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

## G

get(int) - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees.NexusTranslationTable
get(String) - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees.NexusTranslationTable
getAbout() - Method in class info.bioinfweb.jphyloio.events.meta.ResourceMetadataEvent
getAdditionalResourceMetaRel() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLReaderStreamDataProvider
  Returns a {link URIOrStringIdentifier} if an additional `ResourceMetadataEvent` is to be created to enclose meta data of elements without a `JPhyloIOEvent` representation or `null` if this the enclosing event was already generated.
getAfferentBranchID() - Method in class info.bioinfweb.jphyloio.utils.TopoplogicalNodeInfo
getAlignmentInfoByIDMap() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterStreamDataProvider
getAlignmentLength() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterAlignmentInformation
getAlignmentLength() - Method in class info.bioinfweb.jphyloio.formats.pde.PDEReaderStreamDataProvider
getAlignmentType() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterAlignmentInformation
getAllowedChildren() - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLPredicateInfo
getAlternativeStringRepresentation() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLReaderStreamDataProvider
  Returns the value of the content attribute of the current literal meta element to be used as an alternative string representation by a following `LiteralMetadataContentEvent`.
getAlternativeStringValue() - Method in class info.bioinfweb.jphyloio.events.meta.LiteralMetadataEvent
  Returns the alternative string representation of the literal value modeled by the following sequence of `LiteralMetadataContentEvent`s.
getAnnotations() - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreAnnotatedDataAdapter
getAttributeCount() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader
getAttributeInformationMap() - Method in class info.bioinfweb.jphyloio.formats.xml.elementreaders.XMLStartElementReader
getAttributeLocalName(int) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader
getAttributeName() - Method in class info.bioinfweb.jphyloio.formats.xml.AttributeInfo
getAttributeName(int) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader
getAttributeNamespace(int) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader
getAttributePrefix(int) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader
getAttributeToValueMap() - Method in class info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLAttributeMetadataReceiver
getAttributeType(int) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader
getAttributeValue(int) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader
getAttributeValue(String, String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader
getBlockLinks() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusReaderStreamDataProvider
  Returns the map that contains links to other blocks that are explicitly linked to this block.
getBlockName() - Method in class info.bioinfweb.jphyloio.formats.nexus.blockhandlers.ENewickNetworksBlockHandler
getBlockName() - Method in class info.bioinfweb.jphyloio.formats.nexus.blockhandlers.TreesBlockHandler
getBlockNames() - Method in class info.bioinfweb.jphyloio.formats.nexus.blockhandlers.AbstractNexusBlockHandler
getBlockNames() - Method in interface info.bioinfweb.jphyloio.formats.nexus.blockhandlers.NexusBlockHandler
  Returns a collection of the block names this handler supports.
getBlockTitleToIDMap() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusReaderStreamDataProvider
  Returns a map object that can translate Nexus block titles to the IDs of the according JPhyloIO start events.
getCharacterCount() - Method in class info.bioinfweb.jphyloio.formats.phylip.AbstractPhylipEventReader
getCharacterDefinitions(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.NoCharDefsNoSetsMatrixDataAdapter
  Default implementation that always returns an empty object list adapter.
getCharacterDefinitions(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreMatrixDataAdapter
getCharacterDefinitions(ReadWriteParameterMap) - Method in interface info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter
  Returns a list of character definitions for the matrix modeled by this instance.
getCharacterEncodingScheme() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader
getCharacterOffset() - Method in exception info.bioinfweb.jphyloio.exception.JPhyloIOReaderException
  Returns the index of the character in the underlying data source, where the error occurred.
getCharacterSets(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.NoCharDefsNoSetsMatrixDataAdapter
  Default implementation that always returns an empty object list adapter
getCharacterSets(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreMatrixDataAdapter
getCharacterSets(ReadWriteParameterMap) - Method in interface info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter
  Returns a list of character sets defined for the matrix modeled by this instance.
getCharacterSetType() - Method in class info.bioinfweb.jphyloio.formats.xml.XMLReaderStreamDataProvider
getCharIDs() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLReaderStreamDataProvider
  Returns a list of column IDs obtained from NeXML char elements.
getCharIDToIndexMap() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLReaderStreamDataProvider
  Returns a map linking column indices to column IDs obtained from NeXML char elements.
getCharIDToStatesMap() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLReaderStreamDataProvider
  Returns a map linking a token set definition ID to a column ID obtained from a NeXML char elements.
getCharSets() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterAlignmentInformation
getChildIDs() - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLMetaEventInfo
getChildNodeIDs() - Method in class info.bioinfweb.jphyloio.utils.TopoplogicalNodeInfo
getColumnCount(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreMatrixDataAdapter
getColumnCount(ReadWriteParameterMap) - Method in interface info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter
  Returns the number of columns the modeled matrix has, if it contains aligned data or -1 if it contains unaligned data and each sequence may have a different length.
getColumnIndexToIDMap() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterAlignmentInformation
getColumnIndexToStatesMap() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterAlignmentInformation
getColumnNumber() - Method in exception info.bioinfweb.jphyloio.exception.JPhyloIOReaderException
  Returns the index of the column in the underlying data source, where the error occurred.
getCommandName() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.AbstractNexusCommandEventReader
getCommandName() - Method in interface info.bioinfweb.jphyloio.formats.nexus.commandreaders.NexusCommandEventReader
  Returns the name of the Nexus command that can be parsed by this instance.
getCommentContent() - Method in class info.bioinfweb.jphyloio.formats.xml.XMLWriterStreamDataProvider
getCommentEnd() - Method in class info.bioinfweb.jphyloio.formats.text.BasicTextCommentEventReceiver
getCommentStart() - Method in class info.bioinfweb.jphyloio.formats.text.BasicTextCommentEventReceiver
getConstituents() - Method in class info.bioinfweb.jphyloio.events.SingleTokenDefinitionEvent
  Returns a collection of tokens that are constituents of this token (e.g.
getConstituents() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLSingleTokenDefinitionInformation
getContent() - Method in class info.bioinfweb.jphyloio.events.CommentEvent
  Returns the content of the comment.
getContentType() - Method in class info.bioinfweb.jphyloio.events.type.EventType
getContentTypes() - Method in class info.bioinfweb.jphyloio.formatinfo.MetadataModeling
  Returns the set of metadata content types (simple or XML) that may be nested between literal metaevents under start and end events of the according content type.
getCount(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.EmptyObjectListDataAdapter
  This default implementation always returns 0.
getCount(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreObjectListDataAdapter
getCount(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreOTUListDataAdapter
getCount(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.UndefinedOTUListDataAdapter
getCount(ReadWriteParameterMap) - Method in interface info.bioinfweb.jphyloio.dataadapters.ObjectListDataAdapter
  Returns the number of objects to be returned by `ObjectListDataAdapter.getIDIterator(ReadWriteParameterMap)`.
getCreateUnknownCommandEvents() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusEventReader
  Specifies whether `UnknownCommandEvent`s will be fired for all Nexus commands with no according reader stored in the factory.
getCurrentAlignmentID() - Method in class info.bioinfweb.jphyloio.formats.pde.PDEReaderStreamDataProvider
  Returns the ID of the characters element (representing an alignment) that is currently read.
