ubic.erminej

Class classScoreCMD

java.lang.Object

ubic.erminej.classScoreCMD

public class classScoreCMD
extends Object

Run ermineJ from the command line (or fire up the GUI).

Version:

$Id: classScoreCMD.java,v 1.30 2013/05/20 05:21:15 paul Exp $

Author:

Paul Pavlidis, keshav

Field Summary

Fields

Modifier and Type	Field and Description
protected GeneAnnotations	geneData
protected GeneSetTerms	goData
protected Settings	settings
protected StatusViewer	statusMessenger

Constructor Summary

Constructors

Constructor and Description
classScoreCMD()

Method Summary

Methods

Modifier and Type	Method and Description
protected GeneSetPvalRun	analyze()
String	getSaveFileName()
SettingsHolder	getSettings()
StatusViewer	getStatusMessenger()
protected void	initialize()
boolean	isSaveAllGenes()
boolean	isUseCommandLineInterface()
static void	main(String[] args)
protected void	printHelp(String command)
protected boolean	processCommandLine(String commandName, String[] args)
protected boolean	run(String[] args)

Methods inherited from class java.lang.Object

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

Field Detail

settings

protected Settings settings

statusMessenger

protected StatusViewer statusMessenger

goData

protected GeneSetTerms goData

geneData

protected GeneAnnotations geneData

Constructor Detail

classScoreCMD

public classScoreCMD()

Method Detail

main

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

Throws:

Exception

run

protected boolean run(String[] args)
               throws Exception

Parameters:

args -

Throws:

IOException

Exception

getSaveFileName

public String getSaveFileName()

getSettings

public SettingsHolder getSettings()

getStatusMessenger

public StatusViewer getStatusMessenger()

isSaveAllGenes

public boolean isSaveAllGenes()

isUseCommandLineInterface

public boolean isUseCommandLineInterface()

analyze

protected GeneSetPvalRun analyze()
                          throws IOException

Returns:

Throws:

IllegalArgumentException

IOException

initialize

protected void initialize()

See Also:

ubic.erminej.gui.MainFrame.readDataFilesForStartup

printHelp

protected void printHelp(String command)

Parameters:

command - The name of the command as used at the command line.

processCommandLine

protected final boolean processCommandLine(String commandName,
                         String[] args)
                                    throws Exception

Throws:

Exception