Cytoscape 2.8.0 API

cytoscape.init
Interface CyInitParams

All Known Implementing Classes:
CyMain

public interface CyInitParams

An interface that describes the initialization parameters needed by cytoscape. Anything initialing Cytoscape should implement this interface and pass that object into CytoscapeInit. By setting the mode you can control how Cytoscape is initialized.


Field Summary
static int EMBEDDED_WINDOW
          A gui mode, but where cytoscape is embedded within a different application meaning the usual menus and/or toolbars may not be present.
static int ERROR
          Error.
static int GUI
          Normal gui mode.
static int LIBRARY
          Another headless mode (no gui), but meant for a server or daemon that runs in the background without exiting.
static int TEXT
          Headless mode (no gui) were cytoscape acts like a normal command line app and exits once finished processing.
 
Method Summary
 String[] getArgs()
          Returns the arguments used to trigger the initialization.
 List getEdgeAttributeFiles()
          A list of Strings that describe edge attribute file locations.
 List getExpressionFiles()
          A list of Strings that describe expression matrix file locations.
 List getGraphFiles()
          A list of Strings that describe graph file locations.
 int getMode()
          Returns and int representing the mode cytoscape runs in.
 List getNodeAttributeFiles()
          A list of Strings that describe node attribute file locations.
 List getPlugins()
          A list of Strings that describe plugins.
 Properties getProps()
          Returns the properties that were defined at initialization.
 String getSessionFile()
          A single string describing the session file location.
 Properties getVizProps()
          Returns properties specific to the VizMapper.
 

Field Detail

ERROR

static final int ERROR
Error. Something is wrong.

See Also:
Constant Field Values

GUI

static final int GUI
Normal gui mode.

See Also:
Constant Field Values

TEXT

static final int TEXT
Headless mode (no gui) were cytoscape acts like a normal command line app and exits once finished processing.

See Also:
Constant Field Values

LIBRARY

static final int LIBRARY
Another headless mode (no gui), but meant for a server or daemon that runs in the background without exiting.

See Also:
Constant Field Values

EMBEDDED_WINDOW

static final int EMBEDDED_WINDOW
A gui mode, but where cytoscape is embedded within a different application meaning the usual menus and/or toolbars may not be present.

See Also:
Constant Field Values
Method Detail

getProps

Properties getProps()
Returns the properties that were defined at initialization.

Returns:
A Properties object containing whatever property values that were defined at initialization.

getVizProps

Properties getVizProps()
Returns properties specific to the VizMapper. These properties aren't necessarily intended for human consumption.

Returns:
A Properties object containing VizMapper specific properties.

getGraphFiles

List getGraphFiles()
A list of Strings that describe graph file locations. The strings may represent URLs.

Returns:
A list of Strings representing graph file locations.

getEdgeAttributeFiles

List getEdgeAttributeFiles()
A list of Strings that describe edge attribute file locations.

Returns:
A list of Strings representing edge attribute file locations.

getNodeAttributeFiles

List getNodeAttributeFiles()
A list of Strings that describe node attribute file locations.

Returns:
A list of Strings representing node attribute file locations.

getExpressionFiles

List getExpressionFiles()
A list of Strings that describe expression matrix file locations.

Returns:
A list of Strings representing expression matrixfile locations.

getPlugins

List getPlugins()
A list of Strings that describe plugins. The descriptions can be any of the following:

Returns:
A list of strings describing the plugin locations.

getSessionFile

String getSessionFile()
A single string describing the session file location.

Returns:
A string describing the session file locaton.

getMode

int getMode()
Returns and int representing the mode cytoscape runs in. The possible modes are:

Returns:
the int representing the mode

getArgs

String[] getArgs()
Returns the arguments used to trigger the initialization. While args are appropriate for the command line, they're not really appropriate for other modes. Therefore, to pass initialization information to cytoscape, it's better to use getProperties().

Returns:
An array of strings representing arguments used to intialize cytoscape.

Cytoscape 2.8.0 API

Copyright 2010 Cytoscape Consortium. All rights reserved.