jaroslav-kuchar · joancf · Jan 8, 2015 · Jan 9, 2015 · Jan 9, 2015 · Jan 9, 2015
diff --git a/manifest.mf b/manifest.mf
@@ -2,5 +2,5 @@ Manifest-Version: 1.0
 OpenIDE-Module: cz.cvut.fit.gephi.multimode
 OpenIDE-Module-Localizing-Bundle: cz/cvut/fit/gephi/multimode/Bundle.properties
 OpenIDE-Module-Requires: org.openide.windows.WindowManager
-OpenIDE-Module-Specification-Version: 0.1.2
+OpenIDE-Module-Specification-Version: 0.1.3
 
diff --git a/src/cz/cvut/fit/gephi/multimode/Bundle.properties b/src/cz/cvut/fit/gephi/multimode/Bundle.properties
@@ -3,7 +3,8 @@ OpenIDE-Module-Long-Description=\
     This plugin allows multimode networks projection. \
     You can project your bipartite (2-mode) graph to monopartite (one-mode) graph. \
     The projection/transformation is based on the matrix multiplication approach and allows different types of transformations. \
-    The limitation is matrix multiplication - large matrix multiplication takes time and memory.
+    The limitation is matrix multiplication - large matrix multiplication takes time and memory.\n\
+    Threshold to limit the number of generated edges and option to convert directed graphs to undirected has been added\nThe weights are taken into account
 OpenIDE-Module-Name=MultimodeNetworksTransformationPlugin
 OpenIDE-Module-Short-Description=Multimode Networks Transformations
 MultiModeWindowTopComponent.attributes.toolTipText=Attribute column which represents node type.
@@ -20,3 +21,6 @@ MultiModeWindowTopComponent.removeNodes.toolTipText=Remove affected Nodes
 MultiModeWindowTopComponent.load.text=Load attributes
 MultiModeWindowTopComponent.graphColoring.text=Graph Coloring
 MultiModeWindowTopComponent.bipartiteLabel.text=Bipartite: ?
+MultiModeWindowTopComponent.jLabel1.text=Threshold
+MultiModeWindowTopComponent.threshold.text=0.0
+MultiModeWindowTopComponent.directed.text=directed
diff --git a/src/cz/cvut/fit/gephi/multimode/LongTaskTransformation.java b/src/cz/cvut/fit/gephi/multimode/LongTaskTransformation.java
@@ -25,14 +25,19 @@ public class LongTaskTransformation implements LongTask, Runnable {
     private String outDimension;
     private boolean removeEdges = true;
     private boolean removeNodes = true;
+    private boolean directed=false;
+    private boolean considerDirected=false;
+    private double threshold=0.0;
 
-    public LongTaskTransformation(AttributeColumn attributeColumn, String inDimension, String commonDimension, String outDimension, boolean removeEdges, boolean removeNodes) {
+    public LongTaskTransformation(AttributeColumn attributeColumn, String inDimension, String commonDimension, String outDimension,double threshold, boolean removeEdges, boolean removeNodes, boolean considerDirected) {
         this.attributeColumn = attributeColumn;
         this.inDimension = inDimension;
         this.commonDimension = commonDimension;
         this.outDimension = outDimension;
         this.removeEdges = removeEdges;
         this.removeNodes = removeNodes;
+        this.considerDirected=considerDirected;
+        this.threshold=threshold;
     }
 
     @Override
@@ -43,8 +48,14 @@ public void run() {
         // graph
         GraphController graphController = Lookup.getDefault().lookup(GraphController.class);
         GraphModel graphModel = graphController.getModel();
-        Graph graph = graphModel.getGraphVisible();
-        //Graph graph = graphModel.getUndirectedGraphVisible();
+        Graph graph;
+        if (considerDirected){
+            graph = graphModel.getGraphVisible();
+            directed=graphModel.isDirected();
+        } else { 
+            graph = graphModel.getUndirectedGraphVisible();
+            directed=false;        
+        }
         Node[] nodes = graph.getNodes().toArray();
 
