Index: /branches/localSpectral/build.xml
===================================================================
--- /branches/localSpectral/build.xml (revision 27)
+++ /branches/localSpectral/build.xml (revision 27)
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+
+
+
+
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+
+
+ Builds, tests, and runs the project Jung.
+
+
+
Index: /branches/localSpectral/build/built-jar.properties
===================================================================
--- /branches/localSpectral/build/built-jar.properties (revision 27)
+++ /branches/localSpectral/build/built-jar.properties (revision 27)
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+#Sat, 09 Oct 2010 22:35:12 +0200
+
+/home/luke/NetBeansProjects/Jung=
Index: /branches/localSpectral/dist/README.TXT
===================================================================
--- /branches/localSpectral/dist/README.TXT (revision 27)
+++ /branches/localSpectral/dist/README.TXT (revision 27)
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+========================
+BUILD OUTPUT DESCRIPTION
+========================
+
+When you build an Java application project that has a main class, the IDE
+automatically copies all of the JAR
+files on the projects classpath to your projects dist/lib folder. The IDE
+also adds each of the JAR files to the Class-Path element in the application
+JAR files manifest file (MANIFEST.MF).
+
+To run the project from the command line, go to the dist folder and
+type the following:
+
+java -jar "Jung.jar"
+
+To distribute this project, zip up the dist folder (including the lib folder)
+and distribute the ZIP file.
+
+Notes:
+
+* If two JAR files on the project classpath have the same name, only the first
+JAR file is copied to the lib folder.
+* Only JAR files are copied to the lib folder.
+If the classpath contains other types of files or folders, none of the
+classpath elements are copied to the lib folder. In such a case,
+you need to copy the classpath elements to the lib folder manually after the build.
+* If a library on the projects classpath also has a Class-Path element
+specified in the manifest,the content of the Class-Path element has to be on
+the projects runtime path.
+* To set a main class in a standard Java project, right-click the project node
+in the Projects window and choose Properties. Then click Run and enter the
+class name in the Main Class field. Alternatively, you can manually type the
+class name in the manifest Main-Class element.
Index: /branches/localSpectral/manifest.mf
===================================================================
--- /branches/localSpectral/manifest.mf (revision 27)
+++ /branches/localSpectral/manifest.mf (revision 27)
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+Manifest-Version: 1.0
+X-COMMENT: Main-Class will be added automatically by build
+
Index: /branches/localSpectral/nbproject/build-impl.xml
===================================================================
--- /branches/localSpectral/nbproject/build-impl.xml (revision 27)
+++ /branches/localSpectral/nbproject/build-impl.xml (revision 27)
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+ Must set src.dir
+ Must set test.src.dir
+ Must set build.dir
+ Must set dist.dir
+ Must set build.classes.dir
+ Must set dist.javadoc.dir
+ Must set build.test.classes.dir
+ Must set build.test.results.dir
+ Must set build.classes.excludes
+ Must set dist.jar
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+ Must set javac.includes
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+ Must select some files in the IDE or set javac.includes
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+ To run this application from the command line without Ant, try:
+
+
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+
+
+ java -cp "${run.classpath.with.dist.jar}" ${main.class}
+
+
+
+
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+
+
+
+ To run this application from the command line without Ant, try:
+
+ java -jar "${dist.jar.resolved}"
+
+
+
+
+
+
+
+ To run this application from the command line without Ant, try:
+
+ java -jar "${dist.jar.resolved}"
+
+
+
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+ Must select one file in the IDE or set run.class
+
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+ Must select one file in the IDE or set run.class
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+ Must select one file in the IDE or set debug.class
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+ Must select one file in the IDE or set debug.class
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+ Must set fix.includes
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+ Must select some files in the IDE or set javac.includes
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+ Some tests failed; see details above.
+
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+ Must select some files in the IDE or set test.includes
+
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+ Some tests failed; see details above.
