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.

Field Summary

protected String[]	args
protected String[]	edgeAttrFiles
protected String[]	expressionFiles
protected String[]	graphFiles
protected int	mode
protected String[]	nodeAttrFiles
protected org.apache.commons.cli.Options	options
protected String[]	plugins
protected Properties	props
protected String	sessionFile
protected Properties	vizmapProps

Fields inherited from interface cytoscape.init.CyInitParams

EMBEDDED_WINDOW, ERROR, GUI, LIBRARY, TEXT

Constructor Summary

CyMain(String[] args)

Method Summary

String[]	getArgs()
List	getEdgeAttributeFiles()
List	getExpressionFiles()
List	getGraphFiles()
int	getMode()
List	getNodeAttributeFiles()
List	getPlugins()
Properties	getProps()
String	getSessionFile()
Properties	getVizProps()
static void	main(String[] args)
protected void	parseCommandLine(String[] args)
protected void	printHelp()
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 String sessionFile

nodeAttrFiles

protected String[] nodeAttrFiles

edgeAttrFiles

protected String[] edgeAttrFiles

expressionFiles

protected String[] expressionFiles

mode

protected int mode

options

protected org.apache.commons.cli.Options options

Constructor Detail

CyMain

public CyMain(String[] args)
       throws Exception

Throws:

Exception

Method Detail

main

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

Throws:

Exception

parseCommandLine

protected void parseCommandLine(String[] args)

setupLookAndFeel

protected void setupLookAndFeel()

printHelp

protected void printHelp()

getProps

public Properties getProps()

Specified by:

getProps in interface CyInitParams

getVizProps

public Properties getVizProps()

Specified by:

getVizProps in interface CyInitParams

getGraphFiles

public List getGraphFiles()

Specified by:

getGraphFiles in interface CyInitParams

getEdgeAttributeFiles

public List getEdgeAttributeFiles()

Specified by:

getEdgeAttributeFiles in interface CyInitParams

getNodeAttributeFiles

public List getNodeAttributeFiles()

Specified by:

getNodeAttributeFiles in interface CyInitParams

getExpressionFiles

public List getExpressionFiles()

Specified by:

getExpressionFiles in interface CyInitParams

getPlugins

public List getPlugins()

Specified by:

getPlugins in interface CyInitParams

getSessionFile

public String getSessionFile()

Specified by:

getSessionFile in interface CyInitParams

getMode

public int getMode()

Specified by:

getMode in interface CyInitParams

getArgs

public String[] getArgs()

Specified by:

getArgs in interface CyInitParams