath/ms2_math-core/Spectra/Centroids.vb:56-72 | src/mzmath/ms2_math-core/Spectra/Centroids.vb:105-121 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at `src/mzmath/ms2_math-core/Spectra/Centroids.vb:56` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
D4 · Code Duplication · Duplicated block (9 lines × 4) · ×3
  • Duplicated block (9 lines × 4) src/mzmath/mz_deco/Preprocessing/Normalization.vb:395 — src/mzmath/mz_deco/Preprocessing/Normalization.vb:395-403 | src/mzmath/mz_deco/Preprocessing/Normalization.vb:434-442 | src/mzmath/mz_deco/Preprocessing/Normalization.vb:473-481 | src/mzmath/mz_deco/Preprocessing/Normalization.vb:514-522 — all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, `src/mzmath/mz_deco/Preprocessing/Normalization.vb:524` calls `CV` and `src/mzmath/mz_deco/Preprocessing/Normalization.vb:406` does not — after which the two agree again for 3 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live.
  • Duplicated block (9 lines × 4) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1217 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1217-1225 | src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:2979-2988 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5722-5731 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15904-15913 — before extracting anything, compare `src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb` and `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb` as WHOLE FILES: this scan already matched 32 separate duplicated blocks between them, totalling at least 530 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
  • Duplicated block (9 lines × 4) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1425 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1425-1433 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14746-14757 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14815-14824 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14956-14970 — before extracting anything, compare `src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb` and `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb` as WHOLE FILES: this scan already matched 32 separate duplicated blocks between them, totalling at least 530 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
D4 · Code Duplication · Duplicated block (9 lines × 3) · ×3
  • Duplicated block (9 lines × 3) src/visualize/MsImaging/Plot/DualRegionUnionPlot.vb:149 — src/visualize/MsImaging/Plot/DualRegionUnionPlot.vb:149-157 | src/visualize/MsImaging/Plot/MSIPlot.vb:120-128 | src/visualize/MsImaging/Plot/RGBMSIPlot.vb:101-109 — the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach — a file they already depend on, or a new one alongside them — and call it from all 3 call sites, so a change lands once.
  • Duplicated block (9 lines × 3) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:3544 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:3544-3554 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6287-6297 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:8139-8147 — before extracting anything, compare `src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb` and `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb` as WHOLE FILES: this scan already matched 32 separate duplicated blocks between them, totalling at least 530 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
  • Duplicated block (9 lines × 3) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:9904 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:9904-9913 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:9987-9996 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:10794-10802 — all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited.
D18 · Solution Shape · Solution references 13 projects that do not exist · ×2
  • Solution references 13 projects that do not exist src/assembly/MzPackExtensions.sln — `src/assembly/MzPackExtensions.sln` declares 13 project file(s) that are missing from the tree (`biocore-netcore5.vbproj`, `binarydata-netcore5.vbproj`, `HDSPack.vbproj`, `msgpack-netcore5.vbproj`, `netCDF.vbproj`, `graph-netcore5.vbproj`, +7 more). A solution-level restore or build fails on a dangling reference, so anyone building the solution rather than an individual project is blocked. Delete the stale entry from the solution, or restore the missing project file.
  • Solution references 13 projects that do not exist src/assembly/vendors.sln — `src/assembly/vendors.sln` declares 13 project file(s) that are missing from the tree (`R.vbproj`, `BinaryData.vbproj`, `DataStorage.vbproj`, `47_dotnet_ms-vb_data.framework.vbproj`, `math-core.vbproj`, `SignalProcessing.vbproj`, +7 more). A solution-level restore or build fails on a dangling reference, so anyone building the solution rather than an individual project is blocked. Delete the stale entry from the solution, or restore the missing project file.
D18 · Solution Shape · Solution references 9 projects that do not exist · ×2
  • Solution references 9 projects that do not exist src/mzmath/TargetedMetabolomics.sln — `src/mzmath/TargetedMetabolomics.sln` declares 9 project file(s) that are missing from the tree (`binarydata-netcore5.vbproj`, `msgpack-netcore5.vbproj`, `netCDF.vbproj`, `dataframework-netcore5.vbproj`, `linear-netcore5.vbproj`, `Math.NET5.vbproj`, +3 more). A solution-level restore or build fails on a dangling reference, so anyone building the solution rather than an individual project is blocked. Delete the stale entry from the solution, or restore the missing project file.
  • Solution references 9 projects that do not exist src/metadb/MoNA.sln — `src/metadb/MoNA.sln` declares 9 project file(s) that are missing from the tree (`Bio.Assembly.vbproj`, `47_dotnet_ms-vb_data.framework.vbproj`, `math-core.vbproj`, `47-dotnet_Microsoft.VisualBasic.vbproj`, `src/Assembly/assembly/assembly.vbproj`, `src/metadb/Chemoinformatics/Chemoinformatics.vbproj`, +3 more). A solution-level restore or build fails on a dangling reference, so anyone building the solution rather than an individual project is blocked. Delete the stale entry from the solution, or restore the missing project file.
D18 · Solution Shape · Solution references 2 projects that do not exist · ×2
  • Solution references 2 projects that do not exist src/assembly/ProteoWizard.d.sln — `src/assembly/ProteoWizard.d.sln` declares 2 project file(s) that are missing from the tree (`Flute.NET5.vbproj`, `Core.vbproj`). A solution-level restore or build fails on a dangling reference, so anyone building the solution rather than an individual project is blocked. Delete the stale entry from the solution, or restore the missing project file.
  • Solution references 2 projects that do not exist src/metadb/KNApSAcK.sln — `src/metadb/KNApSAcK.sln` declares 2 project file(s) that are missing from the tree (`47-dotnet_Microsoft.VisualBasic.vbproj`, `src/metadb/KNApSAcK/KNApSAcK.vbproj`). A solution-level restore or build fails on a dangling reference, so anyone building the solution rather than an individual project is blocked. Delete the stale entry from the solution, or restore the missing project file.
D4 · Code Duplication · Members sharing a duplicated core (16 members, 50+ identical tokens) · ×2
  • Members sharing a duplicated core (16 members, 50+ identical tokens) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1425 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1425-1459 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3090-3123 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4195-4240 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6169-6255 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6259-6332 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6336-6368 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7685-7703 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7761-7811 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:9061-9118 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13544-13577 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13581-13609 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14235-14270 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14746-14777 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14781-14811 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14815-14831 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14956-14988 — These 16 members share a duplicated core: a run of at least 50 identical tokens appears in every one of them. That run is NOT broken out as duplicated-block rows below — it is what admitted this row, and the blocks below cover only the part of it that clears the block floor, so they understate the correspondence. Read the members as one construct written 16 times. The repair is at the members' grain — factor the shared implementation out once and have all of them call it with their differences as parameters or as an injected step, or, where the difference is systematic, generate them from one template. Extracting the individual blocks below is not the same fix: it leaves every body in place and the next edit still has to be made 16 times.
  • Members sharing a duplicated core (16 members, 50+ identical tokens) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:385 — src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:385-549 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:553-699 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:703-830 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:834-943 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:947-1038 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1042-1116 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1120-1174 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1178-1214 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1284-1501 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1505-1698 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1702-1873 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1877-2026 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:2030-2156 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:2160-2259 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:2263-2334 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:2338-2385 — These 16 members share a duplicated core: a run of at least 50 identical tokens appears in every one of them. That run is NOT broken out as duplicated-block rows below — it is what admitted this row, and the blocks below cover only the part of it that clears the block floor, so they understate the correspondence. Read the members as one construct written 16 times. The repair is at the members' grain — factor the shared implementation out once and have all of them call it with their differences as parameters or as an injected step, or, where the difference is systematic, generate them from one template. Extracting the individual blocks below is not the same fix: it leaves every body in place and the next edit still has to be made 16 times.
D4 · Code Duplication · Duplicated block (21 lines × 2) · ×2
  • Duplicated block (21 lines × 2) src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:1570 — src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:1570-1590 | src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:1611-1631 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (21 lines × 2) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1288 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1288-1308 | src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:3053-3073 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
D4 · Code Duplication · Duplicated block (16–17 lines × 2) · ×2
  • Duplicated block (16–17 lines × 2) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1215 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1215-1230 | src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:2977-2993 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (16–17 lines × 2) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:3528 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:3528-3544 | src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:3605-3620 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
D4 · Code Duplication · Duplicated block (14 lines × 4) · ×2
  • Duplicated block (14 lines × 4) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3649 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3649-3662 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3681-3694 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15820-15833 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15848-15861 — all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited.
  • Duplicated block (14 lines × 4) src/mzmath/ms2_math-core/Chromatogram/ChromXType.vb:144 — src/mzmath/ms2_math-core/Chromatogram/ChromXType.vb:144-157 | src/mzmath/ms2_math-core/Chromatogram/ChromXType.vb:206-219 | src/mzmath/ms2_math-core/Chromatogram/ChromXType.vb:268-281 | src/mzmath/ms2_math-core/Chromatogram/ChromXType.vb:331-344 — all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited.
D4 · Code Duplication · Duplicated block (14–15 lines × 2) · ×2
  • Duplicated block (14–15 lines × 2) src/mzmath/MSEngine/SpectrumHandler.vb:181 — src/mzmath/MSEngine/SpectrumHandler.vb:181-194 | src/mzmath/MSEngine/SpectrumHandler.vb:202-216 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
  • Duplicated block (14–15 lines × 2) src/mzmath/mz_deco/Preprocessing/MissingValueImputation.vb:156 — src/mzmath/mz_deco/Preprocessing/MissingValueImputation.vb:156-170 | src/mzmath/mz_deco/Preprocessing/MissingValueImputation.vb:192-205 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
D4 · Code Duplication · Duplicated block (11–14 lines × 4) · ×2
  • Duplicated block (11–14 lines × 4) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11592 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11592-11605 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11928-11938 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11998-12008 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12071-12081 — all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
  • Duplicated block (11–14 lines × 4) src/metadb/Lipidomics/OadSpectrumPeakGenerator.vb:85 — src/metadb/Lipidomics/OadSpectrumPeakGenerator.vb:85-95 | src/metadb/Lipidomics/OadSpectrumPeakGenerator.vb:399-409 | src/metadb/Lipidomics/SpectrumPeakGenerator.vb:81-94 | src/metadb/Lipidomics/SpectrumPeakGenerator.vb:230-240 — there are 4 copies across 2 file(s) — more copies than files, so at least one file holds the block twice. Extract it once into a single shared function every call site can reach and call it from all 4 sites; resolving a subset leaves the remainder to drift apart.
D4 · Code Duplication · Duplicated block (13–14 lines × 2) · ×2
  • Duplicated block (13–14 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:1200 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:1200-1213 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:1257-1269 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:1257` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
  • Duplicated block (13–14 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13798 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13798-13810 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13820-13833 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
D4 · Code Duplication · Duplicated block (11 lines × 4) · ×2
  • Duplicated block (11 lines × 4) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5730 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5730-5740 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5815-5825 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15912-15922 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15997-16007 — all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited.
  • Duplicated block (11 lines × 4) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4099 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4099-4111 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4415-4427 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4532-4545 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13375-13385 — all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
D4 · Code Duplication · Duplicated block (12–13 lines × 2) · ×2
  • Duplicated block (12–13 lines × 2) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1173 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1173-1185 | src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1197-1208 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (12–13 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5590 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5590-5602 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14092-14103 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
D4 · Code Duplication · Duplicated block (13 lines × 2) · ×2
  • Duplicated block (13 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3997 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3997-4009 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4313-4325 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
  • Duplicated block (13 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7685 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7685-7697 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7761-7773 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
D4 · Code Duplication · Duplicated block (8 lines × 4) · ×2
  • Duplicated block (8 lines × 4) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:422 — src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:422-429 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:586-593 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1328-1335 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1545-1552 — all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited.
  • Duplicated block (8 lines × 4) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1223 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1223-1230 | src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1297-1309 | src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:2986-2993 | src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:3062-3074 — all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited.
D4 · Code Duplication · Duplicated block (8 lines × 7) · ×2
  • Duplicated block (8 lines × 7) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3996 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3996-4003 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4095-4102 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4312-4319 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4411-4418 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4528-4535 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4649-4656 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4762-4769 — all 7 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited.
  • Duplicated block (8 lines × 7) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11640 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11640-11653 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11780-11793 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11804-11817 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11828-11841 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11895-11902 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11966-11973 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12035-12042 — all 7 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
D4 · Code Duplication · Duplicated block (7 lines × 4) · ×2
  • Duplicated block (7 lines × 4) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1787 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1787-1793 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12143-12154 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12197-12204 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12250-12258 — before extracting anything, compare `src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb` and `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb` as WHOLE FILES: this scan already matched 32 separate duplicated blocks between them, totalling at least 530 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
  • Duplicated block (7 lines × 4) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13550 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13550-13557 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13587-13594 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14242-14248 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14253-14259 — all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited.
D4 · Code Duplication · Duplicated block (24 lines × 3) · ×2
  • Duplicated block (24 lines × 3) src/metadb/Lipidomics/SpectrumGenerator/CLEidSpectrumGenerator.vb:144 — src/metadb/Lipidomics/SpectrumGenerator/CLEidSpectrumGenerator.vb:144-167 | src/metadb/Lipidomics/SpectrumGenerator/PGSpectrumGenerator.vb:129-162 | src/metadb/Lipidomics/SpectrumGenerator/PGd5SpectrumGenerator.vb:128-161 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/PGSpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/PGd5SpectrumGenerator.vb` as WHOLE FILES: this scan already matched 3 separate duplicated blocks between them, totalling at least 68 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
  • Duplicated block (24 lines × 3) src/metadb/Lipidomics/SpectrumGenerator/TGEidSpectrumGenerator.vb:194 — src/metadb/Lipidomics/SpectrumGenerator/TGEidSpectrumGenerator.vb:194-222 | src/metadb/Lipidomics/SpectrumGenerator/TGSpectrumGenerator.vb:195-221 | src/metadb/Lipidomics/SpectrumGenerator/TGd5SpectrumGenerator.vb:196-219 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/TGEidSpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/TGSpectrumGenerator.vb` as WHOLE FILES: this scan already matched 3 separate duplicated blocks between them, totalling at least 49 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
D1 · Cyclomatic Complexity · LipoqualityRest.getLqUrl (cyclomatic 313) · ×1
  • LipoqualityRest.getLqUrl (cyclomatic 313) src/metadb/Lipidomics/LipoqualityRest.vb:93 — LipoqualityRest.getLqUrl has cyclomatic complexity 313 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidAnnotation.Characterize (cyclomatic 198) · ×1
  • LipidAnnotation.Characterize (cyclomatic 198) src/metadb/Lipidomics/Annotation/Lipidomics.vb:148 — LipidAnnotation.Characterize has cyclomatic complexity 198 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · MsScanMatching.GetLipidMoleculerSpeciesLevelAnnotationResultForEIEIO (cyclomatic 193) · ×1
  • MsScanMatching.GetLipidMoleculerSpeciesLevelAnnotationResultForEIEIO (cyclomatic 193) src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:289 — MsScanMatching.GetLipidMoleculerSpeciesLevelAnnotationResultForEIEIO has cyclomatic complexity 193 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table. This shape REPEATS in the file: one other method here (MsScanMatching.GetLipidMoleculeAnnotationResult) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D1 · Cyclomatic Complexity · MsScanMatching.GetLipidMoleculeAnnotationResult (cyclomatic 193) · ×1
  • MsScanMatching.GetLipidMoleculeAnnotationResult (cyclomatic 193) src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:871 — MsScanMatching.GetLipidMoleculeAnnotationResult has cyclomatic complexity 193 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table. This shape REPEATS in the file: one other method here (MsScanMatching.GetLipidMoleculerSpeciesLevelAnnotationResultForEIEIO) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D1 · Cyclomatic Complexity · DSPPhaseCorrection.dspPhaseCorrection (cyclomatic 71) · ×1
  • DSPPhaseCorrection.dspPhaseCorrection (cyclomatic 71) src/assembly/NMRFidTool/Math/phasing/DSPPhaseCorrection.vb:77 — DSPPhaseCorrection.dspPhaseCorrection has cyclomatic complexity 71 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · FormulaCalculateUtility.GetFormulaString (cyclomatic 58) · ×1
  • FormulaCalculateUtility.GetFormulaString (cyclomatic 58) src/metadb/Chemoinformatics/Formula/FormulaCalculateUtility.vb:389 — FormulaCalculateUtility.GetFormulaString has cyclomatic complexity 58 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · FormulaGenerator.getFormulaResults (cyclomatic 58) · ×1
  • FormulaGenerator.getFormulaResults (cyclomatic 58) src/mzmath/MSFinder/FormulaGenerator.vb:326 — FormulaGenerator.getFormulaResults has cyclomatic complexity 58 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · SpectrumHandler.EstimateIsotopes (cyclomatic 47) · ×1
  • SpectrumHandler.EstimateIsotopes (cyclomatic 47) src/mzmath/MSEngine/SpectrumHandler.vb:259 — SpectrumHandler.EstimateIsotopes has cyclomatic complexity 47 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfCardiolipin (cyclomatic 44) · ×1
  • LipidMsmsCharacterization.JudgeIfCardiolipin (cyclomatic 44) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7147 — LipidMsmsCharacterization.JudgeIfCardiolipin has cyclomatic complexity 44 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfHexceramideeos (cyclomatic 44) · ×1
  • LipidMsmsCharacterization.JudgeIfHexceramideeos (cyclomatic 44) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:10557 — LipidMsmsCharacterization.JudgeIfHexceramideeos has cyclomatic complexity 44 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · centWave.DetectByCentWave (cyclomatic 44) · ×1
  • centWave.DetectByCentWave (cyclomatic 44) src/mzmath/mz_deco/Signals/centWave/centWave.vb:26 — centWave.DetectByCentWave has cyclomatic complexity 44 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfCeramideeos (cyclomatic 43) · ×1
  • LipidMsmsCharacterization.JudgeIfCeramideeos (cyclomatic 43) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:10243 — LipidMsmsCharacterization.JudgeIfCeramideeos has cyclomatic complexity 43 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · SequenceToSpec.GetSpectrumPeaksByHCD (cyclomatic 43) · ×1
  • SequenceToSpec.GetSpectrumPeaksByHCD (cyclomatic 43) src/mzmath/MSEngine/Proteomics/SequenceToSpec.vb:118 — SequenceToSpec.GetSpectrumPeaksByHCD has cyclomatic complexity 43 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · FormulaCalculateUtility.GetFormulaString (cyclomatic 42) · ×1
  • FormulaCalculateUtility.GetFormulaString (cyclomatic 42) src/metadb/Chemoinformatics/Formula/FormulaCalculateUtility.vb:414 — FormulaCalculateUtility.GetFormulaString has cyclomatic complexity 42 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · PeakAnalyzer.MultiPeakFit (cyclomatic 42) · ×1
  • PeakAnalyzer.MultiPeakFit (cyclomatic 42) src/assembly/RamanSpectroscopy/RamanDataProcessor.vb:1568 — PeakAnalyzer.MultiPeakFit has cyclomatic complexity 42 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfHexceramideo (cyclomatic 41) · ×1
  • LipidMsmsCharacterization.JudgeIfHexceramideo (cyclomatic 41) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:8546 — LipidMsmsCharacterization.JudgeIfHexceramideo has cyclomatic complexity 41 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfCeramideo (cyclomatic 41) · ×1
  • LipidMsmsCharacterization.JudgeIfCeramideo (cyclomatic 41) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:8882 — LipidMsmsCharacterization.JudgeIfCeramideo has cyclomatic complexity 41 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfCeramidens (cyclomatic 40) · ×1
  • LipidMsmsCharacterization.JudgeIfCeramidens (cyclomatic 40) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7943 — LipidMsmsCharacterization.JudgeIfCeramidens has cyclomatic complexity 40 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfCeramidensD7) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfCeramidensD7 (cyclomatic 40) · ×1
  • LipidMsmsCharacterization.JudgeIfCeramidensD7 (cyclomatic 40) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:16340 — LipidMsmsCharacterization.JudgeIfCeramidensD7 has cyclomatic complexity 40 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfCeramidens) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D1 · Cyclomatic Complexity · MsScanMatching.GetWeightedDotProduct (cyclomatic 39) · ×1
  • MsScanMatching.GetWeightedDotProduct (cyclomatic 39) src/mzmath/MSEngine/Search/MsScanMatching.vb:902 — MsScanMatching.GetWeightedDotProduct has cyclomatic complexity 39 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · MathHelpers.NIPALSWithMissing (cyclomatic 39) · ×1
  • MathHelpers.NIPALSWithMissing (cyclomatic 39) src/mzmath/mz_deco/Preprocessing/MathHelpers.vb:909 — MathHelpers.NIPALSWithMissing has cyclomatic complexity 39 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfAcylhexcer (cyclomatic 38) · ×1
  • LipidMsmsCharacterization.JudgeIfAcylhexcer (cyclomatic 38) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11064 — LipidMsmsCharacterization.JudgeIfAcylhexcer has cyclomatic complexity 38 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · MS_Peak_ID.MakeTheoryList (cyclomatic 38) · ×1
  • MS_Peak_ID.MakeTheoryList (cyclomatic 38) src/mzmath/Oligonucleotide_MS/MS_Peak/Oligonucleotide_MS_Peak_ID_Given_Sequence_v8.vb:121 — MS_Peak_ID.MakeTheoryList has cyclomatic complexity 38 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfCeramidends (cyclomatic 37) · ×1
  • LipidMsmsCharacterization.JudgeIfCeramidends (cyclomatic 37) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:8193 — LipidMsmsCharacterization.JudgeIfCeramidends has cyclomatic complexity 37 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfPhosphatidylcholineD5 (cyclomatic 37) · ×1
  • LipidMsmsCharacterization.JudgeIfPhosphatidylcholineD5 (cyclomatic 37) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15067 — LipidMsmsCharacterization.JudgeIfPhosphatidylcholineD5 has cyclomatic complexity 37 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfEthermgdg (cyclomatic 36) · ×1
  • LipidMsmsCharacterization.JudgeIfEthermgdg (cyclomatic 36) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5163 — LipidMsmsCharacterization.JudgeIfEthermgdg has cyclomatic complexity 36 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfHexceramidens (cyclomatic 36) · ×1
  • LipidMsmsCharacterization.JudgeIfHexceramidens (cyclomatic 36) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:8374 — LipidMsmsCharacterization.JudgeIfHexceramidens has cyclomatic complexity 36 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfHexceramideap (cyclomatic 36) · ×1
  • LipidMsmsCharacterization.JudgeIfHexceramideap (cyclomatic 36) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:9518 — LipidMsmsCharacterization.JudgeIfHexceramideap has cyclomatic complexity 36 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · Scanner.WalkChar (cyclomatic 36) · ×1
  • Scanner.WalkChar (cyclomatic 36) src/metadb/SMILES/Language/Scanner.vb:196 — Scanner.WalkChar has cyclomatic complexity 36 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · FragmentAssigner.getValenceCheckedFragmentFormulaList (cyclomatic 36) · ×1
  • FragmentAssigner.getValenceCheckedFragmentFormulaList (cyclomatic 36) src/mzmath/MSFinder/FragmentAssigner.vb:602 — FragmentAssigner.getValenceCheckedFragmentFormulaList has cyclomatic complexity 36 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · BatchCorrection.CorrectComBat (cyclomatic 36) · ×1
  • BatchCorrection.CorrectComBat (cyclomatic 36) src/mzmath/mz_deco/Preprocessing/BatchCorrection.vb:401 — BatchCorrection.CorrectComBat has cyclomatic complexity 36 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · MathHelpers.PCA (cyclomatic 36) · ×1
  • MathHelpers.PCA (cyclomatic 36) src/mzmath/mz_deco/Preprocessing/MathHelpers.vb:755 — MathHelpers.PCA has cyclomatic complexity 36 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · DimensionalityReducer.PCA (cyclomatic 36) · ×1
  • DimensionalityReducer.PCA (cyclomatic 36) src/assembly/RamanSpectroscopy/RamanDataProcessor.vb:1899 — DimensionalityReducer.PCA has cyclomatic complexity 36 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfCeramideap (cyclomatic 35) · ×1
  • LipidMsmsCharacterization.JudgeIfCeramideap (cyclomatic 35) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:9355 — LipidMsmsCharacterization.JudgeIfCeramideap has cyclomatic complexity 35 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfCeramidenp (cyclomatic 35) · ×1
  • LipidMsmsCharacterization.JudgeIfCeramidenp (cyclomatic 35) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:10073 — LipidMsmsCharacterization.JudgeIfCeramidenp has cyclomatic complexity 35 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · SevenGoldenRulesCheck.HeteroAtomCheck (cyclomatic 35) · ×1
  • SevenGoldenRulesCheck.HeteroAtomCheck (cyclomatic 35) src/metadb/Chemoinformatics/Formula/SevenGoldenRulesCheck.vb:407 — SevenGoldenRulesCheck.HeteroAtomCheck has cyclomatic complexity 35 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfPhosphatidylcholine (cyclomatic 34) · ×1
  • LipidMsmsCharacterization.JudgeIfPhosphatidylcholine (cyclomatic 34) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:1789 — LipidMsmsCharacterization.JudgeIfPhosphatidylcholine has cyclomatic complexity 34 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfAcylsm (cyclomatic 34) · ×1
  • LipidMsmsCharacterization.JudgeIfAcylsm (cyclomatic 34) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:10855 — LipidMsmsCharacterization.JudgeIfAcylsm has cyclomatic complexity 34 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfBetaMethylPhosphatidylcholine (cyclomatic 34) · ×1
  • LipidMsmsCharacterization.JudgeIfBetaMethylPhosphatidylcholine (cyclomatic 34) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:16542 — LipidMsmsCharacterization.JudgeIfBetaMethylPhosphatidylcholine has cyclomatic complexity 34 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · MsScanMatching.GetReverseDotProduct (cyclomatic 34) · ×1
  • MsScanMatching.GetReverseDotProduct (cyclomatic 34) src/mzmath/MSEngine/Search/MsScanMatching.vb:757 — MsScanMatching.GetReverseDotProduct has cyclomatic complexity 34 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · FormulaGenerator.getFormulaSearchResults (cyclomatic 34) · ×1
  • FormulaGenerator.getFormulaSearchResults (cyclomatic 34) src/mzmath/MSFinder/FormulaGenerator.vb:825 — FormulaGenerator.getFormulaSearchResults has cyclomatic complexity 34 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfEtherdgdg (cyclomatic 33) · ×1
  • LipidMsmsCharacterization.JudgeIfEtherdgdg (cyclomatic 33) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5442 — LipidMsmsCharacterization.JudgeIfEtherdgdg has cyclomatic complexity 33 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · SevenGoldenRulesCheck.ProbabilityCheck (cyclomatic 33) · ×1
  • SevenGoldenRulesCheck.ProbabilityCheck (cyclomatic 33) src/metadb/Chemoinformatics/Formula/SevenGoldenRulesCheck.vb:498 — SevenGoldenRulesCheck.ProbabilityCheck has cyclomatic complexity 33 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfTriacylglycerol (cyclomatic 32) · ×1
  • LipidMsmsCharacterization.JudgeIfTriacylglycerol (cyclomatic 32) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3126 — LipidMsmsCharacterization.JudgeIfTriacylglycerol has cyclomatic complexity 32 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfTriacylglycerolD5 (cyclomatic 32) · ×1
  • LipidMsmsCharacterization.JudgeIfTriacylglycerolD5 (cyclomatic 32) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:16086 — LipidMsmsCharacterization.JudgeIfTriacylglycerolD5 has cyclomatic complexity 32 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · PeakDetector.DetectByFirstDerivative (cyclomatic 32) · ×1
  • PeakDetector.DetectByFirstDerivative (cyclomatic 32) src/mzmath/mz_deco/Signals/PeakFinding/PeakDetector.vb:357 — PeakDetector.DetectByFirstDerivative has cyclomatic complexity 32 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · PeakAnalyzer.SinglePeakFit (cyclomatic 32) · ×1
  • PeakAnalyzer.SinglePeakFit (cyclomatic 32) src/assembly/RamanSpectroscopy/RamanDataProcessor.vb:1412 — PeakAnalyzer.SinglePeakFit has cyclomatic complexity 32 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfLysopc (cyclomatic 31) · ×1
  • LipidMsmsCharacterization.JudgeIfLysopc (cyclomatic 31) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3535 — LipidMsmsCharacterization.JudgeIfLysopc has cyclomatic complexity 31 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfHexceramidends (cyclomatic 31) · ×1
  • LipidMsmsCharacterization.JudgeIfHexceramidends (cyclomatic 31) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:8718 — LipidMsmsCharacterization.JudgeIfHexceramidends has cyclomatic complexity 31 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfCeramideas (cyclomatic 31) · ×1
  • LipidMsmsCharacterization.JudgeIfCeramideas (cyclomatic 31) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:9692 — LipidMsmsCharacterization.JudgeIfCeramideas has cyclomatic complexity 31 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · CrossReferenceData.Compares (cyclomatic 31) · ×1
  • CrossReferenceData.Compares (cyclomatic 31) src/metadb/Chemoinformatics/Metabolite/CrossReference/CrossReferenceData.vb:254 — CrossReferenceData.Compares has cyclomatic complexity 31 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · AdductIonParser.GetOrganicAdductFormulaAndMass (cyclomatic 31) · ×1
  • AdductIonParser.GetOrganicAdductFormulaAndMass (cyclomatic 31) src/mzmath/ms2_math-core/Ms1/PrecursorType/AdductIonParser.vb:317 — AdductIonParser.GetOrganicAdductFormulaAndMass has cyclomatic complexity 31 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · DensityGroup.DensityGroupAlignment (cyclomatic 31) · ×1
  • DensityGroup.DensityGroupAlignment (cyclomatic 31) src/mzmath/mz_deco/PeakAlignment/Algorithm/DensityGroup.vb:24 — DensityGroup.DensityGroupAlignment has cyclomatic complexity 31 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · GolotvinWilliamsBaselineCorrector.calculateBaselineModel (cyclomatic 30) · ×1
  • GolotvinWilliamsBaselineCorrector.calculateBaselineModel (cyclomatic 30) src/assembly/NMRFidTool/Math/baseline/GolotvinWilliamsBaselineCorrector.vb:114 — GolotvinWilliamsBaselineCorrector.calculateBaselineModel has cyclomatic complexity 30 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · XcaliburRawFileIO.GetScanInfoInternal (cyclomatic 30) · ×1
  • XcaliburRawFileIO.GetScanInfoInternal (cyclomatic 30) src/assembly/ThermoRawFileReader/XcaliburRawFileIO.vb:1192 — XcaliburRawFileIO.GetScanInfoInternal has cyclomatic complexity 30 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfSphingomyelin (cyclomatic 30) · ×1
  • LipidMsmsCharacterization.JudgeIfSphingomyelin (cyclomatic 30) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:2924 — LipidMsmsCharacterization.JudgeIfSphingomyelin has cyclomatic complexity 30 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfSphingomyelinD9) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfDgdg (cyclomatic 30) · ×1
  • LipidMsmsCharacterization.JudgeIfDgdg (cyclomatic 30) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5016 — LipidMsmsCharacterization.JudgeIfDgdg has cyclomatic complexity 30 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfCeramideads (cyclomatic 30) · ×1
  • LipidMsmsCharacterization.JudgeIfCeramideads (cyclomatic 30) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:9787 — LipidMsmsCharacterization.JudgeIfCeramideads has cyclomatic complexity 30 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfSphingomyelinD9 (cyclomatic 30) · ×1
  • LipidMsmsCharacterization.JudgeIfSphingomyelinD9 (cyclomatic 30) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:16232 — LipidMsmsCharacterization.JudgeIfSphingomyelinD9 has cyclomatic complexity 30 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfSphingomyelin) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D1 · Cyclomatic Complexity · MsScanMatching.GetTotalSimilarity (cyclomatic 30) · ×1
  • MsScanMatching.GetTotalSimilarity (cyclomatic 30) src/mzmath/MSEngine/Search/MsScanMatching.vb:1211 — MsScanMatching.GetTotalSimilarity has cyclomatic complexity 30 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · XcaliburRawFileIO.ExtractParentIonMZFromFilterText (cyclomatic 29) · ×1
  • XcaliburRawFileIO.ExtractParentIonMZFromFilterText (cyclomatic 29) src/assembly/ThermoRawFileReader/XcaliburRawFileIO.vb:597 — XcaliburRawFileIO.ExtractParentIonMZFromFilterText has cyclomatic complexity 29 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidEieioMsmsCharacterization.JudgeIfPhosphatidylcholine (cyclomatic 29) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfPhosphatidylcholine (cyclomatic 29) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:230 — LipidEieioMsmsCharacterization.JudgeIfPhosphatidylcholine has cyclomatic complexity 29 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table. This shape REPEATS in the file: one other method here (LipidEieioMsmsCharacterization.JudgeIfPhosphatidylcholineD5) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D1 · Cyclomatic Complexity · LipidEieioMsmsCharacterization.JudgeIfPhosphatidylcholineD5 (cyclomatic 29) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfPhosphatidylcholineD5 (cyclomatic 29) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:2052 — LipidEieioMsmsCharacterization.JudgeIfPhosphatidylcholineD5 has cyclomatic complexity 29 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table. This shape REPEATS in the file: one other method here (LipidEieioMsmsCharacterization.JudgeIfPhosphatidylcholine) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfEtheroxpc (cyclomatic 29) · ×1
  • LipidMsmsCharacterization.JudgeIfEtheroxpc (cyclomatic 29) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3995 — LipidMsmsCharacterization.JudgeIfEtheroxpc has cyclomatic complexity 29 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfLysopcD5 (cyclomatic 29) · ×1
  • LipidMsmsCharacterization.JudgeIfLysopcD5 (cyclomatic 29) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15717 — LipidMsmsCharacterization.JudgeIfLysopcD5 has cyclomatic complexity 29 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · PeakDetector.DetectByMatchedFilter (cyclomatic 29) · ×1
  • PeakDetector.DetectByMatchedFilter (cyclomatic 29) src/mzmath/mz_deco/Signals/PeakFinding/PeakDetector.vb:194 — PeakDetector.DetectByMatchedFilter has cyclomatic complexity 29 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfDgts (cyclomatic 28) · ×1
  • LipidMsmsCharacterization.JudgeIfDgts (cyclomatic 28) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6007 — LipidMsmsCharacterization.JudgeIfDgts has cyclomatic complexity 28 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · IsotopeCalculator.getNominalIsotopeElementPropertyForTenIsotopomerElement (cyclomatic 28) · ×1
  • IsotopeCalculator.getNominalIsotopeElementPropertyForTenIsotopomerElement (cyclomatic 28) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1283 — IsotopeCalculator.getNominalIsotopeElementPropertyForTenIsotopomerElement has cyclomatic complexity 28 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · FormulaStringParcer.setElementNumbers (cyclomatic 28) · ×1
  • FormulaStringParcer.setElementNumbers (cyclomatic 28) src/mzmath/MSFinder/FormulaStringParcer.vb:474 — FormulaStringParcer.setElementNumbers has cyclomatic complexity 28 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · AdductIonParser.IsCommonAdduct (cyclomatic 28) · ×1
  • AdductIonParser.IsCommonAdduct (cyclomatic 28) src/mzmath/ms2_math-core/Ms1/PrecursorType/AdductIonParser.vb:209 — AdductIonParser.IsCommonAdduct has cyclomatic complexity 28 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · MetaDbXref.cbindMeta (cyclomatic 27) · ×1
  • MetaDbXref.cbindMeta (cyclomatic 27) Rscript/Library/mzkit_app/src/mzkit/annotations/MetaDbXref.vb:1049 — MetaDbXref.cbindMeta has cyclomatic complexity 27 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidEieioMsmsCharacterization.JudgeIfPhosphatidylethanolamine (cyclomatic 27) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfPhosphatidylethanolamine (cyclomatic 27) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:414 — LipidEieioMsmsCharacterization.JudgeIfPhosphatidylethanolamine has cyclomatic complexity 27 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfEtherpc (cyclomatic 27) · ×1
  • LipidMsmsCharacterization.JudgeIfEtherpc (cyclomatic 27) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3737 — LipidMsmsCharacterization.JudgeIfEtherpc has cyclomatic complexity 27 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfMgdg (cyclomatic 27) · ×1
  • LipidMsmsCharacterization.JudgeIfMgdg (cyclomatic 27) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4873 — LipidMsmsCharacterization.JudgeIfMgdg has cyclomatic complexity 27 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfCeramidebs (cyclomatic 27) · ×1
  • LipidMsmsCharacterization.JudgeIfCeramidebs (cyclomatic 27) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:9888 — LipidMsmsCharacterization.JudgeIfCeramidebs has cyclomatic complexity 27 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfFahfamidegly (cyclomatic 27) · ×1
  • LipidMsmsCharacterization.JudgeIfFahfamidegly (cyclomatic 27) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12961 — LipidMsmsCharacterization.JudgeIfFahfamidegly has cyclomatic complexity 27 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · OadLipidSpectrumGenerator.GetClassFragmentSpectrum (cyclomatic 27) · ×1
  • OadLipidSpectrumGenerator.GetClassFragmentSpectrum (cyclomatic 27) src/metadb/Lipidomics/SpectrumGenerator/OadLipidsSpectrumGenerator.vb:62 — OadLipidSpectrumGenerator.GetClassFragmentSpectrum has cyclomatic complexity 27 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · MsScanMatching.GetTotalSimilarity (cyclomatic 27) · ×1
  • MsScanMatching.GetTotalSimilarity (cyclomatic 27) src/mzmath/MSEngine/Search/MsScanMatching.vb:1342 — MsScanMatching.GetTotalSimilarity has cyclomatic complexity 27 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · NCAAnalyzer.Analyze (cyclomatic 27) · ×1
  • NCAAnalyzer.Analyze (cyclomatic 27) src/mzmath/TargetedMetabolomics/PKAnalysis.vb:143 — NCAAnalyzer.Analyze has cyclomatic complexity 27 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfEthertag (cyclomatic 26) · ×1
  • LipidMsmsCharacterization.JudgeIfEthertag (cyclomatic 26) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5842 — LipidMsmsCharacterization.JudgeIfEthertag has cyclomatic complexity 26 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfSulfonolipid (cyclomatic 26) · ×1
  • LipidMsmsCharacterization.JudgeIfSulfonolipid (cyclomatic 26) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13210 — LipidMsmsCharacterization.JudgeIfSulfonolipid has cyclomatic complexity 26 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · MsScanMatching.GetSimpleDotProduct (cyclomatic 26) · ×1
  • MsScanMatching.GetSimpleDotProduct (cyclomatic 26) src/mzmath/MSEngine/Search/MsScanMatching.vb:1034 — MsScanMatching.GetSimpleDotProduct has cyclomatic complexity 26 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · FormulaGenerator.getFormulaSearchResults (cyclomatic 26) · ×1
  • FormulaGenerator.getFormulaSearchResults (cyclomatic 26) src/mzmath/MSFinder/FormulaGenerator.vb:467 — FormulaGenerator.getFormulaSearchResults has cyclomatic complexity 26 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · PeakDetector.DetectByLocalMaximum (cyclomatic 26) · ×1
  • PeakDetector.DetectByLocalMaximum (cyclomatic 26) src/mzmath/mz_deco/Signals/PeakFinding/PeakDetector.vb:55 — PeakDetector.DetectByLocalMaximum has cyclomatic complexity 26 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · SpectralPreprocessor.DerivativeSpikeRemoval (cyclomatic 26) · ×1
  • SpectralPreprocessor.DerivativeSpikeRemoval (cyclomatic 26) src/assembly/RamanSpectroscopy/RamanDataProcessor.vb:1030 — SpectralPreprocessor.DerivativeSpikeRemoval has cyclomatic complexity 26 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidomicsConverter.acylChainStringSeparatorVS2 (cyclomatic 25) · ×1
  • LipidomicsConverter.acylChainStringSeparatorVS2 (cyclomatic 25) src/metadb/Lipidomics/Annotation/LipidomicsConverter.vb:3508 — LipidomicsConverter.acylChainStringSeparatorVS2 has cyclomatic complexity 25 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table. This is NOT this file's highest cyclomatic complexity: LipidomicsConverter.ConvertMsdialClassDefinitionToSuperClassVS2 (cyclomatic 237) is higher and carries no row of its own — it was excluded as a flat dispatcher (a long switch/match over independent cases: many branches, almost no nesting), which this dimension does not treat as a refactor obligation. It is named here so the ranking you see in this file is not mistaken for the whole of it; the excluded method is counted neither in this dimension's figures nor in its score.
