info.bioinfweb.jphyloio.dataadapters

Interface TreeNetworkDataAdapter

All Superinterfaces:

AnnotatedDataAdapter, ElementDataAdapter<LabeledIDEvent>

All Known Implementing Classes:

NoSetsTreeNetworkDataAdapter, StoreTreeNetworkDataAdapter

public interface TreeNetworkDataAdapter
extends ElementDataAdapter<LabeledIDEvent>

Data adapter interface that provides data for a tree or a network.

Applications implementing this adapter may consider to inherit their implementation from EmptyAnnotatedDataAdapter or NoSetsTreeNetworkDataAdapter.

Note that TreeTopologyExtractor can be used by event writer implementations to easily generate a tree topology from the data provided by this adapter, if isTree(ReadWriteParameterMap) returns true.

Since:

0.0.0

Author:

Ben Stöver

See Also:

TreeTopologyExtractor, NoSetsTreeNetworkDataAdapter

Method Summary

Modifier and Type	Method and Description
ObjectListDataAdapter<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.
ObjectListDataAdapter<NodeEvent>	getNodes(ReadWriteParameterMap parameters) Returns the set of nodes contained in this tree or network.
boolean	isTree(ReadWriteParameterMap parameters) Determines whether this instance represents a phylogenetic tree or a phylogenetic network.

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

getStartEvent

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

writeMetadata

Method Detail

isTree

boolean isTree(ReadWriteParameterMap parameters)

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

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

ObjectListDataAdapter<NodeEvent> getNodes(ReadWriteParameterMap parameters)

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

Parameters:

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

Returns:

a list of all nodes

getEdges

ObjectListDataAdapter<EdgeEvent> getEdges(ReadWriteParameterMap parameters)

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

Parameters:

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

Returns:

a list of all edges

getNodeEdgeSets

ObjectListDataAdapter<LinkedLabeledIDEvent> getNodeEdgeSets(ReadWriteParameterMap parameters)

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

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