Hierarchy For All Packages

Package Hierarchies:

• bacnet,
• bacnet.datamodel.annotation,
• bacnet.datamodel.dataset,
• bacnet.datamodel.expdesign,
• bacnet.datamodel.phylogeny,
• bacnet.datamodel.proteomics,
• bacnet.datamodel.sequence,
• bacnet.datamodel.sequenceNCBI,
• bacnet.e4.rap,
• bacnet.e4.rap.setup,
• bacnet.expressionAtlas,
• bacnet.expressionAtlas.core,
• bacnet.genomeBrowser,
• bacnet.genomeBrowser.core,
• bacnet.genomeBrowser.dialog,
• bacnet.genomeBrowser.tracksGUI,
• bacnet.handler,
• bacnet.raprcp,
• bacnet.reader,
• bacnet.scripts,
• bacnet.scripts.arrayexpress,
• bacnet.scripts.blast,
• bacnet.scripts.core,
• bacnet.scripts.core.normalization,
• bacnet.scripts.core.stat,
• bacnet.scripts.core.vennDiagram,
• bacnet.scripts.database,
• bacnet.scripts.genome,
• bacnet.scripts.listeriomics,
• bacnet.scripts.listeriomics.ArrayExpress,
• bacnet.scripts.listeriomics.nterm,
• bacnet.scripts.listeriomics.srna,
• bacnet.scripts.listeriomics.technology,
• bacnet.scripts.phylogeny,
• bacnet.sequenceTools,
• bacnet.swt,
• bacnet.table,
• bacnet.table.core,
• bacnet.table.gui,
• bacnet.utils,
• bacnet.views,
• org.biojava3.core.exceptions,
• org.biojava3.core.sequence,
• org.biojava3.core.sequence.compound,
• org.biojava3.core.sequence.edits,
• org.biojava3.core.sequence.features,
• org.biojava3.core.sequence.io,
• org.biojava3.core.sequence.io.template,
• org.biojava3.core.sequence.io.util,
• org.biojava3.core.sequence.loader,
• org.biojava3.core.sequence.location,
• org.biojava3.core.sequence.location.template,
• org.biojava3.core.sequence.storage,
• org.biojava3.core.sequence.template,
• org.biojava3.core.sequence.transcription,
• org.biojava3.core.sequence.views,
• org.biojava3.core.util,
• org.biojava3.genome,
• org.biojava3.genome.parsers.geneid,
• org.biojava3.genome.parsers.gff,
• org.biojava3.genome.query,
• org.biojava3.genome.uniprot,
• org.biojava3.genome.util

Class Hierarchy

• java.lang.Object
  • java.util.AbstractCollection<E> (implements java.util.Collection<E>)
    • java.util.AbstractList<E> (implements java.util.List<E>)
      • java.util.ArrayList<E> (implements java.lang.Cloneable, java.util.List<E>, java.util.RandomAccess, java.io.Serializable)
        • org.biojava3.genome.parsers.gff.FeatureList
  • org.biojava3.core.sequence.template.AbstractCompound (implements org.biojava3.core.sequence.template.Compound)
    • org.biojava3.core.sequence.compound.AminoAcidCompound
    • org.biojava3.core.sequence.compound.CodonCompound
    • org.biojava3.core.sequence.compound.NucleotideCompound (implements org.biojava3.core.sequence.template.ComplementCompound)
  • org.biojava3.core.sequence.template.AbstractCompoundSet<C> (implements org.biojava3.core.sequence.template.CompoundSet<C>)
    • org.biojava3.core.sequence.template.AbstractNucleotideCompoundSet<C>
      • org.biojava3.core.sequence.compound.DNACompoundSet
        • org.biojava3.core.sequence.compound.AmbiguityDNACompoundSet
      • org.biojava3.core.sequence.compound.RNACompoundSet
        • org.biojava3.core.sequence.compound.AmbiguityRNACompoundSet
  • org.biojava3.core.sequence.template.AbstractCompoundTranslator<F,T> (implements org.biojava3.core.sequence.template.CompoundTranslator<F,T>)
    • org.biojava3.core.sequence.transcription.DNAToRNATranslator
    • org.biojava3.core.sequence.transcription.RNAToAminoAcidTranslator
  • org.biojava3.core.sequence.features.AbstractFeature<S,C> (implements org.biojava3.core.sequence.features.FeatureInterface<S,C>)
    • org.biojava3.core.sequence.features.QualityFeature<S,C>
    • org.biojava3.core.sequence.features.QuantityFeature<S,C>
    • org.biojava3.core.sequence.features.TextFeature<S,C>
  • org.biojava3.core.sequence.location.template.AbstractLocation (implements org.biojava3.core.sequence.location.template.Location)
    • org.biojava3.core.sequence.location.InsdcLocations.BondLocation
    • org.biojava3.core.sequence.location.InsdcLocations.OneOfLocation
    • org.biojava3.core.sequence.location.SimpleLocation
      • org.biojava3.core.sequence.location.InsdcLocations.GroupLocation
      • org.biojava3.core.sequence.location.InsdcLocations.OrderLocation
