Package org.biopax.paxtools

Class PaxtoolsMain

java.lang.Object

org.biopax.paxtools.PaxtoolsMain

public final class PaxtoolsMain
extends Object

Various console utility functions

Method Summary

Modifier and Type	Method	Description
static void	blacklist(String[] argv)
static void	fetch(String[] argv)
static void	getNeighbors(String[] argv)
static void	integrate(String[] argv)
static void	merge(String[] argv)
static void	pattern(String[] argv)
static void	sifnxToSif(String inputFile, String outputFile)
static void	summarize(String[] argv)
static void	summarize(Model model, PrintStream out)	A summary of BioPAX class and property values in the model (experimental, messy; for data troubleshooting).
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

Method Details

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

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, messy; for data troubleshooting).

Parameters:

model - input Model

out - output file

Throws:

IOException - when an I/O exception occurs