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

## T

TAG_ABSENT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_ACCESSION - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_ADAPTER - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
TAG_ALIGNMENT - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
TAG_ALPHA - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_ALT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_ANNOTATION - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_AUTHORITY - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_BC - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_BINARY_CHARACTERS - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_BLOCK - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
TAG_BLUE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_BRANCH - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
TAG_BRANCH_COLOR - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_BRANCH_LENGTH - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_BRANCH_WIDTH - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_CELL - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
TAG_CHAR - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
TAG_CHARACTERS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
TAG_CHARSET - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
TAG_CHARSETS - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
TAG_CLADE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_CLADE_RELATION - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_CODE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_COMMON_NAME - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_CONFIDENCE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_CROSS_REFERENCES - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_DATE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_DESC - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_DESCRIPTION - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
TAG_DESCRIPTION - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_DISTRIBUTION - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_DOCUMENT_MARGIN - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
TAG_DOMAIN - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_DOMAIN_ARCHITECTURE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_DUPLICATIONS - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_EDGE - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
TAG_EVENTS - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_FORMAT - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
TAG_GAINED - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_GENE_NAME - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_GLOBAL_FORMATS - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
TAG_GREEN - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_HEADER - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
TAG_HIDDEN_DATA - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
TAG_ICON_LABEL - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
TAG_ID - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_LABEL_MARGIN - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
TAG_LAT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_LEAF_MARGIN - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
TAG_LEGEND - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
TAG_LEGEND_MARGIN - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
TAG_LOCATION - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_LONG - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_LOSSES - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_LOST - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_MATRIX - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
TAG_MATRIX - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
TAG_MAXIMUM - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_MEMBER - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
TAG_META - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
TAG_META_TYPE_DEFINITIONS - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
TAG_MINIMUM - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_MOL_SEQ - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_NAME - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_NETWORK - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
TAG_NODE - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
TAG_NODE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
TAG_NODE_BRANCH_DATA_ADAPTERS - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
TAG_NODE_ID - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_OTU - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
TAG_OTUS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
TAG_PARENT_OF_ROOT - Static variable in class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventReader
TAG_PHYLOGENY - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_PIE_CHART_ID - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
TAG_PIE_CHART_IDS - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
TAG_PIE_CHART_LABEL - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
TAG_POINT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_POLYGON - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_POLYMORPHIC - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
TAG_PRESENT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_PROPERTY - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_RANK - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_RED - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_REFERENCE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_ROOT - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
TAG_ROOT - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
TAG_ROOT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_ROOT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
TAG_ROOTEDGE - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
TAG_ROW - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
TAG_SCALE_BAR - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
TAG_SCI_NAME - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_SEQ - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
TAG_SEQUENCE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_SEQUENCE_INFORMATION - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
TAG_SEQUENCE_META_INFORMATION - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
TAG_SEQUENCE_RELATION - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_SET - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
TAG_SPECIATIONS - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_STATE - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
TAG_STATES - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
TAG_SYMBOL - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_SYNONYM - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_TAXONOMY - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_TEXT_LABEL - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
TAG_TREE - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
TAG_TREE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
TAG_TREES - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
TAG_TYPE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_UNCERTAIN - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