      • org.biojava3.core.sequence.location.SequenceLocation<S,C>
  • java.util.AbstractMap<K,V> (implements java.util.Map<K,V>)
    • org.biojava3.core.util.SoftHashMap<K,V>
  • org.biojava3.core.sequence.template.AbstractSequence<C> (implements org.biojava3.core.sequence.template.Sequence<C>)
    • org.biojava3.core.sequence.BasicSequence<C>
    • org.biojava3.core.sequence.DNASequence
      • org.biojava3.core.sequence.CDSSequence
      • org.biojava3.core.sequence.ChromosomeSequence
        • bacnet.datamodel.sequence.Chromosome
        • bacnet.datamodel.sequence.ChromosomeBacteriaSequence
      • org.biojava3.core.sequence.ExonSequence
      • org.biojava3.core.sequence.GeneSequence
      • org.biojava3.core.sequence.IntronSequence
      • org.biojava3.core.sequence.StartCodonSequence
      • org.biojava3.core.sequence.StopCodonSequence
      • org.biojava3.core.sequence.TranscriptSequence
    • org.biojava3.core.sequence.ProteinSequence
    • org.biojava3.core.sequence.RNASequence
  • org.biojava3.core.sequence.AccessionID
  • bacnet.e4.rap.setup.Activator (implements org.osgi.framework.BundleActivator, org.osgi.framework.BundleListener)
  • bacnet.scripts.Activator (implements org.osgi.framework.BundleActivator, org.osgi.framework.BundleListener)
  • bacnet.scripts.listeriomics.technology.Agilent
  • org.biojava3.core.sequence.compound.AminoAcidCompoundSet (implements org.biojava3.core.sequence.template.CompoundSet<C>)
  • bacnet.scripts.core.stat.AMtools
  • bacnet.datamodel.annotation.Annotation (implements java.io.Serializable)
  • bacnet.sequenceTools.AnnotationView (implements org.eclipse.swt.events.SelectionListener)
  • org.biojava3.genome.App
  • bacnet.e4.rap.AppSpecificMethods
  • bacnet.scripts.arrayexpress.ArrayExpress
  • bacnet.scripts.arrayexpress.ArrayExpressDataImport
  • bacnet.scripts.arrayexpress.ArrayExpressDataUtils
  • bacnet.scripts.listeriomics.ArrayExpress.ArrayExpressDataUtils
  • bacnet.scripts.listeriomics.ArrayExpress.ArrayExpressListeriomics
  • bacnet.scripts.listeriomics.ArrayExpressListeriomics
  • bacnet.scripts.arrayexpress.ArrayExpressTechnology
  • bacnet.scripts.listeriomics.ArrayExpress.ArrayExpressTechnology
  • org.biojava3.core.sequence.storage.ArrayListSequenceReader<C> (implements org.biojava3.core.sequence.template.SequenceReader<C>)
    • org.biojava3.core.sequence.loader.ArrayListProxySequenceReader<C> (implements org.biojava3.core.sequence.template.ProxySequenceReader<C>)
  • bacnet.utils.ArrayUtils
  • bacnet.e4.rap.BannerView (implements org.eclipse.swt.events.SelectionListener)
  • bacnet.views.BannerView (implements org.eclipse.swt.events.SelectionListener)
  • bacnet.e4.rap.BasicApplication (implements org.eclipse.rap.rwt.application.ApplicationConfiguration)
  • bacnet.e4.rap.setup.BasicApplication (implements org.eclipse.rap.rwt.application.ApplicationConfiguration)
  • bacnet.utils.BasicColor
  • bacnet.datamodel.expdesign.BioCondition (implements java.io.Serializable)
  • bacnet.scripts.database.BioConditionCreation
  • org.biojava3.core.sequence.storage.BitSequenceReader<C> (implements org.biojava3.core.sequence.template.ProxySequenceReader<C>)
    • org.biojava3.core.sequence.storage.FourBitSequenceReader<C>
    • org.biojava3.core.sequence.storage.TwoBitSequenceReader<C>
  • org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker<C>
    • org.biojava3.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker<C>
    • org.biojava3.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker<C>
  • bacnet.scripts.blast.Blast
  • bacnet.scripts.blast.BlastDatabase
  • bacnet.scripts.blast.BlastOutput
  • bacnet.scripts.blast.BlastResult
  • bacnet.scripts.blast.BlastResult.BlastResultCompare (implements java.util.Comparator<T>)
  • org.biojava3.genome.query.BlastXMLQuery
  • org.biojava3.core.sequence.transcription.CaseInsensitiveCompound (implements org.biojava3.core.sequence.template.Compound)
  • org.biojava3.core.sequence.CDSComparator (implements java.util.Comparator<T>)
  • org.biojava3.core.sequence.io.util.ClasspathResource
  • bacnet.utils.CMD
  • bacnet.datamodel.sequence.Codon
  • bacnet.datamodel.annotation.CodonUsage
  • bacnet.views.CoExprNetworkView (implements org.eclipse.swt.events.SelectionListener)
