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  • bioknime-master
    • Alignment Writer
      • src
        • au
          • com
            • acpfg
              • phylogeny
                • writer
                  • AlignmentWriterNodeDialog.java
                  • AlignmentWriterNodeFactory.java
                  • AlignmentWriterNodeModel.java
                  • AlignmentWriterNodePlugin.java
                  • AlignmentWriterNodeView.java
                  • UnsupportedAlignmentException.java
    • BioJava Processor
      • src
        • au
          • com
            • acpfg
              • misc
                • biojava
                  • AlternateTranslationProcessor.java
                  • BioJavaProcessorInterface.java
                  • BioJavaProcessorNodeDialog.java
                  • BioJavaProcessorNodeFactory.java
                  • BioJavaProcessorNodeModel.java
                  • BioJavaProcessorNodePlugin.java
                  • BioJavaProcessorNodeView.java
                  • FrameTranslationProcessor.java
                  • HydrophobicityProcessor.java
                  • InvalidIUPACException.java
                  • LongestFrameProcessor.java
                  • ModeSummary.java
                  • PositionByResidueProcessor.java
                  • ResidueFrequencyProcessor.java
                  • SNPFrameshiftDetector.java
                  • SequenceTranslationProcessor.java
                  • TrypticPeptideExtractor.java
                  • TrypticPeptideExtractor_v2.java
                  • WeightedHomopolymerRateProcessor.java
    • Fasta Reader
      • src
        • au
          • com
            • acpfg
              • misc
                • fasta
                  • FastaReaderNodeDialog.java
                  • FastaReaderNodeFactory.java
                  • FastaReaderNodeModel.java
                  • FastaReaderNodePlugin.java
                  • FastaReaderNodeView.java
                  • SequenceStatistics.java
    • Fasta Writer
      • src
        • au
          • com
            • acpfg
              • misc
                • fastawriter
                  • FastaWriterNodeDialog.java
                  • FastaWriterNodeFactory.java
                  • FastaWriterNodeModel.java
                  • FastaWriterNodePlugin.java
                  • FastaWriterNodeView.java
    • GenBank Reader
      • src
        • au
          • com
            • acpfg
              • io
                • genbank
                  • reader
                    • FastGenbankNodeModel.java
                    • GenBankReaderNodeDialog.java
                    • GenBankReaderNodeFactory.java
                    • GenBankReaderNodeModel.java
                    • GenBankReaderNodePlugin.java
                    • GenbankFeatureListener.java
                    • GenbankRecord.java
                    • InvalidGenbankRecordException.java
                    • SectionStart.java
    • InterProScan (EBI)
      • src
        • au
          • com
            • acpfg
              • pfa
                • interproscan
                  • FailedJobException.java
                  • InterProScanNodeDialog.java
                  • InterProScanNodeFactory.java
                  • InterProScanNodeModel.java
                  • InterProScanNodePlugin.java
                  • InterProScanNodeView.java
    • JEmboss (local)
      • src
        • au
          • com
            • acpfg
              • misc
                • jemboss
                  • io
                    • FastaUnmarshaller.java
                    • FormattedUnmarshallerInterface.java
                    • GFFUnmarshaller.java
                    • UnmarshallerInterface.java
                  • local
                    • AbstractTableMapper.java
                    • EmbossProgramDescription.java
                    • JEmbossProcessorNodeDialog.java
                    • JEmbossProcessorNodeFactory.java
                    • JEmbossProcessorNodeModel.java
                    • JEmbossProcessorNodePlugin.java
                    • MyFilteredProgTreeModel.java
                    • MyProgTreeModel.java
                    • MyRunnable.java
                    • MyTreeFilter.java
                    • MyTreeSelectionListener.java
                    • ProgramSettingsListener.java
                    • ProgramSettingsModel.java
                    • ProgsInCategory.java
                    • RawAndFormattedTableMapper.java
                    • StringCellTableRenderer.java
                    • UnmarshallerInterface.java
