├── .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 ├── testAddSelfDefinedList_AA.properties ├── testAddSelfDefinedList_BiochemElements.properties ├── testCleave.fas ├── testFile.jpg ├── testMCServlet.properties ├── testMassCalc.properties ├── testModificationConversionParser_control.txt ├── testModificationParser_control.txt ├── testMonitor.zip └── testSelfDefinedList.properties /.gitignore: -------------------------------------------------------------------------------- 1 | /target/ 2 | derby.log 3 | /.idea/ 4 | /src/test/resources/* 5 | /docs/ -------------------------------------------------------------------------------- /compomics-utilities.ico: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompOmics/compomics-utilities/5ec488fea6f02d4c3153891668a9f92c0d109084/compomics-utilities.ico -------------------------------------------------------------------------------- /resources/conf/gene_mappings/ensembl_versions: -------------------------------------------------------------------------------- 1 | sscrofa_gene_ensembl Ensembl 110 2 | hsapiens_gene_ensembl Ensembl 110 3 | -------------------------------------------------------------------------------- /src/main/assembly/zip.xml: -------------------------------------------------------------------------------- 1 | 4 | zip 5 | 6 | zip 7 | 8 | 9 | 10 | ${project.basedir}/target/${project.artifactId}-${project.version} 11 | / 12 | 13 | 14 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/cli/enzymes/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Command line for the handling of enzymes. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/cli/fasta/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Command line for the handling of fasta files. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/cli/identification_parameters/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Command line for the handling of identification parameters. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/cli/modifications/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Command line for the handling of modifications. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/cli/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Package for the use of compomics-utilities via command line. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/cli/paths/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Command line for the handling of paths. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/cli/peptide_mapper/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Command line for PeptideMapper. 4 | 5 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/scripts_marc/Dummy.java: -------------------------------------------------------------------------------- 1 | package com.compomics.scripts_marc; 2 | 3 | /** 4 | * 5 | * @author Marc Vaudel 6 | */ 7 | public class Dummy { 8 | 9 | public synchronized void delay(long delay) throws InterruptedException { 10 | 11 | this.wait(delay); 12 | 13 | } 14 | 15 | } 16 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/software/autoupdater/HeadlessFileDAO.java: -------------------------------------------------------------------------------- 1 | package com.compomics.software.autoupdater; 2 | 3 | import java.io.File; 4 | import java.io.IOException; 5 | 6 | /** 7 | * HeadlessFileDAO. 8 | * 9 | * @author Davy Maddelein 10 | */ 11 | public class HeadlessFileDAO extends FileDAO { 12 | 13 | /** 14 | * {@inheritDoc } 15 | */ 16 | @Override 17 | public boolean createDesktopShortcut(MavenJarFile file, String iconName, String toolName, boolean deleteOldShortcut) throws IOException { 18 | throw new UnsupportedOperationException("Not supported yet."); // @TODO: implement me... 19 | } 20 | 21 | /** 22 | * {@inheritDoc } 23 | */ 24 | @Override 25 | public File getLocationToDownloadOnDisk(String targetDownloadFolder) throws IOException { 26 | throw new UnsupportedOperationException("Not supported yet."); // @TODO: implement me... 27 | } 28 | } 29 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/software/autoupdater/JarFileFilter.java: -------------------------------------------------------------------------------- 1 | package com.compomics.software.autoupdater; 2 | 3 | import java.io.File; 4 | import java.io.FilenameFilter; 5 | 6 | /** 7 | * JarFileFilter. 8 | * 9 | * @author Davy Maddelein 10 | */ 11 | public class JarFileFilter implements FilenameFilter { 12 | 13 | @Override 14 | public boolean accept(File dir, String name) { 15 | boolean accept = false; 16 | if (dir.getName().contains(name)) { 17 | accept = true; 18 | } 19 | return accept; 20 | } 21 | } 22 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/software/autoupdater/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes related to auto updating compomics-utilities tools. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/software/cli/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Convenience classes for the handling of command lines. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/software/dialogs/JavaHomeOrMemoryDialogParent.java: -------------------------------------------------------------------------------- 1 | package com.compomics.software.dialogs; 2 | 3 | import com.compomics.util.parameters.UtilitiesUserParameters; 4 | 5 | /** 6 | * Interface for parents of JavaMemoryDialog and JavaHomeDialog. 7 | * 8 | * @author Harald Barsnes 9 | */ 10 | public interface JavaHomeOrMemoryDialogParent { 11 | 12 | /** 13 | * Restart the given tool with the new Java options. 14 | */ 15 | public void restart(); 16 | 17 | /** 18 | * Returns the utilities user preferences. 19 | * 20 | * @return the utilities user preferences 21 | */ 22 | public UtilitiesUserParameters getUtilitiesUserParameters(); 23 | } 24 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/software/dialogs/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Dialogs for starting compomics-utilities tools and setting their Java options. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/software/log/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes related to software log. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/software/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Convenience classes for command line usage of compomics-utilities tools. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/software/settings/PathKey.java: -------------------------------------------------------------------------------- 1 | package com.compomics.software.settings; 2 | 3 | /** 4 | * Interface for a path key. 5 | * 6 | * @author Marc Vaudel 7 | */ 8 | public interface PathKey { 9 | 10 | /** 11 | * Returns the id of the path. 12 | * 13 | * @return the id of the path 14 | */ 15 | public String getId(); 16 | 17 | /** 18 | * Returns the description of the path. 19 | * 20 | * @return the description of the path 21 | */ 22 | public String getDescription(); 23 | } 24 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/software/settings/gui/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | GUI settings for compomics-utilities tools. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/software/settings/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Settings for compomics-utilities tools. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/StreamUtil.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util; 2 | 3 | import java.util.Collection; 4 | import java.util.stream.Stream; 5 | 6 | /** 7 | * Convenience methods to work with lambdas. 8 | * 9 | * @author Marc Vaudel 10 | */ 11 | public class StreamUtil { 12 | 13 | /** 14 | * Returns a concatenation of the streams of the given collections. If a 15 | * collection is null it is ignored. Returns null if all collections are 16 | * null. 17 | * 18 | * @param the collections 19 | * @param collections the collections 20 | * 21 | * @return the concatenated stream 22 | */ 23 | public static Stream concatenate(Collection... collections) { 24 | 25 | Stream result = null; 26 | 27 | for (Collection collection : collections) { 28 | 29 | if (collection != null) { 30 | 31 | result = result == null ? collection.stream() : Stream.concat(result, collection.stream()); 32 | 33 | } 34 | } 35 | 36 | return result; 37 | 38 | } 39 | 40 | } 41 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/TempByteArray.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util; 2 | 3 | /** 4 | * Convenience class for storing an array buffer and a length. 5 | * 6 | * @author Marc Vaudel 7 | */ 8 | public class TempByteArray { 9 | 10 | /** 11 | * The byte array. 12 | */ 13 | public final byte[] array; 14 | /** 15 | * The length used. 16 | */ 17 | public final int length; 18 | 19 | /** 20 | * Constructor. 21 | * 22 | * @param array The array. 23 | * @param length The length used. 24 | */ 25 | public TempByteArray( 26 | byte[] array, 27 | int length 28 | ) { 29 | 30 | this.array = array; 31 | this.length = length; 32 | 33 | } 34 | 35 | } 36 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/db/components/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Database related components. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/db/interfaces/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Database related interfaces. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/db/object/DbMutex.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.db.object; 2 | 3 | import com.compomics.util.threading.SimpleSemaphore; 4 | 5 | /** 6 | * Placeholder for the db mutex. 7 | * 8 | * @author Marc Vaudel 9 | */ 10 | public class DbMutex { 11 | 12 | /** 13 | * The db mutex. 14 | */ 15 | public static final SimpleSemaphore dbMutex = new SimpleSemaphore(1); 16 | 17 | /** 18 | * The cache load objects mutex. 19 | */ 20 | public static final SimpleSemaphore loadObjectMutex = new SimpleSemaphore(1); 21 | 22 | } 23 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/db/object/objects/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | This package contains classes of objects that can be stored in the database. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/db/object/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | This package contains the classes relative to the object database. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/db/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Database related classes. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/enumeration/ImageType.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.enumeration; 2 | 3 | /** 4 | * Enumerator for supported export plot file types. 5 | * 6 | * @author Harald Barsnes 7 | */ 8 | public enum ImageType { 9 | 10 | /** 11 | * Supported image types. 12 | */ 13 | JPEG(".jpg"), TIFF(".tiff"), PNG(".png"), PDF(".pdf"), SVG(".svg"); 14 | /** 15 | * The image file extension. 16 | */ 17 | private final String extension; 18 | 19 | /** 20 | * Constructor setting the image type extension. 21 | * 22 | * @param extension 23 | */ 24 | ImageType(String extension) { 25 | this.extension = extension; 26 | } 27 | 28 | /** 29 | * Returns the extension. 30 | * 31 | * @return the extension 32 | */ 33 | public String getExtension() { 34 | return this.extension; 35 | } 36 | 37 | /** 38 | * Empty default constructor 39 | */ 40 | private ImageType() { 41 | extension = ""; 42 | } 43 | } 44 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/enumeration/MolecularElement.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.enumeration; 2 | 3 | /** 4 | * This ENUM types the distinct molecular elements. 5 | * 6 | * Created by IntelliJ IDEA. 7 | * User: Niklaas 8 | * Date: 16-Aug-2010 9 | * Time: 08:28:22 10 | */ 11 | public enum MolecularElement { 12 | 13 | H,C,N,O,S,HDeut,C13,N15,O18,Se; 14 | 15 | /** 16 | * Private constructor to initialize variables for each type. 17 | */ 18 | private MolecularElement() { 19 | } 20 | } 21 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/enumeration/OperatingSystemEnum.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.enumeration; 2 | 3 | /** 4 | * This ENUM types the distinct OS systems. 5 | * 6 | * Created by IntelliJ IDEA. 7 | * User: kenny 8 | * Date: Feb 22, 2010 9 | * Time: 1:42:27 PM 10 | */ 11 | public enum OperatingSystemEnum { 12 | MACOS, WINDOWS, UNIX; 13 | 14 | /** 15 | * Empty default constructor 16 | */ 17 | private OperatingSystemEnum() { 18 | } 19 | } 20 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/enumeration/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Enumeration used by compomics-utilities. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/examples/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Examples of how the compomics-utilities library can 4 | can be used by other projects. 5 | 6 | 7 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/exceptions/exception_handlers/CommandLineExceptionHandler.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.exceptions.exception_handlers; 2 | 3 | import com.compomics.util.exceptions.ExceptionHandler; 4 | import java.util.ArrayList; 5 | 6 | /** 7 | * Exception handler for command line processes. 8 | * 9 | * @author Marc Vaudel 10 | */ 11 | public class CommandLineExceptionHandler extends ExceptionHandler { 12 | 13 | /** 14 | * List of caught exceptions. 15 | */ 16 | private final ArrayList exceptionCaught = new ArrayList<>(); 17 | 18 | /** 19 | * Constructor. 20 | */ 21 | public CommandLineExceptionHandler() { 22 | 23 | } 24 | 25 | @Override 26 | public void notifyUser(Exception e) { 27 | // Do something here? 28 | } 29 | } 30 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/exceptions/exception_handlers/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Implementations of the ExceptionHandler interface. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/exceptions/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes for the handling of exceptions. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/Constants.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.experiment; 2 | 3 | /** 4 | * Convenience class listing constants used throughout the library. 5 | * 6 | * @author Marc Vaudel 7 | */ 8 | public class Constants { 9 | 10 | /** 11 | * Empty default constructor 12 | */ 13 | public Constants() { 14 | } 15 | 16 | /** 17 | * The Avogadro constant without exponent. 18 | */ 19 | public static final double AVOGADRO_NO_EXP = 6.02214129; 20 | /** 21 | * The Avogadro constant. 22 | */ 23 | public static final double Avogadro = AVOGADRO_NO_EXP * Math.pow(10, 23); 24 | /** 25 | * The atomic mass unit without exponent. 26 | */ 27 | public static final double AMU_NO_EXP = 1.660538921; 28 | /** 29 | * The atomic mass unit in kg. 30 | */ 31 | public static final double AMU = AMU_NO_EXP * Math.pow(10, -27); 32 | } 33 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/biology/aminoacids/impl/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | The amino acid implementations. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/biology/aminoacids/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | The amino acid classes. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/biology/aminoacids/sequence/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes related to the handling of protein sequences. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/biology/atoms/impl/Chlorine.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.experiment.biology.atoms.impl; 2 | 3 | import com.compomics.util.experiment.biology.atoms.Atom; 4 | import java.util.HashMap; 5 | 6 | /** 7 | * The Chlorine atom. 8 | * 9 | * @author Harald Barsnes 10 | */ 11 | public class Chlorine extends Atom { 12 | 13 | /** 14 | * Constructor. 15 | */ 16 | public Chlorine() { 17 | monoisotopicMass = 34.96885269; 18 | isotopeMap = new HashMap<>(3); 19 | isotopeMap.put(0, monoisotopicMass); 20 | isotopeMap.put(1, 35.96830682); 21 | isotopeMap.put(2, 36.96590258); 22 | representativeComposition = new HashMap<>(2); 23 | representativeComposition.put(0, 0.76); 24 | representativeComposition.put(2, 0.24); 25 | this.name = "Chlorine"; 26 | this.letter = "Cl"; 27 | } 28 | } -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/biology/atoms/impl/Cobalt.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.experiment.biology.atoms.impl; 2 | 3 | import com.compomics.util.experiment.biology.atoms.Atom; 4 | import java.util.HashMap; 5 | 6 | /** 7 | * The Cobalt atom. 8 | * 9 | * @author Harald Barsnes 10 | */ 11 | public class Cobalt extends Atom { 12 | 13 | /** 14 | * Constructor. 15 | */ 16 | public Cobalt() { 17 | monoisotopicMass = 58.9331950; 18 | isotopeMap = new HashMap<>(1); 19 | isotopeMap.put(0, monoisotopicMass); 20 | representativeComposition = new HashMap<>(1); 21 | representativeComposition.put(0, 1.0); 22 | this.name = "Cobalt"; 23 | this.letter = "Co"; 24 | } 25 | } -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/biology/atoms/impl/Copper.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.experiment.biology.atoms.impl; 2 | 3 | import com.compomics.util.experiment.biology.atoms.Atom; 4 | import java.util.HashMap; 5 | 6 | /** 7 | * The copper atom. 8 | * 9 | * @author Harald Barsnes 10 | */ 11 | public class Copper extends Atom { 12 | 13 | /** 14 | * Constructor. 15 | */ 16 | public Copper() { 17 | 18 | monoisotopicMass = 62.9295975; 19 | 20 | isotopeMap = new HashMap(3); 21 | isotopeMap.put(0, monoisotopicMass); 22 | isotopeMap.put(1, 63.9297642); 23 | isotopeMap.put(2, 64.9277895); 24 | 25 | representativeComposition = new HashMap(2); 26 | representativeComposition.put(0, 0.6915); 27 | representativeComposition.put(2, 0.3085); 28 | 29 | this.name = "Copper"; 30 | this.letter = "Cu"; 31 | } 32 | } 33 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/biology/atoms/impl/Helium.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.experiment.biology.atoms.impl; 2 | 3 | import com.compomics.util.experiment.biology.atoms.Atom; 4 | import java.util.HashMap; 5 | 6 | /** 7 | * The helium atom. 8 | * 9 | * @author Marc Vaudel 10 | */ 11 | public class Helium extends Atom { 12 | 13 | /** 14 | * Constructor. 15 | */ 16 | public Helium() { 17 | monoisotopicMass = 2.015894; 18 | isotopeMap = new HashMap<>(9); 19 | isotopeMap.put(0, monoisotopicMass); 20 | isotopeMap.put(1, 3.0160293191); 21 | isotopeMap.put(2, 4.00260325415); 22 | isotopeMap.put(3, 5.01222); 23 | isotopeMap.put(4, 6.0188891); 24 | isotopeMap.put(5, 7.028021); 25 | isotopeMap.put(6, 8.033922); 26 | isotopeMap.put(7, 9.04395); 27 | isotopeMap.put(8, 10.05240); 28 | representativeComposition = new HashMap<>(2); 29 | representativeComposition.put(0, 0.9999); 30 | representativeComposition.put(1, 0.0001); 31 | this.name = "Helium"; 32 | this.letter = "He"; 33 | } 34 | } 35 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/biology/atoms/impl/Hydrogen.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.experiment.biology.atoms.impl; 2 | 3 | import com.compomics.util.experiment.biology.atoms.Atom; 4 | import java.util.HashMap; 5 | 6 | /** 7 | * The hydrogen atom. 8 | * 9 | * @author Marc Vaudel 10 | */ 11 | public class Hydrogen extends Atom { 12 | 13 | /** 14 | * Constructor. 15 | */ 16 | public Hydrogen() { 17 | monoisotopicMass = 1.00782503207; 18 | isotopeMap = new HashMap<>(2); 19 | isotopeMap.put(0, monoisotopicMass); 20 | isotopeMap.put(1, 2.0141017778); 21 | representativeComposition = new HashMap<>(2); 22 | representativeComposition.put(0, 0.999885); 23 | representativeComposition.put(1, 0.000115); 24 | this.name = "Hydrogen"; 25 | this.letter = "H"; 26 | } 27 | } 28 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/biology/atoms/impl/Iodine.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.experiment.biology.atoms.impl; 2 | 3 | import com.compomics.util.experiment.biology.atoms.Atom; 4 | import java.util.HashMap; 5 | 6 | /** 7 | * Iodine. 8 | * 9 | * @author Marc Vaudel 10 | */ 11 | public class Iodine extends Atom { 12 | 13 | /** 14 | * Constructor. 15 | */ 16 | public Iodine() { 17 | monoisotopicMass = 126.904473; 18 | isotopeMap = new HashMap<>(1); 19 | isotopeMap.put(0, monoisotopicMass); 20 | representativeComposition = new HashMap<>(1); 21 | representativeComposition.put(0, 1.0); 22 | 23 | this.name = "Iodine"; 24 | this.letter = "I"; 25 | } 26 | } 27 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/biology/atoms/impl/Lithium.