cytoscape
Class CytoscapeInit

java.lang.Object
  cytoscape.CytoscapeInit

public class CytoscapeInit

extends Object

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()

Method Summary

static String[]	getArgs() Deprecated. Use Properties (getProperties()) instead of args for accessing initialization information. This method will be removed April 2007.
static String	getBioDataServer() Deprecated. This method will be removed April 2007. Use getProperty("bioDataServer") instead.
static URLClassLoader	getClassLoader()
static File	getConfigDirectory() If .cytoscape directory does not exist, it creates it and returns it
static File	getConfigDirectoy() Deprecated. This method is only deprecated because it is misspelled. Just use the correctly spelled method: getConfigDirectory(). This method will be removed 12/2006.
static File	getConfigFile(String file_name)
static cytoscape.init.CyInitParams	getCyInitParams() Returns the CyInitParams object used to initialize Cytoscape.
static String	getDefaultSpeciesName() Deprecated. Will be removed April 2007. Use getProperty( "defaultSpeciesName" ) instead.
static String	getDefaultVisualStyle() Deprecated. Will be removed April 2007. Use getProperties().getProperty( "defaultVisualStyle" ) instead.
static Set	getEdgeAttributes() Deprecated. Will be removed April 2007. No one appears to be using this method, so don't start.
static Set	getExpressionFiles() Deprecated. Will be removed April 2007. No one appears to be using this method, so don't start.
static Set	getGraphFiles() Deprecated. Will be removed April 2007. No one appears to be using this method, so don't start.
String	getHelp() Deprecated. This method will be removed April 2007. No one appears to use this method, so don't start.
static File	getMRUD()
static File	getMRUF()
static Set	getNodeAttributes() Deprecated. Will be removed April 2007. No one appears to be using this method, so don't start.
static Set	getPluginURLs()
static Properties	getProperties() Returns the properties used by Cytoscape, the result of cytoscape.props and command line options.
static String	getPropertiesLocation() Deprecated. This method will be removed April 2007.
static String	getProperty(String key) Deprecated. Use getProperties().getProperty( ) instead. Since this method never made it into a release, it will be removed Summer 2006.
static Set	getResourcePlugins()
static int	getSecondaryViewThreshold() Deprecated. Will be removed April 2007. Use getProperty( "secondaryViewThreshold" ) instead.
static int	getViewThreshold() Deprecated. Will be removed April 2007. Use getProperty( "viewThreshold" ) instead.
static int	getViewType() Deprecated. Will be removed April 2007. Use CytoscapeDesktop.parseViewType(CytoscapeInit.getProperties().getProperty("viewType"));
static Properties	getVisualProperties()
static String	getVizmapPropertiesLocation() Deprecated. Will be removed April 2007. Use getProperties().getProperty( "TODO" ) instead.
boolean	init(cytoscape.init.CyInitParams params) Cytoscape Init must be initialized using the command line arguments.
static boolean	isHeadless() Deprecated. This method will be removed April 2007. Use getMode() instead.
void	loadPlugin(Class plugin)
static boolean	noCanonicalization() Deprecated. Will be removed April 2007. Use getProperty( "canonicalizeNames" ) instead.
static void	setDefaultSpeciesName() Deprecated. Will be removed April 2007. This doesn't do anything. To set the default species name use getProperties().setProperty("defaultSpeciesName", newName), which you were presumably doing already.
static void	setMRUD(File mrud_new)
static void	setMRUF(File mruf_new)
static void	setProperty(String key, String value) Deprecated. Use getProperties().setProperty( ) instead. Since this method never made it into a release, it will be removed Summer 2006.
static void	setSecondaryViewThreshold(int threshold) Deprecated. Will be removed April 2007. Use getProperties().setProperty( "secondaryViewThreshold", thresh ) instead.
static void	setViewThreshold(int threshold) Deprecated. Will be removed April 2007. Use setProperty( "viewThreshold", thresh ) instead.
static boolean	suppressView() Deprecated. This method will be removed April 2007. No one appears to use this method, so don't start.
static boolean	useView() Deprecated. This method will be removed April 2007. Use getMode() instead.

