Hierarchy For All Packages

Package Hierarchies:

• com.compomics.software,
• com.compomics.software.autoupdater,
• com.compomics.software.dialogs,
• com.compomics.software.settings,
• com.compomics.software.settings.gui,
• com.compomics.util,
• com.compomics.util.db,
• com.compomics.util.db.components,
• com.compomics.util.db.interfaces,
• com.compomics.util.enumeration,
• com.compomics.util.examples,
• com.compomics.util.exceptions,
• com.compomics.util.exceptions.exception_handlers,
• com.compomics.util.experiment,
• com.compomics.util.experiment.biology,
• com.compomics.util.experiment.biology.aminoacids,
• com.compomics.util.experiment.biology.atoms,
• com.compomics.util.experiment.biology.genes,
• com.compomics.util.experiment.biology.genes.ensembl,
• com.compomics.util.experiment.biology.genes.go,
• com.compomics.util.experiment.biology.ions,
• com.compomics.util.experiment.biology.mutations,
• com.compomics.util.experiment.biology.taxonomy,
• com.compomics.util.experiment.biology.taxonomy.mappings,
• com.compomics.util.experiment.filtering,
• com.compomics.util.experiment.identification,
• com.compomics.util.experiment.identification.amino_acid_tags,
• com.compomics.util.experiment.identification.amino_acid_tags.matchers,
• com.compomics.util.experiment.identification.filtering,
• com.compomics.util.experiment.identification.identification_parameters,
• com.compomics.util.experiment.identification.identification_parameters.tool_specific,
• com.compomics.util.experiment.identification.identifications,
• com.compomics.util.experiment.identification.matches,
• com.compomics.util.experiment.identification.matches_iterators,
• com.compomics.util.experiment.identification.parameters_cli,
• com.compomics.util.experiment.identification.protein_inference.proteintree,
• com.compomics.util.experiment.identification.protein_sequences,
• com.compomics.util.experiment.identification.psm_scoring,
• com.compomics.util.experiment.identification.psm_scoring.psm_scores,
• com.compomics.util.experiment.identification.ptm,
• com.compomics.util.experiment.identification.ptm.ptmscores,
• com.compomics.util.experiment.identification.spectrum_annotation,
• com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators,
• com.compomics.util.experiment.identification.spectrum_assumptions,
• com.compomics.util.experiment.io,
• com.compomics.util.experiment.io.identifications,
• com.compomics.util.experiment.io.identifications.idfilereaders,
• com.compomics.util.experiment.io.massspectrometry,
• com.compomics.util.experiment.io.massspectrometry.export,
• com.compomics.util.experiment.massspectrometry,
• com.compomics.util.experiment.massspectrometry.proteowizard,
• com.compomics.util.experiment.massspectrometry.proteowizard.gui,
• com.compomics.util.experiment.normalization,
• com.compomics.util.experiment.patient,
• com.compomics.util.experiment.personalization,
• com.compomics.util.experiment.quantification,
• com.compomics.util.experiment.quantification.reporterion,
• com.compomics.util.experiment.quantification.spectrumcounting,
• com.compomics.util.experiment.refinementparameters,
• com.compomics.util.experiment.units,
• com.compomics.util.general,
• com.compomics.util.general.servlet,
• com.compomics.util.gui,
• com.compomics.util.gui.atoms,
• com.compomics.util.gui.error_handlers,
• com.compomics.util.gui.error_handlers.notification,
• com.compomics.util.gui.events,
• com.compomics.util.gui.export.graphics,
• com.compomics.util.gui.export.report,
• com.compomics.util.gui.filehandling,
• com.compomics.util.gui.genes,
• com.compomics.util.gui.interfaces,
• com.compomics.util.gui.isotopic_calculator,
• com.compomics.util.gui.parameters,
• com.compomics.util.gui.parameters.identification_parameters,
• com.compomics.util.gui.parameters.identification_parameters.algorithm_settings,
• com.compomics.util.gui.protein,
• com.compomics.util.gui.ptm,
• com.compomics.util.gui.renderers,
• com.compomics.util.gui.spectrum,
• com.compomics.util.gui.tablemodels,
• com.compomics.util.gui.utils,
• com.compomics.util.gui.utils.user_choice,
• com.compomics.util.gui.utils.user_choice.list_choosers,
• com.compomics.util.gui.waiting.waitinghandlers,
• com.compomics.util.interfaces,
• com.compomics.util.io,
• com.compomics.util.io.compression,
• com.compomics.util.io.export,
• com.compomics.util.io.export.styles,
• com.compomics.util.io.export.writers,
• com.compomics.util.io.filefilters,
• com.compomics.util.io.json,
• com.compomics.util.io.json.adapter,
• com.compomics.util.io.json.marshallers,
• com.compomics.util.junit,
• com.compomics.util.maps,
• com.compomics.util.math,
• com.compomics.util.math.clustering,
• com.compomics.util.math.clustering.settings,
• com.compomics.util.math.matrix,
• com.compomics.util.math.roc,
• com.compomics.util.math.statistics,
• com.compomics.util.math.statistics.distributions,
• com.compomics.util.math.statistics.linear_regression,
• com.compomics.util.math.statistics.linear_regression.filters,
• com.compomics.util.math.statistics.linear_regression.regressions,
• com.compomics.util.memory,
• com.compomics.util.messages,
• com.compomics.util.nucleotide,
• com.compomics.util.pdbfinder,
• com.compomics.util.pdbfinder.das.readers,
• com.compomics.util.pdbfinder.pdb,
• com.compomics.util.preferences,
• com.compomics.util.pride,
• com.compomics.util.pride.prideobjects,
• com.compomics.util.pride.prideobjects.webservice,
• com.compomics.util.pride.prideobjects.webservice.file,
• com.compomics.util.pride.prideobjects.webservice.query,
• com.compomics.util.pride.validation,
• com.compomics.util.protein,
• com.compomics.util.protein_sequences_manager,
• com.compomics.util.protein_sequences_manager.enums,
• com.compomics.util.protein_sequences_manager.gui,
• com.compomics.util.protein_sequences_manager.gui.preferences,
• com.compomics.util.protein_sequences_manager.gui.sequences_import,
• com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy,
• com.compomics.util.sun,
• com.compomics.util.waiting

Class Hierarchy

• java.lang.Object
  • com.compomics.util.experiment.identification.psm_scoring.psm_scores.AAIntensityRankScore
  • com.compomics.util.experiment.identification.psm_scoring.psm_scores.AAMS2MzFidelityScore
  • com.compomics.util.protein.AASequenceImpl (implements com.compomics.util.interfaces.Sequence)
  • com.compomics.util.experiment.identification.parameters_cli.AbstractIdentificationParametersCli (implements java.util.concurrent.Callable<V>)
  • javax.swing.table.AbstractTableModel (implements java.io.Serializable, javax.swing.table.TableModel)
    • com.compomics.util.db.DBResultSet