D1 · Cyclomatic Complexity · CeramideLipidParser.Parse (cyclomatic 25) · ×1
  • CeramideLipidParser.Parse (cyclomatic 25) src/metadb/Lipidomics/LipidParser/CeramideLipidParser.vb:74 — CeramideLipidParser.Parse has cyclomatic complexity 25 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfOxpc (cyclomatic 25) · ×1
  • LipidMsmsCharacterization.JudgeIfOxpc (cyclomatic 25) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4311 — LipidMsmsCharacterization.JudgeIfOxpc has cyclomatic complexity 25 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfHemiismonoacylglycerophosphate (cyclomatic 25) · ×1
  • LipidMsmsCharacterization.JudgeIfHemiismonoacylglycerophosphate (cyclomatic 25) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7003 — LipidMsmsCharacterization.JudgeIfHemiismonoacylglycerophosphate has cyclomatic complexity 25 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfCeramidebds (cyclomatic 25) · ×1
  • LipidMsmsCharacterization.JudgeIfCeramidebds (cyclomatic 25) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:9970 — LipidMsmsCharacterization.JudgeIfCeramidebds has cyclomatic complexity 25 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfAcylcerbds (cyclomatic 25) · ×1
  • LipidMsmsCharacterization.JudgeIfAcylcerbds (cyclomatic 25) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:10985 — LipidMsmsCharacterization.JudgeIfAcylcerbds has cyclomatic complexity 25 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfAshexcer (cyclomatic 25) · ×1
  • LipidMsmsCharacterization.JudgeIfAshexcer (cyclomatic 25) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11270 — LipidMsmsCharacterization.JudgeIfAshexcer has cyclomatic complexity 25 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · FormulaCalculateUtility.GetFormulaString (cyclomatic 25) · ×1
  • FormulaCalculateUtility.GetFormulaString (cyclomatic 25) src/metadb/Chemoinformatics/Formula/FormulaCalculateUtility.vb:291 — FormulaCalculateUtility.GetFormulaString has cyclomatic complexity 25 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · IsotopeCalculator.getNominalIsotopeElementPropertyForNineIsotopomerElement (cyclomatic 25) · ×1
  • IsotopeCalculator.getNominalIsotopeElementPropertyForNineIsotopomerElement (cyclomatic 25) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1504 — IsotopeCalculator.getNominalIsotopeElementPropertyForNineIsotopomerElement has cyclomatic complexity 25 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · FragmentAssigner.AnnotateIsotopes (cyclomatic 25) · ×1
  • FragmentAssigner.AnnotateIsotopes (cyclomatic 25) src/mzmath/MSFinder/FragmentAssigner.vb:779 — FragmentAssigner.AnnotateIsotopes has cyclomatic complexity 25 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · MissingValueImputation.ImputePCA (cyclomatic 25) · ×1
  • MissingValueImputation.ImputePCA (cyclomatic 25) src/mzmath/mz_deco/Preprocessing/MissingValueImputation.vb:422 — MissingValueImputation.ImputePCA has cyclomatic complexity 25 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfLysope (cyclomatic 24) · ×1
  • LipidMsmsCharacterization.JudgeIfLysope (cyclomatic 24) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3638 — LipidMsmsCharacterization.JudgeIfLysope has cyclomatic complexity 24 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfCeramideeods (cyclomatic 24) · ×1
  • LipidMsmsCharacterization.JudgeIfCeramideeods (cyclomatic 24) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:10458 — LipidMsmsCharacterization.JudgeIfCeramideeods has cyclomatic complexity 24 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfCeramideos (cyclomatic 24) · ×1
  • LipidMsmsCharacterization.JudgeIfCeramideos (cyclomatic 24) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:10774 — LipidMsmsCharacterization.JudgeIfCeramideos has cyclomatic complexity 24 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfFahfaTriacylglycerol (cyclomatic 24) · ×1
  • LipidMsmsCharacterization.JudgeIfFahfaTriacylglycerol (cyclomatic 24) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14651 — LipidMsmsCharacterization.JudgeIfFahfaTriacylglycerol has cyclomatic complexity 24 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · MS_Peak_ID.GetMatches (cyclomatic 24) · ×1
  • MS_Peak_ID.GetMatches (cyclomatic 24) src/mzmath/Oligonucleotide_MS/MS_Peak/Oligonucleotide_MS_Peak_ID_Given_Sequence_v8.vb:455 — MS_Peak_ID.GetMatches has cyclomatic complexity 24 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · Extensions.InchiKey (cyclomatic 24) · ×1
  • Extensions.InchiKey (cyclomatic 24) src/metadb/Chemoinformatics/InChI/Extensions.vb:103 — Extensions.InchiKey has cyclomatic complexity 24 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · FormulaStringParcer.IsOrganicFormula (cyclomatic 24) · ×1
  • FormulaStringParcer.IsOrganicFormula (cyclomatic 24) src/mzmath/MSFinder/FormulaStringParcer.vb:116 — FormulaStringParcer.IsOrganicFormula has cyclomatic complexity 24 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · PeakAssign.PlotInternal (cyclomatic 23) · ×1
  • PeakAssign.PlotInternal (cyclomatic 23) src/visualize/plot/PeakAssign.vb:185 — PeakAssign.PlotInternal has cyclomatic complexity 23 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · XcaliburRawFileIO.GetScanTypeNameFromThermoScanFilterText (cyclomatic 23) · ×1
  • XcaliburRawFileIO.GetScanTypeNameFromThermoScanFilterText (cyclomatic 23) src/assembly/ThermoRawFileReader/XcaliburRawFileIO.vb:1478 — XcaliburRawFileIO.GetScanTypeNameFromThermoScanFilterText has cyclomatic complexity 23 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidEieioMsmsCharacterization.JudgeIfLysopc (cyclomatic 23) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfLysopc (cyclomatic 23) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1067 — LipidEieioMsmsCharacterization.JudgeIfLysopc has cyclomatic complexity 23 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidEieioMsmsCharacterization.JudgeIfPhosphatidylethanolamineD5 (cyclomatic 23) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfPhosphatidylethanolamineD5 (cyclomatic 23) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:2235 — LipidEieioMsmsCharacterization.JudgeIfPhosphatidylethanolamineD5 has cyclomatic complexity 23 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfPhosphatidylethanolamine (cyclomatic 23) · ×1
  • LipidMsmsCharacterization.JudgeIfPhosphatidylethanolamine (cyclomatic 23) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:1989 — LipidMsmsCharacterization.JudgeIfPhosphatidylethanolamine has cyclomatic complexity 23 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfPhosphatidylethanolamineD5) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfLysocardiolipin (cyclomatic 23) · ×1
  • LipidMsmsCharacterization.JudgeIfLysocardiolipin (cyclomatic 23) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7504 — LipidMsmsCharacterization.JudgeIfLysocardiolipin has cyclomatic complexity 23 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfPhosphatidylethanolamineD5 (cyclomatic 23) · ×1
  • LipidMsmsCharacterization.JudgeIfPhosphatidylethanolamineD5 (cyclomatic 23) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15234 — LipidMsmsCharacterization.JudgeIfPhosphatidylethanolamineD5 has cyclomatic complexity 23 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfPhosphatidylethanolamine) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D1 · Cyclomatic Complexity · FormulaStringParcer.setElementNumbers (cyclomatic 23) · ×1
  • FormulaStringParcer.setElementNumbers (cyclomatic 23) src/mzmath/MSFinder/FormulaStringParcer.vb:351 — FormulaStringParcer.setElementNumbers has cyclomatic complexity 23 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · FragmentAssigner.isotopicPeakAssignmnet (cyclomatic 23) · ×1
  • FragmentAssigner.isotopicPeakAssignmnet (cyclomatic 23) src/mzmath/MSFinder/FragmentAssigner.vb:701 — FragmentAssigner.isotopicPeakAssignmnet has cyclomatic complexity 23 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidEieioMsmsCharacterization.JudgeIfPhosphatidylinositol (cyclomatic 22) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfPhosphatidylinositol (cyclomatic 22) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:892 — LipidEieioMsmsCharacterization.JudgeIfPhosphatidylinositol has cyclomatic complexity 22 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table. This shape REPEATS in the file: one other method here (LipidEieioMsmsCharacterization.JudgeIfPhosphatidylinositolD5) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D1 · Cyclomatic Complexity · LipidEieioMsmsCharacterization.JudgeIfSphingomyelin (cyclomatic 22) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfSphingomyelin (cyclomatic 22) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1326 — LipidEieioMsmsCharacterization.JudgeIfSphingomyelin has cyclomatic complexity 22 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table. This shape REPEATS in the file: one other method here (LipidEieioMsmsCharacterization.JudgeIfSphingomyelinD9) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D1 · Cyclomatic Complexity · LipidEieioMsmsCharacterization.JudgeIfPhosphatidylinositolD5 (cyclomatic 22) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfPhosphatidylinositolD5 (cyclomatic 22) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:2659 — LipidEieioMsmsCharacterization.JudgeIfPhosphatidylinositolD5 has cyclomatic complexity 22 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table. This shape REPEATS in the file: one other method here (LipidEieioMsmsCharacterization.JudgeIfPhosphatidylinositol) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D1 · Cyclomatic Complexity · LipidEieioMsmsCharacterization.JudgeIfSphingomyelinD9 (cyclomatic 22) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfSphingomyelinD9 (cyclomatic 22) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:3309 — LipidEieioMsmsCharacterization.JudgeIfSphingomyelinD9 has cyclomatic complexity 22 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table. This shape REPEATS in the file: one other method here (LipidEieioMsmsCharacterization.JudgeIfSphingomyelin) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfAcylglcadg (cyclomatic 22) · ×1
  • LipidMsmsCharacterization.JudgeIfAcylglcadg (cyclomatic 22) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6468 — LipidMsmsCharacterization.JudgeIfAcylglcadg has cyclomatic complexity 22 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfOxTriacylglycerol (cyclomatic 22) · ×1
  • LipidMsmsCharacterization.JudgeIfOxTriacylglycerol (cyclomatic 22) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14570 — LipidMsmsCharacterization.JudgeIfOxTriacylglycerol has cyclomatic complexity 22 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfLysopeD5 (cyclomatic 22) · ×1
  • LipidMsmsCharacterization.JudgeIfLysopeD5 (cyclomatic 22) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15809 — LipidMsmsCharacterization.JudgeIfLysopeD5 has cyclomatic complexity 22 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · SpectrumPeakGenerator.GetDoubleBondSpectrum (cyclomatic 22) · ×1
  • SpectrumPeakGenerator.GetDoubleBondSpectrum (cyclomatic 22) src/metadb/Lipidomics/SpectrumPeakGenerator.vb:65 — SpectrumPeakGenerator.GetDoubleBondSpectrum has cyclomatic complexity 22 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · IsotopeCalculator.getNominalIsotopeElementPropertyForEightIsotopomerElement (cyclomatic 22) · ×1
  • IsotopeCalculator.getNominalIsotopeElementPropertyForEightIsotopomerElement (cyclomatic 22) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1701 — IsotopeCalculator.getNominalIsotopeElementPropertyForEightIsotopomerElement has cyclomatic complexity 22 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · SequenceToSpec.GetSpectrumPeaksByHotECD (cyclomatic 22) · ×1
  • SequenceToSpec.GetSpectrumPeaksByHotECD (cyclomatic 22) src/mzmath/MSEngine/Proteomics/SequenceToSpec.vb:255 — SequenceToSpec.GetSpectrumPeaksByHotECD has cyclomatic complexity 22 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · TICplot.RunPlot (cyclomatic 21) · ×1
  • TICplot.RunPlot (cyclomatic 21) src/visualize/plot/ChromatogramPlot/TICplot.vb:200 — TICplot.RunPlot has cyclomatic complexity 21 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidomicsConverter.ConvertMsdialLipidnameToLipidMoleculeObjectVS2 (cyclomatic 21) · ×1
  • LipidomicsConverter.ConvertMsdialLipidnameToLipidMoleculeObjectVS2 (cyclomatic 21) src/metadb/Lipidomics/Annotation/LipidomicsConverter.vb:507 — LipidomicsConverter.ConvertMsdialLipidnameToLipidMoleculeObjectVS2 has cyclomatic complexity 21 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table. This is NOT this file's highest cyclomatic complexity: LipidomicsConverter.ConvertMsdialClassDefinitionToSuperClassVS2 (cyclomatic 237) is higher and carries no row of its own — it was excluded as a flat dispatcher (a long switch/match over independent cases: many branches, almost no nesting), which this dimension does not treat as a refactor obligation. It is named here so the ranking you see in this file is not mistaken for the whole of it; the excluded method is counted neither in this dimension's figures nor in its score.
D1 · Cyclomatic Complexity · EieioMsCharacterizationUtility.GetDefaultScore (cyclomatic 21) · ×1
  • EieioMsCharacterizationUtility.GetDefaultScore (cyclomatic 21) src/metadb/Lipidomics/MsCharacterization/EieioMsCharacterizationUtility.vb:381 — EieioMsCharacterizationUtility.GetDefaultScore has cyclomatic complexity 21 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidEieioMsmsCharacterization.JudgeIfPhosphatidylserine (cyclomatic 21) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfPhosphatidylserine (cyclomatic 21) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:726 — LipidEieioMsmsCharacterization.JudgeIfPhosphatidylserine has cyclomatic complexity 21 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table. This shape REPEATS in the file: one other method here (LipidEieioMsmsCharacterization.JudgeIfPhosphatidylserineD5) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D1 · Cyclomatic Complexity · LipidEieioMsmsCharacterization.JudgeIfPhosphatidylserineD5 (cyclomatic 21) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfPhosphatidylserineD5 (cyclomatic 21) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:2492 — LipidEieioMsmsCharacterization.JudgeIfPhosphatidylserineD5 has cyclomatic complexity 21 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table. This shape REPEATS in the file: one other method here (LipidEieioMsmsCharacterization.JudgeIfPhosphatidylserine) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D1 · Cyclomatic Complexity · LipidEieioMsmsCharacterization.JudgeIfLysopcD5 (cyclomatic 21) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfLysopcD5 (cyclomatic 21) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:2833 — LipidEieioMsmsCharacterization.JudgeIfLysopcD5 has cyclomatic complexity 21 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidEieioMsmsCharacterization.JudgeIfTriacylglycerolD5 (cyclomatic 21) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfTriacylglycerolD5 (cyclomatic 21) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:3176 — LipidEieioMsmsCharacterization.JudgeIfTriacylglycerolD5 has cyclomatic complexity 21 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfLdgts (cyclomatic 21) · ×1
  • LipidMsmsCharacterization.JudgeIfLdgts (cyclomatic 21) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6168 — LipidMsmsCharacterization.JudgeIfLdgts has cyclomatic complexity 21 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfHexhexceramidens (cyclomatic 21) · ×1
  • LipidMsmsCharacterization.JudgeIfHexhexceramidens (cyclomatic 21) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:9121 — LipidMsmsCharacterization.JudgeIfHexhexceramidens has cyclomatic complexity 21 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfHexhexhexceramidens (cyclomatic 21) · ×1
  • LipidMsmsCharacterization.JudgeIfHexhexhexceramidens (cyclomatic 21) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:9239 — LipidMsmsCharacterization.JudgeIfHexhexhexceramidens has cyclomatic complexity 21 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfShexcer (cyclomatic 21) · ×1
  • LipidMsmsCharacterization.JudgeIfShexcer (cyclomatic 21) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11440 — LipidMsmsCharacterization.JudgeIfShexcer has cyclomatic complexity 21 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfEtherSmgdg (cyclomatic 21) · ×1
  • LipidMsmsCharacterization.JudgeIfEtherSmgdg (cyclomatic 21) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14140 — LipidMsmsCharacterization.JudgeIfEtherSmgdg has cyclomatic complexity 21 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · IsotopeCalculator.GetBasicCompoundElementProfile (cyclomatic 21) · ×1
  • IsotopeCalculator.GetBasicCompoundElementProfile (cyclomatic 21) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:122 — IsotopeCalculator.GetBasicCompoundElementProfile has cyclomatic complexity 21 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · PeptideCalc.Sequence2FastPeptidesByVariableModifications (cyclomatic 21) · ×1
  • PeptideCalc.Sequence2FastPeptidesByVariableModifications (cyclomatic 21) src/mzmath/MSEngine/Proteomics/PeptideCalc.vb:255 — PeptideCalc.Sequence2FastPeptidesByVariableModifications has cyclomatic complexity 21 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · MetaDbXref.searchTable (cyclomatic 20) · ×1
  • MetaDbXref.searchTable (cyclomatic 20) Rscript/Library/mzkit_app/src/mzkit/annotations/MetaDbXref.vb:898 — MetaDbXref.searchTable has cyclomatic complexity 20 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · Assembly.writeMgfIons (cyclomatic 20) · ×1
  • Assembly.writeMgfIons (cyclomatic 20) Rscript/Library/mzkit_app/src/mzkit/assembly/Assembly.vb:336 — Assembly.writeMgfIons has cyclomatic complexity 20 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidomicsConverter.ConvertMsdialLipidnameToLipidMoleculeObjectVS2 (cyclomatic 20) · ×1
  • LipidomicsConverter.ConvertMsdialLipidnameToLipidMoleculeObjectVS2 (cyclomatic 20) src/metadb/Lipidomics/Annotation/LipidomicsConverter.vb:542 — LipidomicsConverter.ConvertMsdialLipidnameToLipidMoleculeObjectVS2 has cyclomatic complexity 20 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table. This is NOT this file's highest cyclomatic complexity: LipidomicsConverter.ConvertMsdialClassDefinitionToSuperClassVS2 (cyclomatic 237) is higher and carries no row of its own — it was excluded as a flat dispatcher (a long switch/match over independent cases: many branches, almost no nesting), which this dimension does not treat as a refactor obligation. It is named here so the ranking you see in this file is not mistaken for the whole of it; the excluded method is counted neither in this dimension's figures nor in its score.
D1 · Cyclomatic Complexity · MsScanMatching.GetRefinedLipidAnnotationLevel (cyclomatic 20) · ×1
  • MsScanMatching.GetRefinedLipidAnnotationLevel (cyclomatic 20) src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:1471 — MsScanMatching.GetRefinedLipidAnnotationLevel has cyclomatic complexity 20 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table. This shape REPEATS in the file: one other method here (MsScanMatching.GetRefinedLipidAnnotationLevelForEIEIO) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared. This is NOT this file's highest cyclomatic complexity: MsScanMatching.GetEieioBasedLipidMoleculeAnnotationResult (cyclomatic 56) is higher and carries no row of its own — it was excluded as a flat dispatcher (a long switch/match over independent cases: many branches, almost no nesting), which this dimension does not treat as a refactor obligation. It is named here so the ranking you see in this file is not mistaken for the whole of it; the excluded method is counted neither in this dimension's figures nor in its score.
D1 · Cyclomatic Complexity · MsScanMatching.GetRefinedLipidAnnotationLevelForEIEIO (cyclomatic 20) · ×1
  • MsScanMatching.GetRefinedLipidAnnotationLevelForEIEIO (cyclomatic 20) src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:1635 — MsScanMatching.GetRefinedLipidAnnotationLevelForEIEIO has cyclomatic complexity 20 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table. This shape REPEATS in the file: one other method here (MsScanMatching.GetRefinedLipidAnnotationLevel) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared. This is NOT this file's highest cyclomatic complexity: MsScanMatching.GetEieioBasedLipidMoleculeAnnotationResult (cyclomatic 56) is higher and carries no row of its own — it was excluded as a flat dispatcher (a long switch/match over independent cases: many branches, almost no nesting), which this dimension does not treat as a refactor obligation. It is named here so the ranking you see in this file is not mistaken for the whole of it; the excluded method is counted neither in this dimension's figures nor in its score.
D1 · Cyclomatic Complexity · HexCerLipidParser.Parse (cyclomatic 20) · ×1
  • HexCerLipidParser.Parse (cyclomatic 20) src/metadb/Lipidomics/LipidParser/HexCerLipidParser.vb:73 — HexCerLipidParser.Parse has cyclomatic complexity 20 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidEieioMsmsCharacterization.JudgeIfEtherpe (cyclomatic 20) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfEtherpe (cyclomatic 20) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1497 — LipidEieioMsmsCharacterization.JudgeIfEtherpe has cyclomatic complexity 20 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfEtherpe (cyclomatic 20) · ×1
  • LipidMsmsCharacterization.JudgeIfEtherpe (cyclomatic 20) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3857 — LipidMsmsCharacterization.JudgeIfEtherpe has cyclomatic complexity 20 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfEtheroxpe (cyclomatic 20) · ×1
  • LipidMsmsCharacterization.JudgeIfEtheroxpe (cyclomatic 20) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4094 — LipidMsmsCharacterization.JudgeIfEtheroxpe has cyclomatic complexity 20 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · MummichogAnnotator.PerformPathwayEnrichment (cyclomatic 20) · ×1
  • MummichogAnnotator.PerformPathwayEnrichment (cyclomatic 20) src/mzmath/Mummichog/MummichogModule.vb:456 — MummichogAnnotator.PerformPathwayEnrichment has cyclomatic complexity 20 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · Composition.FindCompositions (cyclomatic 20) · ×1
  • Composition.FindCompositions (cyclomatic 20) src/mzmath/Oligonucleotide_MS/OligonucleotideComposition/Oligonucleotide_Composition_from_Mass_Calculator_v2.vb:125 — Composition.FindCompositions has cyclomatic complexity 20 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · FormulaScanner.Convert2FormulaObjV2 (cyclomatic 20) · ×1
  • FormulaScanner.Convert2FormulaObjV2 (cyclomatic 20) src/metadb/Chemoinformatics/Formula/FormulaScanner.vb:96 — FormulaScanner.Convert2FormulaObjV2 has cyclomatic complexity 20 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · FormulaScanner.ScanFormula (cyclomatic 20) · ×1
  • FormulaScanner.ScanFormula (cyclomatic 20) src/metadb/Chemoinformatics/Formula/FormulaScanner.vb:376 — FormulaScanner.ScanFormula has cyclomatic complexity 20 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · PeakAreaCalculator.GaussianFittingIntegration (cyclomatic 20) · ×1
  • PeakAreaCalculator.GaussianFittingIntegration (cyclomatic 20) src/mzmath/mz_deco/Signals/PeakFinding/PeakArea/PeakAreaCalculator.vb:100 — PeakAreaCalculator.GaussianFittingIntegration has cyclomatic complexity 20 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · XcaliburRawFileIO.GetTuneData (cyclomatic 19) · ×1
  • XcaliburRawFileIO.GetTuneData (cyclomatic 19) src/assembly/ThermoRawFileReader/XcaliburRawFileIO.vb:1630 — XcaliburRawFileIO.GetTuneData has cyclomatic complexity 19 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfPhosphatidylserine (cyclomatic 19) · ×1
  • LipidMsmsCharacterization.JudgeIfPhosphatidylserine (cyclomatic 19) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:2151 — LipidMsmsCharacterization.JudgeIfPhosphatidylserine has cyclomatic complexity 19 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfPhosphatidylserineD5) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfPhosphatidylglycerol (cyclomatic 19) · ×1
  • LipidMsmsCharacterization.JudgeIfPhosphatidylglycerol (cyclomatic 19) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:2402 — LipidMsmsCharacterization.JudgeIfPhosphatidylglycerol has cyclomatic complexity 19 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfPhosphatidylglycerolD5) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfNacylphosphatidylserine (cyclomatic 19) · ×1
  • LipidMsmsCharacterization.JudgeIfNacylphosphatidylserine (cyclomatic 19) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:2700 — LipidMsmsCharacterization.JudgeIfNacylphosphatidylserine has cyclomatic complexity 19 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfOxpe (cyclomatic 19) · ×1
  • LipidMsmsCharacterization.JudgeIfOxpe (cyclomatic 19) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4410 — LipidMsmsCharacterization.JudgeIfOxpe has cyclomatic complexity 19 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfPhosphatidylserineD5 (cyclomatic 19) · ×1
  • LipidMsmsCharacterization.JudgeIfPhosphatidylserineD5 (cyclomatic 19) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15379 — LipidMsmsCharacterization.JudgeIfPhosphatidylserineD5 has cyclomatic complexity 19 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfPhosphatidylserine) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfPhosphatidylglycerolD5 (cyclomatic 19) · ×1
  • LipidMsmsCharacterization.JudgeIfPhosphatidylglycerolD5 (cyclomatic 19) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15501 — LipidMsmsCharacterization.JudgeIfPhosphatidylglycerolD5 has cyclomatic complexity 19 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfPhosphatidylglycerol) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D1 · Cyclomatic Complexity · EidSpecificSpectrumGenerator.EidSpecificSpectrumGen (cyclomatic 19) · ×1
  • EidSpecificSpectrumGenerator.EidSpecificSpectrumGen (cyclomatic 19) src/metadb/Lipidomics/SpectrumGenerator/EidSpecificSpectrumGenerator.vb:64 — EidSpecificSpectrumGenerator.EidSpecificSpectrumGen has cyclomatic complexity 19 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · MummichogAnnotator.ReverseAnnotation (cyclomatic 19) · ×1
  • MummichogAnnotator.ReverseAnnotation (cyclomatic 19) src/mzmath/Mummichog/MummichogModule.vb:584 — MummichogAnnotator.ReverseAnnotation has cyclomatic complexity 19 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · IsotopeCalculator.getAllIsotopeElementPropertyForTenIsotopomerElement (cyclomatic 19) · ×1
  • IsotopeCalculator.getAllIsotopeElementPropertyForTenIsotopomerElement (cyclomatic 19) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:384 — IsotopeCalculator.getAllIsotopeElementPropertyForTenIsotopomerElement has cyclomatic complexity 19 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · IsotopeCalculator.getNominalIsotopeElementPropertyForSevenIsotopomerElement (cyclomatic 19) · ×1
  • IsotopeCalculator.getNominalIsotopeElementPropertyForSevenIsotopomerElement (cyclomatic 19) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1876 — IsotopeCalculator.getNominalIsotopeElementPropertyForSevenIsotopomerElement has cyclomatic complexity 19 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · Scanner.MeasureElement (cyclomatic 19) · ×1
  • Scanner.MeasureElement (cyclomatic 19) src/metadb/SMILES/Language/Scanner.vb:327 — Scanner.MeasureElement has cyclomatic complexity 19 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · PeptideCalc.GetAminoAcidByFixedModifications (cyclomatic 19) · ×1
  • PeptideCalc.GetAminoAcidByFixedModifications (cyclomatic 19) src/mzmath/MSEngine/Proteomics/PeptideCalc.vb:169 — PeptideCalc.GetAminoAcidByFixedModifications has cyclomatic complexity 19 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table. This shape REPEATS in the file: one other method here (PeptideCalc.GetAminoAcidByVariableModifications) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D1 · Cyclomatic Complexity · PeptideCalc.GetAminoAcidByVariableModifications (cyclomatic 19) · ×1
  • PeptideCalc.GetAminoAcidByVariableModifications (cyclomatic 19) src/mzmath/MSEngine/Proteomics/PeptideCalc.vb:390 — PeptideCalc.GetAminoAcidByVariableModifications has cyclomatic complexity 19 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table. This shape REPEATS in the file: one other method here (PeptideCalc.GetAminoAcidByFixedModifications) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D1 · Cyclomatic Complexity · DTW.ComputeDTW (cyclomatic 19) · ×1
  • DTW.ComputeDTW (cyclomatic 19) src/mzmath/mz_deco/PeakAlignment/Algorithm/DTW.vb:21 — DTW.ComputeDTW has cyclomatic complexity 19 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LOESS.LOESSAlignment (cyclomatic 19) · ×1
  • LOESS.LOESSAlignment (cyclomatic 19) src/mzmath/mz_deco/PeakAlignment/Algorithm/LOESS.vb:25 — LOESS.LOESSAlignment has cyclomatic complexity 19 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · FastSeekIndex.LoadIndex_mzML (cyclomatic 18) · ×1
  • FastSeekIndex.LoadIndex_mzML (cyclomatic 18) src/assembly/assembly/MarkupData/FastSeekIndex.vb:120 — FastSeekIndex.LoadIndex_mzML has cyclomatic complexity 18 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · ScanPopulator.Load (cyclomatic 18) · ×1
  • ScanPopulator.Load (cyclomatic 18) src/assembly/assembly/mzPack/mzWebCache/ScanPopulator.vb:178 — ScanPopulator.Load has cyclomatic complexity 18 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidEieioMsmsCharacterization.JudgeIfDag (cyclomatic 18) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfDag (cyclomatic 18) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1840 — LipidEieioMsmsCharacterization.JudgeIfDag has cyclomatic complexity 18 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfPhosphatidylinositol (cyclomatic 18) · ×1
  • LipidMsmsCharacterization.JudgeIfPhosphatidylinositol (cyclomatic 18) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:2580 — LipidMsmsCharacterization.JudgeIfPhosphatidylinositol has cyclomatic complexity 18 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfPhosphatidylinositolD5) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfOxpg (cyclomatic 18) · ×1
  • LipidMsmsCharacterization.JudgeIfOxpg (cyclomatic 18) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4527 — LipidMsmsCharacterization.JudgeIfOxpg has cyclomatic complexity 18 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfEtherDAG (cyclomatic 18) · ×1
  • LipidMsmsCharacterization.JudgeIfEtherDAG (cyclomatic 18) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5392 — LipidMsmsCharacterization.JudgeIfEtherDAG has cyclomatic complexity 18 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfGlcadg (cyclomatic 18) · ×1
  • LipidMsmsCharacterization.JudgeIfGlcadg (cyclomatic 18) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6371 — LipidMsmsCharacterization.JudgeIfGlcadg has cyclomatic complexity 18 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfPicermide (cyclomatic 18) · ×1
  • LipidMsmsCharacterization.JudgeIfPicermide (cyclomatic 18) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12459 — LipidMsmsCharacterization.JudgeIfPicermide has cyclomatic complexity 18 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfMipc (cyclomatic 18) · ×1
  • LipidMsmsCharacterization.JudgeIfMipc (cyclomatic 18) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14477 — LipidMsmsCharacterization.JudgeIfMipc has cyclomatic complexity 18 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfPhosphatidylinositolD5 (cyclomatic 18) · ×1
  • LipidMsmsCharacterization.JudgeIfPhosphatidylinositolD5 (cyclomatic 18) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15607 — LipidMsmsCharacterization.JudgeIfPhosphatidylinositolD5 has cyclomatic complexity 18 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfPhosphatidylinositol) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D1 · Cyclomatic Complexity · CerNSd7SpectrumGenerator.GetSphingoDoubleBondSpectrum (cyclomatic 18) · ×1
  • CerNSd7SpectrumGenerator.GetSphingoDoubleBondSpectrum (cyclomatic 18) src/metadb/Lipidomics/SpectrumGenerator/CeramideNsD7SpectrumGenerator.vb:172 — CerNSd7SpectrumGenerator.GetSphingoDoubleBondSpectrum has cyclomatic complexity 18 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · MsScanMatching.GetMatchedPeaksScores (cyclomatic 18) · ×1
  • MsScanMatching.GetMatchedPeaksScores (cyclomatic 18) src/mzmath/MSEngine/Search/MsScanMatching.vb:394 — MsScanMatching.GetMatchedPeaksScores has cyclomatic complexity 18 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · MsScanMatching.GetMachedSpectralPeaks (cyclomatic 18) · ×1
  • MsScanMatching.GetMachedSpectralPeaks (cyclomatic 18) src/mzmath/MSEngine/Search/MsScanMatching.vb:648 — MsScanMatching.GetMachedSpectralPeaks has cyclomatic complexity 18 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · Math.RunMaxLFQ (cyclomatic 18) · ×1
  • Math.RunMaxLFQ (cyclomatic 18) src/mzmath/mz_deco/MaxLFQ/Math.vb:9 — Math.RunMaxLFQ has cyclomatic complexity 18 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · PeakProcessor.ProcessPeaksCombined (cyclomatic 18) · ×1
  • PeakProcessor.ProcessPeaksCombined (cyclomatic 18) src/mzmath/mz_deco/Signals/PeakFinding/PeakProcessor.vb:154 — PeakProcessor.ProcessPeaksCombined has cyclomatic complexity 18 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · PeakQualityEvaluator.EvaluatePeakQuality (cyclomatic 18) · ×1
  • PeakQualityEvaluator.EvaluatePeakQuality (cyclomatic 18) src/mzmath/mz_deco/Signals/PeakFinding/PeakQualityEvaluator.vb:24 — PeakQualityEvaluator.EvaluatePeakQuality has cyclomatic complexity 18 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · SpectralPreprocessor.SolveALS (cyclomatic 18) · ×1
  • SpectralPreprocessor.SolveALS (cyclomatic 18) src/assembly/RamanSpectroscopy/RamanDataProcessor.vb:568 — SpectralPreprocessor.SolveALS has cyclomatic complexity 18 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · XcaliburRawFileIO.GetScanDataSumScans (cyclomatic 17) · ×1
  • XcaliburRawFileIO.GetScanDataSumScans (cyclomatic 17) src/assembly/ThermoRawFileReader/XcaliburRawFileIO.vb:2367 — XcaliburRawFileIO.GetScanDataSumScans has cyclomatic complexity 17 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · DoubleBondIndeterminateState.Indeterminate (cyclomatic 17) · ×1
  • DoubleBondIndeterminateState.Indeterminate (cyclomatic 17) src/metadb/Lipidomics/DoubleBondIndeterminateState.vb:90 — DoubleBondIndeterminateState.Indeterminate has cyclomatic complexity 17 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidEieioMsmsCharacterization.JudgeIfPhosphatidylglycerol (cyclomatic 17) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfPhosphatidylglycerol (cyclomatic 17) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:575 — LipidEieioMsmsCharacterization.JudgeIfPhosphatidylglycerol has cyclomatic complexity 17 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidEieioMsmsCharacterization.JudgeIfLysope (cyclomatic 17) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfLysope (cyclomatic 17) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1146 — LipidEieioMsmsCharacterization.JudgeIfLysope has cyclomatic complexity 17 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidEieioMsmsCharacterization.JudgeIfDagD5 (cyclomatic 17) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfDagD5 (cyclomatic 17) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:3090 — LipidEieioMsmsCharacterization.JudgeIfDagD5 has cyclomatic complexity 17 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfOxpi (cyclomatic 17) · ×1
  • LipidMsmsCharacterization.JudgeIfOxpi (cyclomatic 17) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4648 — LipidMsmsCharacterization.JudgeIfOxpi has cyclomatic complexity 17 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfPmeoh (cyclomatic 17) · ×1
  • LipidMsmsCharacterization.JudgeIfPmeoh (cyclomatic 17) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6806 — LipidMsmsCharacterization.JudgeIfPmeoh has cyclomatic complexity 17 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfGm3 (cyclomatic 17) · ×1
  • LipidMsmsCharacterization.JudgeIfGm3 (cyclomatic 17) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11577 — LipidMsmsCharacterization.JudgeIfGm3 has cyclomatic complexity 17 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfGM1 (cyclomatic 17) · ×1
  • LipidMsmsCharacterization.JudgeIfGM1 (cyclomatic 17) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11848 — LipidMsmsCharacterization.JudgeIfGM1 has cyclomatic complexity 17 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfGT1b (cyclomatic 17) · ×1
  • LipidMsmsCharacterization.JudgeIfGT1b (cyclomatic 17) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11916 — LipidMsmsCharacterization.JudgeIfGT1b has cyclomatic complexity 17 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfGQ1b) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfGQ1b (cyclomatic 17) · ×1
  • LipidMsmsCharacterization.JudgeIfGQ1b (cyclomatic 17) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11986 — LipidMsmsCharacterization.JudgeIfGQ1b has cyclomatic complexity 17 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfGT1b) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfNGcGM3 (cyclomatic 17) · ×1
  • LipidMsmsCharacterization.JudgeIfNGcGM3 (cyclomatic 17) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12056 — LipidMsmsCharacterization.JudgeIfNGcGM3 has cyclomatic complexity 17 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfFahfamideglyser (cyclomatic 17) · ×1
  • LipidMsmsCharacterization.JudgeIfFahfamideglyser (cyclomatic 17) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13084 — LipidMsmsCharacterization.JudgeIfFahfamideglyser has cyclomatic complexity 17 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfMonoMethylPE (cyclomatic 17) · ×1
  • LipidMsmsCharacterization.JudgeIfMonoMethylPE (cyclomatic 17) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14275 — LipidMsmsCharacterization.JudgeIfMonoMethylPE has cyclomatic complexity 17 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfDiMethylPE) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfDiMethylPE (cyclomatic 17) · ×1
  • LipidMsmsCharacterization.JudgeIfDiMethylPE (cyclomatic 17) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14376 — LipidMsmsCharacterization.JudgeIfDiMethylPE has cyclomatic complexity 17 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfMonoMethylPE) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D1 · Cyclomatic Complexity · Omega3nChainGenerator.GenerateDoubleBondsForSphingosine (cyclomatic 17) · ×1
  • Omega3nChainGenerator.GenerateDoubleBondsForSphingosine (cyclomatic 17) src/metadb/Lipidomics/Omega3nChainGenerator.vb:203 — Omega3nChainGenerator.GenerateDoubleBondsForSphingosine has cyclomatic complexity 17 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · SpectrumPeakGenerator.GetSphingoDoubleBondSpectrum (cyclomatic 17) · ×1
  • SpectrumPeakGenerator.GetSphingoDoubleBondSpectrum (cyclomatic 17) src/metadb/Lipidomics/SpectrumPeakGenerator.vb:211 — SpectrumPeakGenerator.GetSphingoDoubleBondSpectrum has cyclomatic complexity 17 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · IsotopeCalculator.getAllIsotopeElementPropertyForNineIsotopomerElement (cyclomatic 17) · ×1
  • IsotopeCalculator.getAllIsotopeElementPropertyForNineIsotopomerElement (cyclomatic 17) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:552 — IsotopeCalculator.getAllIsotopeElementPropertyForNineIsotopomerElement has cyclomatic complexity 17 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · GlycosylNameSolver.SplitByTopLevelStack (cyclomatic 17) · ×1
  • GlycosylNameSolver.SplitByTopLevelStack (cyclomatic 17) src/metadb/Chemoinformatics/NaturalProduct/GlycosylNameSolver.vb:280 — GlycosylNameSolver.SplitByTopLevelStack has cyclomatic complexity 17 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · MetaData.EqualsAny (cyclomatic 17) · ×1
  • MetaData.EqualsAny (cyclomatic 17) src/metadb/Massbank/Public/lipidMAPS/SDF.vb:151 — MetaData.EqualsAny has cyclomatic complexity 17 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · SequenceToSpec.GetSpectrumPeaksByECD (cyclomatic 17) · ×1
  • SequenceToSpec.GetSpectrumPeaksByECD (cyclomatic 17) src/mzmath/MSEngine/Proteomics/SequenceToSpec.vb:397 — SequenceToSpec.GetSpectrumPeaksByECD has cyclomatic complexity 17 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · FragmentAssigner.GetRefinedPeaklist (cyclomatic 17) · ×1
  • FragmentAssigner.GetRefinedPeaklist (cyclomatic 17) src/mzmath/MSFinder/FragmentAssigner.vb:457 — FragmentAssigner.GetRefinedPeaklist has cyclomatic complexity 17 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · MissingValueImputation.ImputeKNN (cyclomatic 17) · ×1
  • MissingValueImputation.ImputeKNN (cyclomatic 17) src/mzmath/mz_deco/Preprocessing/MissingValueImputation.vb:310 — MissingValueImputation.ImputeKNN has cyclomatic complexity 17 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · WiffScanFileReader.loadScan (cyclomatic 17) · ×1
  • WiffScanFileReader.loadScan (cyclomatic 17) src/assembly/sciexWiffReader/WiffFileReader/WiffScanFileReader.vb:277 — WiffScanFileReader.loadScan has cyclomatic complexity 17 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · RamanProcessingPipeline.Process (cyclomatic 17) · ×1
  • RamanProcessingPipeline.Process (cyclomatic 17) src/assembly/RamanSpectroscopy/RamanDataProcessor.vb:2486 — RamanProcessingPipeline.Process has cyclomatic complexity 17 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · Massbank.lipidnameMapping (cyclomatic 16) · ×1
  • Massbank.lipidnameMapping (cyclomatic 16) Rscript/Library/mzkit_app/src/mzkit/annotations/Massbank.vb:883 — Massbank.lipidnameMapping has cyclomatic complexity 16 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · FastSeekIndex.LoadIndex_mzXML (cyclomatic 16) · ×1
  • FastSeekIndex.LoadIndex_mzXML (cyclomatic 16) src/assembly/assembly/MarkupData/FastSeekIndex.vb:192 — FastSeekIndex.LoadIndex_mzXML has cyclomatic complexity 16 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · Converter.LoadScanStream (cyclomatic 16) · ×1
  • Converter.LoadScanStream (cyclomatic 16) src/assembly/mzPack/Converter.vb:207 — Converter.LoadScanStream has cyclomatic complexity 16 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidomicsConverter.getTotalChainString (cyclomatic 16) · ×1
  • LipidomicsConverter.getTotalChainString (cyclomatic 16) src/metadb/Lipidomics/Annotation/LipidomicsConverter.vb:2833 — LipidomicsConverter.getTotalChainString has cyclomatic complexity 16 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table. This is NOT this file's highest cyclomatic complexity: LipidomicsConverter.ConvertMsdialClassDefinitionToSuperClassVS2 (cyclomatic 237) is higher and carries no row of its own — it was excluded as a flat dispatcher (a long switch/match over independent cases: many branches, almost no nesting), which this dimension does not treat as a refactor obligation. It is named here so the ranking you see in this file is not mistaken for the whole of it; the excluded method is counted neither in this dimension's figures nor in its score.
D1 · Cyclomatic Complexity · MsScanMatching.GetLipidomicsMatchedPeaksScores (cyclomatic 16) · ×1
  • MsScanMatching.GetLipidomicsMatchedPeaksScores (cyclomatic 16) src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:1551 — MsScanMatching.GetLipidomicsMatchedPeaksScores has cyclomatic complexity 16 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table. This is NOT this file's highest cyclomatic complexity: MsScanMatching.GetEieioBasedLipidMoleculeAnnotationResult (cyclomatic 56) is higher and carries no row of its own — it was excluded as a flat dispatcher (a long switch/match over independent cases: many branches, almost no nesting), which this dimension does not treat as a refactor obligation. It is named here so the ranking you see in this file is not mistaken for the whole of it; the excluded method is counted neither in this dimension's figures nor in its score.
