org.biopax.paxtools

Class PaxtoolsMain

java.lang.Object

org.biopax.paxtools.PaxtoolsMain

public class PaxtoolsMain
extends Object

A command line accessible utility for basic Paxtools operations.

Field Summary

Fields

Modifier and Type	Field and Description
static org.apache.commons.logging.Log	log

Constructor Summary

Constructors

Constructor and Description
PaxtoolsMain()

Method Summary

Modifier and Type	Method and Description
static void	blacklist(String[] argv)
static void	fetch(String[] argv)
static void	getNeighbors(String[] argv)
static void	help()
static void	integrate(String[] argv)
static void	main(String[] argv)
static void	merge(String[] argv)
static void	pattern(String[] argv)
static void	summarize(Model model, PrintStream out)
static void	summarize(String[] argv)
static void	toGSEA(String[] argv)
static void	toLevel3(String[] argv)
static void	toSBGN(String[] argv)
static void	toSif(String[] argv)
static void	toSifnx(String[] argv)
static void	validate(String[] argv)

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(String[] argv)
                 throws IOException,
                        InvocationTargetException,
                        IllegalAccessException

Throws:

IOException

InvocationTargetException

IllegalAccessException

toGSEA

public static void toGSEA(String[] argv)
                   throws IOException

Throws:

IOException

getNeighbors

public static void getNeighbors(String[] argv)
                         throws IOException

Throws:

IOException

fetch

public static void fetch(String[] argv)
                  throws IOException

Throws:

IOException

toLevel3

public static void toLevel3(String[] argv)
                     throws IOException

Throws:

IOException

toSBGN

public static void toSBGN(String[] argv)
                   throws IOException

Throws:

IOException

validate

public static void validate(String[] argv)
                     throws IOException

Throws:

IOException

toSifnx

public static void toSifnx(String[] argv)
                    throws IOException

Throws:

IOException

toSif

public static void toSif(String[] argv)
                  throws IOException

Throws:

IOException

integrate

public static void integrate(String[] argv)
                      throws IOException

Throws:

IOException

merge

public static void merge(String[] argv)
                  throws IOException

Throws:

IOException

blacklist

public static void blacklist(String[] argv)
                      throws IOException

Throws:

IOException

help

public static void help()

pattern

public static void pattern(String[] argv)

summarize

public static void summarize(String[] argv)
                      throws IOException

Throws:

IOException

summarize

public static void summarize(Model model,
                             PrintStream out)
                      throws IOException

Throws:

IOException