Author: ghuck
Date: 2011-06-20 19:40:22 -0700 (Mon, 20 Jun 2011)
New Revision: 25828
Added:
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/CircleLayout.java
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IgraphAPI.java
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IsConnected.java.nocompile
Removed:
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IsConnected.java
Modified:
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IgraphInterface.java
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IgraphPlugin.java
csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/igraphJNA.cpp
csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/igraphJNA.h
Log:
Circle layout working
Added:
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/CircleLayout.java
===================================================================
---
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/CircleLayout.java
(rev 0)
+++
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/CircleLayout.java
2011-06-21 02:40:22 UTC (rev 25828)
@@ -0,0 +1,405 @@
+/**************************************************************************************
+Copyright (C) Gerardo Huck, 2011
+
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+**************************************************************************************/
+
+package cytoscape.plugins.igraph;
+
+import cytoscape.Cytoscape;
+import cytoscape.layout.AbstractLayout;
+import cytoscape.layout.LayoutProperties;
+import cytoscape.layout.Tunable;
+import cytoscape.CyNode;
+import cytoscape.logger.CyLogger;
+
+import cytoscape.view.CyNetworkView;
+import cytoscape.data.CyAttributes;
+
+import csplugins.layout.LayoutPartition;
+import csplugins.layout.LayoutEdge;
+import csplugins.layout.LayoutNode;
+import csplugins.layout.EdgeWeighter;
+import csplugins.layout.algorithms.graphPartition.*;
+
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+
+import java.awt.Dimension;
+import java.awt.GridLayout;
+import java.util.*;
+
+public class CircleLayout extends AbstractGraphPartition
+{
+ private String message;
+ private LayoutProperties layoutProperties;
+
+
+ /**
+ * Creates a new layout object.
+ */
+ public CircleLayout() {
+ super();
+
+ logger = CyLogger.getLogger(CircleLayout.class);
+ // logger.setDebug(true);
+
+ layoutProperties = new LayoutProperties(getName());
+ initialize_properties();
+ }
+
+ /**
+ * This plugin supports laying out only selected nodes
+ */
+ public boolean supportsSelectedOnly() {
+ return true;
+ }
+
+ /**
+ * Adds tunable objects for adjusting plugin parameters
+ * Initializes default values for those parameters
+ */
+ protected void initialize_properties() {
+
+ // Add new properties to layout
+
+ // Initialize layout properties
+ layoutProperties.initializeProperties();
+
+ // Force the settings update
+ updateSettings(true);
+ }
+
+ /**
+ * getName is used to construct property strings
+ * for this layout.
+ */
+ public String getName() {
+ return "Igraph Circle Layout";
+ }
+
+ /**
+ * toString is used to get the user-visible name
+ * of the layout
+ */
+ public String toString(){
+ return "Circle Layout";
+ }
+
+ /**
+ * Overload updateSettings for using it without arguments
+ */
+ public void updateSettings() {
+ updateSettings(false);
+ }
+
+ /**
+ * Get new values from tunables and update parameters
+ */
+ public void updateSettings(boolean force) {
+ layoutProperties.updateValues();
+ }
+
+ /**
+ * Get the settings panel for this layout
+ */
+ public JPanel getSettingsPanel() {
+ JPanel panel = new JPanel(new GridLayout(1, 1));
+ panel.add(layoutProperties.getTunablePanel());
+
+ return panel;
+ }
+
+ /**
+ * Revert previous settings
+ */
+ public void revertSettings() {
+ layoutProperties.revertProperties();
+ }
+
+ /**
+ * Get layout properties
+ */
+ public LayoutProperties getSettings() {
