info.bioinfweb.jphyloio.dataadapters

Interface DocumentDataAdapter

All Superinterfaces:

AnnotatedDataAdapter

All Known Implementing Classes:

EmptyDocumentDataAdapter, ListBasedDocumentDataAdapter, StoreDocumentDataAdapter

public interface DocumentDataAdapter
extends AnnotatedDataAdapter

The root adapter interface to be used with JPhyloIOEventWriters. Implementations model a document containing phylogenetic data, consisting of taxon lists, character matrices and trees or networks.

Application developers need to implement this and one or more of the references interfaces with an adapter class, that allows JPhyloIOEventWriters to access the business model of their application. (Alternatively the business model classes of the application may also implement these interfaces directly, if suitable.)

JPhyloIO offers a set of default implementations in info.bioinfweb.jphyloio.dataadapters.implementations that could be used as superclasses of application adapter implementations, which may reduce the workload in application development.

Author:

Ben Stöver

See Also:

ListBasedDocumentDataAdapter, JPhyloIOEventWriter, OTUListDataAdapter, MatrixDataAdapter, TreeNetworkDataAdapter

Method Summary

Modifier and Type	Method and Description
java.util.Iterator<MatrixDataAdapter>	getMatrixIterator(ReadWriteParameterMap parameters) Returns an iterator providing access to all matrices contained in the document to be written.
OTUListDataAdapter	getOTUList(ReadWriteParameterMap parameters, java.lang.String id) Returns the OTU list referenced by the specified ID.
long	getOTUListCount(ReadWriteParameterMap parameters) Returns the number of OTU lists provided by this document adapter.
java.util.Iterator<OTUListDataAdapter>	getOTUListIterator(ReadWriteParameterMap parameters) Returns an iterator providing access to all OTU lists contained in the document to be written.
java.util.Iterator<TreeNetworkGroupDataAdapter>	getTreeNetworkGroupIterator(ReadWriteParameterMap parameters) Returns an iterator providing access to all trees and network groups contained in the document to be written.

Methods inherited from interface info.bioinfweb.jphyloio.dataadapters.AnnotatedDataAdapter

writeMetadata

Method Detail

getOTUListIterator

java.util.Iterator<OTUListDataAdapter> getOTUListIterator(ReadWriteParameterMap parameters)

Returns an iterator providing access to all OTU lists contained in the document to be written.

Parameters:

parameters - the parameter map of the calling writer that provides context information for the data request

Returns:

the iterator (May be empty but not null.)

getOTUListCount

long getOTUListCount(ReadWriteParameterMap parameters)

Returns the number of OTU lists provided by this document adapter.

Parameters:

parameters - the parameter map of the calling writer that provides context information for the data request

Returns:

the number of OTU lists, that will be returned by getOTUListIterator(ReadWriteParameterMap)

getOTUList

OTUListDataAdapter getOTUList(ReadWriteParameterMap parameters,
                              java.lang.String id)
                       throws java.lang.IllegalArgumentException

Returns the OTU list referenced by the specified ID.

Parameters:

parameters - the parameter map of the calling writer that provides context information for the data request

id - the ID of the OTU list to be returned

Returns:

the OTU list referenced by the specified ID

Throws:

java.lang.IllegalArgumentException - if no OTU list with the specified ID is available

getMatrixIterator

java.util.Iterator<MatrixDataAdapter> getMatrixIterator(ReadWriteParameterMap parameters)

Returns an iterator providing access to all matrices contained in the document to be written.

Parameters:

parameters - the parameter map of the calling writer that provides context information for the data request

Returns:

the iterator (Maybe empty but not null.)

getTreeNetworkGroupIterator

java.util.Iterator<TreeNetworkGroupDataAdapter> getTreeNetworkGroupIterator(ReadWriteParameterMap parameters)

Returns an iterator providing access to all trees and network groups contained in the document to be written.

Parameters:

parameters - the parameter map of the calling writer that provides context information for the data request

Returns:

the iterator (Maybe empty but not null.)