edu.iastate.metnet.graphmodel
Class PathwayModel

java.lang.Object
  org._3pq.jgrapht.graph.AbstractGraph
      org._3pq.jgrapht.graph.GraphDelegator
          org._3pq.jgrapht.graph.DefaultListenableGraph
              org._3pq.jgrapht.graph.ListenableDirectedGraph
                  edu.iastate.metnet.graphmodel.PathwayModel

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, org._3pq.jgrapht.DirectedGraph, org._3pq.jgrapht.Graph, org._3pq.jgrapht.ListenableGraph

public class PathwayModel
extends org._3pq.jgrapht.graph.ListenableDirectedGraph

special graph model, which only add interaction nodes, and automatically add entitywithlocation nodes and edges related to these nodes

Author:

Jie Li

See Also:

Serialized Form

Field Summary

(package private) static org.apache.log4j.Logger	logger log4j facility
protected MetnetPathway	pathway current pathway object

Constructor Summary

PathwayModel(org._3pq.jgrapht.DirectedGraph network, java.util.Map typeMap)
construct the model based on the networks

PathwayModel(org._3pq.jgrapht.DirectedGraph network, java.util.Map dataMap, org.apache.commons.collections.map.MultiKeyMap coefficientMap)
create a pathway model from network

PathwayModel(java.util.Map pathwayMap)
set up the mixture of the pathway based on the ID

Method Summary

void	applyProcessor(IGraphProcessor graphProcessor) general method for post-modification on the graph data model
java.util.Map	getBlockunitMap(java.util.Collection blockIdList)
org.apache.commons.collections.map.MultiKeyMap	getBridgeMap()
org.apache.commons.collections.map.MultiKeyMap	getCoeffMap()
java.util.Map	getLocalPathwayMap()
org.apache.commons.collections.MultiMap	getMbidPbidMap() get the relation among all member blockid and pathway blockid mapping relation
java.util.ArrayList	getPbidMembership(java.lang.Integer mbid) detect the membership of pathway
int	size() return the number of pathway in this model

Methods inherited from class org._3pq.jgrapht.graph.DefaultListenableGraph

addEdge, addEdge, addGraphListener, addVertex, addVertexSetListener, clone, fireEdgeAdded, fireEdgeRemoved, fireVertexAdded, fireVertexRemoved, isReuseEvents, removeEdge, removeEdge, removeGraphListener, removeVertex, removeVertexSetListener, setReuseEvents

Methods inherited from class org._3pq.jgrapht.graph.GraphDelegator

containsEdge, containsVertex, degreeOf, edgeSet, edgesOf, getAllEdges, getEdge, getEdgeFactory, incomingEdgesOf, inDegreeOf, outDegreeOf, outgoingEdgesOf, toString, vertexSet

Methods inherited from class org._3pq.jgrapht.graph.AbstractGraph

addAllEdges, addAllVertices, assertVertexExist, containsEdge, removeAllEdges, removeAllEdges, removeAllEdges, removeAllVertices, toStringFromSets

Methods inherited from class java.lang.Object

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

Methods inherited from interface org._3pq.jgrapht.DirectedGraph

incomingEdgesOf, inDegreeOf, outDegreeOf, outgoingEdgesOf

Methods inherited from interface org._3pq.jgrapht.Graph

addAllEdges, addAllVertices, addEdge, addEdge, addVertex, containsEdge, containsEdge, containsVertex, edgeSet, edgesOf, getAllEdges, getEdge, getEdgeFactory, removeAllEdges, removeAllEdges, removeAllVertices, removeEdge, removeEdge, removeVertex, vertexSet

Field Detail

logger

static org.apache.log4j.Logger logger

log4j facility

pathway

protected MetnetPathway pathway

current pathway object

Constructor Detail

PathwayModel

public PathwayModel(org._3pq.jgrapht.DirectedGraph network,
                    java.util.Map typeMap)

construct the model based on the networks

Parameters:

network - the network containing only the blockid

PathwayModel

public PathwayModel(org._3pq.jgrapht.DirectedGraph network,
                    java.util.Map dataMap,
                    org.apache.commons.collections.map.MultiKeyMap coefficientMap)

create a pathway model from network

Parameters:

network - the network, containing sequence ID

dataMap - the data map from sequence ID to BlockUnit

dummy - the dummy param to distinguish another constructor

PathwayModel

public PathwayModel(java.util.Map pathwayMap)

set up the mixture of the pathway based on the ID

Parameters:

pathwayMap - pathway list

Method Detail

applyProcessor

public void applyProcessor(IGraphProcessor graphProcessor)

general method for post-modification on the graph data model

Parameters:

graphProcessor - the post-modification processor

size

public int size()

return the number of pathway in this model

Returns:

the number of pathway in this model

getMbidPbidMap

public org.apache.commons.collections.MultiMap getMbidPbidMap()

get the relation among all member blockid and pathway blockid mapping relation

Returns:

Returns the mbidPbidMap.

getPbidMembership

public java.util.ArrayList getPbidMembership(java.lang.Integer mbid)

detect the membership of pathway

Parameters:

mbid - the member element's blockid

Returns:

blockid list of pathway in current preview window which the member belongs to

getLocalPathwayMap

public java.util.Map getLocalPathwayMap()

Returns:

Returns the localPathwayMap.

getBlockunitMap

public java.util.Map getBlockunitMap(java.util.Collection blockIdList)

Returns:

the blockunitMap

getBridgeMap

public org.apache.commons.collections.map.MultiKeyMap getBridgeMap()

Returns:

the bridge map, in which the two key is the source node and target node, the value is the interaction removed from the pathway model

getCoeffMap

public org.apache.commons.collections.map.MultiKeyMap getCoeffMap()

Returns:

the coeffMap