+ return layoutProperties;
+ }
+
+
+ /**
+ *
+ */
+ public void layoutPartition (LayoutPartition part) {
+
+ // Check whether it has been canceled by the user
+ if (canceled)
+ return;
+
+ // Show message on the task monitor
+ taskMonitor.setStatus("Initializing: Partition: " +
part.getPartitionNumber());
+
+ // The completed percentage is indeterminable
+ taskMonitor.setPercentCompleted(-1);
+
+ // Figure out our starting point if we are only laying out selected
nodes
+ Dimension initialLocation = null;
+ if (selectedOnly) {
+ initialLocation = part.getAverageLocation();
+ }
+
+ // Get the number of edges and nodes
+ int numNodes = part.nodeCount();
+
+ // Allocate memory for storing graph edges information (to be used as
arguments for JNI call)
+ double[] x = new double[numNodes];
+ double[] y = new double[numNodes];
+
+ // Load graph into native library
+ HashMap<Integer,Integer> mapping = loadGraphPartition(part);
+
+ // Simplify graph
+ IgraphInterface.simplify();
+
+ // Check whether it has been canceled by the user
+ if (canceled)
+ return;
+
+ // Show message on the task monitor
+ taskMonitor.setStatus("Calling native code: Partition: " +
part.getPartitionNumber());
+
+ // Make native method call
+ IgraphInterface.layoutCircle(x, y);
+
+ // Check whether it has been canceled by the user
+ if (canceled)
+ return;
+ // Show message on the task monitor
+ taskMonitor.setStatus("Updating display");
+
+
+
+
+ // Find which ratio is required to 'scale up' the node positions so
that nodes don't overlap
+ double upRatio = 0.0;
+ double actualRatio = 0.0;
+
+ for (LayoutEdge edge: part.getEdgeList()) {
+ LayoutNode n1 = edge.getSource();
+ LayoutNode n2 = edge.getTarget();
+
+ double n1Size = Math.max(n1.getHeight(), n1.getWidth());
+ double n2Size = Math.max(n2.getHeight(), n2.getWidth());
+
+ double edgeSize = Math.sqrt( Math.pow(x[mapping.get(n1.getIndex())]
- x[mapping.get(n2.getIndex())], 2)
+ + Math.pow(y[mapping.get(n1.getIndex())]
- y[mapping.get(n2.getIndex())], 2)
+ );
+ // Check if edgeSize is not zero
+ if (edgeSize > 0.0){
+
+ // actualRatio = minimun_desired_length / actual_length
+ actualRatio = (n1Size + n2Size) / edgeSize;
+
+ // Update upRatio if necessary
+ if (actualRatio > upRatio)
+ upRatio = actualRatio;
+ }
+
+ }
+
+ //if (upRatio > 1000)
+ // upRatio = Math.log(upRatio) + 1000;
+ //upRatio = Math.min(upRatio, 100.0);
+
+ // Check whether the ratio is not zero
+ if (upRatio < 1.0){
+ upRatio = 1.0;
+ }
+
+ double oldUpRatio = upRatio;
+
+ // logger.info("upRatio = " + upRatio);
+ //message = "upRatio = " + upRatio;
+ //JOptionPane.showMessageDialog(Cytoscape.getDesktop(), message);
+
+
+ // Move nodes to their position
+ boolean success = false;
+ while (!success){
+
+ try{
+ // We will keep track of the offset of the whole part so that
we can eliminate it
+ double minX = x[0];
+ double minY = y[0];
+
+ // Get the 'offset' of the whole partition, so that we can
eliminate it
+ for (int i = 1; i < numNodes; i++) {
+
+ if (x[i] < minX)
+ minX = x[i];
+
+ if (y[i] < minY)
+ minY = y[i];
+ }
+
+ minX = upRatio * minX;
+ minY = upRatio * minY;
+
+ // Reset the nodes so we get the new average location
+ part.resetNodes();
+
+ // Iterate over all nodes
+ int currentNode = 0;
+
+ // Create an iterator for processing the nodes
+ Iterator<LayoutNode> iterator2 = part.getNodeList().iterator();
+
+ while (iterator2.hasNext()){
+
+ // Get next node
+ LayoutNode node = (LayoutNode) iterator2.next();
+
+ // Set node's X and Y positions
+ node.setX(upRatio * x[mapping.get(node.getIndex())] - minX);
+ node.setY(upRatio * y[mapping.get(node.getIndex())] - minY);
+
+ //logger.debug("moving node " + currentNode + "to:\nX = " +
(upRatio * node_positions[currentNode][0]) + "\nY = " + (upRatio *
node_positions[currentNode][1]));
+