+
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+ Must select one file in the IDE or set test.class
+
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+ Must select one file in the IDE or set applet.url
+
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+ Must select one file in the IDE or set applet.url
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Index: /branches/localSpectral/nbproject/genfiles.properties
===================================================================
--- /branches/localSpectral/nbproject/genfiles.properties (revision 27)
+++ /branches/localSpectral/nbproject/genfiles.properties (revision 27)
@@ -0,0 +1,8 @@
+build.xml.data.CRC32=c1a09fce
+build.xml.script.CRC32=e5e47792
+build.xml.stylesheet.CRC32=28e38971@1.38.2.45
+# This file is used by a NetBeans-based IDE to track changes in generated files such as build-impl.xml.
+# Do not edit this file. You may delete it but then the IDE will never regenerate such files for you.
+nbproject/build-impl.xml.data.CRC32=c1a09fce
+nbproject/build-impl.xml.script.CRC32=4da45a17
+nbproject/build-impl.xml.stylesheet.CRC32=f33e10ff@1.38.2.45
Index: /branches/localSpectral/nbproject/private/private.properties
===================================================================
--- /branches/localSpectral/nbproject/private/private.properties (revision 27)
+++ /branches/localSpectral/nbproject/private/private.properties (revision 27)
@@ -0,0 +1,2 @@
+compile.on.save=true
+user.properties.file=/home/luke/.netbeans/6.9/build.properties
Index: /branches/localSpectral/nbproject/private/private.xml
===================================================================
--- /branches/localSpectral/nbproject/private/private.xml (revision 27)
+++ /branches/localSpectral/nbproject/private/private.xml (revision 27)
@@ -0,0 +1,4 @@
+
+
+
+
Index: /branches/localSpectral/nbproject/project.properties
===================================================================
--- /branches/localSpectral/nbproject/project.properties (revision 27)
+++ /branches/localSpectral/nbproject/project.properties (revision 27)
@@ -0,0 +1,86 @@
+annotation.processing.enabled=true
+annotation.processing.enabled.in.editor=false
+annotation.processing.processor.options=
+annotation.processing.processors.list=
+annotation.processing.run.all.processors=true
+annotation.processing.source.output=${build.generated.sources.dir}/ap-source-output
+build.classes.dir=${build.dir}/classes
+build.classes.excludes=**/*.java,**/*.form
+# This directory is removed when the project is cleaned:
+build.dir=build
+build.generated.dir=${build.dir}/generated
+build.generated.sources.dir=${build.dir}/generated-sources
+# Only compile against the classpath explicitly listed here:
+build.sysclasspath=ignore
+build.test.classes.dir=${build.dir}/test/classes
+build.test.results.dir=${build.dir}/test/results
+# Uncomment to specify the preferred debugger connection transport:
+#debug.transport=dt_socket
+debug.classpath=\
+ ${run.classpath}
+debug.test.classpath=\
+ ${run.test.classpath}
+# This directory is removed when the project is cleaned:
+dist.dir=dist
+dist.jar=${dist.dir}/Jung.jar
+dist.javadoc.dir=${dist.dir}/javadoc
+excludes=
+file.reference.collections-generic-4.01.jar=/home/luke/Desktop/jung2-2_0_1/collections-generic-4.01.jar