getCurrentAlignmentInfo() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterStreamDataProvider
getCurrentBlockLength() - Method in class info.bioinfweb.jphyloio.utils.SequenceTokensEventManager
getCurrentBlockName() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusEventReader
  Returns the name of the current Nexus block (e.g.
getCurrentBlockStartPosition() - Method in class info.bioinfweb.jphyloio.utils.SequenceTokensEventManager
getCurrentCellsBuffer() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLReaderStreamDataProvider
  The returned map is used to buffer `SingleTokenDefinitionEvent`s and their nested events, in cases where the order of `cell` tags does not match the order of the referenced columns.
getCurrentCladeIDSource() - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLWriterStreamDataProvider
getCurrentEventCollection() - Method in class info.bioinfweb.jphyloio.AbstractEventReader
  Returns the event collection that is currently used to take up new events.
getCurrentEventCollection() - Method in class info.bioinfweb.jphyloio.ReaderStreamDataProvider
  Returns the event collection that is currently used to take up new events.
getCurrentExpectedCharID() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLReaderStreamDataProvider
  Returns the column ID that has been the result of the last call of `NeXMLReaderStreamDataProvider.nextCharID()`.
getCurrentLinkedBlockID(String) - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusReaderStreamDataProvider
  Returns the JPhyloIO ID of the start event describing the Nexus block of the specified type that is linked to the current block.
getCurrentLiteralContentSequenceType() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLReaderStreamDataProvider
  Returns the `LiteralContentSequenceType` of the content nested under the current literal meta element.
getCurrentLiteralMetaDatatype() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterStreamDataProvider
getCurrentLiteralMetaSequenceType() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterStreamDataProvider
getCurrentPosition() - Method in class info.bioinfweb.jphyloio.utils.SequenceTokensEventManager
getCurrentSequenceID() - Method in class info.bioinfweb.jphyloio.formats.pde.PDEReaderStreamDataProvider
getCurrentSequenceIndex() - Method in class info.bioinfweb.jphyloio.formats.pde.PDEReaderStreamDataProvider
getCurrentSequenceLength() - Method in class info.bioinfweb.jphyloio.formats.pde.PDEReaderStreamDataProvider
getCurrentSequenceName() - Method in class info.bioinfweb.jphyloio.utils.SequenceTokensEventManager
getCurrentSingleTokenDefinition() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLReaderStreamDataProvider
  Returns the `NeXMLSingleTokenDefinitionInformation` instance of the currently read single token definition, e.g to add more constituents.
getCurrentTokenSetInfo() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterStreamDataProvider
getCustomXMLElements() - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLWriterStreamDataProvider
getDataReader() - Method in class info.bioinfweb.jphyloio.formats.text.TextReaderStreamDataProvider
getDatatype() - Method in class info.bioinfweb.jphyloio.formats.xml.AttributeInfo
getDefaultBlockID(String) - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.all.BlockTitleToIDMap
getDefaultNamespacePrefix(XMLStreamWriter, String, String) - Static method in class info.bioinfweb.jphyloio.formats.xml.XMLReadWriteUtils
  This method returns a predefined default prefix for a number of namespaces or, if the given namespace does not have a predefined prefix and the given prefix was `null`, `DEFAULT_NAMESPACE_PREFIX`.
getDefaultTokenSetID() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterAlignmentInformation
getDefaultTranslator(QName) - Method in class info.bioinfweb.jphyloio.objecttranslation.ObjectTranslatorFactory
getDefaultTranslatorWithPossiblyInvalidNamespace(QName) - Method in class info.bioinfweb.jphyloio.objecttranslation.ObjectTranslatorFactory
getDefinedTokens() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterAlignmentInformation
getDelimiter() - Method in class info.bioinfweb.jphyloio.formats.text.KeyValueInformation
  Returns the delimiter that was used to delimit the value of this instance.
getDirectParent() - Method in class info.bioinfweb.jphyloio.ParentEventInformation
getDirectParentContentType() - Method in class info.bioinfweb.jphyloio.ParentEventInformation
getDocument() - Method in class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventWriter
getDocumentIDs() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterStreamDataProvider
getEdgeInfos() - Method in class info.bioinfweb.jphyloio.formats.xml.XMLReaderStreamDataProvider
getEdges(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreTreeNetworkDataAdapter
getEdges(ReadWriteParameterMap) - Method in interface info.bioinfweb.jphyloio.dataadapters.TreeNetworkDataAdapter
  Returns the set of edges contained in this tree or network.
getEditedLabel(EventContentType, String) - Method in class info.bioinfweb.jphyloio.utils.LabelEditingReporter
  Returns the (edited) label associated with the specified data element.
getEditedLabel(LabeledIDEvent) - Method in class info.bioinfweb.jphyloio.utils.LabelEditingReporter
  Returns the (edited) label associated with the specified data element.
getElementContentType() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees.ENewickNetworkReader
getElementContentType() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees.TreeReader
getElementCount() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets.AbstractNexusSetReader
  Returns the number of elements which can potentially be contained in this set (e.g.
getElementCount() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets.CharSetReader
getElementCount() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets.IDBasedSetsReader
getElementList(EventContentType, String) - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusReaderStreamDataProvider
getElementName() - Method in class info.bioinfweb.jphyloio.formats.xml.XMLReaderStreamDataProvider
getElementReader(QName, QName, int) - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLEventReader
getElementReader(QName, QName, int) - Method in class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventReader
getElementReaderMap() - Method in class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventReader
getElementText() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLEventReader
getElementText() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader
getElementTypeToCurrentIDMap() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLReaderStreamDataProvider
  Returns a map that links the currently used ID to an `EventContentType`.
getEncoding() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader
getEncounteredTags() - Method in class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventReader
getEnd() - Method in class info.bioinfweb.jphyloio.events.CharacterSetIntervalEvent
  The first index after the new segment to be add to the character set with the specified name.