                  • settings
                    • AlignmentSetting.java
                    • ArraySetting.java
                    • BooleanSetting.java
                    • CodonUsageTableSetting.java
                    • DataFileSetting.java
                    • DummySetting.java
                    • GraphSetting.java
                    • ListSetting.java
                    • MatrixSetting.java
                    • NumberSetting.java
                    • OutputFileSetting.java
                    • ProgramSetting.java
                    • RangeSetting.java
                    • RegexpSetting.java
                    • SequenceSetSetting.java
                    • SequenceSetting.java
                    • StringSetting.java
    • MUSCLE (EBI)
      • src
        • au
          • com
            • acpfg
              • align
                • muscle
                  • AlignmentCellFactory.java
                  • AlignmentSummaryRenderer.java
                  • AlignmentValue.java
                  • FormattedRenderer.java
                  • MultiAlignmentCell.java
                  • MuscleAlignerNodeDialog.java
                  • MuscleAlignerNodeFactory.java
                  • MuscleAlignerNodeModel.java
                  • MuscleAlignerNodePlugin.java
                  • MuscleAlignerNodeView.java
              • misc
                • muscle
                  • AlignmentCellFactory.java
                  • AlignmentSummaryRenderer.java
                  • AlignmentValue.java
                  • FormattedRenderer.java
                  • MultiAlignmentCell.java
                  • MuscleAccessorNodeDialog.java
                  • MuscleAccessorNodeFactory.java
                  • MuscleAccessorNodeModel.java
                  • MuscleAccessorNodePlugin.java
                  • MuscleAccessorNodeView.java
    • Mascot Reader
      • src
        • au
          • com
            • acpfg
              • proteomics
                • mascotrdr
                  • MascotReaderNodeDialog.java
                  • MascotReaderNodeFactory.java
                  • MascotReaderNodeModel.java
                  • MascotReaderNodePlugin.java
                  • MascotReaderNodeView.java
    • Minimum Protein List
      • src
        • au
          • com
            • acpfg
              • proteomics
                • MinProteinListNodeDialog.java
                • MinProteinListNodeFactory.java
                • MinProteinListNodeModel.java
                • MinProteinListNodePlugin.java
                • UnknownPeptideException.java
    • PICR Accessor (EBI)
      • src
        • au
          • com
            • acpfg
              • misc
                • picr
                  • PICRAccessorNodeDialog.java
                  • PICRAccessorNodeFactory.java
                  • PICRAccessorNodeModel.java
                  • PICRAccessorNodePlugin.java
                  • PICRAccessorNodeView.java
        • uk
          • ac
            • ebi
              • picr
                • AccessionMapperInterface.java
                • AccessionMapperService.java
                • CrossReference.java
                • GetMappedDatabaseNames.java
                • GetMappedDatabaseNamesResponse.java
                • GetUPIForAccession.java
                • GetUPIForAccessionResponse.java
                • GetUPIForSequence.java
                • GetUPIForSequenceResponse.java
                • ObjectFactory.java
                • UPEntry.java
                • package-info.java
    • PNG Image Writer
      • src
        • au
          • com
            • acpfg
              • io
                • pngwriter
                  • PNGImageWriterNodeDialog.java
                  • PNGImageWriterNodeFactory.java
                  • PNGImageWriterNodeModel.java
                  • PNGImageWriterNodePlugin.java
                  • PNGImageWriterNodeView.java
    • PepXML Reader
      • src
        • au
          • com
            • acpfg
              • tpp
                • PepXMLGlobals.java
                • PepXMLReaderNodeDialog.java
                • PepXMLReaderNodeFactory.java
                • PepXMLReaderNodeModel.java
                • PepXMLReaderNodePlugin.java
                • PepXMLReaderNodeView.java
                • PepXMLResultInterface.java
                • pepXML.java
    • Phobius Accessor (EBI)
      • src
        • au
          • com
            • acpfg
              • align
                • phobius
                  • PhobiusSourceNodeDialog.java
