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:

• A jar file location, file or URL
• A directory name
• A plugin class name
• A local file location where the file lists one plugin jar per line

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:

• ERROR
• GUI - normal operation as a gui
• TEXT - headless mode where cytoscape acts as a command line app
• LIBRARY - headless mode wehre cytoscape acts as a server or daemon
• EMBEDDED_WINDOW - gui mode where cytoscape is embedded in another app

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.