  • bacnet.views.CoExprNetworkView.InitNetworkThread (implements org.eclipse.jface.operation.IRunnableWithProgress)
  • bacnet.datamodel.annotation.COGannotation
  • bacnet.table.core.ColorMapper (implements java.lang.Cloneable, java.io.Serializable)
  • bacnet.table.core.ColorMapperList (implements java.lang.Cloneable)
  • bacnet.table.core.ColorMapperRCP (implements java.lang.Cloneable, java.io.Serializable)
  • bacnet.table.core.ColorMapperRCPList (implements java.lang.Cloneable)
  • bacnet.table.core.ColorSWT (implements java.io.Serializable)
  • bacnet.scripts.core.vennDiagram.CombinationGenerator
  • bacnet.utils.CombinationGenerator
  • bacnet.scripts.core.Comparison
  • bacnet.expressionAtlas.core.ComparisonAtlas (implements java.io.Serializable)
  • bacnet.scripts.database.ComparisonsCreation
  • 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.JPanel (implements javax.accessibility.Accessible)
          • bacnet.scripts.genome.CircularGenomeJPanel
  • bacnet.datamodel.sequence.CompoundColorization
  • org.biojava3.core.util.ConcurrencyTools
  • org.biojava3.core.util.CRC64Checksum (implements java.util.zip.Checksum)
  • bacnet.views.CRISPRPredictView (implements org.eclipse.swt.events.SelectionListener)
  • bacnet.views.CRISPRPredictView2 (implements org.eclipse.swt.events.SelectionListener)
  • bacnet.scripts.listeriomics.technology.CUFSL
  • bacnet.Database
  • bacnet.Database.InitDatabaseThread (implements org.eclipse.jface.operation.IRunnableWithProgress)
  • bacnet.scripts.database.DatabaseCreation
  • bacnet.scripts.database.DataFolder
  • bacnet.genomeBrowser.core.DataTrack
  • bacnet.scripts.database.DataValidation
  • org.biojava3.core.sequence.features.DBReferenceInfo
  • org.eclipse.jface.dialogs.DialogPage (implements org.eclipse.jface.dialogs.IDialogPage, org.eclipse.jface.dialogs.IMessageProvider)
    • org.eclipse.jface.wizard.WizardPage (implements org.eclipse.jface.wizard.IWizardPage)
      • bacnet.table.gui.ColorMapperWizardPage (implements org.eclipse.swt.widgets.Listener)
  • bacnet.scripts.database.DNASeqCreation
  • org.biojava3.core.sequence.io.DNASequenceCreator (implements org.biojava3.core.sequence.io.template.SequenceCreatorInterface<C>)
  • bacnet.raprcp.DownloadServiceHandler (implements org.eclipse.rap.rwt.service.ServiceHandler)
  • org.eclipse.rap.e4.E4EntryPointFactory (implements org.eclipse.rap.rwt.application.EntryPointFactory)
    • bacnet.e4.rap.BacnetE4PointFactory
    • bacnet.e4.rap.setup.BacnetE4PointFactory
  • org.biojava3.core.sequence.edits.Edit.AbstractEdit<C> (implements org.biojava3.core.sequence.edits.Edit<C>)
    • org.biojava3.core.sequence.edits.Edit.Delete<C>
    • org.biojava3.core.sequence.edits.Edit.Insert<C>
    • org.biojava3.core.sequence.edits.Edit.Substitute<C>
  • bacnet.datamodel.dataset.EGDeWTdata
  • org.biojava3.core.util.Equals
  • org.biojava3.core.sequence.ExonComparator (implements java.util.Comparator<T>)
  • bacnet.datamodel.expdesign.Experiment (implements java.io.Serializable)
  • bacnet.scripts.core.Expression
  • bacnet.reader.ExpressionMatrixReader
  • bacnet.utils.ExpressionMatrixStat
  • bacnet.reader.FastaFileReader<S,C>
  • org.biojava3.core.sequence.io.FastaGeneWriter
  • org.biojava3.core.sequence.io.FastaReader<S,C>
  • org.biojava3.core.sequence.io.FastaReaderHelper
  • org.biojava3.core.sequence.io.FastaSequenceParser (implements org.biojava3.core.sequence.io.template.SequenceParserInterface)
  • org.biojava3.core.sequence.io.FastaWriter<S,C>
  • org.biojava3.core.sequence.io.FastaWriterHelper
  • bacnet.scripts.core.stat.FDR
  • org.biojava3.genome.parsers.gff.Feature (implements org.biojava3.genome.parsers.gff.FeatureI)
  • org.biojava3.genome.parsers.gff.FeatureHelper
  • bacnet.scripts.listeriomics.technology.Febit
  • org.biojava3.core.sequence.io.FileProxyDNASequenceCreator (implements org.biojava3.core.sequence.io.template.SequenceCreatorInterface<C>)
  • org.biojava3.core.sequence.io.FileProxyProteinSequenceCreator (implements org.biojava3.core.sequence.io.template.SequenceCreatorInterface<C>)
  • bacnet.utils.FileUtils
  • bacnet.table.core.Filter (implements java.io.Serializable)
