edu.iastate.metnet.dao
Class MultiPathwayGraphImpl

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

All Implemented Interfaces:

MultiPathwayGraph, java.io.Serializable

public class MultiPathwayGraphImpl
extends java.lang.Object
implements java.io.Serializable, MultiPathwayGraph

implementation of multi-pathway graph

Author:

Jie Li

See Also:

Serialized Form

Constructor Summary

MultiPathwayGraphImpl()
default constructor

MultiPathwayGraphImpl(PathwayAlignment alignment)
get a merged multi-pathway graph based on the alignment information

Method Summary

void	alignPathwayGraph(PathwayAlignment alignment) standard interface to align two patway graph to generate a single graph model
PathwayAlignment	getAlignment()
MultiPathwayElementNode	getNode(java.lang.String guid) get a node
java.util.Map	getNodeMap()
java.util.List	getPredEntityNodeGuidList(java.lang.String guid) return pred entity node guid list
java.util.List	getPredInteractionNodeGuidList(java.lang.String guid) return pred interaction node guid list
java.util.List	getPredNodeGuidList(java.lang.String guid) return all pred multi-node
int	getSimilarity(java.lang.Integer leftIbid, java.lang.Integer rightIbid) get the number of identical elements in the two context sets
java.util.List	getSuccEntityNodeGuidList(java.lang.String guid) return succ entity node guid list
java.util.List	getSuccInteractionNodeGuidList(java.lang.String guid) return succ interaction node guid list
java.util.List	getSuccNodeGuidList(java.lang.String guid) return succ multi-node
boolean	isEntitywithlocation(java.lang.String guid) determine if this is an entity node
boolean	isInteraction(java.lang.String guid) determine if this is an interaction node
void	setAlignment(PathwayAlignment alignment)

Methods inherited from class java.lang.Object

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

Constructor Detail

MultiPathwayGraphImpl

public MultiPathwayGraphImpl()

default constructor

MultiPathwayGraphImpl

public MultiPathwayGraphImpl(PathwayAlignment alignment)

get a merged multi-pathway graph based on the alignment information

Parameters:

alignment - the alignment

Method Detail

alignPathwayGraph

public void alignPathwayGraph(PathwayAlignment alignment)

standard interface to align two patway graph to generate a single graph model

Specified by:

alignPathwayGraph in interface MultiPathwayGraph

Parameters:

alignment - the alignment information

getPredNodeGuidList

public java.util.List getPredNodeGuidList(java.lang.String guid)

return all pred multi-node

Specified by:

getPredNodeGuidList in interface MultiPathwayGraph

Parameters:

guid - the guid of the multi-node

Returns:

all pred node guid

getSuccNodeGuidList

public java.util.List getSuccNodeGuidList(java.lang.String guid)

return succ multi-node

Specified by:

getSuccNodeGuidList in interface MultiPathwayGraph

Parameters:

guid - the guid of the multi-node

Returns:

all succ node guid

getPredEntityNodeGuidList

public java.util.List getPredEntityNodeGuidList(java.lang.String guid)

return pred entity node guid list

Specified by:

getPredEntityNodeGuidList in interface MultiPathwayGraph

Parameters:

guid - the guid of the multi-node

Returns:

pred entity node guid list

getSuccEntityNodeGuidList

public java.util.List getSuccEntityNodeGuidList(java.lang.String guid)

return succ entity node guid list

Specified by:

getSuccEntityNodeGuidList in interface MultiPathwayGraph

Parameters:

guid - the guid of the multi-node

Returns:

succ entity node guid list

getPredInteractionNodeGuidList

public java.util.List getPredInteractionNodeGuidList(java.lang.String guid)

return pred interaction node guid list

Specified by:

getPredInteractionNodeGuidList in interface MultiPathwayGraph

Parameters:

guid - the guid of the multi-node

Returns:

pred interaction node guid list

getSuccInteractionNodeGuidList

public java.util.List getSuccInteractionNodeGuidList(java.lang.String guid)

return succ interaction node guid list

Specified by:

getSuccInteractionNodeGuidList in interface MultiPathwayGraph

Parameters:

guid - the guid of the multi-node

Returns:

succ interaction node guid list

isEntitywithlocation

public boolean isEntitywithlocation(java.lang.String guid)
                             throws NoSuchNodeException

determine if this is an entity node

Specified by:

isEntitywithlocation in interface MultiPathwayGraph

Parameters:

guid - guid of the multi-node

Returns:

true if it is an entity

Throws:

NoSuchNodeException - no such nodes

isInteraction

public boolean isInteraction(java.lang.String guid)
                      throws NoSuchNodeException

determine if this is an interaction node

Specified by:

isInteraction in interface MultiPathwayGraph

Parameters:

guid - guid of the multi-node

Returns:

true if it is an interaction

Throws:

NoSuchNodeException - no such nodes

getNodeMap

public java.util.Map getNodeMap()

Specified by:

getNodeMap in interface MultiPathwayGraph

Returns:

Returns the nodeMap.

getNode

public MultiPathwayElementNode getNode(java.lang.String guid)

get a node

Specified by:

getNode in interface MultiPathwayGraph

Parameters:

guid - the guid

Returns:

the node

getAlignment

public PathwayAlignment getAlignment()

Specified by:

getAlignment in interface MultiPathwayGraph

Returns:

Returns the alignment.

setAlignment

public void setAlignment(PathwayAlignment alignment)

Parameters:

alignment - The alignment to set.

getSimilarity

public int getSimilarity(java.lang.Integer leftIbid,
                         java.lang.Integer rightIbid)

get the number of identical elements in the two context sets

Specified by:

getSimilarity in interface MultiPathwayGraph

Parameters:

leftIbid - the left interaction

rightIbid - the right interaction

Returns:

number of identical elements in the two context sets