         // matrix axis
@@ -72,11 +83,12 @@ public void run() {
                 secondHorizontal.add(n);
             }
         }
-
+        Progress.start(progressTicket, firstVertical.size()+5);
+
         if (cancelled) {
             return;
         }
-        Progress.progress(progressTicket);
+        Progress.progress(progressTicket,1);
 
         // first matrix
         Matrix firstMatrix = new Matrix(firstVertical.size(), firstHorizontal.size());
@@ -86,9 +98,15 @@ public void run() {
                 try {
                     intersection.retainAll(firstHorizontal);
                     for (Node neighbour : intersection) {
-                        firstMatrix.set(i, firstHorizontal.indexOf(neighbour), 1);
+                     int j=firstHorizontal.indexOf(neighbour);
+                     if (j > -1){
+                        Edge edge = graph.getEdge(firstVertical.get(i), firstHorizontal.get(j));
+                        if (edge!= null) {
+                            float w=edge.getWeight();
+                            firstMatrix.set(i, j, w);
+                       }
                     }
-                } catch (UnsupportedOperationException ex) {
+                }} catch (UnsupportedOperationException ex) {
                     System.out.println("exception");
                     // TODO - exception handler
                 }
@@ -102,9 +120,16 @@ public void run() {
             if (intersection != null && intersection.size() > 0) {
                 try {
                     intersection.retainAll(secondHorizontal);
-                    for (Node neighbour : intersection) {
-                        secondMatrix.set(i, secondHorizontal.indexOf(neighbour), 1);
-                    }
+                         for (Node neighbour : intersection) {
+                            int j=secondHorizontal.indexOf(neighbour);
+                            if (j>-1){                    
+                                Edge edge =graph.getEdge(secondVertical.get(i), secondHorizontal.get(j));
+                                 if (edge!= null) {
+                                    float w=edge.getWeight();
+                                    secondMatrix.set(i, j, w);
+                                }
+                            }
+                         }
                 } catch (UnsupportedOperationException ex) {
                     System.out.println("exception");
                     // TODO - exception handler
@@ -114,13 +139,13 @@ public void run() {
         if (cancelled) {
             return;
         }
-        Progress.progress(progressTicket, "Multiplication");
+        Progress.progress(progressTicket, "Multiplication",2);
 
         Matrix result = firstMatrix.timesParallelIndexed(secondMatrix);
         if (cancelled) {
             return;
         }
-        Progress.progress(progressTicket, "Removing nodes/edges");
+        Progress.progress(progressTicket, "Removing nodes/edges",3);
 
 
         if (removeNodes) {
@@ -150,7 +175,7 @@ public void run() {
         if (cancelled) {
             return;
         }
-        Progress.progress(progressTicket, "Creating new edges");
+        Progress.progress(progressTicket, "Creating new edges",4);
         AttributeController ac = Lookup.getDefault().lookup(AttributeController.class);
         AttributeModel model = ac.getModel();        
         AttributeColumn edgeTypeCol = model.getEdgeTable().getColumn("MMNT-EdgeType");        
@@ -162,15 +187,19 @@ public void run() {
         Edge ee = null;
         for (int i = 0; i < result.getM(); i++) {
             for (int j = 0; j < result.getN(); j++) {
-                if (graph.contains(firstVertical.get(i)) && graph.contains(secondHorizontal.get(j)) && graph.getEdge(firstVertical.get(i), secondHorizontal.get(j)) == null && result.get(i, j) > 0) {
-                    ee = graphModel.factory().newEdge(firstVertical.get(i), secondHorizontal.get(j), (float) result.get(i, j), graphModel.isDirected());
+                if (graph.contains(firstVertical.get(i)) && graph.contains(secondHorizontal.get(j)) && graph.getEdge(firstVertical.get(i), secondHorizontal.get(j)) == null && result.get(i, j) > threshold) {
+                    ee = graphModel.factory().newEdge(firstVertical.get(i), secondHorizontal.get(j), (float) result.get(i, j),this.directed );
                     if (!ee.isSelfLoop()) {
                         ee.getEdgeData().getAttributes().setValue(edgeTypeCol.getIndex(), inDimension + "<--->" + outDimension);
                         //ee.getEdgeData().setLabel(inDimension + "-" + outDimension);
                         graph.addEdge(ee);
                     }
                 }
             }
+        if (cancelled) {
+                return;
+         }
+         Progress.progress (progressTicket,i+5);
         }
         Progress.finish(progressTicket);
     }

