org.biopax.paxtools
Class PaxtoolsMain

java.lang.Object
  org.biopax.paxtools.PaxtoolsMain

public class PaxtoolsMain
extends java.lang.Object

A command line accessible utility for basic Paxtools operations.

Field Summary

static org.apache.commons.logging.Log

log

Constructor Summary

PaxtoolsMain()

Method Summary

static void	fetch(java.lang.String[] argv)
static void	fromPsimi(java.lang.String[] argv)
static void	getNeighbors(java.lang.String[] argv)
static void	integrate(java.lang.String[] argv)
static void	main(java.lang.String[] argv)
static void	merge(java.lang.String[] argv)
static void	toGSEA(java.lang.String[] argv)
static void	toLevel3(java.lang.String[] argv)
static void	toSif(java.lang.String[] argv)
static void	toSifnx(java.lang.String[] argv)
static void	validate(java.lang.String[] argv) Checks files by the online BioPAX validator using the validator client.

Methods inherited from class java.lang.Object

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

Field Detail

log

public static org.apache.commons.logging.Log log

Constructor Detail

PaxtoolsMain

public PaxtoolsMain()

Method Detail

main

public static void main(java.lang.String[] argv)
                 throws java.io.IOException,
                        java.lang.reflect.InvocationTargetException,
                        java.lang.IllegalAccessException

Throws:

java.io.IOException

java.lang.reflect.InvocationTargetException

java.lang.IllegalAccessException

fromPsimi

public static void fromPsimi(java.lang.String[] argv)
                      throws java.io.IOException

Throws:

java.io.IOException

toGSEA

public static void toGSEA(java.lang.String[] argv)
                   throws java.io.IOException

Throws:

java.io.IOException

getNeighbors

public static void getNeighbors(java.lang.String[] argv)
                         throws java.io.IOException

Throws:

java.io.IOException

fetch

public static void fetch(java.lang.String[] argv)
                  throws java.io.IOException

Throws:

java.io.IOException

toLevel3

public static void toLevel3(java.lang.String[] argv)
                     throws java.io.IOException

Throws:

java.io.IOException

validate

public static void validate(java.lang.String[] argv)
                     throws java.io.IOException

Checks files by the online BioPAX validator using the validator client.

Parameters:

argv -

Throws:

java.io.IOException

See Also:

http://www.biopax.org/biopax-validator/ws.html

toSifnx

public static void toSifnx(java.lang.String[] argv)
                    throws java.io.IOException

Throws:

java.io.IOException

toSif

public static void toSif(java.lang.String[] argv)
                  throws java.io.IOException

Throws:

java.io.IOException

integrate

public static void integrate(java.lang.String[] argv)
                      throws java.io.IOException

Throws:

java.io.IOException

merge

public static void merge(java.lang.String[] argv)
                  throws java.io.IOException

Throws:

java.io.IOException