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.experiment.biology.atoms.impl; 2 | 3 | import com.compomics.util.experiment.biology.atoms.Atom; 4 | import java.util.HashMap; 5 | 6 | /** 7 | * The Lithium atom. 8 | * 9 | * @author Marc Vaudel 10 | */ 11 | public class Lithium extends Atom { 12 | 13 | /** 14 | * Constructor. 15 | */ 16 | public Lithium() { 17 | monoisotopicMass = 3.030775; 18 | isotopeMap = new HashMap<>(10); 19 | isotopeMap.put(0, monoisotopicMass); 20 | isotopeMap.put(1, 4.02719); 21 | isotopeMap.put(2, 5.01254); 22 | isotopeMap.put(3, 6.015122795); 23 | isotopeMap.put(4, 7.01600455); 24 | isotopeMap.put(5, 8.02248736); 25 | isotopeMap.put(6, 9.0267895); 26 | isotopeMap.put(7, 10.035481); 27 | isotopeMap.put(8, 11.043798); 28 | isotopeMap.put(9, 12.05378); 29 | representativeComposition = new HashMap<>(1); 30 | representativeComposition.put(0, 1.0); 31 | this.name = "Lithium"; 32 | this.letter = "Li"; 33 | } 34 | } -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/biology/atoms/impl/Magnesium.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.experiment.biology.atoms.impl; 2 | 3 | import com.compomics.util.experiment.biology.atoms.Atom; 4 | import java.util.HashMap; 5 | 6 | /** 7 | * The magnesium atom. 8 | * 9 | * @author Harald Barsnes 10 | */ 11 | public class Magnesium extends Atom { 12 | 13 | /** 14 | * Constructor. 15 | */ 16 | public Magnesium() { 17 | 18 | monoisotopicMass = 23.985041697; 19 | 20 | isotopeMap = new HashMap(3); 21 | isotopeMap.put(0, monoisotopicMass); 22 | isotopeMap.put(1, 24.98583696); 23 | isotopeMap.put(2, 25.98259297); 24 | 25 | representativeComposition = new HashMap(3); 26 | representativeComposition.put(0, 0.7899); 27 | representativeComposition.put(1, 0.1000); 28 | representativeComposition.put(2, 0.1101); 29 | 30 | this.name = "Magnesium"; 31 | this.letter = "Mg"; 32 | } 33 | } 34 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/biology/atoms/impl/Manganese.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.experiment.biology.atoms.impl; 2 | 3 | import com.compomics.util.experiment.biology.atoms.Atom; 4 | import java.util.HashMap; 5 | 6 | /** 7 | * The Manganese atom. 8 | * 9 | * @author Harald Barsnes 10 | */ 11 | public class Manganese extends Atom { 12 | 13 | /** 14 | * Constructor. 15 | */ 16 | public Manganese() { 17 | monoisotopicMass = 54.9380451; 18 | isotopeMap = new HashMap<>(1); 19 | isotopeMap.put(0, monoisotopicMass); 20 | representativeComposition = new HashMap<>(1); 21 | representativeComposition.put(0, 1.0); 22 | this.name = "Manganese"; 23 | this.letter = "Mn"; 24 | } 25 | } -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/biology/atoms/impl/Nickel.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.experiment.biology.atoms.impl; 2 | 3 | import com.compomics.util.experiment.biology.atoms.Atom; 4 | import java.util.HashMap; 5 | 6 | /** 7 | * The Nickel atom. 8 | * 9 | * @author Harald Barsnes 10 | */ 11 | public class Nickel extends Atom { 12 | 13 | /** 14 | * Constructor. 15 | */ 16 | public Nickel() { 17 | monoisotopicMass = 57.9353429; 18 | isotopeMap = new HashMap<>(7); 19 | isotopeMap.put(0, monoisotopicMass); 20 | isotopeMap.put(1, 58.9343467); 21 | isotopeMap.put(2, 59.9307864); 22 | isotopeMap.put(3, 60.9310560); 23 | isotopeMap.put(4, 61.9283451); 24 | isotopeMap.put(5, 62.9296694); 25 | isotopeMap.put(6, 63.9279660); 26 | representativeComposition = new HashMap<>(5); 27 | representativeComposition.put(0, 0.68); 28 | representativeComposition.put(2, 0.26); 29 | representativeComposition.put(3, 0.01); 30 | representativeComposition.put(4, 0.036); 31 | representativeComposition.put(6, 0.009); 32 | this.name = "Nickel"; 33 | this.letter = "Ni"; 34 | } 35 | } -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/biology/atoms/impl/Potassium.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.experiment.biology.atoms.impl; 2 | 3 | import com.compomics.util.experiment.biology.atoms.Atom; 4 | import java.util.HashMap; 5 | 6 | /** 7 | * The potassium atom. 8 | * 9 | * @author Harald Barsnes 10 | */ 11 | public class Potassium extends Atom { 12 | 13 | /** 14 | * Constructor. 15 | */ 16 | public Potassium() { 17 | 18 | monoisotopicMass = 38.963706487; 19 | 20 | isotopeMap = new HashMap(3); 21 | isotopeMap.put(0, monoisotopicMass); 22 | isotopeMap.put(1, 56.9353928); 23 | isotopeMap.put(2, 57.9332744); 24 | 25 | representativeComposition = new HashMap(3); 26 | representativeComposition.put(0, 0.932581); 27 | representativeComposition.put(1, 0.000117); 28 | representativeComposition.put(2, 0.067302); 29 | 30 | this.name = "Potassium"; 31 | this.letter = "K"; 32 | } 33 | } 34 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/biology/atoms/impl/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Atoms implementations. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/biology/atoms/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | The atom classes. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/biology/enzymes/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes related to enzymes. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/biology/genes/ensembl/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes for the handling of Ensembl data. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/biology/genes/go/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes for the handling of GO terms. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/biology/genes/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes related to genes. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/biology/ions/impl/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Ion implementations. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/biology/ions/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Experiment classes related to ions. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/biology/modifications/ModificationProvider.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.experiment.biology.modifications; 2 | 3 | /** 4 | * Interface for a modification provider. 5 | * 6 | * @author Marc Vaudel 7 | */ 8 | public interface ModificationProvider { 9 | 10 | /** 11 | * Returns the modification with the given name name. Null if none found. 12 | * 13 | * @param name The name of the modification of interest. 14 | * 15 | * @return The modification of interest 16 | */ 17 | public Modification getModification(String name); 18 | 19 | } 20 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/biology/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Experiment classes related to biological entities. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/biology/proteins/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes related to proteins. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/biology/taxonomy/mappings/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes related to species mapping. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/biology/taxonomy/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes related to species and taxonomy. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/biology/variants/AminoAcidSubstitution.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.experiment.biology.variants; 2 | 3 | /** 4 | * Class representing an amino acid substitution. 5 | * 6 | * @author Marc Vaudel 7 | */ 8 | public class AminoAcidSubstitution { 9 | 10 | /** 11 | * Empty default constructor 12 | */ 13 | public AminoAcidSubstitution() { 14 | originalAminoAcid = '0'; 15 | variantAminoAcid = '0'; 16 | } 17 | 18 | /** 19 | * The original amino acid represented by its single letter code. 20 | */ 21 | public final char originalAminoAcid; 22 | /** 23 | * The variant amino acid represented by its single letter code. 24 | */ 25 | public final char variantAminoAcid; 26 | 27 | /** 28 | * Constructor. 29 | * 30 | * @param originalAminoAcid the original amino acid 31 | * @param variantAminoAcid the variant amino acid 32 | */ 33 | public AminoAcidSubstitution(char originalAminoAcid, char variantAminoAcid) { 34 | this.originalAminoAcid = originalAminoAcid; 35 | this.variantAminoAcid = variantAminoAcid; 36 | } 37 | } 38 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/biology/variants/Variant.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.experiment.biology.variants; 2 | 3 | /** 4 | * Interface for a variant. 5 | * 6 | * @author Marc Vaudel 7 | */ 8 | public interface Variant { 9 | 10 | /** 11 | * Returns the description of the variant as string. 12 | * 13 | * @return the description of the variant as string 14 | */ 15 | public String getDescription(); 16 | } 17 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/biology/variants/amino_acids/Deletion.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.experiment.biology.variants.amino_acids; 2 | 3 | import com.compomics.util.experiment.biology.variants.Variant; 4 | 5 | /** 6 | * Class representing an amino acid deletion. 7 | * 8 | * @author Marc Vaudel 9 | */ 10 | public class Deletion implements Variant { 11 | 12 | /** 13 | * Empty default constructor 14 | */ 15 | public Deletion() { 16 | } 17 | 18 | /** 19 | * The single character code of the deleted amino acid. 20 | */ 21 | char aa; 22 | /** 23 | * Constructor. 24 | * 25 | * @param aa the single character code of the deleted amino acid 26 | */ 27 | public Deletion(char aa) { 28 | this.aa = aa; 29 | } 30 | 31 | @Override 32 | public String getDescription() { 33 | return "Deletion of " + aa; 34 | } 35 | 36 | public char getDeletedAminoAcid(){ 37 | return aa; 38 | } 39 | } 40 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/biology/variants/amino_acids/Insertion.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.experiment.biology.variants.amino_acids; 2 | 3 | import com.compomics.util.experiment.biology.variants.Variant; 4 | 5 | /** 6 | * Class representing an amino acid insertion. 7 | * 8 | * @author Marc Vaudel 9 | */ 10 | public class Insertion implements Variant { 11 | 12 | /** 13 | * Empty default constructor 14 | */ 15 | public Insertion() { 16 | } 17 | 18 | /** 19 | * The single character code of the inserted amino acid. 20 | */ 21 | char aa; 22 | /** 23 | * Constructor. 24 | * 25 | * @param aa the single character code of the inserted amino acid 26 | */ 27 | public Insertion(char aa) { 28 | this.aa = aa; 29 | } 30 | 31 | @Override 32 | public String getDescription() { 33 | return "Insertion of " + aa; 34 | } 35 | 36 | 37 | public char getInsertedAminoAcid(){ 38 | return aa; 39 | } 40 | } 41 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/biology/variants/amino_acids/Swap.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.experiment.biology.variants.amino_acids; 2 | 3 | import com.compomics.util.experiment.biology.variants.Variant; 4 | 5 | /** 6 | * Class representing an amino acid swap. 7 | * 8 | * @author Marc Vaudel 9 | */ 10 | public class Swap implements Variant { 11 | 12 | /** 13 | * Empty default constructor 14 | */ 15 | public Swap() { 16 | } 17 | 18 | /** 19 | * The single character code of the amino acid originally to the left. 20 | */ 21 | char leftAa; 22 | /** 23 | * The single character code of the amino acid originally to the right. 24 | */ 25 | char rightAa; 26 | /** 27 | * Constructor. 28 | * 29 | * @param leftAa the single character code of the amino acid originally to the left 30 | * @param rightAa the single character code of the amino acid originally to the right 31 | */ 32 | public Swap(char leftAa, char rightAa) { 33 | this.leftAa = leftAa; 34 | this.rightAa = rightAa; 35 | } 36 | 37 | @Override 38 | public String getDescription() { 39 | return "Swap of " + leftAa + " and " + rightAa; 40 | } 41 | 42 | } 43 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/biology/variants/amino_acids/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Type of implemented variants. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/biology/variants/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Experiment classes related to variants. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/filtering/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Filtering classes. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/IdentificationMatch.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.experiment.identification; 2 | 3 | import com.compomics.util.experiment.personalization.ExperimentObject; 4 | 5 | /** 6 | * This is an abstract class for an identification match. 7 | * 8 | * @author Marc Vaudel 9 | */ 10 | public abstract class IdentificationMatch extends ExperimentObject { 11 | 12 | /** 13 | * Empty default constructor 14 | */ 15 | public IdentificationMatch() { 16 | } 17 | 18 | /** 19 | * Serial number for backward compatibility. 20 | */ 21 | static final long serialVersionUID = -9132138792119651421L; 22 | 23 | /** 24 | * The type of match. 25 | */ 26 | public enum MatchType { 27 | 28 | Protein, 29 | Peptide, 30 | Spectrum, 31 | Ion, 32 | PTM 33 | } 34 | 35 | /** 36 | * Returns the type of match. 37 | * 38 | * @return the type of match 39 | */ 40 | public abstract MatchType getType(); 41 | 42 | /** 43 | * Returns the key of a match. 44 | * 45 | * @return the key of a match 46 | */ 47 | public abstract long getKey(); 48 | } 49 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/amino_acid_tags/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Amino Acid Tag classes. Tags are small sequences of amino acids. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/features/MutexMap.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.experiment.identification.features; 2 | 3 | import java.util.HashMap; 4 | import java.util.concurrent.Semaphore; 5 | 6 | /** 7 | * Mutex map for the features cache. Note that the current implementation supports a single cache only. 8 | * 9 | * @author Marc Vaudel 10 | */ 11 | public class MutexMap { 12 | 13 | /** 14 | * Empty default constructor 15 | */ 16 | public MutexMap() { 17 | } 18 | 19 | /** 20 | * Semaphore for the different object types. 21 | */ 22 | final static HashMap mutexMap = new HashMap(IdentificationFeaturesCache.ObjectType.values().length); 23 | 24 | 25 | 26 | } 27 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/features/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes for the generation of identification features. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/filtering/items/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Items used by the filters to filter on. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/filtering/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes for the filtering of identification objects. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/identification_parameters/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Parameters settings for the spectrum identification algorithms. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/matches/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Experiment classes related to matches. e.g., 4 | peptides, proteins, modifications and spectra. 5 | 6 | 7 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/matches_iterators/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Identification match iterators. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/modification/mapping/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Mapping between search engine and Utilities modifications. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/modification/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Modification mapping and localization. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/modification/peptide_mapping/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes used to map modifications to acceptor sites in peptides. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/modification/peptide_mapping/performance/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes used to benchmark the modification mapping. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/modification/scores/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | PTM scores. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/modification/search_engine_mapping/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Mapping between search engine and Utilities modifications. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Experiment classes related to identifications. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/peptide_fragmentation/models/UniformFragmentation.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.experiment.identification.peptide_fragmentation.models; 2 | 3 | /** 4 | * Dummy intensity predictor that returns 1.0 for every ion. 5 | * 6 | * @author Marc Vaudel 7 | */ 8 | public class UniformFragmentation { 9 | 10 | /** 11 | * Empty default constructor 12 | */ 13 | public UniformFragmentation() { 14 | } 15 | 16 | /** 17 | * Returns a default intensity of 1.0. 18 | * 19 | * @return a default intensity of 1.0 20 | */ 21 | public static Double getIntensity() { 22 | return 1.0; 23 | } 24 | } 25 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/peptide_fragmentation/models/ms2pip/features_configuration/MultipleAAPropertyFeature.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration; 2 | 3 | import com.compomics.util.experiment.biology.aminoacids.AminoAcid; 4 | 5 | /** 6 | * Interface for the ms2pip features having multiple amino acid properties. 7 | * 8 | * @author Marc Vaudel 9 | */ 10 | public interface MultipleAAPropertyFeature { 11 | 12 | /** 13 | * Returns the amino acid properties to consider. 14 | * 15 | * @return the amino acid properties to consider 16 | */ 17 | public AminoAcid.Property[] getAminoAcidProperties(); 18 | 19 | } 20 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/peptide_fragmentation/models/ms2pip/features_configuration/SingleAAPropertyFeature.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration; 2 | 3 | import com.compomics.util.experiment.biology.aminoacids.AminoAcid; 4 | 5 | /** 6 | * Interface for the ms2pip features having a single amino acid property. 7 | * 8 | * @author Marc Vaudel 9 | */ 10 | public interface SingleAAPropertyFeature { 11 | 12 | /** 13 | * Returns the amino acid property to consider. 14 | * 15 | * @return the amino acid property to consider 16 | */ 17 | public AminoAcid.Property getAminoAcidProperty(); 18 | 19 | /** 20 | * Sets the amino acid property to consider. 21 | * 22 | * @param aminoAcidProperty the amino acid property to consider 23 | */ 24 | public void setAminoAcidProperty(AminoAcid.Property aminoAcidProperty); 25 | } 26 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/peptide_fragmentation/models/ms2pip/features_configuration/features/ForwardIonFeature.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features; 2 | 3 | import com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.IonFeature; 4 | 5 | /** 6 | * Feature based on a property of the forward ion. 7 | * 8 | * @author Marc Vaudel 9 | */ 10 | public class ForwardIonFeature extends IonFeature { 11 | 12 | /** 13 | * Empty default constructor 14 | */ 15 | public ForwardIonFeature() { 16 | } 17 | 18 | /** 19 | * The index of this ms2pip feature. 20 | */ 21 | public static final int index = 2; 22 | /** 23 | * Constructor. 24 | * 25 | * @param property the peptide property 26 | */ 27 | public ForwardIonFeature(IonFeature.Property property) { 28 | this.property = property; 29 | } 30 | 31 | @Override 32 | public String getDescription() { 33 | return property.description; 34 | } 35 | 36 | @Override 37 | public int getIndex() { 38 | return index; 39 | } 40 | } 41 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/peptide_fragmentation/models/ms2pip/features_configuration/features/generic/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | This package contains generic features implemented for ms2pip. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/peptide_fragmentation/models/ms2pip/features_configuration/features/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | This package contains features implemented for ms2pip. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/peptide_fragmentation/models/ms2pip/features_configuration/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | This package contains the classes needed to configure the ms2pip features. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/peptide_fragmentation/models/ms2pip/features_generation/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | This package contains the classes needed to generate ms2pip features. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/peptide_fragmentation/models/ms2pip/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | This package contains classes for the use of ms2PIP. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/peptide_fragmentation/models/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Predictors for peptide fragment intensities. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/peptide_fragmentation/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Peptide fragment intensities. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/peptide_inference/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes related to peptide inference. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/peptide_shaker/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Experiment classes used in PeptideShaker calculations. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/protein_inference/fm_index/CacheElement.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.experiment.identification.protein_inference.fm_index; 2 | 3 | import com.compomics.util.experiment.personalization.ExperimentObject; 4 | import java.util.ArrayList; 5 | 6 | /** 7 | * The cache element. 8 | * 9 | * @author Dominik Kopczynski 10 | */ 11 | public class CacheElement extends ExperimentObject { 12 | 13 | Double massFirst; 14 | String sequence; 15 | Double massSecond; 16 | ArrayList cachedPrimary; 17 | 18 | /** 19 | * Constructor. 20 | * 21 | * @param massFirst the first mass 22 | * @param sequence the sequence 23 | * @param massSecond the second mass 24 | * @param cachedPrimary cached primary 25 | */ 26 | public CacheElement(Double massFirst, String sequence, Double massSecond, ArrayList cachedPrimary) { 27 | this.sequence = sequence; 28 | this.massFirst = massFirst; 29 | this.massSecond = massSecond; 30 | this.cachedPrimary = cachedPrimary; 31 | } 32 | } 33 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/protein_inference/fm_index/MassIndexMap.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.experiment.identification.protein_inference.fm_index; 2 | 3 | import com.compomics.util.experiment.personalization.ExperimentObject; 4 | 5 | /** 6 | * The mass index map. 7 | * 8 | * @author Dominik Kopczynski 9 | */ 10 | public class MassIndexMap extends ExperimentObject { 11 | 12 | public double mass; 13 | public int[] indexes; 14 | 15 | /** 16 | * Empty default constructor 17 | */ 18 | public MassIndexMap() { 19 | } 20 | 21 | public MassIndexMap(double mass, int[] indexes) { 22 | this.mass = mass; 23 | this.indexes = indexes; 24 | } 25 | } 26 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/protein_inference/fm_index/SNPElement.java: -------------------------------------------------------------------------------- 1 | /* 2 | * To change this license header, choose License Headers in Project Properties. 3 | * To change this template file, choose Tools | Templates 4 | * and open the template in the editor. 5 | */ 6 | package com.compomics.util.experiment.identification.protein_inference.fm_index; 7 | 8 | import com.compomics.util.experiment.personalization.ExperimentObject; 9 | 10 | /** 11 | * 12 | * @author dominik.kopczynski 13 | */ 14 | public class SNPElement extends ExperimentObject { 15 | public int position; 16 | public char sourceAA; 17 | public char targetAA; 18 | 19 | 20 | 21 | public SNPElement(int _position, char source, char target){ 22 | position = _position; 23 | sourceAA = source; 24 | targetAA = target; 25 | } 26 | } 27 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/protein_inference/fm_index/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Protein sequence database indexing classes based on Burrows-Wheeler transform. 4 | 5 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/protein_inference/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes related to protein inference. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/protein_sequences/digestion/SequenceIterator.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.experiment.identification.protein_sequences.digestion; 2 | 3 | /** 4 | * Interface for an iterator returning peptides along a protein sequence. 5 | * 6 | * @author Marc Vaudel 7 | */ 8 | public interface SequenceIterator { 9 | 10 | /** 11 | * Returns the next peptide that can be generated from the iterator. Null if none left. 12 | * 13 | * @return the next peptide that can be generated from the iterator 14 | * 15 | * @throws java.lang.InterruptedException exception thrown if a thread is 16 | * interrupted 17 | */ 18 | public ExtendedPeptide getNextPeptide() throws InterruptedException; 19 | } 20 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/protein_sequences/digestion/iterators/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | This package contains implementations of the SequenceIterator interface. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/protein_sequences/digestion/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | This package contains classes used to digest protein sequences into peptides. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/protein_sequences/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Protein sequence handling related classes. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/psm_scoring/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Main PSM scoring class. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/psm_scoring/psm_scores/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Main PTM scoring classes. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/spectrum_annotation/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes used for ms2 spectrum annotation. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/spectrum_annotation/simple_annotators/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | This package contains implementations of the SimpleAnnotator allowing the annotation of specific sets of ions. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/spectrum_annotation/spectrum_annotators/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | This package contains implementations of the SpectrumAnnotator allowing the annotation of all ions. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/spectrum_assumptions/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Implementations of the SpectrumIdentificationAssumption. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/utils/TagUtils.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.experiment.identification.utils; 2 | 3 | /** 4 | * This class groups functions that can be used to work with peptides. 5 | * 6 | * @author Marc Vaudel 7 | */ 8 | public class TagUtils { 9 | 10 | /** 11 | * Empty default constructor 12 | */ 13 | public TagUtils() { 14 | } 15 | } 16 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/utils/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | This package contains utilities classes to handle identification objects. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/validation/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Experiment classes related to identification matches validation. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/validation/percolator/PercolatorFeature.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.experiment.identification.validation.percolator; 2 | 3 | /** 4 | * Enum for the features of Percolator kept in cache. 5 | * 6 | * @author Marc Vaudel 7 | */ 8 | public enum PercolatorFeature { 9 | 10 | measuredAndDeltaMz, intensityCoverage, enzymaticity; 11 | 12 | } 13 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/identification/validation/percolator/PercolatorFeaturesCache.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.experiment.identification.validation.percolator; 2 | 3 | import com.compomics.util.experiment.personalization.UrParameter; 4 | import java.io.ObjectStreamClass; 5 | import java.io.Serializable; 6 | import java.util.EnumMap; 7 | 8 | /** 9 | * This class serves as a cache for Percolator features. 10 | * 11 | * @author Marc Vaudel 12 | */ 13 | public class PercolatorFeaturesCache implements UrParameter, Serializable { 14 | 15 | /** 16 | * Dummy object for instantiation purposes. 17 | */ 18 | public final static PercolatorFeaturesCache dummy = new PercolatorFeaturesCache(); 19 | 20 | /** 21 | * Map of the Percolator values. 22 | */ 23 | public final EnumMap cache = new EnumMap<>(PercolatorFeature.class); 24 | 25 | @Override 26 | public long getParameterKey() { 27 | 28 | return ObjectStreamClass.lookup(PercolatorFeaturesCache.class).getSerialVersionUID(); 29 | 30 | } 31 | 32 | } 33 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/io/biology/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Experiment IO classes for sequences. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/io/biology/protein/ProteinIterator.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.experiment.io.biology.protein; 2 | 3 | import com.compomics.util.experiment.biology.proteins.Protein; 4 | 5 | /** 6 | * Interface for a protein iterator. 7 | * 8 | * 9 | * @author Marc Vaudel 10 | */ 11 | public interface ProteinIterator { 12 | 13 | /** 14 | * Returns the next protein. Null if end was reached. If an error is encountered while iterating, the exception is thrown as runtime exception. 15 | * 16 | * @return the next protein 17 | */ 18 | public Protein getNextProtein(); 19 | 20 | } 21 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/io/biology/protein/converters/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Fasta file converters. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/io/biology/protein/iterators/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Fasta file iterators. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/io/biology/protein/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Experiment IO classes for biological resources. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/io/identification/idfilereaders/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Experiment classes related to reading search engine files. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/io/identification/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Experiment identification classes. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/io/identification/writers/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Writer for identification results. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/io/mass_spectrometry/apl/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes for the handling of Andromeda peak list (apl) files. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/io/mass_spectrometry/cms/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes for the handling of Compomics mass spectrometry (cms) files. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/io/mass_spectrometry/mgf/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes for the handling of mgf files. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/io/mass_spectrometry/ms2/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes for the handling of ms2 files. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/io/mass_spectrometry/mzml/MzmlFileUtils.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.experiment.io.mass_spectrometry.mzml; 2 | 3 | /** 4 | * Utilities for the handling of mzml files. 5 | * 6 | * @author Harald Barsnes 7 | */ 8 | public class MzmlFileUtils { 9 | 10 | /** 11 | * The file extension for mzml files. 12 | */ 13 | public static final String[] EXTENSIONS = new String[]{".mzml", ".mzml.gz"}; 14 | 15 | } 16 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/io/mass_spectrometry/mzml/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes for the handling of mzml files. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/io/mass_spectrometry/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes for the handling of mass spectrometry files. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/io/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Experiment IO classes. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/io/parameters/DummyParameters.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.experiment.io.parameters; 2 | 3 | 4 | /** 5 | * Dummy parameters used to retrieve the parameters type and version. 6 | * 7 | * @author Marc Vaudel 8 | */ 9 | public class DummyParameters implements MarshallableParameter { 10 | 11 | /** 12 | * Empty default constructor 13 | */ 14 | public DummyParameters() { 15 | } 16 | 17 | /** 18 | * Name of the type of marshalled parameter. 19 | */ 20 | private final String marshallableParameterType = null; 21 | 22 | /** 23 | * Version number. 24 | */ 25 | public final String version = null; 26 | 27 | 28 | @Override 29 | public MarshallableParameter.Type getType() { 30 | if (marshallableParameterType == null) { 31 | return null; 32 | } 33 | return MarshallableParameter.Type.valueOf(marshallableParameterType); 34 | } 35 | 36 | @Override 37 | public void setType() { 38 | throw new UnsupportedOperationException("Read only."); 39 | } 40 | } 41 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/io/parameters/MarshallableParameter.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.experiment.io.parameters; 2 | 3 | /** 4 | * Interface for a parameter which can be marshalled as .par file. 5 | * 6 | * @author Marc Vaudel 7 | */ 8 | public interface MarshallableParameter { 9 | 10 | /** 11 | * Enum of the type of parameter which can be encountered in a .par file. 12 | */ 13 | public static enum Type { 14 | search_parameters, identification_parameters; 15 | } 16 | 17 | /** 18 | * Sets the parameters type. The type must be set before writing a file but not in the constructor. 19 | */ 20 | public void setType(); 21 | 22 | /** 23 | * Returns the type of marshalled parameter from an unmarshalled object. The type must be written in the file but not set in the constructor. Null if not a MarshallableParameter. 24 | * 25 | * @return the type of marshalled parameter from an unmarshalled object 26 | */ 27 | public Type getType(); 28 | 29 | 30 | } 31 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/io/parameters/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Experiment IO classes relative to the handling of parameters. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/io/temp/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Experiment IO classes relative to the handling of temporary files. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/mass_spectrometry/FragmentationMethod.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.experiment.mass_spectrometry; 2 | 3 | 4 | /** 5 | * Enum for the different fragmentation methods. 6 | * 7 | * @author Marc Vaudel 8 | */ 9 | public enum FragmentationMethod { 10 | 11 | CID("CID"), HCD("HCD"), ETD("ETD"); 12 | 13 | /** 14 | * The name of the fragmentation method. 15 | */ 16 | public final String name; 17 | 18 | /** 19 | * Constructor. 20 | * 21 | * @param name the name of the fragmentation method 22 | */ 23 | private FragmentationMethod(String name) { 24 | this.name = name; 25 | } 26 | 27 | /** 28 | * Empty default constructor 29 | */ 30 | private FragmentationMethod() { 31 | name = ""; 32 | } 33 | } 34 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/mass_spectrometry/indexes/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes related to the indexing of spectra. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/mass_spectrometry/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Experiment classes related to mass spectrometry. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/mass_spectrometry/proteowizard/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Package containing the classes used to interact with ProteoWizard. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/mass_spectrometry/spectra/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Experiment classes related to spectra. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/mass_spectrometry/thermo_raw_file_parser/gui/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Package containing the GUI classes used to interact with ThermoRawFileParser. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/mass_spectrometry/thermo_raw_file_parser/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Package containing the classes used to interact with ThermoRawFileParser. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/mass_spectrometry/utils/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Utility classes for mass spectrometry. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/normalization/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes related to quantification values normalization. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Gene factory classes. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/patient/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Experiment classes related to patent information. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/personalization/UrParameter.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.experiment.personalization; 2 | 3 | /** 4 | * This interface is used to reference refinement parameters. 5 | * 6 | * @author Marc Vaudel 7 | */ 8 | public interface UrParameter { 9 | 10 | /** 11 | * This method returns the key of the parameter. The key must be unique to 12 | * the type of parameter. 13 | * 14 | * @return the parameter key 15 | */ 16 | public long getParameterKey(); 17 | } -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/personalization/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Experiment customization classes. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/quantification/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Experiment classes related to quantification. 4 | The quantification methods implemented are: 5 | - MS2 reporter ion based quantification (for instance iTRAQ and TMT) 6 | - Spectrum counting (emPAI and NSAF, in PeptideShaker) 7 | 8 | TODO: 9 | - MS1 labeling strategies (like SILAC, 18O, ICAT, AQUA, ICPL) 10 | - MS1 label free quantification 11 | - TIC 12 | 13 | 14 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/quantification/reporterion/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Experiment classes related to reporter ions. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/quantification/spectrumcounting/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Experiment classes related to spectrum counting. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/refinement_parameters/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Experiment classes related to specific parametrization of experiment objects. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/units/Units.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.experiment.units; 2 | 3 | /** 4 | * Convenience class providing units. 5 | * 6 | * @author Marc Vaudel 7 | */ 8 | public class Units { 9 | 10 | /** 11 | * Empty default constructor 12 | */ 13 | public Units() { 14 | } 15 | 16 | /** 17 | * Femtomol. 18 | */ 19 | public final static UnitOfMeasurement fmol = new UnitOfMeasurement(StandardUnit.mol, MetricsPrefix.femto); 20 | 21 | /** 22 | * ppm. 23 | */ 24 | public final static UnitOfMeasurement ppm = new UnitOfMeasurement(StandardUnit.ppm); 25 | 26 | /** 27 | * percent. 28 | */ 29 | public final static UnitOfMeasurement percent = new UnitOfMeasurement(StandardUnit.percentage); 30 | 31 | } 32 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/experiment/units/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Unit related classes. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/general/BoxedObject.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.general; 2 | 3 | import com.compomics.util.experiment.personalization.ExperimentObject; 4 | 5 | /** 6 | * Convenience class allowing the boxing of an object. 7 | * 8 | * @author Marc Vaudel 9 | * 10 | * @param the type of object to box 11 | */ 12 | public class BoxedObject extends ExperimentObject { 13 | 14 | /** 15 | * The object to box. 16 | */ 17 | private K object; 18 | 19 | /** 20 | * Constructor. 21 | */ 22 | public BoxedObject() { 23 | 24 | } 25 | /** 26 | * Constructor. 27 | * 28 | * @param initialValue the initial value 29 | */ 30 | public BoxedObject(K initialValue) { 31 | object = initialValue; 32 | } 33 | 34 | /** 35 | * Returns the boxed object. 36 | * 37 | * @return the boxed object 38 | */ 39 | public K getObject() { 40 | 41 | return object; 42 | } 43 | 44 | /** 45 | * Sets the boxed object. 46 | * 47 | * @param object the boxed object 48 | */ 49 | public void setObject(K object) { 50 | 51 | this.object = object; 52 | } 53 | } 54 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/general/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | General, top-level tasks that are used throughout the other packages in the util section. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/general/servlet/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Servlet representation of the 4 | classes from the general utilities package (com.compomics.util.general) 5 |
