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 LiteralMetadataContentEvents.

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 UnknownCommandEvents 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 SingleTokenDefinitionEvents 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 SequenceTokensEvents.

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 LiteralMetadataContentEvents 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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