From de17a6ef391910a37c6d207d27fc393f8e684b48 Mon Sep 17 00:00:00 2001
From: Philipp Spohr <spohr.philipp@web.de>
Date: Fri, 15 Sep 2017 18:43:43 +0200
Subject: [PATCH] Some work on invalidating a result upon change in the
original graph
---
.../graphModel/YoshikoCluster.java | 55 ++++---
.../graphModel/YoshikoResult.java | 59 ++++++--
.../graphModel/YoshikoSolution.java | 35 ++---
.../swing/components/ClusterView.java | 40 +++---
.../swing/components/ClusterViewList.java | 28 ++++
.../swing/components/ResultPanel.java | 135 ++++++++++++++----
.../swing/components/SolutionTab.java | 120 ++++++++++------
.../yoshikoWrapper/tasks/AlgorithmTask.java | 17 +--
.../tasks/CreateClusterViews.java | 52 +++++++
.../tasks/CreateMetaGraphTask.java | 10 +-
src/main/resources/YoshikoStrings.properties | 5 +
11 files changed, 401 insertions(+), 155 deletions(-)
create mode 100644 src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateClusterViews.java
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 0292e61..6495bbe 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoCluster.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoCluster.java
@@ -23,6 +23,7 @@ package de.hhu.ba.yoshikoWrapper.graphModel;
import java.awt.Image;
import java.util.ArrayList;
+import java.util.Comparator;
import java.util.List;
import javax.swing.ImageIcon;
@@ -57,41 +58,63 @@ public class YoshikoCluster {
private final long id;
private ArrayList<CyNode> nodes;
- private CySubNetwork net;
private Image img;
//SYMBOLIC LINKS
- private final CyNetwork originalGraph;
+ private final YoshikoSolution solution;
private Logger logger = YoshikoLogger.getInstance().getLogger();
+ //STATICS
- public YoshikoCluster(long id, CyNetwork originalGraph) {
+ public static Comparator<YoshikoCluster> lessThanComparator = new Comparator<YoshikoCluster>() {
+
+ @Override
+ public int compare(YoshikoCluster o1, YoshikoCluster o2) {
+ if (o1.getSize() == o2.getSize()) {
+ return 0;
+ }
+ else if(o1.getSize() < o2.getSize()) {
+ return 1;
+ }
+ return -1;
+ }
+
+ };
+
+
+ public YoshikoCluster(YoshikoSolution solution, long id) {
this.id = id;
- this.originalGraph = originalGraph;
+ this.solution = solution;
this.nodes = new ArrayList<CyNode>();
}
- public void createSubNetwork() {
+ /**
+ * Generates a subgraph for this cluster by choosing the nodes and induced edges from the original graph
+ * @return
+ */
+ public CySubNetwork getSubNetwork() {
- CyRootNetwork originalGraphAsRoot = CyCore.rootNetworkManager.getRootNetwork(originalGraph);
+ CyRootNetwork originalGraphAsRoot =
+ CyCore.rootNetworkManager.getRootNetwork(solution.getOriginalGraph());
//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);
+ List<CyEdge> adjacentEdges = solution.getOriginalGraph().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
+ return subnet;
}
/**
@@ -99,13 +122,13 @@ public class YoshikoCluster {
*/
public void highlightInOriginalGraph() {
try {
- List<CyRow> allRows = originalGraph.getDefaultNodeTable().getAllRows();
+ List<CyRow> allRows = solution.getOriginalGraph().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);
+ solution.getOriginalGraph().getRow(n).set("selected", true);
}
}
catch (Exception e) {
@@ -116,10 +139,6 @@ public class YoshikoCluster {
public void applyImage(JLabel label, int width, int height) throws Exception {
- if (net == null) {
- throw new Exception("Can't have an image without having a network associated");
- }
-
if (img != null) {
label.setIcon(new ImageIcon(img));
}
@@ -129,7 +148,7 @@ public class YoshikoCluster {
}
private void getImage(int width, int height,JLabel label) {
- final CyNetworkView view = CyCore.networkViewFactory.createNetworkView(net);
+ final CyNetworkView view = CyCore.networkViewFactory.createNetworkView(getSubNetwork());
//layout cluster
final CyLayoutAlgorithm layout = CyCore.layoutAlgorithmManager.getDefaultLayout();
@@ -188,16 +207,12 @@ public class YoshikoCluster {
return id;
}
- public CySubNetwork getSubNetwork() {
- return net;
- }
-
public void addNode(CyNode node) {
nodes.add(node);
}
public String getNodeName(CyNode n) {
- return originalGraph.getRow(n).get("name", String.class);
+ return solution.getOriginalGraph().getRow(n).get("name", String.class);
}
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoResult.java b/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoResult.java
index cc8b34e..c3247f1 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoResult.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoResult.java
@@ -1,16 +1,16 @@
/*******************************************************************************
* Copyright (C) 2017 Philipp Spohr
- *
+ *
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
- *
+ *
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
- *
+ *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
@@ -23,22 +23,59 @@ package de.hhu.ba.yoshikoWrapper.graphModel;
import java.util.ArrayList;
+import org.cytoscape.model.CyNetwork;
+
import de.hhu.ba.yoshikoWrapper.swig.SolutionFlags;
/**Basic data class that represents a CES instance internally. By using this class the C++ resources can be freed upon retrieval.