  • bacnet.utils.Filter (implements java.io.Serializable)
  • bacnet.table.core.FilterList (implements java.lang.Cloneable)
  • org.biojava3.core.util.FlatFileCache
  • bacnet.reader.GBKReader
  • org.biojava3.genome.parsers.gff.GCStats
  • bacnet.genomeBrowser.tracksGUI.GElement
  • org.biojava3.genome.GeneFeatureHelper
  • org.biojava3.genome.parsers.gff.GeneIDGFF2Reader
  • org.biojava3.genome.parsers.geneid.GeneIDXMLReader
  • org.biojava3.genome.parsers.gff.GeneMarkGTFReader
  • bacnet.datamodel.sequenceNCBI.GeneNCBITools
  • bacnet.scripts.listeriomics.technology.GeneralArray
  • org.biojava3.core.sequence.io.GenericFastaHeaderFormat<S,C> (implements org.biojava3.core.sequence.io.template.FastaHeaderFormatInterface<S,C>)
  • org.biojava3.core.sequence.io.GenericFastaHeaderParser<S,C> (implements org.biojava3.core.sequence.io.template.FastaHeaderParserInterface<S,C>)
  • bacnet.sequenceTools.GeneView (implements org.eclipse.swt.events.MouseListener, org.eclipse.swt.events.SelectionListener)
  • bacnet.sequenceTools.GeneViewHomologTools
  • bacnet.sequenceTools.GeneViewLocalizationTools
  • bacnet.sequenceTools.GeneViewProteomeTools
  • bacnet.sequenceTools.GeneViewTranscriptomeTools
  • bacnet.datamodel.sequence.Genome
  • bacnet.datamodel.sequence.Genome.GetMultiFastaThread (implements org.eclipse.jface.operation.IRunnableWithProgress)
  • bacnet.datamodel.sequence.Genome.OpenGenomesThread (implements org.eclipse.jface.operation.IRunnableWithProgress)
  • bacnet.datamodel.sequenceNCBI.GenomeConversion
  • bacnet.datamodel.sequenceNCBI.GenomeConversionElement
  • bacnet.expressionAtlas.core.GenomeElementAtlas (implements java.io.Serializable)
  • bacnet.datamodel.sequenceNCBI.GenomeNCBI
  • bacnet.scripts.blast.GenomeNCBIFolderTools
  • bacnet.datamodel.sequenceNCBI.GenomeNCBITools
  • bacnet.scripts.phylogeny.GenomePhylogeny
  • bacnet.scripts.database.GenomesCreation
  • bacnet.scripts.listeriomics.GenomesListeriomics
  • bacnet.genomeBrowser.GenomeTranscriptomeView
  • bacnet.sequenceTools.GenomicsView (implements org.eclipse.swt.events.SelectionListener)
  • bacnet.scripts.core.normalization.GENormalization
  • org.biojava3.genome.parsers.gff.GFF3Reader
  • org.biojava3.genome.parsers.gff.GFF3Writer
  • bacnet.reader.GFFNCBIReader
  • bacnet.datamodel.annotation.GlaserFCannotation
  • bacnet.scripts.core.normalization.GRNormalization
  • org.biojava3.core.util.Hashcoder
  • bacnet.expressionAtlas.HeatMapMultiOmicsView (implements org.eclipse.swt.events.SelectionListener)
  • bacnet.expressionAtlas.HeatMapMultiOmicsView.InitOmicsMatrixThread (implements org.eclipse.jface.operation.IRunnableWithProgress)
  • bacnet.expressionAtlas.HeatMapProteomicsExpressionView (implements org.eclipse.swt.events.SelectionListener)
  • bacnet.expressionAtlas.HeatMapProteomicsView (implements org.eclipse.swt.events.SelectionListener)
  • bacnet.expressionAtlas.HeatMapTranscriptomicsView (implements org.eclipse.swt.events.SelectionListener)
  • bacnet.views.HelpPage
  • bacnet.scripts.database.HomologCreation
  • bacnet.utils.HTMLUtils
  • bacnet.scripts.listeriomics.technology.IHM
  • bacnet.utils.ImageMagick
  • bacnet.views.InitView (implements org.eclipse.swt.events.SelectionListener)
  • bacnet.e4.rap.InitViewBacnet (implements org.eclipse.swt.events.SelectionListener)
  • bacnet.e4.rap.InitViewListeria (implements org.eclipse.swt.events.SelectionListener)
  • bacnet.e4.rap.InitViewListeriaSample (implements org.eclipse.swt.events.SelectionListener)
  • bacnet.e4.rap.InitViewYersinia (implements org.eclipse.swt.events.SelectionListener)
  • java.io.InputStream (implements java.io.Closeable)
    • java.io.FilterInputStream
      • org.biojava3.core.util.UncompressInputStream
  • org.biojava3.core.util.InputStreamProvider
  • org.biojava3.core.sequence.location.InsdcLocations
  • org.biojava3.core.sequence.location.InsdcParser
  • bacnet.views.InternalBrowser
  • org.biojava3.core.sequence.io.util.IOUtils
  • org.biojava3.core.sequence.io.IUPACParser
  • org.biojava3.core.sequence.io.IUPACParser.IUPACTable (implements org.biojava3.core.sequence.transcription.Table)
  • bacnet.scripts.listeriomics.technology.JCVI