D1 · Cyclomatic Complexity · LipidEieioMsmsCharacterization.JudgeIfPhosphatidylglycerolD5 (cyclomatic 16) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfPhosphatidylglycerolD5 (cyclomatic 16) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:2392 — LipidEieioMsmsCharacterization.JudgeIfPhosphatidylglycerolD5 has cyclomatic complexity 16 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidEieioMsmsCharacterization.JudgeIfLysopeD5 (cyclomatic 16) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfLysopeD5 (cyclomatic 16) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:2913 — LipidEieioMsmsCharacterization.JudgeIfLysopeD5 has cyclomatic complexity 16 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidEieioMsmsCharacterization.JudgeIfCeramidensD7 (cyclomatic 16) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfCeramidensD7 (cyclomatic 16) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:3409 — LipidEieioMsmsCharacterization.JudgeIfCeramidensD7 has cyclomatic complexity 16 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfPhosphatidylThreonine (cyclomatic 16) · ×1
  • LipidMsmsCharacterization.JudgeIfPhosphatidylThreonine (cyclomatic 16) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:2288 — LipidMsmsCharacterization.JudgeIfPhosphatidylThreonine has cyclomatic complexity 16 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfSqdg) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfSphingomyelinPhyto (cyclomatic 16) · ×1
  • LipidMsmsCharacterization.JudgeIfSphingomyelinPhyto (cyclomatic 16) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3089 — LipidMsmsCharacterization.JudgeIfSphingomyelinPhyto has cyclomatic complexity 16 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfEtherlysopc) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfAcylcarnitine (cyclomatic 16) · ×1
  • LipidMsmsCharacterization.JudgeIfAcylcarnitine (cyclomatic 16) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3287 — LipidMsmsCharacterization.JudgeIfAcylcarnitine has cyclomatic complexity 16 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfEtherlysopc (cyclomatic 16) · ×1
  • LipidMsmsCharacterization.JudgeIfEtherlysopc (cyclomatic 16) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4194 — LipidMsmsCharacterization.JudgeIfEtherlysopc has cyclomatic complexity 16 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfSphingomyelinPhyto) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfEtherlysope (cyclomatic 16) · ×1
  • LipidMsmsCharacterization.JudgeIfEtherlysope (cyclomatic 16) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4243 — LipidMsmsCharacterization.JudgeIfEtherlysope has cyclomatic complexity 16 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfOxps (cyclomatic 16) · ×1
  • LipidMsmsCharacterization.JudgeIfOxps (cyclomatic 16) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4761 — LipidMsmsCharacterization.JudgeIfOxps has cyclomatic complexity 16 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfDgmg (cyclomatic 16) · ×1
  • LipidMsmsCharacterization.JudgeIfDgmg (cyclomatic 16) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5347 — LipidMsmsCharacterization.JudgeIfDgmg has cyclomatic complexity 16 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfSqdg (cyclomatic 16) · ×1
  • LipidMsmsCharacterization.JudgeIfSqdg (cyclomatic 16) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6596 — LipidMsmsCharacterization.JudgeIfSqdg has cyclomatic complexity 16 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfPhosphatidylThreonine) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfPetoh (cyclomatic 16) · ×1
  • LipidMsmsCharacterization.JudgeIfPetoh (cyclomatic 16) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6709 — LipidMsmsCharacterization.JudgeIfPetoh has cyclomatic complexity 16 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfPbtoh) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfPbtoh (cyclomatic 16) · ×1
  • LipidMsmsCharacterization.JudgeIfPbtoh (cyclomatic 16) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6906 — LipidMsmsCharacterization.JudgeIfPbtoh has cyclomatic complexity 16 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfPetoh) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D1 · Cyclomatic Complexity · LipidMsmsCharacterization.JudgeIfFahfa (cyclomatic 16) · ×1
  • LipidMsmsCharacterization.JudgeIfFahfa (cyclomatic 16) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7814 — LipidMsmsCharacterization.JudgeIfFahfa has cyclomatic complexity 16 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · IsotopeCalculator.getNominalIsotopeElementPropertyForSixIsotopomerElement (cyclomatic 16) · ×1
  • IsotopeCalculator.getNominalIsotopeElementPropertyForSixIsotopomerElement (cyclomatic 16) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:2029 — IsotopeCalculator.getNominalIsotopeElementPropertyForSixIsotopomerElement has cyclomatic complexity 16 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · XrefSchema.PullCollection (cyclomatic 16) · ×1
  • XrefSchema.PullCollection (cyclomatic 16) src/metadb/Chemoinformatics/Metabolite/CrossReference/XrefSchema.vb:138 — XrefSchema.PullCollection has cyclomatic complexity 16 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · FormulaStringParcer.TokenizeFormulaCharacter (cyclomatic 16) · ×1
  • FormulaStringParcer.TokenizeFormulaCharacter (cyclomatic 16) src/mzmath/MSFinder/FormulaStringParcer.vb:287 — FormulaStringParcer.TokenizeFormulaCharacter has cyclomatic complexity 16 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · DirectMatch.DirectMatchAlignment (cyclomatic 16) · ×1
  • DirectMatch.DirectMatchAlignment (cyclomatic 16) src/mzmath/mz_deco/PeakAlignment/Algorithm/DirectMatch.vb:22 — DirectMatch.DirectMatchAlignment has cyclomatic complexity 16 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · MathHelpers.MatrixInverse (cyclomatic 16) · ×1
  • MathHelpers.MatrixInverse (cyclomatic 16) src/mzmath/mz_deco/Preprocessing/MathHelpers.vb:342 — MathHelpers.MatrixInverse has cyclomatic complexity 16 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · MissingValueImputation.ImputeQRILC (cyclomatic 16) · ×1
  • MissingValueImputation.ImputeQRILC (cyclomatic 16) src/mzmath/mz_deco/Preprocessing/MissingValueImputation.vb:529 — MissingValueImputation.ImputeQRILC has cyclomatic complexity 16 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D1 · Cyclomatic Complexity · StandardCurveWorker.Regression (cyclomatic 16) · ×1
  • StandardCurveWorker.Regression (cyclomatic 16) src/mzmath/TargetedMetabolomics/MRM/QuantitativeAnalysis/StandardCurveWorker.vb:124 — StandardCurveWorker.Regression has cyclomatic complexity 16 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function, or replace a long branch ladder over a single value with a data-driven lookup or dispatch table.
D15 · Churn × Complexity Hotspots · Hotspot · ×1
  • Hotspot: src/visualize/plot/ChromatogramPlot/TICplot.vb src/visualize/plot/ChromatogramPlot/TICplot.vb:200 — src/visualize/plot/ChromatogramPlot/TICplot.vb changed 2 times in last 90 days, and the most complex body those changes touched has cyclomatic complexity 21 in TICplot.RunPlot at line 200. 2 of those changes were fix/bug commits, so the churn is repair rather than feature work. Before the next change lands here, make sure the area it touches is under test, then split that area out of the file so the following change is smaller than this one — a file this often edited pays the complexity back every time. Counted over 2026-07-15..2026-10-13, the 90 days ending at the analysed commit. Reproduce with `git log --since='2026-07-15 23:20:08 +08:00' --until='2026-10-13 23:20:08 +08:00' --full-history --no-merges -- src/visualize/plot/ChromatogramPlot/TICplot.vb`: merges are excluded because a merge re-states changes already counted at their own commits, and history is NOT path-simplified because a change that reached the file through a merged branch is still a change to it. That command counts raw commits and can read HIGHER than this row, which counts a cherry-picked re-land, and a revert together with the commit it undoes, once each — a difference of several commits on a file whose history was re-landed or reverted inside the window.
D15 · Churn × Complexity Hotspots · Repeated repair · ×1
  • Repeated repair: Rscript/Library/mzkit_app/src/mzplot/src/Visual.vb Rscript/Library/mzkit_app/src/mzplot/src/Visual.vb:727 — Rscript/Library/mzkit_app/src/mzplot/src/Visual.vb changed 3 times in last 90 days and 3 of those changes were fix/bug commits, so repair is the majority of this file's churn. Its max cyclomatic complexity is 7 (its worst body is Visual.Snapshot3D at line 727), UNDER the 15 threshold, so this is deliberately not filed as a churn × complexity hotspot — the difficulty here is in the behaviour the file has to get right, not in its control flow, and refactoring it for complexity would be the wrong move. The repairs counted were: “fix for the plot module re-construct error”; “fix of the data plots namespace reference error”; “fix of the namespace imports”. Each one is a case this code did not handle. Before the next change lands here, check that every one of them is pinned by a test that fails without its fix; where the same area keeps coming back, the durable fix is usually at the interface that keeps being misused rather than at the line that was last corrected. Counted over 2026-07-15..2026-10-13, the 90 days ending at the analysed commit. Reproduce with `git log --since='2026-07-15 23:20:08 +08:00' --until='2026-10-13 23:20:08 +08:00' --full-history --no-merges -- Rscript/Library/mzkit_app/src/mzplot/src/Visual.vb`: merges are excluded because a merge re-states changes already counted at their own commits, and history is NOT path-simplified because a change that reached the file through a merged branch is still a change to it. That command counts raw commits and can read HIGHER than this row, which counts a cherry-picked re-land, and a revert together with the commit it undoes, once each — a difference of several commits on a file whose history was re-landed or reverted inside the window.
D17 · Explicit Debt · TodoComment repeated across 13 files · ×1
  • TodoComment repeated across 13 files Rscript/Library/mzkit_app/src/mzkit/functions/z_assembler.vb:86 — The identical TodoComment appears in 13 files (13 occurrences) — almost certainly one boilerplate line from a single migration or decision, not 13 independent debts. Fix the systemic cause once rather than file-by-file. Text: "' TODO: 释放未托管的资源(未托管的对象)并重写终结器". Source code is not a task system: track the cleanup where tasks live. (Every occurrence still counts toward the score and metrics.)
D17 · Explicit Debt · XxxComment · ×1
  • XxxComment Rscript/Library/mzkit_app/src/mzquant/Math.vb:584 — ' example as pos: XXX -> sample1 — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `' REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
D18 · Solution Shape · Solution references 74 projects that do not exist · ×1
  • Solution references 74 projects that do not exist Rscript/Library/mzkit.NET5.slnx — `Rscript/Library/mzkit.NET5.slnx` declares 74 project file(s) that are missing from the tree (`STRaid.vbproj`, `SingleExpression.vbproj`, `HTS_matrix-netcore5.vbproj`, `Fisher.NET5.vbproj`, `gsea-netcore5.vbproj`, `annotation.NET5.vbproj`, +68 more). A solution-level restore or build fails on a dangling reference, so anyone building the solution rather than an individual project is blocked. Delete the stale entry from the solution, or restore the missing project file.
D18 · Solution Shape · Solution references 27 projects that do not exist · ×1
  • Solution references 27 projects that do not exist src/visualize/MsPlot.NET5.sln — `src/visualize/MsPlot.NET5.sln` declares 27 project file(s) that are missing from the tree (`binarydata-netcore5.vbproj`, `datastorage-netcore5.vbproj`, `FeatherFormat.vbproj`, `HDSPack.vbproj`, `SQLite3.vbproj`, `msgpack-netcore5.vbproj`, +21 more). A solution-level restore or build fails on a dangling reference, so anyone building the solution rather than an individual project is blocked. Delete the stale entry from the solution, or restore the missing project file.
D18 · Solution Shape · Solution references 19 projects that do not exist · ×1
  • Solution references 19 projects that do not exist src/assembly/Comprehensive/Comprehensive.sln — `src/assembly/Comprehensive/Comprehensive.sln` declares 19 project file(s) that are missing from the tree (`STRaid.vbproj`, `SingleExpression.vbproj`, `HTS_matrix-netcore5.vbproj`, `CDF.PInvoke.vbproj`, `HDF.PInvoke.Core.csproj`, `binarydata-netcore5.vbproj`, +13 more). A solution-level restore or build fails on a dangling reference, so anyone building the solution rather than an individual project is blocked. Delete the stale entry from the solution, or restore the missing project file.
D18 · Solution Shape · Solution references 10 projects that do not exist · ×1
  • Solution references 10 projects that do not exist src/mzmath/ms2_simulator.sln — `src/mzmath/ms2_simulator.sln` declares 10 project file(s) that are missing from the tree (`biocore-netcore5.vbproj`, `Trinity.NET5.vbproj`, `word2vec.vbproj`, `DataMining.NET5.vbproj`, `graph-netcore5.vbproj`, `Bootstrapping.vbproj`, +4 more). A solution-level restore or build fails on a dangling reference, so anyone building the solution rather than an individual project is blocked. Delete the stale entry from the solution, or restore the missing project file.
D18 · Solution Shape · Solution references 14 projects that do not exist · ×1
  • Solution references 14 projects that do not exist src/mzmath/Mummichog.sln — `src/mzmath/Mummichog.sln` declares 14 project file(s) that are missing from the tree (`HTS_matrix-netcore5.vbproj`, `Fisher.NET5.vbproj`, `biocore-netcore5.vbproj`, `DataMining.NET5.vbproj`, `graph-netcore5.vbproj`, `machine_learning-netcore5.vbproj`, +8 more). A solution-level restore or build fails on a dangling reference, so anyone building the solution rather than an individual project is blocked. Delete the stale entry from the solution, or restore the missing project file.
D18 · Solution Shape · Solution references 11 projects that do not exist · ×1
  • Solution references 11 projects that do not exist src/mzmath/TargetedMetabolomics/TargetedMetabolomics.sln — `src/mzmath/TargetedMetabolomics/TargetedMetabolomics.sln` declares 11 project file(s) that are missing from the tree (`binarydata-netcore5.vbproj`, `datastorage-netcore5.vbproj`, `FeatherFormat.vbproj`, `msgpack-netcore5.vbproj`, `netCDF.vbproj`, `dataframework-netcore5.vbproj`, +5 more). A solution-level restore or build fails on a dangling reference, so anyone building the solution rather than an individual project is blocked. Delete the stale entry from the solution, or restore the missing project file.
D18 · Solution Shape · Solution references 8 projects that do not exist · ×1
  • Solution references 8 projects that do not exist src/mzmath/mz_deco.sln — `src/mzmath/mz_deco.sln` declares 8 project file(s) that are missing from the tree (`BinaryData.vbproj`, `47_dotnet_ms-vb_data.framework.vbproj`, `math-core.vbproj`, `SignalProcessing.vbproj`, `47-dotnet_Microsoft.VisualBasic.vbproj`, `src/assembly/assembly/assembly.vbproj`, +2 more). A solution-level restore or build fails on a dangling reference, so anyone building the solution rather than an individual project is blocked. Delete the stale entry from the solution, or restore the missing project file.
D18 · Solution Shape · Solution references 5 projects that do not exist · ×1
  • Solution references 5 projects that do not exist src/metadb/Massbank.sln — `src/metadb/Massbank.sln` declares 5 project file(s) that are missing from the tree (`Bio.Assembly.vbproj`, `47_dotnet_ms-vb_data.framework.vbproj`, `47-dotnet_Microsoft.VisualBasic.vbproj`, `src/metadb/Chemoinformatics/Chemoinformatics.vbproj`, `src/metadb/Massbank/Massbank.vbproj`). A solution-level restore or build fails on a dangling reference, so anyone building the solution rather than an individual project is blocked. Delete the stale entry from the solution, or restore the missing project file.
D18 · Solution Shape · Solution references 15 projects that do not exist · ×1
  • Solution references 15 projects that do not exist src/metadb/PubChem.NET6.sln — `src/metadb/PubChem.NET6.sln` declares 15 project file(s) that are missing from the tree (`Fisher.NET5.vbproj`, `gsea-netcore5.vbproj`, `biocore-netcore5.vbproj`, `go_owl-netcore5.vbproj`, `obo_foundry-netcore5.vbproj`, `biopax-netcore5.vbproj`, +9 more). A solution-level restore or build fails on a dangling reference, so anyone building the solution rather than an individual project is blocked. Delete the stale entry from the solution, or restore the missing project file.
D18 · Solution Shape · Solution references 6 projects that do not exist · ×1
  • Solution references 6 projects that do not exist src/assembly/LoadR.NET5.sln — `src/assembly/LoadR.NET5.sln` declares 6 project file(s) that are missing from the tree (`Rsharp-netcore5.vbproj`, `RData.NET5.vbproj`, `binarydata-netcore5.vbproj`, `graph-netcore5.vbproj`, `Math.NET5.vbproj`, `Core.vbproj`). A solution-level restore or build fails on a dangling reference, so anyone building the solution rather than an individual project is blocked. Delete the stale entry from the solution, or restore the missing project file.
D18 · Solution Shape · Solution references 18 projects that do not exist · ×1
  • Solution references 18 projects that do not exist src/metadna/metaDNA.sln — `src/metadna/metaDNA.sln` declares 18 project file(s) that are missing from the tree (`Bio.Assembly.vbproj`, `BinaryData.vbproj`, `MessagePack.vbproj`, `47_dotnet_ms-vb_data.framework.vbproj`, `GraphTheory.vbproj`, `Math.Statistics.vbproj`, +12 more). A solution-level restore or build fails on a dangling reference, so anyone building the solution rather than an individual project is blocked. Delete the stale entry from the solution, or restore the missing project file.
D18 · Solution Shape · Solution references 12 projects that do not exist · ×1
  • Solution references 12 projects that do not exist src/metadna/MetaDNA_visual.sln — `src/metadna/MetaDNA_visual.sln` declares 12 project file(s) that are missing from the tree (`Bio.Assembly.vbproj`, `47_dotnet_ms-vb_data.framework.vbproj`, `GraphTheory.vbproj`, `math-core.vbproj`, `47-dotnet_Microsoft.VisualBasic.vbproj`, `Microsoft.VisualBasic.Imaging.vbproj`, +6 more). A solution-level restore or build fails on a dangling reference, so anyone building the solution rather than an individual project is blocked. Delete the stale entry from the solution, or restore the missing project file.
D2 · Cognitive Complexity · LipoqualityRest.getLqUrl (cognitive 356) · ×1
  • LipoqualityRest.getLqUrl (cognitive 356) src/metadb/Lipidomics/LipoqualityRest.vb:93 — LipoqualityRest.getLqUrl has cognitive complexity 356 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · FormulaGenerator.getFormulaResults (cognitive 318) · ×1
  • FormulaGenerator.getFormulaResults (cognitive 318) src/mzmath/MSFinder/FormulaGenerator.vb:326 — FormulaGenerator.getFormulaResults has cognitive complexity 318 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · FragmentAssigner.getValenceCheckedFragmentFormulaList (cognitive 233) · ×1
  • FragmentAssigner.getValenceCheckedFragmentFormulaList (cognitive 233) src/mzmath/MSFinder/FragmentAssigner.vb:602 — FragmentAssigner.getValenceCheckedFragmentFormulaList has cognitive complexity 233 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfCardiolipin (cognitive 219) · ×1
  • LipidMsmsCharacterization.JudgeIfCardiolipin (cognitive 219) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7147 — LipidMsmsCharacterization.JudgeIfCardiolipin has cognitive complexity 219 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · IsotopeCalculator.getNominalIsotopeElementPropertyForTenIsotopomerElement (cognitive 144) · ×1
  • IsotopeCalculator.getNominalIsotopeElementPropertyForTenIsotopomerElement (cognitive 144) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1283 — IsotopeCalculator.getNominalIsotopeElementPropertyForTenIsotopomerElement has cognitive complexity 144 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · SpectrumHandler.EstimateIsotopes (cognitive 141) · ×1
  • SpectrumHandler.EstimateIsotopes (cognitive 141) src/mzmath/MSEngine/SpectrumHandler.vb:259 — SpectrumHandler.EstimateIsotopes has cognitive complexity 141 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · FormulaGenerator.getFormulaSearchResults (cognitive 139) · ×1
  • FormulaGenerator.getFormulaSearchResults (cognitive 139) src/mzmath/MSFinder/FormulaGenerator.vb:825 — FormulaGenerator.getFormulaSearchResults has cognitive complexity 139 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfHexceramideeos (cognitive 119) · ×1
  • LipidMsmsCharacterization.JudgeIfHexceramideeos (cognitive 119) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:10557 — LipidMsmsCharacterization.JudgeIfHexceramideeos has cognitive complexity 119 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · IsotopeCalculator.getNominalIsotopeElementPropertyForNineIsotopomerElement (cognitive 116) · ×1
  • IsotopeCalculator.getNominalIsotopeElementPropertyForNineIsotopomerElement (cognitive 116) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1504 — IsotopeCalculator.getNominalIsotopeElementPropertyForNineIsotopomerElement has cognitive complexity 116 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfHexceramideo (cognitive 111) · ×1
  • LipidMsmsCharacterization.JudgeIfHexceramideo (cognitive 111) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:8546 — LipidMsmsCharacterization.JudgeIfHexceramideo has cognitive complexity 111 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfCeramideeos (cognitive 109) · ×1
  • LipidMsmsCharacterization.JudgeIfCeramideeos (cognitive 109) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:10243 — LipidMsmsCharacterization.JudgeIfCeramideeos has cognitive complexity 109 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfCeramidens (cognitive 103) · ×1
  • LipidMsmsCharacterization.JudgeIfCeramidens (cognitive 103) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7943 — LipidMsmsCharacterization.JudgeIfCeramidens has cognitive complexity 103 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfCeramidensD7) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfCeramidensD7 (cognitive 103) · ×1
  • LipidMsmsCharacterization.JudgeIfCeramidensD7 (cognitive 103) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:16340 — LipidMsmsCharacterization.JudgeIfCeramidensD7 has cognitive complexity 103 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfCeramidens) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfCeramideo (cognitive 102) · ×1
  • LipidMsmsCharacterization.JudgeIfCeramideo (cognitive 102) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:8882 — LipidMsmsCharacterization.JudgeIfCeramideo has cognitive complexity 102 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · centWave.DetectByCentWave (cognitive 101) · ×1
  • centWave.DetectByCentWave (cognitive 101) src/mzmath/mz_deco/Signals/centWave/centWave.vb:26 — centWave.DetectByCentWave has cognitive complexity 101 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MathHelpers.NIPALSWithMissing (cognitive 100) · ×1
  • MathHelpers.NIPALSWithMissing (cognitive 100) src/mzmath/mz_deco/Preprocessing/MathHelpers.vb:909 — MathHelpers.NIPALSWithMissing has cognitive complexity 100 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · IsotopeCalculator.getAllIsotopeElementPropertyForTenIsotopomerElement (cognitive 99) · ×1
  • IsotopeCalculator.getAllIsotopeElementPropertyForTenIsotopomerElement (cognitive 99) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:384 — IsotopeCalculator.getAllIsotopeElementPropertyForTenIsotopomerElement has cognitive complexity 99 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MathHelpers.PCA (cognitive 99) · ×1
  • MathHelpers.PCA (cognitive 99) src/mzmath/mz_deco/Preprocessing/MathHelpers.vb:755 — MathHelpers.PCA has cognitive complexity 99 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfEthermgdg (cognitive 96) · ×1
  • LipidMsmsCharacterization.JudgeIfEthermgdg (cognitive 96) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5163 — LipidMsmsCharacterization.JudgeIfEthermgdg has cognitive complexity 96 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · GolotvinWilliamsBaselineCorrector.calculateBaselineModel (cognitive 94) · ×1
  • GolotvinWilliamsBaselineCorrector.calculateBaselineModel (cognitive 94) src/assembly/NMRFidTool/Math/baseline/GolotvinWilliamsBaselineCorrector.vb:114 — GolotvinWilliamsBaselineCorrector.calculateBaselineModel has cognitive complexity 94 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfAcylsm (cognitive 94) · ×1
  • LipidMsmsCharacterization.JudgeIfAcylsm (cognitive 94) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:10855 — LipidMsmsCharacterization.JudgeIfAcylsm has cognitive complexity 94 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfEtherdgdg (cognitive 92) · ×1
  • LipidMsmsCharacterization.JudgeIfEtherdgdg (cognitive 92) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5442 — LipidMsmsCharacterization.JudgeIfEtherdgdg has cognitive complexity 92 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · IsotopeCalculator.getNominalIsotopeElementPropertyForEightIsotopomerElement (cognitive 91) · ×1
  • IsotopeCalculator.getNominalIsotopeElementPropertyForEightIsotopomerElement (cognitive 91) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1701 — IsotopeCalculator.getNominalIsotopeElementPropertyForEightIsotopomerElement has cognitive complexity 91 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfTriacylglycerol (cognitive 89) · ×1
  • LipidMsmsCharacterization.JudgeIfTriacylglycerol (cognitive 89) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3126 — LipidMsmsCharacterization.JudgeIfTriacylglycerol has cognitive complexity 89 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfPhosphatidylcholineD5 (cognitive 89) · ×1
  • LipidMsmsCharacterization.JudgeIfPhosphatidylcholineD5 (cognitive 89) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15067 — LipidMsmsCharacterization.JudgeIfPhosphatidylcholineD5 has cognitive complexity 89 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfHexceramidens (cognitive 88) · ×1
  • LipidMsmsCharacterization.JudgeIfHexceramidens (cognitive 88) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:8374 — LipidMsmsCharacterization.JudgeIfHexceramidens has cognitive complexity 88 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfAcylhexcer (cognitive 88) · ×1
  • LipidMsmsCharacterization.JudgeIfAcylhexcer (cognitive 88) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11064 — LipidMsmsCharacterization.JudgeIfAcylhexcer has cognitive complexity 88 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfTriacylglycerolD5 (cognitive 88) · ×1
  • LipidMsmsCharacterization.JudgeIfTriacylglycerolD5 (cognitive 88) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:16086 — LipidMsmsCharacterization.JudgeIfTriacylglycerolD5 has cognitive complexity 88 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfHemiismonoacylglycerophosphate (cognitive 87) · ×1
  • LipidMsmsCharacterization.JudgeIfHemiismonoacylglycerophosphate (cognitive 87) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7003 — LipidMsmsCharacterization.JudgeIfHemiismonoacylglycerophosphate has cognitive complexity 87 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · PeakAnalyzer.MultiPeakFit (cognitive 87) · ×1
  • PeakAnalyzer.MultiPeakFit (cognitive 87) src/assembly/RamanSpectroscopy/RamanDataProcessor.vb:1568 — PeakAnalyzer.MultiPeakFit has cognitive complexity 87 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · Composition.FindCompositions (cognitive 85) · ×1
  • Composition.FindCompositions (cognitive 85) src/mzmath/Oligonucleotide_MS/OligonucleotideComposition/Oligonucleotide_Composition_from_Mass_Calculator_v2.vb:125 — Composition.FindCompositions has cognitive complexity 85 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfCeramidends (cognitive 84) · ×1
  • LipidMsmsCharacterization.JudgeIfCeramidends (cognitive 84) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:8193 — LipidMsmsCharacterization.JudgeIfCeramidends has cognitive complexity 84 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfHexceramideap (cognitive 83) · ×1
  • LipidMsmsCharacterization.JudgeIfHexceramideap (cognitive 83) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:9518 — LipidMsmsCharacterization.JudgeIfHexceramideap has cognitive complexity 83 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfAshexcer (cognitive 83) · ×1
  • LipidMsmsCharacterization.JudgeIfAshexcer (cognitive 83) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11270 — LipidMsmsCharacterization.JudgeIfAshexcer has cognitive complexity 83 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfBetaMethylPhosphatidylcholine (cognitive 82) · ×1
  • LipidMsmsCharacterization.JudgeIfBetaMethylPhosphatidylcholine (cognitive 82) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:16542 — LipidMsmsCharacterization.JudgeIfBetaMethylPhosphatidylcholine has cognitive complexity 82 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfPhosphatidylcholine (cognitive 80) · ×1
  • LipidMsmsCharacterization.JudgeIfPhosphatidylcholine (cognitive 80) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:1789 — LipidMsmsCharacterization.JudgeIfPhosphatidylcholine has cognitive complexity 80 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfCeramideap (cognitive 80) · ×1
  • LipidMsmsCharacterization.JudgeIfCeramideap (cognitive 80) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:9355 — LipidMsmsCharacterization.JudgeIfCeramideap has cognitive complexity 80 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · IsotopeCalculator.getAllIsotopeElementPropertyForNineIsotopomerElement (cognitive 80) · ×1
  • IsotopeCalculator.getAllIsotopeElementPropertyForNineIsotopomerElement (cognitive 80) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:552 — IsotopeCalculator.getAllIsotopeElementPropertyForNineIsotopomerElement has cognitive complexity 80 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · DensityGroup.DensityGroupAlignment (cognitive 79) · ×1
  • DensityGroup.DensityGroupAlignment (cognitive 79) src/mzmath/mz_deco/PeakAlignment/Algorithm/DensityGroup.vb:24 — DensityGroup.DensityGroupAlignment has cognitive complexity 79 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfEtheroxpc (cognitive 78) · ×1
  • LipidMsmsCharacterization.JudgeIfEtheroxpc (cognitive 78) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3995 — LipidMsmsCharacterization.JudgeIfEtheroxpc has cognitive complexity 78 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfSulfonolipid (cognitive 78) · ×1
  • LipidMsmsCharacterization.JudgeIfSulfonolipid (cognitive 78) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13210 — LipidMsmsCharacterization.JudgeIfSulfonolipid has cognitive complexity 78 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · BatchCorrection.CorrectComBat (cognitive 78) · ×1
  • BatchCorrection.CorrectComBat (cognitive 78) src/mzmath/mz_deco/Preprocessing/BatchCorrection.vb:401 — BatchCorrection.CorrectComBat has cognitive complexity 78 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidEieioMsmsCharacterization.JudgeIfPhosphatidylcholine (cognitive 77) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfPhosphatidylcholine (cognitive 77) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:230 — LipidEieioMsmsCharacterization.JudgeIfPhosphatidylcholine has cognitive complexity 77 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidEieioMsmsCharacterization.JudgeIfPhosphatidylcholineD5) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidEieioMsmsCharacterization.JudgeIfPhosphatidylcholineD5 (cognitive 77) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfPhosphatidylcholineD5 (cognitive 77) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:2052 — LipidEieioMsmsCharacterization.JudgeIfPhosphatidylcholineD5 has cognitive complexity 77 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidEieioMsmsCharacterization.JudgeIfPhosphatidylcholine) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfEthertag (cognitive 77) · ×1
  • LipidMsmsCharacterization.JudgeIfEthertag (cognitive 77) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5842 — LipidMsmsCharacterization.JudgeIfEthertag has cognitive complexity 77 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfCeramidenp (cognitive 75) · ×1
  • LipidMsmsCharacterization.JudgeIfCeramidenp (cognitive 75) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:10073 — LipidMsmsCharacterization.JudgeIfCeramidenp has cognitive complexity 75 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MS_Peak_ID.MakeTheoryList (cognitive 75) · ×1
  • MS_Peak_ID.MakeTheoryList (cognitive 75) src/mzmath/Oligonucleotide_MS/MS_Peak/Oligonucleotide_MS_Peak_ID_Given_Sequence_v8.vb:121 — MS_Peak_ID.MakeTheoryList has cognitive complexity 75 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfSphingomyelin (cognitive 72) · ×1
  • LipidMsmsCharacterization.JudgeIfSphingomyelin (cognitive 72) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:2924 — LipidMsmsCharacterization.JudgeIfSphingomyelin has cognitive complexity 72 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfSphingomyelinD9) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfSphingomyelinD9 (cognitive 72) · ×1
  • LipidMsmsCharacterization.JudgeIfSphingomyelinD9 (cognitive 72) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:16232 — LipidMsmsCharacterization.JudgeIfSphingomyelinD9 has cognitive complexity 72 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfSphingomyelin) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidEieioMsmsCharacterization.JudgeIfPhosphatidylethanolamine (cognitive 71) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfPhosphatidylethanolamine (cognitive 71) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:414 — LipidEieioMsmsCharacterization.JudgeIfPhosphatidylethanolamine has cognitive complexity 71 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · DimensionalityReducer.PCA (cognitive 71) · ×1
  • DimensionalityReducer.PCA (cognitive 71) src/assembly/RamanSpectroscopy/RamanDataProcessor.vb:1899 — DimensionalityReducer.PCA has cognitive complexity 71 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · Scanner.WalkChar (cognitive 70) · ×1
  • Scanner.WalkChar (cognitive 70) src/metadb/SMILES/Language/Scanner.vb:196 — Scanner.WalkChar has cognitive complexity 70 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · AdductIonParser.GetOrganicAdductFormulaAndMass (cognitive 70) · ×1
  • AdductIonParser.GetOrganicAdductFormulaAndMass (cognitive 70) src/mzmath/ms2_math-core/Ms1/PrecursorType/AdductIonParser.vb:317 — AdductIonParser.GetOrganicAdductFormulaAndMass has cognitive complexity 70 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfDgdg (cognitive 69) · ×1
  • LipidMsmsCharacterization.JudgeIfDgdg (cognitive 69) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5016 — LipidMsmsCharacterization.JudgeIfDgdg has cognitive complexity 69 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · IsotopeCalculator.getNominalIsotopeElementPropertyForSevenIsotopomerElement (cognitive 69) · ×1
  • IsotopeCalculator.getNominalIsotopeElementPropertyForSevenIsotopomerElement (cognitive 69) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1876 — IsotopeCalculator.getNominalIsotopeElementPropertyForSevenIsotopomerElement has cognitive complexity 69 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidEieioMsmsCharacterization.JudgeIfPhosphatidylinositol (cognitive 68) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfPhosphatidylinositol (cognitive 68) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:892 — LipidEieioMsmsCharacterization.JudgeIfPhosphatidylinositol has cognitive complexity 68 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidEieioMsmsCharacterization.JudgeIfPhosphatidylinositolD5) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidEieioMsmsCharacterization.JudgeIfPhosphatidylinositolD5 (cognitive 68) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfPhosphatidylinositolD5 (cognitive 68) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:2659 — LipidEieioMsmsCharacterization.JudgeIfPhosphatidylinositolD5 has cognitive complexity 68 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidEieioMsmsCharacterization.JudgeIfPhosphatidylinositol) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfAcylglcadg (cognitive 68) · ×1
  • LipidMsmsCharacterization.JudgeIfAcylglcadg (cognitive 68) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6468 — LipidMsmsCharacterization.JudgeIfAcylglcadg has cognitive complexity 68 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfFahfaTriacylglycerol (cognitive 68) · ×1
  • LipidMsmsCharacterization.JudgeIfFahfaTriacylglycerol (cognitive 68) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14651 — LipidMsmsCharacterization.JudgeIfFahfaTriacylglycerol has cognitive complexity 68 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MissingValueImputation.ImputePCA (cognitive 68) · ×1
  • MissingValueImputation.ImputePCA (cognitive 68) src/mzmath/mz_deco/Preprocessing/MissingValueImputation.vb:422 — MissingValueImputation.ImputePCA has cognitive complexity 68 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfFahfamidegly (cognitive 67) · ×1
  • LipidMsmsCharacterization.JudgeIfFahfamidegly (cognitive 67) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12961 — LipidMsmsCharacterization.JudgeIfFahfamidegly has cognitive complexity 67 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · PeakAssign.PlotInternal (cognitive 66) · ×1
  • PeakAssign.PlotInternal (cognitive 66) src/visualize/plot/PeakAssign.vb:185 — PeakAssign.PlotInternal has cognitive complexity 66 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfMgdg (cognitive 66) · ×1
  • LipidMsmsCharacterization.JudgeIfMgdg (cognitive 66) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4873 — LipidMsmsCharacterization.JudgeIfMgdg has cognitive complexity 66 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfHexceramidends (cognitive 66) · ×1
  • LipidMsmsCharacterization.JudgeIfHexceramidends (cognitive 66) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:8718 — LipidMsmsCharacterization.JudgeIfHexceramidends has cognitive complexity 66 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MS_Peak_ID.GetMatches (cognitive 66) · ×1
  • MS_Peak_ID.GetMatches (cognitive 66) src/mzmath/Oligonucleotide_MS/MS_Peak/Oligonucleotide_MS_Peak_ID_Given_Sequence_v8.vb:455 — MS_Peak_ID.GetMatches has cognitive complexity 66 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MsScanMatching.GetWeightedDotProduct (cognitive 65) · ×1
  • MsScanMatching.GetWeightedDotProduct (cognitive 65) src/mzmath/MSEngine/Search/MsScanMatching.vb:902 — MsScanMatching.GetWeightedDotProduct has cognitive complexity 65 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidEieioMsmsCharacterization.JudgeIfPhosphatidylethanolamineD5 (cognitive 64) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfPhosphatidylethanolamineD5 (cognitive 64) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:2235 — LipidEieioMsmsCharacterization.JudgeIfPhosphatidylethanolamineD5 has cognitive complexity 64 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfEtheroxpe (cognitive 64) · ×1
  • LipidMsmsCharacterization.JudgeIfEtheroxpe (cognitive 64) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4094 — LipidMsmsCharacterization.JudgeIfEtheroxpe has cognitive complexity 64 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfDgts (cognitive 64) · ×1
  • LipidMsmsCharacterization.JudgeIfDgts (cognitive 64) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6007 — LipidMsmsCharacterization.JudgeIfDgts has cognitive complexity 64 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · IsotopeCalculator.getAllIsotopeElementPropertyForEightIsotopomerElement (cognitive 63) · ×1
  • IsotopeCalculator.getAllIsotopeElementPropertyForEightIsotopomerElement (cognitive 63) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:702 — IsotopeCalculator.getAllIsotopeElementPropertyForEightIsotopomerElement has cognitive complexity 63 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfOxpe (cognitive 61) · ×1
  • LipidMsmsCharacterization.JudgeIfOxpe (cognitive 61) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4410 — LipidMsmsCharacterization.JudgeIfOxpe has cognitive complexity 61 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfCeramideas (cognitive 61) · ×1
  • LipidMsmsCharacterization.JudgeIfCeramideas (cognitive 61) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:9692 — LipidMsmsCharacterization.JudgeIfCeramideas has cognitive complexity 61 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfShexcer (cognitive 61) · ×1
  • LipidMsmsCharacterization.JudgeIfShexcer (cognitive 61) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11440 — LipidMsmsCharacterization.JudgeIfShexcer has cognitive complexity 61 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidEieioMsmsCharacterization.JudgeIfPhosphatidylserine (cognitive 60) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfPhosphatidylserine (cognitive 60) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:726 — LipidEieioMsmsCharacterization.JudgeIfPhosphatidylserine has cognitive complexity 60 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidEieioMsmsCharacterization.JudgeIfPhosphatidylserineD5) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidEieioMsmsCharacterization.JudgeIfPhosphatidylserineD5 (cognitive 60) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfPhosphatidylserineD5 (cognitive 60) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:2492 — LipidEieioMsmsCharacterization.JudgeIfPhosphatidylserineD5 has cognitive complexity 60 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidEieioMsmsCharacterization.JudgeIfPhosphatidylserine) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfPhosphatidylethanolamine (cognitive 60) · ×1
  • LipidMsmsCharacterization.JudgeIfPhosphatidylethanolamine (cognitive 60) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:1989 — LipidMsmsCharacterization.JudgeIfPhosphatidylethanolamine has cognitive complexity 60 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfPhosphatidylethanolamineD5) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfLysope (cognitive 60) · ×1
  • LipidMsmsCharacterization.JudgeIfLysope (cognitive 60) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3638 — LipidMsmsCharacterization.JudgeIfLysope has cognitive complexity 60 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfEtherpc (cognitive 60) · ×1
  • LipidMsmsCharacterization.JudgeIfEtherpc (cognitive 60) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3737 — LipidMsmsCharacterization.JudgeIfEtherpc has cognitive complexity 60 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfPhosphatidylethanolamineD5 (cognitive 60) · ×1
  • LipidMsmsCharacterization.JudgeIfPhosphatidylethanolamineD5 (cognitive 60) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15234 — LipidMsmsCharacterization.JudgeIfPhosphatidylethanolamineD5 has cognitive complexity 60 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfPhosphatidylethanolamine) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · PeakAnalyzer.SinglePeakFit (cognitive 60) · ×1
  • PeakAnalyzer.SinglePeakFit (cognitive 60) src/assembly/RamanSpectroscopy/RamanDataProcessor.vb:1412 — PeakAnalyzer.SinglePeakFit has cognitive complexity 60 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfLysopc (cognitive 58) · ×1
  • LipidMsmsCharacterization.JudgeIfLysopc (cognitive 58) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3535 — LipidMsmsCharacterization.JudgeIfLysopc has cognitive complexity 58 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MsScanMatching.GetReverseDotProduct (cognitive 58) · ×1
  • MsScanMatching.GetReverseDotProduct (cognitive 58) src/mzmath/MSEngine/Search/MsScanMatching.vb:757 — MsScanMatching.GetReverseDotProduct has cognitive complexity 58 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfEtherpe (cognitive 57) · ×1
  • LipidMsmsCharacterization.JudgeIfEtherpe (cognitive 57) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3857 — LipidMsmsCharacterization.JudgeIfEtherpe has cognitive complexity 57 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · FormulaCalculateUtility.GetFormulaString (cognitive 57) · ×1
  • FormulaCalculateUtility.GetFormulaString (cognitive 57) src/metadb/Chemoinformatics/Formula/FormulaCalculateUtility.vb:389 — FormulaCalculateUtility.GetFormulaString has cognitive complexity 57 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · SequenceToSpec.GetSpectrumPeaksByHCD (cognitive 56) · ×1
  • SequenceToSpec.GetSpectrumPeaksByHCD (cognitive 56) src/mzmath/MSEngine/Proteomics/SequenceToSpec.vb:118 — SequenceToSpec.GetSpectrumPeaksByHCD has cognitive complexity 56 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · PeakDetector.DetectByFirstDerivative (cognitive 56) · ×1
  • PeakDetector.DetectByFirstDerivative (cognitive 56) src/mzmath/mz_deco/Signals/PeakFinding/PeakDetector.vb:357 — PeakDetector.DetectByFirstDerivative has cognitive complexity 56 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · XcaliburRawFileIO.GetScanInfoInternal (cognitive 55) · ×1
  • XcaliburRawFileIO.GetScanInfoInternal (cognitive 55) src/assembly/ThermoRawFileReader/XcaliburRawFileIO.vb:1192 — XcaliburRawFileIO.GetScanInfoInternal has cognitive complexity 55 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfCeramideads (cognitive 55) · ×1
  • LipidMsmsCharacterization.JudgeIfCeramideads (cognitive 55) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:9787 — LipidMsmsCharacterization.JudgeIfCeramideads has cognitive complexity 55 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · FormulaScanner.ScanFormula (cognitive 55) · ×1
  • FormulaScanner.ScanFormula (cognitive 55) src/metadb/Chemoinformatics/Formula/FormulaScanner.vb:376 — FormulaScanner.ScanFormula has cognitive complexity 55 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MetaDbXref.searchTable (cognitive 54) · ×1
  • MetaDbXref.searchTable (cognitive 54) Rscript/Library/mzkit_app/src/mzkit/annotations/MetaDbXref.vb:898 — MetaDbXref.searchTable has cognitive complexity 54 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfOxpc (cognitive 54) · ×1
  • LipidMsmsCharacterization.JudgeIfOxpc (cognitive 54) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4311 — LipidMsmsCharacterization.JudgeIfOxpc has cognitive complexity 54 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfLysopcD5 (cognitive 54) · ×1
  • LipidMsmsCharacterization.JudgeIfLysopcD5 (cognitive 54) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15717 — LipidMsmsCharacterization.JudgeIfLysopcD5 has cognitive complexity 54 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfAcylcerbds (cognitive 53) · ×1
  • LipidMsmsCharacterization.JudgeIfAcylcerbds (cognitive 53) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:10985 — LipidMsmsCharacterization.JudgeIfAcylcerbds has cognitive complexity 53 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · FormulaStringParcer.setElementNumbers (cognitive 53) · ×1
  • FormulaStringParcer.setElementNumbers (cognitive 53) src/mzmath/MSFinder/FormulaStringParcer.vb:474 — FormulaStringParcer.setElementNumbers has cognitive complexity 53 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfEtherDAG (cognitive 52) · ×1
