org.biopax.paxtools

Class PaxtoolsMain

java.lang.Object

org.biopax.paxtools.PaxtoolsMain

public class PaxtoolsMain
extends Object

Paxtools console application (very useful BioPAX utilities).

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	sifnxToSif(String inputFile, String outputFile)
static void	summarize(Model model, PrintStream out) A summary of BioPAX class and property values in the model (experimental; for troubleshooting and debugging).
static void	summarize(String[] argv)
static void	toGSEA(String[] argv)
static void	toLevel3(String[] argv)
static void	toSbgn(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

Constructor Detail

PaxtoolsMain

public PaxtoolsMain()

Method Detail

main

public static void main(String[] argv)
                 throws Exception

Throws:

Exception

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

sifnxToSif

public static void sifnxToSif(String inputFile,
                              String outputFile)
                       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

A summary of BioPAX class and property values in the model (experimental; for troubleshooting and debugging).

Parameters:

model - input Model

out - output file

Throws:

IOException - when an I/O exception occurs