## 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)`