6 | @see com.compomics.util.general 7 | 8 | 9 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/gui/CheckableItem.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.gui; 2 | 3 | /** 4 | * Objects used in CheckBoxCellRenderer. 5 | * 6 | * @author Harald Barsnes 7 | */ 8 | public class CheckableItem { 9 | 10 | /** 11 | * The text to display. 12 | */ 13 | public final String text; 14 | /** 15 | * Whether the item is selected or not. 16 | */ 17 | public boolean selected; 18 | 19 | /** 20 | * Create a new CheckableItem. 21 | * 22 | * @param text the text to display 23 | * @param selected whether the item is selected or not 24 | */ 25 | public CheckableItem(String text, boolean selected) { 26 | this.text = text; 27 | this.selected = selected; 28 | } 29 | 30 | @Override 31 | public String toString() { 32 | return text; 33 | } 34 | 35 | } 36 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/gui/TableScrollBarListener.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.gui; 2 | 3 | import com.compomics.util.gui.tablemodels.SelfUpdatingTableModel; 4 | import java.awt.event.AdjustmentEvent; 5 | import java.awt.event.AdjustmentListener; 6 | import javax.swing.JTable; 7 | 8 | /** 9 | * AdjustmentListener for SelfUpdatingTableModels supporting scrolling in a more 10 | * efficient way. 11 | * 12 | * @author Harald Barsnes 13 | */ 14 | public class TableScrollBarListener implements AdjustmentListener { 15 | 16 | /** 17 | * The table to be monitored. Must have a SelfUpdatingTableModel as the 18 | * table model. 19 | */ 20 | private final JTable table; 21 | 22 | /** 23 | * Constructor. 24 | * 25 | * @param table the table 26 | */ 27 | public TableScrollBarListener(JTable table) { 28 | this.table = table; 29 | } 30 | 31 | public void adjustmentValueChanged(AdjustmentEvent evt) { 32 | ((SelfUpdatingTableModel) table.getModel()).setIsScrolling(evt.getValueIsAdjusting()); 33 | table.revalidate(); 34 | table.repaint(); 35 | } 36 | } 37 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/gui/atoms/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Atoms GUI dialogs. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/gui/enzymes/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Dialogs for enzymes. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/gui/error_handlers/notification/NotificationDialogParent.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.gui.error_handlers.notification; 2 | 3 | /** 4 | * A NotificationDialog parent interface. 5 | * 6 | * @author Harald Barsnes 7 | */ 8 | public interface NotificationDialogParent { 9 | 10 | public void notificationClicked(String notificationType); 11 | } 12 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/gui/error_handlers/notification/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Notification dialogs. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/gui/error_handlers/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Help handlers. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/gui/events/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | GUI event classes. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/gui/export/graphics/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Exporting of graphics. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/gui/export/report/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Report editor GUI. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/gui/file_handling/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | GUI related file filters. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/gui/filtering/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | GUI filters. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/gui/genes/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Dialogs for the handling of genes. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/gui/interfaces/SpectrumPanelListener.java: -------------------------------------------------------------------------------- 1 | /** 2 | * Created by IntelliJ IDEA. 3 | * User: Lennart 4 | * Date: 18-feb-2005 5 | * Time: 7:23:04 6 | */ 7 | package com.compomics.util.gui.interfaces; 8 | 9 | import com.compomics.util.gui.events.RescalingEvent; 10 | 11 | /* 12 | * CVS information: 13 | * 14 | * $Revision: 1.1 $ 15 | * $Date: 2007/10/22 10:09:02 $ 16 | */ 17 | 18 | /** 19 | * This interface describes the behaviour for a listener that wants to receive information 20 | * about events that occurred on a SpectrumPanel. 21 | * 22 | * @author Lennart Martens 23 | * @version $Id: SpectrumPanelListener.java,v 1.1 2007/10/22 10:09:02 lennart Exp $ 24 | */ 25 | public interface SpectrumPanelListener { 26 | 27 | /** 28 | * This method will be called whenever the SpectrumPanel is rescaled. 29 | * 30 | * @param aSe ResizinEvent with the details of the rescaling. 31 | */ 32 | public void rescaled(RescalingEvent aSe); 33 | } 34 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/gui/interfaces/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | GUI related interfaces. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/gui/isotopic_calculator/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | GUI class for the Isotopic Distribution calculator. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/gui/modification/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | PTM GUI dialogs. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/gui/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Basic GUI classes. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/gui/parameters/identification/AlgorithmParametersDialog.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.gui.parameters.identification; 2 | 3 | /** 4 | * Interface for an algorithm settings dialog. 5 | * 6 | * @author Marc Vaudel 7 | */ 8 | public interface AlgorithmParametersDialog { 9 | 10 | /** 11 | * Indicates whether the user canceled the editing. 12 | * 13 | * @return true if cancel was pressed 14 | */ 15 | public boolean isCancelled(); 16 | 17 | /** 18 | * Returns the parameters as set by the user. 19 | * 20 | * @return the parameters as set by the user 21 | */ 22 | public IdentificationAlgorithmParameter getParameters(); 23 | 24 | } 25 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/gui/parameters/identification/IdentificationAlgorithmParameter.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.gui.parameters.identification; 2 | 3 | import com.compomics.util.experiment.identification.Advocate; 4 | 5 | /** 6 | * Interface for the algorithm specific parameters. 7 | * 8 | * @author Marc Vaudel 9 | */ 10 | public interface IdentificationAlgorithmParameter { 11 | 12 | /** 13 | * Returns the identification algorithm. 14 | * 15 | * @return the identification algorithm 16 | */ 17 | public Advocate getAlgorithm(); 18 | 19 | /** 20 | * Indicates whether another identificationAlgorithmParameter has the same 21 | * parameters. 22 | * 23 | * @param identificationAlgorithmParameter the other 24 | * identificationAlgorithmParameter 25 | * 26 | * @return true if the algorithm and parameters are the same 27 | */ 28 | public boolean equals(IdentificationAlgorithmParameter identificationAlgorithmParameter); 29 | 30 | /** 31 | * Returns the parameters as a string. 32 | * 33 | * @param html use HTML formatting 34 | * @return the parameters as a string 35 | */ 36 | public String toString(boolean html); 37 | } 38 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/gui/parameters/identification/advanced/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Dialogs for advanced identification parameters. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/gui/parameters/identification/algorithm/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Search algorithm settings dialogs. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/gui/parameters/identification/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | GUI classes for parameters, settings and preferences used for identification. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/gui/parameters/identification/pride/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Dialogs for pride reprocessing parameters. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/gui/parameters/identification/search/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Dialogs for search parameters. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/gui/parameters/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | GUI classes for parameters, settings and preferences. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/gui/parameters/proteowizard/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Package containing the GUI classes used to interact with ProteoWizard. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/gui/parameters/tools/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | GUI classes for parameters, settings and preferences used in tools. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/gui/protein/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | GUI class related to protein sequence formatting. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/gui/renderers/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | GUI renderer classes. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/gui/spectrum/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Spectrum and Chromatogram visualization GUI classes. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/gui/tablemodels/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Self updating table model classes. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/gui/utils/EmptyCollections.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.gui.utils; 2 | 3 | import java.util.HashSet; 4 | import java.util.TreeSet; 5 | 6 | /** 7 | * This class contains empty collections that can be used for empty results without creating new objects. 8 | * 9 | * @author Marc Vaudel 10 | */ 11 | public class EmptyCollections { 12 | 13 | /** 14 | * Empty default constructor 15 | */ 16 | public EmptyCollections() { 17 | } 18 | 19 | /** 20 | * Convenience result of an empty set. 21 | */ 22 | public static final HashSet emptyStringSet = new HashSet<>(0); 23 | /** 24 | * Convenience result of an empty set. 25 | */ 26 | public static final TreeSet emptyStringTreeSet = new TreeSet<>(); 27 | /** 28 | * Convenience result of an empty set. 29 | */ 30 | public static final HashSet emptyIntSet = new HashSet<>(0); 31 | /** 32 | * Convenience result of an empty set. 33 | */ 34 | public static final TreeSet emptyIntTreeSet = new TreeSet<>(); 35 | 36 | } 37 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/gui/utils/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | GUI utilities classes. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/gui/utils/user_choice/list_choosers/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Implementations of the ListChooser. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/gui/utils/user_choice/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | GUI utils allowing the user to choose something. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/gui/variants/aa_substitutions/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | GUI classes relative to amino acid substitution. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/gui/variants/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | GUI classes relative to variants. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/gui/waiting/waitinghandlers/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Waiting handler classes. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/interfaces/Connectable.java: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright (C) Lennart Martens 3 | * 4 | * Contact: lennart.martens AT UGent.be (' AT ' to be replaced with '@') 5 | */ 6 | 7 | /** 8 | * Created by IntelliJ IDEA. 9 | * User: Lennart 10 | * Date: 18-jun-2003 11 | * Time: 13:56:17 12 | */ 13 | package com.compomics.util.interfaces; 14 | 15 | import java.sql.Connection; 16 | 17 | /* 18 | * CVS information: 19 | * 20 | * $Revision: 1.3 $ 21 | * $Date: 2007/07/06 09:41:53 $ 22 | */ 23 | 24 | /** 25 | * This interface describes the behaviour for classes that can accept an 26 | * incoming DB connection. 27 | * 28 | * @author Lennart Martens 29 | */ 30 | public interface Connectable { 31 | 32 | /** 33 | * This method will be called by the class actually making the connection. 34 | * It will pass the connection and an identifier String for that connection 35 | * (typically the name of the database connected to). 36 | * 37 | * @param aConn Connection with the DB connection. 38 | * @param aDBName String with an identifier for the connection, typically the 39 | * name of the DB connected to. 40 | */ 41 | public void passConnection(Connection aConn, String aDBName); 42 | } 43 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/interfaces/Monitorable.java: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright (C) Lennart Martens 3 | * 4 | * Contact: lennart.martens AT UGent.be (' AT ' to be replaced with '@') 5 | */ 6 | 7 | /* 8 | * Created by IntelliJ IDEA. 9 | * User: Lennart 10 | * Date: 16-okt-02 11 | * Time: 13:38:49 12 | */ 13 | package com.compomics.util.interfaces; 14 | 15 | /* 16 | * CVS information: 17 | * 18 | * $Revision: 1.3 $ 19 | * $Date: 2007/07/06 09:41:53 $ 20 | */ 21 | 22 | /** 23 | * This interface describes the behaviour for any Object whose progressing state 24 | * can be monitored. 25 | * 26 | * @author Lennart Martens 27 | */ 28 | public interface Monitorable { 29 | 30 | /** 31 | * This method reports on the total amount steps the task can take before 32 | * completion. 33 | * 34 | * @return int with the total bytes that can be read from the InputStream. 35 | */ 36 | public abstract int getMaximum(); 37 | 38 | /** 39 | * This method returns the progress of the task. 40 | * 41 | * @return int with the progress. 42 | */ 43 | public abstract int monitorProgress(); 44 | } 45 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/interfaces/PickUp.java: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright (C) Lennart Martens 3 | * 4 | * Contact: lennart.martens AT UGent.be (' AT ' to be replaced with '@') 5 | */ 6 | 7 | /* 8 | * Created by IntelliJ IDEA. 9 | * User: Lennart 10 | * Date: 11-feb-03 11 | * Time: 18:19:45 12 | */ 13 | package com.compomics.util.interfaces; 14 | 15 | /* 16 | * CVS information: 17 | * 18 | * $Revision: 1.3 $ 19 | * $Date: 2007/07/06 09:41:53 $ 20 | */ 21 | 22 | /** 23 | * This interface describes the behaviour for a class that can pick up results. 24 | * 25 | * @author Lennart Martens 26 | */ 27 | public interface PickUp { 28 | 29 | /** 30 | * This method should be called by the notifier when appropriate. 31 | * 32 | * @param aObject Object with the data that should be sent. 33 | */ 34 | public void sendIncoming(Object aObject); 35 | } 36 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/interfaces/TableValueWrapper.java: -------------------------------------------------------------------------------- 1 | /** 2 | * Created by IntelliJ IDEA. 3 | * User: Lennart 4 | * Date: 31-jan-2005 5 | * Time: 17:53:30 6 | */ 7 | package com.compomics.util.interfaces; 8 | 9 | /* 10 | * CVS information: 11 | * 12 | * $Revision: 1.1 $ 13 | * $Date: 2005/02/02 10:40:14 $ 14 | */ 15 | 16 | /** 17 | * This interface describes the behaviour for a class that wraps a table element. 18 | * 19 | * @author Lennart Martens 20 | * @version $Id: TableValueWrapper.java,v 1.1 2005/02/02 10:40:14 lennart Exp $ 21 | */ 22 | public interface TableValueWrapper { 23 | 24 | /** 25 | * This method returns the Object that this instance wraps around. 26 | * 27 | * @return Object with the original instance to be put on the table. 28 | */ 29 | public abstract Object getValue(); 30 | } 31 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/interfaces/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Interfaces for the more specific implementations in the util package. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/io/compression/SectionGzWriter/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Package for writing gzfiles with multiple sections. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/io/compression/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes related to file compression. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/io/export/features/ReporterExportFeature.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.io.export.features; 2 | 3 | import com.compomics.util.io.export.ExportFeature; 4 | 5 | /** 6 | * Reporter extension of the utilities export features. 7 | * 8 | * @author Marc Vaudel 9 | * @author Harald Barsnes 10 | */ 11 | public interface ReporterExportFeature extends ExportFeature { 12 | 13 | /** 14 | * Indicates whether the feature is channel dependent. 15 | * 16 | * @return a boolean indicating whether the feature is channel dependent 17 | */ 18 | public boolean hasChannels(); 19 | } 20 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/io/export/features/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes related to exporting Reporter features. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/io/export/features/peptideshaker/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Package containing classes listing the possible export features for PeptideShaker. 4 | 5 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/io/export/features/reporter/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Package containing classes listing the possible export features for Reporter. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/io/export/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes related to exporting reports. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/io/export/styles/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Export styles. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/io/export/writers/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Export writer. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/io/export/xml/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Convenience classes for xml exports. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/io/file/filefilters/SequestParamsFileFilter.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.io.file.filefilters; 2 | 3 | import java.io.File; 4 | import javax.swing.filechooser.*; 5 | 6 | /** 7 | * File filter for sequest.params files. 8 | * 9 | * @author Harald Barsnes 10 | */ 11 | public class SequestParamsFileFilter extends FileFilter { 12 | 13 | /** 14 | * Empty default constructor 15 | */ 16 | public SequestParamsFileFilter() { 17 | } 18 | 19 | /** 20 | * Accept all directories, sequest.params files. 21 | * 22 | * @param f the file 23 | * @return true if the file passes the filter 24 | */ 25 | public boolean accept(File f) { 26 | if (f.isDirectory()) { 27 | return true; 28 | } 29 | 30 | return f.getName().toLowerCase().equalsIgnoreCase("sequest.params"); 31 | } 32 | 33 | /** 34 | * The description of the filter. 