Class Hierarchy
- java.lang.Object
- com.compomics.util.protein.AASequenceImpl (implements com.compomics.util.interfaces.Sequence)
- javax.swing.table.AbstractTableModel (implements java.io.Serializable, javax.swing.table.TableModel)
- com.compomics.util.experiment.identification.AdvocateFactory
- 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.biology.AminoAcidPattern (implements java.io.Serializable)
- com.compomics.util.preferences.AnnotationPreferences (implements java.io.Serializable)
- com.compomics.util.examples.BareBonesBrowserLaunch
- com.compomics.util.math.BasicMathFunctions
- com.compomics.util.BinaryArrayImpl
- com.compomics.util.db.ColumnTypeConverter
- com.compomics.util.general.CommandLineParser
- com.compomics.software.CommandLineUtils
- com.compomics.util.CompareVersionNumbers (implements java.util.Comparator<T>)
- com.compomics.software.CompomicsWrapper
- java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
- 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.experiment.quantification.reporterion.CorrectionFactor
- 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.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.db.components.DeleteableCode
- com.compomics.util.experiment.biology.ElementaryElement
- com.compomics.util.protein.Enzyme (implements java.lang.Cloneable)
- com.compomics.util.experiment.biology.EnzymeFactory
- com.compomics.util.general.ExceptionHandler
- com.compomics.util.experiment.io.ExperimentIO
- com.compomics.util.experiment.personalization.ExperimentObject (implements java.lang.Cloneable, java.io.Serializable)
- 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.Hydrogen
- 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.Sulfur
- com.compomics.util.experiment.massspectrometry.Charge
- com.compomics.util.experiment.biology.Enzyme
- com.compomics.util.experiment.identification.FastaIndex
- com.compomics.util.experiment.identification.Identification
- 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.identification.matches.IonMatch
- com.compomics.util.experiment.io.massspectrometry.MgfIndex
- com.compomics.util.experiment.identification.matches.ModificationMatch
- com.compomics.util.experiment.MsExperiment
- com.compomics.util.experiment.biology.NeutralLoss
- com.compomics.util.experiment.massspectrometry.Peak
- com.compomics.util.experiment.biology.Peptide
- com.compomics.util.experiment.identification.PeptideAssumption
- com.compomics.util.experiment.identification.advocates.PostProcessor (implements com.compomics.util.experiment.identification.Advocate)
- 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.QuantificationMatch
- com.compomics.util.experiment.quantification.Ratio
- com.compomics.util.experiment.quantification.reporterion.ReporterMethodFactory
- com.compomics.util.experiment.biology.Sample
- com.compomics.util.experiment.SampleAnalysisSet
- com.compomics.util.experiment.identification.advocates.SearchEngine (implements com.compomics.util.experiment.identification.Advocate)
- com.compomics.util.experiment.massspectrometry.Spectrum
- com.compomics.util.experiment.massspectrometry.MS1Spectrum
- com.compomics.util.experiment.massspectrometry.MSnSpectrum
- com.compomics.util.Export
- com.compomics.util.messages.FeedBack
- javax.swing.filechooser.FileFilter
- 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.gui.renderers.FragmentIonTableCellRenderer (implements javax.swing.table.TableCellRenderer)
- com.compomics.util.io.FTP
- com.compomics.util.io.FTPClient
- com.compomics.util.experiment.annotation.gene.GeneFactory
- 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.db.components.GettersAndSetters
- com.compomics.util.experiment.biology.GlyconFactory
- com.compomics.util.experiment.annotation.go.GOFactory
- 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.experiment.io.identifications.IdentificationParametersReader
- com.compomics.util.experiment.io.identifications.IdfileReaderFactory
- com.compomics.util.preferences.IdFilter (implements java.io.Serializable)
- java.io.InputStream (implements java.io.Closeable)
- 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.biology.IonFactory
- com.compomics.util.general.IsotopicDistribution
- com.compomics.util.general.IsotopicDistributionSpectrum (implements com.compomics.util.interfaces.SpectrumFile)
- com.compomics.util.general.IsotopicElement