- *
*
*/
public class YoshikoResult {
-
- public ArrayList<YoshikoSolution> solutions;
-
- public SolutionFlags flags;
-
- public YoshikoResult() {
+ private CyNetwork originalGraph;
+
+ private ArrayList<YoshikoSolution> solutions;
+
+ private SolutionFlags flags;
+
+
+ public YoshikoResult(CyNetwork net, SolutionFlags flags) {
solutions = new ArrayList<YoshikoSolution>();
- }
+
+ this.originalGraph = net;
+ this.flags = flags;
+ }
+
+ public void dispose() {
+ flags.delete();
+ originalGraph.dispose();
+ }
+
+
+ //___________SETTER GETTER_____________//
+
+ /**
+ * @return the flags asspciated with this result
+ */
+ public SolutionFlags getFlags() {
+ return flags;
+ }
+
+
+ public void addSolution(YoshikoSolution solution) {
+ solutions.add(solution);
+ }
+
+
+ public ArrayList<YoshikoSolution> getSolutions() {
+ return solutions;
+ }
+
+
+ public CyNetwork getOriginalGraph() {
+ return originalGraph;
+ }
+
}
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 f351f01..bf4a8a1 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoSolution.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoSolution.java
@@ -22,52 +22,29 @@
package de.hhu.ba.yoshikoWrapper.graphModel;
import java.util.ArrayList;
-import java.util.HashMap;
-import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
-import org.cytoscape.model.CyNode;
-import org.cytoscape.model.CyEdge.Type;
-
-import org.cytoscape.model.subnetwork.CySubNetwork;
-import org.cytoscape.view.layout.CyLayoutAlgorithm;
-import org.cytoscape.view.model.CyNetworkView;
-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 de.hhu.ba.yoshikoWrapper.cytoUtil.StyleManager;
public class YoshikoSolution {
- /**
- * The original Graph from which the solution was generated.
