Uses of Class
info.bioinfweb.jphyloio.events.LinkedLabeledIDEvent

Packages that use LinkedLabeledIDEvent

Package	Description
info.bioinfweb.jphyloio	The main package of JPhyloIO.
info.bioinfweb.jphyloio.dataadapters	Contains adapter interfaces that should be implemented by adapters mediating between the business model of an application and implementations of JPhyloIOEventWriter.
info.bioinfweb.jphyloio.dataadapters.implementations	Contains some basic (abstract) implementations of JPhyloIOEventWriter.
info.bioinfweb.jphyloio.dataadapters.implementations.store	Contains implementations of data adapters that directly store their modeled data in mutable lists or maps instead of delegating to an application business model.
info.bioinfweb.jphyloio.events	Contains implementations of JPhyloIO events, triggered during event based parsing.
info.bioinfweb.jphyloio.formats.newick	Contains classes for reading from and writing to streams/files in Newick tree format.
info.bioinfweb.jphyloio.formats.nexml	Contains classes for reading from and writing to streams/files in NeXML format.
info.bioinfweb.jphyloio.formats.nexus	Contains classes for reading from and writing to streams/files in Nexus format.

Uses of LinkedLabeledIDEvent in info.bioinfweb.jphyloio

Methods in info.bioinfweb.jphyloio with parameters of type LinkedLabeledIDEvent

Modifier and Type	Method and Description
static java.lang.String	AbstractEventWriter.createUniqueLinkedOTULabel(ReadWriteParameterMap parameters, AbstractEventWriter.UniqueLabelHandler handler, LinkedLabeledIDEvent event, OTUListDataAdapter otuList, boolean otuFirst)
protected java.lang.String	AbstractSingleMatrixEventWriter.editSequenceOrNodeLabel(LinkedLabeledIDEvent event, ReadWriteParameterMap parameters, OTUListDataAdapter otuList)
static java.lang.String	AbstractEventWriter.getLinkedOTUNameOTUFirst(LinkedLabeledIDEvent linkedOTUEvent, OTUListDataAdapter otuList, ReadWriteParameterMap parameters) Determines the name (label) to be used for the specified event when writing its data to a file.
static java.lang.String	AbstractEventWriter.getLinkedOTUNameOwnFirst(LinkedLabeledIDEvent linkedOTUEvent, OTUListDataAdapter otuList, ReadWriteParameterMap parameters) Determines the name (label) to be used for the specified event when writing its data to a file.

Method parameters in info.bioinfweb.jphyloio with type arguments of type LinkedLabeledIDEvent

Modifier and Type	Method and Description
static OTUListDataAdapter	AbstractEventWriter.getReferencedOTUList(DocumentDataAdapter document, ElementDataAdapter<LinkedLabeledIDEvent> source, ReadWriteParameterMap parameters) Returns the OTU list found in document which is referenced by the specified event.

Uses of LinkedLabeledIDEvent in info.bioinfweb.jphyloio.dataadapters

Methods in info.bioinfweb.jphyloio.dataadapters that return LinkedLabeledIDEvent

Modifier and Type	Method and Description
LinkedLabeledIDEvent	MatrixDataAdapter.getSequenceStartEvent(ReadWriteParameterMap parameters, java.lang.String sequenceID) Returns an event describing the sequence with the specified ID.

Methods in info.bioinfweb.jphyloio.dataadapters that return types with arguments of type LinkedLabeledIDEvent

Modifier and Type	Method and Description
ObjectListDataAdapter<LinkedLabeledIDEvent>	MatrixDataAdapter.getCharacterSets(ReadWriteParameterMap parameters) Returns a list of character sets defined for the matrix modeled by this instance.
ObjectListDataAdapter<LinkedLabeledIDEvent>	TreeNetworkDataAdapter.getNodeEdgeSets(ReadWriteParameterMap parameters) Returns a list of node-and-edge-sets defined for the tree modeled by this instance.
ObjectListDataAdapter<LinkedLabeledIDEvent>	OTUListDataAdapter.getOTUSets(ReadWriteParameterMap parameters) Returns a list of OTU sets defined for the OTU list modeled by this instance.
ObjectListDataAdapter<LinkedLabeledIDEvent>	MatrixDataAdapter.getSequenceSets(ReadWriteParameterMap parameters) Returns a list of sequence sets defined for the matrix modeled by this instance.
ObjectListDataAdapter<LinkedLabeledIDEvent>	TreeNetworkGroupDataAdapter.getTreeSets(ReadWriteParameterMap parameters) Returns a list of tree sets defined for the tree-network-group modeled by this instance.

Uses of LinkedLabeledIDEvent in info.bioinfweb.jphyloio.dataadapters.implementations

Methods in info.bioinfweb.jphyloio.dataadapters.implementations that return types with arguments of type LinkedLabeledIDEvent

Modifier and Type	Method and Description
ObjectListDataAdapter<LinkedLabeledIDEvent>	NoCharDefsNoSetsMatrixDataAdapter.getCharacterSets(ReadWriteParameterMap parameters) Default implementation that always returns an empty object list adapter
ObjectListDataAdapter<LinkedLabeledIDEvent>	NoSetsTreeNetworkDataAdapter.getNodeEdgeSets(ReadWriteParameterMap parameters) Default implementation that always returns an empty object list adapter.
ObjectListDataAdapter<LinkedLabeledIDEvent>	UndefinedOTUListDataAdapter.getOTUSets(ReadWriteParameterMap parameters)
ObjectListDataAdapter<LinkedLabeledIDEvent>	NoCharDefsNoSetsMatrixDataAdapter.getSequenceSets(ReadWriteParameterMap parameters) Default implementation that always returns an empty object list adapter.
ObjectListDataAdapter<LinkedLabeledIDEvent>	NoSetsTreeNetworkGroupDataAdapter.getTreeSets(ReadWriteParameterMap parameters) Default implementation that always returns an empty object list adapter.