    • javax.swing.table.DefaultTableModel (implements java.io.Serializable)
      • com.compomics.util.gui.spectrum.IonLabelColorTableModel
      • com.compomics.util.gui.tablemodels.SelfUpdatingTableModel
    • com.compomics.util.sun.TableMap (implements javax.swing.event.TableModelListener)
      • com.compomics.util.sun.TableSorter
  • com.compomics.util.experiment.identification.Advocate
  • com.compomics.util.gui.renderers.AlignedTableCellRenderer (implements javax.swing.table.TableCellRenderer)
  • com.compomics.util.pdbfinder.das.readers.AlignmentBlock
  • com.compomics.util.experiment.biology.AminoAcid (implements java.io.Serializable)
    • com.compomics.util.experiment.biology.aminoacids.Alanine
    • com.compomics.util.experiment.biology.aminoacids.Arginine
    • com.compomics.util.experiment.biology.aminoacids.Asparagine
    • com.compomics.util.experiment.biology.aminoacids.AsparticAcid
    • com.compomics.util.experiment.biology.aminoacids.B
    • com.compomics.util.experiment.biology.aminoacids.Cysteine
    • com.compomics.util.experiment.biology.aminoacids.GlutamicAcid
    • com.compomics.util.experiment.biology.aminoacids.Glutamine
    • com.compomics.util.experiment.biology.aminoacids.Glycine
    • com.compomics.util.experiment.biology.aminoacids.Histidine
    • com.compomics.util.experiment.biology.aminoacids.Isoleucine
    • com.compomics.util.experiment.biology.aminoacids.J
    • com.compomics.util.experiment.biology.aminoacids.Leucine
    • com.compomics.util.experiment.biology.aminoacids.Lysine
    • com.compomics.util.experiment.biology.aminoacids.Methionine
    • com.compomics.util.experiment.biology.aminoacids.Phenylalanine
    • com.compomics.util.experiment.biology.aminoacids.Proline
    • com.compomics.util.experiment.biology.aminoacids.Pyrrolysine
    • com.compomics.util.experiment.biology.aminoacids.Selenocysteine
    • com.compomics.util.experiment.biology.aminoacids.Serine
    • com.compomics.util.experiment.biology.aminoacids.Threonine
    • com.compomics.util.experiment.biology.aminoacids.Tryptophan
    • com.compomics.util.experiment.biology.aminoacids.Tyrosine
    • com.compomics.util.experiment.biology.aminoacids.Valine
    • com.compomics.util.experiment.biology.aminoacids.X
    • com.compomics.util.experiment.biology.aminoacids.Z
  • com.compomics.util.experiment.identification.identification_parameters.tool_specific.AndromedaParameters (implements com.compomics.util.experiment.identification.identification_parameters.IdentificationAlgorithmParameter)
  • com.compomics.util.experiment.identification.spectrum_annotation.AnnotationSettings (implements java.io.Serializable)
  • com.compomics.util.experiment.io.massspectrometry.export.AplExporter
  • com.compomics.util.experiment.identification.ptm.ptmscores.AScore
  • com.compomics.util.experiment.biology.AtomChain (implements java.io.Serializable)
  • com.compomics.util.experiment.biology.AtomImpl (implements java.io.Serializable)
  • com.compomics.util.examples.BareBonesBrowserLaunch
  • com.compomics.util.math.BasicMathFunctions
  • com.compomics.util.math.BigFunctions
  • com.compomics.util.math.BigMathUtils
  • com.compomics.util.BinaryArrayImpl
  • com.compomics.util.math.statistics.linear_regression.filters.BinningFilter
  • com.compomics.util.math.statistics.distributions.BinomialDistribution (implements com.compomics.util.math.statistics.Distribution)
  • com.compomics.util.experiment.biology.taxonomy.mappings.BiomartMapping
  • com.compomics.util.db.ColumnTypeConverter
  • com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters (implements com.compomics.util.experiment.identification.identification_parameters.IdentificationAlgorithmParameter)
  • com.compomics.util.general.CommandLineParser
  • com.compomics.software.CommandLineUtils
  • com.compomics.software.autoupdater.CompareVersionNumbers (implements java.util.Comparator<T>)
  • com.compomics.util.CompareVersionNumbers (implements java.util.Comparator<T>)
  • com.compomics.util.experiment.identification.psm_scoring.psm_scores.ComplementarityScore
  • com.compomics.software.CompomicsWrapper
  • java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
    • java.awt.Container
      • javax.swing.JComponent (implements java.io.Serializable)
        • javax.swing.JLabel (implements javax.accessibility.Accessible, javax.swing.SwingConstants)
          • javax.swing.plaf.basic.BasicComboBoxRenderer (implements javax.swing.ListCellRenderer<E>, java.io.Serializable)
            • com.compomics.util.gui.renderers.ToolTipComboBoxRenderer
          • javax.swing.DefaultListCellRenderer (implements javax.swing.ListCellRenderer<E>, java.io.Serializable)
            • com.compomics.util.gui.renderers.AlignedListCellRenderer
          • javax.swing.table.DefaultTableCellRenderer (implements java.io.Serializable, javax.swing.table.TableCellRenderer)
            • com.compomics.util.gui.renderers.ByteArrayRenderer
            • com.compomics.util.gui.renderers.TimestampRenderer
          • com.compomics.util.gui.renderers.GraphicsPanelTableCellRenderer (implements javax.swing.table.TableCellRenderer)
        • javax.swing.JPanel (implements javax.accessibility.Accessible)
          • com.compomics.util.gui.atoms.AtomPanel
          • com.compomics.util.gui.spectrum.GraphicsPanel
            • com.compomics.util.gui.spectrum.ChromatogramPanel
            • com.compomics.util.gui.spectrum.IsotopicDistributionPanel
            • com.compomics.util.gui.spectrum.SpectrumPanel
          • com.compomics.util.gui.spectrum.IntensityHistogram
          • com.compomics.util.gui.JLabelAndComponentPanel
          • com.compomics.util.gui.spectrum.MassErrorBubblePlot
          • com.compomics.util.gui.spectrum.MassErrorPlot
          • com.compomics.util.gui.spectrum.SequenceFragmentationPanel
          • com.compomics.util.gui.protein.SequenceModificationPanel
          • com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy.TaxonomyTreePanel
          • com.compomics.util.gui.VennDiagramPanel
        • javax.swing.JTable (implements javax.accessibility.Accessible, javax.swing.event.CellEditorListener, javax.swing.event.ListSelectionListener, javax.swing.event.RowSorterListener, javax.swing.Scrollable, javax.swing.event.TableColumnModelListener, javax.swing.event.TableModelListener)
          • com.compomics.util.AlternateRowColoursJTable
            • com.compomics.util.gui.JTableForDB
          • com.compomics.util.gui.spectrum.FragmentIonTable
      • java.awt.Window (implements javax.accessibility.Accessible)
        • java.awt.Dialog