  • org.biojava3.core.sequence.storage.JoiningSequenceReader<C> (implements org.biojava3.core.sequence.template.ProxySequenceReader<C>)
  • bacnet.utils.ListUtils
  • bacnet.handler.LoadExpressionMatrixHandler
  • org.biojava3.genome.parsers.gff.Location (implements java.lang.Iterable<T>)
  • org.biojava3.core.sequence.location.template.Location.Tools
  • org.biojava3.core.sequence.location.LocationHelper
  • org.biojava3.genome.parsers.gff.LocIterator (implements java.util.Iterator<E>)
  • bacnet.datamodel.annotation.LocusTag
  • bacnet.scripts.core.stat.LPE
  • bacnet.scripts.listeriomics.technology.LT
  • bacnet.scripts.listeriomics.technology.Macroarray
  • bacnet.scripts.listeriomics.MainListeriomics
  • bacnet.utils.MathUtils
  • bacnet.table.core.MatrixSize (implements java.io.Serializable)
  • bacnet.scripts.core.normalization.MedianNormalization
  • org.biojava3.core.sequence.MultipleSequenceAlignment<S,C> (implements org.biojava3.core.sequence.template.LightweightProfile<S,C>)
  • bacnet.scripts.blast.MultiSequenceBlastProtein
  • bacnet.scripts.blast.MultiSequenceTBlastNProtein
  • bacnet.raprcp.NavigationManagement
  • bacnet.reader.NCBIFastaHeaderParser<S,C> (implements org.biojava3.core.sequence.io.template.FastaHeaderParserInterface<S,C>)
  • bacnet.scripts.database.NetworkCreation
  • bacnet.scripts.database.NGSCreation
  • bacnet.scripts.listeriomics.technology.NimbleGen
  • bacnet.scripts.listeriomics.nterm.NTermConservationWithRiboProfiling
  • bacnet.datamodel.proteomics.NTermCreateData
  • bacnet.scripts.listeriomics.nterm.NTermCreateFinalData
  • bacnet.scripts.listeriomics.nterm.NTermDatabase
  • bacnet.datamodel.proteomics.NTermFilter
  • bacnet.genomeBrowser.NTerminomicsView (implements org.eclipse.swt.events.SelectionListener)
  • bacnet.scripts.listeriomics.nterm.NTermMain
  • bacnet.scripts.listeriomics.nterm.NTermStat
  • bacnet.scripts.listeriomics.nterm.NTermStatProteolyse
  • bacnet.datamodel.proteomics.NTermSummaryTable
  • bacnet.scripts.listeriomics.nterm.NTermTranscriptome
  • bacnet.datamodel.proteomics.NTermUtils
  • bacnet.datamodel.dataset.OmicsData (implements java.io.Serializable)
    • bacnet.datamodel.dataset.ExpressionData (implements java.io.Serializable)
      • bacnet.datamodel.dataset.GeneExpression
      • bacnet.datamodel.dataset.Tiling
    • bacnet.datamodel.dataset.ExpressionMatrix (implements java.lang.Cloneable, java.io.Serializable)
      • bacnet.datamodel.dataset.ProteomicsData (implements java.io.Serializable)
    • bacnet.datamodel.dataset.Network
    • bacnet.datamodel.dataset.NGS (implements java.io.Serializable)
    • bacnet.datamodel.dataset.NTermData (implements java.io.Serializable)
  • bacnet.expressionAtlas.core.OpenExpressionMatrixAndComparisons (implements org.eclipse.jface.operation.IRunnableWithProgress)
  • org.biojava3.genome.query.OutputHitsGFF
  • bacnet.scripts.listeriomics.Peptidomics
  • bacnet.datamodel.phylogeny.Phylogenomic
  • bacnet.scripts.database.PhylogenomicsCreation
  • bacnet.scripts.listeriomics.PhylogenyListeriomics
  • bacnet.scripts.blast.PhylogenySmallORFs
  • bacnet.scripts.phylogeny.PhylogenySmallORFs
  • bacnet.scripts.phylogeny.PhylogenyTools
  • bacnet.scripts.phylogeny.PhylogenyToolsJolley
  • bacnet.scripts.core.PredaTerm
  • org.biojava3.core.util.PrettyXMLWriter (implements org.biojava3.core.util.XMLWriter)
  • org.biojava3.core.sequence.io.ProteinSequenceCreator (implements org.biojava3.core.sequence.io.template.SequenceCreatorInterface<C>)
    • org.biojava3.core.sequence.io.CasePreservingProteinSequenceCreator
  • bacnet.scripts.blast.ProteinTools
  • bacnet.scripts.database.ProteomicsCreation
  • bacnet.expressionAtlas.ProteomicsExpressionView (implements org.eclipse.swt.events.SelectionListener)
  • bacnet.expressionAtlas.ProteomicsView (implements org.eclipse.swt.events.SelectionListener)
  • bacnet.reader.PTTReader
  • bacnet.scripts.genome.RASTEGDeGenome
  • bacnet.scripts.listeriomics.nterm.RASToverlap
  • java.io.Reader (implements java.io.Closeable, java.lang.Readable)
    • org.biojava3.core.sequence.io.BufferedReaderBytesRead
  • bacnet.genomeBrowser.core.Region (implements java.lang.Cloneable, java.io.Serializable)