Uses of LinkedLabeledIDEvent in info.bioinfweb.jphyloio.dataadapters.implementations.store

Methods in info.bioinfweb.jphyloio.dataadapters.implementations.store that return LinkedLabeledIDEvent

Modifier and Type	Method and Description
LinkedLabeledIDEvent	StoreMatrixDataAdapter.getSequenceStartEvent(ReadWriteParameterMap parameters, java.lang.String sequenceID)
LinkedLabeledIDEvent	StoreMatrixDataAdapter.getStartEvent(ReadWriteParameterMap parameters)
LinkedLabeledIDEvent	StoreTreeNetworkGroupDataAdapter.getStartEvent(ReadWriteParameterMap parameters)

Methods in info.bioinfweb.jphyloio.dataadapters.implementations.store that return types with arguments of type LinkedLabeledIDEvent

Modifier and Type	Method and Description
StoreObjectListDataAdapter<LinkedLabeledIDEvent>	StoreMatrixDataAdapter.getCharacterSets(ReadWriteParameterMap parameters)
StoreObjectListDataAdapter<LinkedLabeledIDEvent>	StoreMatrixDataAdapter.getMatrix()
ObjectListDataAdapter<LinkedLabeledIDEvent>	StoreTreeNetworkDataAdapter.getNodeEdgeSets(ReadWriteParameterMap parameters)
StoreObjectListDataAdapter<LinkedLabeledIDEvent>	StoreOTUListDataAdapter.getOTUSets(ReadWriteParameterMap parameters)
StoreObjectListDataAdapter<LinkedLabeledIDEvent>	StoreMatrixDataAdapter.getSequenceSets(ReadWriteParameterMap parameters)
StoreObjectListDataAdapter<LinkedLabeledIDEvent>	StoreTreeNetworkGroupDataAdapter.getTreeSets(ReadWriteParameterMap parameters)

Constructors in info.bioinfweb.jphyloio.dataadapters.implementations.store with parameters of type LinkedLabeledIDEvent

Constructor and Description
StoreMatrixDataAdapter(LinkedLabeledIDEvent alignmentStartEvent, boolean longTokens, java.util.List<JPhyloIOEvent> annotations)
StoreTreeNetworkGroupDataAdapter(LinkedLabeledIDEvent treeOrNetworkGroupStartEvent, java.util.List<JPhyloIOEvent> annotations)

Uses of LinkedLabeledIDEvent in info.bioinfweb.jphyloio.events

Subclasses of LinkedLabeledIDEvent in info.bioinfweb.jphyloio.events

Modifier and Type	Class and Description
class	NodeEvent Event indicating a node in a tree or network.

Methods in info.bioinfweb.jphyloio.events that return LinkedLabeledIDEvent

Modifier and Type	Method and Description
LinkedLabeledIDEvent	ConcreteJPhyloIOEvent.asLinkedLabeledIDEvent()
LinkedLabeledIDEvent	JPhyloIOEvent.asLinkedLabeledIDEvent() Casts this event to a basic OTU event.

Uses of LinkedLabeledIDEvent in info.bioinfweb.jphyloio.formats.newick

Methods in info.bioinfweb.jphyloio.formats.newick with parameters of type LinkedLabeledIDEvent

Modifier and Type	Method and Description
java.lang.String	DefaultNewickWriterNodeLabelProcessor.createNodeName(LinkedLabeledIDEvent nodeEvent)
java.lang.String	NewickWriterNodeLabelProcessor.createNodeName(LinkedLabeledIDEvent nodeEvent)

Uses of LinkedLabeledIDEvent in info.bioinfweb.jphyloio.formats.nexml

Methods in info.bioinfweb.jphyloio.formats.nexml with parameters of type LinkedLabeledIDEvent

Modifier and Type	Method and Description
void	NeXMLWriterStreamDataProvider.writeLinkedLabeledIDAttributes(LinkedLabeledIDEvent event, javax.xml.namespace.QName linkAttribute, boolean forceOTULink)

Uses of LinkedLabeledIDEvent in info.bioinfweb.jphyloio.formats.nexus

Methods in info.bioinfweb.jphyloio.formats.nexus that return types with arguments of type LinkedLabeledIDEvent

Modifier and Type	Method and Description
protected abstract ObjectListDataAdapter<LinkedLabeledIDEvent>	AbstractNexusSetWriter.getSets(ElementDataAdapter<? extends LabeledIDEvent> dataSource)

Methods in info.bioinfweb.jphyloio.formats.nexus with parameters of type LinkedLabeledIDEvent

Modifier and Type	Method and Description
java.lang.String	NexusNewickWriterNodeLabelProcessor.createNodeName(LinkedLabeledIDEvent nodeEvent)