          • javax.swing.JDialog (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • com.compomics.util.gui.AaMass
            • com.compomics.util.gui.protein.AdvancedProteinDatabaseDialog
            • com.compomics.util.gui.AminoAcidPatternDialog
            • com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.AndromedaSettingsDialog (implements com.compomics.util.gui.parameters.identification_parameters.AlgorithmSettingsDialog)
            • com.compomics.util.gui.parameters.identification_parameters.AnnotationSettingsDialog
            • com.compomics.util.gui.atoms.AtomChainDialog
            • com.compomics.util.gui.error_handlers.BugReport
            • com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.CometSettingsDialog (implements com.compomics.util.gui.parameters.identification_parameters.AlgorithmSettingsDialog)
            • com.compomics.util.gui.utils.ConnectionDialog
            • com.compomics.util.gui.utils.DateChooser
            • com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.DirecTagSettingsDialog (implements com.compomics.util.gui.parameters.identification_parameters.AlgorithmSettingsDialog)
            • com.compomics.util.gui.parameters.identification_parameters.EnzymeSelectionDialog
            • com.compomics.util.gui.ExportFormatSelectionDialog
            • com.compomics.util.gui.export.graphics.ExportGraphicsDialog
            • com.compomics.util.gui.filehandling.FileDisplayDialog
            • com.compomics.util.gui.filehandling.FileSelectionDialog
            • com.compomics.util.gui.parameters.identification_parameters.FractionSettingsDialog
            • com.compomics.util.gui.genes.GeneDetailsDialog
            • com.compomics.util.gui.parameters.identification_parameters.GenePreferencesDialog
            • com.compomics.util.gui.error_handlers.HelpDialog
            • com.compomics.util.gui.parameters.IdentificationParametersEditionDialog
            • com.compomics.util.gui.parameters.identification_parameters.IdentificationParametersNameDialog
            • com.compomics.util.gui.parameters.IdentificationParametersOverviewDialog
            • com.compomics.util.gui.parameters.IdentificationParametersSelectionDialog
            • com.compomics.util.protein_sequences_manager.gui.sequences_import.ImportSequencesFromDnaDialog
            • com.compomics.util.protein_sequences_manager.gui.sequences_import.ImportSequencesFromFilesDialog
            • com.compomics.util.protein_sequences_manager.gui.sequences_import.ImportSequencesFromUniprotDialog
            • com.compomics.software.dialogs.JavaHomeDialog
            • com.compomics.software.dialogs.JavaMemoryDialog
            • com.compomics.software.dialogs.JavaSettingsDialog
            • com.compomics.util.gui.JExceptionDialog
            • com.compomics.util.gui.utils.user_choice.ListChooser
              • com.compomics.util.gui.utils.user_choice.list_choosers.PtmChooser
              • com.compomics.util.gui.utils.user_choice.list_choosers.StringListChooser
            • com.compomics.util.gui.parameters.identification_parameters.MatchesImportFiltersDialog
            • com.compomics.util.examples.MirroredSpectraTestDialog
            • com.compomics.util.gui.ptm.ModificationsDialog
            • com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.MsAmandaSettingsDialog (implements com.compomics.util.gui.parameters.identification_parameters.AlgorithmSettingsDialog)
            • com.compomics.util.experiment.massspectrometry.proteowizard.gui.MsConvertParametersDialog
            • com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.MsgfSettingsDialog (implements com.compomics.util.gui.parameters.identification_parameters.AlgorithmSettingsDialog)
            • com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.MyriMatchSettingsDialog (implements com.compomics.util.gui.parameters.identification_parameters.AlgorithmSettingsDialog)
            • com.compomics.util.gui.error_handlers.notification.NotesDialog
            • com.compomics.util.gui.error_handlers.notification.NotificationDialog
            • com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.NovorSettingsDialog (implements com.compomics.util.gui.parameters.identification_parameters.AlgorithmSettingsDialog)
            • com.compomics.util.gui.parameters.OldProcessingPreferencesDialog
            • com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.OmssaSettingsDialog (implements com.compomics.util.gui.parameters.identification_parameters.AlgorithmSettingsDialog)
            • com.compomics.software.settings.gui.PathSettingsDialog
            • com.compomics.software.dialogs.PeptideShakerSetupDialog
            • com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.PNovoSettingsDialog (implements com.compomics.util.gui.parameters.identification_parameters.AlgorithmSettingsDialog)
            • com.compomics.util.gui.PrivacySettingsDialog
            • com.compomics.util.gui.parameters.ProcessingPreferencesDialog
            • com.compomics.util.gui.waiting.waitinghandlers.ProgressDialog
            • com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX (implements com.compomics.util.waiting.WaitingHandler)
            • com.compomics.util.gui.parameters.identification_parameters.ProteinInferenceSettingsDialog
            • com.compomics.util.protein_sequences_manager.gui.ProteinSequencesManagerGUI
            • com.compomics.util.protein_sequences_manager.gui.preferences.ProteinSequencesPreferencesDialog
            • com.compomics.software.dialogs.ProteoWizardSetupDialog
            • com.compomics.util.gui.parameters.identification_parameters.PsmScoringSettingsDialog
            • com.compomics.util.gui.ptm.PtmDialog
            • com.compomics.util.gui.parameters.identification_parameters.PTMLocalizationParametersDialog
            • com.compomics.util.gui.export.report.ReportEditor
            • com.compomics.software.dialogs.ReporterSetupDialog
            • com.compomics.util.gui.SampleSelection
            • com.compomics.software.dialogs.SearchGuiSetupDialog
            • com.compomics.util.gui.parameters.identification_parameters.SearchSettingsDialog
            • com.compomics.util.protein_sequences_manager.gui.SequenceDbDetailsDialog
            • com.compomics.util.gui.parameters.identification_parameters.SequenceMatchingSettingsDialog
            • com.compomics.util.gui.genes.SpeciesDialog
            • com.compomics.util.gui.parameters.identification_parameters.SpectrumMatchingSettingsDialog
            • com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy.TaxonomyTreeDialog