+ // Move node to desired location
+ part.moveNodeToLocation(node);
+
+ currentNode++;
+ }
+
+
+ // Not quite done, yet. If we're only laying out selected
nodes, we need
+ // to migrate the selected nodes back to their starting position
+ if (selectedOnly) {
+ double xDelta = 0.0;
+ double yDelta = 0.0;
+ Dimension finalLocation = part.getAverageLocation();
+ xDelta = finalLocation.getWidth() -
initialLocation.getWidth();
+ yDelta = finalLocation.getHeight() -
initialLocation.getHeight();
+ for (LayoutNode v: part.getNodeList()) {
+ if (!v.isLocked()) {
+ v.decrement(xDelta, yDelta);
+ part.moveNodeToLocation(v);
+ }
+ }
+ }
+
+ success = true;
+
+ }
+ catch(Exception excep){
+
+ upRatio = upRatio / 10.0;
+ if (upRatio <= 0.0){
+ message = "Sorry, cannot produce layout";
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(),
message);
+ return;
+ }
+ success = false;
+ }
+
+ }//while(!success)
+
+
+
+
+
+
+
+ // Actually move the pieces around
+ // Note that we reset our min/max values before we start this
+ // so we can get an accurate min/max for paritioning
+// part.resetNodes();
+
+// for (LayoutNode v: part.getNodeList()) {
+// // Set node's X and Y positions
+// v.setX(x[mapping.get(v.getIndex())]);
+// v.setY(y[mapping.get(v.getIndex())]);
+
+// // Actually move the node
+// part.moveNodeToLocation(v);
+// }
+
+// // Not quite done, yet. If we're only laying out selected nodes, we
need
+// // to migrate the selected nodes back to their starting position
+// if (selectedOnly) {
+// double xDelta = 0.0;
+// double yDelta = 0.0;
+// Dimension finalLocation = part.getAverageLocation();
+// xDelta = finalLocation.getWidth() - initialLocation.getWidth();
+// yDelta = finalLocation.getHeight() - initialLocation.getHeight();
+
+// for (LayoutNode v: part.getNodeList()) {
+// if (!v.isLocked()) {
+// v.decrement(xDelta, yDelta);
+// part.moveNodeToLocation(v);
+// }
+// }
+// }
+
+
+ }// layoutPartion(LayoutPartition part)
+
+
+ /**
+ * This function loads a partition into igraph
+ *
+ */
+ public static HashMap<Integer,Integer> loadGraphPartition(LayoutPartition
part){
+
+ CyLogger logger = CyLogger.getLogger(CircleLayout.class);
+
+ // Create a reverse mapping
+ int nodeCount = part.nodeCount();
+
+ HashMap<Integer, Integer> nodeIdMapping = new HashMap<Integer,
Integer>(nodeCount);
+ int j = 0;
+
+ Iterator<LayoutNode> nodeIt = part.getNodeList().iterator();
+ while(nodeIt.hasNext()){
+ LayoutNode node = (LayoutNode) nodeIt.next();
+ nodeIdMapping.put(node.getIndex(), j);
+ j++;
+ }
+
+ // Write edges (as pairs of consecutive nodes) in edgeArray
+ int[] edgeArray = new int[part.edgeCount() * 2];
+ int i = 0;
+
+ Iterator<LayoutEdge> it = part.getEdgeList().iterator();
+
+ while (it.hasNext()) {
+ LayoutEdge e = (LayoutEdge) it.next();
+
+ LayoutNode source = e.getSource();
+ LayoutNode target = e.getTarget();
+
+ edgeArray[i] = nodeIdMapping.get(source.getIndex());
+ edgeArray[i + 1] = nodeIdMapping.get(target.getIndex());
+ i += 2;
+
+ }
+
+ IgraphInterface.createGraph(edgeArray, i);
+ // IgraphInterface.simplify();
+
+ return nodeIdMapping;
+ } // loadGraphPartition()
+
+
+}
\ No newline at end of file
Added:
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IgraphAPI.java
===================================================================
---
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IgraphAPI.java
(rev 0)
+++
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IgraphAPI.java
2011-06-21 02:40:22 UTC (rev 25828)
@@ -0,0 +1,119 @@
+/**************************************************************************************
+Copyright (C) Gerardo Huck, 2011
+
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+**************************************************************************************/
+
+package cytoscape.plugins.igraph;
+
+import java.awt.event.ActionEvent;
