info.bioinfweb.jphyloio.dataadapters.implementations.store

Class StoreTreeNetworkDataAdapter

java.lang.Object

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

info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreTreeNetworkDataAdapter

All Implemented Interfaces:

AnnotatedDataAdapter, ElementDataAdapter<LabeledIDEvent>, TreeNetworkDataAdapter

public class StoreTreeNetworkDataAdapter
extends StoreAnnotatedDataAdapter<LinkedLabeledIDEvent>
implements TreeNetworkDataAdapter

Constructor Summary

Constructors

Constructor and Description
StoreTreeNetworkDataAdapter(LabeledIDEvent startEvent, boolean isTree, java.util.List<JPhyloIOEvent> annotations)

Method Summary

Modifier and Type	Method and Description
StoreObjectListDataAdapter<EdgeEvent>	getEdges(ReadWriteParameterMap parameters) Returns the set of edges contained in this tree or network.
ObjectListDataAdapter<LinkedLabeledIDEvent>	getNodeEdgeSets(ReadWriteParameterMap parameters) Returns a list of node-and-edge-sets defined for the tree modeled by this instance.
StoreObjectListDataAdapter<NodeEvent>	getNodes(ReadWriteParameterMap parameters) Returns the set of nodes contained in this tree or network.
LabeledIDEvent	getStartEvent(ReadWriteParameterMap parameters) Returns the start event of this data element.
boolean	isTree(ReadWriteParameterMap parameters) Determines whether this instance represents a phylogenetic tree or a phylogenetic network.

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

StoreTreeNetworkDataAdapter

public StoreTreeNetworkDataAdapter(LabeledIDEvent startEvent,
                                   boolean isTree,
                                   java.util.List<JPhyloIOEvent> annotations)

Method Detail

getStartEvent

public LabeledIDEvent getStartEvent(ReadWriteParameterMap parameters)

Description copied from interface: ElementDataAdapter

Returns the start event of this data element. The returned event can be used to determine the label and ID of the modeled data element or an optionally linked data element.

Specified by:

getStartEvent in interface ElementDataAdapter<LabeledIDEvent>

Parameters:

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

Returns:

the start event of this data element

isTree

public boolean isTree(ReadWriteParameterMap parameters)

Description copied from interface: TreeNetworkDataAdapter

Determines whether this instance represents a phylogenetic tree or a phylogenetic network. (Not all formats accept networks.)

Specified by:

isTree in interface TreeNetworkDataAdapter

Parameters:

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

Returns:

true if this instance represents a tree or false otherwise

getNodes

public StoreObjectListDataAdapter<NodeEvent> getNodes(ReadWriteParameterMap parameters)

Description copied from interface: TreeNetworkDataAdapter

Returns the set of nodes contained in this tree or network.

Specified by:

getNodes in interface TreeNetworkDataAdapter

Parameters:

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

Returns:

a list of all nodes

getEdges

public StoreObjectListDataAdapter<EdgeEvent> getEdges(ReadWriteParameterMap parameters)

Description copied from interface: TreeNetworkDataAdapter

Returns the set of edges contained in this tree or network. All nodes referenced by these edges are contained on TreeNetworkDataAdapter.getEdges(ReadWriteParameterMap).

Specified by:

getEdges in interface TreeNetworkDataAdapter

Parameters:

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

Returns:

a list of all edges

getNodeEdgeSets

public ObjectListDataAdapter<LinkedLabeledIDEvent> getNodeEdgeSets(ReadWriteParameterMap parameters)

Description copied from interface: TreeNetworkDataAdapter

Returns a list of node-and-edge-sets defined for the tree modeled by this instance.

Specified by:

getNodeEdgeSets in interface TreeNetworkDataAdapter

Parameters:

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

Returns:

a (possibly empty) list of node-edge-sets