- * NOTE: This can be destroyed or modified during runtime while the solution still exists and may become invalid
- */
- private final CyNetwork originalGraph;
+ private final YoshikoResult result;
public ArrayList<YoshikoCluster> cluster;
private final long id;
- public YoshikoSolution(CyNetwork originalGraph, long id) {
+ public YoshikoSolution(YoshikoResult yoshikoResult, long id) {
cluster = new ArrayList<YoshikoCluster>();
- this.originalGraph = originalGraph;
+ this.result = yoshikoResult;
this.id = id;
}
//_____________GETTER / SETTER ________________//
- public ArrayList<YoshikoCluster> getCluster() {
+ public ArrayList<YoshikoCluster> getClusters() {
return cluster;
}
- public CyNetwork getOriginalGraph() {
- return originalGraph;
- }
-
/**
* @return the id
*/
@@ -75,4 +52,8 @@ public class YoshikoSolution {
return id;
}
+ public CyNetwork getOriginalGraph() {
+ return result.getOriginalGraph();
+ }
+
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ClusterView.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ClusterView.java
index 3259160..ea067d9 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ClusterView.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ClusterView.java
@@ -25,13 +25,10 @@ import static javax.swing.GroupLayout.DEFAULT_SIZE;
import static javax.swing.GroupLayout.PREFERRED_SIZE;
import java.awt.Color;
-import java.awt.Dimension;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import javax.swing.BorderFactory;
-import javax.swing.Box;
-import javax.swing.BoxLayout;
import javax.swing.GroupLayout;
import javax.swing.JLabel;
import javax.swing.JPanel;
@@ -49,28 +46,34 @@ import de.hhu.ba.yoshikoWrapper.swing.SwingUtil;
@SuppressWarnings("serial")
public class ClusterView extends JPanel {
+ //MACRO / STATIC
private final static int CLUSTER_ICON_SIZE = 128;
+ private static final Border regularBorder = BorderFactory.createLineBorder(Color.GRAY,3);
+ private static final Border highlightBorder = BorderFactory.createLineBorder(GraphicsLoader.yoshikoGreen,3);
+ private static final Border selectedBorder = BorderFactory.createLineBorder(Color.BLUE,3);
+
+ //SWING COMPONENTS
+
private final JLabel title;
private final JLabel clusterSize;
private final JLabel icon;
private final BasicCollapsiblePanel nodeList;
- private final Border regularBorder = BorderFactory.createLineBorder(Color.GRAY,3);
- private final Border highlightBorder = BorderFactory.createLineBorder(GraphicsLoader.yoshikoGreen,3);
- private final Border selectedBorder = BorderFactory.createLineBorder(Color.BLUE,3);
+ //INTERNAL
+
+ private boolean isSelected;
//SYMBOLIC LINKS
- /**Simple array list containing references to the nodes that are represented by this cluster view
- *
- */
private YoshikoCluster cluster;
public ClusterView(YoshikoCluster c) throws Exception {
this.cluster = c;
+ this.isSelected = false;
+
//Swing init
title = new JLabel(LocalizationManager.get("cluster")+" "+(c.getID()+1));
@@ -108,7 +111,7 @@ public class ClusterView extends JPanel {
.addComponent(title,DEFAULT_SIZE,DEFAULT_SIZE,PREFERRED_SIZE)
.addComponent(clusterSize,DEFAULT_SIZE,DEFAULT_SIZE,PREFERRED_SIZE)
)
- .addGap(6)
+ .addGap(12)
.addComponent(icon)
)
.addComponent(nodeList)
@@ -119,7 +122,7 @@ public class ClusterView extends JPanel {
.addComponent(title)
.addComponent(clusterSize)
)
- .addGap(6)
+ .addGap(12)
.addComponent(icon)
)
.addComponent(nodeList)
@@ -132,24 +135,25 @@ public class ClusterView extends JPanel {
private MouseListener mouseListener = new MouseListener() {
@Override
- public void mouseClicked(MouseEvent e) {}
-
- @Override
- public void mousePressed(MouseEvent e) {
- cluster.highlightInOriginalGraph();
+ public void mouseClicked(MouseEvent e) {
+ isSelected = !isSelected;
+ setBorder(isSelected ? selectedBorder : regularBorder);
}
+ @Override
+ public void mousePressed(MouseEvent e) {}
@Override
public void mouseReleased(MouseEvent e) {}
@Override
public void mouseEntered(MouseEvent e) {
- setBorder(highlightBorder);
+ cluster.highlightInOriginalGraph();
+ setBorder(isSelected ? selectedBorder : highlightBorder);
}
@Override
public void mouseExited(MouseEvent e) {
- setBorder(regularBorder);
+ setBorder(isSelected ? selectedBorder : regularBorder);
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ClusterViewList.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ClusterViewList.java