getEndPos() - Method in class info.bioinfweb.jphyloio.formats.newick.NewickUtils.ReadElement
getEventFactory() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.AbstractMetaXMLReader
getEventReader() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLReaderStreamDataProvider
getEventReader() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusReaderStreamDataProvider
getEventReader() - Method in class info.bioinfweb.jphyloio.ReaderStreamDataProvider
getEventType() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader
getEventWriter() - Method in class info.bioinfweb.jphyloio.WriterStreamDataProvider
getExpectedStart() - Method in class info.bioinfweb.jphyloio.factory.AbstractStartStringSingleFactory
getExpectENewick() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees.ENewickNetworkReader
getExpectENewick() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees.TreeReader
getFileStartInfo(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.AbstractEventWriter
getFirstSequence() - Method in class info.bioinfweb.jphyloio.utils.SequenceTokensEventManager
getFirstSequenceName() - Method in class info.bioinfweb.jphyloio.utils.SequenceTokensEventManager
getFormatID() - Method in class info.bioinfweb.jphyloio.factory.JPhyloIOContentExtensionFileFilter
getFormatID() - Method in class info.bioinfweb.jphyloio.formatinfo.DefaultFormatInfo
getFormatID() - Method in class info.bioinfweb.jphyloio.formats.fasta.FASTAEventReader
getFormatID() - Method in class info.bioinfweb.jphyloio.formats.fasta.FASTAEventWriter
getFormatID() - Method in class info.bioinfweb.jphyloio.formats.mega.MEGAEventReader
getFormatID() - Method in class info.bioinfweb.jphyloio.formats.newick.NewickEventReader
getFormatID() - Method in class info.bioinfweb.jphyloio.formats.newick.NewickEventWriter
getFormatID() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLEventReader
getFormatID() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLEventWriter
getFormatID() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusEventReader
getFormatID() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusEventWriter
getFormatID() - Method in class info.bioinfweb.jphyloio.formats.pde.PDEEventReader
getFormatID() - Method in class info.bioinfweb.jphyloio.formats.phylip.PhylipEventReader
getFormatID() - Method in class info.bioinfweb.jphyloio.formats.phylip.PhylipEventWriter
getFormatID() - Method in class info.bioinfweb.jphyloio.formats.phylip.SequentialPhylipEventReader
getFormatID() - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLEventReader
getFormatID() - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLEventWriter
getFormatID() - Method in class info.bioinfweb.jphyloio.formats.xtg.XTGEventReader
getFormatID() - Method in interface info.bioinfweb.jphyloio.JPhyloIOFormatSpecificObject
  Returns a string ID uniquely identifying the target format of this instance.
getFormatIDsSet() - Method in class info.bioinfweb.jphyloio.factory.JPhyloIOReaderWriterFactory
  Returns the set of IDs of formats that are currently supported by this factory.
getFormatInfo() - Method in class info.bioinfweb.jphyloio.factory.AbstractSingleReaderWriterFactory
getFormatInfo(String) - Method in class info.bioinfweb.jphyloio.factory.JPhyloIOReaderWriterFactory
  Returns an information object for the specified format.
getFormatInfo() - Method in interface info.bioinfweb.jphyloio.factory.SingleReaderWriterFactory
  Returns an information objects describing the target format and providing according file filters.
getFormatName() - Method in class info.bioinfweb.jphyloio.formatinfo.DefaultFormatInfo
getFormatName() - Method in interface info.bioinfweb.jphyloio.formatinfo.JPhyloIOFormatInfo
  Returns the human readable name of the modeled format.
getHandler(String) - Method in class info.bioinfweb.jphyloio.formats.nexus.blockhandlers.NexusBlockHandlerMap
  Returns the handler that is registered for the specified block name.
getHRef() - Method in class info.bioinfweb.jphyloio.events.meta.ResourceMetadataEvent
getID() - Method in class info.bioinfweb.jphyloio.events.LabeledIDEvent
  Returns the document-wide unique ID of the data element represented by this event.
getID() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLReaderTokenSetInformation
getID() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLSingleTokenDefinitionInformation
getID(String, String) - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.all.BlockTitleToIDMap
getID() - Method in class info.bioinfweb.jphyloio.formats.NodeEdgeInfo
getId() - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLMetaEventInfo
getID(String) - Method in class info.bioinfweb.jphyloio.utils.IDToNameManager
  Makes sure that only one ID as assigned to each sequence Nexus name.
getIDIndex() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterStreamDataProvider
getIDIterator(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.EmptyObjectListDataAdapter
  This default implementation always returns an empty iterator.
getIDIterator(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreObjectListDataAdapter
getIDIterator(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreOTUListDataAdapter
getIDIterator(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.UndefinedOTUListDataAdapter
getIDIterator(ReadWriteParameterMap) - Method in interface info.bioinfweb.jphyloio.dataadapters.ObjectListDataAdapter
  Returns an iterator returning the IDs of all objects contained in the list modeled by this instance.
getIDManager() - Method in class info.bioinfweb.jphyloio.AbstractEventReader
getIDManager() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusEventReader
getIDManager() - Method in class info.bioinfweb.jphyloio.ReaderStreamDataProvider
  Returns the ID manager of the associated reader.
getIdSources() - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLWriterStreamDataProvider
getIdSourceToEventIDMap() - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLReaderStreamDataProvider
getIDToNodeInfoMap() - Method in class info.bioinfweb.jphyloio.utils.TreeTopologyExtractor
getIDToTokenSetInfoMap() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterAlignmentInformation
getIgnoredComments() - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.BasicEventReceiver
getIgnoredLiteralMetadata() - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.BasicEventReceiver
getIgnoredMetadata() - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.BasicEventReceiver
getIgnoredResourceMetadata() - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.BasicEventReceiver
getIncompleteToken() - Method in class info.bioinfweb.jphyloio.formats.xml.XMLReaderStreamDataProvider
getIndention() - Method in class info.bioinfweb.jphyloio.AbstractEventWriter
getIndex() - Method in class info.bioinfweb.jphyloio.events.CharacterDefinitionEvent
getIndex() - Method in class info.bioinfweb.jphyloio.formats.pde.PDEMetaColumnDefintion
getInstance() - Static method in class info.bioinfweb.jphyloio.formats.newick.NHXUtils
  Returns the shared instance of this class
getInstance() - Static method in class info.bioinfweb.jphyloio.JPhyloIO
getInvalidEvent() - Method in exception info.bioinfweb.jphyloio.exception.IllegalEventException
getJPhyloIOEventReader() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.AbstractMetaXMLReader
getKey() - Method in class info.bioinfweb.jphyloio.events.UnknownCommandEvent
  Returns the name or key of the unknown command, if provided in the document.
getLabel() - Method in class info.bioinfweb.jphyloio.events.LabeledEvent
  A text label associated with the data element represented by this event.
getLabel() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLReaderTokenSetInformation
getLabel() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLSingleTokenDefinitionInformation
getLabel() - Method in class info.bioinfweb.jphyloio.formats.NodeEdgeInfo
getLabeledIDEventInformation(NeXMLReaderStreamDataProvider, StartElement) - Method in class info.bioinfweb.jphyloio.formats.nexml.elementreader.AbstractNeXMLElementReader
  Obtains information about the ID and label associated with a `StartElement` by reading its attributes.
getLabeledIDName(LabeledIDEvent) - Static method in class info.bioinfweb.jphyloio.AbstractEventWriter
  Returns a name for the specified event.
getLabelEditingReporter() - Method in class info.bioinfweb.jphyloio.ReadWriteParameterMap
  Returns the label editing reporter of this map stored under `ReadWriteParameterNames.KEY_LABEL_EDITING_REPORTER`.
getLabelHandling() - Method in class info.bioinfweb.jphyloio.ReadWriteParameterMap
getLabelStatus(EventContentType, String) - Method in class info.bioinfweb.jphyloio.utils.LabelEditingReporter
  Returns the status of the specified data element and its label.
getLabelStatus(LabeledIDEvent) - Method in class info.bioinfweb.jphyloio.utils.LabelEditingReporter
  Returns the status of the specified data element and its label.
getLastNodeID() - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLReaderStreamDataProvider
getLastNonCommentEvent() - Method in class info.bioinfweb.jphyloio.AbstractEventReader
  Returns the last event that has been returned by previous calls of `AbstractEventReader.readNextEvent()` that was not a comment event.
