Author: ghuck
Date: 2011-07-03 08:21:41 -0700 (Sun, 03 Jul 2011)
New Revision: 26014
Modified:
csplugins/trunk/soc/ghuck/IgraphPlugin/build.xml
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/cytoscape/plugins/igraph/layouts/FruchtermanReingoldLayout.java
csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/igraphJNA.cpp
csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/igraphJNA.h
Log:
Support for weighted layout added on the C side
Modified: csplugins/trunk/soc/ghuck/IgraphPlugin/build.xml
===================================================================
--- csplugins/trunk/soc/ghuck/IgraphPlugin/build.xml 2011-07-02 14:07:24 UTC
(rev 26013)
+++ csplugins/trunk/soc/ghuck/IgraphPlugin/build.xml 2011-07-03 15:21:41 UTC
(rev 26014)
@@ -152,7 +152,15 @@
</exec>
</target>
+ <!-- =================================================================== -->
+ <!-- Clean up libraries extracted in plugins folder -->
+ <!-- =================================================================== -->
+ <target name="clean-libs" depends="init">
+ <delete file="${cytoscape.plugin.dir}/libigraphWrapper.dylib"/>
+ <delete file="${cytoscape.plugin.dir}/libigraph.0.dylib"/>
+ </target>
+
</project>
<!-- 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
2011-07-02 14:07:24 UTC (rev 26013)
+++
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IgraphInterface.java
2011-07-03 15:21:41 UTC (rev 26014)
@@ -17,7 +17,7 @@
Native.register("igraphWrapper");
}
-// public static native int nativeAdd(int a, int b);
+ public static native int nativeAdd(int a, int b);
// Create an igraph's graph
public static native void createGraph(int edgeArray[], int length);
@@ -42,6 +42,9 @@
double area,
double coolExp,
double repulserad,
- boolean useSeed);
+ boolean useSeed,
+ boolean isWeighted,
+ double weights[]);
-}
\ 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
2011-07-02 14:07:24 UTC (rev 26013)
+++
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IgraphPlugin.java
2011-07-03 15:21:41 UTC (rev 26014)
@@ -55,10 +55,10 @@
checkLib("igraph.0");
String userDir = System.getProperty("user.dir");
-// JOptionPane.showMessageDialog( Cytoscape.getDesktop(), "user dir:"+
userDir);
+ // JOptionPane.showMessageDialog( Cytoscape.getDesktop(), "user dir:"+
userDir);
NativeLibrary.addSearchPath("igraphWrapper", userDir + "/plugins");
-// JOptionPane.showMessageDialog(Cytoscape.getDesktop(),
IgraphInterface.nativeAdd(10, 20));
+ // JOptionPane.showMessageDialog(Cytoscape.getDesktop(),
IgraphInterface.nativeAdd(10, 20));
// Create Igraph object
IgraphAPI igraph = new IgraphAPI();
@@ -123,54 +123,54 @@
} // checkLib
- protected boolean loadIgraph() {
+// protected boolean loadIgraph() {
- boolean res = true;
+// boolean res = true;
- // Reset the "sys_paths" field of the ClassLoader to null.
- Class clazz = ClassLoader.class;
- Field field;
- try {
- field = clazz.getDeclaredField("sys_paths");
- boolean accessible = field.isAccessible();
- if (!accessible)
- field.setAccessible(true);
- Object original = field.get(clazz);
+// // Reset the "sys_paths" field of the ClassLoader to null.
+// Class clazz = ClassLoader.class;
+// Field field;
+// try {
+// field = clazz.getDeclaredField("sys_paths");
+// boolean accessible = field.isAccessible();
+// if (!accessible)
+// field.setAccessible(true);
+// Object original = field.get(clazz);
- // Get original PATH
- String orig_path = System.getProperty("java.library.path");
+// // Get original PATH
+// String orig_path = System.getProperty("java.library.path");
- // Reset it to null so that whenever "System.loadLibrary" is
called, it will be reconstructed with the changed value
- field.set(clazz, null);
- try {
- // Change the value and load the library.
- System.setProperty("java.library.path", "./plugins" + ":" +
orig_path);
- // System.loadLibrary("igraph.0");
- System.loadLibrary("igraphWrapper");
- }
+// // Reset it to null so that whenever "System.loadLibrary" is
called, it will be reconstructed with the changed value
+// field.set(clazz, null);
+// try {
+// // Change the value and load the library.
