cytoscape.data.readers
Class NNFReader

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

All Implemented Interfaces:

GraphReader, NestedNetworkReader

public class NNFReader
extends AbstractGraphReader
implements NestedNetworkReader

Graph file reader for NNF files.

Since:

Cytoscape 2.7.0

Author:

kono, ruschein

Field Summary

Fields inherited from class cytoscape.data.readers.AbstractGraphReader

fileName, title

Constructor Summary

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

NNFReader(String filename)
Creates an interaction reader based on the string file name.

NNFReader(String filename, TaskMonitor monitor)
Creates an interaction reader based on the string file name.

Method Summary

int[]	getEdgeIndicesArray() DOCUMENT ME!
String	getNetworkName() Always returns root network title.
List<CyNetwork>	getNetworks() Returns root network.
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

doPostProcessing, getLayoutAlgorithm

Methods inherited from class java.lang.Object

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

Constructor Detail

NNFReader

public NNFReader(String filename)

Creates an interaction reader based on the string file name.

Parameters:

filename - The filename that contains the interaction data to be read.

NNFReader

public NNFReader(String filename,
                 TaskMonitor monitor)

Creates an interaction reader based on the string file name.

Parameters:

filename - The filename that contains the interaction data to be read.

monitor - An optional task monitor. May be null.

NNFReader

public NNFReader(InputStream is,
                 String name)

Constructor.
This is usually used for remote file loading.

Parameters:

is - Input stream of GML file,

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

Description copied from class: AbstractGraphReader

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!

getNetworks

public List<CyNetwork> getNetworks()

Returns root network.

Usually used by the caller of reader.

Specified by:

getNetworks in interface NestedNetworkReader

Returns:

A list of networks.

getNetworkName

public String getNetworkName()

Always returns root network title.

Specified by:

getNetworkName in interface GraphReader

Overrides:

getNetworkName in class AbstractGraphReader

Returns:

DOCUMENT ME!