getLastNonCommentEvent() - Method in interface info.bioinfweb.jphyloio.JPhyloIOEventReader
  Returns the last event that has been returned by previous calls of `#readNextEvent()` that was not a comment event.
getLength() - Method in class info.bioinfweb.jphyloio.events.EdgeEvent
  Returns the length of this edge.
getLength() - Method in class info.bioinfweb.jphyloio.formats.newick.NewickToken
getLength() - Method in class info.bioinfweb.jphyloio.formats.NodeEdgeInfo
getLibraryName() - Method in class info.bioinfweb.jphyloio.JPhyloIO
getLibraryNameAndVersion() - Method in class info.bioinfweb.jphyloio.JPhyloIO
getLineNumber() - Method in exception info.bioinfweb.jphyloio.exception.JPhyloIOReaderException
  Returns the index of the line in the underlying data source, where the error occurred.
getLinkedBlockName(ElementDataAdapter<? extends LabeledIDEvent>) - Method in class info.bioinfweb.jphyloio.formats.nexus.AbstractNexusSetWriter
getLinkedID() - Method in interface info.bioinfweb.jphyloio.events.LinkedIDEvent
  Returns the ID of a data element, linked to the element modeled by this event.
getLinkedID() - Method in class info.bioinfweb.jphyloio.events.LinkedLabeledIDEvent
  Returns the ID of a data element, linked to the element modeled by this event.
getLinkedID() - Method in class info.bioinfweb.jphyloio.events.SetElementEvent
  Returns the ID of the event modeling the member of the set this event is nested in.
getLinkedID() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets.AbstractNexusSetReader
  Returns the ID if the object that is linked to this set (e.g.
getLinkedID() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets.CharSetReader
getLinkedID() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets.IDBasedSetsReader
getLinkedObjectType() - Method in class info.bioinfweb.jphyloio.events.SetElementEvent
  Returns the type of event that is linked to this set.
getLinkedOTUID(String) - Method in class info.bioinfweb.jphyloio.formats.newick.DefaultNewickReaderNodeLabelProcessor
getLinkedOTUID(String) - Method in interface info.bioinfweb.jphyloio.formats.newick.NewickReaderNodeLabelProcessor
  Returns the OTU ID that is associated with the specified label.
getLinkedOTUID(String) - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees.NexusNewickReaderNodeLabelProcessor
getLinkedOTUNameOTUFirst(LinkedLabeledIDEvent, OTUListDataAdapter, ReadWriteParameterMap) - Static method in class info.bioinfweb.jphyloio.AbstractEventWriter
  Determines the name (label) to be used for the specified event when writing its data to a file.
getLinkedOTUNameOwnFirst(LinkedLabeledIDEvent, OTUListDataAdapter, ReadWriteParameterMap) - Static method in class info.bioinfweb.jphyloio.AbstractEventWriter
  Determines the name (label) to be used for the specified event when writing its data to a file.
getListeners() - Method in class info.bioinfweb.jphyloio.push.EventForwarder
  Returns the list of listeners to which this instance forwards its consumed events.
getLocalName() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader
getLocation() - Method in class info.bioinfweb.jphyloio.formats.newick.NewickToken
getLocation() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader
getLogger() - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.BasicEventReceiver
getLogger() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusEventWriter
getLogger() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusWriterStreamDataProvider
getLogger() - Method in class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventWriter
getLogger() - Method in class info.bioinfweb.jphyloio.ReadWriteParameterMap
getMap(String) - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusReaderStreamDataProvider
  Gets a map object from the shared information map.
getMatchToken() - Method in class info.bioinfweb.jphyloio.ReadWriteParameterMap
getMatchToken() - Method in class info.bioinfweb.jphyloio.utils.SequenceTokensEventManager
getMatrices() - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.ListBasedDocumentDataAdapter
getMatrices() - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreDocumentDataAdapter
getMatrix() - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreMatrixDataAdapter
getMatrixIDToBlockTypeMap() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusEventWriter
getMatrixIDToBlockTypeMap() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusWriterStreamDataProvider
getMatrixIterator(ReadWriteParameterMap) - Method in interface info.bioinfweb.jphyloio.dataadapters.DocumentDataAdapter
  Returns an iterator providing access to all matrices contained in the document to be written.
getMatrixIterator(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.EmptyDocumentDataAdapter
getMatrixIterator(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.ListBasedDocumentDataAdapter
getMatrixIterator(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreDocumentDataAdapter
getMatrixLink() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusReaderStreamDataProvider
  Returns the ID if a `CHARACTERS`, `DATA` or `UNALIGNED` block that is linked to the current block.
getMatrixWidthsMap() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusReaderStreamDataProvider
  Returns a map object that stores the widths of all sequence matrices encountered until now.
getMaxCommentLength() - Method in class info.bioinfweb.jphyloio.ReadWriteParameterMap
getMaxTokensToRead() - Method in class info.bioinfweb.jphyloio.ReadWriteParameterMap
getMeaning() - Method in class info.bioinfweb.jphyloio.events.SingleTokenDefinitionEvent
  Returns the meaning of the new token.
getMetaColumns() - Method in class info.bioinfweb.jphyloio.formats.pde.PDEReaderStreamDataProvider
getMetadataModeling(EventContentType, boolean) - Method in class info.bioinfweb.jphyloio.formatinfo.DefaultFormatInfo
getMetadataModeling(EventContentType, boolean) - Method in interface info.bioinfweb.jphyloio.formatinfo.JPhyloIOFormatInfo
  Determines which kind of metadata the represented format allows to model nested under the specified data element Readers will not produce metaevents under an unsupported type, while writers will accept but ignore metaevents under this type.
getMetaEvents() - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLWriterStreamDataProvider
getMetaIDs() - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLWriterStreamDataProvider
getMetaLevel() - Method in class info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLPredicateMetaReceiver
getMetaType() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLReaderStreamDataProvider
  Returns a stack of `EventContentType` that represents the currently encountered nested meta events.
getName() - Method in class info.bioinfweb.jphyloio.formats.pde.PDEMetaColumnDefintion
getName() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader
getNamespaceContext() - Method in class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventReader
  Returns the currently valid namespace context object or `null`, if the root element was not yet read.
getNamespaceContext() - Method in class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventWriter
getNamespaceContext() - Method in interface info.bioinfweb.jphyloio.formats.xml.JPhyloIOXMLEventReader
  Returns the namespace context that is valid at the current position of the document.
getNamespaceContext() - Method in interface info.bioinfweb.jphyloio.formats.xml.JPhyloIOXMLEventWriter
  Returns the currently valid namespace context of the writer.
getNamespaceContext() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLEventWriter
  Returns the current namespace context of the underlying XML event writer, if
getNamespaceContext() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader
getNamespaceContext() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
getNamespaceCount() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader
getNamespacePrefix(int) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader
getNamespacePrefixes() - Method in class info.bioinfweb.jphyloio.formats.xml.XMLWriterStreamDataProvider
getNamespaceURI() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader
getNamespaceURI(int) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader
getNamespaceURI(String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader
getNestedEdgeEvents() - Method in class info.bioinfweb.jphyloio.formats.NodeEdgeInfo
getNestedEvents() - Method in class info.bioinfweb.jphyloio.formats.BufferedEventInfo
getNestedEvents() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLReaderTokenSetInformation
getNestedMetaNames() - Method in class info.bioinfweb.jphyloio.formats.xml.XMLReaderStreamDataProvider
getNestedNodeEvents() - Method in class info.bioinfweb.jphyloio.formats.NodeEdgeInfo
getNetworkEdgeIDs() - Method in class info.bioinfweb.jphyloio.utils.TreeTopologyExtractor
getNeXMLPrefix(XMLStreamWriter) - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterStreamDataProvider
getNexusNameToIDMap(EventContentType, String) - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusReaderStreamDataProvider
  Returns a map object that translates between a Nexus name and the JPhyloIO ID of the according event.