TAG_URI - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TAG_VALUE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TaxaBlockHandler - Class in info.bioinfweb.jphyloio.formats.nexus.blockhandlers
TaxaBlockHandler() - Constructor for class info.bioinfweb.jphyloio.formats.nexus.blockhandlers.TaxaBlockHandler
TaxLabelsReader - Class in info.bioinfweb.jphyloio.formats.nexus.commandreaders.taxa
TaxLabelsReader(NexusReaderStreamDataProvider) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.commandreaders.taxa.TaxLabelsReader
TaxSetReader - Class in info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets
TaxSetReader(NexusReaderStreamDataProvider) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets.TaxSetReader
TERMINAL_SYMBOL - Static variable in interface info.bioinfweb.jphyloio.formats.newick.NewickConstants
TextReaderStreamDataProvider<R extends AbstractTextEventReader<? extends TextReaderStreamDataProvider<R>>> - Class in info.bioinfweb.jphyloio.formats.text
TextReaderStreamDataProvider(R) - Constructor for class info.bioinfweb.jphyloio.formats.text.TextReaderStreamDataProvider
TextSequenceContentReceiver<P extends TextWriterStreamDataProvider<? extends AbstractTextEventWriter<P>>> - Class in info.bioinfweb.jphyloio.formats.text
  Receiver that writes all encountered sequence tokens and comments to the current line and ignores all metadata.
TextSequenceContentReceiver(P, ReadWriteParameterMap, boolean, String, String) - Constructor for class info.bioinfweb.jphyloio.formats.text.TextSequenceContentReceiver
TextWriterStreamDataProvider<W extends AbstractTextEventWriter<? extends TextWriterStreamDataProvider<W>>> - Class in info.bioinfweb.jphyloio.formats.text
TextWriterStreamDataProvider(W) - Constructor for class info.bioinfweb.jphyloio.formats.text.TextWriterStreamDataProvider
TimeTranslator - Class in info.bioinfweb.jphyloio.objecttranslation.implementations
  An object translator between {link `Calendar`} and xsd:time.
TimeTranslator() - Constructor for class info.bioinfweb.jphyloio.objecttranslation.implementations.TimeTranslator
TitleReader - Class in info.bioinfweb.jphyloio.formats.nexus.commandreaders.all
  Reads the `TITLE` command of a Nexus block and stores the title in the shared information map of the stream data provider under the key `NexusReaderStreamDataProvider.INFO_KEY_BLOCK_TITLE`.
TitleReader(NexusReaderStreamDataProvider) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.commandreaders.all.TitleReader
toBlockName() - Method in enum info.bioinfweb.jphyloio.formats.nexus.NexusMatrixWriteResult
TokenDefinitionLabelHandling - Enum in info.bioinfweb.jphyloio.formats.nexml
  Instances of this enum can be used as parameter values for `ReadWriteParameterNames.KEY_NEXML_TOKEN_DEFINITION_LABEL_METADATA`.
TokenSetDefinitionEvent - Class in info.bioinfweb.jphyloio.events
  Event that indicates that a (predefined) definition of a character state set was found in the parsed file.
TokenSetDefinitionEvent(CharacterStateSetType, String, String) - Constructor for class info.bioinfweb.jphyloio.events.TokenSetDefinitionEvent
  Creates a new instance of this class.
TokenSetEventReceiver - Class in info.bioinfweb.jphyloio.formats.nexus.receivers
TokenSetEventReceiver(NexusWriterStreamDataProvider) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.receivers.TokenSetEventReceiver
TokenTranslationStrategy - Enum in info.bioinfweb.jphyloio.formats.nexml
  Instances of this enum can be used as parameter values for `ReadWriteParameterNames#KEY_NEXML_TOKEN_TRANSLATION_STRATEGY`.
TopoplogicalNodeInfo - Class in info.bioinfweb.jphyloio.utils
  This class is used by `TreeTopologyExtractor` to model a node in a phylogenetic tree or network.
TopoplogicalNodeInfo() - Constructor for class info.bioinfweb.jphyloio.utils.TopoplogicalNodeInfo
toString() - Method in class info.bioinfweb.jphyloio.events.EdgeEvent
toString() - Method in class info.bioinfweb.jphyloio.events.meta.LiteralMetadataContentEvent
  Returns the stored string representation of the modeled metadata element if available.
toString() - Method in class info.bioinfweb.jphyloio.events.meta.URIOrStringIdentifier
toString() - Method in class info.bioinfweb.jphyloio.events.type.EventType
toString() - Method in enum info.bioinfweb.jphyloio.formats.newick.NewickTokenType
toString() - Method in enum info.bioinfweb.jphyloio.formats.pde.PDEMetaColumnType
toString() - Method in enum info.bioinfweb.jphyloio.formats.phyloxml.PropertyOwner
toString() - Method in class info.bioinfweb.jphyloio.formats.xml.elementreaders.XMLElementReaderKey
TranslateReader - Class in info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees
TranslateReader(NexusReaderStreamDataProvider) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees.TranslateReader
TreeNetworkDataAdapter - Interface in info.bioinfweb.jphyloio.dataadapters
  Data adapter interface that provides data for a tree or a network.
TreeNetworkGroupDataAdapter - Interface in info.bioinfweb.jphyloio.dataadapters
TreeReader - Class in info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees
TreeReader(NexusReaderStreamDataProvider) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees.TreeReader
TreeReader(String, String[], NexusReaderStreamDataProvider) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees.TreeReader
TreesBlockHandler - Class in info.bioinfweb.jphyloio.formats.nexus.blockhandlers
TreesBlockHandler() - Constructor for class info.bioinfweb.jphyloio.formats.nexus.blockhandlers.TreesBlockHandler
TreesBlockHandler(String[]) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.blockhandlers.TreesBlockHandler
TreeSetReader - Class in info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets
TreeSetReader(NexusReaderStreamDataProvider) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets.TreeSetReader
TreeTopologyExtractor - Class in info.bioinfweb.jphyloio.utils
  Tool class that allows to determine a tree topology from a `TreeNetworkDataAdapter`.
TreeTopologyExtractor(TreeNetworkDataAdapter, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.utils.TreeTopologyExtractor
TYPE_CONTIN_CELLS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
TYPE_CONTIN_SEQ - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
TYPE_DNA_CELLS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
TYPE_DNA_SEQS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
TYPE_FLOAT_NETWORK - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
TYPE_FLOAT_TREE - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
TYPE_INT_NETWORK - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
TYPE_INT_TREE - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
TYPE_LITERAL_META - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
TYPE_NETWORK_EDGE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
TYPE_PROTEIN_CELLS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
TYPE_PROTEIN_SEQS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
TYPE_RESOURCE_META - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
TYPE_RESTRICTION_CELLS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
TYPE_RESTRICTION_SEQS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
TYPE_RNA_CELLS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
TYPE_RNA_SEQS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
TYPE_STANDARD_CELLS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
TYPE_STANDARD_SEQ - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants

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