cytoscape.data.readers
Class GMLReader

java.lang.Object
  cytoscape.data.readers.AbstractGraphReader
      cytoscape.data.readers.GMLReader

All Implemented Interfaces:

GraphReader

public class GMLReader
extends AbstractGraphReader

This class is responsible for converting a gml object tree into cytoscape objects New features to the current version: 1. Small bug fixes. 2. Translate all features in the GML file. This includes 3. New Visual Style will be generated when you call this class. The new style saves all visual features (like node shape) and will not be lost even after other style selected.

Constructor Summary

GMLReader(InputStream is, String name)
Constructor.

GMLReader(String filename)
Constructor.

GMLReader(String filename, TaskMonitor taskMonitor)
Constructor.

Method Summary

void	applyMaps(String mapSuffix, String VSName) Deprecated. Don't use this. Gone 2/2009.
void	doPostProcessing(CyNetwork net) DOCUMENT ME!
void	extract() DOCUMENT ME!
Color	getColor(String colorString) Create a color object from the string like it is stored in a gml file
int[]	getEdgeIndicesArray() Part of interace contract
CyLayoutAlgorithm	getLayoutAlgorithm() getLayoutAlgorithm is called to get the Layout Algorithm that will be used to layout the resulting graph.
static LineType	getLineType(int width) Deprecated. Don't use this. Set the line width directly. Gone 5/2008.
List	getList() Returns a list containing the gml object tree
int[]	getNodeIndicesArray() Part of interface contract
void	layout(CyNetworkView myView) layout the graph based on the GML values we read
void	read() DOCUMENT ME!
void	setEdgeMaps(VisualMappingManager vizmapper) Deprecated. Don't use this. Gone 2/2009.
void	setNodeMaps(VisualMappingManager vizmapper) Deprecated. Don't use this. Gone 2/2009.
void	setTaskMonitor(TaskMonitor monitor) Sets the task monitor we want to use
void	showMaps() DOCUMENT ME!

Methods inherited from class cytoscape.data.readers.AbstractGraphReader

getNetworkName, layout

Methods inherited from class java.lang.Object

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

Constructor Detail

GMLReader

public GMLReader(String filename)

Constructor.

Parameters:

filename - File name.

GMLReader

public GMLReader(InputStream is,
                 String name)

Constructor.
This is usually used for remote file loading.

Parameters:

is - Input stream of GML file,

GMLReader

public GMLReader(String filename,
                 TaskMonitor taskMonitor)

Constructor.

Parameters:

filename - File name.

taskMonitor - TaskMonitor Object.

Method Detail

setTaskMonitor

public void setTaskMonitor(TaskMonitor monitor)

Sets the task monitor we want to use

Overrides:

setTaskMonitor in class AbstractGraphReader

Parameters:

monitor - the TaskMonitor to use

setNodeMaps

@Deprecated
public void setNodeMaps(VisualMappingManager vizmapper)

Deprecated. Don't use this. Gone 2/2009.

DOCUMENT ME!

Parameters:

vizmapper - DOCUMENT ME!

setEdgeMaps

@Deprecated
public void setEdgeMaps(VisualMappingManager vizmapper)

Deprecated. Don't use this. Gone 2/2009.

DOCUMENT ME!

Parameters:

vizmapper - DOCUMENT ME!

applyMaps

@Deprecated
public void applyMaps(String mapSuffix,
                                 String VSName)

Deprecated. Don't use this. Gone 2/2009.

DOCUMENT ME!

Parameters:

mapSuffix - DOCUMENT ME!

VSName - DOCUMENT ME!

read

public void read()

DOCUMENT ME!

Specified by:

read in interface GraphReader

Specified by:

read in class AbstractGraphReader

getList

public List getList()

Returns a list containing the gml object tree

getLayoutAlgorithm

public CyLayoutAlgorithm getLayoutAlgorithm()

getLayoutAlgorithm is called to get the Layout Algorithm that will be used to layout the resulting graph. In our case, we just return a stub that will call our internal layout routine, which will just use the default layout, but with our task monitor

Specified by:

getLayoutAlgorithm in interface GraphReader

Overrides:

getLayoutAlgorithm in class AbstractGraphReader

Returns:

the CyLayoutAlgorithm to use

layout

public void layout(CyNetworkView myView)

layout the graph based on the GML values we read

Parameters:

myView - the view of the network we want to layout

extract

public void extract()

DOCUMENT ME!

getLineType

@Deprecated
public static LineType getLineType(int width)

Deprecated. Don't use this. Set the line width directly. Gone 5/2008.

showMaps

public void showMaps()

DOCUMENT ME!

getNodeIndicesArray

public int[] getNodeIndicesArray()

Part of interface contract

Specified by:

getNodeIndicesArray in interface GraphReader

Overrides:

getNodeIndicesArray in class AbstractGraphReader

Returns:

DOCUMENT ME!

getEdgeIndicesArray

public int[] getEdgeIndicesArray()

Part of interace contract

Specified by:

getEdgeIndicesArray in interface GraphReader

Overrides:

getEdgeIndicesArray in class AbstractGraphReader

Returns:

DOCUMENT ME!

getColor

public Color getColor(String colorString)

Create a color object from the string like it is stored in a gml file

doPostProcessing

public void doPostProcessing(CyNetwork net)

DOCUMENT ME!

Specified by:

doPostProcessing in interface GraphReader

Overrides:

doPostProcessing in class AbstractGraphReader

Parameters:

net - DOCUMENT ME!