            • com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.TideSettingsDialog (implements com.compomics.util.gui.parameters.identification_parameters.AlgorithmSettingsDialog)
            • com.compomics.util.gui.parameters.identification_parameters.ValidationQCPreferencesDialog
            • com.compomics.util.gui.parameters.identification_parameters.ValidationSettingsDialog
            • com.compomics.util.gui.VennDiagramDialog
            • com.compomics.util.gui.VennDiagramLegendLocationDialog
            • com.compomics.util.gui.VisibleTableColumnsDialog
            • com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog (implements com.compomics.util.waiting.WaitingHandler)
            • com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.XTandemSettingsDialog (implements com.compomics.util.gui.parameters.identification_parameters.AlgorithmSettingsDialog)
            • com.compomics.util.gui.XYPlotFiltersDialog
            • com.compomics.util.gui.XYPlottingDialog (implements com.compomics.util.gui.VisibleTableColumnsDialogParent)
        • java.awt.Frame (implements java.awt.MenuContainer)
          • javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • com.compomics.util.gui.DummyFrame
            • com.compomics.util.gui.FlamableJFrame (implements com.compomics.util.interfaces.Flamable)
            • com.compomics.util.examples.HelpWindow
            • com.compomics.util.gui.isotopic_calculator.IsotopeDistributionGui
            • com.compomics.util.gui.JFrameForBytes
            • com.compomics.util.examples.UtilitiesDemo
  • com.compomics.util.io.ConfigurationFile
  • com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy.ConnectionManager
  • com.compomics.util.experiment.Constants
  • com.compomics.util.db.components.Constructors
  • com.compomics.util.pride.prideobjects.Contact (implements com.compomics.util.pride.PrideObject, java.io.Serializable)
  • com.compomics.util.pride.prideobjects.ContactGroup (implements com.compomics.util.pride.PrideObject, java.io.Serializable)
  • com.compomics.util.pride.CvTerm (implements java.io.Serializable)
  • com.compomics.util.pdbfinder.das.readers.DasAlignment
  • com.compomics.util.pdbfinder.das.readers.DasAnnotationServerAlingmentReader
  • com.compomics.util.pdbfinder.das.readers.DasAnnotationServerResultReader
  • com.compomics.util.pdbfinder.das.readers.DasFeature
  • com.compomics.util.math.roc.DataRoc (implements com.compomics.util.math.statistics.ROC)
  • com.compomics.util.db.DBAccessor
  • com.compomics.util.db.DBAccessorGenerator
  • com.compomics.util.db.DBMetaData
  • com.compomics.util.general.DefaultOutputLoggerImplementation (implements com.compomics.util.interfaces.Logger)
  • com.compomics.util.gui.spectrum.DefaultSpectrumAnnotation (implements com.compomics.util.gui.interfaces.SpectrumAnnotation)
  • com.compomics.util.io.export.styles.DefaultStyle (implements com.compomics.util.io.export.WorkbookStyle)
  • com.compomics.util.db.components.DeleteableCode
  • com.compomics.util.db.DerbyUtil
  • com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters (implements com.compomics.util.experiment.identification.identification_parameters.IdentificationAlgorithmParameter, java.io.Serializable)
  • com.compomics.util.math.roc.DistributionRoc (implements com.compomics.util.math.statistics.ROC)
  • com.compomics.util.math.matrix.DoubleMatrix
  • com.compomics.util.protein_sequences_manager.DownloadingUtil
  • com.compomics.software.autoupdater.DownloadLatestZipFromRepo
  • com.compomics.util.preferences.DummyParameters (implements com.compomics.util.preferences.MarshallableParameter)
  • com.compomics.util.waiting.Duration
  • com.compomics.util.experiment.biology.ElementaryElement
  • com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblGenomesSpecies
  • com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblSpecies
  • com.compomics.util.experiment.biology.genes.ensembl.EnsemblVersion
  • com.compomics.util.protein.Enzyme (implements java.lang.Cloneable)
    • com.compomics.util.protein.DualEnzyme
    • com.compomics.util.protein.RegExEnzyme
  • com.compomics.util.experiment.biology.EnzymeFactory
  • com.compomics.util.exceptions.ExceptionHandler
    • com.compomics.util.exceptions.exception_handlers.CommandLineExceptionHandler
    • com.compomics.util.exceptions.exception_handlers.FrameExceptionHandler
    • com.compomics.util.exceptions.exception_handlers.WaitingDialogExceptionHandler
  • com.compomics.util.experiment.io.ExperimentIO
  • com.compomics.util.experiment.personalization.ExperimentObject (implements java.lang.Cloneable, java.io.Serializable)
    • com.compomics.util.experiment.biology.AminoAcidPattern (implements com.compomics.util.experiment.identification.amino_acid_tags.TagComponent)
    • com.compomics.util.experiment.biology.AminoAcidSequence (implements com.compomics.util.experiment.identification.amino_acid_tags.TagComponent)
    • com.compomics.util.experiment.io.identifications.idfilereaders.AndromedaIdfileReader (implements com.compomics.util.experiment.io.identifications.IdfileReader)
    • com.compomics.util.experiment.biology.Atom
      • com.compomics.util.experiment.biology.atoms.Carbon
      • com.compomics.util.experiment.biology.atoms.Helium
      • com.compomics.util.experiment.biology.atoms.Hydrogen
      • com.compomics.util.experiment.biology.atoms.Iodine
      • com.compomics.util.experiment.biology.atoms.Lithium
      • com.compomics.util.experiment.biology.atoms.Nitrogen
      • com.compomics.util.experiment.biology.atoms.Oxygen
      • com.compomics.util.experiment.biology.atoms.Phosphorus
      • com.compomics.util.experiment.biology.atoms.Selenium
      • com.compomics.util.experiment.biology.atoms.Sodium
      • com.compomics.util.experiment.biology.atoms.Sulfur
    • com.compomics.util.experiment.massspectrometry.Charge
    • com.compomics.util.experiment.io.identifications.idfilereaders.DirecTagIdfileReader (implements com.compomics.util.experiment.io.identifications.IdfileReader)
    • com.compomics.util.experiment.biology.Enzyme
    • com.compomics.util.experiment.identification.protein_sequences.FastaIndex
    • com.compomics.util.experiment.identification.Identification
      • com.compomics.util.experiment.identification.identifications.Ms2Identification
    • com.compomics.util.experiment.identification.IdentificationMatch
      • com.compomics.util.experiment.identification.matches.PeptideMatch
      • com.compomics.util.experiment.identification.matches.ProteinMatch
      • com.compomics.util.experiment.identification.matches.SpectrumMatch
    • com.compomics.util.experiment.identification.IdentificationMethod
