## Uses of Interface
info.bioinfweb.jphyloio.dataadapters.OTUListDataAdapter

- Packages that use OTUListDataAdapter
  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.formats.newick | Contains classes for reading from and writing to streams/files in Newick tree format.
  info.bioinfweb.jphyloio.formats.nexus | Contains classes for reading from and writing to streams/files in Nexus format.

- - ### Uses of OTUListDataAdapter in info.bioinfweb.jphyloio

    Methods in info.bioinfweb.jphyloio that return OTUListDataAdapter
    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.

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

  - ### Uses of OTUListDataAdapter in info.bioinfweb.jphyloio.dataadapters

    Methods in info.bioinfweb.jphyloio.dataadapters that return OTUListDataAdapter
    Modifier and Type | Method and Description
    --- | ---
    `OTUListDataAdapter` | DocumentDataAdapter.`getOTUList(ReadWriteParameterMap parameters, java.lang.String id)` Returns the OTU list referenced by the specified ID.

    Methods in info.bioinfweb.jphyloio.dataadapters that return types with arguments of type OTUListDataAdapter
    Modifier and Type | Method and Description
    --- | ---
    `java.util.Iterator<OTUListDataAdapter>` | DocumentDataAdapter.`getOTUListIterator(ReadWriteParameterMap parameters)` Returns an iterator providing access to all OTU lists contained in the document to be written.

  - ### Uses of OTUListDataAdapter in info.bioinfweb.jphyloio.dataadapters.implementations

    Classes in info.bioinfweb.jphyloio.dataadapters.implementations that implement OTUListDataAdapter
    Modifier and Type | Class and Description
    --- | ---
    `class` | `UndefinedOTUListDataAdapter`

    Methods in info.bioinfweb.jphyloio.dataadapters.implementations that return OTUListDataAdapter
    Modifier and Type | Method and Description
    --- | ---
    `OTUListDataAdapter` | EmptyDocumentDataAdapter.`getOTUList(ReadWriteParameterMap parameters, java.lang.String id)`
    `OTUListDataAdapter` | ListBasedDocumentDataAdapter.`getOTUList(ReadWriteParameterMap parameters, java.lang.String id)`

    Methods in info.bioinfweb.jphyloio.dataadapters.implementations that return types with arguments of type OTUListDataAdapter
    Modifier and Type | Method and Description
    --- | ---
    `java.util.Iterator<OTUListDataAdapter>` | EmptyDocumentDataAdapter.`getOTUListIterator(ReadWriteParameterMap parameters)`
    `java.util.Iterator<OTUListDataAdapter>` | ListBasedDocumentDataAdapter.`getOTUListIterator(ReadWriteParameterMap parameters)`
    `org.apache.commons.collections4.map.ListOrderedMap<java.lang.String,OTUListDataAdapter>` | ListBasedDocumentDataAdapter.`getOTUListsMap()`

    Constructor parameters in info.bioinfweb.jphyloio.dataadapters.implementations with type arguments of type OTUListDataAdapter
    Constructor and Description
    `ListBasedDocumentDataAdapter(org.apache.commons.collections4.map.ListOrderedMap<java.lang.String,OTUListDataAdapter> otusMap, java.util.List<MatrixDataAdapter> matrices, java.util.List<TreeNetworkGroupDataAdapter> treeNetworkGroups)` Creates a new instance of this class using the specified lists.

  - ### Uses of OTUListDataAdapter in info.bioinfweb.jphyloio.dataadapters.implementations.store

    Classes in info.bioinfweb.jphyloio.dataadapters.implementations.store that implement OTUListDataAdapter
    Modifier and Type | Class and Description
    --- | ---
    `class` | `StoreOTUListDataAdapter`

    Methods in info.bioinfweb.jphyloio.dataadapters.implementations.store that return OTUListDataAdapter
    Modifier and Type | Method and Description
    --- | ---
    `OTUListDataAdapter` | StoreDocumentDataAdapter.`getOTUList(ReadWriteParameterMap parameters, java.lang.String id)`

    Methods in info.bioinfweb.jphyloio.dataadapters.implementations.store that return types with arguments of type OTUListDataAdapter
    Modifier and Type | Method and Description
    --- | ---
    `java.util.Iterator<OTUListDataAdapter>` | StoreDocumentDataAdapter.`getOTUListIterator(ReadWriteParameterMap parameters)`
    `org.apache.commons.collections4.OrderedMap<java.lang.String,OTUListDataAdapter>` | StoreDocumentDataAdapter.`getOTUListsMap()`

    Constructor parameters in info.bioinfweb.jphyloio.dataadapters.implementations.store with type arguments of type OTUListDataAdapter
    Constructor and Description
    `StoreDocumentDataAdapter(java.util.List<JPhyloIOEvent> annotations, org.apache.commons.collections4.OrderedMap<java.lang.String,OTUListDataAdapter> otusMap, java.util.List<MatrixDataAdapter> matrices, java.util.List<TreeNetworkGroupDataAdapter> treeNetworkGroups)`

  - ### Uses of OTUListDataAdapter in info.bioinfweb.jphyloio.formats.newick

    Methods in info.bioinfweb.jphyloio.formats.newick that return OTUListDataAdapter
    Modifier and Type | Method and Description
    --- | ---
    `OTUListDataAdapter` | DefaultNewickWriterNodeLabelProcessor.`getOTUList()`

    Constructors in info.bioinfweb.jphyloio.formats.newick with parameters of type OTUListDataAdapter
    Constructor and Description
    `DefaultNewickWriterNodeLabelProcessor(OTUListDataAdapter otuList, ReadWriteParameterMap parameters)`

  - ### Uses of OTUListDataAdapter in info.bioinfweb.jphyloio.formats.nexus

    Constructors in info.bioinfweb.jphyloio.formats.nexus with parameters of type OTUListDataAdapter
    Constructor and Description
    `NexusNewickWriterNodeLabelProcessor(OTUListDataAdapter otuList, java.util.Map<java.lang.String,java.lang.Long> indexMap, ReadWriteParameterMap parameters)`