+file.reference.jung-algorithms-2.0.1.jar=/home/luke/Desktop/jung2-2_0_1/jung-algorithms-2.0.1.jar
+file.reference.jung-api-2.0.1.jar=/home/luke/Desktop/jung2-2_0_1/jung-api-2.0.1.jar
+file.reference.jung-graph-impl-2.0.1.jar=/home/luke/Desktop/jung2-2_0_1/jung-graph-impl-2.0.1.jar
+file.reference.jung-io-2.0.1.jar=/home/luke/Desktop/jung2-2_0_1/jung-io-2.0.1.jar
+file.reference.jung-jai-2.0.1.jar=/home/luke/Desktop/jung2-2_0_1/jung-jai-2.0.1.jar
+file.reference.jung-visualization-2.0.1.jar=/home/luke/Desktop/jung2-2_0_1/jung-visualization-2.0.1.jar
+includes=**
+jar.compress=false
+javac.classpath=\
+ ${file.reference.collections-generic-4.01.jar}:\
+ ${file.reference.jung-algorithms-2.0.1.jar}:\
+ ${file.reference.jung-api-2.0.1.jar}:\
+ ${file.reference.jung-visualization-2.0.1.jar}:\
+ ${file.reference.jung-graph-impl-2.0.1.jar}:\
+ ${file.reference.jung-io-2.0.1.jar}:\
+ ${file.reference.jung-jai-2.0.1.jar}
+# Space-separated list of extra javac options
+javac.compilerargs=
+javac.deprecation=false
+javac.processorpath=\
+ ${javac.classpath}
+javac.source=1.5
+javac.target=1.5
+javac.test.classpath=\
+ ${javac.classpath}:\
+ ${build.classes.dir}:\
+ ${libs.junit.classpath}:\
+ ${libs.junit_4.classpath}
+javac.test.processorpath=\
+ ${javac.test.classpath}
+javadoc.additionalparam=
+javadoc.author=false
+javadoc.encoding=${source.encoding}
+javadoc.noindex=false
+javadoc.nonavbar=false
+javadoc.notree=false
+javadoc.private=false
+javadoc.splitindex=true
+javadoc.use=true
+javadoc.version=false
+javadoc.windowtitle=
+main.class=jung.Main
+manifest.file=manifest.mf
+meta.inf.dir=${src.dir}/META-INF
+platform.active=default_platform
+run.classpath=\
+ ${javac.classpath}:\
+ ${build.classes.dir}
+# Space-separated list of JVM arguments used when running the project
+# (you may also define separate properties like run-sys-prop.name=value instead of -Dname=value
+# or test-sys-prop.name=value to set system properties for unit tests):
+run.jvmargs=
+run.test.classpath=\
+ ${javac.test.classpath}:\
+ ${build.test.classes.dir}
+source.encoding=UTF-8
+src.dir=src
+test.src.dir=test
Index: /branches/localSpectral/nbproject/project.xml
===================================================================
--- /branches/localSpectral/nbproject/project.xml (revision 27)
+++ /branches/localSpectral/nbproject/project.xml (revision 27)
@@ -0,0 +1,15 @@
+
+
+ org.netbeans.modules.java.j2seproject
+
+
+ Jung
+
+
+
+
+
+
+
+
+
Index: /branches/localSpectral/src/clustering/LocalSpectral.java
===================================================================
--- /branches/localSpectral/src/clustering/LocalSpectral.java (revision 27)
+++ /branches/localSpectral/src/clustering/LocalSpectral.java (revision 27)
@@ -0,0 +1,143 @@
+
+package clustering;
+
+import edu.uci.ics.jung.algorithms.scoring.PageRank;
+import edu.uci.ics.jung.algorithms.scoring.PageRankWithPriors;
+import edu.uci.ics.jung.graph.Graph;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Iterator;
+import java.util.List;
+import org.apache.commons.collections15.Transformer;
+
+
+public class LocalSpectral {
+
+ Graph graph;
+
+ double alpha = 0.15;
+
+ public Graph getGraph() {
+ return graph;
+ }
+
