Hierarchy For All Packages

Package Hierarchies:

• info.bioinfweb.jphyloio,
• info.bioinfweb.jphyloio.dataadapters,
• info.bioinfweb.jphyloio.dataadapters.implementations,
• info.bioinfweb.jphyloio.dataadapters.implementations.receivers,
• info.bioinfweb.jphyloio.dataadapters.implementations.store,
• info.bioinfweb.jphyloio.events,
• info.bioinfweb.jphyloio.events.meta,
• info.bioinfweb.jphyloio.events.type,
• info.bioinfweb.jphyloio.exception,
• info.bioinfweb.jphyloio.factory,
• info.bioinfweb.jphyloio.formatinfo,
• info.bioinfweb.jphyloio.formats,
• info.bioinfweb.jphyloio.formats.fasta,
• info.bioinfweb.jphyloio.formats.mega,
• info.bioinfweb.jphyloio.formats.newick,
• info.bioinfweb.jphyloio.formats.nexml,
• info.bioinfweb.jphyloio.formats.nexml.elementreader,
• info.bioinfweb.jphyloio.formats.nexml.receivers,
• info.bioinfweb.jphyloio.formats.nexus,
• info.bioinfweb.jphyloio.formats.nexus.blockhandlers,
• info.bioinfweb.jphyloio.formats.nexus.commandreaders,
• info.bioinfweb.jphyloio.formats.nexus.commandreaders.all,
• info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters,
• info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets,
• info.bioinfweb.jphyloio.formats.nexus.commandreaders.taxa,
• info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees,
• info.bioinfweb.jphyloio.formats.nexus.receivers,
• info.bioinfweb.jphyloio.formats.pde,
• info.bioinfweb.jphyloio.formats.phylip,
• info.bioinfweb.jphyloio.formats.phyloxml,
• info.bioinfweb.jphyloio.formats.phyloxml.elementreader,
• info.bioinfweb.jphyloio.formats.phyloxml.receivers,
• info.bioinfweb.jphyloio.formats.text,
• info.bioinfweb.jphyloio.formats.xml,
• info.bioinfweb.jphyloio.formats.xml.elementreaders,
• info.bioinfweb.jphyloio.formats.xml.receivers,
• info.bioinfweb.jphyloio.formats.xml.stax,
• info.bioinfweb.jphyloio.formats.xtg,
• info.bioinfweb.jphyloio.objecttranslation,
• info.bioinfweb.jphyloio.objecttranslation.implementations,
• info.bioinfweb.jphyloio.push,
• info.bioinfweb.jphyloio.utils

Class Hierarchy

• java.lang.Object
  • info.bioinfweb.jphyloio.AbstractEventReader<P> (implements info.bioinfweb.jphyloio.JPhyloIOEventReader, info.bioinfweb.jphyloio.ReadWriteConstants)
    • info.bioinfweb.jphyloio.formats.text.AbstractTextEventReader<P>
      • info.bioinfweb.jphyloio.formats.phylip.AbstractPhylipEventReader<P> (implements info.bioinfweb.jphyloio.formats.phylip.PhylipConstants)
        • info.bioinfweb.jphyloio.formats.phylip.PhylipEventReader
        • info.bioinfweb.jphyloio.formats.phylip.SequentialPhylipEventReader
      • info.bioinfweb.jphyloio.formats.fasta.FASTAEventReader (implements info.bioinfweb.jphyloio.formats.fasta.FASTAConstants)
      • info.bioinfweb.jphyloio.formats.mega.MEGAEventReader (implements info.bioinfweb.jphyloio.formats.mega.MEGAConstants, info.bioinfweb.jphyloio.ReadWriteConstants)
      • info.bioinfweb.jphyloio.formats.newick.NewickEventReader (implements info.bioinfweb.jphyloio.formats.newick.NewickConstants)
      • info.bioinfweb.jphyloio.formats.nexus.NexusEventReader (implements info.bioinfweb.jphyloio.formats.nexus.NexusConstants)
    • info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventReader<P> (implements info.bioinfweb.jphyloio.formats.xml.JPhyloIOXMLEventReader)
      • info.bioinfweb.jphyloio.formats.nexml.NeXMLEventReader (implements info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants)
      • info.bioinfweb.jphyloio.formats.pde.PDEEventReader (implements info.bioinfweb.jphyloio.formats.pde.PDEConstants)
      • info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLEventReader (implements info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants)
      • info.bioinfweb.jphyloio.formats.xtg.XTGEventReader (implements info.bioinfweb.jphyloio.formats.xtg.XTGConstants)
  • info.bioinfweb.jphyloio.AbstractEventWriter<P> (implements info.bioinfweb.jphyloio.JPhyloIOEventWriter)
    • info.bioinfweb.jphyloio.formats.text.AbstractTextEventWriter<P>
      • info.bioinfweb.jphyloio.AbstractSingleMatrixEventWriter<P>
        • info.bioinfweb.jphyloio.formats.fasta.FASTAEventWriter (implements info.bioinfweb.jphyloio.formats.fasta.FASTAConstants)
        • info.bioinfweb.jphyloio.formats.phylip.PhylipEventWriter (implements info.bioinfweb.jphyloio.formats.phylip.PhylipConstants)
      • info.bioinfweb.jphyloio.formats.newick.NewickEventWriter (implements info.bioinfweb.jphyloio.formats.newick.NewickConstants)
