From a2b8880fb63798af2741bb3c091d548dc597675a Mon Sep 17 00:00:00 2001
From: Philipp Spohr <spohr.philipp@web.de>
Date: Fri, 1 Sep 2017 20:20:45 +0200
Subject: [PATCH] Implemented graphic visualization of cluster in solution view
Various small fixes / stuff
---
.../de/hhu/ba/yoshikoWrapper/CyActivator.java | 5 +-
.../ba/yoshikoWrapper/core/AlgorithmTask.java | 2 +-
.../de/hhu/ba/yoshikoWrapper/core/CyCore.java | 3 +
.../graphModel/YoshikoCluster.java | 149 +++++++++++++++++-
.../graphModel/YoshikoSolution.java | 38 ++---
.../ba/yoshikoWrapper/gui/ClusterView.java | 42 ++---
.../hhu/ba/yoshikoWrapper/gui/MainPanel.java | 9 +-
src/main/resources/YoshikoStrings.properties | 1 +
8 files changed, 196 insertions(+), 53 deletions(-)
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java b/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
index aff1010..32a50c0 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
@@ -42,6 +42,7 @@ import org.cytoscape.task.visualize.ApplyVisualStyleTaskFactory;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.model.CyNetworkViewManager;
+import org.cytoscape.view.presentation.RenderingEngineFactory;
import org.cytoscape.view.vizmap.VisualMappingFunctionFactory;
import org.cytoscape.view.vizmap.VisualMappingManager;
import org.cytoscape.view.vizmap.VisualStyleFactory;
@@ -85,7 +86,9 @@ public class CyActivator extends AbstractCyActivator {
CyCore.continuousMappingFactory = getService(context,VisualMappingFunctionFactory.class, "(mapping.type=continuous)");
CyCore.rootNetworkManager = getService(context,CyRootNetworkManager.class);
CyCore.applyVisualStyleTaskFactory = getService(context,ApplyVisualStyleTaskFactory.class);
-
+ //TODO: Not sure how to infer type here
+ CyCore.renderingEngineFactory = getService(context,RenderingEngineFactory.class);
+
//Set language according to settings
LocalizationManager.switchLanguage(cm.getProperties().getProperty("locale", "enUS"));
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/core/AlgorithmTask.java b/src/main/java/de/hhu/ba/yoshikoWrapper/core/AlgorithmTask.java
index 77b7ca9..ba75280 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/AlgorithmTask.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/AlgorithmTask.java
@@ -182,7 +182,7 @@ public class AlgorithmTask extends AbstractTask {
taskMonitor.setStatusMessage("Processing entry "+(l+1)+ " of "+sizeOfCluster);
int nodeID = LibraryInterface.IntVector_get(clusterVector, l);
CyNode node = nodeMap.indexOf(nodeID); //<<< Another int/long conversion
- cluster.nodes.add(node);
+ cluster.addNode(node);
net.getRow(node).set(columnName, ""+(k+1)); //Add Cluster ID in table (Remove in final version?)
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/core/CyCore.java b/src/main/java/de/hhu/ba/yoshikoWrapper/core/CyCore.java
index 2bd7ce6..fd3c1cd 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/CyCore.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/CyCore.java
@@ -23,6 +23,7 @@ package de.hhu.ba.yoshikoWrapper.core;
import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.application.swing.CySwingApplication;
+import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkFactory;
import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.model.subnetwork.CyRootNetworkManager;
@@ -31,6 +32,7 @@ import org.cytoscape.task.visualize.ApplyVisualStyleTaskFactory;
import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.view.model.CyNetworkViewManager;
+import org.cytoscape.view.presentation.RenderingEngineFactory;
import org.cytoscape.view.vizmap.VisualMappingFunctionFactory;
import org.cytoscape.view.vizmap.VisualMappingManager;
import org.cytoscape.view.vizmap.VisualStyleFactory;
@@ -59,6 +61,7 @@ public class CyCore {
public static VisualMappingFunctionFactory continuousMappingFactory;
public static CyRootNetworkManager rootNetworkManager;
public static ApplyVisualStyleTaskFactory applyVisualStyleTaskFactory;
+ public static RenderingEngineFactory<CyNetwork> renderingEngineFactory;
//