+ public void setGraph(Graph graph) {
+ this.graph = graph;
+ }
+
+ public LocalSpectral(Graph input){
+ graph = input;
+ }
+
+ public void removeCutEdges(List cut){
+ for(V vertex : cut){
+ Collection out_edges = graph.getOutEdges(vertex);
+ for(E edge : out_edges){
+ V opposite_vertex = graph.getOpposite(vertex, edge);
+ if (!cut.contains(opposite_vertex)){
+ graph.removeEdge(edge);
+ }
+ }
+ }
+
+ }
+
+ public List> getGlobalRank(){
+ PageRankWithPriors rank;
+ rank = new PageRank(graph, alpha);
+ rank.evaluate();
+ Collection vertexs = graph.getVertices();
+ Iterator vertexsIterator = vertexs.iterator();
+ ArrayList> vertexsScore = new ArrayList>();
+ while(vertexsIterator.hasNext()){
+ V vertex = (V) vertexsIterator.next();
+ Double score = (Double) rank.getVertexScore(vertex);
+ VertexScore vertexscore = new VertexScore(vertex,score);
+ vertexsScore.add(vertexscore);
+ }
+
+ Collections.sort(vertexsScore,new VertexScoreComparator());
+ return vertexsScore;
+ }
+
+ public List clusterPageRankPriors(V seed, double min_volume){
+ PageRankWithPriors rank;
+ if(seed != null){
+ Transformer transf = new SeedTransformer(seed);
+ rank = new PageRankWithPriors(graph, transf, alpha);
+ }
+ else{
+ rank = new PageRank(graph, alpha);
+ }
+
+ rank.evaluate();
+ Collection vertexs = graph.getVertices();
+ Iterator vertexsIterator = vertexs.iterator();
+ ArrayList> vertexsScore = new ArrayList>();
+ while(vertexsIterator.hasNext()){
+ V vertex = (V) vertexsIterator.next();
+ Double score = (Double) rank.getVertexScore(vertex);
+ int degree = graph.getIncidentEdges(vertex).size();
+ VertexScore vertexscore = new VertexScore(vertex,score/degree);
+ vertexsScore.add(vertexscore);
+ }
+
+ Collections.sort(vertexsScore,new VertexScoreComparator());
+
+ double sum=0;
+ for(VertexScore v : vertexsScore){
+ System.out.println(v.getVertex().toString()+ " " + v.getScore());
+ sum+=v.getScore();
+ }
+ System.out.println("SUM SCORES: "+sum);
+
+ int volume_graph = 2 * graph.getEdgeCount();
+ System.out.println("GRAPH VOLUME: " + volume_graph);
+ double max_volume = (volume_graph / 3) * 2;
+ double min_conductance_subset=100;
+ int min_conductance_index = -1;
+
+ int subsets_count = vertexsScore.size();
+ for(int i=0; i cluster = new ArrayList();
+ for(int i=0; i< min_conductance_index; i++)
+ cluster.add(vertexsScore.get(i).getVertex());
+
+ return cluster;
+
+ }
+
+}
Index: /branches/localSpectral/src/clustering/SeedTransformer.java
===================================================================
--- /branches/localSpectral/src/clustering/SeedTransformer.java (revision 27)
+++ /branches/localSpectral/src/clustering/SeedTransformer.java (revision 27)
@@ -0,0 +1,22 @@
+
+package clustering;
+
+import org.apache.commons.collections15.Transformer;
+
+public class SeedTransformer implements Transformer{
+
+ private V seed;
+
+ public SeedTransformer(V vertexSeed) {
+ this.seed = vertexSeed;
+ }
+
+ public Object transform(Object vertex) {
+ if (seed.equals(vertex))
+ return 1.0;
+ else
+ return 0.0;
+
+ }
+
+}
Index: /branches/localSpectral/src/clustering/VertexScore.java
===================================================================
--- /branches/localSpectral/src/clustering/VertexScore.java (revision 27)
