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.

Since:

Cytoscape 1.0

Author:

Cytoscape Core Team

Constructor Summary

CytoscapeInit()
Creates a new CytoscapeInit object.

Method Summary

static File	getConfigDirectory() If .cytoscape directory does not exist, it creates it and returns it
static File	getConfigFile(String file_name) DOCUMENT ME!
static File	getConfigVersionDirectory() Within the .cytoscape directory create a version-specific directory
static CyInitParams	getCyInitParams() Returns the CyInitParams object used to initialize Cytoscape.
static File	getMRUD()
static File	getMRUF()
static Properties	getProperties() Returns the properties used by Cytoscape, the result of cytoscape.props and command line options.
static Properties	getVisualProperties() DOCUMENT ME!
boolean	init(CyInitParams params) Cytoscape Init must be initialized using the command line arguments.
static void	setMRUD(File mrud_new)
static void	setMRUF(File mruf_new)

Methods inherited from class java.lang.Object

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

Constructor Detail

CytoscapeInit

public CytoscapeInit()

Creates a new CytoscapeInit object.

Method Detail

init

public boolean init(CyInitParams params)

Cytoscape Init must be initialized using the command line arguments.

Parameters:

args - the arguments from the command line

Returns:

false, if we fail to initialize for some reason

getCyInitParams

public static 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.

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)

Parameters:

mrud - the most recently used directory

setMRUF

public static void setMRUF(File mruf_new)

Parameters:

mruf - the most recently used file

getConfigVersionDirectory

public static File getConfigVersionDirectory()

Within the .cytoscape directory create a version-specific directory

Returns:

the directory ".cytoscape/[cytoscape version]

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)

DOCUMENT ME!

Parameters:

file_name - DOCUMENT ME!

Returns:

DOCUMENT ME!

getVisualProperties

public static Properties getVisualProperties()

DOCUMENT ME!

Returns:

DOCUMENT ME!