A B C D E F G H I J K L M N O P Q R S T U V W X

## D

DATA_TYPE_BRANCH_COLOR - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
DATA_TYPE_COLOR - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
DATA_TYPE_EVENTTYPE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
DATA_TYPE_LEGEND_STYLE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
DATA_TYPE_NAMESPACE_FOLDER - Static variable in interface info.bioinfweb.jphyloio.ReadWriteConstants
DATA_TYPE_NEWICK_ARRAY - Static variable in interface info.bioinfweb.jphyloio.formats.newick.NewickConstants
DATA_TYPE_PIE_CHART_LABEL_CAPTION_LINK_TYPE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
DATA_TYPE_PIE_CHART_LABEL_CAPTION_TYPE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
DATA_TYPE_RANK - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
DATA_TYPE_SCALE_BAR_ALIGNMENT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
DATA_TYPE_SCALE_VALUE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
DATA_TYPE_SEQUENCE_SYMBOL - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
DATA_TYPE_SIMPLE_VALUE_LIST - Static variable in interface info.bioinfweb.jphyloio.ReadWriteConstants
  A custom data type defined in JPhyloIO that indicates that a list in the Newick/Nexus metadata notation as processed by `ListTranslator` is stored in an XML format.
DATA_TYPE_TAXONOMY_CODE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
DATA_TYPE_TEXT_ORIENTATION - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
DateTimeTranslator - Class in info.bioinfweb.jphyloio.objecttranslation.implementations
  An object translator between {link `Calendar`} and xsd:dateTime.
DateTimeTranslator() - Constructor for class info.bioinfweb.jphyloio.objecttranslation.implementations.DateTimeTranslator
DateTranslator - Class in info.bioinfweb.jphyloio.objecttranslation.implementations
  An object translator between {link `Calendar`} and xsd:date.
DateTranslator() - Constructor for class info.bioinfweb.jphyloio.objecttranslation.implementations.DateTranslator
decreaseIndention() - Method in class info.bioinfweb.jphyloio.AbstractEventWriter
DEFAULT_CHAR_SET_ID_PREFIX - Static variable in interface info.bioinfweb.jphyloio.ReadWriteConstants
DEFAULT_CHARACTER_DEFINITION_ID_PREFIX - Static variable in interface info.bioinfweb.jphyloio.ReadWriteConstants
DEFAULT_EDGE_ID_PREFIX - Static variable in interface info.bioinfweb.jphyloio.ReadWriteConstants
DEFAULT_GENERAL_ID_PREFIX - Static variable in interface info.bioinfweb.jphyloio.ReadWriteConstants
DEFAULT_LABEL_CHAR - Static variable in interface info.bioinfweb.jphyloio.formats.mega.MEGAConstants
DEFAULT_LINE_LENGTH - Static variable in interface info.bioinfweb.jphyloio.formats.fasta.FASTAConstants
DEFAULT_MATRIX_ID_PREFIX - Static variable in interface info.bioinfweb.jphyloio.ReadWriteConstants
DEFAULT_MAX_COMMENT_LENGTH - Static variable in interface info.bioinfweb.jphyloio.ReadWriteConstants
DEFAULT_MAX_TOKENS_TO_READ - Static variable in interface info.bioinfweb.jphyloio.ReadWriteConstants
DEFAULT_META_ID_PREFIX - Static variable in interface info.bioinfweb.jphyloio.ReadWriteConstants
DEFAULT_NAME_LENGTH - Static variable in interface info.bioinfweb.jphyloio.formats.phylip.PhylipConstants
  The default maximum length of sequence names written to the format.