    • com.compomics.util.experiment.biology.Ion
      • com.compomics.util.experiment.biology.ions.ElementaryIon
      • com.compomics.util.experiment.biology.ions.Glycan
      • com.compomics.util.experiment.biology.ions.ImmoniumIon
      • com.compomics.util.experiment.biology.ions.PeptideFragmentIon
      • com.compomics.util.experiment.biology.ions.PrecursorIon
      • com.compomics.util.experiment.biology.ions.RelatedIon
      • com.compomics.util.experiment.biology.ions.ReporterIon
      • com.compomics.util.experiment.biology.ions.TagFragmentIon
    • com.compomics.util.experiment.identification.matches.IonMatch
    • com.compomics.util.experiment.biology.MassGap (implements com.compomics.util.experiment.identification.amino_acid_tags.TagComponent)
    • com.compomics.util.experiment.io.massspectrometry.MgfIndex
    • com.compomics.util.experiment.identification.matches.ModificationMatch
    • com.compomics.util.experiment.io.identifications.idfilereaders.MsAmandaIdfileReader (implements com.compomics.util.experiment.io.identifications.IdfileReader)
    • com.compomics.util.experiment.MsExperiment
    • com.compomics.util.experiment.io.identifications.idfilereaders.MzIdentMLIdfileReader (implements com.compomics.util.experiment.io.identifications.IdfileReader)
    • com.compomics.util.experiment.io.identifications.MzIdentMLIdfileSearchParametersConverter
    • com.compomics.util.experiment.biology.NeutralLoss
    • com.compomics.util.experiment.io.identifications.idfilereaders.NovorIdfileReader (implements com.compomics.util.experiment.io.identifications.IdfileReader)
    • com.compomics.util.experiment.massspectrometry.Peak
    • com.compomics.util.experiment.io.identifications.idfilereaders.PepNovoIdfileReader (implements com.compomics.util.experiment.io.identifications.IdfileReader)
    • com.compomics.util.experiment.biology.Peptide
    • com.compomics.util.experiment.io.identifications.idfilereaders.PNovoIdfileReader (implements com.compomics.util.experiment.io.identifications.IdfileReader)
    • com.compomics.util.experiment.massspectrometry.Precursor
    • com.compomics.util.experiment.biology.Protein
    • com.compomics.util.experiment.ProteomicAnalysis
    • com.compomics.util.experiment.biology.PTM
    • com.compomics.util.experiment.quantification.Quantification
      • com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
    • com.compomics.util.experiment.quantification.reporterion.ReporterMethodFactory
    • com.compomics.util.experiment.biology.Sample
    • com.compomics.util.experiment.SampleAnalysisSet
    • com.compomics.util.experiment.massspectrometry.Spectrum
      • com.compomics.util.experiment.massspectrometry.MS1Spectrum
      • com.compomics.util.experiment.massspectrometry.MSnSpectrum
    • com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
      • com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption
      • com.compomics.util.experiment.identification.spectrum_assumptions.TagAssumption (implements com.compomics.util.experiment.personalization.UrParameter)
    • com.compomics.util.experiment.identification.amino_acid_tags.Tag
    • com.compomics.util.experiment.io.identifications.idfilereaders.TideIdfileReader (implements com.compomics.util.experiment.io.identifications.IdfileReader)
  • com.compomics.util.Export
  • com.compomics.util.io.export.ExportScheme (implements java.io.Serializable)
  • com.compomics.util.io.export.ExportWriter
    • com.compomics.util.io.export.writers.ExcelWriter
    • com.compomics.util.io.export.writers.TextWriter
  • com.compomics.util.messages.FeedBack
  • com.compomics.util.FileAndFileFilter
  • com.compomics.software.autoupdater.FileDAO
    • com.compomics.software.autoupdater.GUIFileDAO
    • com.compomics.software.autoupdater.HeadlessFileDAO
  • javax.swing.filechooser.FileFilter
    • com.compomics.util.io.filefilters.DatFileFilter
    • com.compomics.util.io.filefilters.DtaFileFilter
    • com.compomics.util.io.filefilters.FastaFileFilter
    • com.compomics.util.io.FilenameExtensionFilter (implements java.io.FilenameFilter)
    • com.compomics.util.io.filefilters.JpegFileFilter
    • com.compomics.util.io.filefilters.MgfFileFilter
    • com.compomics.util.io.filefilters.Ms2FileFilter
    • com.compomics.util.io.filefilters.MzDataFileFilter
    • com.compomics.util.io.filefilters.MzMlFileFilter
    • com.compomics.util.io.filefilters.MzXmlFileFilter
    • com.compomics.util.io.filefilters.OmxFileFilter
    • com.compomics.util.io.filefilters.OutFileFilter
    • com.compomics.util.io.filefilters.PdfFileFilter
    • com.compomics.util.io.filefilters.PeffFileFilter
    • com.compomics.util.io.filefilters.PepXmlFileFilter
    • com.compomics.util.io.filefilters.PklFileFilter
    • com.compomics.util.io.filefilters.PklSpoFileFilter
    • com.compomics.util.io.filefilters.PkxFileFilter
    • com.compomics.util.io.filefilters.PngFileFilter
    • com.compomics.util.io.filefilters.ProtXmlFileFilter
    • com.compomics.util.io.filefilters.SequestParamsFileFilter
    • com.compomics.util.io.filefilters.SvgFileFilter
    • com.compomics.util.io.filefilters.TiffFileFilter
    • com.compomics.util.io.filefilters.XmlFileFilter
  • com.compomics.util.io.filefilters.FileFilterUtils
  • com.compomics.util.general.FileLoggerImplementation (implements com.compomics.util.interfaces.Logger)
  • com.compomics.util.io.FileSystemAccessor
  • com.compomics.util.pdbfinder.FindPdbForUniprotAccessions
  • com.compomics.util.io.FolderMonitor (implements java.lang.Runnable)
  • com.compomics.util.preferences.FractionSettings (implements java.io.Serializable)
  • com.compomics.util.gui.renderers.FragmentIonTableCellRenderer (implements javax.swing.table.TableCellRenderer)
  • com.compomics.util.io.FTP
  • com.compomics.util.io.FTPClient
  • com.compomics.util.io.FTPDownloader
  • com.compomics.util.experiment.biology.genes.GeneFactory
  • com.compomics.util.experiment.biology.genes.ensembl.GeneMapping
  • com.compomics.util.experiment.biology.genes.GeneMaps (implements java.io.Serializable)
  • com.compomics.util.preferences.GenePreferences (implements java.io.Serializable)
  • javax.servlet.GenericServlet (implements java.io.Serializable, javax.servlet.Servlet, javax.servlet.ServletConfig)
    • javax.servlet.http.HttpServlet (implements java.io.Serializable)
      • com.compomics.util.general.servlet.MassCalcServlet
  • com.compomics.util.db.components.GettersAndSetters
  • com.compomics.util.experiment.biology.GlyconFactory
  • com.compomics.util.experiment.biology.genes.go.GoDomains
  • com.compomics.util.experiment.biology.genes.go.GoMapping