                  • PhobiusSourceNodeFactory.java
                  • PhobiusSourceNodeModel.java
                  • PhobiusSourceNodePlugin.java
    • Phylogeny Processor
      • src
        • au
          • com
            • acpfg
              • phylogeny
                • CalcDistanceMatrixTask.java
                • PhylogenyProcessorNodeDialog.java
                • PhylogenyProcessorNodeFactory.java
                • PhylogenyProcessorNodeModel.java
                • PhylogenyProcessorNodePlugin.java
                • PhylogenyProcessorNodeView.java
                • RunnableTask.java
    • Sequence Aligner
      • src
        • au
          • com
            • acpfg
              • align
                • local
                  • AlignmentReporter.java
                  • MyAlignment.java
                  • SequenceAlignerNodeDialog.java
                  • SequenceAlignerNodeFactory.java
                  • SequenceAlignerNodeModel.java
                  • SequenceAlignerNodePlugin.java
                  • SequenceAlignerNodeView.java
    • Spectra Phosphorylation Scorer
      • src
        • au
          • com
            • acpfg
              • spectra
                • phosphorylation
                  • InvalidAScoreException.java
                  • InvalidIonException.java
                  • Ion.java
                  • IonFilterInterface.java
                  • IonList.java
                  • Peak.java
                  • PeptideScore.java
                  • PhosphorylationScorerNodeDialog.java
                  • PhosphorylationScorerNodeFactory.java
                  • PhosphorylationScorerNodeModel.java
                  • PhosphorylationScorerNodePlugin.java
                  • PhosphorylationScorerNodeView.java
                  • SiteDeterminingFilter.java
    • Spectra Quality Assessor
      • src
        • au
          • com
            • acpfg
              • misc
                • spectra
                  • quality
                    • SpectraQualityAssessorNodeDialog.java
                    • SpectraQualityAssessorNodeFactory.java
                    • SpectraQualityAssessorNodeModel.java
                    • SpectraQualityAssessorNodePlugin.java
                    • SpectraQualityAssessorNodeView.java
    • Spectra Reader
      • src
        • au
          • com
            • acpfg
              • misc
                • spectra
                  • AbstractDataProcessor.java
                  • AbstractSpectraCell.java
                  • MGFDataProcessor.java
                  • MGFSpectraCell.java
                  • MyMGFPeakList.java
                  • RowSequence.java
                  • SpectraBitVectorRenderer.java
                  • SpectraReaderNodeDialog.java
                  • SpectraReaderNodeFactory.java
                  • SpectraReaderNodeModel.java
                  • SpectraReaderNodePlugin.java
                  • SpectraStringRenderer.java
                  • SpectraTop10Renderer.java
                  • SpectraUtilityFactory.java
                  • SpectraVisualRenderer.java
                  • SpectralDataInterface.java
                  • mzMLDataProcessor.java
                  • mzMLSpectraCell.java
        • org
          • systemsbiology
            • jrap
              • stax
                • Base64.java
                • ByteBufferIterator.java
                • DataProcessingInfo.java
                • EndPatternStringIterator.java
                • FileHeaderParser.java
                • IndexParser.java
                • LineIterator.java
                • MLScanAndHeaderParser.java
                • MSInstrumentInfo.java
                • MSOperator.java
                • MSXMLParser.java
                • MSXMLSequentialParser.java
                • MZXMLFileInfo.java
                • ParentFile.java
                • Scan.java
                • ScanAndHeaderParser.java
                • ScanHeader.java
                • SoftwareInfo.java
                • StringBuilderReader.java
                • TestParser.java
    • Spectra Writer
      • src
        • au
          • com
            • acpfg
              • misc
                • spectra
                  • writer
                    • SpectraAdapter.java
                    • SpectraWriterNodeDialog.java
                    • SpectraWriterNodeFactory.java
                    • SpectraWriterNodeModel.java
                    • SpectraWriterNodePlugin.java
                    • SpectraWriterNodeView.java
    • Spectral Data Extractor
      • src
        • au