+import javax.swing.JOptionPane;
+import java.util.*;
+
+import cytoscape.Cytoscape;
+import cytoscape.*;
+import cytoscape.data.*;
+import cytoscape.plugin.CytoscapePlugin;
+import cytoscape.util.CytoscapeAction;
+
+import giny.model.*;
+
+import com.sun.jna.Library;
+import com.sun.jna.Native;
+import com.sun.jna.Platform;
+
+
+public class IgraphAPI {
+
+ public class IsConnected extends CytoscapeAction {
+
+ Boolean selectedOnly;
+
+ public IsConnected(IgraphPlugin myPlugin, String name, boolean
selectedOnly) {
+ super(name);
+ setPreferredMenu("Plugins.Igraph.IsConnected");
+ this.selectedOnly = new Boolean(selectedOnly);
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(), "Is
Connected?: " + isConnected(this.selectedOnly));
+ }
+
+ public boolean isConnected(boolean selectedOnly) {
+ loadGraph(selectedOnly);
+ return IgraphInterface.isConnected();
+ }
+
+ }
+
+ /**
+ * This function loads the current graph into Igraph.
+ *
+ */
+ public static HashMap<Integer,Integer> loadGraph(boolean selectedOnly){
+
+ CyNetwork network = Cytoscape.getCurrentNetwork();
+
+ // Create a reverse mapping
+ int nodeCount;
+ if(selectedOnly) {
+ nodeCount = network.getSelectedNodes().size();
+ } else {
+ nodeCount = network.getNodeCount();
+ }
+ HashMap<Integer, Integer> nodeIdMapping = new HashMap<Integer,
Integer>(nodeCount);
+ int j = 0;
+ Iterator<Node> nodeIt;
+ if(selectedOnly) {
+ nodeIt = network.getSelectedNodes().iterator();
+ } else {
+ nodeIt = network.nodesIterator();
+ }
+
+ while(nodeIt.hasNext()){
+ Node node = nodeIt.next();
+ nodeIdMapping.put(node.getRootGraphIndex(), j);
+ j++;
+ }
+
+
+ // Write edges (as pairs of consecutive nodes) in edgeArray
+ int[] edgeArray = new int[network.getEdgeCount() * 2];
+ int i = 0;
+
+ Iterator<Edge> it = network.edgesIterator();
+ while (it.hasNext()) {
+ Edge e = (CyEdge) it.next();
+
+ Node source = e.getSource();
+ Node target = e.getTarget();
+
+ if(!selectedOnly || (network.isSelected(source) &&
network.isSelected(target)) ){
+ edgeArray[i] =
nodeIdMapping.get(source.getRootGraphIndex());
+ edgeArray[i + 1] =
nodeIdMapping.get(target.getRootGraphIndex());
+ i += 2;
+ }
+ }
+
+ IgraphInterface.createGraph(edgeArray, i);
+ // IgraphInterface.simplify();
+
+ return nodeIdMapping;
+ } // loadGraph()
+
+
+
+}
\ No newline at end of file
Modified:
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IgraphInterface.java
===================================================================
---
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IgraphInterface.java
2011-06-21 01:59:28 UTC (rev 25827)
+++
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IgraphInterface.java
2011-06-21 02:40:22 UTC (rev 25828)
@@ -21,10 +21,13 @@
public static native void createGraph(int edgeArray[], int length);
- //Test whether the graph is connected
+ // Test whether the graph is connected
public static native boolean isConnected();
- //Simplify the graph for community ananlysis
+ // Simplify the graph
public static native void simplify();
+
+ // Circle layout
+ public static native void layoutCircle(double x[], double y[]);
}
\ No newline at end of file
Modified:
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IgraphPlugin.java
===================================================================
---
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IgraphPlugin.java
2011-06-21 01:59:28 UTC (rev 25827)
+++
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IgraphPlugin.java
2011-06-21 02:40:22 UTC (rev 25828)
@@ -1,26 +1,28 @@
-/**
-* Copyright (C) Gerardo Huck, 2011
-*
-* This program is free software: you can redistribute it and/or modify
-* it under the terms of the GNU Lesser General Public License as published
-* by the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU Lesser General Public License for more details.