  • com.compomics.util.gui.GuiUtilities
  • com.compomics.util.protein.Header (implements java.lang.Cloneable, java.io.Serializable)
  • com.compomics.util.experiment.identification.IdentificationDB (implements java.io.Serializable)
  • com.compomics.util.preferences.IdentificationParameters (implements com.compomics.util.preferences.MarshallableParameter, java.io.Serializable)
  • com.compomics.util.experiment.identification.identification_parameters.IdentificationParametersFactory
  • com.compomics.util.experiment.identification.parameters_cli.IdentificationParametersInputBean
  • com.compomics.util.experiment.io.identifications.IdfileReaderFactory
  • com.compomics.util.preferences.IdMatchValidationPreferences (implements java.io.Serializable)
  • java.io.InputStream (implements java.io.Closeable)
    • java.io.FilterInputStream
      • com.compomics.util.io.MonitorableInputStream (implements com.compomics.util.interfaces.Monitorable)
        • com.compomics.util.io.MonitorableFileInputStream
  • com.compomics.util.db.components.InstanceVariables
  • com.compomics.util.pride.prideobjects.Instrument (implements com.compomics.util.pride.PrideObject, java.io.Serializable)
  • com.compomics.util.experiment.identification.psm_scoring.psm_scores.IntensityRankScore
  • com.compomics.util.io.json.adapter.InterfaceAdapter<T> (implements com.google.gson.JsonDeserializer<T>, com.google.gson.JsonSerializer<T>)
  • com.compomics.util.experiment.biology.IonFactory
  • com.compomics.util.experiment.identification.spectrum_annotation.IonMatchKeysCache
  • com.compomics.util.general.IsotopicDistribution
  • com.compomics.util.general.IsotopicDistributionSpectrum (implements com.compomics.util.interfaces.SpectrumFile)
  • com.compomics.util.general.IsotopicElement
  • com.compomics.software.autoupdater.JarFileFilter (implements java.io.FilenameFilter)
  • com.compomics.util.gui.JOptionEditorPane
  • com.compomics.util.io.json.JsonMarshaller
    • com.compomics.util.io.json.marshallers.IdentificationParametersMarshaller
    • com.compomics.util.io.json.marshallers.PrideMarshaller
    • com.compomics.util.io.json.marshallers.PTMFactoryMarshaller
  • com.compomics.util.maps.KeyUtils
  • com.compomics.util.math.clustering.KMeansClustering
  • com.compomics.util.math.clustering.settings.KMeansClusteringSettings (implements java.io.Serializable)
  • com.compomics.util.preferences.LastSelectedFolder (implements java.io.Serializable)
  • com.compomics.util.math.statistics.linear_regression.LinearRegression
  • com.compomics.util.io.MascotEnzymeReader
  • com.compomics.util.general.MassCalc
  • com.compomics.util.experiment.identification.ptm.ptmscores.MDScore
  • com.compomics.util.math.statistics.linear_regression.regressions.MedianRegression
  • com.compomics.util.memory.MemoryConsumptionStatus
  • com.compomics.software.autoupdater.MetaDataXMLParser
  • com.compomics.util.experiment.io.massspectrometry.MgfFileIterator
  • com.compomics.util.experiment.io.massspectrometry.MgfReader
  • com.compomics.util.protein.ModificationFactory
  • com.compomics.util.protein.ModificationImplementation (implements java.lang.Cloneable, com.compomics.util.interfaces.Modification, java.io.Serializable)
  • com.compomics.util.gui.protein.ModificationProfile
  • com.compomics.util.protein.ModificationTemplate
  • com.compomics.util.protein.MolecularFormula
  • com.compomics.util.gui.MonitorDimension
  • com.compomics.util.experiment.io.massspectrometry.export.Ms2Exporter
  • com.compomics.util.experiment.identification.psm_scoring.psm_scores.MS2MzFidelityScore
  • com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsAmandaParameters (implements com.compomics.util.experiment.identification.identification_parameters.IdentificationAlgorithmParameter)
  • com.compomics.util.experiment.massspectrometry.proteowizard.MsConvertParameters
  • com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsgfParameters (implements com.compomics.util.experiment.identification.identification_parameters.IdentificationAlgorithmParameter)
  • com.compomics.util.experiment.biology.mutations.Mutation
  • com.compomics.util.experiment.biology.mutations.MutationFactory
  • com.compomics.util.experiment.biology.mutations.MutationMatrix (implements java.io.Serializable)
  • com.compomics.util.experiment.identification.identification_parameters.tool_specific.MyriMatchParameters (implements com.compomics.util.experiment.identification.identification_parameters.IdentificationAlgorithmParameter)
  • com.compomics.util.experiment.identification.spectrum_annotation.NeutralLossesMap (implements java.io.Serializable)
  • com.compomics.util.experiment.identification.protein_inference.proteintree.Node (implements java.io.Serializable)
  • com.compomics.util.math.statistics.distributions.NonSymmetricalNormalDistribution (implements com.compomics.util.math.statistics.Distribution)
  • com.compomics.util.math.statistics.distributions.NormalDistribution (implements com.compomics.util.math.statistics.Distribution)
  • com.compomics.util.experiment.normalization.NormalizationFactors (implements java.io.Serializable)
  • com.compomics.util.math.statistics.distributions.NormalKernelDensityEstimator
  • com.compomics.util.experiment.identification.identification_parameters.tool_specific.NovorParameters (implements com.compomics.util.experiment.identification.identification_parameters.IdentificationAlgorithmParameter)
  • com.compomics.util.nucleotide.NucleotideSequence
  • com.compomics.util.nucleotide.NucleotideSequenceImpl (implements com.compomics.util.interfaces.Sequence)
  • com.compomics.util.db.ObjectsCache
  • com.compomics.util.db.ObjectsDB (implements java.io.Serializable)
  • com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters (implements com.compomics.util.experiment.identification.identification_parameters.IdentificationAlgorithmParameter)
  • com.compomics.util.experiment.patient.Patient
  • com.compomics.util.experiment.patient.PatientInformation
  • com.compomics.util.pdbfinder.pdb.PdbBlock
  • com.compomics.util.pdbfinder.pdb.PdbParameter
  • com.compomics.util.experiment.refinementparameters.PepnovoAssumptionDetails (implements com.compomics.util.experiment.personalization.UrParameter)
  • com.compomics.util.experiment.identification.identification_parameters.tool_specific.PepnovoParameters (implements com.compomics.util.experiment.identification.identification_parameters.IdentificationAlgorithmParameter)
  • com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter (implements java.io.Serializable)
  • com.compomics.util.experiment.identification.matches_iterators.PeptideMatchesIterator
