edu.iastate.metnet.graphmodel
Class RemoveBridgeNodes

java.lang.Object
  edu.iastate.metnet.graphmodel.AbstractGraphProcessor
      edu.iastate.metnet.graphmodel.RemoveBridgeNodes

All Implemented Interfaces:

IGraphProcessor

public class RemoveBridgeNodes
extends AbstractGraphProcessor

Author:

Jie Li

Field Summary

(package private) static org.apache.log4j.Logger

logger log4j facility

Constructor Summary

RemoveBridgeNodes()
default constructor

RemoveBridgeNodes(boolean storeInteraction)
default constructor

Method Summary

boolean	isStoreInteraction()
void	run(MultiPathwayModel model) we have to use two version of run() for two types of graph model.
void	run(PathwayModel model) remove single bridge node (interaction with only one substrate and one product) from the pathway
void	setStoreInteraction(boolean storeInteraction)

Methods inherited from class java.lang.Object

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

Field Detail

logger

static org.apache.log4j.Logger logger

log4j facility

Constructor Detail

RemoveBridgeNodes

public RemoveBridgeNodes()

default constructor

RemoveBridgeNodes

public RemoveBridgeNodes(boolean storeInteraction)

default constructor

Parameters:

storeInteraction - if store the interaction in the user object of the bridge edge

Method Detail

run

public void run(PathwayModel model)

remove single bridge node (interaction with only one substrate and one product) from the pathway

Specified by:

run in interface IGraphProcessor

Overrides:

run in class AbstractGraphProcessor

Parameters:

model - the pathway graph model

run

public void run(MultiPathwayModel model)

we have to use two version of run() for two types of graph model. Basically, we still think the multi-node containing interaction and entitywithlocation purely.

Specified by:

run in interface IGraphProcessor

Overrides:

run in class AbstractGraphProcessor

Parameters:

model - the pathway graph model

isStoreInteraction

public boolean isStoreInteraction()

setStoreInteraction

public void setStoreInteraction(boolean storeInteraction)