edu.iastate.metnet.dao
Interface MultiPathwayGraph

All Known Implementing Classes:

MultiPathwayGraphImpl

public interface MultiPathwayGraph

a pathway graph containing several pathways based on the alignment information, we do not use Super- to prevent confusing

Author:

Jie Li

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) return the similarity between context sets of two interactions
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

Method Detail

alignPathwayGraph

void alignPathwayGraph(PathwayAlignment alignment)

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

Parameters:

alignment - the alignment information

getPredNodeGuidList

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

return all pred multi-node

Parameters:

guid - the guid of the multi-node

Returns:

all pred node guid

getSuccNodeGuidList

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

return succ multi-node

Parameters:

guid - the guid of the multi-node

Returns:

all succ node guid

getPredEntityNodeGuidList

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

return pred entity node guid list

Parameters:

guid - the guid of the multi-node

Returns:

pred entity node guid list

getSuccEntityNodeGuidList

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

return succ entity node guid list

Parameters:

guid - the guid of the multi-node

Returns:

succ entity node guid list

getPredInteractionNodeGuidList

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

return pred interaction node guid list

Parameters:

guid - the guid of the multi-node

Returns:

pred interaction node guid list

getSuccInteractionNodeGuidList

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

return succ interaction node guid list

Parameters:

guid - the guid of the multi-node

Returns:

succ interaction node guid list

isEntitywithlocation

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

determine if this is an entity node

Parameters:

guid - guid of the multi-node

Returns:

true if it is an entity

Throws:

NoSuchNodeException - no such nodes

isInteraction

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

determine if this is an interaction node

Parameters:

guid - guid of the multi-node

Returns:

true if it is an interaction

Throws:

NoSuchNodeException - no such nodes

getNodeMap

java.util.Map getNodeMap()

Returns:

Returns the nodeMap.

getNode

MultiPathwayElementNode getNode(java.lang.String guid)

get a node

Parameters:

guid - the guid

Returns:

the node

getAlignment

PathwayAlignment getAlignment()

Returns:

Returns the alignment.

getSimilarity

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

return the similarity between context sets of two interactions

Parameters:

leftIbid - the left interaction

rightIbid - the right interaction

Returns:

number of identical elements in the two context sets