cytoscape.data.readers
Class InteractionsReader

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

All Implemented Interfaces:

GraphReader

public class InteractionsReader
extends AbstractGraphReader

Reader for graphs in the interactions file format. Given the filename, provides the graph and attributes objects constructed from the file.

Constructor Summary

InteractionsReader(BioDataServer dataServer, String species, String filename)
Deprecated. Will be removed 12/2006. BioDataServer and species are no longer needed or used.

InteractionsReader(BioDataServer dataServer, String species, String zip_entry, boolean is_zip)
Deprecated. Will be removed 12/2006. BioDataServer and species are no longer needed or used.

InteractionsReader(BioDataServer dataServer, String species, String filename, cytoscape.task.TaskMonitor taskMonitor)
Deprecated. Will be removed 12/2006. BioDataServer and species are no longer needed or used.

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

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

InteractionsReader(String zip_entry, cytoscape.task.TaskMonitor monitor, boolean is_zip)
Creates an interaction reader based on a string consisting of data that has been read from a zip file.

Method Summary

Interaction[]	getAllInteractions()
int	getCount()
int[]	getEdgeIndicesArray() Gets an array of edges indices that participate in the newly created graph.
int[]	getNodeIndicesArray() Gets an array of node indices that participate in the newly created graph.
void	layout(GraphView view) Lays out the graph.
void	read() Calls read(false)
void	read(boolean canonicalize)

Methods inherited from class cytoscape.data.readers.AbstractGraphReader

doPostProcessing, getEdgeAttributes, getNetworkName, getNodeAttributes, getRootGraph

Methods inherited from class java.lang.Object

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

Constructor Detail

InteractionsReader

public InteractionsReader(BioDataServer dataServer,
                          String species,
                          String filename)

Deprecated. Will be removed 12/2006. BioDataServer and species are no longer needed or used.

InteractionsReader

public InteractionsReader(BioDataServer dataServer,
                          String species,
                          String filename,
                          cytoscape.task.TaskMonitor taskMonitor)

Deprecated. Will be removed 12/2006. BioDataServer and species are no longer needed or used.

InteractionsReader

public InteractionsReader(BioDataServer dataServer,
                          String species,
                          String zip_entry,
                          boolean is_zip)

Deprecated. Will be removed 12/2006. BioDataServer and species are no longer needed or used.

InteractionsReader

public InteractionsReader(String zip_entry,
                          cytoscape.task.TaskMonitor monitor,
                          boolean is_zip)

Creates an interaction reader based on a string consisting of data that has been read from a zip file.

Parameters:

zip_entry - The zip entry data.

monitor - An optional task monitor. May be null.

is_zip - Indicates that the data is from a zip file - Should almost always be true.

InteractionsReader

public InteractionsReader(String filename)

Creates an interaction reader based on the string file name.

Parameters:

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

InteractionsReader

public InteractionsReader(String filename,
                          cytoscape.task.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.

Method Detail

layout

public void layout(GraphView view)

Description copied from interface: GraphReader

Lays out the graph.

Specified by:

layout in interface GraphReader

Overrides:

layout in class AbstractGraphReader

read

public void read(boolean canonicalize)
          throws IOException

Specified by:

read in interface GraphReader

Overrides:

read in class AbstractGraphReader

Throws:

IOException

read

public void read()
          throws IOException

Calls read(false)

Specified by:

read in interface GraphReader

Specified by:

read in class AbstractGraphReader

Throws:

IOException - IO Errors.

getCount

public int getCount()

getAllInteractions

public Interaction[] getAllInteractions()

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

Overrides:

getNodeIndicesArray in class AbstractGraphReader

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

Overrides:

getEdgeIndicesArray in class AbstractGraphReader

Returns:

array of edges indices from the root graph.