org.gersteinlab.tyna.cytoscape
Class InteractionsReader2

java.lang.Object
  extended by 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