  • LipidMsmsCharacterization.JudgeIfEtherDAG (cognitive 52) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5392 — LipidMsmsCharacterization.JudgeIfEtherDAG has cognitive complexity 52 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfLysocardiolipin (cognitive 52) · ×1
  • LipidMsmsCharacterization.JudgeIfLysocardiolipin (cognitive 52) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7504 — LipidMsmsCharacterization.JudgeIfLysocardiolipin has cognitive complexity 52 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfCeramideeods (cognitive 52) · ×1
  • LipidMsmsCharacterization.JudgeIfCeramideeods (cognitive 52) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:10458 — LipidMsmsCharacterization.JudgeIfCeramideeods has cognitive complexity 52 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfLysopeD5 (cognitive 52) · ×1
  • LipidMsmsCharacterization.JudgeIfLysopeD5 (cognitive 52) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15809 — LipidMsmsCharacterization.JudgeIfLysopeD5 has cognitive complexity 52 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfFahfa (cognitive 51) · ×1
  • LipidMsmsCharacterization.JudgeIfFahfa (cognitive 51) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7814 — LipidMsmsCharacterization.JudgeIfFahfa has cognitive complexity 51 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfNacylphosphatidylserine (cognitive 50) · ×1
  • LipidMsmsCharacterization.JudgeIfNacylphosphatidylserine (cognitive 50) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:2700 — LipidMsmsCharacterization.JudgeIfNacylphosphatidylserine has cognitive complexity 50 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfCeramidebs (cognitive 50) · ×1
  • LipidMsmsCharacterization.JudgeIfCeramidebs (cognitive 50) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:9888 — LipidMsmsCharacterization.JudgeIfCeramidebs has cognitive complexity 50 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · IsotopeCalculator.getNominalIsotopeElementPropertyForSixIsotopomerElement (cognitive 50) · ×1
  • IsotopeCalculator.getNominalIsotopeElementPropertyForSixIsotopomerElement (cognitive 50) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:2029 — IsotopeCalculator.getNominalIsotopeElementPropertyForSixIsotopomerElement has cognitive complexity 50 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MetaDbXref.cbindMeta (cognitive 49) · ×1
  • MetaDbXref.cbindMeta (cognitive 49) Rscript/Library/mzkit_app/src/mzkit/annotations/MetaDbXref.vb:1049 — MetaDbXref.cbindMeta has cognitive complexity 49 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidEieioMsmsCharacterization.JudgeIfSphingomyelin (cognitive 49) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfSphingomyelin (cognitive 49) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1326 — LipidEieioMsmsCharacterization.JudgeIfSphingomyelin has cognitive complexity 49 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidEieioMsmsCharacterization.JudgeIfSphingomyelinD9) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidEieioMsmsCharacterization.JudgeIfSphingomyelinD9 (cognitive 49) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfSphingomyelinD9 (cognitive 49) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:3309 — LipidEieioMsmsCharacterization.JudgeIfSphingomyelinD9 has cognitive complexity 49 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidEieioMsmsCharacterization.JudgeIfSphingomyelin) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfOxTriacylglycerol (cognitive 49) · ×1
  • LipidMsmsCharacterization.JudgeIfOxTriacylglycerol (cognitive 49) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14570 — LipidMsmsCharacterization.JudgeIfOxTriacylglycerol has cognitive complexity 49 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · FormulaScanner.Convert2FormulaObjV2 (cognitive 49) · ×1
  • FormulaScanner.Convert2FormulaObjV2 (cognitive 49) src/metadb/Chemoinformatics/Formula/FormulaScanner.vb:96 — FormulaScanner.Convert2FormulaObjV2 has cognitive complexity 49 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfPicermide (cognitive 48) · ×1
  • LipidMsmsCharacterization.JudgeIfPicermide (cognitive 48) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12459 — LipidMsmsCharacterization.JudgeIfPicermide has cognitive complexity 48 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · IsotopeCalculator.getAllIsotopeElementPropertyForSevenIsotopomerElement (cognitive 48) · ×1
  • IsotopeCalculator.getAllIsotopeElementPropertyForSevenIsotopomerElement (cognitive 48) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:833 — IsotopeCalculator.getAllIsotopeElementPropertyForSevenIsotopomerElement has cognitive complexity 48 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · Math.RunMaxLFQ (cognitive 48) · ×1
  • Math.RunMaxLFQ (cognitive 48) src/mzmath/mz_deco/MaxLFQ/Math.vb:9 — Math.RunMaxLFQ has cognitive complexity 48 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidEieioMsmsCharacterization.JudgeIfEtherpe (cognitive 47) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfEtherpe (cognitive 47) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1497 — LipidEieioMsmsCharacterization.JudgeIfEtherpe has cognitive complexity 47 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfPhosphatidylserine (cognitive 47) · ×1
  • LipidMsmsCharacterization.JudgeIfPhosphatidylserine (cognitive 47) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:2151 — LipidMsmsCharacterization.JudgeIfPhosphatidylserine has cognitive complexity 47 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfPhosphatidylserineD5) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfCeramidebds (cognitive 47) · ×1
  • LipidMsmsCharacterization.JudgeIfCeramidebds (cognitive 47) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:9970 — LipidMsmsCharacterization.JudgeIfCeramidebds has cognitive complexity 47 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfFahfamideglyser (cognitive 47) · ×1
  • LipidMsmsCharacterization.JudgeIfFahfamideglyser (cognitive 47) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13084 — LipidMsmsCharacterization.JudgeIfFahfamideglyser has cognitive complexity 47 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfPhosphatidylserineD5 (cognitive 47) · ×1
  • LipidMsmsCharacterization.JudgeIfPhosphatidylserineD5 (cognitive 47) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15379 — LipidMsmsCharacterization.JudgeIfPhosphatidylserineD5 has cognitive complexity 47 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfPhosphatidylserine) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · PeptideCalc.Sequence2FastPeptidesByVariableModifications (cognitive 47) · ×1
  • PeptideCalc.Sequence2FastPeptidesByVariableModifications (cognitive 47) src/mzmath/MSEngine/Proteomics/PeptideCalc.vb:255 — PeptideCalc.Sequence2FastPeptidesByVariableModifications has cognitive complexity 47 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidEieioMsmsCharacterization.JudgeIfLysopc (cognitive 46) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfLysopc (cognitive 46) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1067 — LipidEieioMsmsCharacterization.JudgeIfLysopc has cognitive complexity 46 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfCeramideos (cognitive 46) · ×1
  • LipidMsmsCharacterization.JudgeIfCeramideos (cognitive 46) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:10774 — LipidMsmsCharacterization.JudgeIfCeramideos has cognitive complexity 46 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfEtherSmgdg (cognitive 46) · ×1
  • LipidMsmsCharacterization.JudgeIfEtherSmgdg (cognitive 46) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14140 — LipidMsmsCharacterization.JudgeIfEtherSmgdg has cognitive complexity 46 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · FormulaCalculateUtility.GetFormulaString (cognitive 46) · ×1
  • FormulaCalculateUtility.GetFormulaString (cognitive 46) src/metadb/Chemoinformatics/Formula/FormulaCalculateUtility.vb:291 — FormulaCalculateUtility.GetFormulaString has cognitive complexity 46 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · FormulaStringParcer.IsOrganicFormula (cognitive 46) · ×1
  • FormulaStringParcer.IsOrganicFormula (cognitive 46) src/mzmath/MSFinder/FormulaStringParcer.vb:116 — FormulaStringParcer.IsOrganicFormula has cognitive complexity 46 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · PeakDetector.DetectByMatchedFilter (cognitive 46) · ×1
  • PeakDetector.DetectByMatchedFilter (cognitive 46) src/mzmath/mz_deco/Signals/PeakFinding/PeakDetector.vb:194 — PeakDetector.DetectByMatchedFilter has cognitive complexity 46 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfPhosphatidylglycerol (cognitive 45) · ×1
  • LipidMsmsCharacterization.JudgeIfPhosphatidylglycerol (cognitive 45) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:2402 — LipidMsmsCharacterization.JudgeIfPhosphatidylglycerol has cognitive complexity 45 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfPhosphatidylglycerolD5) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfHexhexceramidens (cognitive 45) · ×1
  • LipidMsmsCharacterization.JudgeIfHexhexceramidens (cognitive 45) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:9121 — LipidMsmsCharacterization.JudgeIfHexhexceramidens has cognitive complexity 45 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfPhosphatidylglycerolD5 (cognitive 45) · ×1
  • LipidMsmsCharacterization.JudgeIfPhosphatidylglycerolD5 (cognitive 45) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15501 — LipidMsmsCharacterization.JudgeIfPhosphatidylglycerolD5 has cognitive complexity 45 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfPhosphatidylglycerol) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LOESS.LOESSAlignment (cognitive 45) · ×1
  • LOESS.LOESSAlignment (cognitive 45) src/mzmath/mz_deco/PeakAlignment/Algorithm/LOESS.vb:25 — LOESS.LOESSAlignment has cognitive complexity 45 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · PeakDetector.DetectByLocalMaximum (cognitive 45) · ×1
  • PeakDetector.DetectByLocalMaximum (cognitive 45) src/mzmath/mz_deco/Signals/PeakFinding/PeakDetector.vb:55 — PeakDetector.DetectByLocalMaximum has cognitive complexity 45 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · XcaliburRawFileIO.ExtractParentIonMZFromFilterText (cognitive 44) · ×1
  • XcaliburRawFileIO.ExtractParentIonMZFromFilterText (cognitive 44) src/assembly/ThermoRawFileReader/XcaliburRawFileIO.vb:597 — XcaliburRawFileIO.ExtractParentIonMZFromFilterText has cognitive complexity 44 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidEieioMsmsCharacterization.JudgeIfLysopcD5 (cognitive 44) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfLysopcD5 (cognitive 44) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:2833 — LipidEieioMsmsCharacterization.JudgeIfLysopcD5 has cognitive complexity 44 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfOxpg (cognitive 44) · ×1
  • LipidMsmsCharacterization.JudgeIfOxpg (cognitive 44) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4527 — LipidMsmsCharacterization.JudgeIfOxpg has cognitive complexity 44 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfGlcadg (cognitive 44) · ×1
  • LipidMsmsCharacterization.JudgeIfGlcadg (cognitive 44) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6371 — LipidMsmsCharacterization.JudgeIfGlcadg has cognitive complexity 44 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfFahfaDMED (cognitive 44) · ×1
  • LipidMsmsCharacterization.JudgeIfFahfaDMED (cognitive 44) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7887 — LipidMsmsCharacterization.JudgeIfFahfaDMED has cognitive complexity 44 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfMipc (cognitive 44) · ×1
  • LipidMsmsCharacterization.JudgeIfMipc (cognitive 44) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14477 — LipidMsmsCharacterization.JudgeIfMipc has cognitive complexity 44 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · FormulaStringParcer.setElementNumbers (cognitive 44) · ×1
  • FormulaStringParcer.setElementNumbers (cognitive 44) src/mzmath/MSFinder/FormulaStringParcer.vb:351 — FormulaStringParcer.setElementNumbers has cognitive complexity 44 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · TICplot.RunPlot (cognitive 42) · ×1
  • TICplot.RunPlot (cognitive 42) src/visualize/plot/ChromatogramPlot/TICplot.vb:200 — TICplot.RunPlot has cognitive complexity 42 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · GlycosylNameSolver.SplitByTopLevelStack (cognitive 42) · ×1
  • GlycosylNameSolver.SplitByTopLevelStack (cognitive 42) src/metadb/Chemoinformatics/NaturalProduct/GlycosylNameSolver.vb:280 — GlycosylNameSolver.SplitByTopLevelStack has cognitive complexity 42 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · Massbank.lipidnameMapping (cognitive 41) · ×1
  • Massbank.lipidnameMapping (cognitive 41) Rscript/Library/mzkit_app/src/mzkit/annotations/Massbank.vb:883 — Massbank.lipidnameMapping has cognitive complexity 41 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidEieioMsmsCharacterization.JudgeIfDag (cognitive 41) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfDag (cognitive 41) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1840 — LipidEieioMsmsCharacterization.JudgeIfDag has cognitive complexity 41 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfOxpi (cognitive 41) · ×1
  • LipidMsmsCharacterization.JudgeIfOxpi (cognitive 41) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4648 — LipidMsmsCharacterization.JudgeIfOxpi has cognitive complexity 41 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfPmeoh (cognitive 41) · ×1
  • LipidMsmsCharacterization.JudgeIfPmeoh (cognitive 41) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6806 — LipidMsmsCharacterization.JudgeIfPmeoh has cognitive complexity 41 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfHexhexhexceramidens (cognitive 41) · ×1
  • LipidMsmsCharacterization.JudgeIfHexhexhexceramidens (cognitive 41) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:9239 — LipidMsmsCharacterization.JudgeIfHexhexhexceramidens has cognitive complexity 41 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfMonoMethylPE (cognitive 41) · ×1
  • LipidMsmsCharacterization.JudgeIfMonoMethylPE (cognitive 41) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14275 — LipidMsmsCharacterization.JudgeIfMonoMethylPE has cognitive complexity 41 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfDiMethylPE) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfDiMethylPE (cognitive 41) · ×1
  • LipidMsmsCharacterization.JudgeIfDiMethylPE (cognitive 41) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14376 — LipidMsmsCharacterization.JudgeIfDiMethylPE has cognitive complexity 41 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfMonoMethylPE) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · FormulaCalculateUtility.GetFormulaString (cognitive 41) · ×1
  • FormulaCalculateUtility.GetFormulaString (cognitive 41) src/metadb/Chemoinformatics/Formula/FormulaCalculateUtility.vb:414 — FormulaCalculateUtility.GetFormulaString has cognitive complexity 41 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · FragmentAssigner.isotopicPeakAssignmnet (cognitive 41) · ×1
  • FragmentAssigner.isotopicPeakAssignmnet (cognitive 41) src/mzmath/MSFinder/FragmentAssigner.vb:701 — FragmentAssigner.isotopicPeakAssignmnet has cognitive complexity 41 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MissingValueImputation.ImputeKNN (cognitive 41) · ×1
  • MissingValueImputation.ImputeKNN (cognitive 41) src/mzmath/mz_deco/Preprocessing/MissingValueImputation.vb:310 — MissingValueImputation.ImputeKNN has cognitive complexity 41 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · SpectralPreprocessor.DerivativeSpikeRemoval (cognitive 41) · ×1
  • SpectralPreprocessor.DerivativeSpikeRemoval (cognitive 41) src/assembly/RamanSpectroscopy/RamanDataProcessor.vb:1030 — SpectralPreprocessor.DerivativeSpikeRemoval has cognitive complexity 41 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · XcaliburRawFileIO.GetTuneData (cognitive 40) · ×1
  • XcaliburRawFileIO.GetTuneData (cognitive 40) src/assembly/ThermoRawFileReader/XcaliburRawFileIO.vb:1630 — XcaliburRawFileIO.GetTuneData has cognitive complexity 40 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfPhosphatidylThreonine (cognitive 40) · ×1
  • LipidMsmsCharacterization.JudgeIfPhosphatidylThreonine (cognitive 40) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:2288 — LipidMsmsCharacterization.JudgeIfPhosphatidylThreonine has cognitive complexity 40 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfSqdg) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfOxps (cognitive 40) · ×1
  • LipidMsmsCharacterization.JudgeIfOxps (cognitive 40) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4761 — LipidMsmsCharacterization.JudgeIfOxps has cognitive complexity 40 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfSqdg (cognitive 40) · ×1
  • LipidMsmsCharacterization.JudgeIfSqdg (cognitive 40) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6596 — LipidMsmsCharacterization.JudgeIfSqdg has cognitive complexity 40 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfPhosphatidylThreonine) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · MsScanMatching.GetSimpleDotProduct (cognitive 39) · ×1
  • MsScanMatching.GetSimpleDotProduct (cognitive 39) src/mzmath/MSEngine/Search/MsScanMatching.vb:1034 — MsScanMatching.GetSimpleDotProduct has cognitive complexity 39 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · StandardCurveWorker.Regression (cognitive 39) · ×1
  • StandardCurveWorker.Regression (cognitive 39) src/mzmath/TargetedMetabolomics/MRM/QuantitativeAnalysis/StandardCurveWorker.vb:124 — StandardCurveWorker.Regression has cognitive complexity 39 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · XcaliburRawFileIO.GetScanTypeNameFromThermoScanFilterText (cognitive 38) · ×1
  • XcaliburRawFileIO.GetScanTypeNameFromThermoScanFilterText (cognitive 38) src/assembly/ThermoRawFileReader/XcaliburRawFileIO.vb:1478 — XcaliburRawFileIO.GetScanTypeNameFromThermoScanFilterText has cognitive complexity 38 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidEieioMsmsCharacterization.JudgeIfDagD5 (cognitive 38) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfDagD5 (cognitive 38) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:3090 — LipidEieioMsmsCharacterization.JudgeIfDagD5 has cognitive complexity 38 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfPetoh (cognitive 38) · ×1
  • LipidMsmsCharacterization.JudgeIfPetoh (cognitive 38) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6709 — LipidMsmsCharacterization.JudgeIfPetoh has cognitive complexity 38 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfPbtoh) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfPbtoh (cognitive 38) · ×1
  • LipidMsmsCharacterization.JudgeIfPbtoh (cognitive 38) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6906 — LipidMsmsCharacterization.JudgeIfPbtoh has cognitive complexity 38 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfPetoh) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · MummichogAnnotator.PerformPathwayEnrichment (cognitive 38) · ×1
  • MummichogAnnotator.PerformPathwayEnrichment (cognitive 38) src/mzmath/Mummichog/MummichogModule.vb:456 — MummichogAnnotator.PerformPathwayEnrichment has cognitive complexity 38 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · IsotopeCalculator.GetBasicCompoundElementProfile (cognitive 38) · ×1
  • IsotopeCalculator.GetBasicCompoundElementProfile (cognitive 38) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:122 — IsotopeCalculator.GetBasicCompoundElementProfile has cognitive complexity 38 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · Extensions.InchiKey (cognitive 38) · ×1
  • Extensions.InchiKey (cognitive 38) src/metadb/Chemoinformatics/InChI/Extensions.vb:103 — Extensions.InchiKey has cognitive complexity 38 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MzWeb.readCache (cognitive 37) · ×1
  • MzWeb.readCache (cognitive 37) Rscript/Library/mzkit_app/src/mzkit/assembly/MzWeb.vb:438 — MzWeb.readCache has cognitive complexity 37 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfLdgts (cognitive 37) · ×1
  • LipidMsmsCharacterization.JudgeIfLdgts (cognitive 37) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6168 — LipidMsmsCharacterization.JudgeIfLdgts has cognitive complexity 37 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · FragmentAssigner.GetRefinedPeaklist (cognitive 37) · ×1
  • FragmentAssigner.GetRefinedPeaklist (cognitive 37) src/mzmath/MSFinder/FragmentAssigner.vb:457 — FragmentAssigner.GetRefinedPeaklist has cognitive complexity 37 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · DirectMatch.DirectMatchAlignment (cognitive 37) · ×1
  • DirectMatch.DirectMatchAlignment (cognitive 37) src/mzmath/mz_deco/PeakAlignment/Algorithm/DirectMatch.vb:22 — DirectMatch.DirectMatchAlignment has cognitive complexity 37 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MissingValueImputation.ImputeQRILC (cognitive 37) · ×1
  • MissingValueImputation.ImputeQRILC (cognitive 37) src/mzmath/mz_deco/Preprocessing/MissingValueImputation.vb:529 — MissingValueImputation.ImputeQRILC has cognitive complexity 37 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · SpectralPreprocessor.SolveALS (cognitive 37) · ×1
  • SpectralPreprocessor.SolveALS (cognitive 37) src/assembly/RamanSpectroscopy/RamanDataProcessor.vb:568 — SpectralPreprocessor.SolveALS has cognitive complexity 37 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidomicsConverter.acylChainStringSeparatorVS2 (cognitive 36) · ×1
  • LipidomicsConverter.acylChainStringSeparatorVS2 (cognitive 36) src/metadb/Lipidomics/Annotation/LipidomicsConverter.vb:3508 — LipidomicsConverter.acylChainStringSeparatorVS2 has cognitive complexity 36 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidEieioMsmsCharacterization.JudgeIfTriacylglycerolD5 (cognitive 36) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfTriacylglycerolD5 (cognitive 36) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:3176 — LipidEieioMsmsCharacterization.JudgeIfTriacylglycerolD5 has cognitive complexity 36 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · FragmentAssigner.AnnotateIsotopes (cognitive 36) · ×1
  • FragmentAssigner.AnnotateIsotopes (cognitive 36) src/mzmath/MSFinder/FragmentAssigner.vb:779 — FragmentAssigner.AnnotateIsotopes has cognitive complexity 36 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · FastSeekIndex.LoadIndex_mzML (cognitive 35) · ×1
  • FastSeekIndex.LoadIndex_mzML (cognitive 35) src/assembly/assembly/MarkupData/FastSeekIndex.vb:120 — FastSeekIndex.LoadIndex_mzML has cognitive complexity 35 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · IsotopeCalculator.getAllIsotopeElementPropertyForSixIsotopomerElement (cognitive 35) · ×1
  • IsotopeCalculator.getAllIsotopeElementPropertyForSixIsotopomerElement (cognitive 35) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:946 — IsotopeCalculator.getAllIsotopeElementPropertyForSixIsotopomerElement has cognitive complexity 35 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · NCAAnalyzer.Analyze (cognitive 35) · ×1
  • NCAAnalyzer.Analyze (cognitive 35) src/mzmath/TargetedMetabolomics/PKAnalysis.vb:143 — NCAAnalyzer.Analyze has cognitive complexity 35 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · CeramideLipidParser.Parse (cognitive 34) · ×1
  • CeramideLipidParser.Parse (cognitive 34) src/metadb/Lipidomics/LipidParser/CeramideLipidParser.vb:74 — CeramideLipidParser.Parse has cognitive complexity 34 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidEieioMsmsCharacterization.JudgeIfCeramidensD7 (cognitive 34) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfCeramidensD7 (cognitive 34) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:3409 — LipidEieioMsmsCharacterization.JudgeIfCeramidensD7 has cognitive complexity 34 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfPhosphatidylinositol (cognitive 34) · ×1
  • LipidMsmsCharacterization.JudgeIfPhosphatidylinositol (cognitive 34) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:2580 — LipidMsmsCharacterization.JudgeIfPhosphatidylinositol has cognitive complexity 34 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfPhosphatidylinositolD5) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfNacylphosphatidylethanolamine (cognitive 34) · ×1
  • LipidMsmsCharacterization.JudgeIfNacylphosphatidylethanolamine (cognitive 34) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:2809 — LipidMsmsCharacterization.JudgeIfNacylphosphatidylethanolamine has cognitive complexity 34 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfGm3 (cognitive 34) · ×1
  • LipidMsmsCharacterization.JudgeIfGm3 (cognitive 34) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11577 — LipidMsmsCharacterization.JudgeIfGm3 has cognitive complexity 34 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfPhosphatidylinositolD5 (cognitive 34) · ×1
  • LipidMsmsCharacterization.JudgeIfPhosphatidylinositolD5 (cognitive 34) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15607 — LipidMsmsCharacterization.JudgeIfPhosphatidylinositolD5 has cognitive complexity 34 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfPhosphatidylinositol) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · MummichogAnnotator.ReverseAnnotation (cognitive 34) · ×1
  • MummichogAnnotator.ReverseAnnotation (cognitive 34) src/mzmath/Mummichog/MummichogModule.vb:584 — MummichogAnnotator.ReverseAnnotation has cognitive complexity 34 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · IsotopeCalculator.getNominalIsotopeElementPropertyForFiveIsotopomerElement (cognitive 34) · ×1
  • IsotopeCalculator.getNominalIsotopeElementPropertyForFiveIsotopomerElement (cognitive 34) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:2159 — IsotopeCalculator.getNominalIsotopeElementPropertyForFiveIsotopomerElement has cognitive complexity 34 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · FragmentAssigner.AnnotateAdducts (cognitive 34) · ×1
  • FragmentAssigner.AnnotateAdducts (cognitive 34) src/mzmath/MSFinder/FragmentAssigner.vb:824 — FragmentAssigner.AnnotateAdducts has cognitive complexity 34 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfAcylcarnitine (cognitive 33) · ×1
  • LipidMsmsCharacterization.JudgeIfAcylcarnitine (cognitive 33) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3287 — LipidMsmsCharacterization.JudgeIfAcylcarnitine has cognitive complexity 33 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidEieioMsmsCharacterization.JudgeIfPhosphatidylglycerol (cognitive 32) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfPhosphatidylglycerol (cognitive 32) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:575 — LipidEieioMsmsCharacterization.JudgeIfPhosphatidylglycerol has cognitive complexity 32 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidEieioMsmsCharacterization.JudgeIfLysope (cognitive 32) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfLysope (cognitive 32) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1146 — LipidEieioMsmsCharacterization.JudgeIfLysope has cognitive complexity 32 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · EidSpecificSpectrumGenerator.EidSpecificSpectrumGen (cognitive 32) · ×1
  • EidSpecificSpectrumGenerator.EidSpecificSpectrumGen (cognitive 32) src/metadb/Lipidomics/SpectrumGenerator/EidSpecificSpectrumGenerator.vb:64 — EidSpecificSpectrumGenerator.EidSpecificSpectrumGen has cognitive complexity 32 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · CrossReferenceData.Compares (cognitive 32) · ×1
  • CrossReferenceData.Compares (cognitive 32) src/metadb/Chemoinformatics/Metabolite/CrossReference/CrossReferenceData.vb:254 — CrossReferenceData.Compares has cognitive complexity 32 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · XrefSchema.PullCollection (cognitive 32) · ×1
  • XrefSchema.PullCollection (cognitive 32) src/metadb/Chemoinformatics/Metabolite/CrossReference/XrefSchema.vb:138 — XrefSchema.PullCollection has cognitive complexity 32 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · PeakAreaCalculator.GaussianFittingIntegration (cognitive 32) · ×1
  • PeakAreaCalculator.GaussianFittingIntegration (cognitive 32) src/mzmath/mz_deco/Signals/PeakFinding/PeakArea/PeakAreaCalculator.vb:100 — PeakAreaCalculator.GaussianFittingIntegration has cognitive complexity 32 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · mzDeco.RI_calc (cognitive 31) · ×1
  • mzDeco.RI_calc (cognitive 31) Rscript/Library/mzkit_app/src/mzquant/mzDeco.vb:928 — mzDeco.RI_calc has cognitive complexity 31 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidEieioMsmsCharacterization.JudgeIfShexcer (cognitive 31) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfShexcer (cognitive 31) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1626 — LipidEieioMsmsCharacterization.JudgeIfShexcer has cognitive complexity 31 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidEieioMsmsCharacterization.JudgeIfEtherpc (cognitive 31) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfEtherpc (cognitive 31) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1925 — LipidEieioMsmsCharacterization.JudgeIfEtherpc has cognitive complexity 31 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfNGcGM3 (cognitive 31) · ×1
  • LipidMsmsCharacterization.JudgeIfNGcGM3 (cognitive 31) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12056 — LipidMsmsCharacterization.JudgeIfNGcGM3 has cognitive complexity 31 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfEtherps (cognitive 31) · ×1
  • LipidMsmsCharacterization.JudgeIfEtherps (cognitive 31) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12341 — LipidMsmsCharacterization.JudgeIfEtherps has cognitive complexity 31 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · SequenceToSpec.GetSpectrumPeaksByHotECD (cognitive 31) · ×1
  • SequenceToSpec.GetSpectrumPeaksByHotECD (cognitive 31) src/mzmath/MSEngine/Proteomics/SequenceToSpec.vb:255 — SequenceToSpec.GetSpectrumPeaksByHotECD has cognitive complexity 31 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MathHelpers.MatrixInverse (cognitive 31) · ×1
  • MathHelpers.MatrixInverse (cognitive 31) src/mzmath/mz_deco/Preprocessing/MathHelpers.vb:342 — MathHelpers.MatrixInverse has cognitive complexity 31 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · ChromatogramTools.toChromatogram (cognitive 30) · ×1
  • ChromatogramTools.toChromatogram (cognitive 30) Rscript/Library/mzkit_app/src/mzkit/assembly/Chromatogram.vb:220 — ChromatogramTools.toChromatogram has cognitive complexity 30 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · FastSeekIndex.LoadIndex_mzXML (cognitive 30) · ×1
  • FastSeekIndex.LoadIndex_mzXML (cognitive 30) src/assembly/assembly/MarkupData/FastSeekIndex.vb:192 — FastSeekIndex.LoadIndex_mzXML has cognitive complexity 30 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · ScanPopulator.Load (cognitive 30) · ×1
  • ScanPopulator.Load (cognitive 30) src/assembly/assembly/mzPack/mzWebCache/ScanPopulator.vb:178 — ScanPopulator.Load has cognitive complexity 30 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidEieioMsmsCharacterization.JudgeIfDgts (cognitive 30) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfDgts (cognitive 30) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:3527 — LipidEieioMsmsCharacterization.JudgeIfDgts has cognitive complexity 30 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfDag (cognitive 30) · ×1
  • LipidMsmsCharacterization.JudgeIfDag (cognitive 30) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3380 — LipidMsmsCharacterization.JudgeIfDag has cognitive complexity 30 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfDagD5) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfGT1b (cognitive 30) · ×1
  • LipidMsmsCharacterization.JudgeIfGT1b (cognitive 30) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11916 — LipidMsmsCharacterization.JudgeIfGT1b has cognitive complexity 30 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfGQ1b) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfGQ1b (cognitive 30) · ×1
  • LipidMsmsCharacterization.JudgeIfGQ1b (cognitive 30) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11986 — LipidMsmsCharacterization.JudgeIfGQ1b has cognitive complexity 30 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfGT1b) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfSteroidWithPa (cognitive 30) · ×1
  • LipidMsmsCharacterization.JudgeIfSteroidWithPa (cognitive 30) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14879 — LipidMsmsCharacterization.JudgeIfSteroidWithPa has cognitive complexity 30 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfDagD5 (cognitive 30) · ×1
  • LipidMsmsCharacterization.JudgeIfDagD5 (cognitive 30) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:16024 — LipidMsmsCharacterization.JudgeIfDagD5 has cognitive complexity 30 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfDag) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · SpectrumPeakGenerator.GetDoubleBondSpectrum (cognitive 30) · ×1
  • SpectrumPeakGenerator.GetDoubleBondSpectrum (cognitive 30) src/metadb/Lipidomics/SpectrumPeakGenerator.vb:65 — SpectrumPeakGenerator.GetDoubleBondSpectrum has cognitive complexity 30 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · GraphBuilder.BuildFragmentFragmentEdges (cognitive 30) · ×1
  • GraphBuilder.BuildFragmentFragmentEdges (cognitive 30) src/mzmath/ms2_simulator/MSGNN/GraphBuilder.vb:302 — GraphBuilder.BuildFragmentFragmentEdges has cognitive complexity 30 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · GlycosylNameSolver.HandleMultiple (cognitive 30) · ×1
  • GlycosylNameSolver.HandleMultiple (cognitive 30) src/metadb/Chemoinformatics/NaturalProduct/GlycosylNameSolver.vb:214 — GlycosylNameSolver.HandleMultiple has cognitive complexity 30 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · Assembly.writeMgfIons (cognitive 29) · ×1
  • Assembly.writeMgfIons (cognitive 29) Rscript/Library/mzkit_app/src/mzkit/assembly/Assembly.vb:336 — Assembly.writeMgfIons has cognitive complexity 29 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidAnnotation.Characterize (cognitive 29) · ×1
  • LipidAnnotation.Characterize (cognitive 29) src/metadb/Lipidomics/Annotation/Lipidomics.vb:148 — LipidAnnotation.Characterize has cognitive complexity 29 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidEieioMsmsCharacterization.JudgeIfPhosphatidylglycerolD5 (cognitive 29) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfPhosphatidylglycerolD5 (cognitive 29) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:2392 — LipidEieioMsmsCharacterization.JudgeIfPhosphatidylglycerolD5 has cognitive complexity 29 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfDgcc (cognitive 29) · ×1
  • LipidMsmsCharacterization.JudgeIfDgcc (cognitive 29) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6258 — LipidMsmsCharacterization.JudgeIfDgcc has cognitive complexity 29 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfCeramidePhosphate (cognitive 29) · ×1
  • LipidMsmsCharacterization.JudgeIfCeramidePhosphate (cognitive 29) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:8130 — LipidMsmsCharacterization.JudgeIfCeramidePhosphate has cognitive complexity 29 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfGM1 (cognitive 29) · ×1
  • LipidMsmsCharacterization.JudgeIfGM1 (cognitive 29) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11848 — LipidMsmsCharacterization.JudgeIfGM1 has cognitive complexity 29 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · GlycosylNameSolver.HandleComponents (cognitive 29) · ×1
  • GlycosylNameSolver.HandleComponents (cognitive 29) src/metadb/Chemoinformatics/NaturalProduct/GlycosylNameSolver.vb:92 — GlycosylNameSolver.HandleComponents has cognitive complexity 29 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MsScanMatching.GetMatchedPeaksScores (cognitive 29) · ×1
  • MsScanMatching.GetMatchedPeaksScores (cognitive 29) src/mzmath/MSEngine/Search/MsScanMatching.vb:394 — MsScanMatching.GetMatchedPeaksScores has cognitive complexity 29 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MsScanMatching.GetMachedSpectralPeaks (cognitive 29) · ×1
  • MsScanMatching.GetMachedSpectralPeaks (cognitive 29) src/mzmath/MSEngine/Search/MsScanMatching.vb:685 — MsScanMatching.GetMachedSpectralPeaks has cognitive complexity 29 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MissingValueImputation.ImputeRandomMin (cognitive 29) · ×1
  • MissingValueImputation.ImputeRandomMin (cognitive 29) src/mzmath/mz_deco/Preprocessing/MissingValueImputation.vb:594 — MissingValueImputation.ImputeRandomMin has cognitive complexity 29 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MathHelper.MatrixInverse (cognitive 29) · ×1
  • MathHelper.MatrixInverse (cognitive 29) src/assembly/RamanSpectroscopy/RamanDataProcessor.vb:2173 — MathHelper.MatrixInverse has cognitive complexity 29 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · Converter.LoadScanStream (cognitive 28) · ×1
  • Converter.LoadScanStream (cognitive 28) src/assembly/mzPack/Converter.vb:207 — Converter.LoadScanStream has cognitive complexity 28 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · mzStreamWriter.WriteStream (cognitive 28) · ×1
  • mzStreamWriter.WriteStream (cognitive 28) src/assembly/mzPack/v2.0/mzStreamWriter.vb:226 — mzStreamWriter.WriteStream has cognitive complexity 28 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · ModificationProtocol.UpdateProtocol (cognitive 28) · ×1
  • ModificationProtocol.UpdateProtocol (cognitive 28) src/mzmath/MSEngine/Proteomics/ModificationProtocol.vb:79 — ModificationProtocol.UpdateProtocol has cognitive complexity 28 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfEtherlysope (cognitive 27) · ×1
  • LipidMsmsCharacterization.JudgeIfEtherlysope (cognitive 27) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4243 — LipidMsmsCharacterization.JudgeIfEtherlysope has cognitive complexity 27 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfGD1a (cognitive 27) · ×1
  • LipidMsmsCharacterization.JudgeIfGD1a (cognitive 27) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11666 — LipidMsmsCharacterization.JudgeIfGD1a has cognitive complexity 27 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfGD1b (cognitive 27) · ×1
  • LipidMsmsCharacterization.JudgeIfGD1b (cognitive 27) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11732 — LipidMsmsCharacterization.JudgeIfGD1b has cognitive complexity 27 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfPecermide (cognitive 27) · ×1
  • LipidMsmsCharacterization.JudgeIfPecermide (cognitive 27) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12390 — LipidMsmsCharacterization.JudgeIfPecermide has cognitive complexity 27 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · OadLipidSpectrumGenerator.GetClassFragmentSpectrum (cognitive 27) · ×1
  • OadLipidSpectrumGenerator.GetClassFragmentSpectrum (cognitive 27) src/metadb/Lipidomics/SpectrumGenerator/OadLipidsSpectrumGenerator.vb:62 — OadLipidSpectrumGenerator.GetClassFragmentSpectrum has cognitive complexity 27 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MummichogAnnotator.ValidateIsotopePattern (cognitive 27) · ×1
  • MummichogAnnotator.ValidateIsotopePattern (cognitive 27) src/mzmath/Mummichog/MummichogModule.vb:742 — MummichogAnnotator.ValidateIsotopePattern has cognitive complexity 27 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LibraryWorkspace.read (cognitive 27) · ×1
  • LibraryWorkspace.read (cognitive 27) src/mzmath/MSEngine/AnnotationPack/WorkspaceReader.vb:188 — LibraryWorkspace.read has cognitive complexity 27 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MsScanMatching.GetMachedSpectralPeaks (cognitive 27) · ×1
  • MsScanMatching.GetMachedSpectralPeaks (cognitive 27) src/mzmath/MSEngine/Search/MsScanMatching.vb:648 — MsScanMatching.GetMachedSpectralPeaks has cognitive complexity 27 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MetaDbXref.searchMz (cognitive 26) · ×1
  • MetaDbXref.searchMz (cognitive 26) Rscript/Library/mzkit_app/src/mzkit/annotations/MetaDbXref.vb:570 — MetaDbXref.searchMz has cognitive complexity 26 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · TissueMorphology.intersect (cognitive 26) · ×1
  • TissueMorphology.intersect (cognitive 26) Rscript/Library/mzkit_app/src/mzkit/comprehensive/TissueMorphology.vb:384 — TissueMorphology.intersect has cognitive complexity 26 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MathHelpers.SolveLinearSystem (cognitive 26) · ×1
  • MathHelpers.SolveLinearSystem (cognitive 26) src/mzmath/mz_deco/Preprocessing/MathHelpers.vb:282 — MathHelpers.SolveLinearSystem has cognitive complexity 26 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · PeakProcessor.ProcessPeaksCombined (cognitive 26) · ×1
  • PeakProcessor.ProcessPeaksCombined (cognitive 26) src/mzmath/mz_deco/Signals/PeakFinding/PeakProcessor.vb:154 — PeakProcessor.ProcessPeaksCombined has cognitive complexity 26 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · PeakQualityEvaluator.EvaluatePeakQuality (cognitive 26) · ×1
  • PeakQualityEvaluator.EvaluatePeakQuality (cognitive 26) src/mzmath/mz_deco/Signals/PeakFinding/PeakQualityEvaluator.vb:24 — PeakQualityEvaluator.EvaluatePeakQuality has cognitive complexity 26 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MsScanMatching.GetLipidomicsMatchedPeaksScores (cognitive 25) · ×1
  • MsScanMatching.GetLipidomicsMatchedPeaksScores (cognitive 25) src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:1551 — MsScanMatching.GetLipidomicsMatchedPeaksScores has cognitive complexity 25 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · HexCerLipidParser.Parse (cognitive 25) · ×1
  • HexCerLipidParser.Parse (cognitive 25) src/metadb/Lipidomics/LipidParser/HexCerLipidParser.vb:73 — HexCerLipidParser.Parse has cognitive complexity 25 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfPhosphatidicacid (cognitive 25) · ×1
  • LipidMsmsCharacterization.JudgeIfPhosphatidicacid (cognitive 25) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5579 — LipidMsmsCharacterization.JudgeIfPhosphatidicacid has cognitive complexity 25 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfEtherpg) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfEtherpg (cognitive 25) · ×1
  • LipidMsmsCharacterization.JudgeIfEtherpg (cognitive 25) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13372 — LipidMsmsCharacterization.JudgeIfEtherpg has cognitive complexity 25 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfPhosphatidicacid) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · SpectrumPool.AddInternal (cognitive 25) · ×1
  • SpectrumPool.AddInternal (cognitive 25) src/mzmath/MoleculeNetworking/SpectrumPool/SpectrumPool.vb:262 — SpectrumPool.AddInternal has cognitive complexity 25 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · SevenGoldenRulesCheck.ProbabilityCheck (cognitive 25) · ×1
  • SevenGoldenRulesCheck.ProbabilityCheck (cognitive 25) src/metadb/Chemoinformatics/Formula/SevenGoldenRulesCheck.vb:498 — SevenGoldenRulesCheck.ProbabilityCheck has cognitive complexity 25 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · SDFReader.FixMzType (cognitive 25) · ×1
  • SDFReader.FixMzType (cognitive 25) src/metadb/MoNA/SDF/SDFReader.vb:202 — SDFReader.FixMzType has cognitive complexity 25 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · FormulaGenerator.getFormulaSearchResults (cognitive 25) · ×1
  • FormulaGenerator.getFormulaSearchResults (cognitive 25) src/mzmath/MSFinder/FormulaGenerator.vb:467 — FormulaGenerator.getFormulaSearchResults has cognitive complexity 25 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · AdductIonParser.IsCommonAdduct (cognitive 25) · ×1
  • AdductIonParser.IsCommonAdduct (cognitive 25) src/mzmath/ms2_math-core/Ms1/PrecursorType/AdductIonParser.vb:209 — AdductIonParser.IsCommonAdduct has cognitive complexity 25 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · DTW.ComputeDTW (cognitive 25) · ×1
  • DTW.ComputeDTW (cognitive 25) src/mzmath/mz_deco/PeakAlignment/Algorithm/DTW.vb:21 — DTW.ComputeDTW has cognitive complexity 25 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · metaDNAInfer.handleSample (cognitive 24) · ×1
  • metaDNAInfer.handleSample (cognitive 24) Rscript/Library/mzkit_app/src/mzDIA/metaDNA.vb:412 — metaDNAInfer.handleSample has cognitive complexity 24 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MergeLayoutSliders.MergeDataWithLayout (cognitive 24) · ×1
  • MergeLayoutSliders.MergeDataWithLayout (cognitive 24) src/assembly/Comprehensive/MsImaging/MergeSliders/MergeLayoutSliders.vb:76 — MergeLayoutSliders.MergeDataWithLayout has cognitive complexity 24 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfDgmg (cognitive 24) · ×1
  • LipidMsmsCharacterization.JudgeIfDgmg (cognitive 24) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5347 — LipidMsmsCharacterization.JudgeIfDgmg has cognitive complexity 24 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · IsotopeCalculator.getAllIsotopeElementPropertyForFiveIsotopomerElement (cognitive 24) · ×1
  • IsotopeCalculator.getAllIsotopeElementPropertyForFiveIsotopomerElement (cognitive 24) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1041 — IsotopeCalculator.getAllIsotopeElementPropertyForFiveIsotopomerElement has cognitive complexity 24 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MsScanMatching.SearchMatchedPeaks (cognitive 24) · ×1
  • MsScanMatching.SearchMatchedPeaks (cognitive 24) src/mzmath/MSEngine/Search/MsScanMatching.vb:511 — MsScanMatching.SearchMatchedPeaks has cognitive complexity 24 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MissingValueImputation.ImputeHalfMin (cognitive 24) · ×1
  • MissingValueImputation.ImputeHalfMin (cognitive 24) src/mzmath/mz_deco/Preprocessing/MissingValueImputation.vb:155 — MissingValueImputation.ImputeHalfMin has cognitive complexity 24 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (MissingValueImputation.ImputeMinValue) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · MissingValueImputation.ImputeMinValue (cognitive 24) · ×1
  • MissingValueImputation.ImputeMinValue (cognitive 24) src/mzmath/mz_deco/Preprocessing/MissingValueImputation.vb:191 — MissingValueImputation.ImputeMinValue has cognitive complexity 24 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (MissingValueImputation.ImputeHalfMin) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · MathHelper.SolveLinearSystem (cognitive 24) · ×1
  • MathHelper.SolveLinearSystem (cognitive 24) src/assembly/RamanSpectroscopy/RamanDataProcessor.vb:2237 — MathHelper.SolveLinearSystem has cognitive complexity 24 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MSI.spatialConvolution (cognitive 23) · ×1
  • MSI.spatialConvolution (cognitive 23) Rscript/Library/mzkit_app/src/mzkit/comprehensive/MSI.vb:1641 — MSI.spatialConvolution has cognitive complexity 23 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · ReferenceTreePkg.addBucket (cognitive 23) · ×1
  • ReferenceTreePkg.addBucket (cognitive 23) Rscript/Library/mzkit_app/src/mzkit/pipeline/ReferenceTree.vb:749 — ReferenceTreePkg.addBucket has cognitive complexity 23 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MsScanMatching.GetRefinedLipidAnnotationLevel (cognitive 23) · ×1
  • MsScanMatching.GetRefinedLipidAnnotationLevel (cognitive 23) src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:1471 — MsScanMatching.GetRefinedLipidAnnotationLevel has cognitive complexity 23 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (MsScanMatching.GetRefinedLipidAnnotationLevelForEIEIO) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · MsScanMatching.GetRefinedLipidAnnotationLevelForEIEIO (cognitive 23) · ×1