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoCluster.java b/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoCluster.java
index 266fe60..f2e3d51 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoCluster.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoCluster.java
@@ -21,24 +21,167 @@
******************************************************************************/
package de.hhu.ba.yoshikoWrapper.graphModel;
+import java.awt.Image;
import java.util.ArrayList;
+import java.util.List;
+import javax.swing.ImageIcon;
+import javax.swing.JLabel;
+import javax.swing.SwingUtilities;
+
+import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
+import org.cytoscape.model.CyRow;
+import org.cytoscape.model.subnetwork.CyRootNetwork;
+import org.cytoscape.model.subnetwork.CySubNetwork;
+import org.cytoscape.view.layout.CyLayoutAlgorithm;
+import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.view.presentation.RenderingEngine;
+import org.cytoscape.work.Task;
+import org.cytoscape.work.TaskIterator;
+import org.cytoscape.work.TaskMonitor;
+
+import de.hhu.ba.yoshikoWrapper.core.CyCore;
+import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
+import static org.cytoscape.view.presentation.property.BasicVisualLexicon.NETWORK_HEIGHT;
+import static org.cytoscape.view.presentation.property.BasicVisualLexicon.NETWORK_WIDTH;
public class YoshikoCluster {
- public final long id;
- public final CyNetwork originalGraph;
+ private final long id;
+
+ private ArrayList<CyNode> nodes;
+ private CySubNetwork net;
+
+ //SYMBOLIC LINKS
+ private final CyNetwork originalGraph;
+
- public ArrayList<CyNode> nodes;
public YoshikoCluster(long id, CyNetwork originalGraph) {
this.id = id;
this.originalGraph = originalGraph;
this.nodes = new ArrayList<CyNode>();
}
+
+ private void createSubNetwork() {
+
+ CyRootNetwork originalGraphAsRoot = CyCore.rootNetworkManager.getRootNetwork(originalGraph);
+
+ //Create nested graph and cluster subnet
+ ArrayList<CyEdge> inducedEdges = new ArrayList<CyEdge>();
+ for (CyNode n: nodes) {
+ //Sadly Cytoscape doesnt provide a comfort function here
+ List<CyEdge> adjacentEdges = originalGraph.getAdjacentEdgeList(n, CyEdge.Type.ANY);
+ for (CyEdge e: adjacentEdges) {
+ if (nodes.contains(e.getSource()) && nodes.contains(e.getTarget())) {
+ inducedEdges.add(e);
+ }
+ }
+ }
+ CySubNetwork subnet = originalGraphAsRoot.addSubNetwork(nodes ,inducedEdges);
+
+ subnet.getRow(subnet).set(CyNetwork.NAME, LocalizationManager.get("cluster")+" "+(id+1));
+
+ net = subnet; //Save for further reference
+ }
+
+ public void select() {
+ List<CyRow> allRows = originalGraph.getDefaultNodeTable().getAllRows();
+ for (CyRow r: allRows) {
+ r.set("selected", false);
+ }
+ //Select nodes corresponding to the cluster
+ for (CyNode n : nodes) {
+ originalGraph.getRow(n).set("selected", true);
+ }
+ }
+
+
+ public void generateImage(JLabel label, int width, int height) {
+ if (net == null) {
+ createSubNetwork();
+ }
+ CyNetworkView view = CyCore.networkViewFactory.createNetworkView(net);
+
+ //layout cluster
+ CyLayoutAlgorithm layout = CyCore.layoutAlgorithmManager.getDefaultLayout();
+ TaskIterator createLayout = layout.createTaskIterator(
+ view,
+ layout.getDefaultLayoutContext(),
+ CyLayoutAlgorithm.ALL_NODE_VIEWS,
+ null
+ );
+
+ createLayout.append(
+ new Task() {
+
+ @Override
+ public void run(TaskMonitor taskMonitor) throws Exception {
+ taskMonitor.setStatusMessage("Generating cluster view for C:"+id);
+ view.setVisualProperty(NETWORK_WIDTH, new Double(width));
+ view.setVisualProperty(NETWORK_HEIGHT, new Double(height));
+ view.fitContent();
+ view.updateView();
+
+ RenderingEngine<CyNetwork> renderingEngine = CyCore.renderingEngineFactory.createRenderingEngine(label, view);
+ SwingUtilities.invokeLater(new Runnable() {
+
+ @Override
+ public void run() {
+ Image img = renderingEngine.createImage(width,height);
+ label.setIcon(new ImageIcon(img));
+
+ renderingEngine.dispose();
+ view.dispose();
+ }
+
+ });
+
+
+ }
+
+ @Override
+ public void cancel() {
+ // TODO Auto-generated method stub
+ }
+
+ }
+ );
+
