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(InputStream is, String name)
Constructor.

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

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

InteractionsReader(String zip_entry, 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

void	doPostProcessing(CyNetwork net) Executes post-processing: no-op.
Interaction[]	getAllInteractions() DOCUMENT ME!
int	getCount() DOCUMENT ME!
int[]	getEdgeIndicesArray() DOCUMENT ME!
int[]	getNodeIndicesArray() DOCUMENT ME!
void	layout(CyNetworkView networkView) Deprecated. Use getLayoutAlgorithm() instead. Gone 5/2008.
void	read() Calls read(false)
void	read(boolean canonicalize) Deprecated. Will be removed 5/2008
void	setTaskMonitor(TaskMonitor monitor) Sets the task monitor we want to use

Methods inherited from class cytoscape.data.readers.AbstractGraphReader

getLayoutAlgorithm, getNetworkName, layout

Methods inherited from class java.lang.Object

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

Constructor Detail

InteractionsReader

public InteractionsReader(String zip_entry,
                          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,
                          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.

InteractionsReader

public InteractionsReader(InputStream is,
                          String name)

Constructor.
This is usually used for remote file loading.

Parameters:

is - Input stream of GML file,

Method Detail

setTaskMonitor

public void setTaskMonitor(TaskMonitor monitor)

Sets the task monitor we want to use

Overrides:

setTaskMonitor in class AbstractGraphReader

Parameters:

monitor - the TaskMonitor to use

layout

public void layout(CyNetworkView networkView)

Deprecated. Use getLayoutAlgorithm() instead. Gone 5/2008.

layout calls the default CyLayoutAlgorithm but forces it to use our own taskMonitor.

Parameters:

networkView - the view of the network we want to layout

read

@Deprecated
public void read(boolean canonicalize)
          throws IOException

Deprecated. Will be removed 5/2008

DOCUMENT ME!

Parameters:

canonicalize - This parameter does not in use from 2.5.

Throws:

IOException - DOCUMENT ME!

read

public void read()
          throws IOException

Calls read(false)

Specified by:

read in interface GraphReader

Specified by:

read in class AbstractGraphReader

Throws:

IOException - DOCUMENT ME!

getCount

public int getCount()

DOCUMENT ME!

Returns:

DOCUMENT ME!

getAllInteractions

public Interaction[] getAllInteractions()

DOCUMENT ME!

Returns:

DOCUMENT ME!

getNodeIndicesArray

public int[] getNodeIndicesArray()

DOCUMENT ME!

Specified by:

getNodeIndicesArray in interface GraphReader

Overrides:

getNodeIndicesArray in class AbstractGraphReader

Returns:

DOCUMENT ME!

getEdgeIndicesArray

public int[] getEdgeIndicesArray()

DOCUMENT ME!

Specified by:

getEdgeIndicesArray in interface GraphReader

Overrides:

getEdgeIndicesArray in class AbstractGraphReader

Returns:

DOCUMENT ME!

doPostProcessing

public void doPostProcessing(CyNetwork net)

Description copied from class: AbstractGraphReader

Executes post-processing: no-op.

Specified by:

doPostProcessing in interface GraphReader

Overrides:

doPostProcessing in class AbstractGraphReader