org.biopax.paxtools.examples
Class ProteinNameLister

java.lang.Object
  org.biopax.paxtools.examples.ProteinNameLister

public class ProteinNameLister
extends java.lang.Object

This example class processes all the Level2 BioPAX OWL files in the input directory to find all the protein names

Notes:

- recent fix: it doesn't traverse into the NEXT-STEP property, as it may lead beyond the boundaries of the pathway of interest!

- one may prefer using the Paxtools' jenaIO instead of the simpleIO:

import org.biopax.paxtools.io.jena.JenaIOHandler; JenaIOHandler handler = new JenaIOHandler(null, BioPAXLevel.L2);

Constructor Summary

ProteinNameLister()

Method Summary

static void	listProteinUnificationXrefsPerPathway(Model model)
static void	listUnificationXrefsPerPathway(Model model) Here is a more elegant way of doing the previous method!
static void	main(java.lang.String[] args)

Methods inherited from class java.lang.Object

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

Constructor Detail

ProteinNameLister

public ProteinNameLister()

Method Detail

main

public static void main(java.lang.String[] args)

listProteinUnificationXrefsPerPathway

public static void listProteinUnificationXrefsPerPathway(Model model)

listUnificationXrefsPerPathway

public static void listUnificationXrefsPerPathway(Model model)

Here is a more elegant way of doing the previous method!

Parameters:

model -