- com.compomics.util.io.MascotEnzymeReader
- com.compomics.util.experiment.refinementparameters.MascotScore (implements com.compomics.util.experiment.personalization.UrParameter)
- com.compomics.util.general.MassCalc
- 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.preferences.ModificationProfile (implements java.io.Serializable)
- com.compomics.util.protein.ModificationTemplate
- com.compomics.util.protein.MolecularFormula
- com.compomics.util.gui.MonitorDimension
- com.compomics.util.experiment.biology.Mutation
- com.compomics.util.experiment.biology.MutationFactory
- com.compomics.util.experiment.identification.NeutralLossesMap (implements java.io.Serializable)
- com.compomics.util.experiment.identification.protein_inference.proteintree.Node
- com.compomics.util.experiment.identification.protein_inference.proteintree.NodeFactory
- 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.pdbfinder.pdb.PdbBlock
- com.compomics.util.pdbfinder.pdb.PdbParameter
- com.compomics.util.denovo.PeptideAssumptionDetails (implements com.compomics.util.experiment.personalization.UrParameter)
- com.compomics.util.db.components.PersistableCode
- com.compomics.util.io.PklFile
- com.compomics.util.pride.PrideObjectsFactory
- com.compomics.util.pride.validation.PrideXmlValidator
- com.compomics.util.preferences.ProcessingPreferences (implements java.io.Serializable)
- com.compomics.util.io.PropertiesManager
- com.compomics.util.protein.Protein
- com.compomics.util.gui.protein.ProteinSequencePane
- com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree
- com.compomics.util.pride.prideobjects.Protocol (implements com.compomics.util.pride.PrideObject, java.io.Serializable)
- com.compomics.util.experiment.identification.scoring.PsmScores
- com.compomics.util.experiment.biology.PTMFactory (implements java.io.Serializable)
- com.compomics.util.experiment.identification.ptm.PTMLocationScores
- com.compomics.util.preferences.PTMScoringPreferences (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.QuantificationDB (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.experiment.quantification.reporterion.ReporterMethod
- com.compomics.util.gui.events.RescalingEvent
- com.compomics.util.db.components.RetrievableCode
- javax.swing.RowFilter<M,I>
- com.compomics.util.pride.prideobjects.Sample (implements com.compomics.util.pride.PrideObject, java.io.Serializable)
- com.compomics.util.experiment.identification.SearchParameters (implements java.io.Serializable)
- com.compomics.util.experiment.identification.SearchParametersInputBean
- com.compomics.util.experiment.identification.SequenceFactory
- com.compomics.util.io.SerializationUtils
- com.compomics.util.experiment.identification.SpectrumAnnotator
- com.compomics.util.experiment.quantification.spectrumcounting.SpectrumCounting
- com.compomics.util.experiment.massspectrometry.SpectrumFactory
- com.compomics.util.experiment.filters.massspectrometry.SpectrumFilter (implements java.io.Serializable)
- com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.And
- com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.CombFilter
- com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.FingerprintPattern
- com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.MzFilter
- com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.Or
- com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.PeakFilter
- 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.sun.SwingWorker
- com.compomics.util.experiment.identification.TagFactory
- com.compomics.util.io.TarUtils
- com.compomics.util.junit.TestCaseLM
- java.lang.Throwable (implements java.io.Serializable)
- com.compomics.software.ToolFactory
- com.compomics.util.general.Translate
- com.compomics.util.db.components.UpdateableCode
- com.compomics.util.Util
- com.compomics.util.gui.UtilitiesGUIDefaults
- com.compomics.util.preferences.UtilitiesUserPreferences (implements java.io.Serializable)
- com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl (implements com.compomics.util.waiting.WaitingHandler)
- com.compomics.util.pride.validation.XMLValidationErrorHandler (implements org.xml.sax.ErrorHandler)
- com.compomics.util.gui.XYPlottingDialog.NormalKernelDensityEstimator
- com.compomics.util.XYZDataPoint
Interface Hierarchy
Enum Hierarchy
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