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

Constructor Summary

XGMMLReader(InputStream is)
Constructor.

XGMMLReader(InputStream is, String name)
Constructor.

XGMMLReader(String fileName)
Constructor.

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

Method Summary

void	doPostProcessing(CyNetwork network) DOCUMENT ME!
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 cytoscape.data.readers.AbstractGraphReader

layout

Methods inherited from class java.lang.Object

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

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)

DOCUMENT ME!

Specified by:

doPostProcessing in interface GraphReader

Overrides:

doPostProcessing in class AbstractGraphReader

Parameters:

network - DOCUMENT ME!