cytoscape.data.readers
Class InteractionsReader

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

All Implemented Interfaces:

GraphReader

public class InteractionsReader
extends Object
implements GraphReader

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

Field Summary

protected Vector	allInteractions A Vector that holds all of the Interactions
protected String	filename The File to be loaded

Constructor Summary

InteractionsReader(BioDataServer dataServer, String species, String filename)
Interactions Reader Constructor Creates a new Interactions Reader This constructor assumes a Y-Files graph is wanted.

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

InteractionsReader(BioDataServer dataServer, String species, String filename, cytoscape.task.TaskMonitor taskMonitor)
Interactions Reader Constructor Creates a new Interactions Reader This constructor assumes a Y-Files graph is wanted.

InteractionsReader(String filename)

Method Summary

protected String	canonicalizeName(String name)
protected void	createRootGraphFromInteractionData(boolean canonicalize)
Interaction[]	getAllInteractions()
int	getCount()
CyAttributes	getEdgeAttributes()
int[]	getEdgeIndicesArray()
CyAttributes	getNodeAttributes()
int[]	getNodeIndicesArray()
giny.model.RootGraph	getRootGraph()
void	layout(giny.view.GraphView view)
void	read() Calls read(false)
void	read(boolean canonicalize)

Methods inherited from class java.lang.Object

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

Field Detail

filename

protected String filename

The File to be loaded

allInteractions

protected Vector allInteractions

A Vector that holds all of the Interactions

Constructor Detail

InteractionsReader

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

Interactions Reader Constructor Creates a new Interactions Reader This constructor assumes a Y-Files graph is wanted. If not then use the other constructor to say so.

Parameters:

dataServer - a BioDataServer

species - the species of the network being loaded

filename - the file to load the network from

InteractionsReader

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

Interactions Reader Constructor Creates a new Interactions Reader This constructor assumes a Y-Files graph is wanted. If not then use the other constructor to say so.

Parameters:

dataServer - a BioDataServer

species - the species of the network being loaded

filename - the file to load the network from

InteractionsReader

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

InteractionsReader

public InteractionsReader(String filename)

Method Detail

layout

public void layout(giny.view.GraphView view)

Specified by:

layout in interface GraphReader

read

public void read(boolean canonicalize)
          throws IOException

Specified by:

read in interface GraphReader

Throws:

IOException

read

public void read()
          throws IOException

Calls read(false)

Specified by:

read in interface GraphReader

Throws:

IOException

getCount

public int getCount()

getAllInteractions

public Interaction[] getAllInteractions()

canonicalizeName

protected String canonicalizeName(String name)

createRootGraphFromInteractionData

protected void createRootGraphFromInteractionData(boolean canonicalize)

getRootGraph

public giny.model.RootGraph getRootGraph()

Specified by:

getRootGraph in interface GraphReader

getNodeAttributes

public CyAttributes getNodeAttributes()

Specified by:

getNodeAttributes in interface GraphReader

getEdgeAttributes

public CyAttributes getEdgeAttributes()

Specified by:

getEdgeAttributes in interface GraphReader

getNodeIndicesArray

public int[] getNodeIndicesArray()

Specified by:

getNodeIndicesArray in interface GraphReader

getEdgeIndicesArray

public int[] getEdgeIndicesArray()

Specified by:

getEdgeIndicesArray in interface GraphReader