cytoscape.data.readers
Class AbstractGraphReader

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

All Implemented Interfaces:

GraphReader

Direct Known Subclasses:

GMLReader, InteractionsReader, XGMMLReader

public abstract class AbstractGraphReader
extends Object
implements GraphReader

Constructor Summary

AbstractGraphReader(String fileName)
Creates a new AbstractGraphReader object.

Method Summary

void	doPostProcessing(CyNetwork network) Executes post-processing: no-op.
int[]	getEdgeIndicesArray() DOCUMENT ME!
CyLayoutAlgorithm	getLayoutAlgorithm() Return the CyLayoutAlgorithm used to layout the graph
String	getNetworkName() DOCUMENT ME!
int[]	getNodeIndicesArray() DOCUMENT ME!
void	layout(GraphView view) Deprecated. Use getLayoutAlgorithm().doLayout(view) instead. Will be removed 5/2008.
abstract void	read() DOCUMENT ME!
void	setTaskMonitor(TaskMonitor monitor) Set the task monitor to use for this reader

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractGraphReader

public AbstractGraphReader(String fileName)

Creates a new AbstractGraphReader object.

Parameters:

fileName - DOCUMENT ME!

Method Detail

read

public abstract void read()
                   throws IOException

DOCUMENT ME!

Specified by:

read in interface GraphReader

Throws:

IOException - DOCUMENT ME!

getNodeIndicesArray

public int[] getNodeIndicesArray()

DOCUMENT ME!

Specified by:

getNodeIndicesArray in interface GraphReader

Returns:

DOCUMENT ME!

getEdgeIndicesArray

public int[] getEdgeIndicesArray()

DOCUMENT ME!

Specified by:

getEdgeIndicesArray in interface GraphReader

Returns:

DOCUMENT ME!

getNetworkName

public String getNetworkName()

DOCUMENT ME!

Specified by:

getNetworkName in interface GraphReader

Returns:

DOCUMENT ME!

doPostProcessing

public void doPostProcessing(CyNetwork network)

Executes post-processing: no-op.

Specified by:

doPostProcessing in interface GraphReader

getLayoutAlgorithm

public CyLayoutAlgorithm getLayoutAlgorithm()

Return the CyLayoutAlgorithm used to layout the graph

Specified by:

getLayoutAlgorithm in interface GraphReader

setTaskMonitor

public void setTaskMonitor(TaskMonitor monitor)

Set the task monitor to use for this reader

Parameters:

monitor - the TaskMonitor to use

layout

public void layout(GraphView view)

Deprecated. Use getLayoutAlgorithm().doLayout(view) instead. Will be removed 5/2008.

Description copied from interface: GraphReader

Lays out the graph.

Specified by:

layout in interface GraphReader