edu.iastate.metnet.dao
Class PathwayAlignmentImpl

java.lang.Object
  edu.iastate.metnet.dao.PathwayAlignmentImpl

All Implemented Interfaces:

PathwayAlignment, java.io.Serializable

public class PathwayAlignmentImpl
extends java.lang.Object
implements PathwayAlignment

implementation of alignment

Author:

Jie Li

See Also:

Serialized Form

Field Summary

(package private) java.util.Map	alignmentMbidMap member element blockid mapping
(package private) PathwayGraph	leftGraph one pathway graph
(package private) PathwayGraph	rightGraph the other pathway graph

Constructor Summary

PathwayAlignmentImpl()

PathwayAlignmentImpl(PathwayGraph graph, PathwayGraph graph2)

Method Summary

java.util.Map	getAlignmentMbidMap() get the mapping betweem member blockid since the isomorphism is a one-to-one mapping, we only need Map data structure
PathwayGraph	getLeftGraph() get one pathway graph
PathwayGraph	getRightGraph() get the other pathway graph
void	setAlignment(java.lang.Integer leftMbid, java.lang.Integer rightMbid) put the alignment relation

Methods inherited from class java.lang.Object

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

Field Detail

leftGraph

PathwayGraph leftGraph

one pathway graph

rightGraph

PathwayGraph rightGraph

the other pathway graph

alignmentMbidMap

java.util.Map alignmentMbidMap

member element blockid mapping

Constructor Detail

PathwayAlignmentImpl

public PathwayAlignmentImpl()

PathwayAlignmentImpl

public PathwayAlignmentImpl(PathwayGraph graph,
                            PathwayGraph graph2)

Method Detail

getAlignmentMbidMap

public java.util.Map getAlignmentMbidMap()

Description copied from interface: PathwayAlignment

get the mapping betweem member blockid since the isomorphism is a one-to-one mapping, we only need Map data structure

Specified by:

getAlignmentMbidMap in interface PathwayAlignment

Returns:

Returns the alignmentMbidMap.

setAlignment

public void setAlignment(java.lang.Integer leftMbid,
                         java.lang.Integer rightMbid)

put the alignment relation

Specified by:

setAlignment in interface PathwayAlignment

Parameters:

leftMbid - the left member blockid

rightMbid - the right blockid

getLeftGraph

public PathwayGraph getLeftGraph()

Description copied from interface: PathwayAlignment

get one pathway graph

Specified by:

getLeftGraph in interface PathwayAlignment

Returns:

Returns the leftGraph.

getRightGraph

public PathwayGraph getRightGraph()

Description copied from interface: PathwayAlignment

get the other pathway graph

Specified by:

getRightGraph in interface PathwayAlignment

Returns:

Returns the rightGraph.