+++ /branches/localSpectral/src/clustering/VertexScore.java (revision 27)
@@ -0,0 +1,37 @@
+
+package clustering;
+
+public class VertexScore {
+
+ private V vertex;
+ private double score;
+
+ public VertexScore(V vertex, double score) {
+ this.vertex = vertex;
+ this.score = score;
+ }
+
+ public double getScore() {
+ return score;
+ }
+
+ public void setScore(double score) {
+ this.score = score;
+ }
+
+ public V getVertex() {
+ return vertex;
+ }
+
+ public void setVertex(V vertex) {
+ this.vertex = vertex;
+ }
+
+ @Override
+ public String toString(){
+ return this.vertex.toString() + " " + score;
+ }
+
+
+
+}
Index: /branches/localSpectral/src/clustering/VertexScoreComparator.java
===================================================================
--- /branches/localSpectral/src/clustering/VertexScoreComparator.java (revision 27)
+++ /branches/localSpectral/src/clustering/VertexScoreComparator.java (revision 27)
@@ -0,0 +1,17 @@
+
+package clustering;
+
+import java.util.Comparator;
+
+public class VertexScoreComparator implements Comparator {
+
+ public int compare(VertexScore t, VertexScore t1) {
+ if(t.getScore() > t1.getScore())
+ return -1;
+ if(t.getScore() < t1.getScore())
+ return 1;
+
+ return 0;
+ }
+
+}
Index: /branches/localSpectral/src/data/GraphBuilder.java
===================================================================
--- /branches/localSpectral/src/data/GraphBuilder.java (revision 27)
+++ /branches/localSpectral/src/data/GraphBuilder.java (revision 27)
@@ -0,0 +1,62 @@
+
+package data;
+
+import edu.uci.ics.jung.graph.Graph;
+import edu.uci.ics.jung.graph.SparseGraph;
+import java.io.BufferedInputStream;
+import java.io.BufferedReader;
+import java.io.DataInputStream;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.util.Arrays;
+import java.util.HashSet;
+import java.util.Set;
+
+
+public class GraphBuilder {
+
+ Graph graph;
+
+ public GraphBuilder(){
+ graph = new SparseGraph();
+
+ }
+
+ public Graph getGraph() {
+ return graph;
+ }
+
+ public void buildGraphFromARFF(String path, int maxreadline){
+ try {
+ FileInputStream fstream = new FileInputStream(path);
+ DataInputStream in = new DataInputStream(fstream);
+ BufferedReader br = new BufferedReader(new InputStreamReader(in));
+
+ Set vertex = new HashSet();
+
+ String read;
+ int edge=0;
+ int count=0;
+ while(((read = br.readLine()) != null) && (count < maxreadline)){
+ count++;
+ if(!(read.contains("@DATA") || read.contains("@RELATION") || read.contains("@ATTRIBUTE") || read.trim().isEmpty())){
+ String[] splitted = read.trim().split(",");
+ vertex.addAll(Arrays.asList(splitted));
+ graph.addEdge(edge, splitted[0], splitted[1]);
+ edge++;
+ }
+ }
+ br.close();
+ in.close();
+ fstream.close();
+
+ } catch (FileNotFoundException e) {
+ System.out.println(" Error: file not found!");
+ } catch(IOException e){
+ System.out.println(" Error: closing FileInputStream");
+ }
+ }
+
+}
Index: /branches/localSpectral/src/jung/Main.java
===================================================================
--- /branches/localSpectral/src/jung/Main.java (revision 27)
+++ /branches/localSpectral/src/jung/Main.java (revision 27)
@@ -0,0 +1,46 @@
+/*
+ * To change this template, choose Tools | Templates
+ * and open the template in the editor.