DEFAULT_NAMESPACE_PREFIX - Static variable in class info.bioinfweb.jphyloio.formats.xml.XMLReadWriteUtils
DEFAULT_NETWORK_ID_PREFIX - Static variable in interface info.bioinfweb.jphyloio.ReadWriteConstants
DEFAULT_NODE_EDGE_SET_ID_PREFIX - Static variable in interface info.bioinfweb.jphyloio.ReadWriteConstants
DEFAULT_NODE_ID_PREFIX - Static variable in interface info.bioinfweb.jphyloio.ReadWriteConstants
DEFAULT_OTU_ID_PREFIX - Static variable in interface info.bioinfweb.jphyloio.ReadWriteConstants
DEFAULT_OTU_LIST_ID_PREFIX - Static variable in interface info.bioinfweb.jphyloio.ReadWriteConstants
DEFAULT_OTU_SET_ID_PREFIX - Static variable in interface info.bioinfweb.jphyloio.ReadWriteConstants
DEFAULT_READ_AHEAD_LIMIT - Static variable in class info.bioinfweb.jphyloio.factory.JPhyloIOReaderWriterFactory
  The number of bytes that are buffered by methods of this factory to determine the format from an input stream.
DEFAULT_SEQUENCE_ID_PREFIX - Static variable in interface info.bioinfweb.jphyloio.ReadWriteConstants
DEFAULT_SEQUENCE_SET_ID_PREFIX - Static variable in interface info.bioinfweb.jphyloio.ReadWriteConstants
DEFAULT_TOKEN_DEFINITION_ID_PREFIX - Static variable in interface info.bioinfweb.jphyloio.ReadWriteConstants
DEFAULT_TOKEN_DEFINITION_SET_ID_PREFIX - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
DEFAULT_TOKEN_SET_ID_PREFIX - Static variable in interface info.bioinfweb.jphyloio.ReadWriteConstants
DEFAULT_TRANSLATE_INTERNAL_NODE_NAMES - Static variable in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees.NexusNewickReaderNodeLabelProcessor
DEFAULT_TREE_ID_PREFIX - Static variable in interface info.bioinfweb.jphyloio.ReadWriteConstants
DEFAULT_TREE_NETWORK_GROUP_ID_PREFIX - Static variable in interface info.bioinfweb.jphyloio.ReadWriteConstants
DEFAULT_TREE_NETWORK_SET_ID_PREFIX - Static variable in interface info.bioinfweb.jphyloio.ReadWriteConstants
DefaultCommandReader - Class in info.bioinfweb.jphyloio.formats.nexus.commandreaders
  Default Nexus command reader for all unsupported Nexus commands.
DefaultCommandReader(String, NexusReaderStreamDataProvider) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.commandreaders.DefaultCommandReader
  Creates a new instance of this class.
DefaultFormatInfo - Class in info.bioinfweb.jphyloio.formatinfo
  Default implementation of `JPhyloIOFormatInfo`.
DefaultFormatInfo(SingleReaderWriterFactory, String, String, Set<EventContentType>, Set<EventContentType>, Map<EventContentType, MetadataModeling>, Map<EventContentType, MetadataModeling>, Set<String>, Set<String>, ReadWriteParameterMap, String, String...) - Constructor for class info.bioinfweb.jphyloio.formatinfo.DefaultFormatInfo
  Creates a new instance of this class.
DefaultNewickReaderNodeLabelProcessor - Class in info.bioinfweb.jphyloio.formats.newick
  Default implementation of `NewickReaderNodeLabelProcessor` that returns the original name unchanged.
DefaultNewickReaderNodeLabelProcessor() - Constructor for class info.bioinfweb.jphyloio.formats.newick.DefaultNewickReaderNodeLabelProcessor
DefaultNewickWriterNodeLabelProcessor - Class in info.bioinfweb.jphyloio.formats.newick
  The node label processor used by `NewickEventWriter`.
