├── .gitignore ├── LICENSE ├── README.md ├── pom.xml └── src ├── main ├── java │ ├── ai │ │ ├── AIGear.java │ │ ├── AIWorker.java │ │ ├── ApexMatch.java │ │ ├── FileIO.java │ │ ├── JMeta.java │ │ ├── JPeakGroup.java │ │ ├── JSequenceProvider.java │ │ ├── JXIC.java │ │ ├── LibFragment.java │ │ ├── LibOutputWorker.java │ │ ├── PSMConfig.java │ │ ├── PeptideCCS.java │ │ ├── PeptideFrag.java │ │ ├── PeptideMatch.java │ │ ├── PeptideRT.java │ │ ├── RTDataGenerator.java │ │ ├── SkylineIO.java │ │ ├── ai.py │ │ └── ai_pred.py │ ├── db │ │ └── DBGear.java │ ├── dia │ │ ├── CCSDIAIndex.java │ │ ├── CCSDIAMap.java │ │ ├── CCSDIAMeta.java │ │ ├── DIAIndex.java │ │ ├── DIAMap.java │ │ ├── DIAMeta.java │ │ ├── IsolationWindow.java │ │ ├── JFragmentIon.java │ │ ├── JFragmentIonIM.java │ │ ├── LPeak.java │ │ ├── LPeakComparatorMax2Min.java │ │ ├── LibSpectrum.java │ │ ├── PeptidePeak.java │ │ └── XICtool.java │ ├── input │ │ ├── CModification.java │ │ ├── CPTM.java │ │ ├── CParameter.java │ │ ├── JMod.java │ │ ├── ModificationUtils.java │ │ ├── PeptideUtils.java │ │ └── ProteinHit.java │ ├── util │ │ ├── Cloger.java │ │ ├── MgfUtils.java │ │ ├── StreamLog.java │ │ └── log4j.properties │ └── xic │ │ ├── SGFilter.java │ │ ├── SGFilter3points.java │ │ ├── SGFilter5points.java │ │ └── SGFilter7points.java └── resources │ ├── log4j2.xml │ ├── project.properties │ ├── top_modifications.tsv │ └── unimod.xml └── test └── java └── ai └── SkylineIOTest.java /.gitignore: -------------------------------------------------------------------------------- 1 | 2 | *.jar 3 | *.class 4 | 5 | target/* 6 | settings.json -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Noble-Lab/Carafe/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: 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