+ */
+
+package jung;
+
+import clustering.LocalSpectral;
+import clustering.VertexScore;
+import data.GraphBuilder;
+import edu.uci.ics.jung.algorithms.scoring.PageRank;
+import edu.uci.ics.jung.graph.Graph;
+import edu.uci.ics.jung.graph.SparseGraph;
+import java.awt.Paint;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import view.VertexPaintTransformer;
+import view.Viewer;
+
+public class Main {
+
+ public static void main(String[] args) {
+ GraphBuilder builder = new GraphBuilder();
+ builder.buildGraphFromARFF("/home/luke/Desktop/reteSemplice.txt", 6000);
+ Graph graph = builder.getGraph();
+ Viewer viewGraph = new Viewer(graph);
+ viewGraph.viewGraph(null);
+ LocalSpectral clusterer = new LocalSpectral(graph);
+ List> global_ranking = clusterer.getGlobalRank();
+ System.out.println("GLOBAL RANKING");
+ for(VertexScore v : global_ranking)
+ System.out.println("VERTEX: "+v + " RANK "+v.getScore());
+ for(VertexScore v : global_ranking){
+ Long stoptime = 5000L;
+ try {
+ Thread.sleep(stoptime);
+ } catch (InterruptedException e) {}
+ List cut = clusterer.clusterPageRankPriors(v.getVertex(),6);
+ viewGraph.viewGraph(cut);
+ }
+
+ }
+
+
+}
Index: /branches/localSpectral/src/view/VertexLabelTransformer.java
===================================================================
--- /branches/localSpectral/src/view/VertexLabelTransformer.java (revision 27)
+++ /branches/localSpectral/src/view/VertexLabelTransformer.java (revision 27)
@@ -0,0 +1,14 @@
+
+
+package view;
+
+import org.apache.commons.collections15.Transformer;
+
+
+public class VertexLabelTransformer implements Transformer{
+
+ public String transform(V vertex) {
+ return (String) vertex.toString();
+ }
+
+}
Index: /branches/localSpectral/src/view/VertexPaintTransformer.java
===================================================================
--- /branches/localSpectral/src/view/VertexPaintTransformer.java (revision 27)
+++ /branches/localSpectral/src/view/VertexPaintTransformer.java (revision 27)
@@ -0,0 +1,27 @@
+
+package view;
+
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import org.apache.commons.collections15.Transformer;
+
+
+public class VertexPaintTransformer implements Transformer{
+
+ Collection cluster;
+
+ public VertexPaintTransformer(Collection cluster){
+ this.cluster = cluster;
+ }
+
+ public Paint transform(V node) {
+ if(cluster.contains(node))
+ return (Paint) Color.GREEN;
+ else
+ return (Paint) Color.RED;
+ }
+
+
+}
Index: /branches/localSpectral/src/view/Viewer.java
===================================================================
--- /branches/localSpectral/src/view/Viewer.java (revision 27)
+++ /branches/localSpectral/src/view/Viewer.java (revision 27)
@@ -0,0 +1,50 @@
+
+package view;
+
+import edu.uci.ics.jung.algorithms.layout.FRLayout;
+import edu.uci.ics.jung.algorithms.layout.Layout;
+import edu.uci.ics.jung.graph.Graph;
+import edu.uci.ics.jung.visualization.BasicVisualizationServer;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Paint;
+import java.util.ArrayList;
+import java.util.List;
+import javax.swing.JFrame;
+import org.apache.commons.collections15.Transformer;
+
+
+
+public class Viewer {
+
+ Graph graph;
+ Layout layout;
+ BasicVisualizationServer vv;
+ JFrame frame;
+
+ public Viewer(Graph graph) {
+ this.graph = graph;
+ this.frame = new JFrame("Graph View");
+ frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+ layout = new FRLayout(graph);
+ layout.setSize(new Dimension(1000,700));
+ vv = new BasicVisualizationServer(layout);
+ vv.setPreferredSize(new Dimension(1000,700));
+ vv.getRenderContext().setVertexLabelTransformer(new VertexLabelTransformer());
+ }
+
+
+ public void viewGraph(List cut){
+
+ if(cut != null){
+ VertexPaintTransformer vertexPaint = new VertexPaintTransformer(cut);
+ vv.getRenderContext().setVertexFillPaintTransformer(vertexPaint);
+ }
+
+ frame.getContentPane().add(vv);
+ frame.pack();
+ frame.repaint();
+ frame.setVisible(true);
+
+ }
+}