  • MsScanMatching.GetRefinedLipidAnnotationLevelForEIEIO (cognitive 23) src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:1635 — MsScanMatching.GetRefinedLipidAnnotationLevelForEIEIO has cognitive complexity 23 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (MsScanMatching.GetRefinedLipidAnnotationLevel) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidEieioMsmsCharacterization.JudgeIfLysopeD5 (cognitive 23) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfLysopeD5 (cognitive 23) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:2913 — LipidEieioMsmsCharacterization.JudgeIfLysopeD5 has cognitive complexity 23 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfBismonoacylglycerophosphate (cognitive 23) · ×1
  • LipidMsmsCharacterization.JudgeIfBismonoacylglycerophosphate (cognitive 23) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:2520 — LipidMsmsCharacterization.JudgeIfBismonoacylglycerophosphate has cognitive complexity 23 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfVitaminaestermolecules (cognitive 23) · ×1
  • LipidMsmsCharacterization.JudgeIfVitaminaestermolecules (cognitive 23) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13612 — LipidMsmsCharacterization.JudgeIfVitaminaestermolecules has cognitive complexity 23 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfFahfamideorn (cognitive 23) · ×1
  • LipidMsmsCharacterization.JudgeIfFahfamideorn (cognitive 23) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13643 — LipidMsmsCharacterization.JudgeIfFahfamideorn has cognitive complexity 23 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfSmgdg) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfSmgdg (cognitive 23) · ×1
  • LipidMsmsCharacterization.JudgeIfSmgdg (cognitive 23) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14076 — LipidMsmsCharacterization.JudgeIfSmgdg has cognitive complexity 23 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfFahfamideorn) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · CerNSd7SpectrumGenerator.GetSphingoDoubleBondSpectrum (cognitive 23) · ×1
  • CerNSd7SpectrumGenerator.GetSphingoDoubleBondSpectrum (cognitive 23) src/metadb/Lipidomics/SpectrumGenerator/CeramideNsD7SpectrumGenerator.vb:172 — CerNSd7SpectrumGenerator.GetSphingoDoubleBondSpectrum has cognitive complexity 23 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · AdductsRanking.RankNegative (cognitive 23) · ×1
  • AdductsRanking.RankNegative (cognitive 23) src/metadb/FormulaSearch.Extensions/AdductsRanking.vb:330 — AdductsRanking.RankNegative has cognitive complexity 23 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · Extensions.GetInformationNumber (cognitive 23) · ×1
  • Extensions.GetInformationNumber (cognitive 23) src/metadb/Massbank/Public/NCBI/PubChem/Web/Extensions.vb:77 — Extensions.GetInformationNumber has cognitive complexity 23 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MetaInfoReader.getSynonyms (cognitive 23) · ×1
  • MetaInfoReader.getSynonyms (cognitive 23) src/metadb/Massbank/Public/NCBI/PubChem/Web/MetaInfoReader.vb:131 — MetaInfoReader.getSynonyms has cognitive complexity 23 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · SequenceToSpec.GetSpectrumPeaksByECD (cognitive 23) · ×1
  • SequenceToSpec.GetSpectrumPeaksByECD (cognitive 23) src/mzmath/MSEngine/Proteomics/SequenceToSpec.vb:397 — SequenceToSpec.GetSpectrumPeaksByECD has cognitive complexity 23 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MsScanMatching.GetTotalSimilarity (cognitive 23) · ×1
  • MsScanMatching.GetTotalSimilarity (cognitive 23) src/mzmath/MSEngine/Search/MsScanMatching.vb:1211 — MsScanMatching.GetTotalSimilarity has cognitive complexity 23 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · FormulaStringParcer.OrganicElementsReader (cognitive 23) · ×1
  • FormulaStringParcer.OrganicElementsReader (cognitive 23) src/mzmath/MSFinder/FormulaStringParcer.vb:65 — FormulaStringParcer.OrganicElementsReader has cognitive complexity 23 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · FragmentAssigner.FastNeutralLossAssigner (cognitive 23) · ×1
  • FragmentAssigner.FastNeutralLossAssigner (cognitive 23) src/mzmath/MSFinder/FragmentAssigner.vb:321 — FragmentAssigner.FastNeutralLossAssigner has cognitive complexity 23 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · Algorithm.FillGaps (cognitive 23) · ×1
  • Algorithm.FillGaps (cognitive 23) src/mzmath/mz_deco/PeakAlignment/PeakAlignment.vb:111 — Algorithm.FillGaps has cognitive complexity 23 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · SaveXcms.GetPeaks (cognitive 23) · ×1
  • SaveXcms.GetPeaks (cognitive 23) src/mzmath/mz_deco/Save/SaveXcms.vb:183 — SaveXcms.GetPeaks has cognitive complexity 23 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · SpectralPreprocessor.ALSBaselineCorrect (cognitive 23) · ×1
  • SpectralPreprocessor.ALSBaselineCorrect (cognitive 23) src/assembly/RamanSpectroscopy/RamanDataProcessor.vb:508 — SpectralPreprocessor.ALSBaselineCorrect has cognitive complexity 23 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · SingleCellsPack.PackSingleCellsInSampleGroup (cognitive 22) · ×1
  • SingleCellsPack.PackSingleCellsInSampleGroup (cognitive 22) Rscript/Library/mzkit_app/src/mzkit/comprehensive/SingleCellsPack.vb:145 — SingleCellsPack.PackSingleCellsInSampleGroup has cognitive complexity 22 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MsScanMatching.GetLipidomicsMoleculerSpeciesLevelAnnotationPeaksScoresForEIEIO (cognitive 22) · ×1
  • MsScanMatching.GetLipidomicsMoleculerSpeciesLevelAnnotationPeaksScoresForEIEIO (cognitive 22) src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:1593 — MsScanMatching.GetLipidomicsMoleculerSpeciesLevelAnnotationPeaksScoresForEIEIO has cognitive complexity 22 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · DoubleBondIndeterminateState.Indeterminate (cognitive 22) · ×1
  • DoubleBondIndeterminateState.Indeterminate (cognitive 22) src/metadb/Lipidomics/DoubleBondIndeterminateState.vb:90 — DoubleBondIndeterminateState.Indeterminate has cognitive complexity 22 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipoqualityDatabaseManagerUtility.getLipidChainsInformation (cognitive 22) · ×1
  • LipoqualityDatabaseManagerUtility.getLipidChainsInformation (cognitive 22) src/metadb/Lipidomics/LipoqualityDatabaseManagerUtility.vb:466 — LipoqualityDatabaseManagerUtility.getLipidChainsInformation has cognitive complexity 22 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfSphingomyelinPhyto (cognitive 22) · ×1
  • LipidMsmsCharacterization.JudgeIfSphingomyelinPhyto (cognitive 22) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3089 — LipidMsmsCharacterization.JudgeIfSphingomyelinPhyto has cognitive complexity 22 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfEtherlysopc) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfEtherlysopc (cognitive 22) · ×1
  • LipidMsmsCharacterization.JudgeIfEtherlysopc (cognitive 22) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4194 — LipidMsmsCharacterization.JudgeIfEtherlysopc has cognitive complexity 22 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfSphingomyelinPhyto) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfMgmg (cognitive 22) · ×1
  • LipidMsmsCharacterization.JudgeIfMgmg (cognitive 22) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5302 — LipidMsmsCharacterization.JudgeIfMgmg has cognitive complexity 22 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfDilysocardiolipin (cognitive 22) · ×1
  • LipidMsmsCharacterization.JudgeIfDilysocardiolipin (cognitive 22) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7603 — LipidMsmsCharacterization.JudgeIfDilysocardiolipin has cognitive complexity 22 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfEtherpi) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfCeramidedos (cognitive 22) · ×1
  • LipidMsmsCharacterization.JudgeIfCeramidedos (cognitive 22) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:9060 — LipidMsmsCharacterization.JudgeIfCeramidedos has cognitive complexity 22 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfEtherpi (cognitive 22) · ×1
  • LipidMsmsCharacterization.JudgeIfEtherpi (cognitive 22) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12288 — LipidMsmsCharacterization.JudgeIfEtherpi has cognitive complexity 22 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfDilysocardiolipin) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfGpnae (cognitive 22) · ×1
  • LipidMsmsCharacterization.JudgeIfGpnae (cognitive 22) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12911 — LipidMsmsCharacterization.JudgeIfGpnae has cognitive complexity 22 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · SpectrumPeakGenerator.GetSphingoDoubleBondSpectrum (cognitive 22) · ×1
  • SpectrumPeakGenerator.GetSphingoDoubleBondSpectrum (cognitive 22) src/metadb/Lipidomics/SpectrumPeakGenerator.vb:211 — SpectrumPeakGenerator.GetSphingoDoubleBondSpectrum has cognitive complexity 22 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · Exporters.ExportJSON (cognitive 22) · ×1
  • Exporters.ExportJSON (cognitive 22) src/mzmath/ms2_simulator/MSGNN/Exporters.vb:19 — Exporters.ExportJSON has cognitive complexity 22 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · FormulaScanner.ScanFormula (cognitive 22) · ×1
  • FormulaScanner.ScanFormula (cognitive 22) src/metadb/Chemoinformatics/Formula/FormulaScanner.vb:270 — FormulaScanner.ScanFormula has cognitive complexity 22 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · ChemicalCalculator.CalculatePossibleCharges (cognitive 22) · ×1
  • ChemicalCalculator.CalculatePossibleCharges (cognitive 22) src/metadb/Chemoinformatics/Formula/Models/ChemicalCalculator.vb:43 — ChemicalCalculator.CalculatePossibleCharges has cognitive complexity 22 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MetaDb.getBioMarkers (cognitive 22) · ×1
  • MetaDb.getBioMarkers (cognitive 22) src/metadb/Massbank/Public/TMIC/HMDB/Tables/MetaDBTable.vb:276 — MetaDb.getBioMarkers has cognitive complexity 22 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · FormulaStringParcer.TokenizeFormulaCharacter (cognitive 22) · ×1
  • FormulaStringParcer.TokenizeFormulaCharacter (cognitive 22) src/mzmath/MSFinder/FormulaStringParcer.vb:287 — FormulaStringParcer.TokenizeFormulaCharacter has cognitive complexity 22 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · Normalization.NormalizePQN (cognitive 22) · ×1
  • Normalization.NormalizePQN (cognitive 22) src/mzmath/mz_deco/Preprocessing/Normalization.vb:249 — Normalization.NormalizePQN has cognitive complexity 22 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · NCAAnalyzer.FitTerminalPhase (cognitive 22) · ×1
  • NCAAnalyzer.FitTerminalPhase (cognitive 22) src/mzmath/TargetedMetabolomics/PKAnalysis.vb:317 — NCAAnalyzer.FitTerminalPhase has cognitive complexity 22 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MzMath.centroid (cognitive 21) · ×1
  • MzMath.centroid (cognitive 21) Rscript/Library/mzkit_app/src/mzkit/math/Math.vb:1041 — MzMath.centroid has cognitive complexity 21 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · ScanTimeCorrection.ScanMeltdown (cognitive 21) · ×1
  • ScanTimeCorrection.ScanMeltdown (cognitive 21) src/assembly/Comprehensive/MsImaging/ScanTimeCorrection.vb:125 — ScanTimeCorrection.ScanMeltdown has cognitive complexity 21 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · KEGGNetwork.CreateNetwork (cognitive 21) · ×1
  • KEGGNetwork.CreateNetwork (cognitive 21) src/metadna/metaDNA/Models/Networking/KEGGNetwork.vb:107 — KEGGNetwork.CreateNetwork has cognitive complexity 21 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · TreeCluster.Union (cognitive 21) · ×1
  • TreeCluster.Union (cognitive 21) src/mzmath/MoleculeNetworking/Tree/TreeCluster.vb:193 — TreeCluster.Union has cognitive complexity 21 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · FormalCharge.CorrectChargeEmpirical (cognitive 21) · ×1
  • FormalCharge.CorrectChargeEmpirical (cognitive 21) src/metadb/Chemoinformatics/Formula/FormalCharge.vb:83 — FormalCharge.CorrectChargeEmpirical has cognitive complexity 21 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · IsotopeCalculator.getNominalIsotopeElementPropertyForFourIsotopomerElement (cognitive 21) · ×1
  • IsotopeCalculator.getNominalIsotopeElementPropertyForFourIsotopomerElement (cognitive 21) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:2262 — IsotopeCalculator.getNominalIsotopeElementPropertyForFourIsotopomerElement has cognitive complexity 21 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · RecordIO.__loadSection (cognitive 21) · ×1
  • RecordIO.__loadSection (cognitive 21) src/metadb/Massbank/Public/Massbank/RecordIO.vb:191 — RecordIO.__loadSection has cognitive complexity 21 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · FragmentAssigner.GetNeutralLossList (cognitive 21) · ×1
  • FragmentAssigner.GetNeutralLossList (cognitive 21) src/mzmath/MSFinder/FragmentAssigner.vb:397 — FragmentAssigner.GetNeutralLossList has cognitive complexity 21 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · PeakAnalyzer.LocalMaximumPeakDetect (cognitive 21) · ×1
  • PeakAnalyzer.LocalMaximumPeakDetect (cognitive 21) src/assembly/RamanSpectroscopy/RamanDataProcessor.vb:1235 — PeakAnalyzer.LocalMaximumPeakDetect has cognitive complexity 21 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MzWeb.Ms2ScanPeaks (cognitive 20) · ×1
  • MzWeb.Ms2ScanPeaks (cognitive 20) Rscript/Library/mzkit_app/src/mzkit/assembly/MzWeb.vb:953 — MzWeb.Ms2ScanPeaks has cognitive complexity 20 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · ReferenceTreePkg.QuerySingle (cognitive 20) · ×1
  • ReferenceTreePkg.QuerySingle (cognitive 20) Rscript/Library/mzkit_app/src/mzkit/pipeline/ReferenceTree.vb:630 — ReferenceTreePkg.QuerySingle has cognitive complexity 20 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · mzDeco.convertDataframeToXcmsPeaks (cognitive 20) · ×1
  • mzDeco.convertDataframeToXcmsPeaks (cognitive 20) Rscript/Library/mzkit_app/src/mzquant/mzDeco.vb:555 — mzDeco.convertDataframeToXcmsPeaks has cognitive complexity 20 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · FileReader.Load (cognitive 20) · ×1
  • FileReader.Load (cognitive 20) src/assembly/assembly/ASCII/MSL/FileReader.vb:111 — FileReader.Load has cognitive complexity 20 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · XcaliburRawFileIO.GetChromatogramData2D (cognitive 20) · ×1
  • XcaliburRawFileIO.GetChromatogramData2D (cognitive 20) src/assembly/ThermoRawFileReader/XcaliburRawFileIO.vb:1000 — XcaliburRawFileIO.GetChromatogramData2D has cognitive complexity 20 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfPhytosphingosine (cognitive 20) · ×1
  • LipidMsmsCharacterization.JudgeIfPhytosphingosine (cognitive 20) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12231 — LipidMsmsCharacterization.JudgeIfPhytosphingosine has cognitive complexity 20 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfAnandamide (cognitive 20) · ×1
  • LipidMsmsCharacterization.JudgeIfAnandamide (cognitive 20) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12870 — LipidMsmsCharacterization.JudgeIfAnandamide has cognitive complexity 20 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfSterolHexoside) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfVitaminEmolecules (cognitive 20) · ×1
  • LipidMsmsCharacterization.JudgeIfVitaminEmolecules (cognitive 20) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13486 — LipidMsmsCharacterization.JudgeIfVitaminEmolecules has cognitive complexity 20 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfSterolHexoside (cognitive 20) · ×1
  • LipidMsmsCharacterization.JudgeIfSterolHexoside (cognitive 20) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13543 — LipidMsmsCharacterization.JudgeIfSterolHexoside has cognitive complexity 20 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfAnandamide) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · CLEidSpectrumGenerator.EidSpecificSpectrum (cognitive 20) · ×1
  • CLEidSpectrumGenerator.EidSpecificSpectrum (cognitive 20) src/metadb/Lipidomics/SpectrumGenerator/CLEidSpectrumGenerator.vb:243 — CLEidSpectrumGenerator.EidSpecificSpectrum has cognitive complexity 20 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · PValue.ComputePValues (cognitive 20) · ×1
  • PValue.ComputePValues (cognitive 20) src/mzmath/Mummichog/PValue.vb:19 — PValue.ComputePValues has cognitive complexity 20 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · ModificationContainer.GetAminoAcidDictionaryUsedInModificationProtocol (cognitive 20) · ×1
  • ModificationContainer.GetAminoAcidDictionaryUsedInModificationProtocol (cognitive 20) src/mzmath/MSEngine/Proteomics/ModificationContainer.vb:190 — ModificationContainer.GetAminoAcidDictionaryUsedInModificationProtocol has cognitive complexity 20 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MsScanMatching.GetTotalSimilarity (cognitive 20) · ×1
  • MsScanMatching.GetTotalSimilarity (cognitive 20) src/mzmath/MSEngine/Search/MsScanMatching.vb:1342 — MsScanMatching.GetTotalSimilarity has cognitive complexity 20 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · data.XIC (cognitive 19) · ×1
  • data.XIC (cognitive 19) Rscript/Library/mzkit_app/src/mzkit/assembly/data.vb:800 — data.XIC has cognitive complexity 19 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · mzDeco.mz_deco (cognitive 19) · ×1
  • mzDeco.mz_deco (cognitive 19) Rscript/Library/mzkit_app/src/mzquant/mzDeco.vb:1058 — mzDeco.mz_deco has cognitive complexity 19 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · ScanContour.CreateMatrix (cognitive 19) · ×1
  • ScanContour.CreateMatrix (cognitive 19) src/visualize/plot/ChromatogramPlot/ScanContour.vb:97 — ScanContour.CreateMatrix has cognitive complexity 19 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MSFileReader.GetLabelData (cognitive 19) · ×1
  • MSFileReader.GetLabelData (cognitive 19) src/assembly/ThermoRawFileReader/MSFileReader.vb:156 — MSFileReader.GetLabelData has cognitive complexity 19 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · XcaliburRawFileIO.GetScanDataSumScans (cognitive 19) · ×1
  • XcaliburRawFileIO.GetScanDataSumScans (cognitive 19) src/assembly/ThermoRawFileReader/XcaliburRawFileIO.vb:2367 — XcaliburRawFileIO.GetScanDataSumScans has cognitive complexity 19 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidLibraryParser.ReadLibrary (cognitive 19) · ×1
  • LipidLibraryParser.ReadLibrary (cognitive 19) src/metadb/Lipidomics/Annotation/Lipidomics.vb:677 — LipidLibraryParser.ReadLibrary has cognitive complexity 19 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · EieioMsCharacterizationUtility.GetDefaultScore (cognitive 19) · ×1
  • EieioMsCharacterizationUtility.GetDefaultScore (cognitive 19) src/metadb/Lipidomics/MsCharacterization/EieioMsCharacterizationUtility.vb:381 — EieioMsCharacterizationUtility.GetDefaultScore has cognitive complexity 19 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfCardiolipin (cognitive 19) · ×1
  • LipidMsmsCharacterization.JudgeIfCardiolipin (cognitive 19) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7428 — LipidMsmsCharacterization.JudgeIfCardiolipin has cognitive complexity 19 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfAhexbrseSpecies (cognitive 19) · ×1
  • LipidMsmsCharacterization.JudgeIfAhexbrseSpecies (cognitive 19) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13866 — LipidMsmsCharacterization.JudgeIfAhexbrseSpecies has cognitive complexity 19 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: 4 other methods here (LipidMsmsCharacterization.JudgeIfAhexcaseSpecies, LipidMsmsCharacterization.JudgeIfAhexceSpecies, LipidMsmsCharacterization.JudgeIfAhexsiseSpecies, …) have the same decision points, in the same order, at the same nesting depths — so this is one pattern written 5 times rather than 5 independent problems. Splitting this body alone leaves the other 4 exactly as they are. Where these are variations on one operation, the change that clears all 5 is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfAhexcaseSpecies (cognitive 19) · ×1
  • LipidMsmsCharacterization.JudgeIfAhexcaseSpecies (cognitive 19) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13908 — LipidMsmsCharacterization.JudgeIfAhexcaseSpecies has cognitive complexity 19 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: 4 other methods here (LipidMsmsCharacterization.JudgeIfAhexbrseSpecies, LipidMsmsCharacterization.JudgeIfAhexceSpecies, LipidMsmsCharacterization.JudgeIfAhexsiseSpecies, …) have the same decision points, in the same order, at the same nesting depths — so this is one pattern written 5 times rather than 5 independent problems. Splitting this body alone leaves the other 4 exactly as they are. Where these are variations on one operation, the change that clears all 5 is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfAhexceSpecies (cognitive 19) · ×1
  • LipidMsmsCharacterization.JudgeIfAhexceSpecies (cognitive 19) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13950 — LipidMsmsCharacterization.JudgeIfAhexceSpecies has cognitive complexity 19 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: 4 other methods here (LipidMsmsCharacterization.JudgeIfAhexbrseSpecies, LipidMsmsCharacterization.JudgeIfAhexcaseSpecies, LipidMsmsCharacterization.JudgeIfAhexsiseSpecies, …) have the same decision points, in the same order, at the same nesting depths — so this is one pattern written 5 times rather than 5 independent problems. Splitting this body alone leaves the other 4 exactly as they are. Where these are variations on one operation, the change that clears all 5 is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfAhexsiseSpecies (cognitive 19) · ×1
  • LipidMsmsCharacterization.JudgeIfAhexsiseSpecies (cognitive 19) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13992 — LipidMsmsCharacterization.JudgeIfAhexsiseSpecies has cognitive complexity 19 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: 4 other methods here (LipidMsmsCharacterization.JudgeIfAhexbrseSpecies, LipidMsmsCharacterization.JudgeIfAhexcaseSpecies, LipidMsmsCharacterization.JudgeIfAhexceSpecies, …) have the same decision points, in the same order, at the same nesting depths — so this is one pattern written 5 times rather than 5 independent problems. Splitting this body alone leaves the other 4 exactly as they are. Where these are variations on one operation, the change that clears all 5 is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfAhexstseSpecies (cognitive 19) · ×1
  • LipidMsmsCharacterization.JudgeIfAhexstseSpecies (cognitive 19) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14034 — LipidMsmsCharacterization.JudgeIfAhexstseSpecies has cognitive complexity 19 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: 4 other methods here (LipidMsmsCharacterization.JudgeIfAhexbrseSpecies, LipidMsmsCharacterization.JudgeIfAhexcaseSpecies, LipidMsmsCharacterization.JudgeIfAhexceSpecies, …) have the same decision points, in the same order, at the same nesting depths — so this is one pattern written 5 times rather than 5 independent problems. Splitting this body alone leaves the other 4 exactly as they are. Where these are variations on one operation, the change that clears all 5 is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfnoChainSterol (cognitive 19) · ×1
  • LipidMsmsCharacterization.JudgeIfnoChainSterol (cognitive 19) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14234 — LipidMsmsCharacterization.JudgeIfnoChainSterol has cognitive complexity 19 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · Omega3nChainGenerator.GenerateDoubleBondsForSphingosine (cognitive 19) · ×1
  • Omega3nChainGenerator.GenerateDoubleBondsForSphingosine (cognitive 19) src/metadb/Lipidomics/Omega3nChainGenerator.vb:203 — Omega3nChainGenerator.GenerateDoubleBondsForSphingosine has cognitive complexity 19 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · Scanner.MeasureElement (cognitive 19) · ×1
  • Scanner.MeasureElement (cognitive 19) src/metadb/SMILES/Language/Scanner.vb:327 — Scanner.MeasureElement has cognitive complexity 19 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · ParseChain.WalkElement (cognitive 19) · ×1
  • ParseChain.WalkElement (cognitive 19) src/metadb/SMILES/ParseChain.vb:221 — ParseChain.WalkElement has cognitive complexity 19 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LibraryWorkspace.ReadWithHandleConflicts (cognitive 19) · ×1
  • LibraryWorkspace.ReadWithHandleConflicts (cognitive 19) src/mzmath/MSEngine/AnnotationPack/WorkspaceReader.vb:253 — LibraryWorkspace.ReadWithHandleConflicts has cognitive complexity 19 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · FragmentAssigner.FastFragmnetAssigner (cognitive 19) · ×1
  • FragmentAssigner.FastFragmnetAssigner (cognitive 19) src/mzmath/MSFinder/FragmentAssigner.vb:218 — FragmentAssigner.FastFragmnetAssigner has cognitive complexity 19 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · PeakAlignments.RIAlignment (cognitive 19) · ×1
  • PeakAlignments.RIAlignment (cognitive 19) src/mzmath/mz_deco/PeakAlignment.vb:116 — PeakAlignments.RIAlignment has cognitive complexity 19 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · BatchCorrection.CorrectMeanCentering (cognitive 19) · ×1
  • BatchCorrection.CorrectMeanCentering (cognitive 19) src/mzmath/mz_deco/Preprocessing/BatchCorrection.vb:128 — BatchCorrection.CorrectMeanCentering has cognitive complexity 19 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · BatchCorrection.CorrectQCRLSC (cognitive 19) · ×1
  • BatchCorrection.CorrectQCRLSC (cognitive 19) src/mzmath/mz_deco/Preprocessing/BatchCorrection.vb:235 — BatchCorrection.CorrectQCRLSC has cognitive complexity 19 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LCMSPreprocessor.Process (cognitive 19) · ×1
  • LCMSPreprocessor.Process (cognitive 19) src/mzmath/mz_deco/Preprocessing/LCMSPreprocessor.vb:73 — LCMSPreprocessor.Process has cognitive complexity 19 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · WiffScanFileReader.loadScan (cognitive 19) · ×1
  • WiffScanFileReader.loadScan (cognitive 19) src/assembly/sciexWiffReader/WiffFileReader/WiffScanFileReader.vb:277 — WiffScanFileReader.loadScan has cognitive complexity 19 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · SpectralPreprocessor.PolynomialBaselineCorrect (cognitive 19) · ×1
  • SpectralPreprocessor.PolynomialBaselineCorrect (cognitive 19) src/assembly/RamanSpectroscopy/RamanDataProcessor.vb:439 — SpectralPreprocessor.PolynomialBaselineCorrect has cognitive complexity 19 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MetaDbXref.makeUniqueQuery (cognitive 18) · ×1
  • MetaDbXref.makeUniqueQuery (cognitive 18) Rscript/Library/mzkit_app/src/mzkit/annotations/MetaDbXref.vb:697 — MetaDbXref.makeUniqueQuery has cognitive complexity 18 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · Assembly.ionMode (cognitive 18) · ×1
  • Assembly.ionMode (cognitive 18) Rscript/Library/mzkit_app/src/mzkit/assembly/Assembly.vb:503 — Assembly.ionMode has cognitive complexity 18 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · Assembly.getMs1Scans (cognitive 18) · ×1
  • Assembly.getMs1Scans (cognitive 18) Rscript/Library/mzkit_app/src/mzkit/assembly/Assembly.vb:553 — Assembly.getMs1Scans has cognitive complexity 18 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · FormulaTools.peakAnnotation_f (cognitive 18) · ×1
  • FormulaTools.peakAnnotation_f (cognitive 18) Rscript/Library/mzkit_app/src/mzkit/math/Formula.vb:214 — FormulaTools.peakAnnotation_f has cognitive complexity 18 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · TreeSearch.Search (cognitive 18) · ×1
  • TreeSearch.Search (cognitive 18) src/assembly/SpectrumTree/Query/TreeSearch.vb:209 — TreeSearch.Search has cognitive complexity 18 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · SoftenScaler.PopulateRectangle (cognitive 18) · ×1
  • SoftenScaler.PopulateRectangle (cognitive 18) src/visualize/MsImaging/Blender/Scaler/SoftenScaler.vb:73 — SoftenScaler.PopulateRectangle has cognitive complexity 18 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidEieioMsmsCharacterization.JudgeIfBismonoacylglycerophosphate (cognitive 18) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfBismonoacylglycerophosphate (cognitive 18) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:679 — LipidEieioMsmsCharacterization.JudgeIfBismonoacylglycerophosphate has cognitive complexity 18 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfWaxEster (cognitive 18) · ×1
  • LipidMsmsCharacterization.JudgeIfWaxEster (cognitive 18) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:16696 — LipidMsmsCharacterization.JudgeIfWaxEster has cognitive complexity 18 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · BondPosition.ParseStructure (cognitive 18) · ×1
  • BondPosition.ParseStructure (cognitive 18) src/metadb/Chemoinformatics/Lipid/BondPosition.vb:75 — BondPosition.ParseStructure has cognitive complexity 18 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · Atom.ensureValidFormat (cognitive 18) · ×1
  • Atom.ensureValidFormat (cognitive 18) src/metadb/Chemoinformatics/SDF/Struct/Atom.vb:157 — Atom.ensureValidFormat has cognitive complexity 18 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MetaInfoReader.GetBiosampleList (cognitive 18) · ×1
  • MetaInfoReader.GetBiosampleList (cognitive 18) src/metadb/Massbank/Public/NCBI/PubChem/Web/MetaInfoReader.vb:295 — MetaInfoReader.GetBiosampleList has cognitive complexity 18 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MathHelpers.LOESS (cognitive 18) · ×1
  • MathHelpers.LOESS (cognitive 18) src/mzmath/mz_deco/Preprocessing/MathHelpers.vb:672 — MathHelpers.LOESS has cognitive complexity 18 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MissingValueImputation.MarkMissingValues (cognitive 18) · ×1
  • MissingValueImputation.MarkMissingValues (cognitive 18) src/mzmath/mz_deco/Preprocessing/MissingValueImputation.vb:68 — MissingValueImputation.MarkMissingValues has cognitive complexity 18 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · DataFile.CreateQuantifyData (cognitive 18) · ×1
  • DataFile.CreateQuantifyData (cognitive 18) src/mzmath/TargetedMetabolomics/LinearQuantitative/Models/DataFile.vb:117 — DataFile.CreateQuantifyData has cognitive complexity 18 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · PeakAnalyzer.DerivativePeakDetect (cognitive 18) · ×1
  • PeakAnalyzer.DerivativePeakDetect (cognitive 18) src/assembly/RamanSpectroscopy/RamanDataProcessor.vb:1137 — PeakAnalyzer.DerivativePeakDetect has cognitive complexity 18 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · TableFromXICData.Solve (cognitive 17) · ×1
  • TableFromXICData.Solve (cognitive 17) Rscript/Library/mzkit_app/src/mzquant/mzDeco.vb:1478 — TableFromXICData.Solve has cognitive complexity 17 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · mzDeco.peakAlignment_func (cognitive 17) · ×1
  • mzDeco.peakAlignment_func (cognitive 17) Rscript/Library/mzkit_app/src/mzquant/mzDeco.vb:1653 — mzDeco.peakAlignment_func has cognitive complexity 17 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · FileReader.ParseTextFile (cognitive 17) · ×1
  • FileReader.ParseTextFile (cognitive 17) src/assembly/assembly/ASCII/Raman/FileReader.vb:96 — FileReader.ParseTextFile has cognitive complexity 17 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · DualRegionUnionPlot.DrawColorBar (cognitive 17) · ×1
  • DualRegionUnionPlot.DrawColorBar (cognitive 17) src/visualize/MsImaging/Plot/DualRegionUnionPlot.vb:241 — DualRegionUnionPlot.DrawColorBar has cognitive complexity 17 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidomicsConverter.setChainPropertiesVS2 (cognitive 17) · ×1
  • LipidomicsConverter.setChainPropertiesVS2 (cognitive 17) src/metadb/Lipidomics/Annotation/LipidomicsConverter.vb:3285 — LipidomicsConverter.setChainPropertiesVS2 has cognitive complexity 17 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidEieioMsmsCharacterization.JudgeIfSphingosine (cognitive 17) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfSphingosine (cognitive 17) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1772 — LipidEieioMsmsCharacterization.JudgeIfSphingosine has cognitive complexity 17 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfLysopg (cognitive 17) · ×1
  • LipidMsmsCharacterization.JudgeIfLysopg (cognitive 17) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5717 — LipidMsmsCharacterization.JudgeIfLysopg has cognitive complexity 17 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: 3 other methods here (LipidMsmsCharacterization.JudgeIfLysops, LipidMsmsCharacterization.JudgeIfLysopgD5, LipidMsmsCharacterization.JudgeIfLysopsD5) have the same decision points, in the same order, at the same nesting depths — so this is one pattern written 4 times rather than 4 independent problems. Splitting this body alone leaves the other 3 exactly as they are. Where these are variations on one operation, the change that clears all 4 is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfLysopi (cognitive 17) · ×1
  • LipidMsmsCharacterization.JudgeIfLysopi (cognitive 17) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5759 — LipidMsmsCharacterization.JudgeIfLysopi has cognitive complexity 17 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfLysopiD5) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfLysops (cognitive 17) · ×1
  • LipidMsmsCharacterization.JudgeIfLysops (cognitive 17) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5802 — LipidMsmsCharacterization.JudgeIfLysops has cognitive complexity 17 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: 3 other methods here (LipidMsmsCharacterization.JudgeIfLysopg, LipidMsmsCharacterization.JudgeIfLysopgD5, LipidMsmsCharacterization.JudgeIfLysopsD5) have the same decision points, in the same order, at the same nesting depths — so this is one pattern written 4 times rather than 4 independent problems. Splitting this body alone leaves the other 3 exactly as they are. Where these are variations on one operation, the change that clears all 4 is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfOxfattyacid (cognitive 17) · ×1
  • LipidMsmsCharacterization.JudgeIfOxfattyacid (cognitive 17) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7706 — LipidMsmsCharacterization.JudgeIfOxfattyacid has cognitive complexity 17 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfSphingosine (cognitive 17) · ×1
  • LipidMsmsCharacterization.JudgeIfSphingosine (cognitive 17) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12178 — LipidMsmsCharacterization.JudgeIfSphingosine has cognitive complexity 17 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfVitaminDmolecules (cognitive 17) · ×1
  • LipidMsmsCharacterization.JudgeIfVitaminDmolecules (cognitive 17) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13513 — LipidMsmsCharacterization.JudgeIfVitaminDmolecules has cognitive complexity 17 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfLysopgD5 (cognitive 17) · ×1
  • LipidMsmsCharacterization.JudgeIfLysopgD5 (cognitive 17) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15899 — LipidMsmsCharacterization.JudgeIfLysopgD5 has cognitive complexity 17 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: 3 other methods here (LipidMsmsCharacterization.JudgeIfLysopg, LipidMsmsCharacterization.JudgeIfLysops, LipidMsmsCharacterization.JudgeIfLysopsD5) have the same decision points, in the same order, at the same nesting depths — so this is one pattern written 4 times rather than 4 independent problems. Splitting this body alone leaves the other 3 exactly as they are. Where these are variations on one operation, the change that clears all 4 is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfLysopiD5 (cognitive 17) · ×1
  • LipidMsmsCharacterization.JudgeIfLysopiD5 (cognitive 17) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15941 — LipidMsmsCharacterization.JudgeIfLysopiD5 has cognitive complexity 17 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidMsmsCharacterization.JudgeIfLysopi) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfLysopsD5 (cognitive 17) · ×1
  • LipidMsmsCharacterization.JudgeIfLysopsD5 (cognitive 17) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15984 — LipidMsmsCharacterization.JudgeIfLysopsD5 has cognitive complexity 17 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: 3 other methods here (LipidMsmsCharacterization.JudgeIfLysopg, LipidMsmsCharacterization.JudgeIfLysops, LipidMsmsCharacterization.JudgeIfLysopgD5) have the same decision points, in the same order, at the same nesting depths — so this is one pattern written 4 times rather than 4 independent problems. Splitting this body alone leaves the other 3 exactly as they are. Where these are variations on one operation, the change that clears all 4 is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · PCEidSpectrumGenerator.EidSpecificSpectrum (cognitive 17) · ×1
  • PCEidSpectrumGenerator.EidSpecificSpectrum (cognitive 17) src/metadb/Lipidomics/SpectrumGenerator/PCEidSpectrumGenerator.vb:172 — PCEidSpectrumGenerator.EidSpecificSpectrum has cognitive complexity 17 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MummichogAnnotator.New.ctor (cognitive 17) · ×1
  • MummichogAnnotator.New.ctor (cognitive 17) src/mzmath/Mummichog/MummichogModule.vb:104 — MummichogAnnotator.New.ctor has cognitive complexity 17 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · BatchCorrection.CorrectLOESS (cognitive 17) · ×1
  • BatchCorrection.CorrectLOESS (cognitive 17) src/mzmath/mz_deco/Preprocessing/BatchCorrection.vb:297 — BatchCorrection.CorrectLOESS has cognitive complexity 17 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · RICalibrate.ConvertRI (cognitive 17) · ×1
  • RICalibrate.ConvertRI (cognitive 17) src/mzmath/mz_deco/RICalibrate.vb:20 — RICalibrate.ConvertRI has cognitive complexity 17 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · NoiseEstimator.EstimateByPeakValley (cognitive 17) · ×1
  • NoiseEstimator.EstimateByPeakValley (cognitive 17) src/mzmath/mz_deco/Signals/PeakFinding/NoiseEstimator.vb:98 — NoiseEstimator.EstimateByPeakValley has cognitive complexity 17 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · PeakDetector.EstimateAsymmetryFactor (cognitive 17) · ×1
  • PeakDetector.EstimateAsymmetryFactor (cognitive 17) src/mzmath/mz_deco/Signals/PeakFinding/PeakDetector.vb:545 — PeakDetector.EstimateAsymmetryFactor has cognitive complexity 17 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MSI.SampleBootstraping (cognitive 16) · ×1
  • MSI.SampleBootstraping (cognitive 16) Rscript/Library/mzkit_app/src/mzkit/comprehensive/MSI.vb:1939 — MSI.SampleBootstraping has cognitive complexity 16 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · Visual.SpectrumPlot (cognitive 16) · ×1
  • Visual.SpectrumPlot (cognitive 16) Rscript/Library/mzkit_app/src/mzplot/src/Visual.vb:819 — Visual.SpectrumPlot has cognitive complexity 16 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · mzDeco.find_peaks (cognitive 16) · ×1
  • mzDeco.find_peaks (cognitive 16) Rscript/Library/mzkit_app/src/mzquant/mzDeco.vb:1203 — mzDeco.find_peaks has cognitive complexity 16 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · PackSingleCellsRaw.PackRawData (cognitive 16) · ×1
  • PackSingleCellsRaw.PackRawData (cognitive 16) src/assembly/Comprehensive/SingleCells/PackSingleCellsRaw.vb:80 — PackSingleCellsRaw.PackRawData has cognitive complexity 16 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · Proc.New.ctor (cognitive 16) · ×1
  • Proc.New.ctor (cognitive 16) src/assembly/NMRFidTool/Proc.vb:149 — Proc.New.ctor has cognitive complexity 16 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMassLibraryGenerator.commonCeramideOxGenerator (cognitive 16) · ×1
  • LipidMassLibraryGenerator.commonCeramideOxGenerator (cognitive 16) src/metadb/Lipidomics/Annotation/LipidMassLibraryGenerator.vb:1177 — LipidMassLibraryGenerator.commonCeramideOxGenerator has cognitive complexity 16 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MsScanMatching.GetLipidMoleculerSpeciesLevelAnnotationResultForEIEIO (cognitive 16) · ×1
  • MsScanMatching.GetLipidMoleculerSpeciesLevelAnnotationResultForEIEIO (cognitive 16) src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:289 — MsScanMatching.GetLipidMoleculerSpeciesLevelAnnotationResultForEIEIO has cognitive complexity 16 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (MsScanMatching.GetLipidMoleculeAnnotationResult) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · MsScanMatching.GetLipidMoleculeAnnotationResult (cognitive 16) · ×1
  • MsScanMatching.GetLipidMoleculeAnnotationResult (cognitive 16) src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:871 — MsScanMatching.GetLipidMoleculeAnnotationResult has cognitive complexity 16 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (MsScanMatching.GetLipidMoleculerSpeciesLevelAnnotationResultForEIEIO) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidEieioMsmsCharacterization.JudgeIfCholesterylEster (cognitive 16) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfCholesterylEster (cognitive 16) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:2021 — LipidEieioMsmsCharacterization.JudgeIfCholesterylEster has cognitive complexity 16 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidEieioMsmsCharacterization.JudgeIfCholesterylEsterD7) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidEieioMsmsCharacterization.JudgeIfCholesterylEsterD7 (cognitive 16) · ×1
  • LipidEieioMsmsCharacterization.JudgeIfCholesterylEsterD7 (cognitive 16) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:3496 — LipidEieioMsmsCharacterization.JudgeIfCholesterylEsterD7 has cognitive complexity 16 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (LipidEieioMsmsCharacterization.JudgeIfCholesterylEster) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfDmedOxfattyacid (cognitive 16) · ×1
  • LipidMsmsCharacterization.JudgeIfDmedOxfattyacid (cognitive 16) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7760 — LipidMsmsCharacterization.JudgeIfDmedOxfattyacid has cognitive complexity 16 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · LipidMsmsCharacterization.JudgeIfCaseSpecies (cognitive 16) · ×1
  • LipidMsmsCharacterization.JudgeIfCaseSpecies (cognitive 16) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13726 — LipidMsmsCharacterization.JudgeIfCaseSpecies has cognitive complexity 16 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · SpectrumGrid.Clustering (cognitive 16) · ×1
  • SpectrumGrid.Clustering (cognitive 16) src/mzmath/MoleculeNetworking/SpectrumGrid/SpectrumGrid.vb:133 — SpectrumGrid.Clustering has cognitive complexity 16 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · SMILESEmbedding.StructureDocuments (cognitive 16) · ×1
  • SMILESEmbedding.StructureDocuments (cognitive 16) src/mzmath/ms2_simulator/SMILESEmbedding.vb:69 — SMILESEmbedding.StructureDocuments has cognitive complexity 16 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MummichogAnnotator.MatchPeaksToLibrary (cognitive 16) · ×1
  • MummichogAnnotator.MatchPeaksToLibrary (cognitive 16) src/mzmath/Mummichog/MummichogModule.vb:318 — MummichogAnnotator.MatchPeaksToLibrary has cognitive complexity 16 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · Canonical.BuildCanonicalFormula (cognitive 16) · ×1
  • Canonical.BuildCanonicalFormula (cognitive 16) src/metadb/Chemoinformatics/Formula/Models/Canonical.vb:76 — Canonical.BuildCanonicalFormula has cognitive complexity 16 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · Formula.CompareFormalCharge (cognitive 16) · ×1
  • Formula.CompareFormalCharge (cognitive 16) src/metadb/Chemoinformatics/Formula/Models/Formula.vb:315 — Formula.CompareFormalCharge has cognitive complexity 16 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MetaData.EqualsAny (cognitive 16) · ×1
  • MetaData.EqualsAny (cognitive 16) src/metadb/Massbank/Public/lipidMAPS/SDF.vb:151 — MetaData.EqualsAny has cognitive complexity 16 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · Statistics.HMDBCoverages (cognitive 16) · ×1
  • Statistics.HMDBCoverages (cognitive 16) src/metadb/Massbank/Statistics.vb:103 — Statistics.HMDBCoverages has cognitive complexity 16 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · FormulaBuilder.WalkElement (cognitive 16) · ×1
  • FormulaBuilder.WalkElement (cognitive 16) src/metadb/SMILES/FormulaBuilder.vb:116 — FormulaBuilder.WalkElement has cognitive complexity 16 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · ChemicalFormula.Decomposition (cognitive 16) · ×1
  • ChemicalFormula.Decomposition (cognitive 16) src/metadb/SMILES/Graph/ChemicalFormula.vb:132 — ChemicalFormula.Decomposition has cognitive complexity 16 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · PeptideCalc.GetAminoAcidByFixedModifications (cognitive 16) · ×1
  • PeptideCalc.GetAminoAcidByFixedModifications (cognitive 16) src/mzmath/MSEngine/Proteomics/PeptideCalc.vb:169 — PeptideCalc.GetAminoAcidByFixedModifications has cognitive complexity 16 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (PeptideCalc.GetAminoAcidByVariableModifications) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · PeptideCalc.GetAminoAcidByVariableModifications (cognitive 16) · ×1
  • PeptideCalc.GetAminoAcidByVariableModifications (cognitive 16) src/mzmath/MSEngine/Proteomics/PeptideCalc.vb:390 — PeptideCalc.GetAminoAcidByVariableModifications has cognitive complexity 16 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (PeptideCalc.GetAminoAcidByFixedModifications) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · MsScanMatching.GetTotalSimilarity (cognitive 16) · ×1
  • MsScanMatching.GetTotalSimilarity (cognitive 16) src/mzmath/MSEngine/Search/MsScanMatching.vb:1168 — MsScanMatching.GetTotalSimilarity has cognitive complexity 16 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · SpectrumHandler.GetNormalizedPeak4SpectralEntropySimilarityCalc (cognitive 16) · ×1
  • SpectrumHandler.GetNormalizedPeak4SpectralEntropySimilarityCalc (cognitive 16) src/mzmath/MSEngine/SpectrumHandler.vb:201 — SpectrumHandler.GetNormalizedPeak4SpectralEntropySimilarityCalc has cognitive complexity 16 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · SpectrumHandler.GetRefinedPeaklist (cognitive 16) · ×1
  • SpectrumHandler.GetRefinedPeaklist (cognitive 16) src/mzmath/MSEngine/SpectrumHandler.vb:229 — SpectrumHandler.GetRefinedPeaklist has cognitive complexity 16 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · BatchCorrection.CorrectMedianCentering (cognitive 16) · ×1
  • BatchCorrection.CorrectMedianCentering (cognitive 16) src/mzmath/mz_deco/Preprocessing/BatchCorrection.vb:177 — BatchCorrection.CorrectMedianCentering has cognitive complexity 16 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D2 · Cognitive Complexity · MissingValueImputation.ImputeMean (cognitive 16) · ×1
  • MissingValueImputation.ImputeMean (cognitive 16) src/mzmath/mz_deco/Preprocessing/MissingValueImputation.vb:244 — MissingValueImputation.ImputeMean has cognitive complexity 16 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (MissingValueImputation.ImputeMedian) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · MissingValueImputation.ImputeMedian (cognitive 16) · ×1
  • MissingValueImputation.ImputeMedian (cognitive 16) src/mzmath/mz_deco/Preprocessing/MissingValueImputation.vb:274 — MissingValueImputation.ImputeMedian has cognitive complexity 16 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function. This shape REPEATS in the file: one other method here (MissingValueImputation.ImputeMean) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.
