cytoscape
Class CyMain

java.lang.Object
  cytoscape.CyMain

All Implemented Interfaces:

CyInitParams

public class CyMain
extends Object
implements CyInitParams

This is the main startup class for Cytoscape. This parses the command line and implements CyInitParams so that it can be used to initialize cytoscape.

Look and Feel is modified for jgoodies 2.1.4 by Kei Ono

Field Summary

protected String[]	args
protected String[]	edgeAttrFiles
protected String[]	expressionFiles
protected String[]	graphFiles
protected CyLogger	logger
protected int	mode
protected String[]	nodeAttrFiles
protected Options	options
protected String[]	plugins
protected Properties	props
protected static String	sessionFile
protected Properties	vizmapProps

Fields inherited from interface cytoscape.init.CyInitParams

EMBEDDED_WINDOW, ERROR, GUI, LIBRARY, TEXT

Constructor Summary

CyMain(String[] args)
Creates a new CyMain object.

Method Summary

String[]	getArgs() DOCUMENT ME!
List	getEdgeAttributeFiles() DOCUMENT ME!
List	getExpressionFiles() DOCUMENT ME!
List	getGraphFiles() DOCUMENT ME!
int	getMode() DOCUMENT ME!
List	getNodeAttributeFiles() DOCUMENT ME!
List	getPlugins() DOCUMENT ME!
Properties	getProps() DOCUMENT ME!
String	getSessionFile() DOCUMENT ME!
Properties	getVizProps() DOCUMENT ME!
static void	main(String[] args) DOCUMENT ME!
protected void	parseCommandLine(String[] args)
protected void	printHelp()
static void	setSessionFile(String sf) Provides access to the session file parsed from arguments intercepted by CyStartupListener
protected void	setupLookAndFeel()

Methods inherited from class java.lang.Object

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

Field Detail

args

protected String[] args

props

protected Properties props

graphFiles

protected String[] graphFiles

plugins

protected String[] plugins

vizmapProps

protected Properties vizmapProps

sessionFile

protected static String sessionFile

nodeAttrFiles

protected String[] nodeAttrFiles

edgeAttrFiles

protected String[] edgeAttrFiles

expressionFiles

protected String[] expressionFiles

mode

protected int mode

options

protected Options options

logger

protected CyLogger logger

Constructor Detail

CyMain

public CyMain(String[] args)
       throws Exception

Creates a new CyMain object.

Parameters:

args - DOCUMENT ME!

Throws:

Exception - DOCUMENT ME!

Method Detail

main

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

DOCUMENT ME!

Parameters:

args - DOCUMENT ME!

Throws:

Exception - DOCUMENT ME!

parseCommandLine

protected void parseCommandLine(String[] args)

setSessionFile

public static void setSessionFile(String sf)

Provides access to the session file parsed from arguments intercepted by CyStartupListener

setupLookAndFeel

protected void setupLookAndFeel()

printHelp

protected void printHelp()

getProps

public Properties getProps()

DOCUMENT ME!

Specified by:

getProps in interface CyInitParams

Returns:

DOCUMENT ME!

getVizProps

public Properties getVizProps()

DOCUMENT ME!

Specified by:

getVizProps in interface CyInitParams

Returns:

DOCUMENT ME!

getGraphFiles

public List getGraphFiles()

DOCUMENT ME!

Specified by:

getGraphFiles in interface CyInitParams

Returns:

DOCUMENT ME!

getEdgeAttributeFiles

public List getEdgeAttributeFiles()

DOCUMENT ME!

Specified by:

getEdgeAttributeFiles in interface CyInitParams

Returns:

DOCUMENT ME!

getNodeAttributeFiles

public List getNodeAttributeFiles()

DOCUMENT ME!

Specified by:

getNodeAttributeFiles in interface CyInitParams

Returns:

DOCUMENT ME!

getExpressionFiles

public List getExpressionFiles()

DOCUMENT ME!

Specified by:

getExpressionFiles in interface CyInitParams

Returns:

DOCUMENT ME!

getPlugins

public List getPlugins()

DOCUMENT ME!

Specified by:

getPlugins in interface CyInitParams

Returns:

DOCUMENT ME!

getSessionFile

public String getSessionFile()

DOCUMENT ME!

Specified by:

getSessionFile in interface CyInitParams

Returns:

DOCUMENT ME!

getMode

public int getMode()

DOCUMENT ME!

Specified by:

getMode in interface CyInitParams

Returns:

DOCUMENT ME!

getArgs

public String[] getArgs()

DOCUMENT ME!

Specified by:

getArgs in interface CyInitParams

Returns:

DOCUMENT ME!