DefaultNewickWriterNodeLabelProcessor(OTUListDataAdapter, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.newick.DefaultNewickWriterNodeLabelProcessor
DEPRECATED_VALUE_LEAVES_ADAPTER - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
determineMaxSequenceLength(MatrixDataAdapter, ReadWriteParameterMap) - Static method in class info.bioinfweb.jphyloio.AbstractEventWriter
  Calculates the maximum sequence length in matrix with unequal lengths.
determineObjectType(QName) - Method in class info.bioinfweb.jphyloio.formats.nexml.elementreader.AbstractIDLinkSetElementReader
determineWriteMeta(String, URIOrStringIdentifier) - Method in class info.bioinfweb.jphyloio.formats.phyloxml.receivers.PhyloXMLMetaDataReceiver
didIgnoreComments() - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.BasicEventReceiver
didIgnoreLiteralMetadata() - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.BasicEventReceiver
didIgnoreMetadata() - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.BasicEventReceiver
didIgnoreResourceMetadata() - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.BasicEventReceiver
DIMENSIONS_SUBCOMMAND_NCHAR - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
DIMENSIONS_SUBCOMMAND_NEW_TAXA - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
DIMENSIONS_SUBCOMMAND_NTAX - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
DimensionsReader - Class in info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters
DimensionsReader(NexusReaderStreamDataProvider) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters.DimensionsReader
DNA_TYPE - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
doAdd(JPhyloIOEvent) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.AbstractSequenceContentReceiver
doAdd(JPhyloIOEvent) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.BasicEventReceiver
  This method is called internally by `BasicEventReceiver.add(JPhyloIOEvent)` to process events that do not model metadata or comments.
doAdd(JPhyloIOEvent) - Method in class info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLCharacterSetEventReceiver
doAdd(JPhyloIOEvent) - Method in class info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLCollectCharSetDataReceiver
doAdd(JPhyloIOEvent) - Method in class info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLCollectSetMetadataReceiver
doAdd(JPhyloIOEvent) - Method in class info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLCollectTokenSetDefinitionDataReceiver
doAdd(JPhyloIOEvent) - Method in class info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLHandleSequenceDataReceiver
doAdd(JPhyloIOEvent) - Method in class info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLMolecularDataTokenDefinitionReceiver
doAdd(JPhyloIOEvent) - Method in class info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLOnlyWriteMetaDataReceiver
doAdd(JPhyloIOEvent) - Method in class info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLTokenSetEventReceiver
doAdd(JPhyloIOEvent) - Method in class info.bioinfweb.jphyloio.formats.nexus.receivers.AbstractNexusSetsEventReceiver
doAdd(JPhyloIOEvent) - Method in class info.bioinfweb.jphyloio.formats.nexus.receivers.TokenSetEventReceiver
DocumentDataAdapter - Interface in info.bioinfweb.jphyloio.dataadapters
  The root adapter interface to be used with `JPhyloIOEventWriter`s.
doReadNextEvent() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.AbstractKeyValueCommandReader
doReadNextEvent() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.AbstractNexusCommandEventReader
doReadNextEvent() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.all.TitleReader
doReadNextEvent() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters.CharLabelsReader
doReadNextEvent() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters.CharStateLabelsReader
doReadNextEvent() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters.MatrixReader
doReadNextEvent() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.DefaultCommandReader
doReadNextEvent() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets.AbstractNexusSetReader
doReadNextEvent() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.taxa.TaxLabelsReader
doReadNextEvent() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees.TranslateReader
doReadNextEvent() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees.TreeReader
DoubleTranslator - Class in info.bioinfweb.jphyloio.objecttranslation.implementations
  An object translator from and to `Double`.
DoubleTranslator() - Constructor for class info.bioinfweb.jphyloio.objecttranslation.implementations.DoubleTranslator
doWriteDocument(DocumentDataAdapter, Writer, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.AbstractEventWriter
doWriteDocument(DocumentDataAdapter, Writer, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.AbstractSingleMatrixEventWriter
doWriteDocument(DocumentDataAdapter, Writer, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.formats.newick.NewickEventWriter
doWriteDocument() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLEventWriter
doWriteDocument(DocumentDataAdapter, Writer, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusEventWriter
doWriteDocument() - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLEventWriter
doWriteDocument(DocumentDataAdapter, Writer, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.formats.text.AbstractTextEventWriter
doWriteDocument() - Method in class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventWriter
doWriteDocument(DocumentDataAdapter, Writer, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventWriter

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