-*
-* You should have received a copy of the GNU Lesser General Public License
-* along with this program. If not, see <http://www.gnu.org/licenses/>.
-*
-*/
+/**************************************************************************************
+Copyright (C) Gerardo Huck, 2011
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+**************************************************************************************/
+
package cytoscape.plugins.igraph;
import cytoscape.plugin.CytoscapePlugin;
import cytoscape.Cytoscape;
import cytoscape.util.CytoscapeAction;
+import cytoscape.layout.CyLayouts;
import giny.view.NodeView;
import giny.view.Label;
@@ -63,15 +65,19 @@
// JOptionPane.showMessageDialog(Cytoscape.getDesktop(),
IgraphInterface.nativeAdd(10, 20));
+ // Create Igraph object
+ IgraphAPI igraph = new IgraphAPI();
+
// Add elements in menu toolbar
- NodeCount nodeCountAction = new NodeCount(this);
-
Cytoscape.getDesktop().getCyMenus().addCytoscapeAction((CytoscapeAction)
nodeCountAction);
-
- IsConnected isConnectedAction1 = new IsConnected(this, "All
nodes",false);
+ IgraphAPI.IsConnected isConnectedAction1 = igraph.new IsConnected(this,
"All nodes", false);
Cytoscape.getDesktop().getCyMenus().addCytoscapeAction((CytoscapeAction)
isConnectedAction1);
- IsConnected isConnectedAction2 = new IsConnected(this, "Selected
Nodes", true);
+ IgraphAPI.IsConnected isConnectedAction2 = igraph.new IsConnected(this,
"Selected Nodes", true);
Cytoscape.getDesktop().getCyMenus().addCytoscapeAction((CytoscapeAction)
isConnectedAction2);
+
+ // Layouts
+ CyLayouts.addLayout(new CircleLayout(), "Igraph");
+
}
private boolean isOldVersion(){
Deleted:
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IsConnected.java
===================================================================
---
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IsConnected.java
2011-06-21 01:59:28 UTC (rev 25827)
+++
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IsConnected.java
2011-06-21 02:40:22 UTC (rev 25828)
@@ -1,143 +0,0 @@
-/**************************************************************************************
-Copyright (C) Gerardo Huck, 2011
-
-
-This program is free software: you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-**************************************************************************************/
-
-package cytoscape.plugins.igraph;
-
-import java.awt.event.ActionEvent;
-import javax.swing.JOptionPane;
-import java.util.*;
-
-import cytoscape.Cytoscape;
-import cytoscape.*;
-import cytoscape.data.*;
-import cytoscape.plugin.CytoscapePlugin;
-import cytoscape.util.CytoscapeAction;
-
-import giny.model.*;
-
-import com.sun.jna.Library;
-import com.sun.jna.Native;
-import com.sun.jna.Platform;
-
-public class IsConnected extends CytoscapeAction {
-
- Boolean selectedOnly;
-
- public IsConnected(IgraphPlugin myPlugin, String name, boolean
selectedOnly) {
- super(name);
- setPreferredMenu("Plugins.Igraph.IsConnected");
- this.selectedOnly = new Boolean(selectedOnly);
- }
-
- public void actionPerformed(ActionEvent e) {
- JOptionPane.showMessageDialog(Cytoscape.getDesktop(), "Is Connected?: "
+ isConnected(this.selectedOnly));
- }
-
- public boolean isConnected(boolean selectedOnly) {
- loadGraph_optimized(selectedOnly);
- return IgraphInterface.isConnected();
- }
-
- //This will load the graph into c
- public static HashMap<Integer,Integer> loadGraph_optimized(boolean
selectedOnly){
-
- // Nodes are ordered according to node array.
