cytoscape.data.readers
Class XGMMLReader

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

All Implemented Interfaces:

GraphReader

public class XGMMLReader
extends AbstractGraphReader

XGMML file reader.
This version is Metanode-compatible.

Since:

Cytoscape 2.3

Version:

1.0

Author:

kono

See Also:

XGMMLWriter

Field Summary

protected static String	BOX
protected static String	CIRCLE
protected static String	CY_NAMESPACE
protected static String	DIAMOND
protected static String	EDGE
protected static String	ELLIPSE
protected static String	GRAPH
protected static String	GRAPHICS
protected static String	HELLIPSIS
protected static String	HEXAGON
protected static String	LABEL
protected static String	LINE
protected static String	NODE
protected static String	OCTAGON
protected static String	PARALELLOGRAM
protected static String	PENTAGON
protected static String	POINT
protected static String	RECTANGLE
protected static String	RHOMBUS
protected static String	ROUNDED_RECTANGLE
protected static String	SOURCE
protected static String	TARGET
protected static String	TRIANGLE
protected static String	VEE
protected static String	VELLIPSIS

Fields inherited from class cytoscape.data.readers.AbstractGraphReader

fileName, title

Constructor Summary

XGMMLReader(InputStream is)
Constructor.
This is usually used for remote file loading.

XGMMLReader(InputStream is, String name)
Constructor.
This is usually used for remote file loading.

XGMMLReader(String fileName)
Constructor.
This is for local XGMML file.

XGMMLReader(String fileName, TaskMonitor monitor)
Creates a new XGMMLReader object.

Method Summary

void	doPostProcessing(CyNetwork network) This method does all of our postprocessing after reading and parsing the file
int[]	getEdgeIndicesArray() DOCUMENT ME!
CyLayoutAlgorithm	getLayoutAlgorithm() getLayoutAlgorithm is called to get the Layout Algorithm that will be used to layout the resulting graph.
String	getNetworkID() DOCUMENT ME!
String	getNetworkName() DOCUMENT ME!
int[]	getNodeIndicesArray() DOCUMENT ME!
void	read() DOCUMENT ME!
void	setTaskMonitor(TaskMonitor monitor) Sets the task monitor we want to use

Methods inherited from class java.lang.Object

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

Field Detail

GRAPH

protected static final String GRAPH

See Also:

Constant Field Values

NODE

protected static final String NODE

See Also:

Constant Field Values

EDGE

protected static final String EDGE

See Also:

Constant Field Values

GRAPHICS

protected static final String GRAPHICS

See Also:

Constant Field Values

LABEL

protected static final String LABEL

See Also:

Constant Field Values

SOURCE

protected static final String SOURCE

See Also:

Constant Field Values

TARGET

protected static final String TARGET

See Also:

Constant Field Values

RECTANGLE

protected static final String RECTANGLE

See Also:

Constant Field Values

ELLIPSE

protected static final String ELLIPSE

See Also:

Constant Field Values

LINE

protected static final String LINE

See Also:

Constant Field Values

POINT

protected static final String POINT

See Also:

Constant Field Values

DIAMOND

protected static final String DIAMOND

See Also:

Constant Field Values

HEXAGON

protected static final String HEXAGON

See Also:

Constant Field Values

OCTAGON

protected static final String OCTAGON

See Also:

Constant Field Values

PARALELLOGRAM

protected static final String PARALELLOGRAM

See Also:

Constant Field Values

TRIANGLE

protected static final String TRIANGLE

See Also:

Constant Field Values

VEE

protected static final String VEE

See Also:

Constant Field Values

ROUNDED_RECTANGLE

protected static final String ROUNDED_RECTANGLE

See Also:

Constant Field Values

BOX

protected static final String BOX

See Also:

Constant Field Values

CIRCLE

protected static final String CIRCLE

See Also:

Constant Field Values

VELLIPSIS

protected static final String VELLIPSIS

See Also:

Constant Field Values

HELLIPSIS

protected static final String HELLIPSIS

See Also:

Constant Field Values

RHOMBUS

protected static final String RHOMBUS

See Also:

Constant Field Values

PENTAGON

protected static final String PENTAGON

See Also:

Constant Field Values

CY_NAMESPACE

protected static final String CY_NAMESPACE

See Also:

Constant Field Values

Constructor Detail

XGMMLReader

public XGMMLReader(String fileName)

Constructor.
This is for local XGMML file.

Parameters:

fileName - File name of local XGMML file.

Throws:

FileNotFoundException

XGMMLReader

public XGMMLReader(InputStream is)

Constructor.
This is usually used for remote file loading.

Parameters:

is - Input stream of XGMML file,

XGMMLReader

public XGMMLReader(InputStream is,
                   String name)

Constructor.
This is usually used for remote file loading.

Parameters:

is - Input stream of XGMML file,

XGMMLReader

public XGMMLReader(String fileName,
                   TaskMonitor monitor)

Creates a new XGMMLReader object.

Parameters:

fileName - DOCUMENT ME!

monitor - DOCUMENT ME!

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

read

public void read()
          throws IOException

DOCUMENT ME!

Specified by:

read in interface GraphReader

Specified by:

read in class AbstractGraphReader

Throws:

IOException - DOCUMENT ME!

getNodeIndicesArray

public int[] getNodeIndicesArray()

Description copied from class: AbstractGraphReader

DOCUMENT ME!

Specified by:

getNodeIndicesArray in interface GraphReader

Overrides:

getNodeIndicesArray in class AbstractGraphReader

Returns:

DOCUMENT ME!

getEdgeIndicesArray

public int[] getEdgeIndicesArray()

Description copied from class: AbstractGraphReader

DOCUMENT ME!

Specified by:

getEdgeIndicesArray in interface GraphReader

Overrides:

getEdgeIndicesArray in class AbstractGraphReader

Returns:

DOCUMENT ME!

getNetworkID

public String getNetworkID()

DOCUMENT ME!

Returns:

DOCUMENT ME!

getNetworkName

public String getNetworkName()

Description copied from class: AbstractGraphReader

DOCUMENT ME!

Specified by:

getNetworkName in interface GraphReader

Overrides:

getNetworkName in class AbstractGraphReader

Returns:

Returns the networkName.

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

doPostProcessing

public void doPostProcessing(CyNetwork network)

This method does all of our postprocessing after reading and parsing the file

Specified by:

doPostProcessing in interface GraphReader

Overrides:

doPostProcessing in class AbstractGraphReader

Parameters:

network - the network we've read in