35 | * 36 | * @return String the description of the filter 37 | */ 38 | public java.lang.String getDescription() { 39 | return "sequest.params"; 40 | } 41 | } 42 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/io/file/filefilters/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes related to file filters. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/io/file/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes related to the handling of files. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/io/flat/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Export of flat files. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/io/ftp/FtpLoginException.java: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright (C) Lennart Martens 3 | * 4 | * Contact: lennart.martens AT UGent.be (' AT ' to be replaced with '@') 5 | */ 6 | 7 | /* 8 | * Created by IntelliJ IDEA. 9 | * User: Lennart 10 | * Date: 29-nov-02 11 | * Time: 13:53:50 12 | */ 13 | package com.compomics.util.io.ftp; 14 | import org.apache.logging.log4j.Logger; 15 | import org.apache.logging.log4j.LogManager; 16 | 17 | /* 18 | * CVS information: 19 | * 20 | * $Revision: 1.3 $ 21 | * $Date: 2007/07/06 09:41:53 $ 22 | */ 23 | 24 | /** 25 | * This class handles an FTP login exception. 26 | * 27 | * @author Lennart 28 | */ 29 | public class FtpLoginException extends FtpProtocolException { 30 | 31 | /** 32 | * Empty default constructor 33 | */ 34 | public FtpLoginException() { 35 | } 36 | 37 | // Class specific log4j logger for FtpLoginException instances. 38 | Logger logger = LogManager.getLogger(FtpLoginException.class); 39 | 40 | /** 41 | * Creates a new FtpLoginException from the given string. 42 | * 43 | * @param s the FTP login exception as a string 44 | */ 45 | FtpLoginException(String s) { 46 | super(s); 47 | } 48 | } 49 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/io/ftp/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes related to the handling of FTP. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/io/json/adapter/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | JSON adapter classes. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/io/json/marshallers/IdentificationParametersMarshaller.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.io.json.marshallers; 2 | 3 | import com.compomics.util.experiment.biology.atoms.Atom; 4 | import com.compomics.util.experiment.filtering.Filter; 5 | import com.compomics.util.gui.parameters.identification.IdentificationAlgorithmParameter; 6 | import com.compomics.util.io.json.JsonMarshaller; 7 | 8 | /** 9 | * This class is a convenience class to have a DefaultJsonConverter with the 10 | * identification parameters interfaces. 11 | * 12 | * @author Kenneth Verheggen 13 | * @author Marc Vaudel 14 | */ 15 | public class IdentificationParametersMarshaller extends JsonMarshaller { 16 | 17 | /** 18 | * Constructor. 19 | */ 20 | public IdentificationParametersMarshaller() { 21 | super(IdentificationAlgorithmParameter.class, Atom.class, Filter.class); 22 | } 23 | } 24 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/io/json/marshallers/PTMFactoryMarshaller.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.io.json.marshallers; 2 | 3 | import com.compomics.util.experiment.biology.atoms.Atom; 4 | import com.compomics.util.io.json.JsonMarshaller; 5 | 6 | /** 7 | * This class is a convenience class to have a DefaultJsonConverter with the 8 | * search parameter interfaces. 9 | * 10 | * @author Kenneth Verheggen 11 | */ 12 | public class PTMFactoryMarshaller extends JsonMarshaller { 13 | 14 | /** 15 | * Constructor. 16 | */ 17 | public PTMFactoryMarshaller() { 18 | super(Atom.class); 19 | } 20 | } 21 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/io/json/marshallers/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | JSON marshaller classes. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/io/json/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes related to the handling of json files. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/io/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes related to input/output. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/junit/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Custom classpath related test class. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/math/clustering/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Basic clustering functions. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/math/clustering/settings/KMeansClusteringSettings.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.math.clustering.settings; 2 | 3 | 4 | /** 5 | * Settings for k-means clustering. 6 | * 7 | * @author Marc Vaudel 8 | */ 9 | public class KMeansClusteringSettings { 10 | 11 | /** 12 | * The number of clusters to use. 13 | */ 14 | private int nClusters = 18; 15 | 16 | /** 17 | * Constructor. 18 | */ 19 | public KMeansClusteringSettings() { 20 | 21 | } 22 | 23 | /** 24 | * Returns the number of clusters to use. 25 | * 26 | * @return the number of clusters to use 27 | */ 28 | public int getnClusters() { 29 | return nClusters; 30 | } 31 | 32 | /** 33 | * Sets the number of clusters to use. 34 | * 35 | * @param nClusters the number of clusters to use 36 | */ 37 | public void setnClusters(int nClusters) { 38 | this.nClusters = nClusters; 39 | } 40 | } 41 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/math/clustering/settings/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Settings for the clustering. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/math/matrix/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Double matrix classes. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/math/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Basic match functions. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/math/roc/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | ROC curve calculation. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/math/statistics/distributions/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Math classes related to distributions. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/math/statistics/linear_regression/filters/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Implementation of algorithms performing linear regression. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/math/statistics/linear_regression/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes to perform linear regressions. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/math/statistics/linear_regression/regressions/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Filters to apply prior to a linear regression. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/math/statistics/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Math classes related to statistics. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/memory/MemoryConsumptionStatus.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.memory; 2 | 3 | /** 4 | * This class provides information on the memory consumption status. 5 | * 6 | * @author Marc Vaudel 7 | */ 8 | public class MemoryConsumptionStatus { 9 | 10 | /** 11 | * Empty default constructor 12 | */ 13 | public MemoryConsumptionStatus() { 14 | } 15 | 16 | /** 17 | * Indicates whether a GB of memory is free. 18 | * 19 | * @return a boolean indicating whether a GB of memory is free 20 | */ 21 | public static boolean halfGbFree() { 22 | return Runtime.getRuntime().maxMemory() - (Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory()) > 536870912; 23 | } 24 | 25 | /** 26 | * Returns the share of memory being used. 27 | * 28 | * @return the share of memory being used 29 | */ 30 | public static double memoryUsed() { 31 | long memoryUsed = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory(); 32 | float memoryAvailable = Runtime.getRuntime().maxMemory(); 33 | double ratio = (double) (memoryUsed / memoryAvailable); 34 | return ratio; 35 | } 36 | } 37 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/memory/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Memory management. 4 | 5 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/messages/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes related to sending messages to the user. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/nucleotide/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Useful objects for modeling and handling nucleotides. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | General utilities classes. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/parameters/identification/advanced/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Advanced Identification parameters. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/parameters/identification/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Identification parameters. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/parameters/identification/search/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Identification parameters relative to the search. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/parameters/identification/tool_specific/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Parameters settings for the search algorithms. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/parameters/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Utilities parameters. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/parameters/peptide_shaker/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | PeptideShaker parameters. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/parameters/quantification/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Quantification parameters. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/parameters/quantification/spectrum_counting/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Spectrum counting parameters. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/parameters/searchgui/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | SearchGUI parameters. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/parameters/tools/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Tool parameters. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/pdbfinder/das/readers/StartEndPosition.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.pdbfinder.das.readers; 2 | 3 | /** 4 | * StartEndPosition. 5 | * 6 | * @author Niklaas Colaert 7 | */ 8 | public class StartEndPosition { 9 | 10 | /** 11 | * Empty default constructor 12 | */ 13 | public StartEndPosition() { 14 | iStart = 0; 15 | iEnd = 0; 16 | } 17 | 18 | /** 19 | * The start. 20 | */ 21 | private final int iStart; 22 | /** 23 | * The end. 24 | */ 25 | private final int iEnd; 26 | 27 | /** 28 | * Constructor. 29 | * 30 | * @param aStart the start position 31 | * @param aEnd the end position 32 | */ 33 | public StartEndPosition(int aStart, int aEnd) { 34 | this.iStart = aStart; 35 | this.iEnd = aEnd; 36 | } 37 | 38 | /** 39 | * Returns the start position. 40 | * 41 | * @return the start position 42 | */ 43 | public int getStartPosition() { 44 | return this.iStart; 45 | } 46 | 47 | /** 48 | * Returns the end position. 49 | * 50 | * @return the end position 51 | */ 52 | public int getEndPosition() { 53 | return this.iEnd; 54 | } 55 | } 56 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/pdbfinder/das/readers/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes for aligning and annotating PDB files when mapped to UniProt accession numbers. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/pdbfinder/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes for mapping between UniProt accession numbers and PDB structures. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/pdbfinder/pdb/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes for parsing PDB files. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/pride/PrideObject.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.pride; 2 | 3 | /** 4 | * Interface for a PRIDE object. 5 | * 6 | * @author Marc Vaudel 7 | */ 8 | public interface PrideObject { 9 | 10 | /** 11 | * Returns the name to use when serializing the object. 12 | * 13 | * @return the name to use when serializing the object 14 | */ 15 | public String getFileName(); 16 | } 17 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/pride/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Objects related to mapping to PRIDE. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/pride/prideobjects/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Objects related to mapping experiment annotation to PRIDE. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/pride/prideobjects/webservice/file/FileType.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.pride.prideobjects.webservice.file; 2 | 3 | /** 4 | * An enum of the possible file types for the PRIDE file type options. 5 | * 6 | * @author Kenneth Verheggen 7 | */ 8 | public enum FileType { 9 | RESULT, PEAK, SEARCH, RAW, QUANT, GEL, FASTA, SPECTRUM_LIBRARY, MS_IMAGE_DATA, OPTICAL_IMAGE, OTHER; 10 | 11 | /** 12 | * Empty default constructor 13 | */ 14 | private FileType() { 15 | } 16 | } 17 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/pride/prideobjects/webservice/file/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes for validating PRIDE web service file types. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/pride/prideobjects/webservice/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes for validating PRIDE web service queries. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/pride/prideobjects/webservice/query/PrideFilterType.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.pride.prideobjects.webservice.query; 2 | 3 | /** 4 | * An enum of the possible filters for the PRIDE Filter options. 5 | * 6 | * @author Kenneth Verheggen 7 | */ 8 | public enum PrideFilterType { 9 | speciesFilter, 10 | ptmsFilter, 11 | tissueFilter, 12 | diseaseFilter, 13 | titleFilter, 14 | instrumentFilter, 15 | experimentTypeFilter, 16 | quantificationFilter, 17 | projectTagFilter, 18 | submissionTypeFilter; 19 | 20 | /** 21 | * Empty default constructor 22 | */ 23 | private PrideFilterType() { 24 | } 25 | } 26 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/pride/prideobjects/webservice/query/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes for validating PRIDE web service filters. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/pride/validation/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes for validating PRIDE XML files. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/protein/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes concerning useful Objects and their operations for modeling and handling proteins. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/sun/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes related to Java's Swing library. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/threading/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Classes related to maps. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/waiting/WaitingActionListener.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.waiting; 2 | 3 | /** 4 | * This class is used to pass actions like cancel while waiting. 5 | * 6 | * @author Marc Vaudel 7 | */ 8 | public interface WaitingActionListener { 9 | 10 | /** 11 | * Method called whenever the user pressed cancel. 12 | */ 13 | public void cancelPressed(); 14 | } 15 | -------------------------------------------------------------------------------- /src/main/java/com/compomics/util/waiting/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Waiting handler interfaces. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/main/resources/DNA_Protein_Translation.properties: -------------------------------------------------------------------------------- 1 | # This code is the 'standard' genetic code! 2 | TCA = S 3 | TCC = S 4 | TCG = S 5 | TCT = S 6 | TTC = F 7 | TTT = F 8 | TTA = L 9 | TTG = L 10 | TAC = Y 11 | TAT = Y 12 | TAA = _ 13 | TAG = _ 14 | TGC = C 15 | TGT = C 16 | TGA = _ 17 | TGG = W 18 | CTA = L 19 | CTC = L 20 | CTG = L 21 | CTT = L 22 | CCA = P 23 | CCC = P 24 | CCG = P 25 | CCT = P 26 | CAC = H 27 | CAT = H 28 | CAA = Q 29 | CAG = Q 30 | CGA = R 31 | CGC = R 32 | CGG = R 33 | CGT = R 34 | ATA = I 35 | ATC = I 36 | ATT = I 37 | ATG = M 38 | ACA = T 39 | ACC = T 40 | ACG = T 41 | ACT = T 42 | AAC = N 43 | AAT = N 44 | AAA = K 45 | AAG = K 46 | AGC = S 47 | AGT = S 48 | AGA = R 49 | AGG = R 50 | GTA = V 51 | GTC = V 52 | GTG = V 53 | GTT = V 54 | GCA = A 55 | GCC = A 56 | GCG = A 57 | GCT = A 58 | GAC = D 59 | GAT = D 60 | GAA = E 61 | GAG = E 62 | GGA = G 63 | GGC = G 64 | GGG = G 65 | GGT = G -------------------------------------------------------------------------------- /src/main/resources/DefaultJavaOptions.txt: -------------------------------------------------------------------------------- 1 | ################################################################################ 2 | # # 3 | # Parameters to the Java virtual machine. # 4 | # # 5 | # To increase the upper memory limit increase the number on the second line # 6 | # below. Your upper limit is the RAM memory available in your computers. Set # 7 | # it to around three times the size of the spectrum file you want to convert. # 8 | # # 9 | # For example, if you computer has 2GB of RAM memory, you can change the # 10 | # second line to a maximum value of: # 11 | # -Xmx2048M # 12 | # # 13 | ################################################################################ 14 | -Xms128M 15 | -Xmx****M 16 | -------------------------------------------------------------------------------- /src/main/resources/FTPClient.properties: -------------------------------------------------------------------------------- 1 | # This file contains settings for the automated unit testing of 2 | # the FTPClient class. 3 | server = polaris 4 | user = ftpUSer 5 | password = openFTP 6 | 7 | destination = C:/Inetpub/ftproot 8 | 9 | performTest = 0 -------------------------------------------------------------------------------- /src/main/resources/MonoAAMasses.properties: -------------------------------------------------------------------------------- 1 | A = 71.03711 2 | R = 156.10111 3 | N = 114.04293 4 | D = 115.02694 5 | C = 103.00919 6 | Q = 128.05858 7 | E = 129.04259 8 | G = 57.02146 9 | H = 137.05891 10 | I = 113.08406 11 | L = 113.08406 12 | J = 113.08406 13 | K = 128.09496 14 | M = 131.04049 15 | F = 147.06841 16 | P = 97.05276 17 | S = 87.03203 18 | T = 101.04768 19 | W = 186.07931 20 | Y = 163.06333 21 | V = 99.06841 22 | B = 114.04293 23 | Z = 128.05858 24 | X = 118.80450 25 | U = 168.96420 26 | O = 114.146 27 | _ = 0.0 28 | - = 0.0 29 | * = 0.0 -------------------------------------------------------------------------------- /src/main/resources/MonoElementMasses.properties: -------------------------------------------------------------------------------- 1 | H = 1.007825 2 | Li = 7.016003 3 | C = 12.000000 4 | N = 14.003074 5 | O = 15.994915 6 | F = 18.998403 7 | Na = 22.989768 8 | Mg = 23.985142 9 | P = 30.973762 10 | S = 31.972071 11 | Cl = 34.968853 12 | K = 38.963707 13 | Ca = 39.962591 14 | Br = 78.918336 15 | I = 126.904473 16 | Cs = 132.905429 -------------------------------------------------------------------------------- /src/main/resources/MonoNucleotideMasses.properties: -------------------------------------------------------------------------------- 1 | G = 329.20894 2 | A = 313.20954 3 | T = 304.19618 4 | C = 289.18454 -------------------------------------------------------------------------------- /src/main/resources/SpectrumPanel.properties: -------------------------------------------------------------------------------- 1 | 71.03711 = A 2 | 156.10111 = R 3 | 114.04293 = N 4 | 115.02694 = D 5 | 103.00919 = C 6 | 128.05858 = Q 7 | 129.04259 = E 8 | 57.02146 = G 9 | 137.05891 = H 10 | 113.08406 = I/L 11 | 128.09496 = K 12 | 131.04049 = M 13 | 147.035405 = M 14 | 147.06841 = F 15 | 97.05276 = P 16 | 87.03203 = S 17 | 101.04768 = T 18 | 186.07931 = W 19 | 163.06333 = Y 20 | 99.06841 = V 21 | 22 | 112.039856 = Q 23 | 160.030649 = C 24 | 144.011925 = C 25 | 115.026943 = N 26 | 129.042594 = Q 27 | 166.998359 = S