      • info.bioinfweb.jphyloio.formats.nexus.NexusEventWriter (implements info.bioinfweb.jphyloio.formats.nexus.NexusConstants)
    • info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventWriter<P> (implements info.bioinfweb.jphyloio.formats.xml.JPhyloIOXMLEventWriter)
      • info.bioinfweb.jphyloio.formats.nexml.NeXMLEventWriter (implements info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants)
      • info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLEventWriter (implements info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants, info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLPrivateConstants)
  • info.bioinfweb.jphyloio.AbstractEventWriter.NoEditUniqueLabelHandler (implements info.bioinfweb.jphyloio.AbstractEventWriter.UniqueLabelHandler)
  • java.util.AbstractMap<K,V> (implements java.util.Map<K,V>)
    • java.util.TreeMap<K,V> (implements java.lang.Cloneable, java.util.NavigableMap<K,V>, java.io.Serializable)
      • info.bioinfweb.commons.collections.ParameterMap
        • info.bioinfweb.jphyloio.ReadWriteParameterMap (implements info.bioinfweb.jphyloio.ReadWriteParameterNames)
  • info.bioinfweb.jphyloio.formats.xml.stax.AbstractMetaXMLReader
    • info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLEventReader (implements javax.xml.stream.XMLEventReader)
    • info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader (implements javax.xml.stream.XMLStreamReader)
  • info.bioinfweb.jphyloio.formats.xml.stax.AbstractMetaXMLWriter
    • info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLEventWriter (implements javax.xml.stream.XMLEventWriter)
    • info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter (implements javax.xml.stream.XMLStreamWriter)
  • info.bioinfweb.jphyloio.formats.nexml.receivers.AbstractNeXMLDataReceiverMixin (implements info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants)
  • info.bioinfweb.jphyloio.formats.nexml.elementreader.AbstractNeXMLElementReader.LabeledIDEventInformation
    • info.bioinfweb.jphyloio.formats.nexml.elementreader.AbstractNeXMLElementReader.OTUorOTUsEventInformation
  • info.bioinfweb.jphyloio.formats.nexus.blockhandlers.AbstractNexusBlockHandler (implements info.bioinfweb.jphyloio.formats.nexus.blockhandlers.NexusBlockHandler)
    • info.bioinfweb.jphyloio.formats.nexus.blockhandlers.CharactersDataUnalignedBlockHandler (implements info.bioinfweb.jphyloio.formats.nexus.blockhandlers.NexusBlockHandler, info.bioinfweb.jphyloio.formats.nexus.NexusConstants, info.bioinfweb.jphyloio.ReadWriteConstants)
    • info.bioinfweb.jphyloio.formats.nexus.blockhandlers.TaxaBlockHandler (implements info.bioinfweb.jphyloio.formats.nexus.blockhandlers.NexusBlockHandler, info.bioinfweb.jphyloio.formats.nexus.NexusConstants)
    • info.bioinfweb.jphyloio.formats.nexus.blockhandlers.TreesBlockHandler (implements info.bioinfweb.jphyloio.formats.nexus.blockhandlers.NexusBlockHandler, info.bioinfweb.jphyloio.formats.nexus.NexusConstants, info.bioinfweb.jphyloio.ReadWriteConstants)
      • info.bioinfweb.jphyloio.formats.nexus.blockhandlers.ENewickNetworksBlockHandler
  • info.bioinfweb.jphyloio.formats.nexus.commandreaders.AbstractNexusCommandEventReader (implements info.bioinfweb.jphyloio.formats.nexus.commandreaders.NexusCommandEventReader)
    • info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters.AbstractCharLabelsReader (implements info.bioinfweb.jphyloio.formats.nexus.NexusConstants, info.bioinfweb.jphyloio.ReadWriteConstants)
      • info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters.CharLabelsReader (implements info.bioinfweb.jphyloio.formats.nexus.NexusConstants, info.bioinfweb.jphyloio.ReadWriteConstants)
      • info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters.CharStateLabelsReader (implements info.bioinfweb.jphyloio.formats.nexus.NexusConstants, info.bioinfweb.jphyloio.ReadWriteConstants)
    • info.bioinfweb.jphyloio.formats.nexus.commandreaders.AbstractKeyValueCommandReader (implements info.bioinfweb.jphyloio.formats.nexus.NexusConstants)
      • info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters.DimensionsReader (implements info.bioinfweb.jphyloio.formats.nexus.NexusConstants, info.bioinfweb.jphyloio.ReadWriteConstants)
      • info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters.FormatReader (implements info.bioinfweb.jphyloio.formats.nexus.NexusConstants, info.bioinfweb.jphyloio.ReadWriteConstants)