+ CyCore.dialogTaskManager.execute(
+ createLayout
+ );
+
+
+ }
+
+ public int getSize() {
+ return nodes.size();
+ }
+
+ public long getID() {
+ return id;
+ }
+
+ public CySubNetwork getSubNetwork() {
+ if (net == null) {
+ createSubNetwork();
+ }
+ return net;
+ }
+
+ public void addNode(CyNode node) {
+ nodes.add(node);
+ }
+
+ public String getNodeName(CyNode n) {
+ return originalGraph.getRow(n).get("name", String.class);
+ }
+
+
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoSolution.java b/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoSolution.java
index 2b1237c..89c6788 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoSolution.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoSolution.java
@@ -23,12 +23,10 @@ package de.hhu.ba.yoshikoWrapper.graphModel;
import java.util.ArrayList;
import java.util.HashMap;
-import java.util.List;
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
-import org.cytoscape.model.subnetwork.CyRootNetwork;
import org.cytoscape.model.subnetwork.CySubNetwork;
import org.cytoscape.view.layout.CyLayoutAlgorithm;
import org.cytoscape.view.model.CyNetworkView;
@@ -68,27 +66,11 @@ public class YoshikoSolution {
//Map Cluster to Nodes for further reference
HashMap<YoshikoCluster,CyNode> map = new HashMap<YoshikoCluster,CyNode>();
- //Convert original graph to root graph to allow embedding of nodes
- CyRootNetwork originalGraphAsRoot = CyCore.rootNetworkManager.getRootNetwork(originalGraph);
//Add nodes
for (YoshikoCluster c: cluster) {
CyNode clusterNode = metaGraph.addNode();
- //Create nested graph and cluster subnet
- ArrayList<CyEdge> inducedEdges = new ArrayList<CyEdge>();
- for (CyNode n: c.nodes) {
- //Sadly Cytoscape doesnt provide a comfort function here
- List<CyEdge> adjacentEdges = originalGraph.getAdjacentEdgeList(n, CyEdge.Type.ANY);
- for (CyEdge e: adjacentEdges) {
- if (c.nodes.contains(e.getSource()) && c.nodes.contains(e.getTarget())) {
- inducedEdges.add(e);
- }
- }
- }
- CySubNetwork subnet = originalGraphAsRoot.addSubNetwork(c.nodes ,inducedEdges);
-
- subnet.getRow(subnet).set(CyNetwork.NAME, LocalizationManager.get("cluster")+" "+(c.id+1));
-
+ CySubNetwork subnet = c.getSubNetwork();
CyCore.networkManager.addNetwork(subnet);
//Create network view and register it
CyNetworkView subnetView = CyCore.networkViewFactory.createNetworkView(subnet);
@@ -104,8 +86,8 @@ public class YoshikoSolution {
);
clusterNode.setNetworkPointer(subnet);
//Set node attributes
- metaGraph.getRow(clusterNode).set("name", LocalizationManager.get("cluster")+" "+c.id);
- metaGraph.getRow(clusterNode).set("clusterSize",c.nodes.size());
+ metaGraph.getRow(clusterNode).set("name", LocalizationManager.get("cluster")+" "+c.getID());
+ metaGraph.getRow(clusterNode).set("clusterSize",c.getSize());
map.put(c, clusterNode);
}
@@ -118,12 +100,16 @@ public class YoshikoSolution {
) {
continue;
}
- clusterloop:
- for (CyNode c1n : c1.nodes) {
- for (CyNode c2n : c2.nodes) {
+ for (CyNode c1n : c1.getSubNetwork().getNodeList()) {
+ for (CyNode c2n : c2.getSubNetwork().getNodeList()) {
if (originalGraph.containsEdge(c1n, c2n) || originalGraph.containsEdge(c2n, c1n)) {
- metaGraph.addEdge(map.get(c1), map.get(c2), false);
- break clusterloop;
+ if (metaGraph.containsEdge(map.get(c1), map.get(c2))){
+ //TODO: Update weight
+ }
+ else {
+ CyEdge edge = metaGraph.addEdge(map.get(c1), map.get(c2), false);
+ metaGraph.getRow(edge).set("edgeStrength",1);
+ }
}
}
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/ClusterView.java b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/ClusterView.java
index 328fa43..91ff582 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/ClusterView.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/ClusterView.java
@@ -24,7 +24,6 @@ package de.hhu.ba.yoshikoWrapper.gui;
import java.awt.Color;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
-import java.util.List;
import javax.swing.BorderFactory;
import javax.swing.Box;
@@ -34,8 +33,9 @@ import javax.swing.JPanel;
import javax.swing.border.Border;