  • bacnet.scripts.listeriomics.RegulatorRegion
  • bacnet.datamodel.annotation.RfamElement
  • org.biojava3.core.sequence.io.RNASequenceCreator (implements org.biojava3.core.sequence.io.template.SequenceCreatorInterface<C>)
  • bacnet.scripts.core.Rscript
  • bacnet.utils.RWTUtils
  • bacnet.raprcp.SaveFileUtils
  • bacnet.scripts.genome.SDProfile
  • bacnet.datamodel.sequence.Sequence (implements java.io.Serializable)
    • bacnet.datamodel.sequence.Gene
      • bacnet.datamodel.sequence.NcRNA
    • bacnet.datamodel.proteomics.NTerm (implements java.io.Serializable)
    • bacnet.datamodel.sequence.Operon
    • bacnet.datamodel.sequence.Srna
    • bacnet.datamodel.proteomics.TIS (implements java.io.Serializable)
  • org.biojava3.core.sequence.storage.SequenceAsStringHelper<C>
  • org.biojava3.core.sequence.SequenceComparator (implements java.util.Comparator<T>)
  • org.biojava3.core.sequence.loader.SequenceFileProxyLoader<C> (implements org.biojava3.core.sequence.template.ProxySequenceReader<C>)
  • org.biojava3.core.sequence.template.SequenceMixin
  • org.biojava3.core.sequence.template.SequenceMixin.SequenceIterator<C> (implements java.util.Iterator<E>)
  • org.biojava3.core.sequence.SequenceOptimizationHints
  • org.biojava3.core.sequence.template.SequenceProxyView<C> (implements org.biojava3.core.sequence.template.SequenceView<C>)
    • org.biojava3.core.sequence.views.ComplementSequenceView<C>
    • org.biojava3.core.sequence.views.ReversedSequenceView<C>
    • org.biojava3.core.sequence.views.RnaSequenceView (implements org.biojava3.core.sequence.template.ProxySequenceReader<C>)
  • org.biojava3.core.util.SequenceTools
  • bacnet.e4.rap.SessionControl
  • bacnet.e4.rap.setup.SessionControl
  • bacnet.e4.rap.setup.SetupPart (implements org.eclipse.swt.events.SelectionListener)
  • bacnet.datamodel.annotation.Signature (implements java.io.Serializable)
  • org.biojava3.core.sequence.location.SimplePoint (implements org.biojava3.core.sequence.location.template.Point)
    • org.biojava3.core.sequence.location.FuzzyPoint
  • org.biojava3.core.sequence.storage.SingleCompoundSequenceReader<C> (implements org.biojava3.core.sequence.template.ProxySequenceReader<C>)
  • bacnet.scripts.listeriomics.srna.SmallPeptidesSearch
  • org.biojava3.genome.util.SplitFasta
  • bacnet.scripts.listeriomics.srna.Srna10403SOliver
  • bacnet.scripts.listeriomics.srna.SrnaAlignmentBlastN
  • bacnet.scripts.listeriomics.srna.SrnaFinalList
  • bacnet.scripts.listeriomics.SrnaListeriomics
  • bacnet.sequenceTools.SrnaSummaryView (implements org.eclipse.swt.events.SelectionListener)
  • bacnet.scripts.listeriomics.srna.SrnaTables
  • bacnet.sequenceTools.SrnaView (implements org.eclipse.swt.events.MouseListener, org.eclipse.swt.events.SelectionListener)
  • bacnet.scripts.genome.StartCodonProfile
  • bacnet.scripts.core.stat.StatTest
  • bacnet.scripts.core.stat.StatUtils
  • bacnet.utils.StringColor
  • org.biojava3.core.util.StringManipulationHelper
  • org.biojava3.core.sequence.loader.StringProxySequenceReader<C> (implements org.biojava3.core.sequence.template.ProxySequenceReader<C>)
  • bacnet.datamodel.annotation.SubCellCompartment
  • bacnet.scripts.listeriomics.SummaryListeriomics
  • bacnet.swt.SWTResourceManager
    • bacnet.swt.ResourceManager
  • bacnet.e4.rap.SynTView (implements org.eclipse.swt.events.SelectionListener)
  • bacnet.scripts.listeriomics.SystemsBiologyListeriomics
  • bacnet.reader.TabDelimitedTableReader
  • org.biojava3.core.sequence.transcription.Table.CaseInsensitiveTriplet
  • org.biojava3.core.sequence.transcription.Table.Codon (implements org.biojava3.core.sequence.template.Compound)
  • bacnet.utils.TableHTMLExport
  • bacnet.table.TableSWTView
  • bacnet.scripts.listeriomics.technology.Tasmania
  • org.biojava3.core.sequence.TaxonomyID
  • bacnet.e4.rap.setup.Test
  • bacnet.genomeBrowser.TestGenomeBrowser
  • bacnet.e4.rap.TestPart
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Error
      • org.biojava3.core.exceptions.CompoundNotFoundError
      • org.biojava3.core.exceptions.FileAccessError
      • org.biojava3.core.exceptions.HeaderParseException
      • org.biojava3.core.exceptions.SequenceLengthError
