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