28 | 181.014010 = T

29 | 243.029660 = Y

30 | 31 | 114.0555 = A 32 | 199.1195 = R 33 | 157.0613 = N 34 | 158.0453 = D 35 | 146.0276 = C 36 | 171.077 = Q 37 | 172.061 = E 38 | 100.0399 = G 39 | 180.0773 = H 40 | 156.1025 = I/L 41 | 171.1134 = K 42 | 174.0589 = M 43 | 190.0868 = F 44 | 140.0712 = P 45 | 130.0504 = S 46 | 144.0661 = T 47 | 229.0977 = W 48 | 206.0817 = Y 49 | 142.0868 = V 50 | 51 | 52 | 18.010565 = H2O 53 | 17.026549 = NH3 54 | 80 = Phos 55 | 4 = 18O 56 | 44 = (P)EG -------------------------------------------------------------------------------- /src/main/resources/complementaryNucleotides.properties: -------------------------------------------------------------------------------- 1 | A = T 2 | G = C 3 | C = G 4 | T = A 5 | N = N -------------------------------------------------------------------------------- /src/main/resources/compomics-utilities.properties: -------------------------------------------------------------------------------- 1 | compomics-utilities.version=${version} -------------------------------------------------------------------------------- /src/main/resources/elements.txt: -------------------------------------------------------------------------------- 1 | #element = H,C,N,O,S,HDeut,C13,N15,018,Se N term of an AA = NH and not NH2/ c term of an AA = CO and not COOH 2 | #aminoacids 3 | Header=H,C,N,O,S,HDeut,C13,N15,018,Se 4 | A=5,3,1,1,0,0,0,0,0,0 5 | R=12,6,4,1,0,0,0,0,0,0 6 | N=6,4,2,2,0,0,0,0,0,0 7 | D=5,4,1,3,0,0,0,0,0,0 8 | C=5,3,1,1,1,0,0,0,0,0 9 | E=7,5,1,3,0,0,0,0,0,0 10 | Q=8,5,2,2,0,0,0,0,0,0 11 | G=3,2,1,1,0,0,0,0,0,0 12 | H=7,6,3,1,0,0,0,0,0,0 13 | I=11,6,1,1,0,0,0,0,0,0 14 | L=11,6,1,1,0,0,0,0,0,0 15 | K=12,6,2,1,0,0,0,0,0,0 16 | M=9,5,1,1,1,0,0,0,0,0 17 | F=9,9,1,1,0,0,0,0,0,0 18 | P=7,5,1,1,0,0,0,0,0,0 19 | S=5,3,1,2,0,0,0,0,0,0 20 | T=7,4,1,2,0,0,0,0,0,0 21 | W=10,11,2,1,0,0,0,0,0,0 22 | Y=9,9,1,2,0,0,0,0,0,0 23 | V=9,5,1,1,0,0,0,0,0,0 24 | U=5,3,1,1,0,0,0,0,0,1 -------------------------------------------------------------------------------- /src/main/resources/enzymes.txt: -------------------------------------------------------------------------------- 1 | Title:Trypsin 2 | Cleavage:KR 3 | Restrict:P 4 | Cterm 5 | * 6 | Title:Trypsin_Mod 7 | Cleavage:R 8 | Restrict:P 9 | Cterm 10 | * 11 | Title:Lys-C 12 | Cleavage:K 13 | Restrict:P 14 | Cterm 15 | * 16 | Title:Lys-N 17 | Cleavage:K 18 | Nterm 19 | * 20 | Title:Lys-C/P 21 | Cleavage:K 22 | Cterm 23 | * 24 | Title:Arg-C 25 | Cleavage:R 26 | Restrict:P 27 | Cterm 28 | * 29 | Title:Asp-N 30 | Cleavage:DB 31 | Nterm 32 | * 33 | Title:V8-E 34 | Cleavage:EZ 35 | Restrict:P 36 | Cterm 37 | * 38 | Title:V8-DE 39 | Cleavage:BDEZ 40 | Restrict:P 41 | Cterm 42 | * 43 | Title:Chymotrypsin 44 | Cleavage:FYWLIVM 45 | Restrict:P 46 | Cterm 47 | * 48 | Title:Trypsin/P 49 | Cleavage:KR 50 | Cterm 51 | * 52 | Title:TrypChymo 53 | Cleavage:FYWLKR 54 | Restrict:P 55 | Cterm 56 | * 57 | Title:PepsinA 58 | Cleavage:FL 59 | Cterm 60 | * 61 | Title:None 62 | Cleavage:none 63 | Restrict:none 64 | Cterm 65 | * 66 | Title:NoCleavage 67 | Cleavage:X 68 | Restrict:ABCDEFGHIJKLMNOPQRSTUVWXYZ 69 | Cterm 70 | * 71 | Title:dualArgC_Cathep 72 | Cleavage:DXR 73 | Restrict:P 74 | Cterm 75 | * 76 | Title:Arg-C/P 77 | Cleavage:R 78 | Cterm 79 | * -------------------------------------------------------------------------------- /src/main/resources/helpFiles/AtomChainDialog.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |

Atomic Composition

10 | 11 | Select the isotope type and the number of copies for each of the atoms making up the given PTM, neutral 12 | loss or reporter ion. 13 |

14 | Note that for PTMs you can also subtract atoms. This is done by setting the number of copies for the given atom to a negative value. 15 |


16 | 17 | 18 | s -------------------------------------------------------------------------------- /src/main/resources/helpFiles/FractionPreferences.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |

Fraction Analysis

10 | 11 | 12 |

Options

13 |
    14 |
  • 15 | Protein Confidence MW (%): the protein confidence, in percent, for inclusion in MW plots in the Fractions panel. 16 |
    • 17 |
    18 |
19 |
20 | Go to top of page 21 |


22 | 23 |


24 | 25 | -------------------------------------------------------------------------------- /src/main/resources/helpFiles/GeneAnnotationPreferences.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |

Gene Annotation

10 | 11 | 12 | more details are coming soon... 13 | 14 | 15 | 16 | 17 | 18 | 19 |


20 | 21 | -------------------------------------------------------------------------------- /src/main/resources/helpFiles/InSilicoProteinDigestion.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |

In Silico Protein Digestion

10 | Insert a protein sequence, either in FASTA format or simply a continuous sequence of amino acids, 11 | and select an enzyme to in silico digest the sequence. The maximum number of missed cleavages and 12 | lower and upper mass limits can also be selected. 13 |

14 | All theoretical peptides are listed in the Peptides table, and the coverage is displayed 15 | in the Sequence Coverage panel to right, where the covered parts of the sequence and the currently 16 | selected peptde (in the Peptide table) are highlighted. 17 |
18 | 19 | -------------------------------------------------------------------------------- /src/main/resources/helpFiles/JavaHomeDialog.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |

Java Home

10 | 11 |

12 | To change the Java version used set the Java Home option to point 13 | to the bin folder of the Java version to use, for example, "C:\Program Files\Java\jre1.8.0_25\bin". 14 |

15 | Note that the tool has to be restarted in order to take the new settings into account. 16 |

17 |
18 | 19 | 20 | -------------------------------------------------------------------------------- /src/main/resources/helpFiles/JavaOptionsDialog.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |

Java Options

10 | 11 |

Memory Limit

12 |

13 | To increase the upper memory limit increase the Memory Limit value. 14 | The upper limit is the RAM memory available in your computers. The 15 | value is given in MB. 16 |

17 | For example, if you computer has 2 GB of RAM memory, you can change 18 | the value to a maximum value of 2048 (and usually the actual limit 19 | is a bit lower than the max). 20 |

21 | If the selected value is not supported by your system (32 bits only), 22 | the value will be reduced automatically. 23 |

24 | Note that the tool has to be restarted in order to take 25 | the new settings into account. 26 |

27 |
28 | 29 | 30 | -------------------------------------------------------------------------------- /src/main/resources/helpFiles/NewEnzymeDialog.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |

New Enzyme

10 | 11 | 14 | 15 | 16 |

Introduction

17 | To create a custom enzyme, simply provide an enzyme name and the cleavage 18 | pattern as comma separated lists of (one letter) amino acids. It is also 19 | recommended to provide a PSI-MS CV term, as this will be used in, for 20 | example, the mzIdentML export. 21 |

22 | If you encounter any issues 23 | with enzymes in SearchGUI, please contact the developers. 24 |

25 | Go to top of page 26 |


27 | 28 | 29 | -------------------------------------------------------------------------------- /src/main/resources/helpFiles/PeptideVariantsPreferences.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |

Peptide Variants

10 | 11 | 12 | more details are coming soon... 13 | 14 | 15 | 16 | 17 | 18 | 19 |


20 | 21 | -------------------------------------------------------------------------------- /src/main/resources/helpFiles/ProteinInferencePreferences.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |

Protein Inference

10 | 11 | 12 | more details are coming soon... 13 | 14 | 15 | 16 | 17 | 18 | 19 |


20 | 21 | -------------------------------------------------------------------------------- /src/main/resources/helpFiles/PsmScoringPreferences.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |

PSM Scoring

10 | 11 | 12 | more details are coming soon... 13 | 14 | 15 | 16 | 17 | 18 | 19 |


20 | 21 | -------------------------------------------------------------------------------- /src/main/resources/helpFiles/PtmLocalizationPreferences.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |

PTM Localization

10 | 11 | 12 | more details are coming soon... 13 | 14 | 15 | 16 | 17 | 18 | 19 |


20 | 21 | -------------------------------------------------------------------------------- /src/main/resources/helpFiles/QualityControlPreferences.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |

Quality Control

10 | 11 | These settings allow you to define which PSMs, peptides and proteins that should be considered as Doubtful. 12 |

13 | For more details, please see our tutorials, in particular Chapter 1.5 about Validation. 14 | 15 |


16 | 17 | -------------------------------------------------------------------------------- /src/main/resources/helpFiles/SequenceMatchingPreferences.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |

Sequence Matching

10 | 11 | more details are coming soon... 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 |


20 | 21 | -------------------------------------------------------------------------------- /src/main/resources/helpFiles/ValidationPreferences.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |

Validation Levels

10 | 11 | 12 | more details are coming soon... 13 | 14 | 15 | 16 | 17 | 18 | 19 |


20 | 21 | -------------------------------------------------------------------------------- /src/main/resources/helpFiles/XTandemSettingsDialog.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |

X!Tandem Advanced Settings

10 | 11 |

12 | X!Tandem comes with many options allowing you to fine tune the search settings. Note that these settings aim to be 13 | used by advanced users only. It is highly recommended to carefully test any change to the default settings, to document them and report them in any publication/report. 14 |

15 | For more help, consult the X!Tandem API. If you are missing a parameter, please contact the developers. 16 |