    • java.lang.Exception
      • java.lang.RuntimeException
        • org.biojava3.core.exceptions.ParserException
        • org.biojava3.core.exceptions.TranslationException
  • bacnet.scripts.listeriomics.TilingGeneExprDataBase
  • bacnet.genomeBrowser.core.Track (implements java.lang.Cloneable, java.io.Serializable)
  • org.biojava3.core.sequence.transcription.TranscriptionEngine
  • org.biojava3.core.sequence.transcription.TranscriptionEngine.Builder
  • bacnet.scripts.database.TranscriptomesCreation
  • bacnet.expressionAtlas.TranscriptomicsView (implements org.eclipse.swt.events.SelectionListener)
  • bacnet.scripts.listeriomics.TSSNTermRiboSeqListeriomics
  • bacnet.scripts.listeriomics.technology.UGiessen
  • bacnet.scripts.core.UNAfold
  • bacnet.utils.UNAfold
  • org.biojava3.core.sequence.loader.UniprotProxySequenceReader<C> (implements org.biojava3.core.sequence.features.DatabaseReferenceInterface, org.biojava3.core.sequence.features.FeaturesKeyWordInterface, org.biojava3.core.sequence.template.ProxySequenceReader<C>)
  • org.biojava3.genome.uniprot.UniprotToFasta
  • bacnet.scripts.core.normalization.VarianceNormalization
  • bacnet.utils.VectorUtils
  • bacnet.scripts.core.vennDiagram.VennDiagram
  • org.eclipse.jface.viewers.ViewerComparator (implements java.io.Serializable)
    • bacnet.table.core.BioConditionComparator
    • bacnet.table.core.TableViewerComparator
  • org.eclipse.jface.viewers.ViewerFilter (implements java.io.Serializable)
    • bacnet.table.gui.TableFilter
  • org.eclipse.swt.widgets.Widget (implements org.eclipse.rap.rwt.Adaptable, org.eclipse.swt.internal.SerializableCompatibility)
    • org.eclipse.swt.widgets.Control (implements org.eclipse.swt.graphics.Drawable)
      • org.eclipse.swt.widgets.Scrollable
        • org.eclipse.swt.widgets.Composite
          • org.eclipse.swt.widgets.Canvas
            • bacnet.genomeBrowser.tracksGUI.TrackCanvasData (implements org.eclipse.swt.events.MouseMoveListener)
            • bacnet.genomeBrowser.tracksGUI.TrackCanvasGenome (implements org.eclipse.swt.events.MouseMoveListener)
          • bacnet.genomeBrowser.CompositeNTermInfo
          • bacnet.expressionAtlas.ProteomicsDataFilterComposite (implements org.eclipse.swt.events.SelectionListener)
          • bacnet.expressionAtlas.TableCompositeHeatMap (implements org.eclipse.swt.events.SelectionListener)
          • bacnet.table.TableSWTComposite (implements org.eclipse.swt.events.SelectionListener)
          • bacnet.genomeBrowser.tracksGUI.TracksComposite (implements org.eclipse.swt.events.MouseListener, org.eclipse.swt.events.SelectionListener)
          • bacnet.expressionAtlas.TranscriptomicsDataFilterComposite (implements org.eclipse.swt.events.SelectionListener)
  • org.eclipse.jface.window.Window (implements org.eclipse.jface.window.IShellProvider, java.io.Serializable)
    • org.eclipse.jface.dialogs.Dialog
      • bacnet.table.gui.FilterDialog (implements org.eclipse.swt.events.SelectionListener)
      • bacnet.sequenceTools.LocalizationDialog
      • bacnet.sequenceTools.SecondStructureRNADialog
      • bacnet.sequenceTools.SequenceDisplayDialog (implements org.eclipse.swt.events.SelectionListener)
      • org.eclipse.jface.dialogs.TrayDialog
        • org.eclipse.jface.dialogs.TitleAreaDialog
          • bacnet.genomeBrowser.dialog.AddProteomicsDataDialog (implements org.eclipse.swt.events.SelectionListener)
          • bacnet.genomeBrowser.dialog.AddTranscriptomicsDataDialog (implements org.eclipse.swt.events.SelectionListener)
          • bacnet.table.gui.FilterExpressionMatrixDialog (implements org.eclipse.swt.events.SelectionListener)
          • bacnet.table.gui.HideExpressionMatrixDialog (implements org.eclipse.swt.events.SelectionListener)
          • bacnet.genomeBrowser.dialog.LegendDialog (implements org.eclipse.swt.events.SelectionListener)
          • bacnet.expressionAtlas.core.SelectGenomeElementDialog (implements org.eclipse.swt.events.SelectionListener)
          • bacnet.expressionAtlas.core.SignatureSelectionDialog
  • org.biojava3.core.sequence.views.WindowedSequence<C> (implements java.lang.Iterable<T>)
