edu.iastate.metnet.export
Class MyPathwayGraph

java.lang.Object
  edu.iastate.metnet.export.MyPathwayGraph

All Implemented Interfaces:

java.io.Serializable

public class MyPathwayGraph
extends java.lang.Object
implements java.io.Serializable

a simple pathway graph to detect the structure change. Like version graph, we store the element here but the adjacency list in node itself

Author:

Jie Li

See Also:

Serialized Form

Constructor Summary

MyPathwayGraph()
default constructor

Method Summary

void	addEdge(java.lang.Integer leftId, java.lang.Integer rightId)
void	addNode(PathwayElementNode node) add an element
java.util.ArrayList	getDownstreamEntityNodeIdList(java.lang.Integer blockId) get the downstream entity node id list
java.util.ArrayList	getDownstreamInteractionNodeIdList(java.lang.Integer blockId) get the downstream interaction node id list
java.util.ArrayList	getDownstreamNodeIdList(java.lang.Integer blockId) get the list of new version record
java.util.Map	getNodeMap()
java.util.ArrayList	getUpstreamEntityNodeIdList(java.lang.Integer blockId) get the upstream entity node id list
java.util.ArrayList	getUpstreamInteractionNodeIdList(java.lang.Integer blockId) get the upstream interaction node id list
java.util.ArrayList	getUpstreamNodeIdList(java.lang.Integer blockId) get the list of old version record
boolean	isControlInteraction(java.lang.Integer blockId) if this is a control interaction
boolean	isEntitywithlocation(java.lang.Integer blockId) if it is an entitywithlocation
boolean	isInteraction(java.lang.Integer blockId) if it is an interaction
boolean	isNormalInteraction(java.lang.Integer blockId) if it is a normal interaction
void	removeNode(java.lang.Integer nodeId) remove a node from the pathway structure

Methods inherited from class java.lang.Object

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

Constructor Detail

MyPathwayGraph

public MyPathwayGraph()

default constructor

Method Detail

addNode

public void addNode(PathwayElementNode node)

add an element

Parameters:

node - the structure node information

removeNode

public void removeNode(java.lang.Integer nodeId)

remove a node from the pathway structure

Parameters:

nodeId - the node id of the pathway element

isEntitywithlocation

public boolean isEntitywithlocation(java.lang.Integer blockId)
                             throws NoSuchNodeException

if it is an entitywithlocation

Parameters:

blockId - the blockid of the entitywithlocation

Returns:

true if it is an entitywithlocation, false if not

Throws:

NoSuchNodeException - the node id does not exist

isInteraction

public boolean isInteraction(java.lang.Integer blockId)
                      throws NoSuchNodeException

if it is an interaction

Parameters:

blockId - the blockid of the node

Returns:

true if it is an interaction, false if not

Throws:

NoSuchNodeException - the node id does not exist

isNormalInteraction

public boolean isNormalInteraction(java.lang.Integer blockId)
                            throws NoSuchNodeException

if it is a normal interaction

Parameters:

blockId - the blockid of the node

Returns:

true if it is a normal interaction, false if not

Throws:

NoSuchNodeException - the node id does not exist

isControlInteraction

public boolean isControlInteraction(java.lang.Integer blockId)
                             throws NoSuchNodeException

if this is a control interaction

Parameters:

blockId - the blockid of current node

Returns:

true if it is a control interaction, false if not

Throws:

NoSuchNodeException - the node id does not exist

getDownstreamNodeIdList

public java.util.ArrayList getDownstreamNodeIdList(java.lang.Integer blockId)

get the list of new version record

Parameters:

blockId - the record id to be query

Returns:

the list of new version record id

getUpstreamNodeIdList

public java.util.ArrayList getUpstreamNodeIdList(java.lang.Integer blockId)

get the list of old version record

Parameters:

blockId - the recordid to be query

Returns:

the list of old version record id

getUpstreamEntityNodeIdList

public java.util.ArrayList getUpstreamEntityNodeIdList(java.lang.Integer blockId)

get the upstream entity node id list

Parameters:

blockId - the current node id

Returns:

the upstream entity node id list

getDownstreamEntityNodeIdList

public java.util.ArrayList getDownstreamEntityNodeIdList(java.lang.Integer blockId)

get the downstream entity node id list

Parameters:

blockId - the current node id

Returns:

the downstream entity node id list

getUpstreamInteractionNodeIdList

public java.util.ArrayList getUpstreamInteractionNodeIdList(java.lang.Integer blockId)

get the upstream interaction node id list

Parameters:

blockId - the current node id

Returns:

the upstream interaction node id list

getDownstreamInteractionNodeIdList

public java.util.ArrayList getDownstreamInteractionNodeIdList(java.lang.Integer blockId)

get the downstream interaction node id list

Parameters:

blockId - the current node id

Returns:

the downstream interaction node id list

addEdge

public void addEdge(java.lang.Integer leftId,
                    java.lang.Integer rightId)
             throws NoSuchNodeException

Throws:

NoSuchNodeException

getNodeMap

public java.util.Map getNodeMap()

Returns:

Returns the nodeMap.