Methods inherited from class java.lang.Object

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

Constructor Detail

CytoscapeInit

public CytoscapeInit()

Method Detail

init

public boolean init(cytoscape.init.CyInitParams params)

Cytoscape Init must be initialized using the command line arguments.

Returns:

false, if we fail to initialize for some reason

getCyInitParams

public static cytoscape.init.CyInitParams getCyInitParams()

Returns the CyInitParams object used to initialize Cytoscape.

getProperties

public static Properties getProperties()

Returns the properties used by Cytoscape, the result of cytoscape.props and command line options.

setProperty

public static void setProperty(String key,
                               String value)

Deprecated. Use getProperties().setProperty( ) instead. Since this method never made it into a release, it will be removed Summer 2006.

getProperty

public static String getProperty(String key)

Deprecated. Use getProperties().getProperty( ) instead. Since this method never made it into a release, it will be removed Summer 2006.

getClassLoader

public static URLClassLoader getClassLoader()

getPluginURLs

public static Set getPluginURLs()

getResourcePlugins

public static Set getResourcePlugins()

getHelp

public String getHelp()

Deprecated. This method will be removed April 2007. No one appears to use this method, so don't start.

isHeadless

public static boolean isHeadless()

Deprecated. This method will be removed April 2007. Use getMode() instead.

useView

public static boolean useView()

Deprecated. This method will be removed April 2007. Use getMode() instead.

suppressView

public static boolean suppressView()

Deprecated. This method will be removed April 2007. No one appears to use this method, so don't start.

getArgs

public static String[] getArgs()

Deprecated. Use Properties (getProperties()) instead of args for accessing initialization information. This method will be removed April 2007.

getPropertiesLocation

public static String getPropertiesLocation()

Deprecated. This method will be removed April 2007.

getBioDataServer

public static String getBioDataServer()

Deprecated. This method will be removed April 2007. Use getProperty("bioDataServer") instead.

noCanonicalization

public static boolean noCanonicalization()

Deprecated. Will be removed April 2007. Use getProperty( "canonicalizeNames" ) instead.

getExpressionFiles

public static Set getExpressionFiles()

Deprecated. Will be removed April 2007. No one appears to be using this method, so don't start.

getGraphFiles

public static Set getGraphFiles()

Deprecated. Will be removed April 2007. No one appears to be using this method, so don't start.

getEdgeAttributes

public static Set getEdgeAttributes()

Deprecated. Will be removed April 2007. No one appears to be using this method, so don't start.

getNodeAttributes

public static Set getNodeAttributes()

Deprecated. Will be removed April 2007. No one appears to be using this method, so don't start.

getDefaultSpeciesName

public static String getDefaultSpeciesName()

Deprecated. Will be removed April 2007. Use getProperty( "defaultSpeciesName" ) instead.

getViewType

public static int getViewType()

Deprecated. Will be removed April 2007. Use CytoscapeDesktop.parseViewType(CytoscapeInit.getProperties().getProperty("viewType"));

getViewThreshold

public static int getViewThreshold()

Deprecated. Will be removed April 2007. Use getProperty( "viewThreshold" ) instead.

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)

Deprecated. Will be removed April 2007. Use setProperty( "viewThreshold", thresh ) instead.

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()

Deprecated. Will be removed April 2007. Use getProperty( "secondaryViewThreshold" ) instead.

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)

Deprecated. Will be removed April 2007. Use getProperties().setProperty( "secondaryViewThreshold", thresh ) instead.

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()

Deprecated. Will be removed April 2007. Use getProperties().getProperty( "TODO" ) instead.

getDefaultVisualStyle

public static String getDefaultVisualStyle()

Deprecated. Will be removed April 2007. Use getProperties().getProperty( "defaultVisualStyle" ) instead.

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()

Deprecated. Will be removed April 2007. This doesn't do anything. To set the default species name use getProperties().setProperty("defaultSpeciesName", newName), which you were presumably doing already.

getConfigDirectoy

public static File getConfigDirectoy()

Deprecated. This method is only deprecated because it is misspelled. Just use the correctly spelled method: getConfigDirectory(). This method will be removed 12/2006.

getConfigDirectory

public static File getConfigDirectory()

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)

getVisualProperties

public static Properties getVisualProperties()