org.gersteinlab.tyna.cytoscape
Class InteractionsReader2

java.lang.Object
  org.gersteinlab.tyna.cytoscape.InteractionsReader2

All Implemented Interfaces:

cytoscape.data.readers.GraphReader

public class InteractionsReader2

extends java.lang.Object

implements cytoscape.data.readers.GraphReader

Field Summary

protected java.util.Vector

allInteractions A Vector that holds all of the Interactions

Constructor Summary

InteractionsReader2(cytoscape.data.servers.BioDataServer dataServer, java.lang.String species, java.lang.String rawText)

Method Summary

protected java.lang.String	canonicalizeName(java.lang.String name)
static cytoscape.CyNetwork	createNetwork(java.lang.String networkData, java.lang.String title) ImportGraphFileAction
protected void	createRootGraphFromInteractionData(boolean canonicalize)
cytoscape.data.Interaction[]	getAllInteractions()
int	getCount()
cytoscape.data.CyAttributes	getEdgeAttributes()
int[]	getEdgeIndicesArray()
java.lang.String	getNetworkName()
cytoscape.data.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

allInteractions

protected java.util.Vector allInteractions

A Vector that holds all of the Interactions

Constructor Detail

InteractionsReader2

public InteractionsReader2(cytoscape.data.servers.BioDataServer dataServer,
                           java.lang.String species,
                           java.lang.String rawText)

Method Detail

createNetwork

public static cytoscape.CyNetwork createNetwork(java.lang.String networkData,
                                                java.lang.String title)
                                         throws java.io.IOException

ImportGraphFileAction

Throws:

java.io.IOException

layout

public void layout(giny.view.GraphView view)

Specified by:

layout in interface cytoscape.data.readers.GraphReader

read

public void read(boolean canonicalize)
          throws java.io.IOException

Specified by:

read in interface cytoscape.data.readers.GraphReader

Throws:

java.io.IOException

read

public void read()
          throws java.io.IOException

Calls read(false)

Specified by:

read in interface cytoscape.data.readers.GraphReader

Throws:

java.io.IOException

getCount

public int getCount()

getAllInteractions

public cytoscape.data.Interaction[] getAllInteractions()

canonicalizeName

protected java.lang.String canonicalizeName(java.lang.String name)

createRootGraphFromInteractionData

protected void createRootGraphFromInteractionData(boolean canonicalize)

getRootGraph

public giny.model.RootGraph getRootGraph()

Specified by:

getRootGraph in interface cytoscape.data.readers.GraphReader

getNodeAttributes

public cytoscape.data.CyAttributes getNodeAttributes()

Specified by:

getNodeAttributes in interface cytoscape.data.readers.GraphReader

getEdgeAttributes

public cytoscape.data.CyAttributes getEdgeAttributes()

Specified by:

getEdgeAttributes in interface cytoscape.data.readers.GraphReader

getNodeIndicesArray

public int[] getNodeIndicesArray()

Specified by:

getNodeIndicesArray in interface cytoscape.data.readers.GraphReader

getEdgeIndicesArray

public int[] getEdgeIndicesArray()

Specified by:

getEdgeIndicesArray in interface cytoscape.data.readers.GraphReader

getNetworkName

public java.lang.String getNetworkName()

Specified by:

getNetworkName in interface cytoscape.data.readers.GraphReader