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)

Method Summary

void	doPostProcessing(CyNetwork network) Executes post-processing: no-op.
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 view) Lays out the graph.
abstract void	read() Reads/imports the graph.
void	read(boolean canonicalizeNodeNames) Deprecated. Use read() instead. Will be removed Dec 2006.

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractGraphReader

public AbstractGraphReader(String fileName)

Method Detail

read

public abstract void read()
                   throws IOException

Description copied from interface: GraphReader

Reads/imports the graph.

Specified by:

read in interface GraphReader

Throws:

IOException - IO Errors.

read

public void read(boolean canonicalizeNodeNames)
          throws IOException

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

Specified by:

read in interface GraphReader

Throws:

IOException

getRootGraph

public RootGraph getRootGraph()

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

Specified by:

getRootGraph in interface GraphReader

getNodeAttributes

public CyAttributes getNodeAttributes()

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

Specified by:

getNodeAttributes in interface GraphReader

getEdgeAttributes

public CyAttributes getEdgeAttributes()

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

Specified by:

getEdgeAttributes in interface GraphReader

layout

public void layout(GraphView view)

Description copied from interface: GraphReader

Lays out the graph.

Specified by:

layout in interface GraphReader

getNodeIndicesArray

public int[] getNodeIndicesArray()

Description copied from interface: GraphReader

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

Specified by:

getNodeIndicesArray in interface GraphReader

Returns:

array of node indices from the root graph.

getEdgeIndicesArray

public int[] getEdgeIndicesArray()

Description copied from interface: GraphReader

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

Specified by:

getEdgeIndicesArray in interface GraphReader

Returns:

array of edges indices from the root graph.

getNetworkName

public String getNetworkName()

Description copied from interface: GraphReader

Gets the name of the network.

Specified by:

getNetworkName in interface GraphReader

Returns:

network name.

doPostProcessing

public void doPostProcessing(CyNetwork network)

Executes post-processing: no-op.

Specified by:

doPostProcessing in interface GraphReader