edu.iastate.metnet.launch
Class RunCytoscape

java.lang.Object
  edu.iastate.metnet.launch.RunCytoscape

All Implemented Interfaces:

cytoscape.init.CyInitParams

public class RunCytoscape
extends java.lang.Object
implements cytoscape.init.CyInitParams

This is the main startup class for Cytoscape. It is similar to the CyMain class provided in Cytoscapes code, except it allow initializing Cytoscape in "embedded window" state.

Author:

Mohammed Alabsi

Field Summary

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

Fields inherited from interface cytoscape.init.CyInitParams

EMBEDDED_WINDOW, ERROR, GUI, LIBRARY, TEXT

Constructor Summary

RunCytoscape()

Method Summary

static void	defineVisualStyle(cytoscape.visual.VisualStyle bpVisualStyle, cytoscape.visual.VisualMappingManager manager, cytoscape.visual.CalculatorCatalog catalog)
java.lang.String[]	getArgs()
java.util.List	getEdgeAttributeFiles()
java.util.List	getExpressionFiles()
java.util.List	getGraphFiles()
int	getMode()
java.util.List	getNodeAttributeFiles()
java.util.List	getPlugins()
java.util.Properties	getProps()
java.lang.String	getSessionFile()
java.util.Properties	getVizProps()
protected void	init()
static void	main(java.lang.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 java.lang.String[] args

props

protected java.util.Properties props

graphFiles

protected java.lang.String[] graphFiles

plugins

protected java.lang.String[] plugins

vizmapProps

protected java.util.Properties vizmapProps

sessionFile

protected java.lang.String sessionFile

nodeAttrFiles

protected java.lang.String[] nodeAttrFiles

edgeAttrFiles

protected java.lang.String[] edgeAttrFiles

expressionFiles

protected java.lang.String[] expressionFiles

mode

protected int mode

options

protected org.apache.commons.cli.Options options

Constructor Detail

RunCytoscape

public RunCytoscape()
             throws java.lang.Exception

Throws:

java.lang.Exception

Method Detail

main

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

Parameters:

args -

Throws:

java.lang.Exception

init

protected void init()

setupLookAndFeel

protected void setupLookAndFeel()

printHelp

protected void printHelp()

getProps

public java.util.Properties getProps()

Specified by:

getProps in interface cytoscape.init.CyInitParams

getVizProps

public java.util.Properties getVizProps()

Specified by:

getVizProps in interface cytoscape.init.CyInitParams

getGraphFiles

public java.util.List getGraphFiles()

Specified by:

getGraphFiles in interface cytoscape.init.CyInitParams

getEdgeAttributeFiles

public java.util.List getEdgeAttributeFiles()

Specified by:

getEdgeAttributeFiles in interface cytoscape.init.CyInitParams

getNodeAttributeFiles

public java.util.List getNodeAttributeFiles()

Specified by:

getNodeAttributeFiles in interface cytoscape.init.CyInitParams

getExpressionFiles

public java.util.List getExpressionFiles()

Specified by:

getExpressionFiles in interface cytoscape.init.CyInitParams

getPlugins

public java.util.List getPlugins()

Specified by:

getPlugins in interface cytoscape.init.CyInitParams

getSessionFile

public java.lang.String getSessionFile()

Specified by:

getSessionFile in interface cytoscape.init.CyInitParams

getMode

public int getMode()

Specified by:

getMode in interface cytoscape.init.CyInitParams

getArgs

public java.lang.String[] getArgs()

Specified by:

getArgs in interface cytoscape.init.CyInitParams

defineVisualStyle

public static void defineVisualStyle(cytoscape.visual.VisualStyle bpVisualStyle,
                                     cytoscape.visual.VisualMappingManager manager,
                                     cytoscape.visual.CalculatorCatalog catalog)