cytoscape
Class CytoscapeInit

java.lang.Object
  cytoscape.CytoscapeInit

All Implemented Interfaces:

EventListener, PropertyChangeListener

public class CytoscapeInit

extends Object

implements PropertyChangeListener

Cytoscape Init is responsible for starting Cytoscape in a way that makes sense. The comments below are more hopeful than accurate. We currently do not support a "headless" mode (meaning there is no GUI). We do, however, hope to support this in the future. The two main modes of running Cytoscape are either in "headless" mode or in "script" mode. This class will use the command-line options to figure out which mode is desired, and run things accordingly. The order for doing things will be the following: 1. deterimine script mode, or headless mode 2. get options from properties files 3. get options from command line ( these overwrite properties ) 4. Load all Networks 5. Load all Data 6. Load all Plugins 7. Initialize all plugins, in order if specified. 8. Start Desktop/ Print Output exit.

Constructor Summary

CytoscapeInit()
Calling the constructor sets up the CytoscapeInit Object to be a CYTOSCAPE_EXIT event listener, and will take care of saving all properties.

Method Summary

static String[]	getArgs()
static String	getBioDataServer()
static URLClassLoader	getClassLoader()
static File	getConfigDirectoy() If .cytoscape directory does not exist, it creates it and returns it
static File	getConfigFile(String file_name)
static String	getDefaultSpeciesName()
static String	getDefaultVisualStyle()
static Set	getEdgeAttributes()
static Set	getExpressionFiles()
static Set	getGraphFiles()
String	getHelp()
static File	getMRUD()
static File	getMRUF()
static Set	getNodeAttributes()
static Set	getPluginURLs()
static Properties	getProperties()
static String	getPropertiesLocation()
static int	getSecondaryViewThreshold() Gets the Secondary View Threshold.
static int	getViewThreshold() Gets the ViewThreshold.
static int	getViewType()
static String	getVizmapPropertiesLocation()
boolean	init(String[] args) Cytoscape Init must be initialized using the command line arguments.
static boolean	isHeadless()
void	loadPlugin(Class plugin)
static boolean	noCanonicalization()
void	propertyChange(PropertyChangeEvent e)
static void	setDefaultSpeciesName()
static void	setMRUD(File mrud_new)
static void	setMRUF(File mruf_new)
static void	setSecondaryViewThreshold(int threshold) Sets the Secondary View Threshold.
static void	setViewThreshold(int threshold) Sets the ViewThreshold.
static boolean	suppressView()
static boolean	useView()

Methods inherited from class java.lang.Object

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

Constructor Detail

CytoscapeInit

public CytoscapeInit()

Calling the constructor sets up the CytoscapeInit Object to be a CYTOSCAPE_EXIT event listener, and will take care of saving all properties.

Method Detail

propertyChange

public void propertyChange(PropertyChangeEvent e)

Specified by:

propertyChange in interface PropertyChangeListener

init

public boolean init(String[] args)

Cytoscape Init must be initialized using the command line arguments.

Parameters:

args - the arguments from the command line

Returns:

false, if we should stop initing, since help has been requested

getHelp

public String getHelp()

isHeadless

public static boolean isHeadless()

useView

public static boolean useView()

suppressView

public static boolean suppressView()

getArgs

public static String[] getArgs()

getProperties

public static Properties getProperties()

getPropertiesLocation

public static String getPropertiesLocation()

getClassLoader

public static URLClassLoader getClassLoader()

getPluginURLs

public static Set getPluginURLs()

getBioDataServer

public static String getBioDataServer()

noCanonicalization

public static boolean noCanonicalization()

getExpressionFiles

public static Set getExpressionFiles()

getGraphFiles

public static Set getGraphFiles()

getEdgeAttributes

public static Set getEdgeAttributes()

getNodeAttributes

public static Set getNodeAttributes()

getDefaultSpeciesName

public static String getDefaultSpeciesName()

getViewType

public static int getViewType()

getViewThreshold

public static int getViewThreshold()

Gets the ViewThreshold. Networks with number of nodes below this threshold will automatically have network views created.

Returns:

view threshold.

setViewThreshold

public static void setViewThreshold(int threshold)

Sets the ViewThreshold. Networks with number of nodes below this threshold will automatically have network views created.

Parameters:

threshold - view threshold.

getSecondaryViewThreshold

public static int getSecondaryViewThreshold()

Gets the Secondary View Threshold. This value is a secondary check on rendering very large networks. It is primarily checked when a user wishes to create a view for a large network.

Returns:

threshold value, indicating number of nodes.

setSecondaryViewThreshold

public static void setSecondaryViewThreshold(int threshold)

Sets the Secondary View Threshold. This value is a secondary check on rendering very large networks. It is primarily checked when a user wishes to create a view for a large network.

Parameters:

threshold - value, indicating number of nodes.

getVizmapPropertiesLocation

public static String getVizmapPropertiesLocation()

getDefaultVisualStyle

public static String getDefaultVisualStyle()

loadPlugin

public void loadPlugin(Class plugin)

getMRUD

public static File getMRUD()

Returns:

the most recently used directory

getMRUF

public static File getMRUF()

Returns:

the most recently used file

setMRUD

public static void setMRUD(File mrud_new)

setMRUF

public static void setMRUF(File mruf_new)

setDefaultSpeciesName

public static void setDefaultSpeciesName()

getConfigDirectoy

public static File getConfigDirectoy()

If .cytoscape directory does not exist, it creates it and returns it

Returns:

the directory ".cytoscape" in the users home directory.

getConfigFile

public static File getConfigFile(String file_name)