diff --git a/src/cz/cvut/fit/gephi/multimode/MultiModeWindowTopComponent.form b/src/cz/cvut/fit/gephi/multimode/MultiModeWindowTopComponent.form
@@ -19,37 +19,45 @@
           <Group type="102" attributes="0">
               <EmptySpace max="-2" attributes="0"/>
               <Group type="103" groupAlignment="0" attributes="0">
-                  <Group type="102" attributes="0">
+                  <Group type="102" alignment="1" attributes="0">
                       <Group type="103" groupAlignment="0" attributes="0">
-                          <Component id="removeNodes" min="-2" max="-2" attributes="0"/>
-                          <Component id="removeEdges" alignment="0" min="-2" max="-2" attributes="0"/>
+                          <Component id="attributeLabel" alignment="0" min="-2" max="-2" attributes="0"/>
+                          <Component id="leftlabel" alignment="0" min="-2" max="-2" attributes="0"/>
+                          <Component id="rightLabel" alignment="0" min="-2" max="-2" attributes="0"/>
                       </Group>
+                      <EmptySpace max="-2" attributes="0"/>
+                      <Group type="103" groupAlignment="0" attributes="0">
+                          <Component id="secondMatrix" max="32767" attributes="0"/>
+                          <Component id="firstMatrix" max="32767" attributes="0"/>
+                          <Component id="attributes" max="32767" attributes="0"/>
+                      </Group>
+                  </Group>
+                  <Component id="jSeparator1" alignment="1" max="32767" attributes="0"/>
+                  <Group type="102" attributes="0">
                       <EmptySpace min="0" pref="0" max="32767" attributes="0"/>
+                      <Component id="start" min="-2" max="-2" attributes="0"/>
+                      <EmptySpace min="-2" pref="172" max="-2" attributes="0"/>
                   </Group>
                   <Group type="102" alignment="1" attributes="0">
+                      <Group type="103" groupAlignment="0" attributes="0">
+                          <Component id="removeEdges" alignment="0" min="-2" max="-2" attributes="0"/>
+                          <Component id="removeNodes" alignment="0" min="-2" max="-2" attributes="0"/>
+                      </Group>
+                      <EmptySpace pref="66" max="32767" attributes="0"/>
                       <Group type="103" groupAlignment="0" attributes="0">
                           <Group type="102" alignment="1" attributes="0">
-                              <Group type="103" groupAlignment="0" attributes="0">
-                                  <Component id="attributeLabel" alignment="0" min="-2" max="-2" attributes="0"/>
-                                  <Component id="leftlabel" alignment="0" min="-2" max="-2" attributes="0"/>
-                                  <Component id="rightLabel" alignment="0" min="-2" max="-2" attributes="0"/>
-                              </Group>
-                              <EmptySpace max="-2" attributes="0"/>
-                              <Group type="103" groupAlignment="0" attributes="0">
-                                  <Component id="secondMatrix" pref="191" max="32767" attributes="0"/>
-                                  <Component id="firstMatrix" max="32767" attributes="0"/>
-                                  <Component id="attributes" max="32767" attributes="0"/>
-                              </Group>
+                              <Component id="jLabel1" min="-2" pref="83" max="-2" attributes="0"/>
+                              <EmptySpace min="-2" pref="1" max="-2" attributes="0"/>
                           </Group>
                           <Group type="102" alignment="1" attributes="0">
-                              <EmptySpace min="0" pref="0" max="32767" attributes="0"/>
-                              <Component id="start" min="-2" max="-2" attributes="0"/>
+                              <Component id="directed" min="-2" max="-2" attributes="0"/>
+                              <EmptySpace type="unrelated" max="-2" attributes="0"/>
                           </Group>
-                          <Component id="jSeparator1" alignment="1" max="32767" attributes="0"/>