      • info.bioinfweb.jphyloio.formats.nexus.commandreaders.all.LinkReader (implements info.bioinfweb.jphyloio.formats.nexus.NexusConstants)
    • info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets.AbstractNexusSetReader (implements info.bioinfweb.jphyloio.formats.nexus.NexusConstants, info.bioinfweb.jphyloio.ReadWriteConstants)
      • info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets.CharSetReader (implements info.bioinfweb.jphyloio.formats.nexus.NexusConstants, info.bioinfweb.jphyloio.ReadWriteConstants)
      • info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets.IDBasedSetsReader (implements info.bioinfweb.jphyloio.formats.nexus.NexusConstants, info.bioinfweb.jphyloio.ReadWriteConstants)
        • info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets.TaxSetReader
        • info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets.TreeSetReader
    • info.bioinfweb.jphyloio.formats.nexus.commandreaders.DefaultCommandReader (implements info.bioinfweb.jphyloio.formats.nexus.NexusConstants)
    • info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters.MatrixReader (implements info.bioinfweb.jphyloio.formats.nexus.NexusConstants, info.bioinfweb.jphyloio.ReadWriteConstants)
    • info.bioinfweb.jphyloio.formats.nexus.commandreaders.taxa.TaxLabelsReader (implements info.bioinfweb.jphyloio.formats.nexus.NexusConstants, info.bioinfweb.jphyloio.ReadWriteConstants)
    • info.bioinfweb.jphyloio.formats.nexus.commandreaders.all.TitleReader (implements info.bioinfweb.jphyloio.formats.nexus.NexusConstants, info.bioinfweb.jphyloio.ReadWriteConstants)
    • info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees.TranslateReader (implements info.bioinfweb.jphyloio.formats.nexus.NexusConstants, info.bioinfweb.jphyloio.ReadWriteConstants)
    • info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees.TreeReader (implements info.bioinfweb.jphyloio.formats.nexus.NexusConstants, info.bioinfweb.jphyloio.ReadWriteConstants)
      • info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees.ENewickNetworkReader
  • info.bioinfweb.jphyloio.formats.nexus.AbstractNexusSetWriter (implements info.bioinfweb.jphyloio.formats.nexus.NexusConstants)
  • info.bioinfweb.jphyloio.objecttranslation.implementations.AbstractObjectTranslator<O> (implements info.bioinfweb.jphyloio.objecttranslation.ObjectTranslator<O>)
    • info.bioinfweb.jphyloio.objecttranslation.implementations.AbstractXMLObjectTranslator<O>
    • info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLColorTranslator (implements info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants)
    • info.bioinfweb.jphyloio.objecttranslation.implementations.SimpleValueTranslator<O>
      • info.bioinfweb.jphyloio.objecttranslation.implementations.IllegalArgumentExceptionSimpleValueTranslator<O>
        • info.bioinfweb.jphyloio.objecttranslation.implementations.Base64BinaryTranslator
        • info.bioinfweb.jphyloio.objecttranslation.implementations.BooleanTranslator
        • info.bioinfweb.jphyloio.objecttranslation.implementations.ColorTranslator
        • info.bioinfweb.jphyloio.objecttranslation.implementations.DateTimeTranslator
        • info.bioinfweb.jphyloio.objecttranslation.implementations.DateTranslator
        • info.bioinfweb.jphyloio.objecttranslation.implementations.EnumTranslator<E>
        • info.bioinfweb.jphyloio.objecttranslation.implementations.HexadecimalColorTranslator
        • info.bioinfweb.jphyloio.objecttranslation.implementations.HexBinaryTranslator
        • info.bioinfweb.jphyloio.objecttranslation.implementations.QNameTranslator
        • info.bioinfweb.jphyloio.objecttranslation.implementations.TimeTranslator
      • info.bioinfweb.jphyloio.objecttranslation.implementations.ListTranslator (implements info.bioinfweb.jphyloio.formats.newick.NewickConstants)
      • info.bioinfweb.jphyloio.objecttranslation.implementations.NumericValueTranslator<O>
        • info.bioinfweb.jphyloio.objecttranslation.implementations.BigDecimalTranslator
        • info.bioinfweb.jphyloio.objecttranslation.implementations.BigIntegerTranslator
        • info.bioinfweb.jphyloio.objecttranslation.implementations.ByteTranslator
        • info.bioinfweb.jphyloio.objecttranslation.implementations.DoubleTranslator
        • info.bioinfweb.jphyloio.objecttranslation.implementations.FloatTranslator