+// System.setProperty("java.library.path", "./plugins" + ":" +
orig_path);
+// // System.loadLibrary("igraph.0");
+// System.loadLibrary("igraphWrapper");
+// }
- catch (UnsatisfiedLinkError error) {
- String message = "Problem detected while loading library.\n"
- + error.getMessage()
- + "\nPlease check your plugins folder.";
- JOptionPane.showMessageDialog(Cytoscape.getDesktop(), message);
+// catch (UnsatisfiedLinkError error) {
+// String message = "Problem detected while loading library.\n"
+// + error.getMessage()
+// + "\nPlease check your plugins folder.";
+// JOptionPane.showMessageDialog(Cytoscape.getDesktop(), message);
- res = false;
- }
+// res = false;
+// }
- finally {
- // Revert back the changes
- field.set(clazz, original);
- field.setAccessible(accessible);
- }
- }
- catch (Exception exception) {
- res = false;
- }
+// finally {
+// // Revert back the changes
+// field.set(clazz, original);
+// field.setAccessible(accessible);
+// }
+// }
+// catch (Exception exception) {
+// res = false;
+// }
- finally {
- return res;
- }
- }
+// finally {
+// return res;
+// }
+// }
}
\ No newline at end of file
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
2011-07-02 14:07:24 UTC (rev 26013)
+++
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/layouts/AbstractIgraphLayout.java
2011-07-03 15:21:41 UTC (rev 26014)
@@ -187,9 +187,6 @@
// Load graph into native library
HashMap<Integer,Integer> mapping = loadGraphPartition(part,
selectedOnly);
- // Store current node positions
- loadPositions(part, mapping, x, y);
-
// Check whether it has been canceled by the user
if (canceled)
return;
@@ -341,6 +338,8 @@
CyLogger logger = CyLogger.getLogger(AbstractIgraphLayout.class);
+ // JOptionPane.showMessageDialog(Cytoscape.getDesktop(), "Load graph
called!");
+
// Create a reverse mapping
int nodeCount = part.nodeCount();
Modified:
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/layouts/FruchtermanReingoldLayout.java
===================================================================
---
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/layouts/FruchtermanReingoldLayout.java
2011-07-02 14:07:24 UTC (rev 26013)
+++
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/layouts/FruchtermanReingoldLayout.java
2011-07-03 15:21:41 UTC (rev 26014)
@@ -132,15 +132,6 @@
}
-// /**
-// * 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
@@ -151,9 +142,17 @@
HashMap<Integer,Integer> mapping) {
- double maxDelta = maxDeltaCoefficient * part.nodeCount();
- double area = areaCoefficient * part.nodeCount() *
part.nodeCount();
- double repulseRad = repulseRadCoefficient * area * part.nodeCount();
+ int numNodes = mapping.size();
+
+ double maxDelta = maxDeltaCoefficient * numNodes;
+ double area = areaCoefficient * numNodes * numNodes;
+ double repulseRad = repulseRadCoefficient * area * numNodes;
+ double[] weights = new double[numNodes];
+
+ // Store current node positions if necessary
+ if (!randomize) {
+ loadPositions(part, mapping, x, y);
+ }
// Make native method call
IgraphInterface.layoutFruchterman(x,
@@ -163,7 +162,9 @@
area,
coolExp,
repulseRad,
- !randomize);
+ !randomize,
+ false,
+ weights);
return 1;
}
Modified: csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/igraphJNA.cpp
===================================================================
--- csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/igraphJNA.cpp
2011-07-02 14:07:24 UTC (rev 26013)
+++ csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/igraphJNA.cpp
2011-07-03 15:21:41 UTC (rev 26014)
@@ -69,6 +69,8 @@
x[i] = MATRIX(locs, i, 0);
y[i] = MATRIX(locs, i, 1);
}
+ // Clean up
+ igraph_matrix_destroy(&locs);
}
void starLayout(double x[], double y[], int centerId) {
@@ -85,8 +87,9 @@
x[i] = MATRIX(locs, i, 0);
y[i] = MATRIX(locs, i, 1);
}
-
-
+
+ // Clean up
+ igraph_matrix_destroy(&locs);
}
//Fruchterman - Reingold Layout
@@ -97,35 +100,76 @@
double area,
double coolExp,
double repulserad,
- bool useSeed){
+ bool useSeed,
+ bool isWeighted,
+ double weights[]){
+
long int vcount = igraph_vcount(&g);
+
igraph_matrix_t locs;
igraph_matrix_init(&locs, vcount, 2);
- for(int i = 0; i < vcount; i++){
+ 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, // weights
- 0,
- 0);
+ igraph_vector_t weights_vector;
+ if (isWeighted) {
+ igraph_vector_init(&weights_vector, vcount);
+ for (int i = 0; i < vcount; i++){
+ VECTOR(weights_vector)[i] = weights[i];
+ }
+ }
+
+
+ if (isWeighted) {
+ igraph_layout_fruchterman_reingold(&g,
+ &locs,
+ iter,
+ maxDelta,
+ area,
+ coolExp,
+ repulserad,
+ useSeed,
+ &weights_vector,
+ 0,
+ 0);
+
+ } else {
+ 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);
}
+
+ // Clean up
+ igraph_matrix_destroy(&locs);
+ igraph_vector_destroy(&weights_vector);
}
+extern "C"{
+ //Simple adding of two integers
+ int nativeAdd(int a, int b)
+ {
+ return( a + b );
+ }
+}
+
//////////////////////////////
//Boolean, test whether the current graph is simple
@@ -628,13 +672,6 @@
// }
-extern "C"{
-//Simple adding of two integers
- int nativeAdd( int a, int b )
- {
- return( a + b );
- }
-}
// //Add one to the passed integer via pointer
// void nativeIncrement(int* iptr){
// *iptr += 1;
Modified: csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/igraphJNA.h
===================================================================
--- csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/igraphJNA.h
2011-07-02 14:07:24 UTC (rev 26013)
+++ csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/igraphJNA.h
2011-07-03 15:21:41 UTC (rev 26014)
@@ -25,7 +25,9 @@
double area,
double coolExp,
double repulserad,
- bool useSeed);
+ bool useSeed,
+ bool isWeighted,
+ double weights[]);
/* void fastGreedy(int membership[], double* modularity, int csize[], int *
numCluster); */
@@ -34,11 +36,10 @@
/* void edgeBetweenness(int membership[], double*modularity, int csize[],
int * numCluster); */
/* void spinGlass(int membership[], double* modularity, int csize[], int*
numCluster); */
/* 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.
+
-
//test functions
-/* int nativeAdd( int a, int b ); */
+ int nativeAdd(int a, int b);
/* void nativeIncrement(int* iptr); */
/* int nativeArrayReset(int data[], int length); */
/* int nativeCountAdd(int value); */
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