org.biopax.paxtools.examples

Class PathwayGenesExtractor

java.lang.Object

org.biopax.paxtools.examples.PathwayGenesExtractor

All Implemented Interfaces:

Visitor

public class PathwayGenesExtractor
extends Object
implements Visitor

Prints all the genes (aka proteins) in the L2 pathway and sub-pathways (*conditions apply), and also - trace where they come from. * Note: it doesn't traverse the 'NEXT-STEP' property! (as doing so may take you beyond the pathway of interest)

Author:

rodch

Constructor Summary

Constructors

Constructor and Description
PathwayGenesExtractor(pathway pw)

Method Summary

Modifier and Type	Method and Description
static void	main(String[] args)
void	visit(BioPAXElement domain1, Object range, Model model, PropertyEditor editor) An implementation of this method should perform a BioPAX element and editor dependent operation on the model.

Methods inherited from class java.lang.Object

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

Constructor Detail

PathwayGenesExtractor

public PathwayGenesExtractor(pathway pw)

Method Detail

main

public static void main(String[] args)
                 throws FileNotFoundException

Throws:

FileNotFoundException

visit

public void visit(BioPAXElement domain1,
                  Object range,
                  Model model,
                  PropertyEditor editor)

Description copied from interface: Visitor

An implementation of this method should perform a BioPAX element and editor dependent operation on the model. Examples of uses of this method include adding a BioPAX element--with all its dependent elements that can be reached via the editor--into the model, or updating an element that is equivalent to the given BioPAX element using the latter's/former's values.

Specified by:

visit in interface Visitor

Parameters:

domain1 - BioPAXElement which is the domain of this property

range - Object which is the range of this property

model - model on which the visiting operation will be done

editor - editor