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Remove standalone scripts, legacy tools, and unused classes that are not referenced by the core MSGF+ search pipeline, reducing codebase by ~22,000 lines. Deleted entire packages: - ims/ (9 files) — legacy IMS utilities - ipa/ (5 files) — unused isotope pattern analysis - msgf2d/ (8 files) — abandoned 2D scoring experiment - msdictionary/ (7 files) — unused genome dictionary tool - mstag/ (3 files) — unused sequence tagging - scripts/ (6 files) — standalone CLI utilities - msutil/test/ (3 files) — misplaced test classes - msgf/test/ (2 files) — legacy test stubs - msgf/analysis/ (1 file) — unused ROC generator Cleaned mixed packages: - misc/: removed 59 standalone scripts, kept 5 core utilities - msgf/: removed 6 unused graph/scoring classes - msutil/: removed 9 unused filter/annotation classes - msdbsearch/: removed 4 standalone DB tools - parser/: removed 9 legacy format parsers (InsPecT, Mascot, etc.) - ui/: removed 6 legacy entry points (MSGF, MSGFLib, etc.) - mzid/: removed 1 unused adapter stub - msscorer/: removed 1 unused stats class - suffixarray/: removed 1 unused mass array class Also removed dead test methods and cleaned dangling imports. Tests: 119 run, 0 failures. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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Pull request overview
Note
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Removes large amounts of dead/legacy code that’s not used by the core MSGF+ pipeline, reducing maintenance surface area and slightly shrinking the build output.
Changes:
- Deleted numerous unused CLI scripts, misc utilities, and ad-hoc “test” drivers under
src/main/java. - Removed legacy/unused parsers and supporting classes (e.g., OMSSA/MSGFDB-related and other analysis helpers).
- Cleaned up
ParamManagerby removing a deprecatedmainentry point and its dependency on the legacyMSGFUI class.
Reviewed changes
Copilot reviewed 141 out of 155 changed files in this pull request and generated 1 comment.
Show a summary per file
| File | Description |
|---|---|
| src/main/java/edu/ucsd/msjava/scripts/SpecFileValidator.java | Removed unused standalone validator script. |
| src/main/java/edu/ucsd/msjava/scripts/SelectSpectra.java | Removed unused standalone spectra-selection script. |
| src/main/java/edu/ucsd/msjava/scripts/MergeSpectra.java | Removed unused standalone spectra-merging script. |
| src/main/java/edu/ucsd/msjava/scripts/GetDBInfo.java | Removed unused standalone FASTA stats script. |
| src/main/java/edu/ucsd/msjava/scripts/CountSpectra.java | Removed unused standalone spectra-count script. |
| src/main/java/edu/ucsd/msjava/scripts/AgilentCyclicSpecPreProcess.java | Removed unused standalone preprocessing script. |
| src/main/java/edu/ucsd/msjava/parser/SortedSpectraIterator.java | Removed unused iterator utility. |
| src/main/java/edu/ucsd/msjava/parser/SearchParameterParser.java | Removed unused parameter parser stub. |
| src/main/java/edu/ucsd/msjava/parser/PSMList.java | Removed legacy PSM container/utilities not used in core pipeline. |
| src/main/java/edu/ucsd/msjava/parser/OMSSAParser.java | Removed legacy OMSSA result parser. |
| src/main/java/edu/ucsd/msjava/parser/MzXMLToMgfConverter.java | Removed unused mzXML→MGF converter. |
| src/main/java/edu/ucsd/msjava/parser/MSGappedDictionaryParser.java | Removed unused MS-Gapped-Dictionary parser. |
| src/main/java/edu/ucsd/msjava/parser/MSGappedDictionaryPSM.java | Removed unused MS-Gapped-Dictionary PSM type. |
| src/main/java/edu/ucsd/msjava/parser/MSGFDBParser.java | Removed legacy MSGFDB text parser. |
| src/main/java/edu/ucsd/msjava/parser/InsPecTPSM.java | Removed legacy InsPecT PSM type. |