  • com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader (implements com.compomics.util.experiment.io.identifications.IdfileReader)
  • com.compomics.util.db.components.PersistableCode
  • com.compomics.util.experiment.identification.ptm.ptmscores.PhosphoRS
  • com.compomics.util.io.PklFile
  • com.compomics.util.experiment.identification.identification_parameters.tool_specific.PNovoParameters (implements com.compomics.util.experiment.identification.identification_parameters.IdentificationAlgorithmParameter)
  • com.compomics.util.experiment.identification.psm_scoring.psm_scores.PrecursorAccuracy
  • com.compomics.util.pride.prideobjects.webservice.query.PrideFilter
  • com.compomics.util.pride.PrideObjectsFactory
  • com.compomics.util.pride.PrideWebService
  • com.compomics.util.pride.validation.PrideXmlValidator
  • com.compomics.util.math.statistics.linear_regression.filters.ProbabilityFilter
  • com.compomics.util.preferences.ProcessingPreferences
  • com.compomics.util.io.PropertiesManager
  • com.compomics.util.protein.Protein
  • com.compomics.util.preferences.ProteinInferencePreferences (implements java.io.Serializable)
  • com.compomics.util.experiment.identification.matches_iterators.ProteinMatchesIterator
  • com.compomics.util.gui.protein.ProteinSequencePane
  • com.compomics.util.protein_sequences_manager.ProteinSequencesManager
  • com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree
  • com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree.PeptideIterator (implements java.util.Iterator<E>)
  • com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory
  • com.compomics.util.pride.prideobjects.Protocol (implements com.compomics.util.pride.PrideObject, java.io.Serializable)
  • com.compomics.util.experiment.identification.matches_iterators.PsmIterator
  • com.compomics.util.preferences.PsmScoringPreferences (implements java.io.Serializable)
  • com.compomics.util.preferences.PSProcessingPreferences (implements java.io.Serializable)
  • com.compomics.util.experiment.biology.PTMFactory (implements java.io.Serializable)
  • com.compomics.util.preferences.PTMScoringPreferences (implements java.io.Serializable)
  • com.compomics.util.experiment.identification.identification_parameters.PtmSettings (implements java.io.Serializable)
  • com.compomics.util.experiment.identification.ptm.PtmSiteMapping
  • com.compomics.util.experiment.identification.ptm.PtmtableContent
  • com.compomics.util.pride.PtmToPrideMap (implements java.io.Serializable)
  • com.compomics.util.io.PushBackStringReader
  • com.compomics.util.experiment.quantification.reporterion.Reagent (implements java.io.Serializable)
  • com.compomics.util.pride.prideobjects.Reference (implements com.compomics.util.pride.PrideObject, java.io.Serializable)
  • com.compomics.util.gui.spectrum.ReferenceArea
  • com.compomics.util.pride.prideobjects.ReferenceGroup (implements com.compomics.util.pride.PrideObject, java.io.Serializable)
  • com.compomics.util.math.statistics.linear_regression.RegressionStatistics
  • com.compomics.util.experiment.quantification.reporterion.ReporterMethod (implements java.io.Serializable)
  • com.compomics.util.gui.events.RescalingEvent
  • com.compomics.util.db.components.RetrievableCode
  • javax.swing.RowFilter<M,I>
    • com.compomics.util.gui.XYPlottingDialog.SelectedValuesTableFilter
  • com.compomics.util.pride.prideobjects.Sample (implements com.compomics.util.pride.PrideObject, java.io.Serializable)
  • com.compomics.util.experiment.identification.identification_parameters.SearchParameters (implements com.compomics.util.preferences.MarshallableParameter, java.io.Serializable)
  • com.compomics.util.experiment.identification.protein_sequences.SequenceFactory
  • com.compomics.util.experiment.identification.protein_sequences.SequenceFactory.HeaderIterator
  • com.compomics.util.experiment.identification.protein_sequences.SequenceFactory.ProteinIterator
  • com.compomics.util.preferences.SequenceMatchingPreferences (implements java.io.Serializable)
  • com.compomics.util.experiment.identification.amino_acid_tags.SequenceSegment
  • com.compomics.util.io.SerializationUtils
  • com.compomics.util.experiment.ShotgunProtocol (implements java.io.Serializable)
  • com.compomics.util.math.statistics.linear_regression.regressions.SimpleLinearRegression
  • com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
  • com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationSettings
  • com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
    • com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator
    • com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.TagSpectrumAnnotator
  • com.compomics.util.experiment.quantification.spectrumcounting.SpectrumCounting
  • com.compomics.util.experiment.massspectrometry.SpectrumFactory
  • com.compomics.software.SplashScreen
  • com.compomics.util.io.StartBrowser
  • com.compomics.util.pdbfinder.das.readers.StartEndPosition
  • com.compomics.util.io.StreamGobbler (implements java.lang.Runnable)
  • com.compomics.util.gui.utils.SwingUtils
  • com.compomics.util.sun.SwingWorker
  • com.compomics.util.gui.TableMouseWheelListener (implements java.awt.event.MouseWheelListener)
  • com.compomics.util.gui.TableProperties
  • com.compomics.util.gui.TableScrollBarListener (implements java.awt.event.AdjustmentListener)
  • com.compomics.util.experiment.identification.TagFactory
  • com.compomics.util.experiment.identification.amino_acid_tags.matchers.TagMatcher
  • com.compomics.util.io.compression.TarUtils
  • com.compomics.util.gui.filehandling.TempFilesManager
  • com.compomics.util.junit.TestCaseLM
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • com.compomics.util.db.GeneratorException
      • java.io.IOException
        • com.compomics.util.io.FtpProtocolException
          • com.compomics.util.io.FtpConnectionException
          • com.compomics.util.io.FtpLoginException
      • com.compomics.util.general.UnknownElementMassException
  • com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters (implements com.compomics.util.experiment.identification.identification_parameters.IdentificationAlgorithmParameter)
  • com.compomics.software.ToolFactory
  • com.compomics.util.general.Translate
  • com.google.gson.TypeAdapter<T>
    • com.compomics.util.io.json.adapter.FileAdapter
  • com.compomics.util.protein_sequences_manager.UniProtQuery
  • com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy
  • com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy.UniprotTaxonomyProvider
