Author: ghuck
Date: 2011-06-28 08:02:18 -0700 (Tue, 28 Jun 2011)
New Revision: 25958
Added:
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/layouts/FruchtermanReingoldLayout.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/cytoscape/plugins/igraph/layouts/AbstractIgraphLayout.java
csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/igraphJNA.cpp
csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/igraphJNA.h
Log:
Added Fruchterman-Reignolds layout
Modified:
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IgraphInterface.java
===================================================================
---
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IgraphInterface.java
2011-06-28 14:58:25 UTC (rev 25957)
+++
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IgraphInterface.java
2011-06-28 15:02:18 UTC (rev 25958)
@@ -35,13 +35,13 @@
public static native void starLayout(double x[], double y[], int centerId);
// Fruchterman - Reingold Layout
-// public static native void layoutFruchterman(double x[],
-// double y[],
-// int iter,
-// double maxDelta,
-// double area,
-// double coolExp,
-// double repulserad,
-// boolean useSeed);
+ public static native void layoutFruchterman(double x[],
+ double y[],
+ int iter,
+ double maxDelta,
+ double area,
+ double coolExp,
+ double repulserad,
+ boolean useSeed);
}
\ 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
2011-06-28 14:58:25 UTC (rev 25957)
+++
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IgraphPlugin.java
2011-06-28 15:02:18 UTC (rev 25958)
@@ -71,10 +71,10 @@
Cytoscape.getDesktop().getCyMenus().addCytoscapeAction((CytoscapeAction)
isConnectedAction2);
// Layouts
- CyLayouts.addLayout(new CircleLayout(), "Igraph");
+ CyLayouts.addLayout(new CircleLayout() , "Igraph");
+ CyLayouts.addLayout(new StarLayout() , "Igraph");
+ CyLayouts.addLayout(new FruchtermanReingoldLayout(), "Igraph");
- CyLayouts.addLayout(new StarLayout(), "Igraph");
-
}
Modified:
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/layouts/AbstractIgraphLayout.java
===================================================================
---
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/layouts/AbstractIgraphLayout.java
2011-06-28 14:58:25 UTC (rev 25957)
+++
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/layouts/AbstractIgraphLayout.java
2011-06-28 15:02:18 UTC (rev 25958)
@@ -109,10 +109,10 @@
}
/**
- * Overload updateSettings for using it without arguments
+ * Get new values from tunables and update parameters
*/
- public void updateSettings() {
- updateSettings(false);
+ public void updateSettings(boolean force) {
+ layoutProperties.updateValues();
}
/**
@@ -128,10 +128,10 @@
// END OF METHODS WHICH MAY BE OVERRIDEN
/**
- * Get new values from tunables and update parameters
+ * Overload updateSettings for using it without arguments
*/
- public void updateSettings(boolean force) {
- layoutProperties.updateValues();
+ public void updateSettings() {
+ updateSettings(false);
}
/**
Added:
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/layouts/FruchtermanReingoldLayout.java
===================================================================
---
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/layouts/FruchtermanReingoldLayout.java
(rev 0)
+++
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/layouts/FruchtermanReingoldLayout.java
2011-06-28 15:02:18 UTC (rev 25958)
@@ -0,0 +1,190 @@
+/**************************************************************************************
+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.layout;
+
+import cytoscape.plugins.igraph.*;
+import cytoscape.logger.CyLogger;
+import cytoscape.layout.LayoutProperties;
+import csplugins.layout.LayoutPartition;
+import cytoscape.layout.Tunable;
+
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+
+import java.awt.GridLayout;
+
+import java.util.*;
+
+public class FruchtermanReingoldLayout extends AbstractIgraphLayout {
+
+ private int iterNumber = 500; // Number of iterations
+ private double maxDeltaCoefficient = 1.0; // Maximum distance to move