| src/main/java/edu/ucsd/msjava/params/ParamManager.java | Removed deprecated main and legacy MSGF dependency. |
| src/main/java/edu/ucsd/msjava/mzid/MzIdAdapter.java | Removed unused mzIdentML adapter stub. |
| src/main/java/edu/ucsd/msjava/msutil/test/SpectraTest.java | Removed ad-hoc main-based test driver. |
| src/main/java/edu/ucsd/msjava/msutil/test/MzXMLSpectraMapTest.java | Removed ad-hoc main-based test driver. |
| src/main/java/edu/ucsd/msjava/msutil/test/MzXMLSpectraIteratorTest.java | Removed ad-hoc main-based test driver. |
| src/main/java/edu/ucsd/msjava/msutil/TopNFilter.java | Removed unused spectrum reshape/filter implementation. |
| src/main/java/edu/ucsd/msjava/msutil/SpectrumTester.java | Removed ad-hoc spectrum parsing tester. |
| src/main/java/edu/ucsd/msjava/msutil/SpectrumRecalibrator.java | Removed incomplete/unused recalibration implementation. |
| src/main/java/edu/ucsd/msjava/msutil/SpectrumAnnotator.java | Removed unused annotation helper. |
| src/main/java/edu/ucsd/msjava/msutil/ScoringFunction.java | Removed unused scoring interface. |
| src/main/java/edu/ucsd/msjava/msutil/NominalMassAASet.java | Removed unused AA-set utility. |
| src/main/java/edu/ucsd/msjava/msutil/IntMassAASet.java | Removed unused AA-set utility. |
| src/main/java/edu/ucsd/msjava/msutil/GappedPeptide.java | Removed unused gapped peptide representation. |
| src/main/java/edu/ucsd/msjava/msutil/CompositionAASet.java | Removed unused AA-set utility. |
| src/main/java/edu/ucsd/msjava/mstag/TagTester.java | Removed ad-hoc tag testing code. |
| src/main/java/edu/ucsd/msjava/mstag/Tag.java | Removed unused tag representation. |
| src/main/java/edu/ucsd/msjava/msscorer/ListStat.java | Removed unused statistics helper. |
| src/main/java/edu/ucsd/msjava/msgf2d/TestMSGF2D.java | Removed unused test stub. |
| src/main/java/edu/ucsd/msjava/msgf2d/ScoreBound2D.java | Removed unused 2D scoring bounds helper. |
| src/main/java/edu/ucsd/msjava/msgf2d/CombinePairedSpectra.java | Removed unused 2D workflow helper. |
| src/main/java/edu/ucsd/msjava/msgf2d/BacktrackTable2D.java | Removed unused 2D backtracking structure. |
| src/main/java/edu/ucsd/msjava/msgf2d/BacktrackPointer2D.java | Removed unused 2D backtracking pointer. |
| src/main/java/edu/ucsd/msjava/msgf/test/MSGFValidation.java | Removed unused/buggy validation CLI. |
| src/main/java/edu/ucsd/msjava/msgf/SpectrumGraphNode.java | Removed unused graph node type. |
| src/main/java/edu/ucsd/msjava/msgf/ScoredSpectrumSumHP.java | Removed unused specialization. |
| src/main/java/edu/ucsd/msjava/msgf/ReachableNode.java | Removed unused reachable-node cache holder. |
| src/main/java/edu/ucsd/msjava/msgf/PercolatorAdapter.java | Removed unused adapter stub. |
| src/main/java/edu/ucsd/msjava/msgf/LengthPredictor.java | Removed unused heuristic predictor. |
| src/main/java/edu/ucsd/msjava/msgf/DeNovoSequencer.java | Removed unused de novo sequencing implementation. |
| src/main/java/edu/ucsd/msjava/msgf/AminoAcidGraph.java | Removed unused graph specialization. |
| src/main/java/edu/ucsd/msjava/msdictionary/TestMSDictionary.java | Removed unused test driver. |
| src/main/java/edu/ucsd/msjava/msdictionary/ProteinLocator.java | Removed unused analysis tool. |
| src/main/java/edu/ucsd/msjava/msdictionary/MSDicLauncher.java | Removed deprecated MS-Dictionary launcher. |
| src/main/java/edu/ucsd/msjava/msdictionary/GenomeLocator.java | Removed unused genome locator utility. |
| src/main/java/edu/ucsd/msjava/msdictionary/Codon.java | Removed unused codon translation table. |
| src/main/java/edu/ucsd/msjava/msdbsearch/ShuffleDB.java | Removed unused database shuffling utility. |
| src/main/java/edu/ucsd/msjava/msdbsearch/ReverseLibDB.java | Removed unused database reverse/concat utility. |
