info.bioinfweb.jphyloio.dataadapters.implementations.store

Class StoreDocumentDataAdapter

java.lang.Object

info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreAnnotatedDataAdapter<ConcreteJPhyloIOEvent>

info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreDocumentDataAdapter

All Implemented Interfaces:

AnnotatedDataAdapter, DocumentDataAdapter

public class StoreDocumentDataAdapter
extends StoreAnnotatedDataAdapter<ConcreteJPhyloIOEvent>
implements DocumentDataAdapter

Constructor Summary

Constructors

Constructor and Description
StoreDocumentDataAdapter() Creates a new instance of this class with empty array lists for all properties.
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)

Method Summary

Modifier and Type	Method and Description
java.util.List<MatrixDataAdapter>	getMatrices()
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.
org.apache.commons.collections4.OrderedMap<java.lang.String,OTUListDataAdapter>	getOTUListsMap()
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.
java.util.List<TreeNetworkGroupDataAdapter>	getTreesNetworks()

Methods inherited from class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreAnnotatedDataAdapter

getAnnotations, writeMetadata

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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

writeMetadata

Constructor Detail

StoreDocumentDataAdapter

public 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)

StoreDocumentDataAdapter

public StoreDocumentDataAdapter()

Creates a new instance of this class with empty array lists for all properties.

Using this constructor is equivalent to calling #StoreDocumentDataAdapter(List, List, List) with only null arguments.

Method Detail

getOTUListsMap

public org.apache.commons.collections4.OrderedMap<java.lang.String,OTUListDataAdapter> getOTUListsMap()

getMatrices

public java.util.List<MatrixDataAdapter> getMatrices()

getTreesNetworks

public java.util.List<TreeNetworkGroupDataAdapter> getTreesNetworks()

getOTUListIterator

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

Description copied from interface: DocumentDataAdapter

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

Specified by:

getOTUListIterator in interface DocumentDataAdapter

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

public long getOTUListCount(ReadWriteParameterMap parameters)

Description copied from interface: DocumentDataAdapter

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

Specified by:

getOTUListCount in interface DocumentDataAdapter

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 DocumentDataAdapter.getOTUListIterator(ReadWriteParameterMap)

getOTUList

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

Description copied from interface: DocumentDataAdapter

Returns the OTU list referenced by the specified ID.

Specified by:

getOTUList in interface DocumentDataAdapter

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

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

Description copied from interface: DocumentDataAdapter

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

Specified by:

getMatrixIterator in interface DocumentDataAdapter

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

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

Description copied from interface: DocumentDataAdapter

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

Specified by:

getTreeNetworkGroupIterator in interface DocumentDataAdapter

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.)