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 JPhyloIOEventWriters.

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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