| src/main/java/edu/ucsd/msjava/msdbsearch/MakePairedSpectra.java | Removed unused paired-spectra tool. |
| src/main/java/edu/ucsd/msjava/msdbsearch/FilterDatabase.java | Removed unused database filtering tool. |
| src/main/java/edu/ucsd/msjava/misc/VennDiagram.java | Removed unused results comparison CLI. |
| src/main/java/edu/ucsd/msjava/misc/TrainScoringParameters.java | Removed unused training helper. |
| src/main/java/edu/ucsd/msjava/misc/TopDownAnalysis.java | Removed unused analysis stub. |
| src/main/java/edu/ucsd/msjava/misc/SuffixArrayTest.java | Removed unused suffix-array test tool. |
| src/main/java/edu/ucsd/msjava/misc/SplitMgf.java | Removed unused MGF splitting CLI. |
| src/main/java/edu/ucsd/msjava/misc/SplitFasta.java | Removed unused FASTA splitting CLI. |
| src/main/java/edu/ucsd/msjava/misc/SpectraSTToTSV.java | Removed unused format conversion CLI. |
| src/main/java/edu/ucsd/msjava/misc/SpectraSTToMSGFInput.java | Removed unused format conversion CLI. |
| src/main/java/edu/ucsd/msjava/misc/RunOMSSAOnCCMS.java | Removed unused OMSSA grid helper. |
| src/main/java/edu/ucsd/msjava/misc/RunMSGFDBOnGrid.java | Removed commented-out/unused grid runner. |
| src/main/java/edu/ucsd/msjava/misc/PepIdxToFasta.java | Removed unused conversion CLI. |
| src/main/java/edu/ucsd/msjava/misc/ParamToTxt.java | Removed unused parameter conversion CLI. |
| src/main/java/edu/ucsd/msjava/misc/PEMMRProcessor.java | Removed unused TSV post-processor. |
| src/main/java/edu/ucsd/msjava/misc/MzXMLToMgf.java | Removed duplicate mzXML→MGF CLI. |
| src/main/java/edu/ucsd/msjava/misc/MultiThreadExercise.java | Removed unrelated threading exercise code. |
| src/main/java/edu/ucsd/msjava/misc/MergeTargetDecoyFiles.java | Removed unused results-merging helper. |
| src/main/java/edu/ucsd/msjava/misc/MassCalc.java | Removed interactive mass calculator CLI. |
| src/main/java/edu/ucsd/msjava/misc/MakePrefixDB.java | Removed unused DB transformation tool. |
| src/main/java/edu/ucsd/msjava/misc/MSGFDBToQSpec.java | Removed unused result conversion tool. |
| src/main/java/edu/ucsd/msjava/misc/MSGFDBToInspect.java | Removed unused result conversion tool. |
| src/main/java/edu/ucsd/msjava/misc/MS2ToMgf.java | Removed unused MS2→MGF converter. |
| src/main/java/edu/ucsd/msjava/misc/ISBETDAnalysis.java | Removed unused analysis tool. |
| src/main/java/edu/ucsd/msjava/misc/IPA.java | Removed unused IPA helper (distinct from edu.ucsd.msjava.ipa). |
| src/main/java/edu/ucsd/msjava/misc/GetSearchParams.java | Removed unused CLI stub. |
| src/main/java/edu/ucsd/msjava/misc/GetProteinLength.java | Removed unused conversion helper. |
| src/main/java/edu/ucsd/msjava/misc/FindPSMIntersection.java | Removed unused intersection-finding tool. |
| src/main/java/edu/ucsd/msjava/misc/FilteringEfficiency.java | Removed unused analysis code. |
| src/main/java/edu/ucsd/msjava/misc/FileFilter.java | Removed file filter helpers only used by deleted tools. |
| src/main/java/edu/ucsd/msjava/misc/Deconvolution.java | Removed unused spectrum deconvolution CLI. |
| src/main/java/edu/ucsd/msjava/misc/DatToTxt.java | Removed unused Mascot .dat conversion tool. |
| src/main/java/edu/ucsd/msjava/misc/CountSequestIDs.java | Removed unused stub. |
| src/main/java/edu/ucsd/msjava/misc/CountID.java | Removed unused ID counting CLI. |
| src/main/java/edu/ucsd/msjava/misc/ConvertToMgf.java | Removed unused “convert to MGF” CLI. |
| src/main/java/edu/ucsd/msjava/misc/ControlNew.java | Removed unused dataset-specific tool. |
| src/main/java/edu/ucsd/msjava/misc/CompositionFirst.java | Removed unused stub. |
| src/main/java/edu/ucsd/msjava/misc/CompareSearchResults.java | Removed unused result comparison tool. |