getNodeEdgeSets(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.NoSetsTreeNetworkDataAdapter
  Default implementation that always returns an empty object list adapter.
getNodeEdgeSets(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreTreeNetworkDataAdapter
getNodeEdgeSets(ReadWriteParameterMap) - Method in interface info.bioinfweb.jphyloio.dataadapters.TreeNetworkDataAdapter
  Returns a list of node-and-edge-sets defined for the tree modeled by this instance.
getNodeEventIDToIDSourceMap() - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLWriterStreamDataProvider
getNodes(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreTreeNetworkDataAdapter
getNodes(ReadWriteParameterMap) - Method in interface info.bioinfweb.jphyloio.dataadapters.TreeNetworkDataAdapter
  Returns the set of nodes contained in this tree or network.
getNumericValue() - Method in class info.bioinfweb.jphyloio.formats.newick.NewickUtils.ReadElement
getObjectClass() - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLColorTranslator
getObjectClass() - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.Base64BinaryTranslator
getObjectClass() - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.BigDecimalTranslator
getObjectClass() - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.BigIntegerTranslator
getObjectClass() - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.BooleanTranslator
getObjectClass() - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.ByteTranslator
getObjectClass() - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.ColorTranslator
getObjectClass() - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.DateTimeTranslator
getObjectClass() - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.DateTranslator
getObjectClass() - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.DoubleTranslator
getObjectClass() - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.EnumTranslator
getObjectClass() - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.FloatTranslator
getObjectClass() - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.HexadecimalColorTranslator
getObjectClass() - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.HexBinaryTranslator
getObjectClass() - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.IntegerTranslator
getObjectClass() - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.ListTranslator
getObjectClass() - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.LongTranslator
getObjectClass() - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.QNameTranslator
getObjectClass() - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.ShortTranslator
getObjectClass() - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.StringTranslator
getObjectClass() - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.TimeTranslator
getObjectClass() - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.URITranslator
getObjectClass() - Method in interface info.bioinfweb.jphyloio.objecttranslation.ObjectTranslator
  Returns the Java class of object instances created by this translator.
getObjectContent() - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreObjectData
getObjectContent(String) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreObjectListDataAdapter
getObjectMap() - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreObjectListDataAdapter
getObjectStartEvent(ReadWriteParameterMap, String) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.EmptyObjectListDataAdapter
getObjectStartEvent() - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreObjectData
getObjectStartEvent(ReadWriteParameterMap, String) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreObjectListDataAdapter
getObjectStartEvent(ReadWriteParameterMap, String) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreOTUListDataAdapter
getObjectStartEvent(ReadWriteParameterMap, String) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.UndefinedOTUListDataAdapter
getObjectStartEvent(ReadWriteParameterMap, String) - Method in interface info.bioinfweb.jphyloio.dataadapters.ObjectListDataAdapter
  Returns the start event of an object determined by the specified object ID.
getObjectTranslatorFactory() - Method in class info.bioinfweb.jphyloio.ReadWriteParameterMap
  Returns the object translator factory stored under `ReadWriteParameterNames.KEY_OBJECT_TRANSLATOR_FACTORY`.
getObjectValue() - Method in class info.bioinfweb.jphyloio.events.meta.LiteralMetadataContentEvent
  Returns the Java object representing the metadata element modeled by this event.
getOccuringTokens() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterTokenSetInformation
getOriginalKey() - Method in class info.bioinfweb.jphyloio.formats.text.KeyValueInformation
  Returns the key as it was written from the source stream (file).
getOriginalType() - Method in class info.bioinfweb.jphyloio.events.meta.LiteralMetadataEvent
getOriginalType() - Method in class info.bioinfweb.jphyloio.formats.phyloxml.receivers.PhyloXMLMetaDataReceiver
getOTUIDToLabelMap() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLReaderStreamDataProvider
  Returns a map that links a label to a certain OTU ID.
getOTUList(ReadWriteParameterMap, String) - Method in interface info.bioinfweb.jphyloio.dataadapters.DocumentDataAdapter
  Returns the OTU list referenced by the specified ID.
getOTUList(ReadWriteParameterMap, String) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.EmptyDocumentDataAdapter
getOTUList(ReadWriteParameterMap, String) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.ListBasedDocumentDataAdapter
getOTUList(ReadWriteParameterMap, String) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreDocumentDataAdapter
getOTUList() - Method in class info.bioinfweb.jphyloio.formats.newick.DefaultNewickWriterNodeLabelProcessor
getOTUListCount(ReadWriteParameterMap) - Method in interface info.bioinfweb.jphyloio.dataadapters.DocumentDataAdapter
  Returns the number of OTU lists provided by this document adapter.
getOTUListCount(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.EmptyDocumentDataAdapter
getOTUListCount(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.ListBasedDocumentDataAdapter
getOTUListCount(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreDocumentDataAdapter
getOtuListID() - Method in class info.bioinfweb.jphyloio.formats.pde.PDEReaderStreamDataProvider
getOTUListIterator(ReadWriteParameterMap) - Method in interface info.bioinfweb.jphyloio.dataadapters.DocumentDataAdapter
  Returns an iterator providing access to all OTU lists contained in the document to be written.
getOTUListIterator(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.EmptyDocumentDataAdapter
getOTUListIterator(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.ListBasedDocumentDataAdapter
getOTUListIterator(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreDocumentDataAdapter
getOTUListsMap() - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.ListBasedDocumentDataAdapter
getOTUListsMap() - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreDocumentDataAdapter
getOTUorOTUsEventInformation(NeXMLReaderStreamDataProvider, StartElement) - Method in class info.bioinfweb.jphyloio.formats.nexml.elementreader.AbstractNeXMLElementReader
  Obtains information about the ID, label and linked OTU or OTU list associated with a `StartElement` by reading its attributes.
getOtus() - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreOTUListDataAdapter
getOTUSets(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreOTUListDataAdapter
getOTUSets(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.UndefinedOTUListDataAdapter
getOTUSets(ReadWriteParameterMap) - Method in interface info.bioinfweb.jphyloio.dataadapters.OTUListDataAdapter
  Returns a list of OTU sets defined for the OTU list modeled by this instance.
getOwner() - Method in class info.bioinfweb.jphyloio.utils.SequenceTokensEventManager
  Returns the reader instance using this object.