D2 · Cognitive Complexity · SaveXcms.ReadTextTable (cognitive 16) · ×1
  • SaveXcms.ReadTextTable (cognitive 16) src/mzmath/mz_deco/Save/SaveXcms.vb:80 — SaveXcms.ReadTextTable has cognitive complexity 16 (threshold 15). To reduce it, flatten the nesting: invert conditions into early returns or guard clauses so the happy path stays at one level, and lift the deepest nested block into its own named function.
D29 · Static Analysis (SAST) · REDACTED · ×1
  • REDACTED
D35 · Change Coupling · Change coupling · ×1
  • Change coupling: GCxGCTIC2DPlot.vb ↔ GCxGCTIC3DPeaks.vb src/visualize/ComprehensiveMsPlot/GCxGC/GCxGCTIC2DPlot.vb:1 — `src/visualize/ComprehensiveMsPlot/GCxGC/GCxGCTIC2DPlot.vb` and `src/visualize/ComprehensiveMsPlot/GCxGC/GCxGCTIC3DPeaks.vb` change together 55% of the time (6 of the 11 commits that touched whichever of the two files changed less often, counting a file under its earlier names as well, and counted over this repository's 10,000 most recent commits rather than its whole history — a repo-wide or module-wide sweep is evidence about the sweep rather than about any pair inside it and is left out of BOTH sides of this ratio, while a dependency bump, a formatter/rename sweep, or a commit whose edit to one of the two files was a tool directive such as //go:generate or whitespace only is left out of the shared count ONLY, so the two sides are not taken over identical commit sets). They sit in the same directory, and in this ecosystem sibling files there normally share one namespace/package — so a direct reference between them needs no import and this pass cannot see whether one exists. Read the pair before acting: if one file only DECLARES what the other consumes (a constants/types file beside its user), the co-change is definitional and the question is whether the split earns its keep; if they duplicate structure, extract the common part into a shared function or type they both call; if neither holds, the coupling is hidden and worth breaking. You can check this without leaving the row: of the 6 shared commits counted here, the most recent 3 are `2778ec19` split project into multiple parts; `95fe0050` update source file banner headers![MS data plot] (at that commit the files were still `src/visualize/plot/GCxGC/GCxGCTIC2DPlot.vb` and `src/visualize/plot/GCxGC/GCxGCTIC3DPeaks.vb`); `791e54e6` fix of the missing data model (at that commit the files were still `src/visualize/plot/GCxGC/GCxGCTIC2DPlot.vb` and `src/visualize/plot/GCxGC/GCxGCTIC3DPeaks.vb`) — run `git show` on any of them.
D35 · Change Coupling · Change-coupling hub · ×1
  • Change-coupling hub: PeakTablePlot.vb → GCxGCTIC2DPlot.vb, ChromatogramPeakPlot.vb, TICplot.vb, PeakAssign.vb, RawScatterPlot.vb src/visualize/plot/PeakTablePlot.vb — `src/visualize/plot/PeakTablePlot.vb` changes together with 5 other files — `src/visualize/ComprehensiveMsPlot/GCxGC/GCxGCTIC2DPlot.vb`, `src/visualize/plot/ChromatogramPlot/ChromatogramPeakPlot.vb`, `src/visualize/plot/ChromatogramPlot/TICplot.vb`, `src/visualize/plot/PeakAssign.vb`, `src/visualize/plot/RawScatterPlot.vb` — none of which declares a dependency on it: one file is the hub of 5 separate couplings, not 5 unrelated pairs. Read the hub first: if the others each duplicate a part of what it does, the shared concern belongs in ONE unit and extracting it clears every edge at once; if the hub is a registry, dispatcher or barrel that must name each of them, the coupling is structural and the question is whether that list can be discovered instead of enumerated. Fixing the hub is one change; breaking the couplings one pair at a time is 5.
D4 · Code Duplication · Near-duplicate member family (4 members, 17 shared lines) · ×1
  • Near-duplicate member family (4 members, 17 shared lines) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1773 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1773-1804 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12125-12175 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12179-12228 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12232-12283 — These 4 members are variants of one another: a block of 17 lines reported below appears in every one of them, and the pairwise near-duplicate rows they would otherwise produce are collapsed into this row. Read them as one construct written 4 times. The repair is at the members' grain — factor the shared implementation out once and have all of them call it with their differences as parameters or as an injected step, or, where the difference is systematic, generate them from one template. Extracting the individual blocks below is not the same fix: it leaves every body in place and the next edit still has to be made 4 times.
D4 · Code Duplication · Near-duplicate member pair (501 shared lines) · ×1
  • Near-duplicate member pair (501 shared lines) src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:290 — src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:290-868 | src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:873-1448 — These two members are variants of one another: 501 of their lines are already reported as duplicated blocks below, spread through both bodies rather than gathered into one. Read them as a single construct written twice. The repair is at the members' grain — factor the shared pipeline into one implementation the two call with their differences as parameters or as an injected step, or, where the difference is systematic (sync against async, one transport against another), generate one from the other. Extracting the individual blocks below is not the same fix: it leaves the two bodies in place and the next edit still has to be made twice.
D4 · Code Duplication · Near-duplicate member pair (77 shared lines) · ×1
  • Near-duplicate member pair (77 shared lines) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3639 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3639-3734 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15810-15897 — These two members are variants of one another: 77 of their lines are already reported as duplicated blocks below, spread through both bodies rather than gathered into one. Read them as a single construct written twice. The repair is at the members' grain — factor the shared pipeline into one implementation the two call with their differences as parameters or as an injected step, or, where the difference is systematic (sync against async, one transport against another), generate one from the other. Extracting the individual blocks below is not the same fix: it leaves the two bodies in place and the next edit still has to be made twice.
D4 · Code Duplication · Near-duplicate member pair (42 shared lines) · ×1
  • Near-duplicate member pair (42 shared lines) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1147 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1147-1212 | src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:2914-2974 — These two members are variants of one another: 42 of their lines are already reported as duplicated blocks below, spread through both bodies rather than gathered into one. Read them as a single construct written twice. The repair is at the members' grain — factor the shared pipeline into one implementation the two call with their differences as parameters or as an injected step, or, where the difference is systematic (sync against async, one transport against another), generate one from the other. Extracting the individual blocks below is not the same fix: it leaves the two bodies in place and the next edit still has to be made twice.
D4 · Code Duplication · Edited copy of a member (102 corresponding lines) · ×1
  • Edited copy of a member (102 corresponding lines) src/mzmath/MSFinder/FormulaStringParcer.vb:117 — src/mzmath/MSFinder/FormulaStringParcer.vb:117-239 | src/mzmath/MSFinder/FormulaStringParcer.vb:352-471 — These two members are one piece of code written twice and then edited apart: 102 consecutive lines correspond almost exactly, broken only by small local edits. Most of that correspondence is NOT reported as duplicated blocks below — the edits cut it into fragments and only the largest of them clear the block floor, so the rows below understate it. The repair is at the members' grain — factor the shared implementation into one the two call with their differences as parameters or as an injected step, or, where the difference is systematic (an extra return value, one transport against another), generate one from the other. Left alone, the next edit has to be made twice and the two will drift further apart.
D4 · Code Duplication · Members sharing a duplicated core (44 members, 50+ identical tokens) · ×1
  • Members sharing a duplicated core (44 members, 50+ identical tokens) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1215 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1215-1244 | src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1248-1285 | src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1288-1323 | src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:2977-3008 | src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:3012-3050 | src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:3053-3088 | src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:3528-3601 | src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:3605-3632 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:2581-2697 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3996-4091 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4095-4188 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4312-4407 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4411-4524 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4528-4645 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4649-4758 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4762-4868 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5580-5642 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5646-5714 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5718-5756 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5760-5800 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5803-5840 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6169-6255 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6259-6332 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7604-7660 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7664-7682 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7707-7758 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:8131-8190 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:9061-9118 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11578-11663 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11667-11730 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11733-11797 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11849-11913 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11917-11983 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11987-12053 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12057-12120 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12289-12338 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12342-12387 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13373-13427 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13431-13450 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14077-14137 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15608-15715 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15900-15938 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15942-15982 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15985-16022 — These 44 members share a duplicated core: a run of at least 50 identical tokens appears in every one of them. That run is NOT broken out as duplicated-block rows below — it is what admitted this row, and the blocks below cover only the part of it that clears the block floor, so they understate the correspondence. Read the members as one construct written 44 times. The repair is at the members' grain — factor the shared implementation out once and have all of them call it with their differences as parameters or as an injected step, or, where the difference is systematic, generate them from one template. Extracting the individual blocks below is not the same fix: it leaves every body in place and the next edit still has to be made 44 times.
D4 · Code Duplication · Members sharing a duplicated core (39 members, 50+ identical tokens) · ×1
  • Members sharing a duplicated core (39 members, 50+ identical tokens) src/metadb/Lipidomics/SpectrumGenerator/BMPEidSpectrumGenerator.vb:95 — src/metadb/Lipidomics/SpectrumGenerator/BMPEidSpectrumGenerator.vb:95-105 | src/metadb/Lipidomics/SpectrumGenerator/BMPSpectrumGenerator.vb:95-104 | src/metadb/Lipidomics/SpectrumGenerator/DGEidSpectrumGenerator.vb:91-101 | src/metadb/Lipidomics/SpectrumGenerator/DGSpectrumGenerator.vb:91-100 | src/metadb/Lipidomics/SpectrumGenerator/DGTASpectrumGenerator.vb:98-106 | src/metadb/Lipidomics/SpectrumGenerator/DGTSSpectrumGenerator.vb:102-110 | src/metadb/Lipidomics/SpectrumGenerator/DGd5SpectrumGenerator.vb:92-101 | src/metadb/Lipidomics/SpectrumGenerator/DMEDFAHFASpectrumGenerator.vb:97-106 | src/metadb/Lipidomics/SpectrumGenerator/HBMPSpectrumGenerator.vb:100-112 | src/metadb/Lipidomics/SpectrumGenerator/LDGTASpectrumGenerator.vb:100-108 | src/metadb/Lipidomics/SpectrumGenerator/LDGTSSpectrumGenerator.vb:100-108 | src/metadb/Lipidomics/SpectrumGenerator/LPCEidSpectrumGenerator.vb:103-116 | src/metadb/Lipidomics/SpectrumGenerator/LPCSpectrumGenerator.vb:103-115 | src/metadb/Lipidomics/SpectrumGenerator/LPCd5SpectrumGenerator.vb:103-115 | src/metadb/Lipidomics/SpectrumGenerator/LPEEidSpectrumGenerator.vb:101-110 | src/metadb/Lipidomics/SpectrumGenerator/LPESpectrumGenerator.vb:101-109 | src/metadb/Lipidomics/SpectrumGenerator/LPEd5SpectrumGenerator.vb:101-109 | src/metadb/Lipidomics/SpectrumGenerator/LPGSpectrumGenerator.vb:98-107 | src/metadb/Lipidomics/SpectrumGenerator/LPGd5SpectrumGenerator.vb:97-105 | src/metadb/Lipidomics/SpectrumGenerator/LPISpectrumGenerator.vb:101-109 | src/metadb/Lipidomics/SpectrumGenerator/LPId5SpectrumGenerator.vb:101-109 | src/metadb/Lipidomics/SpectrumGenerator/LPSEidSpectrumGenerator.vb:103-112 | src/metadb/Lipidomics/SpectrumGenerator/LPSSpectrumGenerator.vb:102-110 | src/metadb/Lipidomics/SpectrumGenerator/LPSd5SpectrumGenerator.vb:102-110 | src/metadb/Lipidomics/SpectrumGenerator/PCEidSpectrumGenerator.vb:98-107 | src/metadb/Lipidomics/SpectrumGenerator/PCSpectrumGenerator.vb:98-106 | src/metadb/Lipidomics/SpectrumGenerator/PCd5SpectrumGenerator.vb:98-106 | src/metadb/Lipidomics/SpectrumGenerator/PEEidSpectrumGenerator.vb:99-109 | src/metadb/Lipidomics/SpectrumGenerator/PESpectrumGenerator.vb:99-108 | src/metadb/Lipidomics/SpectrumGenerator/PEd5SpectrumGenerator.vb:101-110 | src/metadb/Lipidomics/SpectrumGenerator/PGEidSpectrumGenerator.vb:99-109 | src/metadb/Lipidomics/SpectrumGenerator/PGSpectrumGenerator.vb:100-109 | src/metadb/Lipidomics/SpectrumGenerator/PGd5SpectrumGenerator.vb:99-108 | src/metadb/Lipidomics/SpectrumGenerator/PIEidSpectrumGenerator.vb:99-110 | src/metadb/Lipidomics/SpectrumGenerator/PISpectrumGenerator.vb:99-108 | src/metadb/Lipidomics/SpectrumGenerator/PId5SpectrumGenerator.vb:99-108 | src/metadb/Lipidomics/SpectrumGenerator/PSEidSpectrumGenerator.vb:102-111 | src/metadb/Lipidomics/SpectrumGenerator/PSSpectrumGenerator.vb:101-110 | src/metadb/Lipidomics/SpectrumGenerator/PSd5SpectrumGenerator.vb:101-110 — These 39 members share a duplicated core: a run of at least 50 identical tokens appears in every one of them. That run is NOT broken out as duplicated-block rows below — it is what admitted this row, and the blocks below cover only the part of it that clears the block floor, so they understate the correspondence. Read the members as one construct written 39 times. The repair is at the members' grain — factor the shared implementation out once and have all of them call it with their differences as parameters or as an injected step, or, where the difference is systematic, generate them from one template. Extracting the individual blocks below is not the same fix: it leaves every body in place and the next edit still has to be made 39 times.
D4 · Code Duplication · Members sharing a duplicated core (9 members, 50+ identical tokens) · ×1
  • Members sharing a duplicated core (9 members, 50+ identical tokens) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:2521 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:2521-2577 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:2581-2697 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3381-3503 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3507-3532 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7429-7499 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:9061-9118 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14652-14741 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15608-15715 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:16025-16084 — These 9 members share a duplicated core: a run of at least 50 identical tokens appears in every one of them. That run is NOT broken out as duplicated-block rows below — it is what admitted this row, and the blocks below cover only the part of it that clears the block floor, so they understate the correspondence. Read the members as one construct written 9 times. The repair is at the members' grain — factor the shared implementation out once and have all of them call it with their differences as parameters or as an injected step, or, where the difference is systematic, generate them from one template. Extracting the individual blocks below is not the same fix: it leaves every body in place and the next edit still has to be made 9 times.
D4 · Code Duplication · Members sharing a duplicated core (5 members, 50+ identical tokens) · ×1
  • Members sharing a duplicated core (5 members, 50+ identical tokens) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:109 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:109-130 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:261-282 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:1118-1138 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:1158-1180 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:1376-1398 — These 5 members share a duplicated core: a run of at least 50 identical tokens appears in every one of them. That run is NOT broken out as duplicated-block rows below — it is what admitted this row, and the blocks below cover only the part of it that clears the block floor, so they understate the correspondence. Read the members as one construct written 5 times. The repair is at the members' grain — factor the shared implementation out once and have all of them call it with their differences as parameters or as an injected step, or, where the difference is systematic, generate them from one template. Extracting the individual blocks below is not the same fix: it leaves every body in place and the next edit still has to be made 5 times.
D4 · Code Duplication · Duplicated block (396–398 lines × 2) · ×1
  • Duplicated block (396–398 lines × 2) src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:414 — src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:414-811 | src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:997-1392 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
D4 · Code Duplication · Duplicated block (98 lines × 3) · ×1
  • Duplicated block (98 lines × 3) src/mzmath/MSFinder/FormulaStringParcer.vb:133 — src/mzmath/MSFinder/FormulaStringParcer.vb:133-230 | src/mzmath/MSFinder/FormulaStringParcer.vb:368-465 | src/mzmath/MSFinder/FormulaStringParcer.vb:497-594 — all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just before the matched lines, `src/mzmath/MSFinder/FormulaStringParcer.vb:491` calls `Contains`, `Replace` and `src/mzmath/MSFinder/FormulaStringParcer.vb:364` does not — after which the two agree again for 2 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live.
D4 · Code Duplication · Duplicated block (61 lines × 2) · ×1
  • Duplicated block (61 lines × 2) src/metadb/Chemoinformatics/Formula/SevenGoldenRulesCheck.vb:215 — src/metadb/Chemoinformatics/Formula/SevenGoldenRulesCheck.vb:215-275 | src/metadb/Chemoinformatics/Formula/SevenGoldenRulesCheck.vb:280-340 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at `src/metadb/Chemoinformatics/Formula/SevenGoldenRulesCheck.vb:215` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
D4 · Code Duplication · Duplicated block (57 lines × 2) · ×1
  • Duplicated block (57 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:2623 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:2623-2679 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15650-15706 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
D4 · Code Duplication · Duplicated block (58 lines × 2) · ×1
  • Duplicated block (58 lines × 2) src/mzmath/MSEngine/Search/MsScanMatching.vb:825 — src/mzmath/MSEngine/Search/MsScanMatching.vb:825-882 | src/mzmath/MSEngine/Search/MsScanMatching.vb:974-1031 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
D4 · Code Duplication · Duplicated block (56 lines × 2) · ×1
  • Duplicated block (56 lines × 2) src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:1473 — src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:1473-1528 | src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:1637-1692 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
D4 · Code Duplication · Duplicated block (54 lines × 2) · ×1
  • Duplicated block (54 lines × 2) src/metadb/Lipidomics/SpectrumGenerator/LPGSpectrumGenerator.vb:127 — src/metadb/Lipidomics/SpectrumGenerator/LPGSpectrumGenerator.vb:127-180 | src/metadb/Lipidomics/SpectrumGenerator/LPGd5SpectrumGenerator.vb:125-178 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/LPGSpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/LPGd5SpectrumGenerator.vb` as WHOLE FILES: this scan already matched 3 separate duplicated blocks between them, totalling at least 79 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
D4 · Code Duplication · Duplicated block (47–48 lines × 2) · ×1
  • Duplicated block (47–48 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4033 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4033-4079 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4130-4177 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
D4 · Code Duplication · Duplicated block (40 lines × 5) · ×1
  • Duplicated block (40 lines × 5) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4351 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4351-4390 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4448-4487 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4569-4608 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4683-4722 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4793-4832 — all 5 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited.
D4 · Code Duplication · Duplicated block (31–41 lines × 3) · ×1
  • Duplicated block (31–41 lines × 3) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:3541 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:3541-3581 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6284-6324 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11594-11624 — before extracting anything, compare `src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb` and `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb` as WHOLE FILES: this scan already matched 32 separate duplicated blocks between them, totalling at least 530 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
D4 · Code Duplication · Duplicated block (4–41 lines × 3) · ×1
  • Duplicated block (4–41 lines × 3) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3381 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3381-3421 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14692-14695 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:16025-16065 — all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14692` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
D4 · Code Duplication · Duplicated block (39–40 lines × 2) · ×1
  • Duplicated block (39–40 lines × 2) src/metadb/Lipidomics/Annotation/LipidomicsConverter.vb:5526 — src/metadb/Lipidomics/Annotation/LipidomicsConverter.vb:5526-5564 | src/metadb/Lipidomics/LipoqualityDatabaseManagerUtility.vb:821-860 — the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach — a location they all depend on today, or a new shared one if there is none — and call it from each site; until then, every change has to be made twice.
D4 · Code Duplication · Duplicated block (33–35 lines × 3) · ×1
  • Duplicated block (33–35 lines × 3) src/metadb/Lipidomics/LipoqualityDatabaseManagerUtility.vb:275 — src/metadb/Lipidomics/LipoqualityDatabaseManagerUtility.vb:275-307 | src/metadb/Lipidomics/LipoqualityDatabaseManagerUtility.vb:318-351 | src/metadb/Lipidomics/LipoqualityDatabaseManagerUtility.vb:363-397 — all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
D4 · Code Duplication · Duplicated block (32–34 lines × 7) · ×1
  • Duplicated block (32–34 lines × 7) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4048 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4048-4079 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4145-4177 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4358-4391 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4455-4488 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4576-4609 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4690-4723 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4800-4833 — all 7 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
D4 · Code Duplication · Duplicated block (34 lines × 2) · ×1
  • Duplicated block (34 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3639 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3639-3672 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15810-15843 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
D4 · Code Duplication · Duplicated block (26–32 lines × 3) · ×1
  • Duplicated block (26–32 lines × 3) src/mzmath/mz_deco/Preprocessing/BatchCorrection.vb:236 — src/mzmath/mz_deco/Preprocessing/BatchCorrection.vb:236-267 | src/mzmath/mz_deco/Preprocessing/BatchCorrection.vb:298-323 | src/mzmath/mz_deco/Preprocessing/BatchCorrection.vb:564-593 — all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited.
D4 · Code Duplication · Duplicated block (18–32 lines × 2) · ×1
  • Duplicated block (18–32 lines × 2) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1787 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1787-1804 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12197-12228 — before extracting anything, compare `src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb` and `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb` as WHOLE FILES: this scan already matched 32 separate duplicated blocks between them, totalling at least 530 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it.
D4 · Code Duplication · Duplicated block (28–32 lines × 2) · ×1
  • Duplicated block (28–32 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:9901 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:9901-9928 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:9979-10010 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it.
D4 · Code Duplication · Duplicated block (18–31 lines × 2) · ×1
  • Duplicated block (18–31 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:2523 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:2523-2540 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7434-7464 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
D4 · Code Duplication · Duplicated block (20–30 lines × 2) · ×1
  • Duplicated block (20–30 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13590 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13590-13609 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14959-14988 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
D4 · Code Duplication · Duplicated block (10–30 lines × 2) · ×1
  • Duplicated block (10–30 lines × 2) src/mzmath/MSFinder/FormulaGenerator.vb:277 — src/mzmath/MSFinder/FormulaGenerator.vb:277-286 | src/mzmath/MSFinder/FormulaGenerator.vb:536-565 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
D4 · Code Duplication · Duplicated block (28–29 lines × 6) · ×1
  • Duplicated block (28–29 lines × 6) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11677 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11677-11705 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11743-11771 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11859-11886 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11930-11957 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12000-12027 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12073-12100 — all 6 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited.
D4 · Code Duplication · Duplicated block (10–29 lines × 4) · ×1
  • Duplicated block (10–29 lines × 4) src/metadb/Lipidomics/SpectrumGenerator/PCOadSpectrumGenerator.vb:93 — src/metadb/Lipidomics/SpectrumGenerator/PCOadSpectrumGenerator.vb:93-121 | src/metadb/Lipidomics/SpectrumGenerator/PEOadSpectrumGenerator.vb:120-129 | src/metadb/Lipidomics/SpectrumGenerator/PGOadSpectrumGenerator.vb:119-128 | src/metadb/Lipidomics/SpectrumGenerator/PIOadSpectrumGenerator.vb:116-125 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/PGOadSpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/PIOadSpectrumGenerator.vb` as WHOLE FILES: 84% of the shorter file's lines also appear in the other, so this reads as one file having been copied from the other rather than as a helper waiting to be extracted. The 2 duplicated block(s) this scan matched between them are fragments of that copy, not the extent of it — treat the file pair as the unit. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
D4 · Code Duplication · Duplicated block (28 lines × 2) · ×1
  • Duplicated block (28 lines × 2) src/metadb/Lipidomics/LipidParser/CeramideLipidParser.vb:75 — src/metadb/Lipidomics/LipidParser/CeramideLipidParser.vb:75-102 | src/metadb/Lipidomics/LipidParser/HexCerLipidParser.vb:74-101 — the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach — a file they already depend on, or a new one alongside them — and call it from both call sites, so a change lands once. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, `src/metadb/Lipidomics/LipidParser/CeramideLipidParser.vb:104` calls `classGroup` and `src/metadb/Lipidomics/LipidParser/HexCerLipidParser.vb:103` does not — after which the two agree again for 4 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live.
D4 · Code Duplication · Duplicated block (27–28 lines × 2) · ×1
  • Duplicated block (27–28 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:1206 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:1206-1232 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:1275-1302 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:1206` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
D4 · Code Duplication · Duplicated block (21–27 lines × 2) · ×1
  • Duplicated block (21–27 lines × 2) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1224 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1224-1244 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5730-5756 — before extracting anything, compare `src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb` and `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb` as WHOLE FILES: this scan already matched 32 separate duplicated blocks between them, totalling at least 530 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
D4 · Code Duplication · Duplicated block (22–27 lines × 2) · ×1
  • Duplicated block (22–27 lines × 2) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:2987 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:2987-3008 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15912-15938 — before extracting anything, compare `src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb` and `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb` as WHOLE FILES: this scan already matched 32 separate duplicated blocks between them, totalling at least 530 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
D4 · Code Duplication · Duplicated block (27 lines × 2) · ×1
  • Duplicated block (27 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3678 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3678-3704 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15845-15871 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
D4 · Code Duplication · Duplicated block (19–27 lines × 2) · ×1
  • Duplicated block (19–27 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:8146 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:8146-8164 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:9080-9106 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
D4 · Code Duplication · Duplicated block (26 lines × 3) · ×1
  • Duplicated block (26 lines × 3) src/assembly/NMRFidTool/Math/phasing/DSPPhaseCorrection.vb:101 — src/assembly/NMRFidTool/Math/phasing/DSPPhaseCorrection.vb:101-126 | src/assembly/NMRFidTool/Math/phasing/DSPPhaseCorrection.vb:149-174 | src/assembly/NMRFidTool/Math/phasing/DSPPhaseCorrection.vb:197-222 — all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited.
D4 · Code Duplication · Duplicated block (24–25 lines × 2) · ×1
  • Duplicated block (24–25 lines × 2) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1248 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1248-1271 | src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:3012-3036 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
D4 · Code Duplication · Duplicated block (24 lines × 2) · ×1
  • Duplicated block (24 lines × 2) src/metadb/Lipidomics/SpectrumGenerator/CLEidSpectrumGenerator.vb:177 — src/metadb/Lipidomics/SpectrumGenerator/CLEidSpectrumGenerator.vb:177-200 | src/metadb/Lipidomics/SpectrumGenerator/CLSpectrumGenerator.vb:163-186 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/CLEidSpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/CLSpectrumGenerator.vb` as WHOLE FILES: this scan already matched 3 separate duplicated blocks between them, totalling at least 38 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
D4 · Code Duplication · Duplicated block (22–24 lines × 2) · ×1
  • Duplicated block (22–24 lines × 2) src/mzmath/TargetedMetabolomics/LinearQuantitative/Linear/InternalStandardMethod.vb:175 — src/mzmath/TargetedMetabolomics/LinearQuantitative/Linear/InternalStandardMethod.vb:175-198 | src/mzmath/TargetedMetabolomics/MRM/QuantitativeAnalysis/StandardCurveWorker.vb:236-257 — the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach — a location they all depend on today, or a new shared one if there is none — and call it from each site; until then, every change has to be made twice.
D4 · Code Duplication · Duplicated block (20–23 lines × 3) · ×1
  • Duplicated block (20–23 lines × 3) src/metadb/Lipidomics/SpectrumGenerator/SMEidSpectrumGenerator.vb:95 — src/metadb/Lipidomics/SpectrumGenerator/SMEidSpectrumGenerator.vb:95-117 | src/metadb/Lipidomics/SpectrumGenerator/SMSpectrumGenerator.vb:98-117 | src/metadb/Lipidomics/SpectrumGenerator/SMd9SpectrumGenerator.vb:95-114 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/SMEidSpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/SMSpectrumGenerator.vb` as WHOLE FILES: this scan already matched 4 separate duplicated blocks between them, totalling at least 66 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
D4 · Code Duplication · Duplicated block (18–22 lines × 6) · ×1
  • Duplicated block (18–22 lines × 6) src/metadb/Lipidomics/SpectrumGenerator/Hex2CerSpectrumGenerator.vb:94 — src/metadb/Lipidomics/SpectrumGenerator/Hex2CerSpectrumGenerator.vb:94-111 | src/metadb/Lipidomics/SpectrumGenerator/HexCerSpectrumGenerator.vb:94-115 | src/metadb/Lipidomics/SpectrumGenerator/SMEidSpectrumGenerator.vb:97-117 | src/metadb/Lipidomics/SpectrumGenerator/SMOadSpectrumGenerator.vb:110-128 | src/metadb/Lipidomics/SpectrumGenerator/SMSpectrumGenerator.vb:100-117 | src/metadb/Lipidomics/SpectrumGenerator/SMd9SpectrumGenerator.vb:97-114 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/SMEidSpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/SMSpectrumGenerator.vb` as WHOLE FILES: this scan already matched 4 separate duplicated blocks between them, totalling at least 66 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
D4 · Code Duplication · Duplicated block (21–22 lines × 6) · ×1
  • Duplicated block (21–22 lines × 6) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:500 — src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:500-521 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:655-676 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:792-812 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:910-930 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1010-1030 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1093-1113 — all 6 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited.
D4 · Code Duplication · Duplicated block (13–22 lines × 4) · ×1
  • Duplicated block (13–22 lines × 4) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:2525 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:2525-2538 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3386-3398 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7441-7462 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:16030-16042 — all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it.
D4 · Code Duplication · Duplicated block (22 lines × 3) · ×1
  • Duplicated block (22 lines × 3) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:3551 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:3551-3580 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5602-5623 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6294-6323 — before extracting anything, compare `src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb` and `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb` as WHOLE FILES: this scan already matched 32 separate duplicated blocks between them, totalling at least 530 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just before the matched lines, `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5600` calls `fattyacidProductIon` and `src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:3549` does not — after which the two agree again for 3 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live.
D4 · Code Duplication · Duplicated block (19–22 lines × 3) · ×1
  • Duplicated block (19–22 lines × 3) src/metadb/Lipidomics/SpectrumGenerator/LPCOadSpectrumGenerator.vb:94 — src/metadb/Lipidomics/SpectrumGenerator/LPCOadSpectrumGenerator.vb:94-114 | src/metadb/Lipidomics/SpectrumGenerator/LPEOadSpectrumGenerator.vb:94-115 | src/metadb/Lipidomics/SpectrumGenerator/TGOadSpectrumGenerator.vb:88-106 — the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach — a file they already depend on, or a new one alongside them — and call it from all 3 call sites, so a change lands once.
D4 · Code Duplication · Duplicated block (19 lines × 2) · ×1
  • Duplicated block (19 lines × 2) Rscript/Library/mzkit_app/src/mzkit/annotations/Massbank.vb:916 — Rscript/Library/mzkit_app/src/mzkit/annotations/Massbank.vb:916-934 | Rscript/Library/mzkit_app/src/mzkit/annotations/Massbank.vb:940-958 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
D4 · Code Duplication · Duplicated block (18–22 lines × 2) · ×1
  • Duplicated block (18–22 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5583 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5583-5600 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7607-7628 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
D4 · Code Duplication · Duplicated block (20–21 lines × 7) · ×1
  • Duplicated block (20–21 lines × 7) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:497 — src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:497-516 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:652-672 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:789-808 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:907-926 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1007-1026 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1090-1109 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1154-1173 — all 7 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, `src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1111` calls `getAccurateMultiplatedIsotopeElement`, `getAccurateMargedIsotopeElement` and `src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1174` does not — after which the two agree again for 2 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live.
D4 · Code Duplication · Duplicated block (18–21 lines × 3) · ×1
  • Duplicated block (18–21 lines × 3) src/metadb/Lipidomics/SpectrumGenerator/EtherPCSpectrumGenerator.vb:101 — src/metadb/Lipidomics/SpectrumGenerator/EtherPCSpectrumGenerator.vb:101-118 | src/metadb/Lipidomics/SpectrumGenerator/EtherPEEidSpectrumGenerator.vb:102-122 | src/metadb/Lipidomics/SpectrumGenerator/EtherPESpectrumGenerator.vb:102-122 — the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach — a file they already depend on, or a new one alongside them — and call it from all 3 call sites, so a change lands once. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, `src/metadb/Lipidomics/SpectrumGenerator/EtherPEEidSpectrumGenerator.vb:122` calls `AddRange`, `EidSpecificSpectrum` and `src/metadb/Lipidomics/SpectrumGenerator/EtherPCSpectrumGenerator.vb:118` does not — after which the two agree again for 5 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live.
D4 · Code Duplication · Duplicated block (19–20 lines × 8) · ×1
  • Duplicated block (19–20 lines × 8) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:492 — src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:492-511 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:647-666 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:784-803 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:902-921 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1002-1021 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1085-1104 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1149-1168 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1194-1212 — all 8 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, `src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1170` calls `getAccurateMultiplatedIsotopeElement`, `getAccurateMargedIsotopeElement` and `src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1214` does not — after which the two agree again for 2 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live.
D4 · Code Duplication · Duplicated block (18–20 lines × 4) · ×1
  • Duplicated block (18–20 lines × 4) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:109 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:109-127 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:261-279 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:1118-1135 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:1158-1177 — before extracting anything, compare `src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb` and `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb` as WHOLE FILES: this scan already matched 32 separate duplicated blocks between them, totalling at least 530 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
D4 · Code Duplication · Duplicated block (18–20 lines × 3) · ×1
  • Duplicated block (18–20 lines × 3) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4025 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4025-4044 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4122-4141 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4433-4450 — all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
D4 · Code Duplication · Duplicated block (16–20 lines × 2) · ×1
  • Duplicated block (16–20 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:575 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:575-590 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:629-648 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:575` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
D4 · Code Duplication · Duplicated block (15–20 lines × 2) · ×1
  • Duplicated block (15–20 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3663 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3663-3677 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3695-3714 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
D4 · Code Duplication · Duplicated block (20 lines × 2) · ×1
  • Duplicated block (20 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12126 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12126-12145 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12180-12199 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
D4 · Code Duplication · Duplicated block (18–19 lines × 6) · ×1
  • Duplicated block (18–19 lines × 6) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:508 — src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:508-526 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:529-546 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:663-681 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:800-817 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:918-935 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1018-1035 — all 6 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited.
D4 · Code Duplication · Duplicated block (18–19 lines × 2) · ×1
  • Duplicated block (18–19 lines × 2) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1186 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1186-1203 | src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:2947-2965 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
D4 · Code Duplication · Duplicated block (17–18 lines × 5) · ×1
  • Duplicated block (17–18 lines × 5) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:149 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:149-165 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:565-581 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:1027-1043 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:1071-1087 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:1328-1345 — before extracting anything, compare `src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb` and `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb` as WHOLE FILES: this scan already matched 32 separate duplicated blocks between them, totalling at least 530 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:581` calls `acyls` and `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:1043` does not — after which the two agree again for 4 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live.
D4 · Code Duplication · Duplicated block (17–18 lines × 3) · ×1
  • Duplicated block (17–18 lines × 3) src/metadb/Lipidomics/Annotation/LipidomicsConverter.vb:2814 — src/metadb/Lipidomics/Annotation/LipidomicsConverter.vb:2814-2830 | src/metadb/Lipidomics/Annotation/LipidomicsConverter.vb:2997-3014 | src/metadb/Lipidomics/Annotation/LipidomicsConverter.vb:3047-3063 — all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited.
D4 · Code Duplication · Duplicated block (11–17 lines × 4) · ×1
  • Duplicated block (11–17 lines × 4) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11777 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11777-11793 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11892-11902 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11963-11973 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12032-12042 — all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
D4 · Code Duplication · Duplicated block (16–17 lines × 3) · ×1
  • Duplicated block (16–17 lines × 3) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4097 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4097-4112 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4413-4428 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4530-4546 — all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it.
D4 · Code Duplication · Duplicated block (15–16 lines × 20) · ×1
  • Duplicated block (15–16 lines × 20) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:432 — src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:432-446 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:448-462 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:464-478 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:480-494 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:595-609 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:611-625 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:627-641 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:643-657 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:740-754 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:756-770 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:772-786 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:866-880 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:882-896 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:898-912 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:974-988 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:990-1004 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1064-1079 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1081-1095 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1137-1151 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1190-1204 — all 20 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at `src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:643` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
D4 · Code Duplication · Duplicated block (16 lines × 8) · ×1
  • Duplicated block (16 lines × 8) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:505 — src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:505-521 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:526-541 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:660-676 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:681-696 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:797-812 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:915-930 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1015-1030 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1098-1113 — all 8 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at `src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:505` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
D4 · Code Duplication · Duplicated block (16 lines × 6) · ×1
  • Duplicated block (16 lines × 6) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:534 — src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:534-549 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:684-699 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:815-830 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:928-943 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1023-1038 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1101-1116 — all 6 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited.
D4 · Code Duplication · Duplicated block (16 lines × 5) · ×1
  • Duplicated block (16 lines × 5) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11640 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11640-11659 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11713-11728 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11780-11795 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11804-11819 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11828-11843 — all 5 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited.
