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(String filename)
Constructor.

GMLReader(String filename, cytoscape.task.TaskMonitor taskMonitor)
Constructor.

Method Summary

void	applyMaps(String mapSuffix, String VSName)
void	doPostProcessing(CyNetwork net) Executes post-processing: no-op.
void	extract()
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
static LineType	getLineType(int width)
List	getList() Returns a list containing the gml object tree
int[]	getNodeIndicesArray() Part of interface contract
void	layout(GraphView myView) Lays out the graph.
void	read() Reads/imports the graph.
void	setEdgeMaps(VisualMappingManager vizmapper)
void	setNodeMaps(VisualMappingManager vizmapper)
void	showMaps()

Methods inherited from class cytoscape.data.readers.AbstractGraphReader

getEdgeAttributes, getNetworkName, getNodeAttributes, getRootGraph, read

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(String filename,
                 cytoscape.task.TaskMonitor taskMonitor)

Constructor.

Parameters:

filename - File name.

taskMonitor - TaskMonitor Object.

Method Detail

setNodeMaps

public void setNodeMaps(VisualMappingManager vizmapper)

setEdgeMaps

public void setEdgeMaps(VisualMappingManager vizmapper)

applyMaps

public void applyMaps(String mapSuffix,
                      String VSName)

read

public void read()

Description copied from interface: GraphReader

Reads/imports the graph.

Specified by:

read in interface GraphReader

Specified by:

read in class AbstractGraphReader

getList

public List getList()

Returns a list containing the gml object tree

layout

public void layout(GraphView myView)

Description copied from interface: GraphReader

Lays out the graph.

Specified by:

layout in interface GraphReader

Overrides:

layout in class AbstractGraphReader

extract

public void extract()

getLineType

public static LineType getLineType(int width)

showMaps

public void showMaps()

getNodeIndicesArray

public int[] getNodeIndicesArray()

Part of interface contract

Specified by:

getNodeIndicesArray in interface GraphReader

Overrides:

getNodeIndicesArray in class AbstractGraphReader

Returns:

array of node indices from the root graph.

getEdgeIndicesArray

public int[] getEdgeIndicesArray()

Part of interace contract

Specified by:

getEdgeIndicesArray in interface GraphReader

Overrides:

getEdgeIndicesArray in class AbstractGraphReader

Returns:

array of edges indices from the root graph.

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)

Description copied from class: AbstractGraphReader

Executes post-processing: no-op.

Specified by:

doPostProcessing in interface GraphReader

Overrides:

doPostProcessing in class AbstractGraphReader