          • com
            • acpfg
              • misc
                • spectra
                  • peakextractor
                    • PeakItemPanel.java
                    • PeakPanel.java
                    • PeakWindow.java
                    • SpectralPeakExtractorNodeDialog.java
                    • SpectralPeakExtractorNodeFactory.java
                    • SpectralPeakExtractorNodeModel.java
                    • SpectralPeakExtractorNodePlugin.java
                    • SpectralPeakExtractorNodeView.java
    • String Matcher
      • src
        • au
          • com
            • acpfg
              • misc
                • StringMatcher
                  • CoverageReporter.java
                  • Extent.java
                  • ExtentReporter.java
                  • HighlightMatchReporter.java
                  • MatchDensityPositionReporter.java
                  • MatchLengthsReporter.java
                  • MatchPositionsReporter.java
                  • MatchReporter.java
                  • MatchesPerPositionReporter.java
                  • MatchesReporter.java
                  • MyPattern.java
                  • NonOverlappingMatchesReporter.java
                  • NumMatchesReporter.java
                  • SearchStringReporter.java
                  • StartDensityPositionReporter.java
                  • StartPositionsReporter.java
                  • StringMatcherNodeDialog.java
                  • StringMatcherNodeFactory.java
                  • StringMatcherNodeModel.java
                  • StringMatcherNodePlugin.java
                  • StringMatcherNodeView.java
                  • UniqueMatchReporter.java
    • UniProtKB Accessor (EBI)
      • src
        • au
          • com
            • acpfg
              • misc
                • uniprot
                  • AccessionMapTask.java
                  • CacheableUniProtRecord.java
                  • DeletedEntryException.java
                  • RetrieveEntryTask.java
                  • UniPARCEntryTask.java
                  • UniProtAccessorNodeDialog.java
                  • UniProtAccessorNodeFactory.java
                  • UniProtAccessorNodeModel.java
                  • UniProtAccessorNodePlugin.java
                  • UniProtAccessorNodeView.java
                  • UniProtHit.java
                  • UniProtTaskInterface.java
                  • UniRefEntryTask.java
    • WU-BLAST (EBI)
      • src
        • au
          • com
            • acpfg
              • misc
                • blast
                  • wublast
                    • BlastHit.java
                    • WUBlastNodeDialog.java
                    • WUBlastNodeFactory.java
                    • WUBlastNodeModel.java
                    • WUBlastNodePlugin.java
                    • WUBlastNodeView.java
    • XML Reader
      • src
        • au
          • com
            • acpfg
              • xml
                • reader
                  • MyNSRemover.java
                  • XMLCell.java
                  • XMLReaderNodeDialog.java
                  • XMLReaderNodeFactory.java
                  • XMLReaderNodeModel.java
                  • XMLReaderNodePlugin.java
                  • XMLUtilityFactory.java
    • XML Writer
      • src
        • au
          • com
            • acpfg
              • xml
                • writer
                  • XMLWriterNodeDialog.java
                  • XMLWriterNodeFactory.java
                  • XMLWriterNodeModel.java
                  • XMLWriterNodePlugin.java
                  • XMLWriterNodeView.java
    • XQuery Processor
      • src
        • au
          • com
            • acpfg
              • xml
                • query
                  • AttributeCollectionReporter.java
                  • BuiltinTemplateListDialog.java
                  • ElementCollectionReporter.java
                  • ElementDistributionReporter.java
                  • FailedPathException.java
                  • MyQueryEntryListModel.java
                  • MyQueryEntryRenderer.java
                  • StringReporter.java
                  • TextCollectionReporter.java
                  • TextReporter.java
                  • XMLQueryEntry.java
                  • XQueryProcessorNodeDialog.java
                  • XQueryProcessorNodeFactory.java
                  • XQueryProcessorNodeModel.java
                  • XQueryProcessorNodePlugin.java
                  • XQueryReporter.java
                  • XQueryReporterInterface.java
                  • XQueryResponseInterface.java