All Classes

AASequenceImpl Advocate AdvocateFactory Alanine AlignedListCellRenderer AlignedTableCellRenderer AlignmentBlock AlternateRowColoursJTable AminoAcid AndromedaIdfileReader Arginine Asparagine AsparticAcid Atom B BareBonesBrowserLaunch BasicMathFunctions BinaryArrayImpl ByteArrayRenderer Carbon CH4OS Charge ChromatogramPanel ColumnTypeConverter CommandLineParser CompomicsTools Connectable ConnectionDialog Constructors Contact CorrectionFactor CvTerm Cysteine DasAlignment DasAnnotationServerAlingmentReader DasAnnotationServerResultReader DasFeature DateChooser DatFileFilter DBAccessor DBAccessorGenerator DBElement DBMetaData DBResultSet DefaultOutputLoggerImplementation DefaultSpectrumAnnotation Deleteable DeleteableCode DtaFileFilter DualEnzyme Enzyme Enzyme EnzymeFactory ExperimentIO ExperimentObject Export FastaFileFilter FastaIndex FileFilterUtils FileLoggerImplementation FilenameExtensionFilter FileSystemAccessor FindPdbForUniprotAccessions Flamable FlamableJFrame FolderMonitor FragmentFactory FragmentIonTable FragmentIonTableCellRenderer FTP FTPClient FtpConnectionException FtpLoginException FtpProtocolException GeneratorException GettersAndSetters GlutamicAcid Glutamine Glycine Glycon GlyconFactory GraphicsPanel GraphicsPanel.GraphicsPanelType GraphicsPanelTableCellRenderer H2O H3PO4 Header Header.DatabaseType HelpWindow Histidine HPO3 Hydrogen Identification IdentificationMatch IdentificationMatch.MatchType IdentificationMethod IdentificationParametersReader IdfileReader IdfileReaderFactory ImageType InstanceVariables Instrument IntensityHistogram Ion IonMatch Isoleucine IsotopeDistributionGui IsotopicDistribution IsotopicDistributionPanel IsotopicDistributionSpectrum IsotopicElement JExceptionDialog JFrameForBytes JLabelAndComponentPanel JpegFileFilter JTableForDB Leucine Logger Lysine MascotEnzymeReader MascotIdfileReader MascotScore MassCalc MassCalcServlet MassErrorBubblePlot MassErrorPlot Methionine MgfFileFilter MgfIndex MgfReader Modification ModificationFactory ModificationImplementation ModificationMatch ModificationProfile ModificationTemplate MolecularElement MolecularFormula Monitorable MonitorableFileInputStream MonitorableInputStream MonitorDimension MS1Spectrum Ms2FileFilter Ms2Identification MsExperiment MSnSpectrum MzDataFileFilter MzMlFileFilter MzXmlFileFilter NeutralLoss NeutralLossesMap NH3 Nitrogen NucleotideSequence NucleotideSequenceImpl OMSSAIdfileReader OmxFileFilter OperatingSystemEnum OutFileFilter Oxygen PdbBlock PdbParameter PdfFileFilter Peak PeffFileFilter Peptide PeptideAssumption PeptideFragmentIon PeptideFragmentIon.PeptideFragmentIonType PeptideMatch PeptideQuantification PepXmlFileFilter Persistable PersistableCode Phenylalanine Phosphorus PickUp PklFile PklFileFilter PklSpoFileFilter PkxFileFilter PngFileFilter PostProcessor Precursor PrideObject PrideObjectsFactory ProgressDialog ProgressDialogParent ProgressDialogX Proline PropertiesManager Protein Protein ProteinMatch ProteinQuantification ProteinSequencePane ProteomicAnalysis Protocol Proton ProtXmlFileFilter PsmQuantification PTM PTMFactory PTMLocationScores PtmtableContent PtmToPrideMap PushBackStringReader Quantification Quantification.QuantificationMethod QuantificationMatch Ratio Reference ReferenceArea RegExEnzyme ReporterIon ReporterIonQuantification ReporterIonQuantification.ReporterIonMethod ReporterMethod ReporterMethodFactory RescalingEvent Retrievable RetrievableCode Sample Sample SampleAnalysisSet SearchEngine Selenocysteine Sequence SequenceFactory SequenceFragmentationPanel SequenceModificationPanel SequestParamsFileFilter Serine Spectrum SpectrumAnnotation SpectrumAnnotator SpectrumCounting SpectrumCounting.SpectrumCountingMethod SpectrumFactory SpectrumFile SpectrumMatch SpectrumPanel SpectrumPanelListener StartBrowser StartEndPosition Sulfur SvgFileFilter SwingWorker TableMap TableSorter TableValueWrapper Threonine TiffFileFilter TimestampRenderer ToolTipComboBoxRenderer Translate Tryptophan Tyrosine UnknownElementMassException Updateable UpdateableCode UrParameter Util UtilitiesDemo UtilitiesGUIDefaults Valine X XmlFileFilter XTandemIdfileReader XYZDataPoint Z