        • info.bioinfweb.jphyloio.objecttranslation.implementations.IntegerTranslator
        • info.bioinfweb.jphyloio.objecttranslation.implementations.LongTranslator
        • info.bioinfweb.jphyloio.objecttranslation.implementations.ShortTranslator
      • info.bioinfweb.jphyloio.objecttranslation.implementations.StringTranslator
      • info.bioinfweb.jphyloio.objecttranslation.implementations.URITranslator
  • info.bioinfweb.jphyloio.factory.AbstractSingleReaderWriterFactory (implements info.bioinfweb.jphyloio.factory.SingleReaderWriterFactory)
    • info.bioinfweb.jphyloio.formats.phylip.AbstractPhylipFactory (implements info.bioinfweb.jphyloio.formats.JPhyloIOFormatIDs, info.bioinfweb.jphyloio.formats.phylip.PhylipConstants, info.bioinfweb.jphyloio.factory.SingleReaderWriterFactory)
      • info.bioinfweb.jphyloio.formats.phylip.PhylipFactory
      • info.bioinfweb.jphyloio.formats.phylip.SequentialPhylipFactory
    • info.bioinfweb.jphyloio.factory.AbstractStartStringSingleFactory (implements info.bioinfweb.jphyloio.factory.SingleReaderWriterFactory)
      • info.bioinfweb.jphyloio.formats.fasta.FASTAFactory (implements info.bioinfweb.jphyloio.formats.fasta.FASTAConstants, info.bioinfweb.jphyloio.formats.JPhyloIOFormatIDs, info.bioinfweb.jphyloio.factory.SingleReaderWriterFactory)
      • info.bioinfweb.jphyloio.formats.mega.MEGAFactory (implements info.bioinfweb.jphyloio.formats.JPhyloIOFormatIDs, info.bioinfweb.jphyloio.formats.mega.MEGAConstants, info.bioinfweb.jphyloio.factory.SingleReaderWriterFactory)
      • info.bioinfweb.jphyloio.formats.nexus.NexusFactory (implements info.bioinfweb.jphyloio.formats.JPhyloIOFormatIDs, info.bioinfweb.jphyloio.formats.nexus.NexusConstants)
    • info.bioinfweb.jphyloio.formats.xml.AbstractXMLFactory
      • info.bioinfweb.jphyloio.formats.nexml.NeXMLFactory (implements info.bioinfweb.jphyloio.formats.JPhyloIOFormatIDs, info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants)
      • info.bioinfweb.jphyloio.formats.pde.PDEFactory (implements info.bioinfweb.jphyloio.formats.JPhyloIOFormatIDs, info.bioinfweb.jphyloio.formats.pde.PDEConstants)
      • info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLFactory (implements info.bioinfweb.jphyloio.formats.JPhyloIOFormatIDs, info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants)
      • info.bioinfweb.jphyloio.formats.xtg.XTGFactory (implements info.bioinfweb.jphyloio.formats.JPhyloIOFormatIDs, info.bioinfweb.jphyloio.formats.xtg.XTGConstants)
    • info.bioinfweb.jphyloio.formats.newick.NewickFactory (implements info.bioinfweb.jphyloio.formats.JPhyloIOFormatIDs, info.bioinfweb.jphyloio.formats.newick.NewickConstants, info.bioinfweb.jphyloio.factory.SingleReaderWriterFactory)
  • info.bioinfweb.jphyloio.formats.xml.elementreaders.AbstractXMLElementReader<P> (implements info.bioinfweb.jphyloio.formats.xml.elementreaders.XMLElementReader<P>)
    • info.bioinfweb.jphyloio.formats.nexml.elementreader.AbstractNeXMLElementReader (implements info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants, info.bioinfweb.jphyloio.ReadWriteConstants, info.bioinfweb.jphyloio.formats.xml.elementreaders.XMLElementReader<P>)
      • info.bioinfweb.jphyloio.formats.nexml.elementreader.AbstractSetElementReader
        • info.bioinfweb.jphyloio.formats.nexml.elementreader.AbstractIDLinkSetElementReader
      • info.bioinfweb.jphyloio.formats.nexml.elementreader.NeXMLMetaEndElementReader
      • info.bioinfweb.jphyloio.formats.nexml.elementreader.NeXMLMetaStartElementReader
      • info.bioinfweb.jphyloio.formats.nexml.elementreader.NeXMLSetEndElementReader
    • info.bioinfweb.jphyloio.formats.xml.elementreaders.CommentElementReader<P>
    • info.bioinfweb.jphyloio.formats.phyloxml.elementreader.PhyloXMLCharactersElementReader
    • info.bioinfweb.jphyloio.formats.xml.elementreaders.StartDocumentElementReader<P>
      • info.bioinfweb.jphyloio.formats.nexml.elementreader.NeXMLStartDocumentElementReader
      • info.bioinfweb.jphyloio.formats.phyloxml.elementreader.PhyloXMLStartDocumentElementReader
    • info.bioinfweb.jphyloio.formats.xml.elementreaders.XMLEndElementReader
    • info.bioinfweb.jphyloio.formats.xml.elementreaders.XMLNoCharactersAllowedElementReader
    • info.bioinfweb.jphyloio.formats.xml.elementreaders.XMLStartElementReader
      • info.bioinfweb.jphyloio.formats.xtg.XTGFormattedTextElementReader (implements info.bioinfweb.jphyloio.formats.xtg.XTGConstants)