D4 · Code Duplication · Duplicated block (13–16 lines × 4) · ×1
  • Duplicated block (13–16 lines × 4) src/metadb/Lipidomics/SpectrumGenerator/CLSpectrumGenerator.vb:104 — src/metadb/Lipidomics/SpectrumGenerator/CLSpectrumGenerator.vb:104-119 | src/metadb/Lipidomics/SpectrumGenerator/CeramideNsD7SpectrumGenerator.vb:98-110 | src/metadb/Lipidomics/SpectrumGenerator/CeramidePhytoSphSpectrumGenerator.vb:97-109 | src/metadb/Lipidomics/SpectrumGenerator/CeramideSpectrumGenerator.vb:100-112 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/CeramidePhytoSphSpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/CeramideSpectrumGenerator.vb` as WHOLE FILES: 88% of the shorter file's lines also appear in the other, so this reads as one file having been copied from the other rather than as a helper waiting to be extracted. The 2 duplicated block(s) this scan matched between them are fragments of that copy, not the extent of it — treat the file pair as the unit. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
D4 · Code Duplication · Duplicated block (11–16 lines × 2) · ×1
  • Duplicated block (11–16 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:9889 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:9889-9899 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:9971-9986 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it.
D4 · Code Duplication · Duplicated block (14–16 lines × 2) · ×1
  • Duplicated block (14–16 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14746 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14746-14761 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14815-14828 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
D4 · Code Duplication · Duplicated block (12–16 lines × 2) · ×1
  • Duplicated block (12–16 lines × 2) src/mzmath/mz_deco/Signals/PeakFinding/PeakProcessor.vb:116 — src/mzmath/mz_deco/Signals/PeakFinding/PeakProcessor.vb:116-131 | src/mzmath/mz_deco/Signals/PeakFinding/PeakProcessor.vb:186-197 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
D4 · Code Duplication · Duplicated block (15 lines × 9) · ×1
  • Duplicated block (15 lines × 9) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:506 — src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:506-521 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:522-536 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:661-676 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:677-691 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:798-812 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:813-827 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:916-930 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1016-1030 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1099-1113 — all 9 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited.
D4 · Code Duplication · Duplicated block (15 lines × 3) · ×1
  • Duplicated block (15 lines × 3) src/metadb/Lipidomics/SpectrumGenerator/TGEidSpectrumGenerator.vb:97 — src/metadb/Lipidomics/SpectrumGenerator/TGEidSpectrumGenerator.vb:97-111 | src/metadb/Lipidomics/SpectrumGenerator/TGSpectrumGenerator.vb:96-110 | src/metadb/Lipidomics/SpectrumGenerator/TGd5SpectrumGenerator.vb:99-113 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/TGEidSpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/TGSpectrumGenerator.vb` as WHOLE FILES: this scan already matched 3 separate duplicated blocks between them, totalling at least 49 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
D4 · Code Duplication · Duplicated block (11–15 lines × 2) · ×1
  • Duplicated block (11–15 lines × 2) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:2030 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:2030-2040 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3348-3362 — before extracting anything, compare `src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb` and `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb` as WHOLE FILES: this scan already matched 32 separate duplicated blocks between them, totalling at least 530 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
D4 · Code Duplication · Duplicated block (13–15 lines × 2) · ×1
  • Duplicated block (13–15 lines × 2) src/mzmath/mz_deco/Signals/PeakFinding/PeakDetector.vb:359 — src/mzmath/mz_deco/Signals/PeakFinding/PeakDetector.vb:359-373 | src/mzmath/mz_deco/Signals/centWave/centWave.vb:27-39 — the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach — a location they all depend on today, or a new shared one if there is none — and call it from each site; until then, every change has to be made twice. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
D4 · Code Duplication · Duplicated block (13–14 lines × 7) · ×1
  • Duplicated block (13–14 lines × 7) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12611 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12611-12623 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12647-12659 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12683-12695 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12719-12731 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12755-12767 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12791-12804 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12834-12846 — all 7 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
D4 · Code Duplication · Duplicated block (14 lines × 3) · ×1
  • Duplicated block (14 lines × 3) src/metadb/Lipidomics/SpectrumGenerator/LPIEidSpectrumGenerator.vb:189 — src/metadb/Lipidomics/SpectrumGenerator/LPIEidSpectrumGenerator.vb:189-202 | src/metadb/Lipidomics/SpectrumGenerator/LPISpectrumGenerator.vb:192-205 | src/metadb/Lipidomics/SpectrumGenerator/LPId5SpectrumGenerator.vb:192-205 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/LPIEidSpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/LPISpectrumGenerator.vb` as WHOLE FILES: this scan already matched 3 separate duplicated blocks between them, totalling at least 71 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
D4 · Code Duplication · Duplicated block (11–14 lines × 2) · ×1
  • Duplicated block (11–14 lines × 2) src/mzmath/mz_deco/Preprocessing/BatchCorrection.vb:268 — src/mzmath/mz_deco/Preprocessing/BatchCorrection.vb:268-281 | src/mzmath/mz_deco/Preprocessing/BatchCorrection.vb:324-334 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
D4 · Code Duplication · Duplicated block (10 lines × 8) · ×1
  • Duplicated block (10 lines × 8) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12592 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12592-12601 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12630-12639 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12666-12675 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12702-12711 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12738-12747 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12774-12783 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12817-12826 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12853-12862 — all 8 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited.
D4 · Code Duplication · Duplicated block (12–13 lines × 6) · ×1
  • Duplicated block (12–13 lines × 6) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1284 — src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1284-1295 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1505-1516 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1702-1713 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1877-1888 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:2030-2041 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:2160-2172 — all 6 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, `src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1519` calls `List` and `src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1717` does not — after which the two agree again for 2 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live.
D4 · Code Duplication · Duplicated block (13 lines × 5) · ×1
  • Duplicated block (13 lines × 5) src/metadb/Lipidomics/SpectrumGenerator/MGEidSpectrumGenerator.vb:184 — src/metadb/Lipidomics/SpectrumGenerator/MGEidSpectrumGenerator.vb:184-196 | src/metadb/Lipidomics/SpectrumGenerator/PGEidSpectrumGenerator.vb:199-211 | src/metadb/Lipidomics/SpectrumGenerator/PIEidSpectrumGenerator.vb:207-219 | src/metadb/Lipidomics/SpectrumGenerator/PSEidSpectrumGenerator.vb:189-201 | src/metadb/Lipidomics/SpectrumGenerator/SMEidSpectrumGenerator.vb:189-201 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/MGEidSpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/PIEidSpectrumGenerator.vb` as WHOLE FILES: this scan already matched 3 separate duplicated blocks between them, totalling at least 41 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
D4 · Code Duplication · Duplicated block (13 lines × 3) · ×1
  • Duplicated block (13 lines × 3) src/metadb/Lipidomics/MsCharacterization/EieioMsCharacterizationUtility.vb:142 — src/metadb/Lipidomics/MsCharacterization/EieioMsCharacterizationUtility.vb:142-154 | src/metadb/Lipidomics/MsCharacterization/EieioMsCharacterizationUtility.vb:170-182 | src/metadb/Lipidomics/MsCharacterization/EieioMsCharacterizationUtility.vb:186-198 — all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited.
D4 · Code Duplication · Duplicated block (7 lines × 3) · ×1
  • Duplicated block (7 lines × 3) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:3543 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:3543-3549 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:2653-2659 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15680-15686 — before extracting anything, compare `src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb` and `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb` as WHOLE FILES: this scan already matched 32 separate duplicated blocks between them, totalling at least 530 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
D4 · Code Duplication · Duplicated block (11–13 lines × 3) · ×1
  • Duplicated block (11–13 lines × 3) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6170 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6170-6182 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6260-6270 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6337-6347 — all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
D4 · Code Duplication · Duplicated block (12–13 lines × 3) · ×1
  • Duplicated block (12–13 lines × 3) src/metadb/Lipidomics/SpectrumGenerator/LPCEidSpectrumGenerator.vb:103 — src/metadb/Lipidomics/SpectrumGenerator/LPCEidSpectrumGenerator.vb:103-115 | src/metadb/Lipidomics/SpectrumGenerator/LPCSpectrumGenerator.vb:103-114 | src/metadb/Lipidomics/SpectrumGenerator/LPCd5SpectrumGenerator.vb:103-114 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/LPCEidSpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/LPCSpectrumGenerator.vb` as WHOLE FILES: this scan already matched 3 separate duplicated blocks between them, totalling at least 37 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
D4 · Code Duplication · Duplicated block (7–12 lines × 39) · ×1
  • Duplicated block (7–12 lines × 39) src/metadb/Lipidomics/SpectrumGenerator/BMPEidSpectrumGenerator.vb:97 — src/metadb/Lipidomics/SpectrumGenerator/BMPEidSpectrumGenerator.vb:97-104 | src/metadb/Lipidomics/SpectrumGenerator/BMPSpectrumGenerator.vb:97-103 | src/metadb/Lipidomics/SpectrumGenerator/DGEidSpectrumGenerator.vb:92-100 | src/metadb/Lipidomics/SpectrumGenerator/DGSpectrumGenerator.vb:92-99 | src/metadb/Lipidomics/SpectrumGenerator/DGTASpectrumGenerator.vb:99-105 | src/metadb/Lipidomics/SpectrumGenerator/DGTSSpectrumGenerator.vb:103-109 | src/metadb/Lipidomics/SpectrumGenerator/DGd5SpectrumGenerator.vb:93-100 | src/metadb/Lipidomics/SpectrumGenerator/DMEDFAHFASpectrumGenerator.vb:99-105 | src/metadb/Lipidomics/SpectrumGenerator/HBMPSpectrumGenerator.vb:101-111 | src/metadb/Lipidomics/SpectrumGenerator/LDGTASpectrumGenerator.vb:101-107 | src/metadb/Lipidomics/SpectrumGenerator/LDGTSSpectrumGenerator.vb:101-107 | src/metadb/Lipidomics/SpectrumGenerator/LPCEidSpectrumGenerator.vb:104-115 | src/metadb/Lipidomics/SpectrumGenerator/LPCSpectrumGenerator.vb:104-114 | src/metadb/Lipidomics/SpectrumGenerator/LPCd5SpectrumGenerator.vb:104-114 | src/metadb/Lipidomics/SpectrumGenerator/LPEEidSpectrumGenerator.vb:102-109 | src/metadb/Lipidomics/SpectrumGenerator/LPESpectrumGenerator.vb:102-108 | src/metadb/Lipidomics/SpectrumGenerator/LPEd5SpectrumGenerator.vb:102-108 | src/metadb/Lipidomics/SpectrumGenerator/LPGSpectrumGenerator.vb:100-106 | src/metadb/Lipidomics/SpectrumGenerator/LPGd5SpectrumGenerator.vb:98-104 | src/metadb/Lipidomics/SpectrumGenerator/LPISpectrumGenerator.vb:102-108 | src/metadb/Lipidomics/SpectrumGenerator/LPId5SpectrumGenerator.vb:102-108 | src/metadb/Lipidomics/SpectrumGenerator/LPSEidSpectrumGenerator.vb:104-111 | src/metadb/Lipidomics/SpectrumGenerator/LPSSpectrumGenerator.vb:103-109 | src/metadb/Lipidomics/SpectrumGenerator/LPSd5SpectrumGenerator.vb:103-109 | src/metadb/Lipidomics/SpectrumGenerator/PCEidSpectrumGenerator.vb:99-106 | src/metadb/Lipidomics/SpectrumGenerator/PCSpectrumGenerator.vb:99-105 | src/metadb/Lipidomics/SpectrumGenerator/PCd5SpectrumGenerator.vb:99-105 | src/metadb/Lipidomics/SpectrumGenerator/PEEidSpectrumGenerator.vb:100-108 | src/metadb/Lipidomics/SpectrumGenerator/PESpectrumGenerator.vb:100-107 | src/metadb/Lipidomics/SpectrumGenerator/PEd5SpectrumGenerator.vb:102-109 | src/metadb/Lipidomics/SpectrumGenerator/PGEidSpectrumGenerator.vb:101-108 | src/metadb/Lipidomics/SpectrumGenerator/PGSpectrumGenerator.vb:102-108 | src/metadb/Lipidomics/SpectrumGenerator/PGd5SpectrumGenerator.vb:101-107 | src/metadb/Lipidomics/SpectrumGenerator/PIEidSpectrumGenerator.vb:101-109 | src/metadb/Lipidomics/SpectrumGenerator/PISpectrumGenerator.vb:101-107 | src/metadb/Lipidomics/SpectrumGenerator/PId5SpectrumGenerator.vb:101-107 | src/metadb/Lipidomics/SpectrumGenerator/PSEidSpectrumGenerator.vb:103-110 | src/metadb/Lipidomics/SpectrumGenerator/PSSpectrumGenerator.vb:103-109 | src/metadb/Lipidomics/SpectrumGenerator/PSd5SpectrumGenerator.vb:103-109 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/BMPEidSpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/BMPSpectrumGenerator.vb` as WHOLE FILES: this scan already matched 4 separate duplicated blocks between them, totalling at least 55 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just before the matched lines, `src/metadb/Lipidomics/SpectrumGenerator/PSSpectrumGenerator.vb:102` calls `If`, `Equals` and `src/metadb/Lipidomics/SpectrumGenerator/PSEidSpectrumGenerator.vb:102` does not — after which the two agree again for 4 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live.
D4 · Code Duplication · Duplicated block (11–12 lines × 3) · ×1
  • Duplicated block (11–12 lines × 3) src/mzmath/mz_deco/Preprocessing/MissingValueImputation.vb:159 — src/mzmath/mz_deco/Preprocessing/MissingValueImputation.vb:159-170 | src/mzmath/mz_deco/Preprocessing/MissingValueImputation.vb:195-205 | src/mzmath/mz_deco/Preprocessing/MissingValueImputation.vb:599-609 — all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
D4 · Code Duplication · Duplicated block (11–12 lines × 2) · ×1
  • Duplicated block (11–12 lines × 2) src/mzmath/Mummichog/MummichogModule.vb:771 — src/mzmath/Mummichog/MummichogModule.vb:771-782 | src/mzmath/Mummichog/MummichogModule.vb:796-806 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
D4 · Code Duplication · Duplicated block (11 lines × 9) · ×1
  • Duplicated block (11 lines × 9) src/metadb/Chemoinformatics/Formula/Models/Element.vb:153 — src/metadb/Chemoinformatics/Formula/Models/Element.vb:153-163 | src/metadb/Chemoinformatics/Formula/Models/Element.vb:164-174 | src/metadb/Chemoinformatics/Formula/Models/Element.vb:175-185 | src/metadb/Chemoinformatics/Formula/Models/Element.vb:190-225 | src/metadb/Chemoinformatics/Formula/Models/Element.vb:226-273 | src/metadb/Chemoinformatics/Formula/Models/Element.vb:282-321 | src/metadb/Chemoinformatics/Formula/Models/Element.vb:322-361 | src/metadb/Chemoinformatics/Formula/Models/Element.vb:362-372 | src/metadb/Chemoinformatics/Formula/Models/Element.vb:373-383 — all 9 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at `src/metadb/Chemoinformatics/Formula/Models/Element.vb:175` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, `src/metadb/Chemoinformatics/Formula/Models/Element.vb:225` calls `Element`, `Isotope` and `src/metadb/Chemoinformatics/Formula/Models/Element.vb:185` does not — after which the two agree again for 4 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live.
D4 · Code Duplication · Duplicated block (11 lines × 7) · ×1
  • Duplicated block (11 lines × 7) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1284 — src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1284-1294 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1505-1515 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1702-1712 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1877-1887 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:2030-2040 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:2160-2170 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:2263-2274 — all 7 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, `src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1715` calls `List` and `src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1891` does not — after which the two agree again for 2 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live.
D4 · Code Duplication · Duplicated block (10–11 lines × 4) · ×1
  • Duplicated block (10–11 lines × 4) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11667 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11667-11676 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11733-11742 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11917-11927 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11987-11997 — all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
D4 · Code Duplication · Duplicated block (7–11 lines × 2) · ×1
  • Duplicated block (7–11 lines × 2) src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:77 — src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:77-83 | src/mzmath/MSEngine/Search/MsScanMatching.vb:264-274 — the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach — a location they all depend on today, or a new shared one if there is none — and call it from each site; until then, every change has to be made twice.
D4 · Code Duplication · Duplicated block (10–11 lines × 2) · ×1
  • Duplicated block (10–11 lines × 2) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13514 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13514-13524 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13613-13622 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
D4 · Code Duplication · Duplicated block (5 lines × 15) · ×1
  • Duplicated block (5 lines × 15) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:395 — src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:395-399 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:562-566 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:711-715 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:841-845 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:953-957 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1047-1051 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1124-1128 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1181-1185 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1301-1305 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1521-1525 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1717-1721 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1891-1895 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:2043-2047 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:2172-2176 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:2274-2278 — all 15 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, `src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1130` calls `isotopeElementPropertyBeanList` and `src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1187` does not — after which the two agree again for 2 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live.
D4 · Code Duplication · Duplicated block (5 lines × 10) · ×1
  • Duplicated block (5 lines × 10) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:422 — src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:422-426 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:586-590 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:732-736 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:859-863 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:968-972 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1328-1332 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1545-1549 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1738-1742 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1909-1913 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:2058-2062 — all 10 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited.
D4 · Code Duplication · Duplicated block (7 lines × 7) · ×1
  • Duplicated block (7 lines × 7) src/metadb/Lipidomics/SpectrumGenerator/LPCOadSpectrumGenerator.vb:107 — src/metadb/Lipidomics/SpectrumGenerator/LPCOadSpectrumGenerator.vb:107-113 | src/metadb/Lipidomics/SpectrumGenerator/LPEOadSpectrumGenerator.vb:108-114 | src/metadb/Lipidomics/SpectrumGenerator/PCOadSpectrumGenerator.vb:114-120 | src/metadb/Lipidomics/SpectrumGenerator/PEOadSpectrumGenerator.vb:122-128 | src/metadb/Lipidomics/SpectrumGenerator/PGOadSpectrumGenerator.vb:121-127 | src/metadb/Lipidomics/SpectrumGenerator/PIOadSpectrumGenerator.vb:118-124 | src/metadb/Lipidomics/SpectrumGenerator/TGOadSpectrumGenerator.vb:99-105 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/PGOadSpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/PIOadSpectrumGenerator.vb` as WHOLE FILES: 84% of the shorter file's lines also appear in the other, so this reads as one file having been copied from the other rather than as a helper waiting to be extracted. The 2 duplicated block(s) this scan matched between them are fragments of that copy, not the extent of it — treat the file pair as the unit. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
D4 · Code Duplication · Duplicated block (10 lines × 5) · ×1
  • Duplicated block (10 lines × 5) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:2521 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:2521-2530 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:2581-2590 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3507-3517 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7429-7446 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15608-15617 — all 5 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
D4 · Code Duplication · Duplicated block (6 lines × 5) · ×1
  • Duplicated block (6 lines × 5) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3090 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3090-3095 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4195-4200 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6169-6174 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6259-6264 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6336-6341 — all 5 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited.
D4 · Code Duplication · Duplicated block (9 lines × 24) · ×1
  • Duplicated block (9 lines × 24) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:396 — src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:396-404 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:405-413 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:414-422 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:563-571 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:572-580 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:712-720 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:721-729 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:842-850 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:851-859 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:954-962 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1048-1056 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1125-1133 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1302-1310 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1311-1319 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1320-1328 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1522-1530 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1531-1539 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1718-1726 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1727-1735 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1892-1900 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1901-1909 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:2044-2052 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:2173-2181 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:2275-2283 — all 24 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, `src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:729` calls `isotopeElementPropertyBeanList` and `src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:422` does not — after which the two agree again for 4 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live.
D4 · Code Duplication · Duplicated block (9 lines × 12) · ×1
  • Duplicated block (9 lines × 12) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:417 — src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:417-425 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:581-589 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:727-735 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:854-862 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:963-971 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1054-1062 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1323-1331 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1540-1548 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1733-1741 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1904-1912 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:2053-2061 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:2179-2187 — all 12 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited.
D4 · Code Duplication · Duplicated block (9 lines × 11) · ×1
  • Duplicated block (9 lines × 11) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5580 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5580-5589 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5646-5655 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5718-5728 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5803-5813 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7604-7614 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12289-12299 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13373-13382 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13431-13439 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14077-14087 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15900-15910 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15985-15995 — all 11 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
D4 · Code Duplication · Duplicated block (9 lines × 8) · ×1
  • Duplicated block (9 lines × 8) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3090 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3090-3098 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4195-4203 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6169-6177 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6259-6267 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6336-6344 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7685-7693 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7761-7769 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:9061-9069 — all 8 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6178` calls `isDiagnosticFragmentExist` and `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4204` does not — after which the two agree again for 2 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live.
D4 · Code Duplication · Duplicated block (7–9 lines × 9) · ×1
  • Duplicated block (7–9 lines × 9) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:136 — src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:136-144 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:148-156 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:160-168 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:172-180 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:184-192 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:196-204 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:208-216 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:220-228 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:232-238 — all 9 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
D4 · Code Duplication · Duplicated block (9 lines × 7) · ×1
  • Duplicated block (9 lines × 7) src/mzmath/mz_deco/Preprocessing/MissingValueImputation.vb:245 — src/mzmath/mz_deco/Preprocessing/MissingValueImputation.vb:245-253 | src/mzmath/mz_deco/Preprocessing/MissingValueImputation.vb:275-283 | src/mzmath/mz_deco/Preprocessing/Normalization.vb:394-403 | src/mzmath/mz_deco/Preprocessing/Normalization.vb:433-442 | src/mzmath/mz_deco/Preprocessing/Normalization.vb:472-481 | src/mzmath/mz_deco/Preprocessing/Normalization.vb:513-522 | src/mzmath/mz_deco/Preprocessing/Normalization.vb:553-562 — there are 7 copies across 2 file(s) — more copies than files, so at least one file holds the block twice. Extract it once into a single shared function every call site can reach and call it from all 7 sites; resolving a subset leaves the remainder to drift apart. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, `src/mzmath/mz_deco/Preprocessing/Normalization.vb:524` calls `CV` and `src/mzmath/mz_deco/Preprocessing/Normalization.vb:406` does not — after which the two agree again for 3 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live.
D4 · Code Duplication · Duplicated block (9 lines × 5) · ×1
  • Duplicated block (9 lines × 5) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3341 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3341-3349 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13704-13713 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13752-13761 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13775-13784 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13843-13852 — all 5 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited.
D4 · Code Duplication · Duplicated block (8 lines × 32) · ×1
  • Duplicated block (8 lines × 32) src/mzmath/MSFinder/FormulaStringParcer.vb:134 — src/mzmath/MSFinder/FormulaStringParcer.vb:134-142 | src/mzmath/MSFinder/FormulaStringParcer.vb:143-151 | src/mzmath/MSFinder/FormulaStringParcer.vb:152-160 | src/mzmath/MSFinder/FormulaStringParcer.vb:161-169 | src/mzmath/MSFinder/FormulaStringParcer.vb:170-178 | src/mzmath/MSFinder/FormulaStringParcer.vb:179-187 | src/mzmath/MSFinder/FormulaStringParcer.vb:188-196 | src/mzmath/MSFinder/FormulaStringParcer.vb:197-205 | src/mzmath/MSFinder/FormulaStringParcer.vb:206-214 | src/mzmath/MSFinder/FormulaStringParcer.vb:215-223 | src/mzmath/MSFinder/FormulaStringParcer.vb:369-377 | src/mzmath/MSFinder/FormulaStringParcer.vb:378-386 | src/mzmath/MSFinder/FormulaStringParcer.vb:387-395 | src/mzmath/MSFinder/FormulaStringParcer.vb:396-404 | src/mzmath/MSFinder/FormulaStringParcer.vb:405-413 | src/mzmath/MSFinder/FormulaStringParcer.vb:414-422 | src/mzmath/MSFinder/FormulaStringParcer.vb:423-431 | src/mzmath/MSFinder/FormulaStringParcer.vb:432-440 | src/mzmath/MSFinder/FormulaStringParcer.vb:441-449 | src/mzmath/MSFinder/FormulaStringParcer.vb:450-458 | src/mzmath/MSFinder/FormulaStringParcer.vb:498-506 | src/mzmath/MSFinder/FormulaStringParcer.vb:507-515 | src/mzmath/MSFinder/FormulaStringParcer.vb:516-524 | src/mzmath/MSFinder/FormulaStringParcer.vb:525-533 | src/mzmath/MSFinder/FormulaStringParcer.vb:534-542 | src/mzmath/MSFinder/FormulaStringParcer.vb:543-551 | src/mzmath/MSFinder/FormulaStringParcer.vb:552-560 | src/mzmath/MSFinder/FormulaStringParcer.vb:561-569 | src/mzmath/MSFinder/FormulaStringParcer.vb:570-578 | src/mzmath/MSFinder/FormulaStringParcer.vb:579-587 | src/mzmath/MSFinder/FormulaStringParcer.vb:588-595 | src/mzmath/MSFinder/FormulaStringParcer.vb:596-603 — all 32 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited.
D4 · Code Duplication · Duplicated block (8 lines × 14) · ×1
  • Duplicated block (8 lines × 14) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5580 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5580-5588 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5646-5654 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5718-5727 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5803-5812 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7604-7613 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7664-7672 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7707-7715 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12289-12297 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12342-12350 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13373-13381 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13431-13438 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14077-14085 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15900-15909 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15985-15994 — all 14 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
D4 · Code Duplication · Duplicated block (7–8 lines × 2) · ×1
  • Duplicated block (7–8 lines × 2) Rscript/Library/mzkit_app/src/mzDIA/DIA.vb:176 — Rscript/Library/mzkit_app/src/mzDIA/DIA.vb:176-183 | Rscript/Library/mzkit_app/src/mzDIA/DIA.vb:185-191 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
D4 · Code Duplication · Duplicated block (6 lines × 6) · ×1
  • Duplicated block (6 lines × 6) src/metadb/Lipidomics/SpectrumGenerator/MGEidSpectrumGenerator.vb:184 — src/metadb/Lipidomics/SpectrumGenerator/MGEidSpectrumGenerator.vb:184-189 | src/metadb/Lipidomics/SpectrumGenerator/PCEidSpectrumGenerator.vb:173-178 | src/metadb/Lipidomics/SpectrumGenerator/PGEidSpectrumGenerator.vb:199-204 | src/metadb/Lipidomics/SpectrumGenerator/PIEidSpectrumGenerator.vb:207-212 | src/metadb/Lipidomics/SpectrumGenerator/PSEidSpectrumGenerator.vb:189-194 | src/metadb/Lipidomics/SpectrumGenerator/SMEidSpectrumGenerator.vb:189-194 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/MGEidSpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/PIEidSpectrumGenerator.vb` as WHOLE FILES: this scan already matched 3 separate duplicated blocks between them, totalling at least 41 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
D4 · Code Duplication · Duplicated block (5 lines × 5) · ×1
  • Duplicated block (5 lines × 5) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11667 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11667-11671 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11733-11737 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11849-11853 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11917-11921 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11987-11991 — all 5 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited.
D4 · Code Duplication · Duplicated block (6 lines × 3) · ×1
  • Duplicated block (6 lines × 3) src/metadb/Lipidomics/Omega3nChainGenerator.vb:215 — src/metadb/Lipidomics/Omega3nChainGenerator.vb:215-220 | src/metadb/Lipidomics/Omega3nChainGenerator.vb:221-226 | src/metadb/Lipidomics/Omega3nChainGenerator.vb:227-233 — all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
D4 · Code Duplication · Duplicated block (4–6 lines × 3) · ×1
  • Duplicated block (4–6 lines × 3) src/mzmath/MSEngine/Search/MsScanMatching.vb:773 — src/mzmath/MSEngine/Search/MsScanMatching.vb:773-778 | src/mzmath/MSEngine/Search/MsScanMatching.vb:918-923 | src/mzmath/MSEngine/Search/MsScanMatching.vb:1052-1055 — all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just before the matched lines, `src/mzmath/MSEngine/Search/MsScanMatching.vb:1052` calls `List`, `Double` and `src/mzmath/MSEngine/Search/MsScanMatching.vb:918` does not — after which the two agree again for 2 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live.
D4 · Code Duplication · Duplicated block (5 lines × 12) · ×1
  • Duplicated block (5 lines × 12) src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:385 — src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:385-389 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:390-395 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:553-557 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:703-707 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:834-838 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:947-951 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1042-1047 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1292-1296 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1513-1517 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1710-1714 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1885-1889 | src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:2038-2043 — all 12 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, `src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:707` calls `List` and `src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:395` does not — after which the two agree again for 3 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live.
D4 · Code Duplication · Duplicated block (5 lines × 4) · ×1
  • Duplicated block (5 lines × 4) src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1180 — src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1180-1184 | src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1203-1207 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3672-3676 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3704-3713 — before extracting anything, compare `src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb` and `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb` as WHOLE FILES: this scan already matched 32 separate duplicated blocks between them, totalling at least 530 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
D4 · Code Duplication · Duplicated block (89 lines × 46) · ×1
  • Duplicated block (89 lines × 46) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:1790 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:1790-1986 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:1991-2147 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:2152-2286 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:2289-2399 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:2403-2517 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:2701-2806 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:2925-3086 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3536-3635 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3738-3854 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3858-3992 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:4874-5013 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5017-5160 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5164-5299 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5443-5575 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6008-6163 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6372-6465 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6597-6706 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6710-6803 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6807-6903 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6907-6999 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7944-8127 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:8194-8371 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:8375-8543 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:8547-8715 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:8719-8879 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:8883-9057 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:9240-9352 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:9356-9515 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:9519-9689 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:9693-9784 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:9788-9885 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:10074-10240 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12962-13081 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13085-13205 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14141-14231 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14276-14373 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14377-14474 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:14478-14566 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15068-15231 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15235-15375 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15380-15498 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15502-15605 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:15718-15806 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:16233-16338 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:16341-16508 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:16543-16693 — all 46 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:8375` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it.
D4 · Code Duplication · Duplicated block (96 lines × 9) · ×1
  • Duplicated block (96 lines × 9) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3127 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:3127-3284 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:5843-6004 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:6469-6593 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7004-7144 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:7505-7600 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:10244-10455 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:10558-10769 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:10856-10981 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:16087-16230 — all 9 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at `src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:10244` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it.
D4 · Code Duplication · Duplicated block (66 lines × 4) · ×1
  • Duplicated block (66 lines × 4) src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11441 — src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:11441-11574 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12391-12456 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:12460-12570 | src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:13211-13369 — all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it.
D4 · Code Duplication · Duplicated block (17 lines × 5) · ×1
  • Duplicated block (17 lines × 5) src/metadb/Lipidomics/SpectrumGenerator/BMPEidSpectrumGenerator.vb:158 — src/metadb/Lipidomics/SpectrumGenerator/BMPEidSpectrumGenerator.vb:158-183 | src/metadb/Lipidomics/SpectrumGenerator/HBMPEidSpectrumGenerator.vb:175-191 | src/metadb/Lipidomics/SpectrumGenerator/HBMPEidSpectrumGenerator.vb:195-214 | src/metadb/Lipidomics/SpectrumGenerator/HBMPSpectrumGenerator.vb:166-185 | src/metadb/Lipidomics/SpectrumGenerator/HBMPSpectrumGenerator.vb:189-208 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/HBMPEidSpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/HBMPSpectrumGenerator.vb` as WHOLE FILES: this scan already matched 4 separate duplicated blocks between them, totalling at least 47 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
D4 · Code Duplication · Duplicated block (19 lines × 7) · ×1
  • Duplicated block (19 lines × 7) src/metadb/Lipidomics/SpectrumGenerator/DGEidSpectrumGenerator.vb:148 — src/metadb/Lipidomics/SpectrumGenerator/DGEidSpectrumGenerator.vb:148-167 | src/metadb/Lipidomics/SpectrumGenerator/DGSpectrumGenerator.vb:147-168 | src/metadb/Lipidomics/SpectrumGenerator/DGd5SpectrumGenerator.vb:147-168 | src/metadb/Lipidomics/SpectrumGenerator/MGEidSpectrumGenerator.vb:151-170 | src/metadb/Lipidomics/SpectrumGenerator/PIEidSpectrumGenerator.vb:175-193 | src/metadb/Lipidomics/SpectrumGenerator/PISpectrumGenerator.vb:172-190 | src/metadb/Lipidomics/SpectrumGenerator/PId5SpectrumGenerator.vb:172-190 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/DGEidSpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/DGSpectrumGenerator.vb` as WHOLE FILES: 85% of the shorter file's lines also appear in the other, so this reads as one file having been copied from the other rather than as a helper waiting to be extracted. The 2 duplicated block(s) this scan matched between them are fragments of that copy, not the extent of it — treat the file pair as the unit. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
D4 · Code Duplication · Duplicated block (28 lines × 5) · ×1
  • Duplicated block (28 lines × 5) src/metadb/Lipidomics/SpectrumGenerator/EtherPCSpectrumGenerator.vb:139 — src/metadb/Lipidomics/SpectrumGenerator/EtherPCSpectrumGenerator.vb:139-166 | src/metadb/Lipidomics/SpectrumGenerator/PCSpectrumGenerator.vb:126-154 | src/metadb/Lipidomics/SpectrumGenerator/PCd5SpectrumGenerator.vb:126-154 | src/metadb/Lipidomics/SpectrumGenerator/PESpectrumGenerator.vb:128-159 | src/metadb/Lipidomics/SpectrumGenerator/PEd5SpectrumGenerator.vb:130-161 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/PCSpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/PCd5SpectrumGenerator.vb` as WHOLE FILES: 89% of the shorter file's lines also appear in the other, so this reads as one file having been copied from the other rather than as a helper waiting to be extracted. The 2 duplicated block(s) this scan matched between them are fragments of that copy, not the extent of it — treat the file pair as the unit. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
D4 · Code Duplication · Duplicated block (25 lines × 3) · ×1
  • Duplicated block (25 lines × 3) src/metadb/Lipidomics/SpectrumGenerator/LPCEidSpectrumGenerator.vb:136 — src/metadb/Lipidomics/SpectrumGenerator/LPCEidSpectrumGenerator.vb:136-160 | src/metadb/Lipidomics/SpectrumGenerator/LPEEidSpectrumGenerator.vb:130-161 | src/metadb/Lipidomics/SpectrumGenerator/LPSEidSpectrumGenerator.vb:132-160 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/LPCEidSpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/LPEEidSpectrumGenerator.vb` as WHOLE FILES: this scan already matched 4 separate duplicated blocks between them, totalling at least 66 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
D4 · Code Duplication · Duplicated block (37 lines × 2) · ×1
  • Duplicated block (37 lines × 2) src/metadb/Lipidomics/SpectrumGenerator/LPESpectrumGenerator.vb:129 — src/metadb/Lipidomics/SpectrumGenerator/LPESpectrumGenerator.vb:129-165 | src/metadb/Lipidomics/SpectrumGenerator/LPEd5SpectrumGenerator.vb:129-165 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/LPESpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/LPEd5SpectrumGenerator.vb` as WHOLE FILES: this scan already matched 3 separate duplicated blocks between them, totalling at least 61 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
D4 · Code Duplication · Duplicated block (42 lines × 3) · ×1
  • Duplicated block (42 lines × 3) src/metadb/Lipidomics/SpectrumGenerator/LPIEidSpectrumGenerator.vb:135 — src/metadb/Lipidomics/SpectrumGenerator/LPIEidSpectrumGenerator.vb:135-176 | src/metadb/Lipidomics/SpectrumGenerator/LPISpectrumGenerator.vb:129-179 | src/metadb/Lipidomics/SpectrumGenerator/LPId5SpectrumGenerator.vb:129-179 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/LPIEidSpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/LPISpectrumGenerator.vb` as WHOLE FILES: this scan already matched 3 separate duplicated blocks between them, totalling at least 71 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
D4 · Code Duplication · Duplicated block (13 lines × 4) · ×1
  • Duplicated block (13 lines × 4) src/metadb/Lipidomics/SpectrumGenerator/PSSpectrumGenerator.vb:178 — src/metadb/Lipidomics/SpectrumGenerator/PSSpectrumGenerator.vb:178-197 | src/metadb/Lipidomics/SpectrumGenerator/PSSpectrumGenerator.vb:201-213 | src/metadb/Lipidomics/SpectrumGenerator/PSd5SpectrumGenerator.vb:178-197 | src/metadb/Lipidomics/SpectrumGenerator/PSd5SpectrumGenerator.vb:201-213 — before extracting anything, compare `src/metadb/Lipidomics/SpectrumGenerator/PSSpectrumGenerator.vb` and `src/metadb/Lipidomics/SpectrumGenerator/PSd5SpectrumGenerator.vb` as WHOLE FILES: 92% of the shorter file's lines also appear in the other, so this reads as one file having been copied from the other rather than as a helper waiting to be extracted. The 2 duplicated block(s) this scan matched between them are fragments of that copy, not the extent of it — treat the file pair as the unit. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place.
D44 · Platform End-of-Life · End-of-life runtime · ×1
  • End-of-life runtime: .NET net6.0 src/mzmath/Oligonucleotide_MS/test/test.vbproj:6 — src/mzmath/Oligonucleotide_MS/test/test.vbproj declares .NET net6.0 as this project's target framework, and .NET 6 LTS, support ended 2024-11-12. An unsupported runtime receives no security patches, so every vulnerability disclosed in it since 2024-11-12 is present and unfixable without moving off it. This is a migration rather than an upgrade: there is no newer release of a runtime that has ended.
D5 · Coupling · Unstable project Targetted.NET5 · ×1
  • Unstable project Targetted.NET5 src/mzmath/TargetedMetabolomics/Targetted.NET5.vbproj:1 — Targetted.NET5 has instability 0.63 with 3 dependents.
D8 · Code Coverage · Coverage not measured · ×1
  • Coverage not measured — no coverage collector is wired up — Coverage NOT MEASURED: `--collect:"XPlat Code Coverage"` names a data collector that ships in the `coverlet.collector` package, and this repository wires up none — no test project references it and no runsettings declares one. The absence of coverage here is therefore not evidence about the suite or about our analyzer environment: without a collector, `--collect` produces nothing even from a suite that builds and passes. Add a `coverlet.collector` PackageReference to the test project(s) (or commit the Cobertura/OpenCover/lcov report your CI produces) and real coverage will be measured. It is excluded from the score rather than counted as a near-zero defect.
M1 · Documentation (README) · README may be stale · ×1
  • README may be stale — 220 code files changed in the last 6 months but the README was not touched — it may no longer reflect the system.
P1 · CI/CD gates · No CI pipeline · ×1
  • No CI pipeline — No CI workflow found (.github/workflows, azure-pipelines.yml, .gitlab-ci.yml, …) — changes aren't gated by an automated build/test.
S1 · Web-Security Posture · Third-party script without Subresource Integrity · ×1
  • Third-party script without Subresource Integrity Rscript/Library/mzkit_app/data/MRM/linears.html:15 — `https://query.biodeep.cn/resources/vendor/jquery-3.7.1.min.js` is executed by this page with no Subresource Integrity. Whoever can answer that request — the CDN, anyone who compromises it, anyone on the network path — runs arbitrary script in this page's origin, with its session. The URL also names no version, so it resolves to whatever that origin serves at fetch time — the executed bytes can change with nobody touching this repository. 2536 such include(s) across the repository's markup.
SC1 · Supply-chain hygiene · NuGet dependencies are not locked · ×1
  • NuGet dependencies are not locked — No packages.lock.json and no central package management — restores aren't reproducible or pinned (SSDF PW.4.4). Enable <RestorePackagesWithLockFile>true</RestorePackagesWithLockFile> (commit the lockfile) or adopt Directory.Packages.props. Advisory — never scored.
Minor — 1088 finding(s)
D34 · Knowledge Freshness · Orphaned file · ×988
  • Orphaned file src/metadb/Chemoinformatics/Formula/Isotopic/IsotopeCalc.vb:1 — No one still active in this repository holds living knowledge of this file: everyone who made a meaningful change to it has gone quiet, or what the current team did to it (moves, reformatting, log-level or import edits, renames) never needed understanding it. If it breaks, no one currently understands it. Attach the read to the next change that touches it: have a second person review that change, and leave behind a short comment or test recording what the file is for.
  • Orphaned file src/metadb/Lipidomics/Annotation/Search/MsScanMatching.vb:1 — No one still active in this repository holds living knowledge of this file: everyone who made a meaningful change to it has gone quiet, or what the current team did to it (moves, reformatting, log-level or import edits, renames) never needed understanding it. If it breaks, no one currently understands it. Attach the read to the next change that touches it: have a second person review that change, and leave behind a short comment or test recording what the file is for.
  • Orphaned file src/assembly/ThermoRawFileReader/XcaliburRawFileIO.vb:1 — No one still active in this repository holds living knowledge of this file: everyone who made a meaningful change to it has gone quiet, or what the current team did to it (moves, reformatting, log-level or import edits, renames) never needed understanding it. If it breaks, no one currently understands it. Attach the read to the next change that touches it: have a second person review that change, and leave behind a short comment or test recording what the file is for.
  • Orphaned file src/metadb/Lipidomics/Annotation/LipidMassLibraryGenerator.vb:1 — No one still active in this repository holds living knowledge of this file: everyone who made a meaningful change to it has gone quiet, or what the current team did to it (moves, reformatting, log-level or import edits, renames) never needed understanding it. If it breaks, no one currently understands it. Attach the read to the next change that touches it: have a second person review that change, and leave behind a short comment or test recording what the file is for.
  • Orphaned file src/mzmath/MSEngine/Search/MsScanMatching.vb:1 — No one still active in this repository holds living knowledge of this file: everyone who made a meaningful change to it has gone quiet, or what the current team did to it (moves, reformatting, log-level or import edits, renames) never needed understanding it. If it breaks, no one currently understands it. Attach the read to the next change that touches it: have a second person review that change, and leave behind a short comment or test recording what the file is for.
  • Orphaned file src/mzmath/MSFinder/FormulaGenerator.vb:1 — No one still active in this repository holds living knowledge of this file: everyone who made a meaningful change to it has gone quiet, or what the current team did to it (moves, reformatting, log-level or import edits, renames) never needed understanding it. If it breaks, no one currently understands it. Attach the read to the next change that touches it: have a second person review that change, and leave behind a short comment or test recording what the file is for.
  • Orphaned file src/metadb/Lipidomics/Annotation/Lipidomics.vb:1 — No one still active in this repository holds living knowledge of this file: everyone who made a meaningful change to it has gone quiet, or what the current team did to it (moves, reformatting, log-level or import edits, renames) never needed understanding it. If it breaks, no one currently understands it. Attach the read to the next change that touches it: have a second person review that change, and leave behind a short comment or test recording what the file is for.