import org.cytoscape.model.CyNode;
-import org.cytoscape.model.CyRow;
+import org.cytoscape.util.swing.BasicCollapsiblePanel;
+import de.hhu.ba.yoshikoWrapper.core.GraphicsLoader;
import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoCluster;
@@ -44,9 +44,11 @@ public class ClusterView extends JPanel {
private final JLabel title;
private final JLabel clusterSize;
+ private final JLabel icon;
+ private final BasicCollapsiblePanel nodeList;
- private final Border regularBorder = BorderFactory.createLineBorder(Color.GRAY);
- private final Border highlightBorder = BorderFactory.createLineBorder(Color.RED);
+ private final Border regularBorder = BorderFactory.createLineBorder(Color.GRAY,3);
+ private final Border highlightBorder = BorderFactory.createLineBorder(GraphicsLoader.yoshikoGreen,3);
//SYMBOLIC LINKS
@@ -62,21 +64,28 @@ public class ClusterView extends JPanel {
//Swing init
this.setLayout(new BoxLayout(this,BoxLayout.Y_AXIS));
- title = new JLabel(LocalizationManager.get("cluster")+" "+(c.id+1));
- clusterSize = new JLabel(LocalizationManager.get("clusterSize")+" "+c.nodes.size());
-
- SwingUtil.addAll(this,title,clusterSize);
+ title = new JLabel(LocalizationManager.get("cluster")+" "+(c.getID()+1));
+ clusterSize = new JLabel(LocalizationManager.get("clusterSize")+" "+c.getSize());
+ icon = new JLabel();
+ icon.setBorder(BorderFactory.createLineBorder(Color.BLACK));
+ cluster.generateImage(icon,128, 128);
+
+ SwingUtil.addAll(this,title,clusterSize,icon);
this.add(Box.createVerticalStrut(4));
+ nodeList = new BasicCollapsiblePanel(LocalizationManager.get("nodes"));
+
//Loop over nodes in the cluster and add them to the view
- for (CyNode n : c.nodes) {
- this.add(
+ for (CyNode n : c.getSubNetwork().getNodeList()) {
+ nodeList.add(
new JLabel(
- c.originalGraph.getRow(n).get("name", String.class)
+ c.getNodeName(n)
)
);
}
+ this.add(nodeList);
+
this.addMouseListener(mouseListener);
this.setBorder(regularBorder);
@@ -90,16 +99,7 @@ public class ClusterView extends JPanel {
@Override
public void mousePressed(MouseEvent e) {
- //Undo previous selection
-
- List<CyRow> allRows = cluster.originalGraph.getDefaultNodeTable().getAllRows();
- for (CyRow r: allRows) {
- r.set("selected", false);
- }
- //Select nodes corresponding to the cluster
- for (CyNode n : cluster.nodes) {
- cluster.originalGraph.getRow(n).set("selected", true);
- }
+ cluster.select();
}
@Override
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/MainPanel.java b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/MainPanel.java
index cbfa232..806fccd 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/gui/MainPanel.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/gui/MainPanel.java
@@ -181,6 +181,7 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
*/
private ActionListener buttonListener = new ActionListener() {
+ private final TaskIterator iterator = new TaskIterator();
@Override
public void actionPerformed(ActionEvent e) {
if (YoshikoLoader.isLibraryLoaded()){
@@ -199,7 +200,13 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
opModePanel.useHeuristic(),
opModePanel.getSolCount()
);
- CyCore.dialogTaskManager.execute(new TaskIterator(1,yoshiko));
+ /**
+ * Don't queue multiple runs at once because that will get messy
+ */
+ if (!iterator.hasNext()) {
+ iterator.append(yoshiko);
+ CyCore.dialogTaskManager.execute(iterator);
+ }
}
else {
JOptionPane.showMessageDialog(
diff --git a/src/main/resources/YoshikoStrings.properties b/src/main/resources/YoshikoStrings.properties
index fa80efd..d7ed53d 100644
--- a/src/main/resources/YoshikoStrings.properties
+++ b/src/main/resources/YoshikoStrings.properties
@@ -52,3 +52,4 @@ switchLanguage = Plugin language
icTooltip = This value is used to determine what the algorithm pays when inserting an edge. Existing mappings overwrite this value. A higher value means that the algorithm is less likely to insert edges in order to generate a cluster.
operationMode = Operation Mode
run = Perform Algorithm
+nodes = Nodes
--
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