  • info.bioinfweb.jphyloio.formats.xml.AttributeInfo
  • info.bioinfweb.jphyloio.dataadapters.implementations.receivers.BasicEventReceiver<P> (implements info.bioinfweb.jphyloio.dataadapters.JPhyloIOEventReceiver)
    • info.bioinfweb.jphyloio.dataadapters.implementations.receivers.AbstractSequenceContentReceiver<P>
      • info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLHandleSequenceDataReceiver (implements info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants)
        • info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLCollectSequenceDataReceiver
        • info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLSequenceTokensReceiver
      • info.bioinfweb.jphyloio.formats.text.TextSequenceContentReceiver<P>
    • info.bioinfweb.jphyloio.formats.xml.receivers.AbstractXMLDataReceiver<P>
      • info.bioinfweb.jphyloio.formats.nexml.receivers.AbstractNeXMLDataReceiver (implements info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants)
        • info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLCollectNamespaceReceiver
          • info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLCollectCharSetDataReceiver
          • info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLCollectSetMetadataReceiver
          • info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLCollectTokenSetDefinitionDataReceiver
        • info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLMetaDataReceiver
          • info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLCharacterSetEventReceiver
          • info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLMolecularDataTokenDefinitionReceiver
          • info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLOnlyWriteMetaDataReceiver
          • info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLPredicateMetaReceiver
            • info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLAttributeMetadataReceiver
            • info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLIgnoreCertainMetadataReceiver
          • info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLTokenSetEventReceiver
      • info.bioinfweb.jphyloio.formats.phyloxml.receivers.PhyloXMLCollectMetadataDataReceiver (implements info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants)
      • info.bioinfweb.jphyloio.formats.phyloxml.receivers.PhyloXMLMetaDataReceiver (implements info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants)
        • info.bioinfweb.jphyloio.formats.phyloxml.receivers.PhyloXMLOnlyCustomXMLDataReceiver
        • info.bioinfweb.jphyloio.formats.phyloxml.receivers.PhyloXMLPropertyMetadataReceiver
        • info.bioinfweb.jphyloio.formats.phyloxml.receivers.PhyloXMLSpecificPredicatesDataReceiver
    • info.bioinfweb.jphyloio.formats.text.BasicTextCommentEventReceiver<P>
      • info.bioinfweb.jphyloio.formats.nexus.receivers.AbstractNexusEventReceiver (implements info.bioinfweb.jphyloio.formats.nexus.NexusConstants)
        • info.bioinfweb.jphyloio.formats.nexus.receivers.AbstractNexusSetsEventReceiver
          • info.bioinfweb.jphyloio.formats.nexus.receivers.CharacterSetEventReceiver
          • info.bioinfweb.jphyloio.formats.nexus.receivers.ReferenceOnlySetReceiver
        • info.bioinfweb.jphyloio.formats.nexus.receivers.TokenSetEventReceiver
    • info.bioinfweb.jphyloio.formats.newick.NewickNodeEdgeEventReceiver<E> (implements info.bioinfweb.jphyloio.formats.newick.NewickConstants)
  • info.bioinfweb.jphyloio.formats.nexus.commandreaders.all.BlockTitleToIDMap
  • info.bioinfweb.jphyloio.formats.BufferedEventInfo<E>
  • info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent (implements info.bioinfweb.jphyloio.events.JPhyloIOEvent)
    • info.bioinfweb.jphyloio.events.CharacterSetIntervalEvent
    • info.bioinfweb.jphyloio.events.ContinuedEvent
      • info.bioinfweb.jphyloio.events.CommentEvent
      • info.bioinfweb.jphyloio.events.meta.LiteralMetadataContentEvent
    • info.bioinfweb.jphyloio.events.LabeledEvent
      • info.bioinfweb.jphyloio.events.LabeledIDEvent
        • info.bioinfweb.jphyloio.events.CharacterDefinitionEvent
        • info.bioinfweb.jphyloio.events.EdgeEvent
        • info.bioinfweb.jphyloio.events.LinkedLabeledIDEvent (implements info.bioinfweb.jphyloio.events.LinkedIDEvent)
          • info.bioinfweb.jphyloio.events.NodeEvent
        • info.bioinfweb.jphyloio.events.meta.LiteralMetadataEvent