getPaintStartID() - Method in class info.bioinfweb.jphyloio.utils.TreeTopologyExtractor
getParameterMap() - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.BasicEventReceiver
getParameters() - Method in class info.bioinfweb.jphyloio.AbstractEventReader
getParameters() - Method in class info.bioinfweb.jphyloio.formats.newick.DefaultNewickWriterNodeLabelProcessor
getParameters() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusEventWriter
getParameters() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusWriterStreamDataProvider
getParameters() - Method in class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventWriter
getParameters() - Method in class info.bioinfweb.jphyloio.ReaderStreamDataProvider
  Returns the parameter map that was specified when the constructor of the associated reader was called.
getParentEvent() - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.BasicEventReceiver
getParentEvent() - Method in exception info.bioinfweb.jphyloio.exception.IllegalEventException
getParentEvents() - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.BasicEventReceiver
getParentFromBottom(int) - Method in class info.bioinfweb.jphyloio.ParentEventInformation
getParentFromTop(int) - Method in class info.bioinfweb.jphyloio.ParentEventInformation
getParentInformation() - Method in class info.bioinfweb.jphyloio.AbstractEventReader
  The returned object provides information on the start events fired by this reader until now.
getParentInformation() - Method in interface info.bioinfweb.jphyloio.JPhyloIOEventReader
  The returned object provides information on the start events fired by this reader until now.
getParentName() - Method in class info.bioinfweb.jphyloio.formats.xml.XMLReaderStreamDataProvider
getParentNodeID() - Method in class info.bioinfweb.jphyloio.utils.TopoplogicalNodeInfo
getParentTag() - Method in class info.bioinfweb.jphyloio.formats.xml.elementreaders.XMLElementReaderKey
getPhylogenyID() - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLWriterStreamDataProvider
getPhylogenyIDProvider() - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLWriterStreamDataProvider
getPhyloXMLEventIDTranslationMap() - Method in class info.bioinfweb.jphyloio.ReadWriteParameterMap
getPhyloXMLMetadataTreatment() - Method in class info.bioinfweb.jphyloio.ReadWriteParameterMap
getPIData() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader
getPITarget() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader
getPredicate() - Method in class info.bioinfweb.jphyloio.events.meta.LiteralMetadataEvent
getPredicate() - Method in class info.bioinfweb.jphyloio.formats.xml.AttributeInfo
getPredicateInfoMap() - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLWriterStreamDataProvider
  This map is used by `PhyloXMLSpecificPredicatesDataReceiver` to translate meta events with certain predicates to PhyloXML tags.
getPredicates() - Method in class info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLPredicateMetaReceiver
getPrefix(String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLEventWriter
getPrefix() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader
getPrefix(String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
getPreviousEvent() - Method in class info.bioinfweb.jphyloio.AbstractEventReader
  Returns the event that has been returned by the previous call of `AbstractEventReader.readNextEvent()`.
getPreviousEvent() - Method in interface info.bioinfweb.jphyloio.JPhyloIOEventReader
  Returns the event that was returned with the last call of `JPhyloIOEventReader.next()`.
getProjectURL() - Method in class info.bioinfweb.jphyloio.JPhyloIO
getProperty(String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.AbstractMetaXMLReader
getProperty(String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
getPropertyOwner() - Method in class info.bioinfweb.jphyloio.formats.phyloxml.receivers.PhyloXMLMetaDataReceiver
getReadAheadLimit() - Method in class info.bioinfweb.jphyloio.factory.JPhyloIOReaderWriterFactory
  Returns the maximal number of bytes this factory will read to determine the format of an input in the `#guess*()` methods.
getReader(String, InputStream, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.factory.JPhyloIOReaderWriterFactory
getReader(String, File, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.factory.JPhyloIOReaderWriterFactory
getReader(String, Reader, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.factory.JPhyloIOReaderWriterFactory
getReader(InputStream, ReadWriteParameterMap) - Method in interface info.bioinfweb.jphyloio.factory.SingleReaderWriterFactory
  Creates a new reader instance for the target format of this factory.
getReader(Reader, ReadWriteParameterMap) - Method in interface info.bioinfweb.jphyloio.factory.SingleReaderWriterFactory
  Creates a new reader instance for the target format of this factory.
getReader(InputStream, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.formats.fasta.FASTAFactory
getReader(Reader, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.formats.fasta.FASTAFactory
getReader(InputStream, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.formats.mega.MEGAFactory
getReader(Reader, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.formats.mega.MEGAFactory
getReader(InputStream, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.formats.newick.NewickFactory
getReader(Reader, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.formats.newick.NewickFactory
getReader(InputStream, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLFactory
getReader(Reader, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLFactory
getReader(InputStream, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusFactory
getReader(Reader, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusFactory
getReader(InputStream, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.formats.pde.PDEFactory
getReader(Reader, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.formats.pde.PDEFactory
getReader(InputStream, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.formats.phylip.PhylipFactory
getReader(Reader, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.formats.phylip.PhylipFactory
getReader(InputStream, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.formats.phylip.SequentialPhylipFactory
getReader(Reader, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.formats.phylip.SequentialPhylipFactory
getReader(InputStream, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLFactory
getReader(Reader, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLFactory
getReader() - Method in class info.bioinfweb.jphyloio.formats.text.AbstractTextEventReader
  Returns the reader providing the document contents.
getReader(InputStream, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.formats.xtg.XTGFactory
getReader(Reader, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.formats.xtg.XTGFactory
getReceiver() - Method in exception info.bioinfweb.jphyloio.exception.IllegalEventException
getReceiver() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.AbstractMetaXMLWriter
getReferencedOTUList(DocumentDataAdapter, ElementDataAdapter<LinkedLabeledIDEvent>, ReadWriteParameterMap) - Static method in class info.bioinfweb.jphyloio.AbstractEventWriter
  Returns the OTU list found in `document` which is referenced by the specified event.
getRel() - Method in class info.bioinfweb.jphyloio.events.meta.ResourceMetadataEvent
getResourcePredicate() - Method in class info.bioinfweb.jphyloio.formats.xml.elementreaders.XMLStartElementReader
getRootTag() - Method in class info.bioinfweb.jphyloio.formats.xml.AbstractXMLFactory
  Returns the root tag that was specified in the constructor.
getSequenceCount(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreMatrixDataAdapter
getSequenceCount(ReadWriteParameterMap) - Method in interface info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter
  Returns the number of sequences contained in this matrix.
getSequenceCount() - Method in class info.bioinfweb.jphyloio.formats.pde.PDEReaderStreamDataProvider
getSequenceCount() - Method in class info.bioinfweb.jphyloio.formats.phylip.AbstractPhylipEventReader
getSequenceIDIterator(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreMatrixDataAdapter
getSequenceIDIterator(ReadWriteParameterMap) - Method in interface info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter
  Returns an iterator returning the IDs of all sequences in the represented matrix.
getSequenceIndexToOTUID() - Method in class info.bioinfweb.jphyloio.formats.pde.PDEReaderStreamDataProvider
getSequenceInformations() - Method in class info.bioinfweb.jphyloio.formats.pde.PDEReaderStreamDataProvider
getSequenceLength(ReadWriteParameterMap, String) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreMatrixDataAdapter
getSequenceLength(ReadWriteParameterMap, String) - Method in interface info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter
  Returns the length for the specified sequence.
getSequenceSets(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.NoCharDefsNoSetsMatrixDataAdapter
  Default implementation that always returns an empty object list adapter.