  • Orphaned file src/metadb/Lipidomics/LipidParser/LipidParsers.vb:1 — No one still active in this repository holds living knowledge of this file: everyone who made a meaningful change to it has gone quiet, or what the current team did to it (moves, reformatting, log-level or import edits, renames) never needed understanding it. If it breaks, no one currently understands it. Attach the read to the next change that touches it: have a second person review that change, and leave behind a short comment or test recording what the file is for.
  • Orphaned file src/mzmath/MSFinder/FragmentAssigner.vb:1 — No one still active in this repository holds living knowledge of this file: everyone who made a meaningful change to it has gone quiet, or what the current team did to it (moves, reformatting, log-level or import edits, renames) never needed understanding it. If it breaks, no one currently understands it. Attach the read to the next change that touches it: have a second person review that change, and leave behind a short comment or test recording what the file is for.
  • Orphaned file src/metadb/Lipidomics/LipoqualityRest.vb:1 — No one still active in this repository holds living knowledge of this file: everyone who made a meaningful change to it has gone quiet, or what the current team did to it (moves, reformatting, log-level or import edits, renames) never needed understanding it. If it breaks, no one currently understands it. Attach the read to the next change that touches it: have a second person review that change, and leave behind a short comment or test recording what the file is for.
  • Orphaned file Rscript/Library/mzkit_app/src/mzDIA/metaDNA.vb:1 — No one still active in this repository holds living knowledge of this file: everyone who made a meaningful change to it has gone quiet, or what the current team did to it (moves, reformatting, log-level or import edits, renames) never needed understanding it. If it breaks, no one currently understands it. Attach the read to the next change that touches it: have a second person review that change, and leave behind a short comment or test recording what the file is for.
  • Orphaned file src/metadb/Lipidomics/LipoqualityDatabaseManagerUtility.vb:1 — No one still active in this repository holds living knowledge of this file: everyone who made a meaningful change to it has gone quiet, or what the current team did to it (moves, reformatting, log-level or import edits, renames) never needed understanding it. If it breaks, no one currently understands it. Attach the read to the next change that touches it: have a second person review that change, and leave behind a short comment or test recording what the file is for.
  • Orphaned file src/metadb/Chemoinformatics/Formula/Models/Element.vb:1 — No one still active in this repository holds living knowledge of this file: everyone who made a meaningful change to it has gone quiet, or what the current team did to it (moves, reformatting, log-level or import edits, renames) never needed understanding it. If it breaks, no one currently understands it. Attach the read to the next change that touches it: have a second person review that change, and leave behind a short comment or test recording what the file is for.
  • Orphaned file Rscript/Library/mzkit_app/src/mzkit/assembly/Assembly.vb:1 — No one still active in this repository holds living knowledge of this file: everyone who made a meaningful change to it has gone quiet, or what the current team did to it (moves, reformatting, log-level or import edits, renames) never needed understanding it. If it breaks, no one currently understands it. Attach the read to the next change that touches it: have a second person review that change, and leave behind a short comment or test recording what the file is for.
  • Orphaned file Rscript/Library/mzkit_app/src/mzDIA/MoleculeNetworking.vb:1 — No one still active in this repository holds living knowledge of this file: everyone who made a meaningful change to it has gone quiet, or what the current team did to it (moves, reformatting, log-level or import edits, renames) never needed understanding it. If it breaks, no one currently understands it. Attach the read to the next change that touches it: have a second person review that change, and leave behind a short comment or test recording what the file is for.
  • Orphaned file src/metadb/Lipidomics/OadSpectrumPeakGenerator.vb:1 — No one still active in this repository holds living knowledge of this file: everyone who made a meaningful change to it has gone quiet, or what the current team did to it (moves, reformatting, log-level or import edits, renames) never needed understanding it. If it breaks, no one currently understands it. Attach the read to the next change that touches it: have a second person review that change, and leave behind a short comment or test recording what the file is for.
  • Orphaned file src/metadb/Lipidomics/MsCharacterization/EieioMsCharacterizationUtility.vb:1 — No one still active in this repository holds living knowledge of this file: everyone who made a meaningful change to it has gone quiet, or what the current team did to it (moves, reformatting, log-level or import edits, renames) never needed understanding it. If it breaks, no one currently understands it. Attach the read to the next change that touches it: have a second person review that change, and leave behind a short comment or test recording what the file is for.
  • Orphaned file src/metadb/Chemoinformatics/Formula/SevenGoldenRulesCheck.vb:1 — No one still active in this repository holds living knowledge of this file: everyone who made a meaningful change to it has gone quiet, or what the current team did to it (moves, reformatting, log-level or import edits, renames) never needed understanding it. If it breaks, no one currently understands it. Attach the read to the next change that touches it: have a second person review that change, and leave behind a short comment or test recording what the file is for.
  • Orphaned file src/mzmath/ms2_math-core/Ms1/PrecursorType/AdductIonParser.vb:1 — No one still active in this repository holds living knowledge of this file: everyone who made a meaningful change to it has gone quiet, or what the current team did to it (moves, reformatting, log-level or import edits, renames) never needed understanding it. If it breaks, no one currently understands it. Attach the read to the next change that touches it: have a second person review that change, and leave behind a short comment or test recording what the file is for.
  • Orphaned file src/mzmath/MSFinder/FormulaStringParcer.vb:1 — No one still active in this repository holds living knowledge of this file: everyone who made a meaningful change to it has gone quiet, or what the current team did to it (moves, reformatting, log-level or import edits, renames) never needed understanding it. If it breaks, no one currently understands it. Attach the read to the next change that touches it: have a second person review that change, and leave behind a short comment or test recording what the file is for.
  • Orphaned file Rscript/Library/mzkit_app/src/mzkit/assembly/MzPackAccess.vb:1 — No one still active in this repository holds living knowledge of this file: everyone who made a meaningful change to it has gone quiet, or what the current team did to it (moves, reformatting, log-level or import edits, renames) never needed understanding it. If it breaks, no one currently understands it. Attach the read to the next change that touches it: have a second person review that change, and leave behind a short comment or test recording what the file is for.
  • Orphaned file src/metadb/Chemoinformatics/Formula/FormulaCalculateUtility.vb:1 — No one still active in this repository holds living knowledge of this file: everyone who made a meaningful change to it has gone quiet, or what the current team did to it (moves, reformatting, log-level or import edits, renames) never needed understanding it. If it breaks, no one currently understands it. Attach the read to the next change that touches it: have a second person review that change, and leave behind a short comment or test recording what the file is for.
  • Orphaned file src/mzmath/MSEngine/Proteomics/PeptideCalc.vb:1 — No one still active in this repository holds living knowledge of this file: everyone who made a meaningful change to it has gone quiet, or what the current team did to it (moves, reformatting, log-level or import edits, renames) never needed understanding it. If it breaks, no one currently understands it. Attach the read to the next change that touches it: have a second person review that change, and leave behind a short comment or test recording what the file is for.
  • Orphaned file src/assembly/assembly/MarkupData/imzML/Writer/mzPackWriter.vb:1 — No one still active in this repository holds living knowledge of this file: everyone who made a meaningful change to it has gone quiet, or what the current team did to it (moves, reformatting, log-level or import edits, renames) never needed understanding it. If it breaks, no one currently understands it. Attach the read to the next change that touches it: have a second person review that change, and leave behind a short comment or test recording what the file is for.
  • Orphaned file src/mzmath/MSEngine/SpectrumHandler.vb:1 — No one still active in this repository holds living knowledge of this file: everyone who made a meaningful change to it has gone quiet, or what the current team did to it (moves, reformatting, log-level or import edits, renames) never needed understanding it. If it breaks, no one currently understands it. Attach the read to the next change that touches it: have a second person review that change, and leave behind a short comment or test recording what the file is for.
  • + 963 more in this group — see findings.md.
D24 · Comment Value · redundant comment · ×63
  • redundant comment src/assembly/ProteoWizard.Interop/My Project/AssemblyInfo.vb:60 — "General Information about an assembly is controlled through the following set of attributes. Change these attribute values to modify the information associated …" is Visual Studio AssemblyInfo template text, left in place. Delete it, or replace it with what the code cannot say (why it is done here, a constraint, or a consequence).
  • redundant comment src/assembly/ProteoWizard.Interop/My Project/AssemblyInfo.vb:64 — "Review the values of the assembly attributes" is Visual Studio AssemblyInfo template text, left in place. Delete it, or replace it with what the code cannot say (why it is done here, a constraint, or a consequence).
  • redundant comment src/assembly/ProteoWizard.Interop/My Project/AssemblyInfo.vb:75 — "The following GUID is for the ID of the typelib if this project is exposed to COM" is Visual Studio AssemblyInfo template text, left in place. Delete it, or replace it with what the code cannot say (why it is done here, a constraint, or a consequence).
  • redundant comment src/assembly/ProteoWizard.Interop/My Project/AssemblyInfo.vb:78 — "Version information for an assembly consists of the following four values: Major Version Minor Version Build Number Revision You can specify all the values or y …" is Visual Studio AssemblyInfo template text, left in place. Delete it, or replace it with what the code cannot say (why it is done here, a constraint, or a consequence).
  • redundant comment src/assembly/ProteoWizard.d/test/My Project/AssemblyInfo.vb:5 — "General Information about an assembly is controlled through the following set of attributes. Change these attribute values to modify the information associated …" is Visual Studio AssemblyInfo template text, left in place. Delete it, or replace it with what the code cannot say (why it is done here, a constraint, or a consequence).
  • redundant comment src/assembly/ProteoWizard.d/test/My Project/AssemblyInfo.vb:9 — "Review the values of the assembly attributes" is Visual Studio AssemblyInfo template text, left in place. Delete it, or replace it with what the code cannot say (why it is done here, a constraint, or a consequence).
  • redundant comment src/assembly/ProteoWizard.d/test/My Project/AssemblyInfo.vb:20 — "The following GUID is for the ID of the typelib if this project is exposed to COM" is Visual Studio AssemblyInfo template text, left in place. Delete it, or replace it with what the code cannot say (why it is done here, a constraint, or a consequence).
  • redundant comment src/assembly/ProteoWizard.d/test/My Project/AssemblyInfo.vb:23 — "Version information for an assembly consists of the following four values: Major Version Minor Version Build Number Revision You can specify all the values or y …" is Visual Studio AssemblyInfo template text, left in place. Delete it, or replace it with what the code cannot say (why it is done here, a constraint, or a consequence).
  • redundant comment src/assembly/ThermoRawFileReader/Enums/IntensityCutoffTypeConstants.vb:49 — "Enum IntensityCutoffTypeConstants /********************************************************************************/" repeats the code it sits on: 4 of its 5 words (intensity, cutoff, type, constants) are already in `<CLSCompliant(True)>`. Delete it, or replace it with what the code cannot say (why it is done here, a constraint, or a consequence).
  • redundant comment src/assembly/ThermoRawFileReader/Enums/MRMScanTypeConstants.vb:49 — "Enum MRMScanTypeConstants /********************************************************************************/" repeats the code it sits on: 4 of its 5 words (mrm, scan, type, constants) are already in `<CLSCompliant(True)>`. Delete it, or replace it with what the code cannot say (why it is done here, a constraint, or a consequence).
  • redundant comment src/assembly/ThermoRawFileReader/XcaliburRawFileIO.vb:1345 — "Unknown format for .FilterText; return an error" repeats the code it sits on: 5 of its 6 words (unknown, format, filter, text, error) are already in `RaiseErrorMessage("Unknown format for Scan Filter: " & scanInfo.FilterText)`. Delete it, or replace it with what the code cannot say (why it is done here, a constraint, or a consequence).
  • redundant comment src/assembly/ThermoRawFileReader/XcaliburRawFileIO.vb:1370 — "Unknown format for .FilterText; return an error" repeats the code it sits on: 5 of its 6 words (unknown, format, filter, text, error) are already in `RaiseErrorMessage("Unknown format for Scan Filter: " & scanInfo.FilterText)`. Delete it, or replace it with what the code cannot say (why it is done here, a constraint, or a consequence).
  • redundant comment src/assembly/ThermoRawFileReader/XcaliburRawFileIO.vb:1405 — "Get the status log nearest to a retention time." repeats the code it sits on: 5 of its 6 words (get, status, log, retention, time) are already in `Dim statusLogEntry = mXRawFile.GetStatusLogForRetentionTime(retentionTime)`. Delete it, or replace it with what the code cannot say (why it is done here, a constraint, or a consequence).
  • redundant comment src/assembly/mzPackExtensions/test/My Project/AssemblyInfo.vb:58 — "General Information about an assembly is controlled through the following set of attributes. Change these attribute values to modify the information associated …" is Visual Studio AssemblyInfo template text, left in place. Delete it, or replace it with what the code cannot say (why it is done here, a constraint, or a consequence).
  • redundant comment src/assembly/mzPackExtensions/test/My Project/AssemblyInfo.vb:62 — "Review the values of the assembly attributes" is Visual Studio AssemblyInfo template text, left in place. Delete it, or replace it with what the code cannot say (why it is done here, a constraint, or a consequence).
  • redundant comment src/assembly/mzPackExtensions/test/My Project/AssemblyInfo.vb:73 — "The following GUID is for the ID of the typelib if this project is exposed to COM" is Visual Studio AssemblyInfo template text, left in place. Delete it, or replace it with what the code cannot say (why it is done here, a constraint, or a consequence).
  • redundant comment src/assembly/mzPackExtensions/test/My Project/AssemblyInfo.vb:76 — "Version information for an assembly consists of the following four values: Major Version Minor Version Build Number Revision You can specify all the values or y …" is Visual Studio AssemblyInfo template text, left in place. Delete it, or replace it with what the code cannot say (why it is done here, a constraint, or a consequence).
  • redundant comment src/metadb/Chemoinformatics/test/inchiTest.vb:65 — "8 9 10 | \ / 7 2 3--4 \/ \ / | 1 5 6 / \ / \ H 12 11" repeats the code it sits on: 3 of its 3 words (10, 12, 11) are already in `Dim bounds As InchiInput = MainLayer.ParseBounds("7-1-2(8)5-3(9)4(10)6(11)12-5")`. Delete it, or replace it with what the code cannot say (why it is done here, a constraint, or a consequence).
  • redundant comment src/metadb/KEGG/My Project/AssemblyInfo.vb:5 — "General Information about an assembly is controlled through the following set of attributes. Change these attribute values to modify the information associated …" is Visual Studio AssemblyInfo template text, left in place. Delete it, or replace it with what the code cannot say (why it is done here, a constraint, or a consequence).
  • redundant comment src/metadb/KEGG/My Project/AssemblyInfo.vb:9 — "Review the values of the assembly attributes" is Visual Studio AssemblyInfo template text, left in place. Delete it, or replace it with what the code cannot say (why it is done here, a constraint, or a consequence).
  • redundant comment src/metadb/KEGG/My Project/AssemblyInfo.vb:20 — "The following GUID is for the ID of the typelib if this project is exposed to COM" is Visual Studio AssemblyInfo template text, left in place. Delete it, or replace it with what the code cannot say (why it is done here, a constraint, or a consequence).
  • redundant comment src/metadb/KEGG/My Project/AssemblyInfo.vb:23 — "Version information for an assembly consists of the following four values: Major Version Minor Version Build Number Revision You can specify all the values or y …" is Visual Studio AssemblyInfo template text, left in place. Delete it, or replace it with what the code cannot say (why it is done here, a constraint, or a consequence).
  • redundant comment src/metadb/Lipidomics/Annotation/LipidomicsConverter.vb:2611 — 28 comments in this file only repeat the code they sit on (lines 2611, 4172, 4181, 4187, 4199, 4207, 4213, 4216, 4220, 4239, 4244, 4250, 4290, 4320, 4331, 4333, 4338, 4343, 4352, 4881, 4893, 4905, 4918, 4942, 4947, 4957, 4963, 5029), for example "set basic properties". Delete it, or replace it with what the code cannot say (why it is done here, a constraint, or a consequence).
  • redundant comment src/metadb/Lipidomics/SpectrumGenerator/CeramideOadSpectrumGenerator.vb:127 — "spectrum.AddRange(GetAcylSpectrum(lipid, acyl, adduct));" repeats the code it sits on: 7 of its 7 words (spectrum, add, range, get, acyl, lipid, adduct) are already in `spectrum.AddRange(spectrumGenerator.GetAcylDoubleBondSpectrum(lipid, acyl, adduct, nlMass, 30.0R, oadId))`. Delete it, or replace it with what the code cannot say (why it is done here, a constraint, or a consequence).
  • redundant comment src/metadb/Lipidomics/SpectrumGenerator/FacadeLipidSpectrumGenerator.vb:118 — "generator.Add(LbmClass.MG, new MGSpectrumGenerator());" repeats the code it sits on: 6 of its 7 words (generator, add, lbm, class, new, spectrum) are already in `generator.Add(LbmClass.DG, New DGSpectrumGenerator())`. Delete it, or replace it with what the code cannot say (why it is done here, a constraint, or a consequence).
  • + 38 more in this group — see findings.md.
D18 · Solution Shape · Thin analysable surface across projects · ×9
  • Thin analysable surface across projects: KEGG src/metadb/KEGG/KEGG.vbproj — 9 project(s) carry only a thin slice of real code; `KEGG` has 21 significant line(s). The mean analysable-surface weight is 84 %; this project lowers Solution Shape by about 0.2 point(s). Consolidate it or grow it into a substantial, well-scoped assembly.
  • Thin analysable surface across projects: test(net10.0-windows) src/assembly/ThermoRawFileReader/test/test.vbproj — 9 project(s) carry only a thin slice of real code; `test(net10.0-windows)` has 27 significant line(s). The mean analysable-surface weight is 84 %; this project lowers Solution Shape by about 0.32 point(s). Consolidate it or grow it into a substantial, well-scoped assembly.
  • Thin analysable surface across projects: test src/metadb/MoNA/test/test.vbproj — 9 project(s) carry only a thin slice of real code; `test` has 28 significant line(s). The mean analysable-surface weight is 84 %; this project lowers Solution Shape by about 0.15 point(s). Consolidate it or grow it into a substantial, well-scoped assembly.
  • Thin analysable surface across projects: test src/assembly/mzPackExtensions/test/test.vbproj — 9 project(s) carry only a thin slice of real code; `test` has 30 significant line(s). The mean analysable-surface weight is 84 %; this project lowers Solution Shape by about 0.14 point(s). Consolidate it or grow it into a substantial, well-scoped assembly.
  • Thin analysable surface across projects: test src/mzmath/Oligonucleotide_MS/test/test.vbproj — 9 project(s) carry only a thin slice of real code; `test` has 32 significant line(s). The mean analysable-surface weight is 84 %; this project lowers Solution Shape by about 0.12 point(s). Consolidate it or grow it into a substantial, well-scoped assembly.
  • Thin analysable surface across projects: test src/assembly/Comprehensive/test/test.vbproj — 9 project(s) carry only a thin slice of real code; `test` has 33 significant line(s). The mean analysable-surface weight is 84 %; this project lowers Solution Shape by about 0.12 point(s). Consolidate it or grow it into a substantial, well-scoped assembly.
  • Thin analysable surface across projects: test src/assembly/BrukerDataReader/test/test.vbproj — 9 project(s) carry only a thin slice of real code; `test` has 38 significant line(s). The mean analysable-surface weight is 84 %; this project lowers Solution Shape by about 0.08 point(s). Consolidate it or grow it into a substantial, well-scoped assembly.
  • Thin analysable surface across projects: test src/metadna/MetaDNA_visual/test/test.vbproj — 9 project(s) carry only a thin slice of real code; `test` has 41 significant line(s). The mean analysable-surface weight is 84 %; this project lowers Solution Shape by about 0.06 point(s). Consolidate it or grow it into a substantial, well-scoped assembly.
  • Thin analysable surface across projects: test src/assembly/LoadR.NET5/test/test.vbproj — 9 project(s) carry only a thin slice of real code; `test` has 43 significant line(s). The mean analysable-surface weight is 84 %; this project lowers Solution Shape by about 0.05 point(s). Consolidate it or grow it into a substantial, well-scoped assembly.
D17 · Explicit Debt · ObsoleteWithoutCallers · ×8
  • ObsoleteWithoutCallers src/assembly/NMRFidTool/Math/FFT/FFTBase.vb:70 — <Obsolete> FFTBase
  • ObsoleteWithoutCallers src/assembly/NMRFidTool/Math/apodization/ApodizationTool.vb:101 — <Obsolete> ApodizationTool
  • ObsoleteWithoutCallers src/assembly/ThermoRawFileReader/DataObjects/SingleScanInfo.vb:180 — <Obsolete> ParentIonMonoisotopicMZ
  • ObsoleteWithoutCallers src/assembly/ThermoRawFileReader/DataObjects/SingleScanInfo.vb:196 — <Obsolete> IsolationWindowTargetMZ
  • ObsoleteWithoutCallers src/assembly/ThermoRawFileReader/XcaliburRawFileIO.vb:2601 — <Obsolete> GetCollisionEnergyUnnormalized
  • ObsoleteWithoutCallers src/metadb/Lipidomics/SpectrumGeneratorUtility.vb:65 — <Obsolete> GetAcylDoubleBondSpectrum
  • ObsoleteWithoutCallers src/metadb/Lipidomics/SpectrumGeneratorUtility.vb:96 — <Obsolete> GetAlkylDoubleBondSpectrum
  • ObsoleteWithoutCallers src/mzmath/MSEngine/MoleculeMsReference.vb:121 — <Obsolete> .ctor
D29 · Static Analysis (SAST) · REDACTED
  • REDACTED
  • REDACTED
  • REDACTED
  • REDACTED
  • REDACTED
  • REDACTED
  • REDACTED
D34 · Knowledge Freshness · Most significant orphaned file · ×3
  • Most significant orphaned file src/metadb/Lipidomics/MsCharacterization/MsmsCharacterization.vb:1 — One of the orphaned files carrying the most lost knowledge — ranked by size weighted by the file's role in the codebase, the same weighting behind the score above, so core code outranks equally large plumbing. A reasonable place to start a read-through before the aggregate risk above bites.
  • Most significant orphaned file src/metadb/Lipidomics/MsCharacterization/LipidEieioMsmsCharacterization.vb:1 — One of the orphaned files carrying the most lost knowledge — ranked by size weighted by the file's role in the codebase, the same weighting behind the score above, so core code outranks equally large plumbing. A reasonable place to start a read-through before the aggregate risk above bites.
  • Most significant orphaned file src/metadb/Lipidomics/Annotation/LipidomicsConverter.vb:1 — One of the orphaned files carrying the most lost knowledge — ranked by size weighted by the file's role in the codebase, the same weighting behind the score above, so core code outranks equally large plumbing. A reasonable place to start a read-through before the aggregate risk above bites.
AX6 · Interface segregation · Fat interface · ×1
  • Fat interface: ICrossReference (20 members) src/metadb/Chemoinformatics/Metabolite/CrossReference/CrossReference.vb:67 — `ICrossReference` declares 20 members: `chebi`, `KEGG`, `KEGGdrug`, `pubchem`, `HMDB`, `metlin`, `DrugBank`, `ChEMBL`, `Wikipedia`, `lipidmaps`, `MeSH`, `ChemIDplus`, `MetaCyc`, `KNApSAcK`, `foodb`, `chemspider`, `CAS`, `InChIkey`, `InChI`, `SMILES`. Counted as the author wrote them — a property is ONE member and its get/set accessors are not counted separately, and an event counts once. A wide interface forces every implementer and caller to depend on methods they don't use (the Interface-Segregation 'I' in SOLID). Split it into focused role-interfaces.
D20 · ADR Quality · No ADRs found · ×1
  • No ADRs found — No ADRs found. No recognised ADR directory (`docs/adr/`, `docs/decisions/`, `adr/`, `docs/rfcs/`, an `ADR0001/` folder, or their siblings) exists anywhere in this tree. What was searched, so you can tell an empty log from a search that missed one: every directory under the tree (build output, dependencies and VCS metadata excepted), for a document that is either any non-index page inside a recognised ADR directory, whatever its name and however deeply nested (`docs/adr/use-postgres.md`, `docs/adr/2024/0001-x.md`); or a file anywhere whose name is ADR-shaped (`0001-use-postgres.md`, `adr-012-caching.md`); or, when neither turned anything up, a document carrying the decision-record signature (an "Architecture Decision Record" heading, or Status / Context / Decision / Consequences as section headings). A decision log that clears none of these — unnumbered files outside any recognised directory, without those headings — is not seen by this check and this row is then wrong. If that is your case, say so rather than renaming anything; otherwise, consider recording architectural decisions in `docs/adr/`.
D26 · Project Cohesion · Projects may be oversized for their cohesion · ×1
  • Projects may be oversized for their cohesion — 5 of 75 project(s) overshoot their size bounds, lowering Project Cohesion to 8.7/10. The most over is `Lipidomics` (52741 LoC, 257 public types across 1 namespaces). Review these for cohesion — split a project that spans unrelated responsibilities.
D28 · Secrets (history) · Rotate the exposed credentials · ×1
  • REDACTED
D34 · Knowledge Freshness · Concentrated knowledge decay · ×1
  • Concentrated knowledge decay — 991 of 1188 significant files have no living knowledge, while the repository is still being changed at a low rate (38 commit(s) in the last 90 days) — so this is one repo-wide knowledge-decay state, not 991 separate risks. Counted over 1188 of the 1306 production source files in this repository: the rest are under the ~2,400-byte size floor this dimension measures over. The code moved on without the people who understood these files: document them or schedule a read-through before the next change lands in them.
D37 · Vulnerability-disclosure Policy · REDACTED · ×1
  • REDACTED
M2 · Architecture documentation · No ADRs · ×1
  • No ADRs — No Architecture Decision Records found — no conventional ADR directory, no numbered `NNNN-title` documents in any markup this check reads, and nothing ADR-shaped by content. Design rationale recorded elsewhere (a design-notes tree, a mailing list, pull-request discussion) is not visible to this check and is not re-findable per decision, so a future maintainer cannot ask why one choice was made and get an answer.
M2 · Architecture documentation · No architecture diagram/doc · ×1
  • No architecture diagram/doc — No C4/Structurizr/PlantUML/Mermaid/Graphviz/D2 diagram, no drawn diagram named for the architecture, no file named `architecture` or `design` in any markup this check reads, and nothing in the README, docs or contributor guides that announces the shape — no `## Architecture` heading, no "architecture overview"/"high-level design" phrasing, no "the architecture is …" introduction, no guided code tour. A shape laid out in prose that never names itself as the architecture is not visible to this check, and neither is one kept outside the repository, so this row reports the absence of a re-findable shape document — not evidence that nobody wrote the shape down.
M3 · Folder & project structure · Inconsistent root namespaces · ×1
  • Inconsistent root namespaces — Only 40/75 projects share a common root namespace — the code's module identity is inconsistent.
P3 · Security & performance tooling · No SAST · ×1
  • No SAST — No static application security testing detected. For this repository's stack, add a Roslyn security analyzer package referenced from the project (the analyzer packages do analyse VB.NET), plus gitleaks for committed secrets — CodeQL has no VB.NET extractor, so its csharp pack would extract nothing from this tree and then report it clean — this repository has no CI pipeline yet, so run it locally to clear the existing findings, then make it a step of the first workflow you add so a regression fails the build. What was searched, so you can tell an absence from a miss: the 0 CI workflow file(s) in this repository, and the scanner and linter configuration checked in beside them. A scan that runs outside CI, one configured in your forge's web UI rather than in a committed file, or a tool whose name is none of those this check carries, is not seen — if that is your case the row is wrong, and saying so is more useful than adding a second scanner.
Minor — 47 finding(s)
D24 · Comment Value · doc comments repeat the names · ×47
  • doc comments repeat the names src/assembly/BrukerDataReader/Raw/DataReader.vb:85 — 0 of 25 documented parameters and 19 of 99 summaries in `BrukerDataReader.NET5` only repeat the member or parameter name (e.g. "Constructor for the DataReader class" for `DataReader`). 12 documentation tag(s) are empty. Delete the restating tags, or add what the name does not say.
  • doc comments repeat the names src/assembly/Comprehensive/GCxGC/D2Chromatogram.vb:80 — 0 of 72 documented parameters and 0 of 44 summaries in `Comprehensive.NET5` only repeat the member or parameter name (e.g. "" for `gcxgc`). 64 documentation tag(s) are empty. Delete the restating tags, or add what the name does not say.
  • doc comments repeat the names src/metadb/FormulaSearch.Extensions/AdductsRanking.vb:92 — 0 of 24 documented parameters and 0 of 19 summaries in `FormulaSearch.Extensions.NET5(net10.0-windows)` only repeat the member or parameter name (e.g. "" for `Rank`). 31 documentation tag(s) are empty. Delete the restating tags, or add what the name does not say.
  • doc comments repeat the names src/mzmath/GCxGC/GCMSPeak1D.vb:67 — 0 of 9 documented parameters and 1 of 23 summaries in `GCxGC` only repeat the member or parameter name (e.g. "A 1-d gcms peak" for `GCMSPeak1D`). 5 documentation tag(s) are empty. Delete the restating tags, or add what the name does not say.
  • doc comments repeat the names src/metadna/KEGG_MetaDNA/Program.vb:82 — 0 of 2 documented parameters and 0 of 0 summaries in `KEGG_MetaDNA` only repeat the member or parameter name (e.g. "" for `args`). 2 documentation tag(s) are empty. Delete the restating tags, or add what the name does not say.
  • doc comments repeat the names src/metadb/Lipidomics/Annotation/LipidSearchMapper.vb:72 — 0 of 19 documented parameters and 0 of 17 summaries in `Lipidomics` only repeat the member or parameter name (e.g. "" for `LipidSearchMapper`). 16 documentation tag(s) are empty. Delete the restating tags, or add what the name does not say.
  • doc comments repeat the names src/assembly/LoadR.NET5/ChromatogramOverlap.vb:105 — 0 of 7 documented parameters and 0 of 10 summaries in `LoadR.NET5` only repeat the member or parameter name (e.g. "" for `getByName`). 6 documentation tag(s) are empty. Delete the restating tags, or add what the name does not say.
  • doc comments repeat the names src/mzmath/MSEngine/AnnotationPack/AnnotationResult.vb:144 — 0 of 59 documented parameters and 0 of 105 summaries in `MSEngine(net10.0-windows)` only repeat the member or parameter name (e.g. "" for `copy`). 42 documentation tag(s) are empty. Delete the restating tags, or add what the name does not say.
  • doc comments repeat the names src/assembly/ThermoRawFileReader/DataObjects/MRMInfo.vb:74 — 7 of 99 documented parameters and 31 of 201 summaries in `MSFileReader.NET5` only repeat the member or parameter name (e.g. "Duplicate the MRM info" for `DuplicateMRMInfo`). 44 documentation tag(s) are empty. Delete the restating tags, or add what the name does not say.
  • doc comments repeat the names src/mzmath/MSFinder/FormulaGenerator.vb:124 — 0 of 42 documented parameters and 0 of 24 summaries in `MSFinder(net10.0-windows)` only repeat the member or parameter name (e.g. "" for `param`). 35 documentation tag(s) are empty. Delete the restating tags, or add what the name does not say.
  • doc comments repeat the names src/metadb/MoNA/Metadata/MetaData.vb:162 — 0 of 11 documented parameters and 1 of 14 summaries in `MoNA.NET5(net10.0-windows)` only repeat the member or parameter name (e.g. "the CAS number" for `cas_number`). 11 documentation tag(s) are empty. Delete the restating tags, or add what the name does not say.
  • doc comments repeat the names src/mzmath/MoleculeNetworking/NLPEmbedding/SpecEmbedding.vb:102 — 0 of 90 documented parameters and 0 of 101 summaries in `MoleculeNetworking` only repeat the member or parameter name (e.g. "" for `AddSample`). 80 documentation tag(s) are empty. Delete the restating tags, or add what the name does not say.
  • doc comments repeat the names src/visualize/MsImaging/Blender/Renderer/Renderer.vb:126 — 0 of 148 documented parameters and 2 of 142 summaries in `MsImaging.NET5` only repeat the member or parameter name (e.g. "draw background" for `DrawBackground`). 148 documentation tag(s) are empty. Delete the restating tags, or add what the name does not say.
  • doc comments repeat the names src/visualize/plot/ChromatogramPlot/ChromatogramPeakPlot.vb:232 — 0 of 86 documented parameters and 0 of 22 summaries in `MsPlot.NET5` only repeat the member or parameter name (e.g. "" for `g`). 76 documentation tag(s) are empty. Delete the restating tags, or add what the name does not say.
  • doc comments repeat the names src/mzmath/Mummichog/PeakCorrelation.vb:117 — 0 of 8 documented parameters and 0 of 15 summaries in `Mummichog(net10.0-windows)` only repeat the member or parameter name (e.g. "" for `peak`). 8 documentation tag(s) are empty. Delete the restating tags, or add what the name does not say.
  • doc comments repeat the names src/assembly/NMRFidTool/Math/apodization/ApodizationTool.vb:108 — 0 of 16 documented parameters and 0 of 37 summaries in `NMRFidTool(net10.0-windows)` only repeat the member or parameter name (e.g. "" for `spectrum`). 8 documentation tag(s) are empty. Delete the restating tags, or add what the name does not say.
  • doc comments repeat the names src/mzmath/Oligonucleotide_MS/MS_Peak/TheoreticalDigestMass.vb:68 — 0 of 8 documented parameters and 1 of 44 summaries in `Oligonucleotide_MS` only repeat the member or parameter name (e.g. "digest" for `TheoreticalDigestMass`). 10 documentation tag(s) are empty. Delete the restating tags, or add what the name does not say.
  • doc comments repeat the names src/assembly/ProteoWizard.Interop/Extensions.vb:66 — 0 of 2 documented parameters and 0 of 10 summaries in `ProteoWizard.Interop.NET5(net10.0-windows)` only repeat the member or parameter name (e.g. "" for `path`). 2 documentation tag(s) are empty. Delete the restating tags, or add what the name does not say.
  • doc comments repeat the names src/assembly/ProteoWizard.d/VBServerScript.vb:66 — 0 of 3 documented parameters and 1 of 1 summaries in `ProteoWizard.d` only repeat the member or parameter name (e.g. "VB server script" for `VBServerScript`). 3 documentation tag(s) are empty. Delete the restating tags, or add what the name does not say.
  • doc comments repeat the names src/assembly/RamanSpectroscopy/read_WDF.vb:90 — 0 of 2 documented parameters and 0 of 7 summaries in `RamanSpectroscopy` only repeat the member or parameter name (e.g. "" for `verbose`). 1 documentation tag(s) are empty. Delete the restating tags, or add what the name does not say.
  • doc comments repeat the names src/visualize/SDF.Extensions/SDF2KCF.vb:71 — 0 of 1 documented parameters and 0 of 1 summaries in `SDF.Extensions.NET5` only repeat the member or parameter name (e.g. "" for `sdf`). 1 documentation tag(s) are empty. Delete the restating tags, or add what the name does not say.
  • doc comments repeat the names src/metadb/SMILES/AtomGroup.vb:91 — 0 of 21 documented parameters and 0 of 45 summaries in `SMILES.NET5` only repeat the member or parameter name (e.g. "" for `label`). 20 documentation tag(s) are empty. Delete the restating tags, or add what the name does not say.
  • doc comments repeat the names src/assembly/SignalReader/UVSpectroscopyReader.vb:93 — 0 of 12 documented parameters and 1 of 7 summaries in `SignalReader(net10.0-windows)` only repeat the member or parameter name (e.g. "electromagnetic radiation spectrum" for `PopulatesElectromagneticRadiationSpectrum`). 12 documentation tag(s) are empty. Delete the restating tags, or add what the name does not say.
  • doc comments repeat the names src/mzmath/SingleCells/Deconvolute/Math.vb:81 — 0 of 49 documented parameters and 0 of 67 summaries in `SingleCells` only repeat the member or parameter name (e.g. "" for `raw`). 46 documentation tag(s) are empty. Delete the restating tags, or add what the name does not say.
  • doc comments repeat the names src/mzmath/SpatialMath/PixelData.vb:214 — 0 of 7 documented parameters and 0 of 24 summaries in `SpatialMath` only repeat the member or parameter name (e.g. "" for `pixels`). 4 documentation tag(s) are empty. Delete the restating tags, or add what the name does not say.
  • + 22 more in this group — see findings.md.

Appendix B — Reproduction & audit trail

Every external tool invocation behind a deep-scan dimension — the tool, its captured version, the exact command, how many findings it yielded, and a link to the retained raw output. To reproduce any finding: check out the same commit and run the command shown (repo-relative — never an absolute scratch path). The complete raw scanner output is retained verbatim under artifacts/raw/ (indexed in artifacts/raw/index.json); per-invocation exit codes and wall-clock durations are in sidecar.json — kept out of this table so the rendered report stays byte-identical across runs of the same commit.

DimensionToolVersionCommandFindingsRaw output
D28 · Secrets (history)gitleaks—gitleaks detect --no-banner --config /opt/gitleaks-rules/watchdog-gitleaks.toml --report-format json --report-path /tmp/watchdog-gitleaks-8c0213c78b0c43ab817a5072462ec640/history.json --exit-code 0 --source .223artifacts/raw/gitleaks-history.json
D28 · Secrets (history)gitleaks—gitleaks detect --no-git --no-banner --config /opt/gitleaks-rules/watchdog-gitleaks.toml --report-format json --report-path /tmp/watchdog-gitleaks-8c0213c78b0c43ab817a5072462ec640/tree.json --exit-code 0 --source .223artifacts/raw/gitleaks-tree.json
D29 · Static Analysis (SAST)semgrep—semgrep --config /opt/semgrep-rules/security-audit.yml --config /opt/semgrep-rules/owasp-top-ten.yml --config /opt/semgrep-rules/watchdog-sast.yml --json --quiet --timeout 10 --timeout-threshold 3 --metrics off --exclude *.arrow --exclude *.avro --exclude *.csv --exclude *.dat --exclude *.db --exclude *.feather --exclude *.geojson --exclude *.h5 --exclude *.hdf5 --exclude *.jsonl --exclude *.log --exclude *.ndjson --exclude *.npy --exclude *.npz --exclude *.orc --exclude *.parquet --exclude *.pickle --exclude *.pkl --exclude *.psv --exclude *.sqlite --exclude *.sqlite3 --exclude *.tfrecord --exclude *.tsv --exclude *.txt --exclude Rscript/R/MetaDNA/man --exclude Rscript/R/mzkit/man .10artifacts/raw/semgrep.json
D30 · Dependency Vulnerabilitiesnuget—nuget: not applicable — nuget: the solution did not restore on the analyzer's .NET SDK (an SDK/target-framework/restore mismatch, common for an older codebase), so there was no restored dependency graph to scan0—
D30 · Dependency Vulnerabilitiesosv-scanner—osv-scanner --format json --recursive --experimental-disable-plugins transitivedependency/requirements --experimental-disable-plugins dotnet/csproj --experimental-disable-plugins dotnet/nugetcpm .0artifacts/raw/osv-scanner.json
D31 · IaC & Container Securitytrivy—trivy: not applicable — No Infrastructure-as-Code or container manifests found (Dockerfile, Docker Compose, Terraform, Kubernetes/Helm, CloudFormation, ARM, Bicep, Ansible); nothing to scan.0—
D32 · Data Compliance (PII/GDPR)semgrep—semgrep: not applicable — No personal data was found crossing a boundary the PII/GDPR ruleset checks — nothing written to a log or console sink, placed in a URL or query string, or persisted to browser storage. That is a clean result for the LEAK surface only: this ruleset detects personal data escaping, it does not inventory the personal data a repository holds, so it is not evidence that this repository has no personal-data surface. The personal-data map (Appendix C) and the C1-C5 compliance cards are what speak to that. semgrep could not parse 16 file(s) — `Rscript/Library/mzkit_app/@export/ChemicalDraw.d.ts`, `Rscript/Library/mzkit_app/@export/GCMS.d.ts`, `Rscript/Library/mzkit_app/@export/MRMLinear.d.ts`, `Rscript/Library/mzkit_app/@export/MSI.d.ts`, `Rscript/Library/mzkit_app/@export/MoleculeNetworking.d.ts`, … (+11 more) — so the PII/GDPR sweep did not cover the unparsed regions of them; rows reported elsewhere in those files are real.0—
D36 · Supply-chain Provenance & Signingprovenance—provenance: not applicable — No CI/build pipeline found (.github/.forgejo/.gitea workflows, .circleci, .buildkite, .woodpecker, .teamcity, .gitlab-ci.yml, .travis.yml, bitbucket-pipelines.yml, .drone.yml, .cirrus.yml, .woodpecker.yml, appveyor.yml, azure-pipelines*.yml, .pipelines/, .vsts-ci/, .azuredevops/, Jenkinsfile); there is no build to attest provenance for.0—
D40 · Network Egress Confinementruntime-hardening—runtime-hardening: not applicable — No Kubernetes/orchestration workloads found in the repository manifests; network egress policy is a cluster-native control that may live at the platform/firewall layer, so there is nothing to assess here.0—
D41 · Kernel & Syscall Confinementruntime-hardening—runtime-hardening: not applicable — No Kubernetes/orchestration workloads found in the repository manifests; seccomp/AppArmor/SELinux confinement is a workload-level control, so there is nothing to assess here.0—
D42 · Runtime Threat Enforcementruntime-hardening—runtime-hardening: not applicable — No Kubernetes/orchestration workloads found in the repository manifests; runtime threat-detection and admission-control policy are cluster-level controls, so there is nothing to assess here.0—
D43 · Malicious Dependenciesosv-scanner—osv-scanner --format json --recursive --experimental-disable-plugins transitivedependency/requirements --experimental-disable-plugins dotnet/csproj --experimental-disable-plugins dotnet/nugetcpm .0artifacts/raw/osv-scanner.json

Run 01a179d3-72bd-7806-bc44-2bf2e8e81a85 · every finding is also locatable in findings.md, and the complete scoring record (with exit codes + durations) in sidecar.json.

Issues: 121 · Warnings: 1247 · Recommendations: 1088 · Info: 47 — Appendix A · all findings · full markdown report.
Generated by Watchdog — deterministic code-health analysis. 26-10-2026 @ 20:07 UTC.

Downloadable artifacts

Machine-readable and reproducible from this commit + frozen rubric — drop them straight into a contract appendix, a CRA dossier, or a downstream SCA / VEX tool.

⬇ Findings, MITRE CWE-tagged .sarif⬇ Health changelog .md