        • info.bioinfweb.jphyloio.events.meta.ResourceMetadataEvent
        • info.bioinfweb.jphyloio.events.SingleTokenDefinitionEvent
        • info.bioinfweb.jphyloio.events.TokenSetDefinitionEvent
      • info.bioinfweb.jphyloio.events.SingleSequenceTokenEvent
    • info.bioinfweb.jphyloio.events.PartEndEvent
    • info.bioinfweb.jphyloio.events.SequenceTokensEvent
    • info.bioinfweb.jphyloio.events.SetElementEvent (implements info.bioinfweb.jphyloio.events.LinkedIDEvent)
    • info.bioinfweb.jphyloio.events.UnknownCommandEvent
  • info.bioinfweb.jphyloio.formatinfo.DefaultFormatInfo (implements info.bioinfweb.jphyloio.formatinfo.JPhyloIOFormatInfo)
  • info.bioinfweb.jphyloio.formats.newick.DefaultNewickReaderNodeLabelProcessor (implements info.bioinfweb.jphyloio.formats.newick.NewickReaderNodeLabelProcessor)
  • info.bioinfweb.jphyloio.formats.newick.DefaultNewickWriterNodeLabelProcessor (implements info.bioinfweb.jphyloio.formats.newick.NewickWriterNodeLabelProcessor)
    • info.bioinfweb.jphyloio.formats.nexus.NexusNewickWriterNodeLabelProcessor
  • info.bioinfweb.jphyloio.dataadapters.implementations.EmptyAnnotatedDataAdapter<E> (implements info.bioinfweb.jphyloio.dataadapters.AnnotatedDataAdapter)
    • info.bioinfweb.jphyloio.dataadapters.implementations.EmptyDocumentDataAdapter (implements info.bioinfweb.jphyloio.dataadapters.DocumentDataAdapter)
    • info.bioinfweb.jphyloio.dataadapters.implementations.ListBasedDocumentDataAdapter (implements info.bioinfweb.jphyloio.dataadapters.DocumentDataAdapter)
    • info.bioinfweb.jphyloio.dataadapters.implementations.NoCharDefsNoSetsMatrixDataAdapter (implements info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter)
    • info.bioinfweb.jphyloio.dataadapters.implementations.NoSetsTreeNetworkDataAdapter (implements info.bioinfweb.jphyloio.dataadapters.TreeNetworkDataAdapter)
    • info.bioinfweb.jphyloio.dataadapters.implementations.NoSetsTreeNetworkGroupDataAdapter (implements info.bioinfweb.jphyloio.dataadapters.TreeNetworkGroupDataAdapter)
  • info.bioinfweb.jphyloio.dataadapters.implementations.EmptyObjectListDataAdapter<E> (implements info.bioinfweb.jphyloio.dataadapters.ObjectListDataAdapter<E>)
  • info.bioinfweb.jphyloio.push.EventForwarder
  • info.bioinfweb.jphyloio.events.type.EventType (implements java.lang.Comparable<T>)
  • javax.swing.filechooser.FileFilter
    • info.bioinfweb.commons.io.ExtensionFileFilter (implements java.io.FileFilter, java.io.FilenameFilter)
      • info.bioinfweb.commons.io.ContentExtensionFileFilter
        • info.bioinfweb.jphyloio.factory.JPhyloIOContentExtensionFileFilter (implements info.bioinfweb.jphyloio.JPhyloIOFormatSpecificObject)
  • info.bioinfweb.jphyloio.formats.newick.HotCommentDataReader (implements info.bioinfweb.jphyloio.formats.newick.NewickConstants, info.bioinfweb.jphyloio.ReadWriteConstants)
  • info.bioinfweb.jphyloio.utils.IDToNameManager
  • info.bioinfweb.jphyloio.JPhyloIO
  • info.bioinfweb.jphyloio.factory.JPhyloIOReaderWriterFactory (implements info.bioinfweb.jphyloio.formats.JPhyloIOFormatIDs)
  • info.bioinfweb.jphyloio.utils.JPhyloIOReadingUtils
  • info.bioinfweb.jphyloio.utils.JPhyloIOWritingUtils
  • info.bioinfweb.jphyloio.formats.text.KeyValueInformation
  • info.bioinfweb.jphyloio.utils.LabelEditingReporter
  • info.bioinfweb.jphyloio.formatinfo.MetadataModeling
  • info.bioinfweb.jphyloio.formats.newick.NewickScanner (implements info.bioinfweb.jphyloio.formats.newick.NewickConstants)
  • info.bioinfweb.jphyloio.formats.newick.NewickStringReader (implements info.bioinfweb.jphyloio.formats.newick.NewickConstants, info.bioinfweb.jphyloio.ReadWriteConstants)
  • info.bioinfweb.jphyloio.formats.newick.NewickStringWriter (implements info.bioinfweb.jphyloio.formats.newick.NewickConstants)
  • info.bioinfweb.jphyloio.formats.newick.NewickToken
  • info.bioinfweb.jphyloio.formats.newick.NewickUtils (implements info.bioinfweb.jphyloio.formats.newick.NewickConstants)
  • info.bioinfweb.jphyloio.formats.newick.NewickUtils.ReadElement
  • info.bioinfweb.jphyloio.formats.nexml.NeXMLReaderTokenSetInformation
  • info.bioinfweb.jphyloio.formats.nexml.NeXMLSingleTokenDefinitionInformation
  • info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterAlignmentInformation (implements info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants)
  • info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterTokenSetInformation
  • info.bioinfweb.jphyloio.formats.nexus.blockhandlers.NexusBlockHandlerMap
  • info.bioinfweb.jphyloio.formats.nexus.commandreaders.NexusCommandReaderFactory
  • info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees.NexusNewickReaderNodeLabelProcessor (implements info.bioinfweb.jphyloio.formats.newick.NewickReaderNodeLabelProcessor, info.bioinfweb.jphyloio.formats.nexus.NexusConstants)
  • info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees.NexusTranslationTable
  • info.bioinfweb.jphyloio.formats.newick.NHXUtils (implements info.bioinfweb.jphyloio.formats.newick.NewickConstants, info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants, info.bioinfweb.jphyloio.ReadWriteConstants)
  • info.bioinfweb.jphyloio.formats.NodeEdgeInfo
  • info.bioinfweb.jphyloio.objecttranslation.ObjectTranslatorFactory (implements info.bioinfweb.jphyloio.ReadWriteConstants, info.bioinfweb.commons.io.W3CXSConstants)
  • info.bioinfweb.jphyloio.ParentEventInformation
  • info.bioinfweb.jphyloio.formats.pde.PDEMetaColumnDefintion
  • info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLMetaEventInfo
  • info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLPredicateInfo
  • info.bioinfweb.jphyloio.ReaderStreamDataProvider<R>
    • info.bioinfweb.jphyloio.formats.text.TextReaderStreamDataProvider<R>
      • info.bioinfweb.jphyloio.formats.nexus.NexusReaderStreamDataProvider (implements info.bioinfweb.jphyloio.formats.nexus.NexusConstants)
    • info.bioinfweb.jphyloio.formats.xml.XMLReaderStreamDataProvider<R>
      • info.bioinfweb.jphyloio.formats.nexml.NeXMLReaderStreamDataProvider
      • info.bioinfweb.jphyloio.formats.pde.PDEReaderStreamDataProvider
      • info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLReaderStreamDataProvider
  • info.bioinfweb.jphyloio.utils.SequenceTokensEventManager
  • info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreAnnotatedDataAdapter<E> (implements info.bioinfweb.jphyloio.dataadapters.AnnotatedDataAdapter)
    • info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreDocumentDataAdapter (implements info.bioinfweb.jphyloio.dataadapters.DocumentDataAdapter)
    • info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreMatrixDataAdapter (implements info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter)
    • info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreOTUListDataAdapter (implements info.bioinfweb.jphyloio.dataadapters.OTUListDataAdapter)
    • info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreTreeNetworkDataAdapter (implements info.bioinfweb.jphyloio.dataadapters.TreeNetworkDataAdapter)
    • info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreTreeNetworkGroupDataAdapter (implements info.bioinfweb.jphyloio.dataadapters.TreeNetworkGroupDataAdapter)
  • info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreObjectData<E>
  • info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreObjectListDataAdapter<E> (implements info.bioinfweb.jphyloio.dataadapters.ObjectListDataAdapter<E>)
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • info.bioinfweb.jphyloio.objecttranslation.InvalidObjectSourceDataException
      • java.io.IOException
        • info.bioinfweb.jphyloio.exception.JPhyloIOReaderException (implements info.bioinfweb.commons.io.StreamLocationProvider)
          • info.bioinfweb.jphyloio.exception.UnsupportedFormatFeatureException
        • info.bioinfweb.jphyloio.exception.JPhyloIOWriterException
      • java.lang.RuntimeException
        • info.bioinfweb.jphyloio.exception.InconsistentAdapterDataException
          • info.bioinfweb.jphyloio.exception.IllegalEventException
  • info.bioinfweb.jphyloio.utils.TopoplogicalNodeInfo
  • info.bioinfweb.jphyloio.utils.TreeTopologyExtractor
  • info.bioinfweb.jphyloio.dataadapters.implementations.UndefinedOTUListDataAdapter (implements info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants, info.bioinfweb.jphyloio.dataadapters.OTUListDataAdapter)
  • info.bioinfweb.jphyloio.events.meta.URIOrStringIdentifier
  • info.bioinfweb.jphyloio.WriterStreamDataProvider<R>
    • info.bioinfweb.jphyloio.formats.text.TextWriterStreamDataProvider<W>
      • info.bioinfweb.jphyloio.formats.nexus.NexusWriterStreamDataProvider
    • info.bioinfweb.jphyloio.formats.xml.XMLWriterStreamDataProvider<R>
      • info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterStreamDataProvider (implements info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants)
