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.
CyAttributes	getEdgeAttributes() Deprecated. Use Cytoscape.getEdgeAttributes() instead. Will be removed Dec 2006.
int[]	getEdgeIndicesArray() Gets an array of edges indices that participate in the newly created graph.
String	getNetworkName() Gets the name of the network.
CyAttributes	getNodeAttributes() Deprecated. Use Cytoscape.getNodeAttributes() instead. Will be removed Dec 2006.
int[]	getNodeIndicesArray() Gets an array of node indices that participate in the newly created graph.
RootGraph	getRootGraph() Deprecated. Use Cytoscape.getRootGraph() instead. Will be removed Dec 2006.
void	layout(GraphView myView) Lays out the graph.
void	read() Reads/imports the graph.
void	read(boolean canonicalizeNodeNames) Deprecated. Use read() instead. Will be removed Dec 2006.

Method Detail

read

void read()
          throws IOException

Reads/imports the graph.

Throws:

IOException - IO Errors.

layout

void layout(GraphView myView)

Lays out 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.

read

void read(boolean canonicalizeNodeNames)
          throws IOException

Deprecated. Use read() instead. Will be removed Dec 2006.

Throws:

IOException

getRootGraph

RootGraph getRootGraph()

Deprecated. Use Cytoscape.getRootGraph() instead. Will be removed Dec 2006.

getNodeAttributes

CyAttributes getNodeAttributes()

Deprecated. Use Cytoscape.getNodeAttributes() instead. Will be removed Dec 2006.

getEdgeAttributes

CyAttributes getEdgeAttributes()

Deprecated. Use Cytoscape.getEdgeAttributes() instead. Will be removed Dec 2006.

getNetworkName

String getNetworkName()

Gets the name of the network.

Returns:

network name.