| src/main/java/edu/ucsd/msjava/misc/CompactSATest.java | Removed unused suffix-array read test tool. |
| src/main/java/edu/ucsd/msjava/misc/CompGraphPaper.java | Removed unused analysis script. |
| src/main/java/edu/ucsd/msjava/misc/Clauser.java | Removed unused conversion helper. |
| src/main/java/edu/ucsd/msjava/misc/ChargePrediction.java | Removed unused experimental tool. |
| src/main/java/edu/ucsd/msjava/misc/CalcFastaDBSize.java | Removed duplicate/legacy FASTA stats tool. |
| src/main/java/edu/ucsd/msjava/misc/AnnotatedMgfToMSGFInput.java | Removed unused conversion CLI. |
| src/main/java/edu/ucsd/msjava/ipa/PSM.java | Removed unused IPA model class. |
| src/main/java/edu/ucsd/msjava/ipa/MSGFPlusResultSet.java | Removed unused IPA result wrapper. |
| src/main/java/edu/ucsd/msjava/ipa/MS1SpectraMap.java | Removed unused IPA MS1 map. |
| src/main/java/edu/ucsd/msjava/ipa/IPA.java | Removed unused IPA processing pipeline. |
| src/main/java/edu/ucsd/msjava/ipa/Feature.java | Removed unused IPA feature model. |
| src/main/java/edu/ucsd/msjava/ims/Summarize.java | Removed unused IMS utility. |
| src/main/java/edu/ucsd/msjava/ims/SplitDta.java | Removed unused IMS utility. |
| src/main/java/edu/ucsd/msjava/ims/OptimizeCE.java | Removed unused IMS utility. |
| src/main/java/edu/ucsd/msjava/ims/Misc.java | Removed unused IMS utility. |
| src/main/java/edu/ucsd/msjava/ims/MaskSpectra.java | Removed unused IMS utility. |
| src/main/java/edu/ucsd/msjava/ims/GetTheBestPerScan.java | Removed unused IMS utility. |
| src/main/java/edu/ucsd/msjava/ims/GetTheBestPerPeptide.java | Removed unused IMS utility. |
| src/main/java/edu/ucsd/msjava/ims/DtaToMSGFInputDB.java | Removed unused IMS conversion tool. |
| src/main/java/edu/ucsd/msjava/ims/DtaToMSGFInput.java | Removed unused IMS conversion tool. |
Comments suppressed due to low confidence (1)
src/main/java/edu/ucsd/msjava/params/ParamManager.java:1
- The PR description frames this as “pure code hygiene” with “no functional changes”, but removing the deprecated
public static void main(String[])entry point fromParamManageris a functional/API behavior change for any downstream users that invoked this class directly (even if strongly discouraged). If maintaining backward compatibility matters, consider keeping a minimalmainthat either delegates to the supported CLI entry point (e.g.,MSGFPlus) or prints a clear deprecation message and exits; otherwise, explicitly call this out as a breaking change in the PR description/release notes.
package edu.ucsd.msjava.params;
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| import edu.ucsd.msjava.sequences.Constants; | ||
| import edu.ucsd.msjava.ui.MSGF; | ||
| import edu.ucsd.msjava.ui.MSGFPlus; |
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The PR description frames this as “pure code hygiene” with “no functional changes”, but removing the deprecated public static void main(String[]) entry point from ParamManager is a functional/API behavior change for any downstream users that invoked this class directly (even if strongly discouraged). If maintaining backward compatibility matters, consider keeping a minimal main that either delegates to the supported CLI entry point (e.g., MSGFPlus) or prints a clear deprecation message and exits; otherwise, explicitly call this out as a breaking change in the PR description/release notes.
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Summary
ims/,ipa/,msgf2d/,msdictionary/,mstag/,scripts/,msutil/test/,msgf/test/,msgf/analysis/misc/utilities (ProgressData, ProgressReporter, ThreadPoolExecutorWithExceptions, ExceptionCapturer, TextParsingUtils) preservedBenchmark (vs original master baseline)
Test plan
mvn compile— clean compilationmvn test— 119 tests run, 0 failures, 0 errors🤖 Generated with Claude Code