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)