getSequenceSets(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreMatrixDataAdapter
getSequenceSets(ReadWriteParameterMap) - Method in interface info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter
  Returns a list of sequence sets defined for the matrix modeled by this instance.
getSequenceStartEvent(ReadWriteParameterMap, String) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreMatrixDataAdapter
getSequenceStartEvent(ReadWriteParameterMap, String) - Method in interface info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter
  Returns an event describing the sequence with the specified ID.
getSequenceTokensEventManager() - Method in class info.bioinfweb.jphyloio.AbstractEventReader
  Returns the manager object used by this instance to create `SequenceTokensEvent`s.
getSequenceTokensEventManager() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusEventReader
getSequenceTokensEventManager() - Method in class info.bioinfweb.jphyloio.ReaderStreamDataProvider
  Returns the sequence tokens event manager of the associated reader.
getSequenceType() - Method in class info.bioinfweb.jphyloio.events.meta.LiteralMetadataEvent
  Determines which type of sequence of `LiteralMetadataContentEvent`s will be nested within this event.
getSetIDToSetElementsMap() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterStreamDataProvider
getSets(ElementDataAdapter<? extends LabeledIDEvent>) - Method in class info.bioinfweb.jphyloio.formats.nexus.AbstractNexusSetWriter
getSetType() - Method in class info.bioinfweb.jphyloio.events.TokenSetDefinitionEvent
  Returns the meaning of the the new character state set.
getSetType() - Method in class info.bioinfweb.jphyloio.formats.nexml.elementreader.AbstractSetElementReader
getSetType() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLReaderTokenSetInformation
getSharedInformationMap() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusReaderStreamDataProvider
  This map can be used to store objects to be shared between different instances of `NexusCommandEventReader`.
getSingleToken() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterStreamDataProvider
getSingleTokenDefinitions() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterTokenSetInformation
getSingleTokens() - Method in class info.bioinfweb.jphyloio.formats.nexus.receivers.TokenSetEventReceiver
getSource() - Method in class info.bioinfweb.jphyloio.formats.NodeEdgeInfo
getSourceID() - Method in class info.bioinfweb.jphyloio.events.EdgeEvent
  Returns the ID of the source node linked by this edge.
getSourceNode() - Method in class info.bioinfweb.jphyloio.formats.xml.XMLReaderStreamDataProvider
getStart() - Method in class info.bioinfweb.jphyloio.events.CharacterSetIntervalEvent
  The first position of the new segment to be add to the character set with the specified name.
getStartDocumentEvent() - Method in class info.bioinfweb.jphyloio.formats.xml.XMLReaderStreamDataProvider
getStartEvent(ReadWriteParameterMap) - Method in interface info.bioinfweb.jphyloio.dataadapters.ElementDataAdapter
  Returns the start event of this data element.
getStartEvent(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreMatrixDataAdapter
getStartEvent(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreOTUListDataAdapter
getStartEvent(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreTreeNetworkDataAdapter
getStartEvent(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreTreeNetworkGroupDataAdapter
getStartEvent(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.UndefinedOTUListDataAdapter
getStartEvent() - Method in class info.bioinfweb.jphyloio.formats.BufferedEventInfo
getStartTriggerCommand() - Method in class info.bioinfweb.jphyloio.formats.nexus.blockhandlers.ENewickNetworksBlockHandler
getStartTriggerCommand() - Method in class info.bioinfweb.jphyloio.formats.nexus.blockhandlers.TreesBlockHandler
getStreamDataProvider() - Method in class info.bioinfweb.jphyloio.AbstractEventReader
getStreamDataProvider() - Method in class info.bioinfweb.jphyloio.AbstractEventWriter
getStreamDataProvider() - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.BasicEventReceiver
getStreamDataProvider() - Method in class info.bioinfweb.jphyloio.formats.newick.NewickNodeEdgeEventReceiver
getStreamDataProvider() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.AbstractNexusCommandEventReader
getStreamDataProvider() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.AbstractMetaXMLReader
getStringRepresentation() - Method in class info.bioinfweb.jphyloio.events.meta.URIOrStringIdentifier
getStringValue() - Method in class info.bioinfweb.jphyloio.events.meta.LiteralMetadataContentEvent
  Returns the string value of the meta information.
getSupportedParameters(boolean) - Method in class info.bioinfweb.jphyloio.formatinfo.DefaultFormatInfo
getSupportedParameters(boolean) - Method in interface info.bioinfweb.jphyloio.formatinfo.JPhyloIOFormatInfo
  Returns a set of the parameters supported by the associated reader or writer.
getSymbol() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLSingleTokenDefinitionInformation
getSymbolTranslationMap() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLReaderTokenSetInformation
getTagName() - Method in class info.bioinfweb.jphyloio.formats.xml.elementreaders.XMLElementReaderKey
getTarget() - Method in class info.bioinfweb.jphyloio.formats.NodeEdgeInfo
getTargetID() - Method in class info.bioinfweb.jphyloio.events.EdgeEvent
  Returns the ID of the target node linked by this edge.
getText() - Method in class info.bioinfweb.jphyloio.formats.newick.NewickToken
getText() - Method in class info.bioinfweb.jphyloio.formats.newick.NewickUtils.ReadElement
getText() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader
getTextCharacters() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader
getTextCharacters(int, char[], int, int) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader
getTextLength() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader
getTextStart() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader
getToken() - Method in class info.bioinfweb.jphyloio.events.SingleSequenceTokenEvent
getTokenDefinitionIDToSymbolMap() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLReaderStreamDataProvider
  Returns a map that links a symbol (i.e.
getTokenIndex() - Method in class info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLHandleSequenceDataReceiver
  Returns the index of the alignment character the currently handled token belongs to.
getTokenName() - Method in class info.bioinfweb.jphyloio.events.SingleTokenDefinitionEvent
  Returns the string representation of the new token.
getTokens() - Method in class info.bioinfweb.jphyloio.events.SequenceTokensEvent
getTokenSetIDtoColumnsMap() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLReaderStreamDataProvider
  Returns a map that links a symbol (i.e.
getTokenSets(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.NoCharDefsNoSetsMatrixDataAdapter
  Default implementation that always returns an empty object list adapter.
getTokenSets(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreMatrixDataAdapter
getTokenSets(ReadWriteParameterMap) - Method in interface info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter
  Returns a list of token sets defined for the matrix modeled by this instance.
getTokenSets() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLReaderStreamDataProvider
  Returns a map that links a `NeXMLReaderTokenSetInformation` to a certain token set ID.
getTokenSetType() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterAlignmentInformation
getTokenTranslationMap() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterTokenSetInformation
getTokenType() - Method in class info.bioinfweb.jphyloio.events.SingleTokenDefinitionEvent
  Returns the type of the new token (e.g.
getTokenType() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterAlignmentInformation
getTopologyType() - Method in class info.bioinfweb.jphyloio.events.type.EventType
getTopologyType() - Method in class info.bioinfweb.jphyloio.formatinfo.MetadataModeling
  Returns the topology type that may be nested between start and end events of the according content type.
