├── .gitignore ├── LICENSE-2.0.txt ├── README.md ├── README.txt ├── compomics-utilities.ico ├── docs └── javadoc │ ├── com │ └── compomics │ │ └── util │ │ └── experiment │ │ └── identification │ │ └── protein_inference │ │ └── fm_index │ │ ├── FMIndex.html │ │ ├── Rank.html │ │ ├── WaveletTree.html │ │ └── package-tree.html │ ├── index-all.html │ ├── overview-tree.html │ └── serialized-form.html ├── exampleFiles ├── PeptideMapping │ ├── yeast-pep-1k.csv │ ├── yeast-tag-1k.csv │ └── yeast.fasta ├── exampleChromatogram.txt ├── exampleSpectrumA.pkl ├── exampleSpectrumB.pkl └── experiment │ ├── enzymes.xml │ ├── glycons.xml │ ├── mods.xml │ ├── reporterMethods.xml │ └── usermods.xml ├── nb-configuration.xml ├── nbactions.xml ├── pom.xml ├── resources └── conf │ ├── gene_mappings │ ├── ensembl_versions │ ├── go_domains │ ├── hsapiens_gene_ensembl_gene_mappings │ ├── hsapiens_gene_ensembl_go_mappings │ ├── sscrofa_gene_ensembl_gene_mappings │ └── sscrofa_gene_ensembl_go_mappings │ └── taxonomy │ ├── ensembl_all_species │ ├── ensembl_biomart_databases │ └── uniprot_species └── src ├── main ├── assembly │ └── zip.xml ├── java │ └── com │ │ └── compomics │ │ ├── cli │ │ ├── enzymes │ │ │ ├── EnzymesCLI.java │ │ │ ├── EnzymesCLIInputBean.java │ │ │ ├── EnzymesCLIParams.java │ │ │ └── package.html │ │ ├── fasta │ │ │ ├── FastaParametersCLIParams.java │ │ │ ├── FastaParametersInputBean.java │ │ │ └── package.html │ │ ├── identification_parameters │ │ │ ├── AbstractIdentificationParametersCli.java │ │ │ ├── IdentificationParametersCLI.java │ │ │ ├── IdentificationParametersCLIParams.java │ │ │ ├── IdentificationParametersInputBean.java │ │ │ └── package.html │ │ ├── modifications │ │ │ ├── ModificationsCLI.java │ │ │ ├── ModificationsCLIInputBean.java │ │ │ ├── ModificationsCLIParams.java │ │ │ └── package.html │ │ ├── package.html │ │ ├── paths │ │ │ ├── PathSettingsCLI.java │ │ │ ├── PathSettingsCLIInputBean.java │ │ │ ├── PathSettingsCLIParams.java │ │ │ └── package.html │ │ └── peptide_mapper │ │ │ ├── MappingWorker.java │ │ │ ├── PeptideMapperCLI.java │ │ │ └── package.html │ │ ├── scripts_marc │ │ ├── Dummy.java │ │ └── MsFilePerformance.java │ │ ├── software │ │ ├── CompomicsWrapper.java │ │ ├── SplashScreen.java │ │ ├── ToolFactory.java │ │ ├── autoupdater │ │ │ ├── CompareVersionNumbers.java │ │ │ ├── DownloadLatestZipFromRepo.java │ │ │ ├── FileDAO.java │ │ │ ├── GUIFileDAO.java │ │ │ ├── HeadlessFileDAO.java │ │ │ ├── JarFileFilter.java │ │ │ ├── MavenJarFile.java │ │ │ ├── MetaDataXMLParser.java │ │ │ ├── WebDAO.java │ │ │ └── package.html │ │ ├── cli │ │ │ ├── CommandLineUtils.java │ │ │ ├── CommandParameter.java │ │ │ └── package.html │ │ ├── dialogs │ │ │ ├── JavaHomeDialog.form │ │ │ ├── JavaHomeDialog.java │ │ │ ├── JavaHomeOrMemoryDialogParent.java │ │ │ ├── JavaMemoryDialog.form │ │ │ ├── JavaMemoryDialog.java │ │ │ ├── JavaParametersDialog.form │ │ │ ├── JavaParametersDialog.java │ │ │ ├── PeptideShakerSetupDialog.form │ │ │ ├── PeptideShakerSetupDialog.java │ │ │ ├── ProteoWizardSetupDialog.form │ │ │ ├── ProteoWizardSetupDialog.java │ │ │ ├── ReporterSetupDialog.form │ │ │ ├── ReporterSetupDialog.java │ │ │ ├── SearchGuiSetupDialog.form │ │ │ ├── SearchGuiSetupDialog.java │ │ │ └── package.html │ │ ├── log │ │ │ ├── CliLogger.java │ │ │ └── package.html │ │ ├── package.html │ │ └── settings │ │ │ ├── PathKey.java │ │ │ ├── UtilitiesPathParameters.java │ │ │ ├── gui │ │ │ ├── PathParametersDialog.form │ │ │ ├── PathParametersDialog.java │ │ │ └── package.html │ │ │ └── package.html │ │ └── util │ │ ├── AlternateRowColoursJTable.java │ │ ├── ArrayUtil.java │ │ ├── BinaryArrayImpl.java │ │ ├── CompareVersionNumbers.java │ │ ├── Export.java │ │ ├── StreamUtil.java │ │ ├── TempByteArray.java │ │ ├── Util.java │ │ ├── XYZDataPoint.java │ │ ├── db │ │ ├── ColumnTypeConverter.java │ │ ├── DBAccessor.java │ │ ├── DBAccessorGenerator.java │ │ ├── DBMetaData.java │ │ ├── DBResultSet.java │ │ ├── GeneratorException.java │ │ ├── components │ │ │ ├── Constructors.java │ │ │ ├── DeleteableCode.java │ │ │ ├── GettersAndSetters.java │ │ │ ├── InstanceVariables.java │ │ │ ├── PersistableCode.java │ │ │ ├── RetrievableCode.java │ │ │ ├── UpdateableCode.java │ │ │ └── package.html │ │ ├── interfaces │ │ │ ├── DBElement.java │ │ │ ├── Deleteable.java │ │ │ ├── Persistable.java │ │ │ ├── Retrievable.java │ │ │ ├── Updateable.java │ │ │ └── package.html │ │ ├── object │ │ │ ├── DbMutex.java │ │ │ ├── ObjectsCache.java │ │ │ ├── ObjectsDB.java │ │ │ ├── objects │ │ │ │ ├── BlobObject.java │ │ │ │ └── package.html │ │ │ └── package.html │ │ └── package.html │ │ ├── enumeration │ │ ├── CompomicsTools.java │ │ ├── ImageType.java │ │ ├── MolecularElement.java │ │ ├── OperatingSystemEnum.java │ │ └── package.html │ │ ├── examples │ │ ├── BareBonesBrowserLaunch.java │ │ ├── HelpWindow.form │ │ ├── HelpWindow.java │ │ ├── MirroredSpectraTestDialog.form │ │ ├── MirroredSpectraTestDialog.java │ │ ├── UtilitiesDemo.form │ │ ├── UtilitiesDemo.java │ │ └── package.html │ │ ├── exceptions │ │ ├── ExceptionHandler.java │ │ ├── exception_handlers │ │ │ ├── CommandLineExceptionHandler.java │ │ │ ├── FrameExceptionHandler.java │ │ │ ├── WaitingDialogExceptionHandler.java │ │ │ └── package.html │ │ └── package.html │ │ ├── experiment │ │ ├── Constants.java │ │ ├── ProjectParameters.java │ │ ├── biology │ │ │ ├── aminoacids │ │ │ │ ├── AminoAcid.java │ │ │ │ ├── impl │ │ │ │ │ ├── Alanine.java │ │ │ │ │ ├── Arginine.java │ │ │ │ │ ├── Asparagine.java │ │ │ │ │ ├── AsparticAcid.java │ │ │ │ │ ├── B.java │ │ │ │ │ ├── Cysteine.java │ │ │ │ │ ├── GlutamicAcid.java │ │ │ │ │ ├── Glutamine.java │ │ │ │ │ ├── Glycine.java │ │ │ │ │ ├── Histidine.java │ │ │ │ │ ├── Isoleucine.java │ │ │ │ │ ├── J.java │ │ │ │ │ ├── Leucine.java │ │ │ │ │ ├── Lysine.java │ │ │ │ │ ├── Methionine.java │ │ │ │ │ ├── Phenylalanine.java │ │ │ │ │ ├── Proline.java │ │ │ │ │ ├── Pyrrolysine.java │ │ │ │ │ ├── Selenocysteine.java │ │ │ │ │ ├── Serine.java │ │ │ │ │ ├── Threonine.java │ │ │ │ │ ├── Tryptophan.java │ │ │ │ │ ├── Tyrosine.java │ │ │ │ │ ├── Valine.java │ │ │ │ │ ├── X.java │ │ │ │ │ ├── Z.java │ │ │ │ │ └── package.html │ │ │ │ ├── package.html │ │ │ │ └── sequence │ │ │ │ │ ├── AminoAcidPattern.java │ │ │ │ │ ├── AminoAcidSequence.java │ │ │ │ │ └── package.html │ │ │ ├── atoms │ │ │ │ ├── Atom.java │ │ │ │ ├── AtomChain.java │ │ │ │ ├── AtomImpl.java │ │ │ │ ├── ElementaryElement.java │ │ │ │ ├── impl │ │ │ │ │ ├── Calcium.java │ │ │ │ │ ├── Carbon.java │ │ │ │ │ ├── Chlorine.java │ │ │ │ │ ├── Cobalt.java │ │ │ │ │ ├── Copper.java │ │ │ │ │ ├── Fluorine.java │ │ │ │ │ ├── Helium.java │ │ │ │ │ ├── Hydrogen.java │ │ │ │ │ ├── Iodine.java │ │ │ │ │ ├── Iron.java │ │ │ │ │ ├── Lithium.java │ │ │ │ │ ├── Magnesium.java │ │ │ │ │ ├── Manganese.java │ │ │ │ │ ├── Nickel.java │ │ │ │ │ ├── Nitrogen.java │ │ │ │ │ ├── Oxygen.java │ │ │ │ │ ├── Phosphorus.java │ │ │ │ │ ├── Potassium.java │ │ │ │ │ ├── Selenium.java │ │ │ │ │ ├── Sodium.java │ │ │ │ │ ├── Sulfur.java │ │ │ │ │ ├── Zinc.java │ │ │ │ │ └── package.html │ │ │ │ └── package.html │ │ │ ├── enzymes │ │ │ │ ├── Enzyme.java │ │ │ │ ├── EnzymeFactory.java │ │ │ │ └── package.html │ │ │ ├── genes │ │ │ │ ├── GeneMaps.java │ │ │ │ ├── ProteinGeneDetailsProvider.java │ │ │ │ ├── ensembl │ │ │ │ │ ├── EnsemblVersion.java │ │ │ │ │ ├── GeneMapping.java │ │ │ │ │ └── package.html │ │ │ │ ├── go │ │ │ │ │ ├── GoDomains.java │ │ │ │ │ ├── GoMapping.java │ │ │ │ │ └── package.html │ │ │ │ └── package.html │ │ │ ├── ions │ │ │ │ ├── Charge.java │ │ │ │ ├── Ion.java │ │ │ │ ├── IonFactory.java │ │ │ │ ├── NeutralLoss.java │ │ │ │ ├── NeutralLossCombination.java │ │ │ │ ├── impl │ │ │ │ │ ├── ElementaryIon.java │ │ │ │ │ ├── Glycan.java │ │ │ │ │ ├── ImmoniumIon.java │ │ │ │ │ ├── PeptideFragmentIon.java │ │ │ │ │ ├── PrecursorIon.java │ │ │ │ │ ├── RelatedIon.java │ │ │ │ │ ├── ReporterIon.java │ │ │ │ │ ├── TagFragmentIon.java │ │ │ │ │ └── package.html │ │ │ │ └── package.html │ │ │ ├── modifications │ │ │ │ ├── Modification.java │ │ │ │ ├── ModificationCategory.java │ │ │ │ ├── ModificationFactory.java │ │ │ │ ├── ModificationProvider.java │ │ │ │ └── ModificationType.java │ │ │ ├── package.html │ │ │ ├── proteins │ │ │ │ ├── Peptide.java │ │ │ │ ├── Protein.java │ │ │ │ └── package.html │ │ │ ├── taxonomy │ │ │ │ ├── SpeciesFactory.java │ │ │ │ ├── mappings │ │ │ │ │ ├── BiomartMapping.java │ │ │ │ │ ├── EnsemblSpecies.java │ │ │ │ │ ├── UniprotTaxonomy.java │ │ │ │ │ └── package.html │ │ │ │ └── package.html │ │ │ └── variants │ │ │ │ ├── AaSubstitutionMatrix.java │ │ │ │ ├── AminoAcidSubstitution.java │ │ │ │ ├── Variant.java │ │ │ │ ├── amino_acids │ │ │ │ ├── Deletion.java │ │ │ │ ├── Insertion.java │ │ │ │ ├── Substitution.java │ │ │ │ ├── Swap.java │ │ │ │ └── package.html │ │ │ │ └── package.html │ │ ├── filtering │ │ │ ├── Filter.java │ │ │ ├── FilterItem.java │ │ │ ├── FilterItemComparator.java │ │ │ └── package.html │ │ ├── identification │ │ │ ├── Advocate.java │ │ │ ├── Identification.java │ │ │ ├── IdentificationKeys.java │ │ │ ├── IdentificationMatch.java │ │ │ ├── IdentificationMethod.java │ │ │ ├── SpectrumIdentificationAssumption.java │ │ │ ├── TagFactory.java │ │ │ ├── amino_acid_tags │ │ │ │ ├── MassGap.java │ │ │ │ ├── Tag.java │ │ │ │ ├── TagComponent.java │ │ │ │ └── package.html │ │ │ ├── features │ │ │ │ ├── IdentificationFeaturesCache.java │ │ │ │ ├── IdentificationFeaturesGenerator.java │ │ │ │ ├── MutexMap.java │ │ │ │ └── package.html │ │ │ ├── filtering │ │ │ │ ├── AssumptionFilter.java │ │ │ │ ├── MatchFilter.java │ │ │ │ ├── PeptideAssumptionFilter.java │ │ │ │ ├── PeptideFilter.java │ │ │ │ ├── ProteinFilter.java │ │ │ │ ├── PsmFilter.java │ │ │ │ ├── items │ │ │ │ │ ├── AssumptionFilterItem.java │ │ │ │ │ ├── PeptideFilterItem.java │ │ │ │ │ ├── ProteinFilterItem.java │ │ │ │ │ ├── PsmFilterItem.java │ │ │ │ │ └── package.html │ │ │ │ └── package.html │ │ │ ├── identification_parameters │ │ │ │ ├── IdentificationParametersFactory.java │ │ │ │ └── package.html │ │ │ ├── matches │ │ │ │ ├── IonMatch.java │ │ │ │ ├── ModificationMatch.java │ │ │ │ ├── PeptideMatch.java │ │ │ │ ├── PeptideVariantMatches.java │ │ │ │ ├── ProteinMatch.java │ │ │ │ ├── SpectrumMatch.java │ │ │ │ └── package.html │ │ │ ├── matches_iterators │ │ │ │ ├── MatchesIterator.java │ │ │ │ ├── PeptideMatchesIterator.java │ │ │ │ ├── ProteinMatchesIterator.java │ │ │ │ ├── SpectrumMatchesIterator.java │ │ │ │ └── package.html │ │ │ ├── modification │ │ │ │ ├── ModificationLocalizationScore.java │ │ │ │ ├── ModificationSiteMapping.java │ │ │ │ ├── ModificationtableContent.java │ │ │ │ ├── mapping │ │ │ │ │ ├── ModificationLocalizationMapper.java │ │ │ │ │ ├── ModificationMassMapper.java │ │ │ │ │ ├── ModificationNameMapper.java │ │ │ │ │ └── package.html │ │ │ │ ├── package.html │ │ │ │ ├── peptide_mapping │ │ │ │ │ ├── ModificationPeptideMapping.java │ │ │ │ │ ├── package.html │ │ │ │ │ └── performance │ │ │ │ │ │ ├── HistoneExample.java │ │ │ │ │ │ ├── PerformanceBenchmark.java │ │ │ │ │ │ ├── PerformanceBenchmarkRunnable.java │ │ │ │ │ │ └── package.html │ │ │ │ ├── scores │ │ │ │ │ ├── MDScore.java │ │ │ │ │ ├── PhosphoRS.java │ │ │ │ │ └── package.html │ │ │ │ └── search_engine_mapping │ │ │ │ │ ├── ModificationLocalizationMapper.java │ │ │ │ │ ├── ModificationMassMapper.java │ │ │ │ │ ├── ModificationNameMapper.java │ │ │ │ │ └── package.html │ │ │ ├── package.html │ │ │ ├── peptide_fragmentation │ │ │ │ ├── FragmentItensityPredictor.java │ │ │ │ ├── PeptideFragmentationModel.java │ │ │ │ ├── models │ │ │ │ │ ├── SequestFragmentationModel.java │ │ │ │ │ ├── UniformFragmentation.java │ │ │ │ │ ├── ms2pip │ │ │ │ │ │ ├── features_configuration │ │ │ │ │ │ │ ├── FeaturesMap.java │ │ │ │ │ │ │ ├── FeaturesMapManager.java │ │ │ │ │ │ │ ├── Ms2pipFeature.java │ │ │ │ │ │ │ ├── MultipleAAPropertyFeature.java │ │ │ │ │ │ │ ├── SingleAAPropertyFeature.java │ │ │ │ │ │ │ ├── features │ │ │ │ │ │ │ │ ├── AAIdentityFeatureAbsolute.java │ │ │ │ │ │ │ │ ├── AAIdentityFeatureRelative.java │ │ │ │ │ │ │ │ ├── AAPropertyFeatureAbsolute.java │ │ │ │ │ │ │ │ ├── AAPropertyFeatureRelative.java │ │ │ │ │ │ │ │ ├── AAPropertyRelationshipFeature.java │ │ │ │ │ │ │ │ ├── ComplementaryIonAminoAcidFeature.java │ │ │ │ │ │ │ │ ├── ComplementaryIonFeature.java │ │ │ │ │ │ │ │ ├── ForwardIonAminoAcidFeature.java │ │ │ │ │ │ │ │ ├── ForwardIonFeature.java │ │ │ │ │ │ │ │ ├── ModificationFeature.java │ │ │ │ │ │ │ │ ├── PeptideAminoAcidFeature.java │ │ │ │ │ │ │ │ ├── PeptideFeature.java │ │ │ │ │ │ │ │ ├── generic │ │ │ │ │ │ │ │ │ ├── AAIdentityFeature.java │ │ │ │ │ │ │ │ │ ├── AAPropertyFeature.java │ │ │ │ │ │ │ │ │ ├── AASequenceFeature.java │ │ │ │ │ │ │ │ │ ├── IonFeature.java │ │ │ │ │ │ │ │ │ └── package.html │ │ │ │ │ │ │ │ └── package.html │ │ │ │ │ │ │ └── package.html │ │ │ │ │ │ ├── features_generation │ │ │ │ │ │ │ ├── FeaturesGenerator.java │ │ │ │ │ │ │ └── package.html │ │ │ │ │ │ └── package.html │ │ │ │ │ └── package.html │ │ │ │ └── package.html │ │ │ ├── peptide_inference │ │ │ │ ├── PeptideInference.java │ │ │ │ └── package.html │ │ │ ├── peptide_shaker │ │ │ │ ├── Metrics.java │ │ │ │ ├── ModificationScoring.java │ │ │ │ ├── PSModificationScores.java │ │ │ │ ├── PSParameter.java │ │ │ │ └── package.html │ │ │ ├── protein_inference │ │ │ │ ├── FastaMapper.java │ │ │ │ ├── PeptideAndProteinBuilder.java │ │ │ │ ├── PeptideProteinMapping.java │ │ │ │ ├── fm_index │ │ │ │ │ ├── AccessionMetaData.java │ │ │ │ │ ├── CacheElement.java │ │ │ │ │ ├── FMIndex.java │ │ │ │ │ ├── MassIndexMap.java │ │ │ │ │ ├── MatrixContent.java │ │ │ │ │ ├── Rank.java │ │ │ │ │ ├── SNPElement.java │ │ │ │ │ ├── TagElement.java │ │ │ │ │ ├── WaveletTree.java │ │ │ │ │ └── package.html │ │ │ │ └── package.html │ │ │ ├── protein_sequences │ │ │ │ ├── AaOccurrence.java │ │ │ │ ├── AmbiguousSequenceIterator.java │ │ │ │ ├── SingleProteinSequenceProvider.java │ │ │ │ ├── digestion │ │ │ │ │ ├── ExtendedPeptide.java │ │ │ │ │ ├── IteratorFactory.java │ │ │ │ │ ├── PeptideDraft.java │ │ │ │ │ ├── ProteinIteratorUtils.java │ │ │ │ │ ├── SequenceIterator.java │ │ │ │ │ ├── iterators │ │ │ │ │ │ ├── NoDigestionCombinationIterator.java │ │ │ │ │ │ ├── NoDigestionIterator.java │ │ │ │ │ │ ├── SpecificSingleEnzymeCombinationIterator.java │ │ │ │ │ │ ├── SpecificSingleEnzymeIterator.java │ │ │ │ │ │ ├── UnspecificCombinationIterator.java │ │ │ │ │ │ ├── UnspecificIterator.java │ │ │ │ │ │ └── package.html │ │ │ │ │ └── package.html │ │ │ │ └── package.html │ │ │ ├── psm_scoring │ │ │ │ ├── PsmScore.java │ │ │ │ ├── PsmScoresEstimator.java │ │ │ │ ├── package.html │ │ │ │ └── psm_scores │ │ │ │ │ ├── HyperScore.java │ │ │ │ │ ├── PrecursorAccuracy.java │ │ │ │ │ ├── SnrScore.java │ │ │ │ │ └── package.html │ │ │ ├── spectrum_annotation │ │ │ │ ├── AnnotationParameters.java │ │ │ │ ├── IonMatchKeysCache.java │ │ │ │ ├── NeutralLossesMap.java │ │ │ │ ├── SpecificAnnotationParameters.java │ │ │ │ ├── SpectrumAnnotator.java │ │ │ │ ├── package.html │ │ │ │ ├── simple_annotators │ │ │ │ │ ├── FragmentAnnotator.java │ │ │ │ │ ├── FragmentAnnotatorNL.java │ │ │ │ │ ├── ImmoniumIonAnnotator.java │ │ │ │ │ ├── PrecursorAnnotator.java │ │ │ │ │ ├── ReporterIonAnnotator.java │ │ │ │ │ └── package.html │ │ │ │ └── spectrum_annotators │ │ │ │ │ ├── PeptideSpectrumAnnotator.java │ │ │ │ │ ├── SimplePeptideAnnotator.java │ │ │ │ │ ├── TagSpectrumAnnotator.java │ │ │ │ │ └── package.html │ │ │ ├── spectrum_assumptions │ │ │ │ ├── PeptideAssumption.java │ │ │ │ ├── PeptideAssumptionParameter.java │ │ │ │ ├── TagAssumption.java │ │ │ │ └── package.html │ │ │ ├── utils │ │ │ │ ├── ModificationUtils.java │ │ │ │ ├── PeptideUtils.java │ │ │ │ ├── ProteinUtils.java │ │ │ │ ├── TagUtils.java │ │ │ │ └── package.html │ │ │ └── validation │ │ │ │ ├── MatchValidationLevel.java │ │ │ │ ├── package.html │ │ │ │ └── percolator │ │ │ │ ├── PercolatorFeature.java │ │ │ │ └── PercolatorFeaturesCache.java │ │ ├── io │ │ │ ├── biology │ │ │ │ ├── package.html │ │ │ │ └── protein │ │ │ │ │ ├── FastaParameters.java │ │ │ │ │ ├── FastaSummary.java │ │ │ │ │ ├── Header.java │ │ │ │ │ ├── ProteinDatabase.java │ │ │ │ │ ├── ProteinDetailsProvider.java │ │ │ │ │ ├── ProteinIterator.java │ │ │ │ │ ├── SequenceProvider.java │ │ │ │ │ ├── converters │ │ │ │ │ ├── DecoyConverter.java │ │ │ │ │ ├── GenericFastaConverter.java │ │ │ │ │ └── package.html │ │ │ │ │ ├── iterators │ │ │ │ │ ├── FastaIterator.java │ │ │ │ │ ├── HeaderIterator.java │ │ │ │ │ └── package.html │ │ │ │ │ └── package.html │ │ │ ├── identification │ │ │ │ ├── IdfileReader.java │ │ │ │ ├── IdfileReaderFactory.java │ │ │ │ ├── MzIdentMLIdfileSearchParametersConverter.java │ │ │ │ ├── MzIdentMLVersion.java │ │ │ │ ├── idfilereaders │ │ │ │ │ ├── AndromedaIdfileReader.java │ │ │ │ │ ├── CossIdfileReader.java │ │ │ │ │ ├── DirecTagIdfileReader.java │ │ │ │ │ ├── MascotIdfileReader.java │ │ │ │ │ ├── MsAmandaIdfileReader.java │ │ │ │ │ ├── MzIdentMLIdfileReader.java │ │ │ │ │ ├── NovorIdfileReader.java │ │ │ │ │ ├── OnyaseIdfileReader.java │ │ │ │ │ ├── PNovoIdfileReader.java │ │ │ │ │ ├── PepNovoIdfileReader.java │ │ │ │ │ ├── PepxmlIdfileReader.java │ │ │ │ │ ├── SageIdfileReader.java │ │ │ │ │ ├── TideIdfileReader.java │ │ │ │ │ ├── XTandemIdfileReader.java │ │ │ │ │ └── package.html │ │ │ │ ├── package.html │ │ │ │ └── writers │ │ │ │ │ ├── SimpleMzIdentMLExporter.java │ │ │ │ │ └── package.html │ │ │ ├── mass_spectrometry │ │ │ │ ├── MsFileExporter.java │ │ │ │ ├── MsFileHandler.java │ │ │ │ ├── MsFileIterator.java │ │ │ │ ├── apl │ │ │ │ │ ├── AplFileWriter.java │ │ │ │ │ └── package.html │ │ │ │ ├── cms │ │ │ │ │ ├── CmsFileIterator.java │ │ │ │ │ ├── CmsFileReader.java │ │ │ │ │ ├── CmsFileUtils.java │ │ │ │ │ ├── CmsFileWriter.java │ │ │ │ │ ├── CmsFolder.java │ │ │ │ │ └── package.html │ │ │ │ ├── mgf │ │ │ │ │ ├── IndexedMgfReader.java │ │ │ │ │ ├── MgfFileIterator.java │ │ │ │ │ ├── MgfFileUtils.java │ │ │ │ │ ├── MgfFileWriter.java │ │ │ │ │ ├── MgfIndex.java │ │ │ │ │ └── package.html │ │ │ │ ├── ms2 │ │ │ │ │ ├── Ms2Exporter.java │ │ │ │ │ ├── Ms2FileWriter.java │ │ │ │ │ └── package.html │ │ │ │ ├── mzml │ │ │ │ │ ├── IntDecoder.java │ │ │ │ │ ├── MSNumpress.java │ │ │ │ │ ├── MzmlFileIterator.java │ │ │ │ │ ├── MzmlFileUtils.java │ │ │ │ │ └── package.html │ │ │ │ └── package.html │ │ │ ├── package.html │ │ │ ├── parameters │ │ │ │ ├── DummyParameters.java │ │ │ │ ├── MarshallableParameter.java │ │ │ │ ├── SdrfExport.java │ │ │ │ └── package.html │ │ │ └── temp │ │ │ │ ├── TempFilesManager.java │ │ │ │ └── package.html │ │ ├── mass_spectrometry │ │ │ ├── FragmentationMethod.java │ │ │ ├── SimpleNoiseDistribution.java │ │ │ ├── SpectrumProvider.java │ │ │ ├── indexes │ │ │ │ ├── PrecursorMap.java │ │ │ │ ├── SpectrumIndex.java │ │ │ │ └── package.html │ │ │ ├── package.html │ │ │ ├── proteowizard │ │ │ │ ├── MsConvertParameters.java │ │ │ │ ├── ProteoWizardFilter.java │ │ │ │ ├── ProteoWizardMsFormat.java │ │ │ │ └── package.html │ │ │ ├── spectra │ │ │ │ ├── Peak.java │ │ │ │ ├── Precursor.java │ │ │ │ ├── PrecursorParameter.java │ │ │ │ ├── RecalibrationUtils.java │ │ │ │ ├── Spectrum.java │ │ │ │ ├── SpectrumUtil.java │ │ │ │ └── package.html │ │ │ ├── thermo_raw_file_parser │ │ │ │ ├── ThermoRawFileParserOutputFormat.java │ │ │ │ ├── ThermoRawFileParserParameters.java │ │ │ │ ├── gui │ │ │ │ │ ├── ThermoRawFileParserParametersDialog.form │ │ │ │ │ ├── ThermoRawFileParserParametersDialog.java │ │ │ │ │ └── package.html │ │ │ │ └── package.html │ │ │ └── utils │ │ │ │ ├── StandardMasses.java │ │ │ │ └── package.html │ │ ├── normalization │ │ │ ├── NormalizationFactors.java │ │ │ └── package.html │ │ ├── package.html │ │ ├── patient │ │ │ ├── Patient.java │ │ │ ├── PatientInformation.java │ │ │ └── package.html │ │ ├── personalization │ │ │ ├── ExperimentObject.java │ │ │ ├── UrParameter.java │ │ │ └── package.html │ │ ├── quantification │ │ │ ├── Quantification.java │ │ │ ├── package.html │ │ │ ├── reporterion │ │ │ │ ├── Reagent.java │ │ │ │ ├── ReporterIonQuantification.java │ │ │ │ ├── ReporterMethod.java │ │ │ │ ├── ReporterMethodFactory.java │ │ │ │ └── package.html │ │ │ └── spectrumcounting │ │ │ │ ├── ScalingFactorsEstimators.java │ │ │ │ ├── SpectrumCountingMethod.java │ │ │ │ └── package.html │ │ ├── refinement_parameters │ │ │ ├── PepnovoAssumptionDetails.java │ │ │ └── package.html │ │ └── units │ │ │ ├── MetricsPrefix.java │ │ │ ├── StandardUnit.java │ │ │ ├── UnitOfMeasurement.java │ │ │ ├── Units.java │ │ │ └── package.html │ │ ├── general │ │ ├── BoxedObject.java │ │ ├── CommandLineParser.java │ │ ├── DefaultOutputLoggerImplementation.java │ │ ├── FileLoggerImplementation.java │ │ ├── IsotopicDistribution.java │ │ ├── IsotopicDistributionSpectrum.java │ │ ├── IsotopicElement.java │ │ ├── MassCalc.java │ │ ├── Translate.java │ │ ├── UnknownElementMassException.java │ │ ├── package.html │ │ └── servlet │ │ │ ├── MassCalcServlet.java │ │ │ └── package.html │ │ ├── gui │ │ ├── AaMass.form │ │ ├── AaMass.java │ │ ├── AminoAcidPatternDialog.form │ │ ├── AminoAcidPatternDialog.java │ │ ├── CheckBoxCellRenderer.java │ │ ├── CheckableItem.java │ │ ├── CheckedComboBox.java │ │ ├── DummyFrame.java │ │ ├── ExportFormatSelectionDialog.form │ │ ├── ExportFormatSelectionDialog.java │ │ ├── FlamableJFrame.java │ │ ├── GuiUtilities.java │ │ ├── JExceptionDialog.java │ │ ├── JFrameForBytes.java │ │ ├── JLabelAndComponentPanel.java │ │ ├── JOptionEditorPane.java │ │ ├── JTableForDB.java │ │ ├── MonitorDimension.java │ │ ├── PrivacyParametersDialog.form │ │ ├── PrivacyParametersDialog.java │ │ ├── SampleSelection.form │ │ ├── SampleSelection.java │ │ ├── TableMouseWheelListener.java │ │ ├── TableProperties.java │ │ ├── TableScrollBarListener.java │ │ ├── UtilitiesGUIDefaults.java │ │ ├── VennDiagramDialog.form │ │ ├── VennDiagramDialog.java │ │ ├── VennDiagramLegendLocationDialog.form │ │ ├── VennDiagramLegendLocationDialog.java │ │ ├── VennDiagramPanel.form │ │ ├── VennDiagramPanel.java │ │ ├── VisibleTableColumnsDialog.form │ │ ├── VisibleTableColumnsDialog.java │ │ ├── VisibleTableColumnsDialogParent.java │ │ ├── XYPlotFiltersDialog.form │ │ ├── XYPlotFiltersDialog.java │ │ ├── XYPlottingDialog.form │ │ ├── XYPlottingDialog.java │ │ ├── atoms │ │ │ ├── AtomChainDialog.form │ │ │ ├── AtomChainDialog.java │ │ │ ├── AtomPanel.form │ │ │ ├── AtomPanel.java │ │ │ └── package.html │ │ ├── enzymes │ │ │ ├── EnzymesDialog.form │ │ │ ├── EnzymesDialog.java │ │ │ ├── NewEnzymeDialog.form │ │ │ ├── NewEnzymeDialog.java │ │ │ └── package.html │ │ ├── error_handlers │ │ │ ├── BugReport.form │ │ │ ├── BugReport.java │ │ │ ├── HelpDialog.form │ │ │ ├── HelpDialog.java │ │ │ ├── notification │ │ │ │ ├── NotesDialog.form │ │ │ │ ├── NotesDialog.java │ │ │ │ ├── NotificationDialog.form │ │ │ │ ├── NotificationDialog.java │ │ │ │ ├── NotificationDialogParent.java │ │ │ │ └── package.html │ │ │ └── package.html │ │ ├── events │ │ │ ├── RescalingEvent.java │ │ │ └── package.html │ │ ├── export │ │ │ ├── graphics │ │ │ │ ├── ExportGraphicsDialog.form │ │ │ │ ├── ExportGraphicsDialog.java │ │ │ │ └── package.html │ │ │ └── report │ │ │ │ ├── ReportEditor.form │ │ │ │ ├── ReportEditor.java │ │ │ │ └── package.html │ │ ├── file_handling │ │ │ ├── FileAndFileFilter.java │ │ │ ├── FileChooserUtil.java │ │ │ ├── FileDisplayDialog.form │ │ │ ├── FileDisplayDialog.java │ │ │ ├── FileSelectionDialog.form │ │ │ ├── FileSelectionDialog.java │ │ │ └── package.html │ │ ├── filtering │ │ │ ├── FilterDialog.form │ │ │ ├── FilterDialog.java │ │ │ ├── FilterParameters.java │ │ │ └── package.html │ │ ├── genes │ │ │ ├── GeneDetailsDialog.form │ │ │ ├── GeneDetailsDialog.java │ │ │ └── package.html │ │ ├── interfaces │ │ │ ├── SpectrumAnnotation.java │ │ │ ├── SpectrumPanelListener.java │ │ │ └── package.html │ │ ├── isotopic_calculator │ │ │ ├── IsotopeDistributionGui.form │ │ │ ├── IsotopeDistributionGui.java │ │ │ └── package.html │ │ ├── modification │ │ │ ├── ModificationDialog.form │ │ │ ├── ModificationDialog.java │ │ │ ├── ModificationTable.java │ │ │ ├── ModificationsDialog.form │ │ │ ├── ModificationsDialog.java │ │ │ └── package.html │ │ ├── package.html │ │ ├── parameters │ │ │ ├── SparklineColorsDialog.form │ │ │ ├── SparklineColorsDialog.java │ │ │ ├── identification │ │ │ │ ├── AlgorithmParametersDialog.java │ │ │ │ ├── IdentificationAlgorithmParameter.java │ │ │ │ ├── IdentificationParametersEditionDialog.form │ │ │ │ ├── IdentificationParametersEditionDialog.java │ │ │ │ ├── IdentificationParametersNameDialog.form │ │ │ │ ├── IdentificationParametersNameDialog.java │ │ │ │ ├── IdentificationParametersOverviewDialog.form │ │ │ │ ├── IdentificationParametersOverviewDialog.java │ │ │ │ ├── advanced │ │ │ │ │ ├── AnnotationParametersDialog.form │ │ │ │ │ ├── AnnotationParametersDialog.java │ │ │ │ │ ├── BackgroundSpeciesDialog.form │ │ │ │ │ ├── BackgroundSpeciesDialog.java │ │ │ │ │ ├── FractionParametersDialog.form │ │ │ │ │ ├── FractionParametersDialog.java │ │ │ │ │ ├── GeneParametersDialog.form │ │ │ │ │ ├── GeneParametersDialog.java │ │ │ │ │ ├── MatchesImportParametersDialog.form │ │ │ │ │ ├── MatchesImportParametersDialog.java │ │ │ │ │ ├── ModificationLocalizationParametersDialog.form │ │ │ │ │ ├── ModificationLocalizationParametersDialog.java │ │ │ │ │ ├── PeptideVariantsParametersDialog.form │ │ │ │ │ ├── PeptideVariantsParametersDialog.java │ │ │ │ │ ├── ProteinInferenceParametersDialog.form │ │ │ │ │ ├── ProteinInferenceParametersDialog.java │ │ │ │ │ ├── PsmScoringParametersDialog.form │ │ │ │ │ ├── PsmScoringParametersDialog.java │ │ │ │ │ ├── SequenceMatchingParametersDialog.form │ │ │ │ │ ├── SequenceMatchingParametersDialog.java │ │ │ │ │ ├── ValidationParametersDialog.form │ │ │ │ │ ├── ValidationParametersDialog.java │ │ │ │ │ ├── ValidationQCParametersDialog.form │ │ │ │ │ ├── ValidationQCParametersDialog.java │ │ │ │ │ └── package.html │ │ │ │ ├── algorithm │ │ │ │ │ ├── AndromedaParametersDialog.form │ │ │ │ │ ├── AndromedaParametersDialog.java │ │ │ │ │ ├── CometParametersDialog.form │ │ │ │ │ ├── CometParametersDialog.java │ │ │ │ │ ├── DirecTagParametersDialog.form │ │ │ │ │ ├── DirecTagParametersDialog.java │ │ │ │ │ ├── MetaMorpheusParametersDialog.form │ │ │ │ │ ├── MetaMorpheusParametersDialog.java │ │ │ │ │ ├── MsAmandaParametersDialog.form │ │ │ │ │ ├── MsAmandaParametersDialog.java │ │ │ │ │ ├── MsgfParametersDialog.form │ │ │ │ │ ├── MsgfParametersDialog.java │ │ │ │ │ ├── MyriMatchParametersDialog.form │ │ │ │ │ ├── MyriMatchParametersDialog.java │ │ │ │ │ ├── NovorParametersDialog.form │ │ │ │ │ ├── NovorParametersDialog.java │ │ │ │ │ ├── OmssaParametersDialog.form │ │ │ │ │ ├── OmssaParametersDialog.java │ │ │ │ │ ├── PNovoParametersDialog.form │ │ │ │ │ ├── PNovoParametersDialog.java │ │ │ │ │ ├── PepNovoParametersDialog.form │ │ │ │ │ ├── PepNovoParametersDialog.java │ │ │ │ │ ├── SageParametersDialog.form │ │ │ │ │ ├── SageParametersDialog.java │ │ │ │ │ ├── TideParametersDialog.form │ │ │ │ │ ├── TideParametersDialog.java │ │ │ │ │ ├── XTandemParametersDialog.form │ │ │ │ │ ├── XTandemParametersDialog.java │ │ │ │ │ └── package.html │ │ │ │ ├── package.html │ │ │ │ ├── pride │ │ │ │ │ ├── EnzymeParametersDialog.form │ │ │ │ │ ├── EnzymeParametersDialog.java │ │ │ │ │ └── package.html │ │ │ │ └── search │ │ │ │ │ ├── SearchParametersDialog.form │ │ │ │ │ ├── SearchParametersDialog.java │ │ │ │ │ ├── SequenceDbDetailsDialog.form │ │ │ │ │ ├── SequenceDbDetailsDialog.java │ │ │ │ │ └── package.html │ │ │ ├── package.html │ │ │ ├── proteowizard │ │ │ │ ├── MsConvertParametersDialog.form │ │ │ │ ├── MsConvertParametersDialog.java │ │ │ │ └── package.html │ │ │ └── tools │ │ │ │ ├── ProcessingParametersDialog.form │ │ │ │ ├── ProcessingParametersDialog.java │ │ │ │ └── package.html │ │ ├── protein │ │ │ ├── FastaParametersDialog.form │ │ │ ├── FastaParametersDialog.java │ │ │ ├── ModificationProfile.java │ │ │ ├── ProteinSequencePane.java │ │ │ ├── SequenceModificationPanel.java │ │ │ └── package.html │ │ ├── renderers │ │ │ ├── AlignedListCellRenderer.java │ │ │ ├── AlignedTableCellRenderer.java │ │ │ ├── ByteArrayRenderer.java │ │ │ ├── FragmentIonTableCellRenderer.java │ │ │ ├── GraphicsPanelTableCellRenderer.java │ │ │ ├── TimestampRenderer.java │ │ │ ├── ToolTipComboBoxRenderer.java │ │ │ └── package.html │ │ ├── spectrum │ │ │ ├── ChromatogramPanel.java │ │ │ ├── DefaultSpectrumAnnotation.java │ │ │ ├── FragmentIonTable.java │ │ │ ├── GraphicsPanel.java │ │ │ ├── IntensityHistogram.java │ │ │ ├── IonLabelColorTableModel.java │ │ │ ├── IsotopicDistributionPanel.java │ │ │ ├── MassErrorBubblePlot.java │ │ │ ├── MassErrorPlot.java │ │ │ ├── ReferenceArea.java │ │ │ ├── SequenceFragmentationPanel.java │ │ │ ├── SpectrumPanel.java │ │ │ └── package.html │ │ ├── tablemodels │ │ │ ├── SelfUpdatingTableModel.java │ │ │ └── package.html │ │ ├── utils │ │ │ ├── ConnectionDialog.java │ │ │ ├── DateChooser.java │ │ │ ├── EmptyCollections.java │ │ │ ├── SwingUtils.java │ │ │ ├── package.html │ │ │ └── user_choice │ │ │ │ ├── ListChooser.form │ │ │ │ ├── ListChooser.java │ │ │ │ ├── list_choosers │ │ │ │ ├── ModificationChooser.java │ │ │ │ ├── StringListChooser.java │ │ │ │ └── package.html │ │ │ │ └── package.html │ │ ├── variants │ │ │ ├── aa_substitutions │ │ │ │ ├── AaSubstitutionMatrixTableModel.java │ │ │ │ └── package.html │ │ │ └── package.html │ │ └── waiting │ │ │ └── waitinghandlers │ │ │ ├── ProgressDialog.java │ │ │ ├── ProgressDialogX.form │ │ │ ├── ProgressDialogX.java │ │ │ ├── WaitingDialog.form │ │ │ ├── WaitingDialog.java │ │ │ ├── WaitingHandlerCLIImpl.java │ │ │ ├── WaitingHandlerDummy.java │ │ │ └── package.html │ │ ├── interfaces │ │ ├── Connectable.java │ │ ├── Flamable.java │ │ ├── Logger.java │ │ ├── Modification.java │ │ ├── Monitorable.java │ │ ├── PickUp.java │ │ ├── Sequence.java │ │ ├── SpectrumFile.java │ │ ├── TableValueWrapper.java │ │ └── package.html │ │ ├── io │ │ ├── IoUtil.java │ │ ├── MascotEnzymeReader.java │ │ ├── PklFile.java │ │ ├── PropertiesManager.java │ │ ├── PushBackStringReader.java │ │ ├── StartBrowser.java │ │ ├── StreamGobbler.java │ │ ├── compression │ │ │ ├── GzUtils.java │ │ │ ├── SectionGzWriter │ │ │ │ ├── WriterBySection.java │ │ │ │ └── package.html │ │ │ ├── TarUtils.java │ │ │ ├── ZipUtils.java │ │ │ ├── ZstdUtils.java │ │ │ └── package.html │ │ ├── export │ │ │ ├── ExportFactory.java │ │ │ ├── ExportFeature.java │ │ │ ├── ExportFormat.java │ │ │ ├── ExportScheme.java │ │ │ ├── ExportWriter.java │ │ │ ├── WorkbookStyle.java │ │ │ ├── features │ │ │ │ ├── ReporterExportFeature.java │ │ │ │ ├── package.html │ │ │ │ ├── peptideshaker │ │ │ │ │ ├── PsAnnotationFeature.java │ │ │ │ │ ├── PsFragmentFeature.java │ │ │ │ │ ├── PsIdentificationAlgorithmMatchesFeature.java │ │ │ │ │ ├── PsInputFilterFeature.java │ │ │ │ │ ├── PsPeptideFeature.java │ │ │ │ │ ├── PsProjectFeature.java │ │ │ │ │ ├── PsProteinFeature.java │ │ │ │ │ ├── PsPsmFeature.java │ │ │ │ │ ├── PsPtmScoringFeature.java │ │ │ │ │ ├── PsSearchFeature.java │ │ │ │ │ ├── PsSpectrumCountingFeature.java │ │ │ │ │ ├── PsValidationFeature.java │ │ │ │ │ └── package.html │ │ │ │ └── reporter │ │ │ │ │ ├── ReporterPeptideFeature.java │ │ │ │ │ ├── ReporterProteinFeatures.java │ │ │ │ │ ├── ReporterPsmFeatures.java │ │ │ │ │ └── package.html │ │ │ ├── package.html │ │ │ ├── styles │ │ │ │ ├── DefaultStyle.java │ │ │ │ └── package.html │ │ │ ├── writers │ │ │ │ ├── ExcelWriter.java │ │ │ │ ├── TextWriter.java │ │ │ │ └── package.html │ │ │ └── xml │ │ │ │ ├── SimpleXmlWriter.java │ │ │ │ └── package.html │ │ ├── file │ │ │ ├── FileSystemAccessor.java │ │ │ ├── FilenameExtensionFilter.java │ │ │ ├── FolderMonitor.java │ │ │ ├── LastSelectedFolder.java │ │ │ ├── MonitorableFileInputStream.java │ │ │ ├── MonitorableInputStream.java │ │ │ ├── SerializationUtils.java │ │ │ ├── filefilters │ │ │ │ ├── DatFileFilter.java │ │ │ │ ├── DtaFileFilter.java │ │ │ │ ├── FastaFileFilter.java │ │ │ │ ├── FileFilterUtils.java │ │ │ │ ├── JpegFileFilter.java │ │ │ │ ├── MgfFileFilter.java │ │ │ │ ├── Ms2FileFilter.java │ │ │ │ ├── MzDataFileFilter.java │ │ │ │ ├── MzMlFileFilter.java │ │ │ │ ├── MzXmlFileFilter.java │ │ │ │ ├── OmxFileFilter.java │ │ │ │ ├── OutFileFilter.java │ │ │ │ ├── PdfFileFilter.java │ │ │ │ ├── PeffFileFilter.java │ │ │ │ ├── PepXmlFileFilter.java │ │ │ │ ├── PklFileFilter.java │ │ │ │ ├── PklSpoFileFilter.java │ │ │ │ ├── PkxFileFilter.java │ │ │ │ ├── PngFileFilter.java │ │ │ │ ├── ProtXmlFileFilter.java │ │ │ │ ├── SequestParamsFileFilter.java │ │ │ │ ├── SvgFileFilter.java │ │ │ │ ├── TiffFileFilter.java │ │ │ │ ├── XmlFileFilter.java │ │ │ │ └── package.html │ │ │ └── package.html │ │ ├── flat │ │ │ ├── SimpleFileReader.java │ │ │ ├── SimpleFileWriter.java │ │ │ ├── package.html │ │ │ └── readers │ │ │ │ ├── SimpleGzReader.java │ │ │ │ └── SimpleTextReader.java │ │ ├── ftp │ │ │ ├── FTP.java │ │ │ ├── FTPClient.java │ │ │ ├── FTPDownloader.java │ │ │ ├── FtpConnectionException.java │ │ │ ├── FtpLoginException.java │ │ │ ├── FtpProtocolException.java │ │ │ └── package.html │ │ ├── json │ │ │ ├── JsonMarshaller.java │ │ │ ├── adapter │ │ │ │ ├── ColorAdapter.java │ │ │ │ ├── FileAdapter.java │ │ │ │ ├── InterfaceAdapter.java │ │ │ │ └── package.html │ │ │ ├── marshallers │ │ │ │ ├── IdentificationParametersMarshaller.java │ │ │ │ ├── PTMFactoryMarshaller.java │ │ │ │ ├── PrideMarshaller.java │ │ │ │ └── package.html │ │ │ └── package.html │ │ └── package.html │ │ ├── junit │ │ ├── TestCaseLM.java │ │ └── package.html │ │ ├── math │ │ ├── BasicMathFunctions.java │ │ ├── BigFunctions.java │ │ ├── BigMathUtils.java │ │ ├── HistogramUtils.java │ │ ├── VennDiagram.java │ │ ├── clustering │ │ │ ├── KMeansClustering.java │ │ │ ├── package.html │ │ │ └── settings │ │ │ │ ├── KMeansClusteringSettings.java │ │ │ │ └── package.html │ │ ├── matrix │ │ │ ├── DoubleMatrix.java │ │ │ └── package.html │ │ ├── package.html │ │ ├── roc │ │ │ ├── DataRoc.java │ │ │ ├── DistributionRoc.java │ │ │ └── package.html │ │ └── statistics │ │ │ ├── Distribution.java │ │ │ ├── ROC.java │ │ │ ├── distributions │ │ │ ├── BinomialDistribution.java │ │ │ ├── NonSymmetricalNormalDistribution.java │ │ │ ├── NormalDistribution.java │ │ │ ├── NormalKernelDensityEstimator.java │ │ │ └── package.html │ │ │ ├── linear_regression │ │ │ ├── LinearRegression.java │ │ │ ├── RegressionStatistics.java │ │ │ ├── filters │ │ │ │ ├── BinningFilter.java │ │ │ │ ├── ProbabilityFilter.java │ │ │ │ └── package.html │ │ │ ├── package.html │ │ │ └── regressions │ │ │ │ ├── MedianRegression.java │ │ │ │ ├── SimpleLinearRegression.java │ │ │ │ └── package.html │ │ │ └── package.html │ │ ├── memory │ │ ├── MemoryConsumptionStatus.java │ │ └── package.html │ │ ├── messages │ │ ├── FeedBack.java │ │ └── package.html │ │ ├── nucleotide │ │ ├── NucleotideSequence.java │ │ ├── NucleotideSequenceImpl.java │ │ └── package.html │ │ ├── package.html │ │ ├── parameters │ │ ├── UtilitiesUserParameters.java │ │ ├── identification │ │ │ ├── IdentificationParameters.java │ │ │ ├── advanced │ │ │ │ ├── FractionParameters.java │ │ │ │ ├── GeneParameters.java │ │ │ │ ├── IdMatchValidationParameters.java │ │ │ │ ├── ModificationLocalizationParameters.java │ │ │ │ ├── PeptideVariantsParameters.java │ │ │ │ ├── ProteinInferenceParameters.java │ │ │ │ ├── PsmScoringParameters.java │ │ │ │ ├── SequenceMatchingParameters.java │ │ │ │ ├── ValidationQcParameters.java │ │ │ │ └── package.html │ │ │ ├── package.html │ │ │ ├── search │ │ │ │ ├── DigestionParameters.java │ │ │ │ ├── ModificationParameters.java │ │ │ │ ├── SearchParameters.java │ │ │ │ └── package.html │ │ │ └── tool_specific │ │ │ │ ├── AndromedaParameters.java │ │ │ │ ├── CometParameters.java │ │ │ │ ├── DirecTagParameters.java │ │ │ │ ├── MetaMorpheusParameters.java │ │ │ │ ├── MsAmandaParameters.java │ │ │ │ ├── MsgfParameters.java │ │ │ │ ├── MyriMatchParameters.java │ │ │ │ ├── NovorParameters.java │ │ │ │ ├── OmssaParameters.java │ │ │ │ ├── PNovoParameters.java │ │ │ │ ├── PepnovoParameters.java │ │ │ │ ├── SageParameters.java │ │ │ │ ├── TideParameters.java │ │ │ │ ├── XtandemParameters.java │ │ │ │ └── package.html │ │ ├── package.html │ │ ├── peptide_shaker │ │ │ ├── ProjectType.java │ │ │ └── package.html │ │ ├── quantification │ │ │ ├── package.html │ │ │ └── spectrum_counting │ │ │ │ ├── SpectrumCountingParameters.java │ │ │ │ └── package.html │ │ ├── searchgui │ │ │ ├── OutputParameters.java │ │ │ └── package.html │ │ └── tools │ │ │ ├── ProcessingParameters.java │ │ │ └── package.html │ │ ├── pdbfinder │ │ ├── FindPdbForUniprotAccessions.java │ │ ├── das │ │ │ └── readers │ │ │ │ ├── AlignmentBlock.java │ │ │ │ ├── DasAlignment.java │ │ │ │ ├── DasAnnotationServerAlingmentReader.java │ │ │ │ ├── DasAnnotationServerResultReader.java │ │ │ │ ├── DasFeature.java │ │ │ │ ├── StartEndPosition.java │ │ │ │ └── package.html │ │ ├── package.html │ │ └── pdb │ │ │ ├── PdbBlock.java │ │ │ ├── PdbParameter.java │ │ │ └── package.html │ │ ├── pride │ │ ├── CvTerm.java │ │ ├── PrideObject.java │ │ ├── PrideObjectsFactory.java │ │ ├── PrideWebService.java │ │ ├── PtmToPrideMap.java │ │ ├── package.html │ │ ├── prideobjects │ │ │ ├── Contact.java │ │ │ ├── ContactGroup.java │ │ │ ├── Instrument.java │ │ │ ├── Protocol.java │ │ │ ├── Reference.java │ │ │ ├── ReferenceGroup.java │ │ │ ├── Sample.java │ │ │ ├── package.html │ │ │ └── webservice │ │ │ │ ├── PrideQuery.java │ │ │ │ ├── file │ │ │ │ ├── FileType.java │ │ │ │ └── package.html │ │ │ │ ├── package.html │ │ │ │ └── query │ │ │ │ ├── PrideFilter.java │ │ │ │ ├── PrideFilterType.java │ │ │ │ └── package.html │ │ └── validation │ │ │ ├── PrideXmlValidator.java │ │ │ ├── XMLValidationErrorHandler.java │ │ │ └── package.html │ │ ├── protein │ │ ├── AASequenceImpl.java │ │ ├── DualEnzyme.java │ │ ├── Enzyme.java │ │ ├── ModificationFactory.java │ │ ├── ModificationImplementation.java │ │ ├── ModificationTemplate.java │ │ ├── MolecularFormula.java │ │ ├── Protein.java │ │ ├── RegExEnzyme.java │ │ └── package.html │ │ ├── sun │ │ ├── SwingWorker.java │ │ ├── TableMap.java │ │ ├── TableSorter.java │ │ └── package.html │ │ ├── threading │ │ ├── ObjectMutex.java │ │ ├── SimpleSemaphore.java │ │ └── package.html │ │ └── waiting │ │ ├── Duration.java │ │ ├── WaitingActionListener.java │ │ ├── WaitingHandler.java │ │ └── package.html └── resources │ ├── DNA_Protein_Translation.properties │ ├── DefaultJavaOptions.txt │ ├── FTPClient.properties │ ├── META-INF │ └── services │ │ └── com.compomics.util.experiment.io.identification.IdfileReader │ ├── MonoAAMasses.properties │ ├── MonoElementMasses.properties │ ├── MonoNucleotideMasses.properties │ ├── SpectrumPanel.properties │ ├── complementaryNucleotides.properties │ ├── compomics-utilities.properties │ ├── elements.txt │ ├── enzymes.txt │ ├── helpFiles │ ├── AnnotationPreferences.html │ ├── AtomChainDialog.html │ ├── ChromatogramPanel.html │ ├── EnzymesDialog.html │ ├── FilterSettings.html │ ├── FractionPreferences.html │ ├── GeneAnnotationPreferences.html │ ├── InSilicoProteinDigestion.html │ ├── IsotopicDistributionPanel.html │ ├── JavaHomeDialog.html │ ├── JavaOptionsDialog.html │ ├── ModificationEditor.html │ ├── NewEnzymeDialog.html │ ├── OmssaSettingsDialog.html │ ├── PeptideVariantsPreferences.html │ ├── PrivacySettingsHelp.html │ ├── ProcessingPreferences.html │ ├── ProteinInferencePreferences.html │ ├── PsmScoringPreferences.html │ ├── PtmDialog.html │ ├── PtmLocalizationPreferences.html │ ├── QualityControlPreferences.html │ ├── SearchSettingsDialog.html │ ├── SequenceMatchingPreferences.html │ ├── SpeciesDialog.html │ ├── SpectrumPanel.html │ ├── StatisticsDialog.html │ ├── ValidationPreferences.html │ └── XTandemSettingsDialog.html │ ├── icons │ ├── accept-new.png │ ├── accept.png │ ├── close.png │ ├── close_grey.png │ ├── compomics-utilities.png │ ├── compomics.png │ ├── contextual_menu_black.png │ ├── contextual_menu_gray.png │ ├── edit.png │ ├── edit_gray.png │ ├── error-new.png │ ├── help.GIF │ ├── help_no_frame.png │ ├── help_no_frame_grey.png │ ├── intelliJ.png │ ├── java.png │ ├── maven.png │ ├── next.png │ ├── next_grey.png │ ├── ols_transparent.GIF │ ├── peptide-shaker-medium-orange-shadow.png │ ├── peptide-shaker-orange.gif │ ├── peptide-shaker.gif │ ├── pinned.png │ ├── previous.png │ ├── previous_grey.png │ ├── pwiz_purple_logo.png │ ├── relims_logo.png │ ├── reporter_logo.png │ ├── searchgui-medium-shadow.png │ ├── searchgui-orange.gif │ ├── searchgui.gif │ ├── selected_green-new.png │ ├── selected_green.png │ ├── ugent.png │ ├── unpinned.png │ ├── vib.png │ ├── warning-new.png │ ├── warning2-new.png │ └── yourkit.png │ ├── isotopicElement.txt │ ├── kyte_doolittle.properties │ ├── meek.properties │ ├── modificationConversion.txt │ ├── modifications.properties │ ├── modifications.txt │ └── pride.xsd └── test ├── java └── com │ └── compomics │ └── util │ └── test │ ├── FullSuite.java │ ├── experiment │ ├── FragmentFactoryTest.java │ ├── io │ │ ├── AminoAcidPatternParsingTest.java │ │ ├── AtomChainParsingTest.java │ │ ├── IdentificationDBTest.java │ │ ├── identifications │ │ │ ├── PepNovoIdfileReaderTest.java │ │ │ ├── TestIdfileReaderFactory.java │ │ │ └── package.html │ │ ├── package.html │ │ └── spectrum │ │ │ ├── SpectrumImportTest.java │ │ │ ├── cms │ │ │ └── CmsFileTest.java │ │ │ └── package.html │ ├── modification │ │ └── ModificationPeptideMappingTest.java │ ├── package.html │ ├── sequences │ │ ├── digestion │ │ │ ├── DigestionTest.java │ │ │ ├── ProteinSequenceIteratorTest.java │ │ │ └── package.html │ │ ├── indexing │ │ │ ├── FMIndexTest.java │ │ │ └── package.html │ │ ├── matching │ │ │ ├── AminoAcidPatternTest.java │ │ │ ├── SequenceMatchingTest.java │ │ │ └── package.html │ │ └── package.html │ └── spectrum │ │ ├── indexing │ │ ├── SpectrumAnnotationTest.java │ │ └── package.html │ │ └── package.html │ ├── general │ ├── PtmsiteMappingTest.java │ ├── TestCommandLineParser.java │ ├── TestIsotopicDistributionCalculator.java │ ├── TestMassCalc.java │ ├── package.html │ └── servlet │ │ ├── TstMassCalcServlet.java │ │ └── package.html │ ├── io │ ├── TestFTPClient.java │ ├── TestFilenameExtensionFilter.java │ ├── TestFolderMonitor.java │ ├── TestMascotEnzymeReader.java │ ├── TestMonitorableFileInputStream.java │ ├── TestMonitorableInputStream.java │ ├── TestPushBackStringReader.java │ ├── TestSearchParameterMarshaller.java │ ├── TestWriterBySection.java │ └── package.html │ ├── math │ ├── TestBigFunctions.java │ ├── TestBinomialDistribution.java │ └── package.html │ ├── nucleotide │ ├── TestNucleotideSequence.java │ ├── TestNucleotideSequenceImpl.java │ └── package.html │ ├── package.html │ └── protein │ ├── TestAASequenceImpl.java │ ├── TestDualEnzyme.java │ ├── TestEnzyme.java │ ├── TestHeader.java │ ├── TestModificationFactory.java │ ├── TestModificationImplementation.java │ ├── TestMolecularFormula.java │ ├── TestProtein.java │ ├── TestRegExEnzyme.java │ └── package.html └── resources ├── DNA_Protein_Translation.properties ├── DefaultJavaOptions.txt ├── FTPClient.properties ├── META-INF └── services │ └── com.compomics.util.experiment.io.identifications.IdfileReader ├── MonoAAMasses.properties ├── MonoElementMasses.properties ├── MonoNucleotideMasses.properties ├── SpectrumPanel.properties ├── complementaryNucleotides.properties ├── compomics-utilities.properties ├── elements.txt ├── enzymes.txt ├── enzymes_test.txt ├── exampleFiles ├── exampleSpectrumA.pkl └── exampleSpectrumB.pkl ├── exampleSpectrumA.pkl ├── exampleSpectrumB.pkl ├── experiment ├── sgd.fasta ├── terminiSequence.fasta ├── test.mgf ├── test.mgf.out ├── testSequences.fasta ├── testSequences_1.fasta └── uniprot.fasta ├── fastaFile.fas ├── fastaFile.fas.phr ├── fastaFile.fas.pin ├── fastaFile.fas.psq ├── fastaNucleotideFile.fas ├── formatdb.log ├── helpFiles ├── AnnotationPreferences.html ├── AtomChainDialog.html ├── ChromatogramPanel.html ├── FilterSettings.html ├── FractionPreferences.html ├── GeneAnnotationPreferences.html ├── InSilicoProteinDigestion.html ├── IsotopicDistributionPanel.html ├── JavaHomeDialog.html ├── JavaOptionsDialog.html ├── ModificationEditor.html ├── OmssaSettingsDialog.html ├── PeptideVariantsPreferences.html ├── PrivacySettingsHelp.html ├── ProcessingPreferences.html ├── ProteinInferencePreferences.html ├── PsmScoringPreferences.html ├── PtmDialog.html ├── PtmLocalizationPreferences.html ├── QualityControlPreferences.html ├── SearchSettingsDialog.html ├── SequenceMatchingPreferences.html ├── SpeciesDialog.html ├── SpectrumPanel.html ├── StatisticsDialog.html ├── ValidationPreferences.html └── XTandemSettingsDialog.html ├── icons ├── accept.png ├── close.png ├── close_grey.png ├── compomics-utilities.png ├── compomics.png ├── contextual_menu_black.png ├── contextual_menu_gray.png ├── edit.png ├── edit_gray.png ├── help.GIF ├── help_no_frame.png ├── help_no_frame_grey.png ├── intelliJ.png ├── java.png ├── maven.png ├── next.png ├── next_grey.png ├── ols_transparent.GIF ├── peptide-shaker-medium-blue-shadow.png ├── peptide-shaker-medium-orange-shadow.png ├── peptide-shaker-orange.gif ├── peptide-shaker.gif ├── pinned.png ├── previous.png ├── previous_grey.png ├── pwiz_purple_logo.png ├── relims_logo.png ├── reporter_logo.png ├── searchgui-medium-shadow.png ├── searchgui-orange.gif ├── searchgui.gif ├── selected_green.png ├── ugent.png ├── unpinned.png ├── vib.png └── yourkit.png ├── isotopicElement.txt ├── kyte_doolittle.properties ├── meek.properties ├── modificationConversion.txt ├── modifications.properties ├── modifications.txt ├── pride.xsd ├── test.spr.gz ├── 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