- CyNetwork network = Cytoscape.getCurrentNetwork();
-
- // ArrayList<Integer> selectedNodeIndices = new
ArrayList<Integer>();
-
- // int[] edgeIndicesArray = network.getEdgeIndicesArray();
- // int[] nodeArray = network.getNodeIndicesArray();
- // Set<Node> selectedNodes = network.geSelectedNodes();
-
- // Create a reverse mapping
- int nodeCount;
- if(selectedOnly) {
- nodeCount = network.getSelectedNodes().size();
- } else {
- nodeCount = network.getNodeCount();
- }
- HashMap<Integer, Integer> nodeIdMapping = new HashMap<Integer,
Integer>(nodeCount);
- int j = 0;
- Iterator<Node> nodeIt;
- if(selectedOnly) {
- nodeIt = network.getSelectedNodes().iterator();
- } else {
- nodeIt = network.nodesIterator();
- }
-
- while(nodeIt.hasNext()){
- Node node = nodeIt.next();
- nodeIdMapping.put(node.getRootGraphIndex(), j);
- j++;
- }
-
-
-// for(int i=0; i<nodeArray.length; i++){
-// nodeIdMapping.put(nodeArray[i],i);
-// }
-
- // Get the selectedNodes
- // Return the selected node array list
-// Iterator<Node> nodeIt = network.getSelectedNodes().iterator();
-// while(nodeIt.hasNext()){
-
-// Node node = nodeIt.next();
-// ////System.out.println("This is gd:" +
nodeIdMapping.get(node.getRootGraphIndex()));
-//
selectedNodeIndices.add(nodeIdMapping.get(node.getRootGraphIndex()));
-// }
-
- //If this works then it will be a lot faster
-
-
- int[] edgeArray = new int[network.getEdgeCount() * 2];
- int i = 0;
-
- Iterator<Edge> it = network.edgesIterator();
-
- while (it.hasNext()) {
- Edge e = (CyEdge) it.next();
-
- Node source = e.getSource();
- Node target = e.getTarget();
-
- if(!selectedOnly || (network.isSelected(source) &&
network.isSelected(target)) ){
- edgeArray[i] =
nodeIdMapping.get(source.getRootGraphIndex());
- edgeArray[i + 1] =
nodeIdMapping.get(target.getRootGraphIndex());
- i += 2;
- }
- }
-
-
-// for(int i = 0; i < edgeIndicesArray.length; i++){
-
-// if(!selectedOnly ||
-// (network.isSelected() && network.isSelected()) ){
-// edgeArray[i * 2] =
nodeIdMapping.get(network.getEdgeTargetIndex(edgeIndicesArray[i]));
-// edgeArray[i * 2 + 1] =
nodeIdMapping.get(network.getEdgeSourceIndex(edgeIndicesArray[i]));
-// }
-// }
-
- IgraphInterface.createGraph(edgeArray, i);
- // IgraphInterface.simplify();
-
- return nodeIdMapping;
- }
-
-}
\ No newline at end of file
Copied:
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IsConnected.java.nocompile
(from rev 25764,
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IsConnected.java)
===================================================================
---
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IsConnected.java.nocompile
(rev 0)
+++
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IsConnected.java.nocompile
2011-06-21 02:40:22 UTC (rev 25828)
@@ -0,0 +1,119 @@
+/**************************************************************************************
+Copyright (C) Gerardo Huck, 2011
+
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+**************************************************************************************/
+
+package cytoscape.plugins.igraph;
+
+import java.awt.event.ActionEvent;
+import javax.swing.JOptionPane;
+import java.util.*;
+
+import cytoscape.Cytoscape;
+import cytoscape.*;
+import cytoscape.data.*;
+import cytoscape.plugin.CytoscapePlugin;
+import cytoscape.util.CytoscapeAction;
+
+import giny.model.*;
+
+import com.sun.jna.Library;
+import com.sun.jna.Native;
+import com.sun.jna.Platform;
+
+
+public class IgraphLib {
+
+ public class IsConnected extends CytoscapeAction {
+
+ Boolean selectedOnly;
+
+ public IsConnected(IgraphPlugin myPlugin, String name, boolean
selectedOnly) {
+ super(name);
+ setPreferredMenu("Plugins.Igraph.IsConnected");
+ this.selectedOnly = new Boolean(selectedOnly);
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(), "Is
Connected?: " + isConnected(this.selectedOnly));
+ }
+
+ public boolean isConnected(boolean selectedOnly) {
+ loadGraph(selectedOnly);
+ return IgraphInterface.isConnected();
+ }
+
+ }
+
+ /**
+ * This function loads the current graph into Igraph.
