cytoscape.data.readers
Interface GraphReader

All Known Implementing Classes:

AbstractGraphReader, GMLReader, InteractionsReader, XGMMLReader

public interface GraphReader

Interface for Reading in Cytoscape Graphs.

Author:

Cytoscape Development Group.

Method Summary

void	doPostProcessing(CyNetwork network) Execute whatever post-processing is required.
int[]	getEdgeIndicesArray() Gets an array of edges indices that participate in the newly created graph.
CyLayoutAlgorithm	getLayoutAlgorithm() Returns the CyLayoutAlgorithm used to layout the graph
String	getNetworkName() Gets the name of the network.
int[]	getNodeIndicesArray() Gets an array of node indices that participate in the newly created graph.
void	layout(GraphView myView) Deprecated. Use getLayoutAlgorithm().doLayout(view) instead. Will be removed 5/2008.
void	read() Reads/imports the graph.

Method Detail

read

void read()
          throws IOException

Reads/imports the graph.

Throws:

IOException - IO Errors.

layout

void layout(GraphView myView)

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

Lays out the graph.

Parameters:

myView -

getLayoutAlgorithm

CyLayoutAlgorithm getLayoutAlgorithm()

Returns the CyLayoutAlgorithm used to layout the graph

Parameters:

myView -

getNodeIndicesArray

int[] getNodeIndicesArray()

Gets an array of node indices that participate in the newly created graph.

Returns:

array of node indices from the root graph.

getEdgeIndicesArray

int[] getEdgeIndicesArray()

Gets an array of edges indices that participate in the newly created graph.

Returns:

array of edges indices from the root graph.

doPostProcessing

void doPostProcessing(CyNetwork network)

Execute whatever post-processing is required.

getNetworkName

String getNetworkName()

Gets the name of the network.

Returns:

network name.