      • info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLWriterStreamDataProvider (implements info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants, info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLPrivateConstants)
  • info.bioinfweb.jphyloio.formats.xml.elementreaders.XMLElementReaderKey
  • info.bioinfweb.jphyloio.formats.xml.XMLReadWriteUtils

Interface Hierarchy

• info.bioinfweb.jphyloio.AbstractEventWriter.UniqueLabelHandler
• info.bioinfweb.jphyloio.dataadapters.AnnotatedDataAdapter
  • info.bioinfweb.jphyloio.dataadapters.DocumentDataAdapter
  • info.bioinfweb.jphyloio.dataadapters.ElementDataAdapter<E>
    • info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter
    • info.bioinfweb.jphyloio.dataadapters.OTUListDataAdapter (also extends info.bioinfweb.jphyloio.dataadapters.ObjectListDataAdapter<E>)
    • info.bioinfweb.jphyloio.dataadapters.TreeNetworkDataAdapter
    • info.bioinfweb.jphyloio.dataadapters.TreeNetworkGroupDataAdapter
  • info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter
  • info.bioinfweb.jphyloio.dataadapters.OTUListDataAdapter (also extends info.bioinfweb.jphyloio.dataadapters.ElementDataAdapter<E>, info.bioinfweb.jphyloio.dataadapters.ObjectListDataAdapter<E>)
  • info.bioinfweb.jphyloio.dataadapters.TreeNetworkDataAdapter
  • info.bioinfweb.jphyloio.dataadapters.TreeNetworkGroupDataAdapter
• info.bioinfweb.jphyloio.formats.fasta.FASTAConstants
• info.bioinfweb.jphyloio.events.JPhyloIOEvent
  • info.bioinfweb.jphyloio.events.LinkedIDEvent
• info.bioinfweb.jphyloio.push.JPhyloIOEventListener
• info.bioinfweb.jphyloio.dataadapters.JPhyloIOEventReceiver
• info.bioinfweb.jphyloio.formats.JPhyloIOFormatIDs
• info.bioinfweb.jphyloio.JPhyloIOFormatSpecificObject
  • info.bioinfweb.jphyloio.JPhyloIOEventReader
    • info.bioinfweb.jphyloio.formats.xml.JPhyloIOXMLEventReader
  • info.bioinfweb.jphyloio.JPhyloIOEventWriter
    • info.bioinfweb.jphyloio.formats.xml.JPhyloIOXMLEventWriter
  • info.bioinfweb.jphyloio.formatinfo.JPhyloIOFormatInfo
  • info.bioinfweb.jphyloio.formats.xml.JPhyloIOXMLEventReader
  • info.bioinfweb.jphyloio.formats.xml.JPhyloIOXMLEventWriter
• info.bioinfweb.jphyloio.formats.mega.MEGAConstants
• info.bioinfweb.jphyloio.formats.newick.NewickConstants
• info.bioinfweb.jphyloio.formats.newick.NewickReaderNodeLabelProcessor
• info.bioinfweb.jphyloio.formats.newick.NewickWriterNodeLabelProcessor
• info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
• info.bioinfweb.jphyloio.formats.nexus.blockhandlers.NexusBlockHandler
• info.bioinfweb.jphyloio.formats.nexus.commandreaders.NexusCommandEventReader
• info.bioinfweb.jphyloio.formats.nexus.NexusConstants
• info.bioinfweb.jphyloio.dataadapters.ObjectListDataAdapter<E>
  • info.bioinfweb.jphyloio.dataadapters.OTUListDataAdapter (also extends info.bioinfweb.jphyloio.dataadapters.ElementDataAdapter<E>)
• info.bioinfweb.jphyloio.objecttranslation.ObjectTranslator<O>
• info.bioinfweb.jphyloio.formats.pde.PDEConstants
• info.bioinfweb.jphyloio.formats.phylip.PhylipConstants
• info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
• info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLPrivateConstants
• info.bioinfweb.jphyloio.ReadWriteConstants
• info.bioinfweb.jphyloio.ReadWriteParameterNames
• info.bioinfweb.jphyloio.factory.SingleReaderWriterFactory
• info.bioinfweb.jphyloio.formats.xml.elementreaders.XMLElementReader<P>
• info.bioinfweb.jphyloio.formats.xtg.XTGConstants

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • info.bioinfweb.jphyloio.events.meta.LiteralContentSequenceType
    • info.bioinfweb.jphyloio.events.type.EventContentType
    • info.bioinfweb.jphyloio.events.type.EventTopologyType
    • info.bioinfweb.jphyloio.formatinfo.MetadataTopologyType
    • info.bioinfweb.jphyloio.formats.newick.NewickTokenType
    • info.bioinfweb.jphyloio.formats.nexml.TokenDefinitionLabelHandling
    • info.bioinfweb.jphyloio.formats.nexml.TokenTranslationStrategy
    • info.bioinfweb.jphyloio.formats.nexus.NexusMatrixWriteResult
    • info.bioinfweb.jphyloio.formats.pde.PDEMetaColumnType
    • info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLMetadataTreatment
    • info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLPredicateTreatment
    • info.bioinfweb.jphyloio.formats.phyloxml.PropertyOwner
    • info.bioinfweb.jphyloio.utils.LabelEditingReporter.LabelStatus