com.dpgil.pathlinker.path_linker.internal.model

Class PathLinkerModel

java.lang.Object

com.dpgil.pathlinker.path_linker.internal.model.PathLinkerModel

public class PathLinkerModel
extends Object

Back end model for the PathLinker plugin

Constructor Summary

Constructors

Constructor and Description

PathLinkerModel(org.cytoscape.model.CyNetwork originalNetwork, boolean allowSourcesTargetsInPaths, boolean includePathScoreTies, Set<String> sourceNames, Set<String> targetNames, List<org.cytoscape.model.CyNode> sourcesList, List<org.cytoscape.model.CyNode> targetsList, String edgeWeightColumnName, int inputK, EdgeWeightType edgeWeightType, Double edgePenalty, Map<org.cytoscape.model.CyNode,String> cyNodeToId) Constructor of the model

Method Summary

Modifier and Type	Method and Description
int	getOutputK() Getter method of output k value
ArrayList<Algorithms.PathWay>	getResult() Getter method of the result
Set<org.cytoscape.model.CyNode>	getSubgraphSources() Getter method of the subgraph sources
Set<org.cytoscape.model.CyNode>	getSubgraphTargets() Getter method of the subgraph targets
void	runKSP() Runs all the necessary algorithms to calculate kth shortest path If path exists, selects corresponding nodes and edges in the network to prepare for the subnetwork creation

Methods inherited from class java.lang.Object

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

Constructor Detail

PathLinkerModel

public PathLinkerModel(org.cytoscape.model.CyNetwork originalNetwork,
                       boolean allowSourcesTargetsInPaths,
                       boolean includePathScoreTies,
                       Set<String> sourceNames,
                       Set<String> targetNames,
                       List<org.cytoscape.model.CyNode> sourcesList,
                       List<org.cytoscape.model.CyNode> targetsList,
                       String edgeWeightColumnName,
                       int inputK,
                       EdgeWeightType edgeWeightType,
                       Double edgePenalty,
                       Map<org.cytoscape.model.CyNode,String> cyNodeToId)

Constructor of the model

Parameters:

originalNetwork - the original network given by the view

allowSourcesTargetsInPaths - boolean deciding if sources and targets should be allow in the result path

includePathScoreTies - the option to include all paths of equal length

sourceNames - set of sources in string

targetNames - set of targets in string

sourcesList - list of sources in CyNode

targetsList - list of targets in CyNode

edgeWeightColumnName - column name that contains the edge weight information

inputK - input k value

edgeWeightType - edge weight type

edgePenalty - edge penalty

cyNodeToId - map mapping all CyNode to its string name

Method Detail

getSubgraphSources

public Set<org.cytoscape.model.CyNode> getSubgraphSources()

Getter method of the subgraph sources

Returns:

subgraphSources

getSubgraphTargets

public Set<org.cytoscape.model.CyNode> getSubgraphTargets()

Getter method of the subgraph targets

Returns:

subgraphTargets

getOutputK

public int getOutputK()

Getter method of output k value

Returns:

output k value

getResult

public ArrayList<Algorithms.PathWay> getResult()

Getter method of the result

Returns:

result

runKSP

public void runKSP()

Runs all the necessary algorithms to calculate kth shortest path If path exists, selects corresponding nodes and edges in the network to prepare for the subnetwork creation