17 | 18 |

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-------------------------------------------------------------------------------- 1 | #The element, dalton difference, occurrence 2 | C,1,0.01107 3 | N,1,0.003663 4 | H,1,0.00015 5 | O,2,0.002036 6 | S,2,0.0421 7 | O,1,0.000374 8 | S,1,0.0075 9 | S,4,0.0002 -------------------------------------------------------------------------------- /src/main/resources/kyte_doolittle.properties: -------------------------------------------------------------------------------- 1 | A = 1.800 2 | R = -4.500 3 | N = -3.500 4 | D = -3.500 5 | C = 2.500 6 | Q = -3.500 7 | E = -3.500 8 | G = -0.400 9 | H = -3.200 10 | I = 4.500 11 | L = 3.800 12 | K = -3.900 13 | M = 1.900 14 | F = 2.800 15 | P = -1.600 16 | S = -0.800 17 | T = -0.700 18 | W = -0.900 19 | Y = -1.300 20 | V = 4.200 -------------------------------------------------------------------------------- /src/main/resources/meek.properties: -------------------------------------------------------------------------------- 1 | A = 7.300 2 | R = -3.600 3 | N = -5.700 4 | D = -2.900 5 | C = -9.200 6 | Q = -0.300 7 | E = -7.100 8 | G = -1.200 9 | H = -2.100 10 | I = 6.600 11 | L = 20.000 12 | K = -3.700 13 | M = 5.600 14 | F = 19.200 15 | P = 5.100 16 | S = -4.100 17 | T = 0.800 18 | W = 16.300 19 | Y = 5.900 20 | V = 3.500 -------------------------------------------------------------------------------- /src/main/resources/modificationConversion.txt: -------------------------------------------------------------------------------- 1 | # No notation as of yet!!! 2 | # Devised these myself! 3 | Carbamidomethyl (C)=Cmm 4 | N-Formyl (Protein)=For 5 | Myristoylation (K)=Myr 6 | Amide (C-term)=Ami 7 | 8 | # These need some work for the N-term!! 9 | Acetyl (K)=Ace 10 | Acetyl (N-term)=Ace 11 | 12 | # Check these. 13 | Me-ester (DE)=Met 14 | Me-ester (C-term)=Met 15 | Phospho (ST)=P 16 | Phospho (Y)=P 17 | Sulphone (M)=Sul 18 | 19 | # Not in Mascot? 20 | NONE1=DiS 21 | NONE2=HOx 22 | #NONE3=For 23 | NONE4=COx 24 | NONE5=Cys 25 | 26 | 27 | # These are OK. 28 | Pyro-glu (N-term Q)=Pyr 29 | Pyro-glu (N-term E)=Pyr 30 | Oxidation (M)=Mox 31 | Deamidation (NQ)=Dam 32 | HSe=Hse 33 | Propionamide (C)=Prp 34 | Carbamyl (N-term)=Car 35 | thioprop (N-term)=Tpr 36 | thiopropcar (N-term)=Tpc 37 | ThiopropLys (K)=Tpl 38 | ThiopropCarbLys (K)=Tcl 39 | Homoarg (K)=Har -------------------------------------------------------------------------------- /src/main/resources/modifications.properties: -------------------------------------------------------------------------------- 1 | Ox = 14, Oxidation 2 | Ace = 28, Acetylation 3 | Spe = -44 4 | Pyr = 12 -------------------------------------------------------------------------------- /src/test/java/com/compomics/util/test/experiment/io/AminoAcidPatternParsingTest.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.test.experiment.io; 2 | 3 | import com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern; 4 | import org.junit.Assert; 5 | import junit.framework.TestCase; 6 | 7 | /** 8 | * This class tests the parsing of amino acid patterns. 9 | * 10 | * @author Marc Vaudel 11 | */ 12 | public class AminoAcidPatternParsingTest extends TestCase { 13 | 14 | 15 | public void testParsing() { 16 | 17 | String testInput = "TEST"; 18 | String expectedOutput = testInput; 19 | AminoAcidPattern aminoAcidPattern = AminoAcidPattern.getAminoAcidPatternFromString(testInput); 20 | String testOutput = aminoAcidPattern.toString(); 21 | Assert.assertTrue(expectedOutput.equals(testOutput)); 22 | 23 | testInput = "[TEST]TE[ST]"; 24 | expectedOutput = testInput; 25 | aminoAcidPattern = AminoAcidPattern.getAminoAcidPatternFromString(testInput); 26 | testOutput = aminoAcidPattern.toString(); 27 | Assert.assertTrue(expectedOutput.equals(testOutput)); 28 | } 29 | 30 | } 31 | -------------------------------------------------------------------------------- /src/test/java/com/compomics/util/test/experiment/io/identifications/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Package containing the tests for the identification parsing. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/test/java/com/compomics/util/test/experiment/io/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Package containing the tests for file IO. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/test/java/com/compomics/util/test/experiment/io/spectrum/SpectrumImportTest.java: -------------------------------------------------------------------------------- 1 | package com.compomics.util.test.experiment.io.spectrum; 2 | 3 | import junit.framework.TestCase; 4 | 5 | import java.io.File; 6 | 7 | /** 8 | * This test case will test the mgf import and spectrum annotation 9 | * 10 | * @author Marc Vaudel 11 | */ 12 | public class SpectrumImportTest extends TestCase { 13 | 14 | public void testSpectrumImportFromMgf() throws Exception { 15 | File mgfFile = new File("src/test/resources/experiment/test.mgf"); 16 | } 17 | } 18 | -------------------------------------------------------------------------------- /src/test/java/com/compomics/util/test/experiment/io/spectrum/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Package containing the tests for the spectrum files parsing. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/test/java/com/compomics/util/test/experiment/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Test classes for the experiment package. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/test/java/com/compomics/util/test/experiment/sequences/digestion/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Package containing the tests for sequence manipulation. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/test/java/com/compomics/util/test/experiment/sequences/indexing/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Package containing the tests for sequence manipulation. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/test/java/com/compomics/util/test/experiment/sequences/matching/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Package containing the tests for sequence manipulation. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/test/java/com/compomics/util/test/experiment/sequences/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Package containing the tests for spectrum indexing. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/test/java/com/compomics/util/test/experiment/spectrum/indexing/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Package containing the tests for sequence manipulation. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/test/java/com/compomics/util/test/experiment/spectrum/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Package containing the tests for sequence manipulation. 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/test/java/com/compomics/util/test/general/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | This package holds all the tests for the classes 4 | from the util.general package. 5 |
6 | @see util.general 7 | 8 | 9 | -------------------------------------------------------------------------------- /src/test/java/com/compomics/util/test/general/servlet/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | Tests for the servlet representations of the general 4 | utilities package. 5 |
6 | @see com.compomics.util.general.servlet 7 | 8 | 9 | -------------------------------------------------------------------------------- /src/test/java/com/compomics/util/test/io/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | This package contains the tests for all the classes 4 | in the com.compomics.util.io package. 5 |
6 | @see com.compomics.util.io 7 | 8 | 9 | -------------------------------------------------------------------------------- /src/test/java/com/compomics/util/test/math/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | This package contains the tests for all the classes 4 | in the com.compomics.util.math package. 5 |
6 | @see com.compomics.util.math 7 | 8 | 9 | -------------------------------------------------------------------------------- /src/test/java/com/compomics/util/test/nucleotide/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | This package contains the tests for all the classes 4 | in the com.compomics.util.nucleotide package. 5 |
6 | @see com.compomics.util.nucleotide 7 | 8 | 9 | -------------------------------------------------------------------------------- /src/test/java/com/compomics/util/test/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | This package groups all the tests for the utilities project. 4 |
5 | The package names inside this package reflect the package 6 | names within util of the utilities the tests are for. 7 | 8 | 9 | -------------------------------------------------------------------------------- /src/test/java/com/compomics/util/test/protein/package.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | This package contains the tests for all the classes 4 | in the com.compomics.util.protein package. 5 |
6 | @see com.compomics.util.protein 7 | 8 | 9 | -------------------------------------------------------------------------------- /src/test/resources/DNA_Protein_Translation.properties: -------------------------------------------------------------------------------- 1 | # This code is the 'standard' genetic code! 2 | TCA = S 3 | TCC = S 4 | TCG = S 5 | TCT = S 6 | TTC = F 7 | TTT = F 8 | TTA = L 9 | TTG = L 10 | TAC = Y 11 | TAT = Y 12 | TAA = _ 13 | TAG = _ 14 | TGC = C 15 | TGT = C 16 | TGA = _ 17 | TGG = W 18 | CTA = L 19 | CTC = L 20 | CTG = L 21 | CTT = L 22 | CCA = P 23 | CCC = P 24 | CCG = P 25 | CCT = P 26 | CAC = H 27 | CAT = H 28 | CAA = Q 29 | CAG = Q 30 | CGA = R 31 | CGC = R 32 | CGG = R 33 | CGT = R 34 | ATA = I 35 | ATC = I 36 | ATT = I 37 | ATG = M 38 | ACA = T 39 | ACC = T 40 | ACG = T 41 | ACT = T 42 | AAC = N 43 | AAT = N 44 | AAA = K 45 | AAG = K 46 | AGC = S 47 | AGT = S 48 | AGA = R 49 | AGG = R 50 | GTA = V 51 | GTC = V 52 | GTG = V 53 | GTT = V 54 | GCA = A 55 | GCC = A 56 | GCG = A 57 | GCT = A 58 | GAC = D 59 | GAT = D 60 | GAA = E 61 | GAG = E 62 | GGA = G 63 | GGC = G 64 | GGG = G 65 | GGT = G -------------------------------------------------------------------------------- /src/test/resources/DefaultJavaOptions.txt: -------------------------------------------------------------------------------- 1 | ################################################################################ 2 | # # 3 | # Parameters to the Java virtual machine. # 4 | # # 5 | # To increase the upper memory limit increase the number on the second line # 6 | # below. Your upper limit is the RAM memory available in your computers. Set # 7 | # it to around three times the size of the spectrum file you want to convert. # 8 | # # 9 | # For example, if you computer has 2GB of RAM memory, you can change the # 10 | # second line to a maximum value of: # 11 | # -Xmx2048M # 12 | # # 13 | ################################################################################ 14 | -Xms128M 15 | -Xmx****M 16 | -------------------------------------------------------------------------------- /src/test/resources/FTPClient.properties: -------------------------------------------------------------------------------- 1 | # This file contains settings for the automated unit testing of 2 | # the FTPClient class. 3 | server = polaris 4 | user = ftpUSer 5 | password = openFTP 6 | 7 | destination = C:/Inetpub/ftproot 8 | 9 | performTest = 0 -------------------------------------------------------------------------------- /src/test/resources/META-INF/services/com.compomics.util.experiment.io.identifications.IdfileReader: -------------------------------------------------------------------------------- 1 | com.compomics.util.experiment.io.identification.idfilereaders.AndromedaIdfileReader 2 | com.compomics.util.experiment.io.identification.idfilereaders.MzIdentMLIdfileReader 3 | com.compomics.util.experiment.io.identification.idfilereaders.MascotIdfileReader 4 | com.compomics.util.experiment.io.identification.idfilereaders.PepNovoIdfileReader 5 | com.compomics.util.experiment.io.identification.idfilereaders.DirecTagIdfileReader 6 | com.compomics.util.experiment.io.identification.idfilereaders.MsAmandaIdfileReader 7 | com.compomics.util.experiment.io.identification.idfilereaders.PepxmlIdfileReader 8 | com.compomics.util.experiment.io.identification.idfilereaders.PNovoIdfileReader 9 | com.compomics.util.experiment.io.identification.idfilereaders.TideIdfileReader 10 | com.compomics.util.experiment.io.identification.idfilereaders.NovorIdfileReader 11 | com.compomics.util.experiment.io.identification.idfilereaders.OnyaseIdfileReader 12 | com.compomics.util.experiment.io.identification.idfilereaders.XTandemIdfileReader -------------------------------------------------------------------------------- /src/test/resources/MonoAAMasses.properties: -------------------------------------------------------------------------------- 1 | A = 71.03711 2 | R = 156.10111 3 | N = 114.04293 4 | D = 115.02694 5 | C = 103.00919 6 | Q = 128.05858 7 | E = 129.04259 8 | G = 57.02146 9 | H = 137.05891 10 | I = 113.08406 11 | L = 113.08406 12 | J = 113.08406 13 | K = 128.09496 14 | M = 131.04049 15 | F = 147.06841 16 | P = 97.05276 17 | S = 87.03203 18 | T = 101.04768 19 | W = 186.07931 20 | Y = 163.06333 21 | V = 99.06841 22 | B = 114.04293 23 | Z = 128.05858 24 | X = 118.80450 25 | U = 168.96420 26 | O = 114.146 27 | _ = 0.0 28 | - = 0.0 29 | * = 0.0 -------------------------------------------------------------------------------- /src/test/resources/MonoElementMasses.properties: -------------------------------------------------------------------------------- 1 | H = 1.007825 2 | Li = 7.016003 3 | C = 12.000000 4 | N = 14.003074 5 | O = 15.994915 6 | F = 18.998403 7 | Na = 22.989768 8 | Mg = 23.985142 9 | P = 30.973762 10 | S = 31.972071 11 | Cl = 34.968853 12 | K = 38.963707 13 | Ca = 39.962591 14 | Br = 78.918336 15 | I = 126.904473 16 | Cs = 132.905429 -------------------------------------------------------------------------------- /src/test/resources/MonoNucleotideMasses.properties: -------------------------------------------------------------------------------- 1 | G = 329.20894 2 | A = 313.20954 3 | T = 304.19618 4 | C = 289.18454 -------------------------------------------------------------------------------- /src/test/resources/SpectrumPanel.properties: -------------------------------------------------------------------------------- 1 | 71.03711 = A 2 | 156.10111 = R 3 | 114.04293 = N 4 | 115.02694 = D 5 | 103.00919 = C 6 | 128.05858 = Q 7 | 129.04259 = E 8 | 57.02146 = G 9 | 137.05891 = H 10 | 113.08406 = I/L 11 | 128.09496 = K 12 | 131.04049 = M 13 | 147.035405 = M 14 | 147.06841 = F 15 | 97.05276 = P 16 | 87.03203 = S 17 | 101.04768 = T 18 | 186.07931 = W 19 | 163.06333 = Y 20 | 99.06841 = V 21 | 22 | 112.039856 = Q 23 | 160.030649 = C 24 | 144.011925 = C 25 | 115.026943 = N 26 | 129.042594 = Q 27 | 166.998359 = S

28 | 181.014010 = T

29 | 243.029660 = Y

30 | 31 | 114.0555 = A 32 | 199.1195 = R 33 | 157.0613 = N 34 | 158.0453 = D 35 | 146.0276 = C 36 | 171.077 = Q 37 | 172.061 = E 38 | 100.0399 = G 39 | 180.0773 = H 40 | 156.1025 = I/L 41 | 171.1134 = K 42 | 174.0589 = M 43 | 190.0868 = F 44 | 140.0712 = P 45 | 130.0504 = S 46 | 144.0661 = T 47 | 229.0977 = W 48 | 206.0817 = Y 49 | 142.0868 = V 50 | 51 | 52 | 18.010565 = H2O 53 | 17.026549 = NH3 54 | 80 = Phos 55 | 4 = 18O 56 | 44 = (P)EG -------------------------------------------------------------------------------- /src/test/resources/complementaryNucleotides.properties: -------------------------------------------------------------------------------- 1 | A = T 2 | G = C 3 | C = G 4 | T = A 5 | N = N -------------------------------------------------------------------------------- /src/test/resources/compomics-utilities.properties: -------------------------------------------------------------------------------- 1 | compomics-utilities.version=${version} -------------------------------------------------------------------------------- /src/test/resources/elements.txt: -------------------------------------------------------------------------------- 1 | #element = H,C,N,O,S,HDeut,C13,N15,018,Se N term of an AA = NH and not NH2/ c term of an AA = CO and not COOH 2 | #aminoacids 3 | Header=H,C,N,O,S,HDeut,C13,N15,018,Se 4 | A=5,3,1,1,0,0,0,0,0,0 5 | R=12,6,4,1,0,0,0,0,0,0 6 | N=6,4,2,2,0,0,0,0,0,0 7 | D=5,4,1,3,0,0,0,0,0,0 8 | C=5,3,1,1,1,0,0,0,0,0 9 | E=7,5,1,3,0,0,0,0,0,0 10 | Q=8,5,2,2,0,0,0,0,0,0 11 | G=3,2,1,1,0,0,0,0,0,0 12 | H=7,6,3,1,0,0,0,0,0,0 13 | I=11,6,1,1,0,0,0,0,0,0 14 | L=11,6,1,1,0,0,0,0,0,0 15 | K=12,6,2,1,0,0,0,0,0,0 16 | M=9,5,1,1,1,0,0,0,0,0 17 | F=9,9,1,1,0,0,0,0,0,0 18 | P=7,5,1,1,0,0,0,0,0,0 19 | S=5,3,1,2,0,0,0,0,0,0 20 | T=7,4,1,2,0,0,0,0,0,0 21 | W=10,11,2,1,0,0,0,0,0,0 22 | Y=9,9,1,2,0,0,0,0,0,0 23 | V=9,5,1,1,0,0,0,0,0,0 24 | U=5,3,1,1,0,0,0,0,0,1 -------------------------------------------------------------------------------- /src/test/resources/enzymes.txt: -------------------------------------------------------------------------------- 1 | Title:Trypsin 2 | Cleavage:KR 3 | Restrict:P 4 | Cterm 5 | * 6 | Title:Trypsin_Mod 7 | Cleavage:R 8 | Restrict:P 9 | Cterm 10 | * 11 | Title:Lys-C 12 | Cleavage:K 13 | Restrict:P 14 | Cterm 15 | * 16 | Title:Lys-N 17 | Cleavage:K 18 | Nterm 19 | * 20 | Title:Lys-C/P 21 | Cleavage:K 22 | Cterm 23 | * 24 | Title:Arg-C 25 | Cleavage:R 26 | Restrict:P 27 | Cterm 28 | * 29 | Title:Asp-N 30 | Cleavage:DB 31 | Nterm 32 | * 33 | Title:V8-E 34 | Cleavage:EZ 35 | Restrict:P 36 | Cterm 37 | * 38 | Title:V8-DE 39 | Cleavage:BDEZ 40 | Restrict:P 41 | Cterm 42 | * 43 | Title:Chymotrypsin 44 | Cleavage:FYWLIVM 45 | Restrict:P 46 | Cterm 47 | * 48 | Title:Trypsin/P 49 | Cleavage:KR 50 | Cterm 51 | * 52 | Title:TrypChymo 53 | Cleavage:FYWLKR 54 | Restrict:P 55 | Cterm 56 | * 57 | Title:PepsinA 58 | Cleavage:FL 59 | Cterm 60 | * 61 | Title:None 62 | Cleavage:none 63 | Restrict:none 64 | Cterm 65 | * 66 | Title:NoCleavage 67 | Cleavage:X 68 | Restrict:ABCDEFGHIJKLMNOPQRSTUVWXYZ 69 | Cterm 70 | * 71 | Title:dualArgC_Cathep 72 | Cleavage:DXR 73 | Restrict:P 74 | Cterm 75 | * 76 | Title:Arg-C/P 77 | Cleavage:R 78 | Cterm 79 | * -------------------------------------------------------------------------------- /src/test/resources/enzymes_test.txt: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | Title:Trypsin 5 | Cleavage:KR 6 | Restrict:P 7 | Cterm 8 | 9 | 10 | * 11 | 12 | Title:Trypsin/P 13 | Cleavage:KR 14 | Cterm 15 | 16 | * 17 | Title:TrypChymo 18 | Cleavage:FYWLKR 19 | Restrict:P 20 | Cterm 21 | * 22 | TiTle:PepsinA 23 | Cleavage:FL 24 | Cterm 25 | * 26 | Title:None 27 | CleAvage : none 28 | RestriCT: none 29 | Nterm 30 | * 31 | 32 | * 33 | 34 | Title:something not correct. 35 | 36 | * 37 | 38 | Title:dualTrypCathep 39 | CleAvage : DXR 40 | RestrIct: P 41 | Cterm 42 | * 43 | Title:DuAlTrypCathep2 44 | CleaVage:DKXRW 45 | Nterm 46 | * 47 | 48 | Title:ReGeXTrypCathep 49 | CleaVage:[KR] 50 | RestriCt: P 51 | Cterm 52 | * 53 | Title:regexTrypCathep2 54 | CleaVage:P+R 55 | Nterm 56 | * 57 | -------------------------------------------------------------------------------- /src/test/resources/experiment/terminiSequence.fasta: -------------------------------------------------------------------------------- 1 | >tr|A0A1C9NAQ8|A0A1C9NAQ8_9DIPT Cytochrome c oxidase subunit 1 (Fragment) OS=Mycetophilidae sp. BOLD-2016 GN=COI PE=3 SV=1 2 | FIXGAWSGMVGTSLSMIIRAELGHPGALIGNDQIYNVIVTAHAFIMIFFMVMPIMIGGFG 3 | NWLVPLMLGAPDMAFPRMNNMSFWMLPPSLTLLLSSSLVEAGAGTGWTVYPPLSSTIAHA 4 | GASVDLAIFSLHLAGISSILGAVNFITTIINMRAPGITFDRMPLFVWSVLITAVLLLLSL 5 | PVLAGAITMLLTDR 6 | -------------------------------------------------------------------------------- /src/test/resources/experiment/test.mgf: -------------------------------------------------------------------------------- 1 | BEGIN IONS 2 | TITLE=controllerType=0 controllerNumber=1 scan=159 3 | RTINSECONDS=218.6808 4 | PEPMASS=1060.86962890625 18161.67578125 5 | CHARGE=2 and 3+ and 4- 6 | 964.581665 0.861346662 7 | END IONS 8 | BEGIN IONS 9 | TITLE=controllerType=0 controllerNumber=1 scan=160 10 | RTINSECONDS=218-219.71 11 | PEPMASS=1060.86962890625 18161.67578125 12 | CHARGE=2 and 3+ and 4- 13 | 964.581665 0.861346662 14 | END IONS -------------------------------------------------------------------------------- /src/test/resources/experiment/testSequences_1.fasta: -------------------------------------------------------------------------------- 1 | >generic|test|test 2 | TESTMRITESTCKTESTKMELTSESTE 3 | >sw|TESTX|foo 4 | SMLTTGFQASNLGKTGMIILGGGLPKHHICNANMMRNGADYDGLSGDTLGXPCXVPINMKILDEEVGGTTTVIVDVMHHQVLYRITDRVKTCFXXTEAVLLPFAITADCY 5 | >foo|Q30592|YR2small 6 | LATAWOIDNXKRRRPDTIEDIXEXIEID 7 | >bar|D0M1N1K|isAwesome 8 | FIXTHISSHITTYERROR -------------------------------------------------------------------------------- /src/test/resources/experiment/uniprot.fasta: -------------------------------------------------------------------------------- 1 | >sp|P31946|1433B_HUMAN 14-3-3 protein beta/alpha OS=Homo sapiens GN=YWHAB PE=1 SV=3 2 | MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFYLKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGDAGEGEN 3 | -------------------------------------------------------------------------------- /src/test/resources/fastaFile.fas: -------------------------------------------------------------------------------- 1 | >sw|O95229|ZWIN_HUMAN ZW10 interactor (ZW10 interacting protein-1) (Zwint-1). 2 | MAAPRPPPAISVSVSAPAFYAPQKKFAPVVAPKPKVNPFRPGDSEPPVAAGAQRAQMG 3 | RVGEIPPPPPEDFPLPPPPLIGEGDDSEGALGGAFPPPPPPMIEEPFPPAPLEEDIFP 4 | SPPPPLEEEGGPEAPTQLPPQPREKVCSIDLEIDSLSSLLDDMTKNDPFKARVSSGYV 5 | PPPVATPFVPKPSTKPAPGGTAPLPPWKTPSSSQPPPQPQRKPQVQLHVQPQAKPHVQ 6 | PQPVSSANTQPRGPLSQAPTPAPKFAPVAPKFTPVVSKFSPGAPSGPGPQPIKKWCLR 7 | MPPSSVSTGSPQPPSFTYAQQKEKPLVQEKQHPQPPPAQNQNQVRSPGGPGPLTLKEV 8 | EELEQLTQQLMQDMEHPQRQSVAVNESCGKCNQPLARAQPAVRALGQLFHITCFTCHQ 9 | CQQQLQGQQFYSLEGAPYCEGCYTDTLEKCNTCGQPITDRMLRATGKAYHPQCFTCVV 10 | CACPLEGTSFIVDQANQPHSVPDYHKQYAPRCSVCSEPIMPEPGRDETVRVVALDKNF 11 | HMKCYKCEDCGKPLSIEADDNGCFPLDGHVLCRKCHSARAQT 12 | >sw|O95230|ZWIN_HUMAN ZW10 interactor (ZW10 interacting protein-2) (Zwint-2). 13 | MAAPRPPPAISVSVGAPAFYAPQKKFAPVVAPKPKVNPFR 14 | -------------------------------------------------------------------------------- /src/test/resources/fastaFile.fas.phr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompOmics/compomics-utilities/5ec488fea6f02d4c3153891668a9f92c0d109084/src/test/resources/fastaFile.fas.phr -------------------------------------------------------------------------------- /src/test/resources/fastaFile.fas.pin: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompOmics/compomics-utilities/5ec488fea6f02d4c3153891668a9f92c0d109084/src/test/resources/fastaFile.fas.pin -------------------------------------------------------------------------------- /src/test/resources/fastaFile.fas.psq: -------------------------------------------------------------------------------- 1 |   2 | 3 |  4 |  5 |             6 |        7 |  8 |  9 |  10 |   11 |  12 |   13 |    14 |  15 |  16 |  17 | 18 |    19 |  20 |   21 |     22 |       23 |          24 |     25 |     26 |    27 |  28 |  29 |  30 |       31 |    32 | 33 |  34 |  35 |   -------------------------------------------------------------------------------- /src/test/resources/fastaNucleotideFile.fas: -------------------------------------------------------------------------------- 1 | >sw|O95229|ZWIN_HUMAN ZW10 interactor (ZW10 interacting NucleotideSequence-1) (Zwint-1). 2 | AGCTAGCTAGCTAGCTAGAGCTAGCTAGCTAGCTAGAGCTAGCTAGCTAGCTAGAGCT 3 | AGCTAGCTAGCTAGAGCTAGCTAGCTAGCTAGAGCTAGCTAGCTAGCTAGAGCTAGCT 4 | AGCTAGCTAGAGCTAGCTAGCTAGCTAGAGCTAGCTAGCTAGCTAGAGCTAGCTAGCT 5 | AGCTAGAGCTAGCTAGCTAGCTAG 6 | >sw|O95230|ZWIN_HUMAN ZW10 interactor (ZW10 interacting NucleotideSequence-2) (Zwint-2). 7 | AGCTAGCTAGCTAGCTAGAGCTAGCTAGCTAGCTAG 8 | -------------------------------------------------------------------------------- /src/test/resources/formatdb.log: -------------------------------------------------------------------------------- 1 | 2 | ========================[ Aug 31, 2010 3:21 PM ]======================== 3 | Version 2.2.11 [Jun-05-2005] 4 | Started database file "fastaFile.fas" 5 | Formatted 2 sequences in volume 0 6 | -------------------------------------------------------------------------------- /src/test/resources/helpFiles/AtomChainDialog.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |

Atomic Composition

10 | 11 | Select the isotope type and the number of copies for each of the atoms making up the given PTM, neutral 12 | loss or reporter ion. 13 |

14 | Note that for PTMs you can also subtract atoms. This is done by setting the number of copies for the given atom to a negative value. 15 |


16 | 17 | 18 | s -------------------------------------------------------------------------------- /src/test/resources/helpFiles/FractionPreferences.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |

Fraction Analysis

10 | 11 | 12 |

Options

13 |
    14 |
  • 15 | Protein Confidence MW (%): the protein confidence, in percent, for inclusion in MW plots in the Fractions panel. 16 |
    • 17 |
    18 |
19 |
20 | Go to top of page 21 |


22 | 23 |


24 | 25 | -------------------------------------------------------------------------------- /src/test/resources/helpFiles/GeneAnnotationPreferences.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |

Gene Annotation

10 | 11 | 12 | more details are coming soon... 13 | 14 | 15 | 16 | 17 | 18 | 19 |


20 | 21 | -------------------------------------------------------------------------------- /src/test/resources/helpFiles/InSilicoProteinDigestion.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |

In Silico Protein Digestion

10 | Insert a protein sequence, either in FASTA format or simply a continuous sequence of amino acids, 11 | and select an enzyme to in silico digest the sequence. The maximum number of missed cleavages and 12 | lower and upper mass limits can also be selected. 13 |

14 | All theoretical peptides are listed in the Peptides table, and the coverage is displayed 15 | in the Sequence Coverage panel to right, where the covered parts of the sequence and the currently 16 | selected peptde (in the Peptide table) are highlighted. 17 |
18 | 19 | -------------------------------------------------------------------------------- /src/test/resources/helpFiles/JavaHomeDialog.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |

Java Home

10 | 11 |

12 | To change the Java version used set the Java Home option to point 13 | to the bin folder of the Java version to use, for example, "C:\Program Files\Java\jre1.8.0_25\bin". 14 |

15 | Note that the tool has to be restarted in order to take the new settings into account. 16 |

17 |
18 | 19 | 20 | -------------------------------------------------------------------------------- /src/test/resources/helpFiles/JavaOptionsDialog.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |

Java Options

10 | 11 |

Memory Limit

12 |

13 | To increase the upper memory limit increase the Memory Limit value. 14 | The upper limit is the RAM memory available in your computers. The 15 | value is given in MB. 16 |

17 | For example, if you computer has 2 GB of RAM memory, you can change 18 | the value to a maximum value of 2048 (and usually the actual limit 19 | is a bit lower than the max). 20 |

21 | If the selected value is not supported by your system (32 bits only), 22 | the value will be reduced automatically. 23 |

24 | Note that the tool has to be restarted in order to take 25 | the new settings into account. 26 |

27 |
28 | 29 | 30 | -------------------------------------------------------------------------------- /src/test/resources/helpFiles/PeptideVariantsPreferences.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |

Peptide Variants

10 | 11 | 12 | more details are coming soon... 13 | 14 | 15 | 16 | 17 | 18 | 19 |


20 | 21 | -------------------------------------------------------------------------------- /src/test/resources/helpFiles/ProteinInferencePreferences.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |

Protein Inference

10 | 11 | 12 | more details are coming soon... 13 | 14 | 15 | 16 | 17 | 18 | 19 |


20 | 21 | -------------------------------------------------------------------------------- /src/test/resources/helpFiles/PsmScoringPreferences.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |

PSM Scoring

10 | 11 | 12 | more details are coming soon... 13 | 14 | 15 | 16 | 17 | 18 | 19 |


20 | 21 | -------------------------------------------------------------------------------- /src/test/resources/helpFiles/PtmLocalizationPreferences.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |

PTM Localization

10 | 11 | 12 | more details are coming soon... 13 | 14 | 15 | 16 | 17 | 18 | 19 |


20 | 21 | -------------------------------------------------------------------------------- /src/test/resources/helpFiles/QualityControlPreferences.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |

Quality Control

10 | 11 | These settings allow you to define which PSMs, peptides and proteins that should be considered as Doubtful. 12 |

13 | For more details, please see our tutorials, in particular Chapter 1.5 about Validation. 14 | 15 |


16 | 17 | -------------------------------------------------------------------------------- /src/test/resources/helpFiles/SequenceMatchingPreferences.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |

Sequence Matching

10 | 11 | more details are coming soon... 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 |


20 | 21 | -------------------------------------------------------------------------------- /src/test/resources/helpFiles/ValidationPreferences.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |

Validation Levels

10 | 11 | 12 | more details are coming soon... 13 | 14 | 15 | 16 | 17 | 18 | 19 |


20 | 21 | -------------------------------------------------------------------------------- /src/test/resources/helpFiles/XTandemSettingsDialog.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |

X!Tandem Advanced Settings

10 | 11 |

12 | X!Tandem comes with many options allowing you to fine tune the search settings. Note that these settings aim to be 13 | used by advanced users only. It is highly recommended to carefully test any change to the default settings, to document them and report them in any publication/report. 14 |

15 | For more help, consult the X!Tandem API. If you are missing a parameter, please contact the developers. 16 |

17 | 18 |

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-------------------------------------------------------------------------------- /src/test/resources/kyte_doolittle.properties: -------------------------------------------------------------------------------- 1 | A = 1.800 2 | R = -4.500 3 | N = -3.500 4 | D = -3.500 5 | C = 2.500 6 | Q = -3.500 7 | E = -3.500 8 | G = -0.400 9 | H = -3.200 10 | I = 4.500 11 | L = 3.800 12 | K = -3.900 13 | M = 1.900 14 | F = 2.800 15 | P = -1.600 16 | S = -0.800 17 | T = -0.700 18 | W = -0.900 19 | Y = -1.300 20 | V = 4.200 -------------------------------------------------------------------------------- /src/test/resources/meek.properties: -------------------------------------------------------------------------------- 1 | A = 7.300 2 | R = -3.600 3 | N = -5.700 4 | D = -2.900 5 | C = -9.200 6 | Q = -0.300 7 | E = -7.100 8 | G = -1.200 9 | H = -2.100 10 | I = 6.600 11 | L = 20.000 12 | K = -3.700 13 | M = 5.600 14 | F = 19.200 15 | P = 5.100 16 | S = -4.100 17 | T = 0.800 18 | W = 16.300 19 | Y = 5.900 20 | V = 3.500 -------------------------------------------------------------------------------- /src/test/resources/modificationConversion.txt: -------------------------------------------------------------------------------- 1 | # No notation as of yet!!! 2 | # Devised these myself! 3 | Carbamidomethyl (C)=Cmm 4 | N-Formyl (Protein)=For 5 | Myristoylation (K)=Myr 6 | Amide (C-term)=Ami 7 | 8 | # These need some work for the N-term!! 9 | Acetyl (K)=Ace 10 | Acetyl (N-term)=Ace 11 | 12 | # Check these. 13 | Me-ester (DE)=Met 14 | Me-ester (C-term)=Met 15 | Phospho (ST)=P 16 | Phospho (Y)=P 17 | Sulphone (M)=Sul 18 | 19 | # Not in Mascot? 20 | NONE1=DiS 21 | NONE2=HOx 22 | #NONE3=For 23 | NONE4=COx 24 | NONE5=Cys 25 | 26 | 27 | # These are OK. 28 | Pyro-glu (N-term Q)=Pyr 29 | Pyro-glu (N-term E)=Pyr 30 | Oxidation (M)=Mox 31 | Deamidation (NQ)=Dam 32 | HSe=Hse 33 | Propionamide (C)=Prp 34 | Carbamyl (N-term)=Car 35 | thioprop (N-term)=Tpr 36 | thiopropcar (N-term)=Tpc 37 | ThiopropLys (K)=Tpl 38 | ThiopropCarbLys (K)=Tcl 39 | Homoarg (K)=Har -------------------------------------------------------------------------------- /src/test/resources/modifications.properties: -------------------------------------------------------------------------------- 1 | Ox = 14, Oxidation 2 | Ace = 28, Acetylation 3 | Spe = -44 4 | Pyr = 12 -------------------------------------------------------------------------------- /src/test/resources/test.spr.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompOmics/compomics-utilities/5ec488fea6f02d4c3153891668a9f92c0d109084/src/test/resources/test.spr.gz -------------------------------------------------------------------------------- /src/test/resources/testAddSelfDefinedList_AA.properties: -------------------------------------------------------------------------------- 1 | Mo = 149.04049 2 | W = 188.07931 -------------------------------------------------------------------------------- /src/test/resources/testAddSelfDefinedList_BiochemElements.properties: -------------------------------------------------------------------------------- 1 | Si = 27.9769 2 | Br = 80.918336 -------------------------------------------------------------------------------- /src/test/resources/testFile.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompOmics/compomics-utilities/5ec488fea6f02d4c3153891668a9f92c0d109084/src/test/resources/testFile.jpg -------------------------------------------------------------------------------- /src/test/resources/testMCServlet.properties: -------------------------------------------------------------------------------- 1 | url=http://beo04.UGent.be/utilities/masscalc 2 | doTest=1 -------------------------------------------------------------------------------- /src/test/resources/testMassCalc.properties: -------------------------------------------------------------------------------- 1 | Br2O3 = 205.821417 2 | CH3CH2COOH = 74.03678 3 | H2O2 = 34.00548 4 | CH3Br = 93.941811 5 | (CH3)Br = 93.941811 6 | (CH3)2Br = 108.96528599999999 7 | (CH3)2Br(CH3)2 = 139.012236 8 | NHCH2CO = 57.021464 9 | NHCHCH3CO = 71.037114 10 | ((CH3)2Br)CH3 = 123.988761 11 | ((CH3)3C)CH2(C(CH3)3) = 128.1565 12 | H3PO4 = 97.97689700000001 13 | (O(H(O(P)O)H)O)H = 97.976897 -------------------------------------------------------------------------------- /src/test/resources/testModificationConversionParser_control.txt: -------------------------------------------------------------------------------- 1 | Acetyl (K)=Ace 2 | Acetyl (N-term)=Ace 3 | Amide (C-term)=Ami 4 | Carbamidomethyl (C)=Cmm 5 | Carbamyl (N-term)=Car 6 | Deamidation (NQ)=Dam 7 | Homoarg (K)=Har 8 | Me-ester (C-term)=Met 9 | Me-ester (DE)=Met 10 | Myristoylation (K)=Myr 11 | N-Formyl (Protein)=For 12 | Oxidation (M)=Mox 13 | Phospho (ST)=P 14 | Phospho (Y)=P 15 | Propionamide (C)=Prp 16 | Pyro-glu (N-term E)=Pyr 17 | Pyro-glu (N-term Q)=Pyr 18 | Sulphone (M)=Sul 19 | ThiopropCarbLys (K)=Tcl 20 | ThiopropLys (K)=Tpl 21 | thioprop (N-term)=Tpr 22 | thiopropcar (N-term)=Tpc -------------------------------------------------------------------------------- /src/test/resources/testMonitor.zip: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompOmics/compomics-utilities/5ec488fea6f02d4c3153891668a9f92c0d109084/src/test/resources/testMonitor.zip -------------------------------------------------------------------------------- /src/test/resources/testSelfDefinedList.properties: -------------------------------------------------------------------------------- 1 | R = 4.0 2 | W = 2.0 3 | X = 1 --------------------------------------------------------------------------------