a node in each iteration
+ private double areaCoefficient = 1.0; // Area parameter
+ private double coolExp = 1.5; // The cooling exponent of
the simulated annealing
+ private double repulseRadCoefficient = 1.0; // Determines the radius at
which vertex-vertex repulsion cancels out attraction of adjacent vertices
+ private boolean randomize = true; // Randomize node position
before layout
+
+
+ public FruchtermanReingoldLayout() {
+ super();
+ logger = CyLogger.getLogger(FruchtermanReingoldLayout.class);
+
+ layoutProperties = new LayoutProperties(getName());
+ initialize_properties();
+ }
+
+ /**
+ * Adds tunable objects for adjusting plugin parameters
+ * Initializes default values for those parameters
+ */
+ protected void initialize_properties() {
+
+ // Add new properties to layout
+ layoutProperties.add(new Tunable("iterNumber",
+ "Number of Iterations",
+ Tunable.INTEGER,
+ new Integer(iterNumber)));
+
+ layoutProperties.add(new Tunable("maxDeltaCoefficient",
+ "Distance to move nodes in each
iteration",
+ Tunable.DOUBLE,
+ new Double(maxDeltaCoefficient)));
+
+ layoutProperties.add(new Tunable("areaCoefficient",
+ "Area to use in layout",
+ Tunable.DOUBLE,
+ new Double(areaCoefficient)));
+
+ layoutProperties.add(new Tunable("coolExp",
+ "Cooling exponent of the simulated
annealing",
+ Tunable.DOUBLE,
+ new Double(coolExp)));
+
+ layoutProperties.add(new Tunable("repulseRadCoefficient",
+ "Radius at which vertex-vertex
repulsion cancels out attraction of adjacent vertices",
+ Tunable.DOUBLE,
+ new Double(repulseRadCoefficient)));
+
+ layoutProperties.add(new Tunable("randomize",
+ "Randomize node locations before
laying out nodes",
+ Tunable.BOOLEAN,
+ new Boolean(randomize)));
+
+ // Initialize layout properties
+ layoutProperties.initializeProperties();
+
+ // Force the settings update
+ updateSettings(true);
+ }
+
+ /**
+ * Get new values from tunables and update parameters
+ */
+ public void updateSettings(boolean force) {
+ layoutProperties.updateValues();
+
+ // Get initialNoIterations
+ Tunable t1 = layoutProperties.get("iterNumber");
+ if ((t1 != null) && (t1.valueChanged() || force))
+ iterNumber = ((Integer) t1.getValue()).intValue();
+
+ // Get maxDeltaCoefficient
+ Tunable t2 = layoutProperties.get("maxDeltaCoefficient");
+ if ((t2 != null) && (t2.valueChanged() || force))
+ maxDeltaCoefficient = ((Double) t2.getValue()).doubleValue();
+
+ // Get areaCoefficient
+ Tunable t3 = layoutProperties.get("areaCoefficient");
+ if ((t3 != null) && (t3.valueChanged() || force))
+ areaCoefficient = ((Double) t3.getValue()).doubleValue();
+
+ // Get coolExp
+ Tunable t4 = layoutProperties.get("coolExp");
+ if ((t4 != null) && (t4.valueChanged() || force))
+ coolExp = ((Double) t4.getValue()).doubleValue();
+
+ // Get repulseRadCoefficient
+ Tunable t5 = layoutProperties.get("repulseRadCoefficient");
+ if ((t5 != null) && (t5.valueChanged() || force))
+ repulseRadCoefficient = ((Double) t5.getValue()).doubleValue();
+
+ // Get randomize
+ Tunable t6 = layoutProperties.get("randomize");
+ if ((t6 != null) && (t6.valueChanged() || force))
+ randomize = ((Boolean) t6.getValue()).booleanValue();
+
+ }
+
+// /**
+// * Get the settings panel for this layout
+// */
+// public JPanel getSettingsPanel() {
+// JPanel panel = new JPanel(new GridLayout(1, 1));
+// panel.add(layoutProperties.getTunablePanel());
+
+// return panel;
+// }
+
+ /**
+ * Do the layout on a graph alrealy loaded into igraph
+ */
+ public int layout(double[] x,
+ double[] y,
+ LayoutPartition part,
+ HashMap<Integer,Integer> mapping) {
+
+
+ double maxDelta = maxDeltaCoefficient * part.nodeCount();
+ double area = areaCoefficient * part.nodeCount() *
part.nodeCount();
+ double repulseRad = repulseRadCoefficient * area * part.nodeCount();
+
+ // Make native method call
+ IgraphInterface.layoutFruchterman(x,
+ y,
+ iterNumber,
+ maxDelta,
+ area,
+ coolExp,
+ repulseRad,
+ !randomize);
+
+ return 1;
+ }
+
+ /**
+ * getName is used to construct property strings
+ * for this layout.