  • org.eclipse.jface.wizard.Wizard (implements org.eclipse.jface.wizard.IWizard)
    • bacnet.table.gui.ColorMapperWizard
  • bacnet.scripts.listeriomics.technology.Wuerzburg
  • bacnet.scripts.listeriomics.technology.WUSTL
  • org.biojava3.core.util.XMLHelper
  • bacnet.utils.XMLUtils
  • bacnet.genomeBrowser.core.Zoom (implements java.lang.Cloneable, java.io.Serializable)

Interface Hierarchy

• org.biojava3.core.sequence.template.Accessioned
  • org.biojava3.core.sequence.location.template.AccesionedLocation (also extends org.biojava3.core.sequence.location.template.Location)
  • org.biojava3.core.sequence.location.template.Location (also extends java.lang.Iterable<T>)
    • org.biojava3.core.sequence.location.template.AccesionedLocation (also extends org.biojava3.core.sequence.template.Accessioned)
  • org.biojava3.core.sequence.template.Sequence<C> (also extends java.lang.Iterable<T>)
    • org.biojava3.core.sequence.template.SequenceReader<C>
      • org.biojava3.core.sequence.template.ProxySequenceReader<C>
    • org.biojava3.core.sequence.template.SequenceView<C>
• java.lang.Comparable<T>
  • org.biojava3.core.sequence.location.template.Point
• org.biojava3.core.sequence.template.Compound
  • org.biojava3.core.sequence.template.ComplementCompound
• org.biojava3.core.sequence.template.CompoundSet<C>
• org.biojava3.core.sequence.template.CompoundTranslator<F,T>
• org.biojava3.core.sequence.features.DatabaseReferenceInterface
• org.biojava3.core.sequence.edits.Edit<C>
• org.biojava3.core.sequence.io.template.FastaHeaderFormatInterface<S,C>
• org.biojava3.core.sequence.io.template.FastaHeaderParserInterface<S,C>
• org.biojava3.genome.parsers.gff.FeatureI
• org.biojava3.core.sequence.features.FeatureInterface<S,C>
• org.biojava3.core.sequence.features.FeaturesKeyWordInterface
• org.biojava3.core.sequence.io.util.IOUtils.ReaderProcessor
• java.lang.Iterable<T>
  • org.biojava3.core.sequence.location.template.Location (also extends org.biojava3.core.sequence.template.Accessioned)
    • org.biojava3.core.sequence.location.template.AccesionedLocation (also extends org.biojava3.core.sequence.template.Accessioned)
  • org.biojava3.core.sequence.template.Sequence<C> (also extends org.biojava3.core.sequence.template.Accessioned)
    • org.biojava3.core.sequence.template.SequenceReader<C>
      • org.biojava3.core.sequence.template.ProxySequenceReader<C>
    • org.biojava3.core.sequence.template.SequenceView<C>
• org.biojava3.core.sequence.template.LightweightProfile<S,C>
• org.biojava3.core.sequence.location.template.Point.Resolver<T>
• bacnet.swt.ResourceManager.PluginResourceProvider
• org.biojava3.core.sequence.io.template.SequenceCreatorInterface<C>
• org.biojava3.core.sequence.io.template.SequenceParserInterface
• org.biojava3.core.sequence.transcription.Table
• org.biojava3.core.util.XMLWriter

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.lang.constant.Constable, java.io.Serializable)
    • org.biojava3.core.sequence.template.AbstractSequence.AnnotationType
    • bacnet.scripts.blast.BlastOutput.BlastOutputTYPE
    • bacnet.table.core.ColorMapper.TypeMapper
    • bacnet.table.core.ColorMapperRCP.Type
    • org.biojava3.core.sequence.DataSource
    • org.biojava3.core.sequence.DNASequence.DNAType
    • bacnet.table.core.Filter.TypeFilter
    • bacnet.utils.Filter.TypeFilter
    • org.biojava3.core.sequence.transcription.Frame
    • org.biojava3.core.sequence.template.LightweightProfile.StringFormat
    • bacnet.datamodel.sequence.NcRNA.TypeNcRNA
    • bacnet.datamodel.proteomics.NTerm.ExperimentName
    • bacnet.datamodel.proteomics.NTerm.MappingFrame
    • bacnet.datamodel.proteomics.NTerm.TypeModif
    • bacnet.datamodel.dataset.OmicsData.ColNames
    • bacnet.datamodel.dataset.OmicsData.TypeData
    • bacnet.datamodel.sequence.Sequence.SeqType
    • org.biojava3.core.sequence.SequenceOptimizationHints.SequenceCollection
    • org.biojava3.core.sequence.SequenceOptimizationHints.SequenceUsage
    • bacnet.datamodel.sequence.Srna.TypeSrna
    • bacnet.scripts.core.stat.StatTest.TypeStat
    • org.biojava3.core.sequence.Strand
    • bacnet.datamodel.annotation.SubCellCompartment.TypeCompartment
    • bacnet.genomeBrowser.core.Track.DisplayType