edu.iastate.metnet.dao
Class PathwayGraphImpl

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

All Implemented Interfaces:

PathwayGraph, java.io.Serializable

public class PathwayGraphImpl
extends java.lang.Object
implements java.io.Serializable, PathwayGraph

a simple pathway graph to detect the structure change.

Author:

Jie Li

See Also:

Serialized Form

Constructor Summary

PathwayGraphImpl()
default constructor

Method Summary

void	addEdge(java.lang.Integer leftId, java.lang.Integer rightId) add an edge
void	addNode(PathwayElementNode node) add an element
java.util.Map	getAllEbidEidMap() get the entity blockid->entityid mapping for comparison
java.util.List	getAllEbidList() get all entity node bid list
java.util.List	getAllIbidList() get all interaction node bid list
java.util.Set	getContext(java.lang.Integer ibid) get all entity id around the interaction in specified steps.
java.util.List	getDownstreamEntityNodeIdList(java.lang.Integer blockId) get the downstream entity node id list
java.util.List	getDownstreamInteractionNodeIdList(java.lang.Integer blockId) get the downstream interaction node id list
java.util.List	getDownstreamNodeIdList(java.lang.Integer blockId) get the list of new version record
PathwayElementNode	getNode(java.lang.Integer nodeId) return a node by id
java.util.Map	getNodeMap()
java.util.Set	getPbidSet()
InteractionStructure	getSignature(java.lang.Integer ibid) generate the signature of an interaction based on the entityid, the format is (left entity id 1, left entity id 2, ...; right id 1, right id 2, ...) without any space.
java.util.List	getUpstreamEntityNodeIdList(java.lang.Integer blockId) get the upstream entity node id list
java.util.List	getUpstreamInteractionNodeIdList(java.lang.Integer blockId) get the upstream interaction node id list
java.util.List	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	isDetachableInteraction(java.lang.Integer ibid) check if the node specified by the blockid can be detached from the pathway structure
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
PathwayAlignment	isomorphism(PathwayGraph graph, AlignmentAlgorithm algorithm) run isomorphism
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

PathwayGraphImpl

public PathwayGraphImpl()

default constructor

Method Detail

addNode

public void addNode(PathwayElementNode node)

Description copied from interface: PathwayGraph

add an element

Specified by:

addNode in interface PathwayGraph

Parameters:

node - the structure node information

getNode

public PathwayElementNode getNode(java.lang.Integer nodeId)

return a node by id

Specified by:

getNode in interface PathwayGraph

Parameters:

nodeId - the blockid of the node

Returns:

the node

removeNode

public void removeNode(java.lang.Integer nodeId)

Description copied from interface: PathwayGraph

remove a node from the pathway structure

Specified by:

removeNode in interface PathwayGraph

Parameters:

nodeId - the node id of the pathway element

isEntitywithlocation

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

Description copied from interface: PathwayGraph

if it is an entitywithlocation

Specified by:

isEntitywithlocation in interface PathwayGraph

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

Description copied from interface: PathwayGraph

if it is an interaction

Specified by:

isInteraction in interface PathwayGraph

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

Description copied from interface: PathwayGraph

if it is a normal interaction

Specified by:

isNormalInteraction in interface PathwayGraph

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

Description copied from interface: PathwayGraph

if this is a control interaction

Specified by:

isControlInteraction in interface PathwayGraph

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.List getDownstreamNodeIdList(java.lang.Integer blockId)

Description copied from interface: PathwayGraph

get the list of new version record

Specified by:

getDownstreamNodeIdList in interface PathwayGraph

Parameters:

blockId - the record id to be query

Returns:

the list of new version record id

getUpstreamNodeIdList

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

Description copied from interface: PathwayGraph

get the list of old version record

Specified by:

getUpstreamNodeIdList in interface PathwayGraph

Parameters:

blockId - the recordid to be query

Returns:

the list of old version record id

getUpstreamEntityNodeIdList

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

Description copied from interface: PathwayGraph

get the upstream entity node id list

Specified by:

getUpstreamEntityNodeIdList in interface PathwayGraph

Parameters:

blockId - the current node id

Returns:

the upstream entity node id list

getDownstreamEntityNodeIdList

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

Description copied from interface: PathwayGraph

get the downstream entity node id list

Specified by:

getDownstreamEntityNodeIdList in interface PathwayGraph

Parameters:

blockId - the current node id

Returns:

the downstream entity node id list

getUpstreamInteractionNodeIdList

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

Description copied from interface: PathwayGraph

get the upstream interaction node id list

Specified by:

getUpstreamInteractionNodeIdList in interface PathwayGraph

Parameters:

blockId - the current node id

Returns:

the upstream interaction node id list

getDownstreamInteractionNodeIdList

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

Description copied from interface: PathwayGraph

get the downstream interaction node id list

Specified by:

getDownstreamInteractionNodeIdList in interface PathwayGraph

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

Description copied from interface: PathwayGraph

add an edge

Specified by:

addEdge in interface PathwayGraph

Parameters:

leftId - the left node id

rightId - the right node id

Throws:

NoSuchNodeException - exception if one of nodes does not exist

isDetachableInteraction

public boolean isDetachableInteraction(java.lang.Integer ibid)

check if the node specified by the blockid can be detached from the pathway structure

Parameters:

graph - the pathway graph structure

checkedBlockId - the blockid of the node to be checked

Returns:

true if can be detached, false if not

getAllIbidList

public java.util.List getAllIbidList()

get all interaction node bid list

Specified by:

getAllIbidList in interface PathwayGraph

Returns:

all interaction node bid list

getAllEbidList

public java.util.List getAllEbidList()

get all entity node bid list

Specified by:

getAllEbidList in interface PathwayGraph

Returns:

all entity node bid list

getAllEbidEidMap

public java.util.Map getAllEbidEidMap()

get the entity blockid->entityid mapping for comparison

Specified by:

getAllEbidEidMap in interface PathwayGraph

Returns:

the blockid->entityid mapping

getNodeMap

public java.util.Map getNodeMap()

Specified by:

getNodeMap in interface PathwayGraph

Returns:

Returns the nodeMap.

isomorphism

public PathwayAlignment isomorphism(PathwayGraph graph,
                                    AlignmentAlgorithm algorithm)

run isomorphism

Specified by:

isomorphism in interface PathwayGraph

Parameters:

graph - the other pathway graph

algorithm - the alignment algorithm

Returns:

the alignment results

getSignature

public InteractionStructure getSignature(java.lang.Integer ibid)

generate the signature of an interaction based on the entityid, the format is (left entity id 1, left entity id 2, ...; right id 1, right id 2, ...) without any space. If the interaction is an control one, how to specify the interaction signature? we attach char 'I' before the blockid to indicate that it is a normal interaction in the right side. For a normal interaction, we do not consider the control interaction when creating the signature.

Specified by:

getSignature in interface PathwayGraph

Parameters:

ibid - the interaction blockid

Returns:

the signature, directional one.

getPbidSet

public java.util.Set getPbidSet()

Specified by:

getPbidSet in interface PathwayGraph

Returns:

Returns the pbidSet.

getContext

public java.util.Set getContext(java.lang.Integer ibid)

get all entity id around the interaction in specified steps.

Specified by:

getContext in interface PathwayGraph

Parameters:

ibid - the blockid of the interaction

Returns:

all entity id around the interaction in specified steps