+ */
+ public String getName() {
+ return "Igraph Fruchterman-Reingold Layout";
+ }
+
+ /**
+ * toString is used to get the user-visible name
+ * of the layout
+ */
+ public String toString() {
+ return "Fruchterman-Reingold Layout";
+ }
+
+}
+
+
+
Modified: csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/igraphJNA.cpp
===================================================================
--- csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/igraphJNA.cpp
2011-06-28 14:58:25 UTC (rev 25957)
+++ csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/igraphJNA.cpp
2011-06-28 15:02:18 UTC (rev 25958)
@@ -89,37 +89,39 @@
}
-// Fruchterman - Reingold Layout
-// void layoutFruchterman(double x[],
-// double y[],
-// int iter,
-// double maxDelta,
-// double area,
-// double coolExp,
-// double repulserad,
-// bool useSeed){
-// long int vcount = igraph_vcount(&g);
-// igraph_matrix_t locs;
-// igraph_matrix_init(&locs, vcount, 2);
-// for(int i=0; i<vcount; i++){
-// MATRIX(locs, i, 0) = x[i];
-// MATRIX(locs, i, 1) = y[i];
-// }
+//Fruchterman - Reingold Layout
+void layoutFruchterman(double x[],
+ double y[],
+ int iter,
+ double maxDelta,
+ double area,
+ double coolExp,
+ double repulserad,
+ bool useSeed){
+ long int vcount = igraph_vcount(&g);
+ igraph_matrix_t locs;
+ igraph_matrix_init(&locs, vcount, 2);
+ for(int i = 0; i < vcount; i++){
+ MATRIX(locs, i, 0) = x[i];
+ MATRIX(locs, i, 1) = y[i];
+ }
-// igraph_layout_fruchterman_reingold(&g,
-// &locs,
-// iter,
-// maxDelta,
-// area,
-// coolExp,
-// repulserad,
-// useSeed,
-// 0);
-// for(int i=0; i<vcount; i++){
-// x[i] = MATRIX(locs, i, 0);
-// y[i] = MATRIX(locs, i, 1);
-// }
-// }
+ igraph_layout_fruchterman_reingold(&g,
+ &locs,
+ iter,
+ maxDelta,
+ area,
+ coolExp,
+ repulserad,
+ useSeed,
+ 0, // weights
+ 0,
+ 0);
+ for(int i=0; i<vcount; i++){
+ x[i] = MATRIX(locs, i, 0);
+ y[i] = MATRIX(locs, i, 1);
+ }
+}
Modified: csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/igraphJNA.h
===================================================================
--- csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/igraphJNA.h
2011-06-28 14:58:25 UTC (rev 25957)
+++ csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/igraphJNA.h
2011-06-28 15:02:18 UTC (rev 25958)
@@ -18,14 +18,14 @@
// Layouts
void layoutCircle(double x[], double y[]);
void starLayout(double x[], double y[], int centerId);
-/* void layoutFruchterman(double x[], */
-/* double y[], */
-/* int iter, */
-/* double maxDelta, */
-/* double area, */
-/* double coolExp, */
-/* double repulserad, */
-/* bool useSeed); */
+ void layoutFruchterman(double x[],
+ double y[],
+ int iter,
+ double maxDelta,
+ double area,
+ double coolExp,
+ double repulserad,
+ bool useSeed);
/* void fastGreedy(int membership[], double* modularity, int csize[], int *
numCluster); */
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