getTranslateTokens() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLEventReader
getTranslateTokens() - Method in class info.bioinfweb.jphyloio.ReadWriteParameterMap
getTranslation() - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLPredicateInfo
getTranslator(QName, Class<O>) - Method in class info.bioinfweb.jphyloio.objecttranslation.ObjectTranslatorFactory
getTreatment() - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLPredicateInfo
getTreeLabel() - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLReaderStreamDataProvider
getTreeNetworkGroupIterator(ReadWriteParameterMap) - Method in interface info.bioinfweb.jphyloio.dataadapters.DocumentDataAdapter
  Returns an iterator providing access to all trees and network groups contained in the document to be written.
getTreeNetworkGroupIterator(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.EmptyDocumentDataAdapter
getTreeNetworkGroupIterator(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.ListBasedDocumentDataAdapter
getTreeNetworkGroupIterator(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreDocumentDataAdapter
getTreeNetworkGroups() - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.ListBasedDocumentDataAdapter
getTreeNetworkIterator(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreTreeNetworkGroupDataAdapter
getTreeNetworkIterator(ReadWriteParameterMap) - Method in interface info.bioinfweb.jphyloio.dataadapters.TreeNetworkGroupDataAdapter
  Returns an iterator providing access to all trees and networks contained in the document to be written.
getTreesAndNetworks() - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreTreeNetworkGroupDataAdapter
getTreeSets(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.NoSetsTreeNetworkGroupDataAdapter
  Default implementation that always returns an empty object list adapter.
getTreeSets(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreTreeNetworkGroupDataAdapter
getTreeSets(ReadWriteParameterMap) - Method in interface info.bioinfweb.jphyloio.dataadapters.TreeNetworkGroupDataAdapter
  Returns a list of tree sets defined for the tree-network-group modeled by this instance.
getTreesNetworks() - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreDocumentDataAdapter
getTreesTranslationTable() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusReaderStreamDataProvider
  Returns the current Nexus translation table object.
getType() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
getType() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
  Returns the type of this event.
getType() - Method in class info.bioinfweb.jphyloio.formats.newick.NewickToken
getType() - Method in class info.bioinfweb.jphyloio.formats.pde.PDEMetaColumnDefintion
getUndefinedOtuID() - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.UndefinedOTUListDataAdapter
getUndefinedOTUID() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterStreamDataProvider
getUndefinedOTUsID() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterStreamDataProvider
getUnderlyingXMLWriter() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.AbstractMetaXMLWriter
getUpcomingEvents() - Method in class info.bioinfweb.jphyloio.AbstractEventReader
  Returns the queue to store events in, that shall be returned by upcoming calls of `AbstractEventReader.next()`.
getURI() - Method in class info.bioinfweb.jphyloio.events.meta.URIOrStringIdentifier
getValidBlocks() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.AbstractNexusCommandEventReader
getValidBlocks() - Method in interface info.bioinfweb.jphyloio.formats.nexus.commandreaders.NexusCommandEventReader
  Returns a collection with the names of the Nexus blocks the command parsed by the implementing class may be contained in.
getValue() - Method in class info.bioinfweb.jphyloio.events.UnknownCommandEvent
  Returns the value of the unknown command.
getValue() - Method in class info.bioinfweb.jphyloio.formats.text.KeyValueInformation
  Returns the value as it was written from the source stream (file).
getVersion() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader
getVersion() - Method in class info.bioinfweb.jphyloio.JPhyloIO
getWriter(String) - Method in class info.bioinfweb.jphyloio.factory.JPhyloIOReaderWriterFactory
getWriter() - Method in interface info.bioinfweb.jphyloio.factory.SingleReaderWriterFactory
  Creates a new writer instance for the target format of this factory.
getWriter() - Method in class info.bioinfweb.jphyloio.formats.fasta.FASTAFactory
getWriter() - Method in class info.bioinfweb.jphyloio.formats.mega.MEGAFactory
getWriter() - Method in class info.bioinfweb.jphyloio.formats.newick.NewickFactory
getWriter() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLFactory
getWriter() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusFactory
getWriter() - Method in class info.bioinfweb.jphyloio.formats.pde.PDEFactory
getWriter() - Method in class info.bioinfweb.jphyloio.formats.phylip.AbstractPhylipFactory
getWriter() - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLFactory
getWriter() - Method in class info.bioinfweb.jphyloio.formats.text.AbstractTextEventWriter
getWriter() - Method in class info.bioinfweb.jphyloio.formats.text.TextWriterStreamDataProvider
getWriter() - Method in class info.bioinfweb.jphyloio.formats.xml.XMLWriterStreamDataProvider
getWriter() - Method in class info.bioinfweb.jphyloio.formats.xtg.XTGFactory
getWriterInstance() - Method in class info.bioinfweb.jphyloio.ReadWriteParameterMap
  Returns the writer instance registered under `ReadWriteParameterNames.KEY_WRITER_INSTANCE`.
getXMLEvent() - Method in class info.bioinfweb.jphyloio.events.meta.LiteralMetadataContentEvent
  Returns the `XMLEvent` modeled by this instance.
getXmlEventType() - Method in class info.bioinfweb.jphyloio.formats.xml.elementreaders.XMLElementReaderKey
getXMLReader() - Method in class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventReader
getXMLReader() - Method in class info.bioinfweb.jphyloio.formats.xml.XMLReaderStreamDataProvider
getXMLWriter() - Method in class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventWriter
getXSDPrefix(XMLStreamWriter) - Static method in class info.bioinfweb.jphyloio.formats.xml.XMLReadWriteUtils
getXSIPrefix(XMLStreamWriter) - Static method in class info.bioinfweb.jphyloio.formats.xml.XMLReadWriteUtils
guessFormat(File, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.factory.JPhyloIOReaderWriterFactory
  Tries to determine the format of the contents of the specified file by examining at its beginning (e.g.
guessFormat(File) - Method in class info.bioinfweb.jphyloio.factory.JPhyloIOReaderWriterFactory
  Tries to determine the format of the contents of the specified file by examining at its beginning (e.g.
guessFormat(Reader, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.factory.JPhyloIOReaderWriterFactory
  Tries to determine the format of the contents of the specified reader by examining at its beginning (e.g.
guessFormat(Reader) - Method in class info.bioinfweb.jphyloio.factory.JPhyloIOReaderWriterFactory
  Tries to determine the format of the contents of the specified reader by examining at its beginning (e.g.
guessFormat(InputStream, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.factory.JPhyloIOReaderWriterFactory
  Tries to determine the format of the contents of the specified input stream by examining at its beginning (e.g.
guessFormat(InputStream) - Method in class info.bioinfweb.jphyloio.factory.JPhyloIOReaderWriterFactory
  Tries to determine the format of the contents of the specified reader by examining at its beginning (e.g.
guessReader(InputStream, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.factory.JPhyloIOReaderWriterFactory
  Tries to determine the format of the contents of the specified input stream as described in the documentation of `JPhyloIOReaderWriterFactory.guessFormat(InputStream)`, resets the input stream and than creates a reader for the according format from that stream.
guessReader(File, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.factory.JPhyloIOReaderWriterFactory
  Tries to determine the format of the contents of the specified file as described in the documentation of `JPhyloIOReaderWriterFactory.guessFormat(File)` and than creates a reader for the according format from that stream.

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