fern.cytoscape
Class CytoscapeNetworkWrapper

java.lang.Object
  extended by fern.network.AbstractNetworkImpl
      extended by fern.cytoscape.CytoscapeNetworkWrapper
All Implemented Interfaces:
Network

public class CytoscapeNetworkWrapper
extends AbstractNetworkImpl


Constructor Summary
CytoscapeNetworkWrapper(NetworkChecker checker, CyNetwork net, CyNetworkView cyView, CyAttributes nodeAttr)
           
 
Method Summary
 long getInitialAmount(int species)
          Gets the initial amount of the specified molecule species.
 NetworkChecker getNetworkChecker()
           
 CyNetworkView getNetworkViewObject()
           
 CyAttributes getNodeAttributeObject()
           
 NodeView getReactionView(int index)
           
 NodeView getSpeciesView(int index)
           
 void setInitialAmount(int species, long value)
          Sets the initial amount of the specified molecule species.
 
Methods inherited from class fern.network.AbstractNetworkImpl
getAmountManager, getAnnotationManager, getName, getNumReactions, getNumSpecies, getProducts, getPropensityCalculator, getReactants, getReactionName, getSpeciesByName, getSpeciesMapping, getSpeciesName
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

CytoscapeNetworkWrapper

public CytoscapeNetworkWrapper(NetworkChecker checker,
                               CyNetwork net,
                               CyNetworkView cyView,
                               CyAttributes nodeAttr)
Method Detail

getInitialAmount

public long getInitialAmount(int species)
Description copied from interface: Network
Gets the initial amount of the specified molecule species.

Parameters:
species - index of the species
Returns:
initial amount of the species

setInitialAmount

public void setInitialAmount(int species,
                             long value)
Description copied from interface: Network
Sets the initial amount of the specified molecule species.

Parameters:
species - index of the species
value - initial amount of the species

getNodeAttributeObject

public CyAttributes getNodeAttributeObject()

getNetworkViewObject

public CyNetworkView getNetworkViewObject()

getReactionView

public NodeView getReactionView(int index)

getSpeciesView

public NodeView getSpeciesView(int index)

getNetworkChecker

public NetworkChecker getNetworkChecker()