Package de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3interactions

Class LVL3ModelConverter

java.lang.Object

de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3interactions.LVL3ModelConverter

public class LVL3ModelConverter
extends Object

takes an OWL model and fills the graph with edges, nodes and attributes

Author:

ricardo

Constructor Summary

Constructors

Constructor	Description
LVL3ModelConverter()

Method Summary

Modifier and Type	Method	Description
void	convertLVL3Model(org.biopax.paxtools.model.Model model, Graph g, boolean all)
Graph	getGraph()
void	readGraph(org.biopax.paxtools.model.Model model, Graph g)	reads all nodes and edges of the graph first all physical entities will be read so pointing in interactions to them is possible afterwards the interactions will be read
void	readInteractionsFromPathway(org.biopax.paxtools.model.Model originalModel, ArrayList<MyPathWay> arrayList)	made for partial import of one or more pathway components

Methods inherited from class java.lang.Object

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

Constructor Details

LVL3ModelConverter

public LVL3ModelConverter()

Method Details

convertLVL3Model

public void convertLVL3Model(org.biopax.paxtools.model.Model model,
Graph g,
boolean all)
                      throws IllegalArgumentException,
IllegalAccessException,
InvocationTargetException

Throws:

IllegalArgumentException

IllegalAccessException

InvocationTargetException

getGraph

public Graph getGraph()

readGraph

public void readGraph(org.biopax.paxtools.model.Model model,
Graph g)

reads all nodes and edges of the graph first all physical entities will be read so pointing in interactions to them is possible afterwards the interactions will be read

Parameters:

model -

g -

readInteractionsFromPathway

public void readInteractionsFromPathway(org.biopax.paxtools.model.Model originalModel,
ArrayList<MyPathWay> arrayList)
                                 throws IllegalArgumentException,
IllegalAccessException,
InvocationTargetException

made for partial import of one or more pathway components

Parameters:

originalModel -

processes -

Throws:

IllegalArgumentException

IllegalAccessException

InvocationTargetException