+ *
+ */
+ public static HashMap<Integer,Integer> loadGraph(boolean selectedOnly){
+
+ CyNetwork network = Cytoscape.getCurrentNetwork();
+
+ // Create a reverse mapping
+ int nodeCount;
+ if(selectedOnly) {
+ nodeCount = network.getSelectedNodes().size();
+ } else {
+ nodeCount = network.getNodeCount();
+ }
+ HashMap<Integer, Integer> nodeIdMapping = new HashMap<Integer,
Integer>(nodeCount);
+ int j = 0;
+ Iterator<Node> nodeIt;
+ if(selectedOnly) {
+ nodeIt = network.getSelectedNodes().iterator();
+ } else {
+ nodeIt = network.nodesIterator();
+ }
+
+ while(nodeIt.hasNext()){
+ Node node = nodeIt.next();
+ nodeIdMapping.put(node.getRootGraphIndex(), j);
+ j++;
+ }
+
+
+ // Write edges (as pairs of consecutive nodes) in edgeArray
+ int[] edgeArray = new int[network.getEdgeCount() * 2];
+ int i = 0;
+
+ Iterator<Edge> it = network.edgesIterator();
+ while (it.hasNext()) {
+ Edge e = (CyEdge) it.next();
+
+ Node source = e.getSource();
+ Node target = e.getTarget();
+
+ if(!selectedOnly || (network.isSelected(source) &&
network.isSelected(target)) ){
+ edgeArray[i] =
nodeIdMapping.get(source.getRootGraphIndex());
+ edgeArray[i + 1] =
nodeIdMapping.get(target.getRootGraphIndex());
+ i += 2;
+ }
+ }
+
+ IgraphInterface.createGraph(edgeArray, i);
+ // IgraphInterface.simplify();
+
+ return nodeIdMapping;
+ } // loadGraph()
+
+
+
+}
\ No newline at end of file
Modified: csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/igraphJNA.cpp
===================================================================
--- csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/igraphJNA.cpp
2011-06-21 01:59:28 UTC (rev 25827)
+++ csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/igraphJNA.cpp
2011-06-21 02:40:22 UTC (rev 25828)
@@ -311,23 +311,21 @@
// }
-// void layoutCircle(double x[], double y[]){
-// igraph_matrix_t locs;
-// igraph_matrix_init(&locs, 0, 0);
+void layoutCircle(double x[], double y[]){
+ igraph_matrix_t locs;
+ igraph_matrix_init(&locs, 0, 0);
-// igraph_layout_circle(&g, &locs);
+ igraph_layout_circle(&g, &locs);
-// long int nRow = igraph_matrix_nrow(&locs);
-// long int nCol = igraph_matrix_ncol(&locs);
-// for(int i=0; i<nRow; i++){
-// x[i] = MATRIX(locs, i, 0);
-// y[i] = MATRIX(locs, i, 1);
-// }
+ long int nRow = igraph_matrix_nrow(&locs);
+ long int nCol = igraph_matrix_ncol(&locs);
+ for(int i=0; i<nRow; i++){
+ x[i] = MATRIX(locs, i, 0);
+ y[i] = MATRIX(locs, i, 1);
+ }
+}
-// }
-
-
// void layoutRandom(double x[], double y[]){
// igraph_matrix_t locs;
// igraph_matrix_init(&locs, 0, 0);
Modified: csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/igraphJNA.h
===================================================================
--- csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/igraphJNA.h
2011-06-21 01:59:28 UTC (rev 25827)
+++ csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/igraphJNA.h
2011-06-21 02:40:22 UTC (rev 25828)
@@ -32,5 +32,6 @@
/* void spinGlassSingle(int target, int community[], int* community_size);
//only compute community close to the target id */
//Can also make a function to compute an array of ids, if possible in later
versions.
+ void layoutCircle(double x[], double y[]);
}
--
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