                       </Group>
-                      <EmptySpace max="-2" attributes="0"/>
+                      <Component id="threshold" min="-2" pref="71" max="-2" attributes="0"/>
                   </Group>
               </Group>
+              <EmptySpace max="-2" attributes="0"/>
           </Group>
           <Group type="102" attributes="0">
               <Group type="103" groupAlignment="0" attributes="0">
@@ -86,9 +94,20 @@
                   <Component id="rightLabel" alignment="3" min="-2" max="-2" attributes="0"/>
               </Group>
               <EmptySpace type="separate" max="-2" attributes="0"/>
-              <Component id="removeEdges" min="-2" max="-2" attributes="0"/>
-              <EmptySpace max="-2" attributes="0"/>
-              <Component id="removeNodes" min="-2" max="-2" attributes="0"/>
+              <Group type="103" groupAlignment="0" attributes="0">
+                  <Group type="102" attributes="0">
+                      <Group type="103" groupAlignment="3" attributes="0">
+                          <Component id="removeEdges" alignment="3" min="-2" max="-2" attributes="0"/>
+                          <Component id="directed" alignment="3" min="-2" max="-2" attributes="0"/>
+                      </Group>
+                      <EmptySpace max="-2" attributes="0"/>
+                      <Group type="103" groupAlignment="0" attributes="0">
+                          <Component id="removeNodes" min="-2" max="-2" attributes="0"/>
+                          <Component id="jLabel1" min="-2" max="-2" attributes="0"/>
+                      </Group>
+                  </Group>
+                  <Component id="threshold" alignment="1" min="-2" max="-2" attributes="0"/>
+              </Group>
               <EmptySpace max="-2" attributes="0"/>
               <Component id="start" min="-2" max="-2" attributes="0"/>
               <EmptySpace max="-2" attributes="0"/>
@@ -98,7 +117,7 @@
                   <Component id="graphColoring" alignment="3" min="-2" max="-2" attributes="0"/>
                   <Component id="bipartiteLabel" alignment="3" min="-2" max="-2" attributes="0"/>
               </Group>
-              <EmptySpace pref="60" max="32767" attributes="0"/>
+              <EmptySpace pref="87" max="32767" attributes="0"/>
           </Group>
       </Group>
     </DimensionLayout>
@@ -215,5 +234,30 @@
         </Property>
       </Properties>
     </Component>
+    <Component class="javax.swing.JCheckBox" name="directed">
+      <Properties>
+        <Property name="text" type="java.lang.String" editor="org.netbeans.modules.i18n.form.FormI18nStringEditor">
+          <ResourceString bundle="cz/cvut/fit/gephi/multimode/Bundle.properties" key="MultiModeWindowTopComponent.directed.text" replaceFormat="org.openide.util.NbBundle.getMessage({sourceFileName}.class, &quot;{key}&quot;)"/>
+        </Property>
+      </Properties>
+    </Component>
+    <Component class="javax.swing.JLabel" name="jLabel1">
+      <Properties>
+        <Property name="text" type="java.lang.String" editor="org.netbeans.modules.i18n.form.FormI18nStringEditor">
+          <ResourceString bundle="cz/cvut/fit/gephi/multimode/Bundle.properties" key="MultiModeWindowTopComponent.jLabel1.text" replaceFormat="org.openide.util.NbBundle.getMessage({sourceFileName}.class, &quot;{key}&quot;)"/>
+        </Property>
+      </Properties>
+    </Component>
+    <Component class="javax.swing.JTextField" name="threshold">
+      <Properties>
+        <Property name="text" type="java.lang.String" editor="org.netbeans.modules.i18n.form.FormI18nStringEditor">
+          <ResourceString bundle="cz/cvut/fit/gephi/multimode/Bundle.properties" key="MultiModeWindowTopComponent.threshold.text" replaceFormat="org.openide.util.NbBundle.getMessage({sourceFileName}.class, &quot;{key}&quot;)"/>
+        </Property>
+      </Properties>
+      <Events>
+        <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="thresholdActionPerformed"/>
+        <EventHandler event="focusLost" listener="java.awt.event.FocusListener" parameters="java.awt.event.FocusEvent" handler="thresholdFocusLost"/>
+      </Events>
+    </Component>
   </SubComponents>
 </Form>