  • com.compomics.util.experiment.units.UnitOfMeasurement (implements java.io.Serializable)
  • com.compomics.util.db.components.UpdateableCode
  • com.compomics.util.Util
  • com.compomics.util.gui.UtilitiesGUIDefaults
  • com.compomics.software.settings.UtilitiesPathPreferences
  • com.compomics.util.preferences.UtilitiesUserPreferences (implements java.io.Serializable)
  • com.compomics.util.preferences.ValidationQCPreferences (implements java.io.Serializable)
  • com.compomics.util.math.VennDiagram
  • com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl (implements com.compomics.util.waiting.WaitingHandler)
  • com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy (implements com.compomics.util.waiting.WaitingHandler)
  • com.compomics.software.autoupdater.WebDAO
  • com.compomics.util.pride.validation.XMLValidationErrorHandler (implements org.xml.sax.ErrorHandler)
  • com.compomics.util.experiment.identification.identification_parameters.tool_specific.XtandemParameters (implements com.compomics.util.experiment.identification.identification_parameters.IdentificationAlgorithmParameter)
  • com.compomics.util.XYZDataPoint
  • java.util.zip.ZipFile (implements java.io.Closeable)
    • java.util.jar.JarFile
      • com.compomics.software.autoupdater.MavenJarFile
  • com.compomics.util.io.compression.ZipUtils

Interface Hierarchy

• com.compomics.util.gui.parameters.identification_parameters.AlgorithmSettingsDialog
• java.lang.Comparable<T>
  • com.compomics.util.interfaces.Modification
  • com.compomics.util.interfaces.SpectrumFile
• com.compomics.util.interfaces.Connectable
• com.compomics.util.db.interfaces.DBElement
• com.compomics.util.db.interfaces.Deleteable
• com.compomics.util.experiment.filtering.Filter
• com.compomics.util.experiment.filtering.FilterItem
• com.compomics.util.interfaces.Flamable
• com.compomics.util.experiment.io.identifications.IdfileReader
• com.compomics.software.dialogs.JavaHomeOrMemoryDialogParent
• com.compomics.util.interfaces.Logger
• com.compomics.util.preferences.MarshallableParameter
• com.compomics.util.interfaces.Monitorable
• com.compomics.util.gui.error_handlers.notification.NotificationDialogParent
• com.compomics.software.settings.PathKey
• com.compomics.util.db.interfaces.Persistable
• com.compomics.util.interfaces.PickUp
• com.compomics.util.pride.PrideObject
• com.compomics.util.db.interfaces.Retrievable
• com.compomics.util.math.statistics.ROC
• com.compomics.util.interfaces.Sequence
• java.io.Serializable
  • com.compomics.util.math.statistics.Distribution
  • com.compomics.util.io.export.ExportFactory
  • com.compomics.util.io.export.ExportFeature
  • com.compomics.util.experiment.identification.identification_parameters.IdentificationAlgorithmParameter
  • com.compomics.util.experiment.personalization.UrParameter
• com.compomics.util.gui.interfaces.SpectrumAnnotation
• com.compomics.util.gui.interfaces.SpectrumPanelListener
• com.compomics.util.interfaces.TableValueWrapper
• com.compomics.util.experiment.identification.amino_acid_tags.TagComponent
• com.compomics.util.db.interfaces.Updateable
• com.compomics.util.gui.parameters.identification_parameters.ValidationQCPreferencesDialogParent
• com.compomics.util.gui.VisibleTableColumnsDialogParent
• com.compomics.util.waiting.WaitingActionListener
• com.compomics.util.waiting.WaitingHandler
• com.compomics.util.io.export.WorkbookStyle

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • com.compomics.software.settings.UtilitiesPathPreferences.UtilitiesPathKey (implements com.compomics.software.settings.PathKey)
    • com.compomics.util.enumeration.OperatingSystemEnum
    • com.compomics.util.enumeration.MolecularElement
    • com.compomics.util.enumeration.ImageType
    • com.compomics.util.enumeration.CompomicsTools
    • com.compomics.util.experiment.biology.Ion.IonType
    • com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblGenomesSpecies.EnsemblGenomeDivision
    • com.compomics.util.experiment.filtering.FilterItemComparator
    • com.compomics.util.experiment.identification.IdentificationMatch.MatchType
    • com.compomics.util.experiment.identification.Advocate.AdvocateType
    • com.compomics.util.experiment.identification.identification_parameters.SearchParameters.MassAccuracyType
    • com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters.CometOutputFormat
    • com.compomics.util.experiment.identification.matches.IonMatch.MzErrorType
    • com.compomics.util.experiment.identification.parameters_cli.IdentificationParametersCLIParams
    • com.compomics.util.experiment.identification.psm_scoring.PsmScores
    • com.compomics.util.experiment.identification.ptm.PtmScore
    • com.compomics.util.experiment.massspectrometry.FragmentationMethod (implements java.io.Serializable)
    • com.compomics.util.experiment.massspectrometry.proteowizard.ProteoWizardFilter
    • com.compomics.util.experiment.massspectrometry.proteowizard.MsFormat
    • com.compomics.util.experiment.quantification.Quantification.QuantificationMethod
    • com.compomics.util.experiment.quantification.spectrumcounting.SpectrumCounting.SpectrumCountingMethod
    • com.compomics.util.experiment.units.StandardUnit
    • com.compomics.util.experiment.units.MetricsPrefix (implements java.io.Serializable)
    • com.compomics.util.gui.XYPlottingDialog.PlottingDialogPlotType
    • com.compomics.util.gui.VennDiagramPanel.VennDiagramType
    • com.compomics.util.gui.parameters.IdentificationParametersSelectionDialog.StartupMode
    • com.compomics.util.gui.spectrum.GraphicsPanel.DrawingStyle
    • com.compomics.util.gui.spectrum.GraphicsPanel.GraphicsPanelType
    • com.compomics.util.io.export.ExportFormat
    • com.compomics.util.math.roc.DataRoc.RocInterpolation
    • com.compomics.util.messages.FeedBack.FeedBackType
    • com.compomics.util.preferences.SequenceMatchingPreferences.MatchingType
    • com.compomics.util.preferences.SearchGuiOutputOption
    • com.compomics.util.preferences.ProcessingPreferences.ProcessingType
    • com.compomics.util.preferences.MarshallableParameter.Type
    • com.compomics.util.pride.prideobjects.webservice.file.FileType
    • com.compomics.util.pride.prideobjects.webservice.PrideQuery
    • com.compomics.util.pride.prideobjects.webservice.query.PrideFilterType
    • com.compomics.util.protein.Header.DatabaseType
    • com.compomics.util.protein_sequences_manager.enums.SequenceInputType
    • com.compomics.util.protein_sequences_manager.enums.SequenceContentType
    • com.compomics.util.protein_sequences_manager.enums.ModelOrganism
    • com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy.QueryType