index 396439f..ad45bb5 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ClusterViewList.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ClusterViewList.java
@@ -1,14 +1,22 @@
package de.hhu.ba.yoshikoWrapper.swing.components;
+import java.awt.Component;
import java.awt.Dimension;
import java.awt.Rectangle;
+import java.util.ArrayList;
import javax.swing.JPanel;
import javax.swing.Scrollable;
+import org.slf4j.Logger;
+
+import de.hhu.ba.yoshikoWrapper.logging.YoshikoLogger;
+
@SuppressWarnings("serial")
public class ClusterViewList extends JPanel implements Scrollable {
+ private static final Logger logger = YoshikoLogger.getInstance().getLogger();
+
@Override
public Dimension getPreferredScrollableViewportSize() {
return this.getPreferredSize();
@@ -34,4 +42,24 @@ public class ClusterViewList extends JPanel implements Scrollable {
return false;
}
+ @Override
+ public ClusterView add(Component c) throws NullPointerException{
+ //Simple type check
+ if (c instanceof ClusterView) {
+ return (ClusterView) super.add(c);
+ }
+ logger.error("Attempted to add a component to ClusterViewList that is not a ClusterView");
+ return null;
+ }
+
+ public ArrayList<ClusterView> getClusterViews() {
+ ArrayList<ClusterView> ret = new ArrayList<ClusterView>();
+ for (Component c : this.getComponents()) {
+ if (c instanceof ClusterView) {
+ ret.add((ClusterView)c);
+ }
+ }
+ return ret;
+ }
+
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ResultPanel.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ResultPanel.java
index 928ffd5..1395910 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ResultPanel.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ResultPanel.java
@@ -25,9 +25,10 @@ import static javax.swing.GroupLayout.*;
import java.awt.Color;
import java.awt.Component;
-import java.awt.Dimension;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.util.ArrayList;
+import java.util.Properties;
import javax.swing.BoxLayout;
import javax.swing.GroupLayout;
@@ -41,6 +42,18 @@ import javax.swing.JTabbedPane;
import org.cytoscape.application.swing.CytoPanelComponent;
import org.cytoscape.application.swing.CytoPanelName;
+import org.cytoscape.event.AbstractCyEvent;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.events.AboutToRemoveEdgesEvent;
+import org.cytoscape.model.events.AboutToRemoveEdgesListener;
+import org.cytoscape.model.events.AboutToRemoveNodesEvent;
+import org.cytoscape.model.events.AboutToRemoveNodesListener;
+import org.cytoscape.model.events.AddedEdgesEvent;
+import org.cytoscape.model.events.AddedEdgesListener;
+import org.cytoscape.model.events.AddedNodesEvent;
+import org.cytoscape.model.events.AddedNodesListener;
+import org.cytoscape.model.events.NetworkAboutToBeDestroyedEvent;
+import org.cytoscape.model.events.NetworkAboutToBeDestroyedListener;
import org.cytoscape.util.swing.BasicCollapsiblePanel;
import de.hhu.ba.yoshikoWrapper.core.CyCore;
@@ -54,13 +67,27 @@ import de.hhu.ba.yoshikoWrapper.swing.SwingUtil;
* Conforms to CY 3.5 by being a CytoPanelComponent which is the norm for "result" panels
*/
@SuppressWarnings("serial")//Will never be serialized
-public class ResultPanel extends JPanel implements CytoPanelComponent{
+public class ResultPanel extends JPanel implements CytoPanelComponent,
+//Implements listeners to invalidate results when the graph the result was generated for changes
+AboutToRemoveEdgesListener,
+AboutToRemoveNodesListener,
+AddedEdgesListener,
+AddedNodesListener,
+NetworkAboutToBeDestroyedListener
+{
+
+ //MACRO
+
+ private static final int HACKFIX_FIXED_WIDTH = 128+256;
+
+ private final JTabbedPane tabbedPane;
- private final JTabbedPane solutionTabs;
private final JButton destroyButton;
private BasicCollapsiblePanel marker;
+ private final JLabel invalidLabel;
+ private ArrayList<SolutionTab> solutionTabs;
private final YoshikoResult result;
public ResultPanel(YoshikoResult result) throws Exception {
@@ -68,17 +95,21 @@ public class ResultPanel extends JPanel implements CytoPanelComponent{
this.result = result;
//Init subcomponents
- solutionTabs = new JTabbedPane();
- for (YoshikoSolution s : result.solutions) {
- addSolutionTab(s);
- }
-
- if (result.flags.getIlpGenerated()) {
- System.out.println("Setting up ILP Info Marker");
+ invalidLabel = new JLabel();
+ tabbedPane = new JTabbedPane();
+ for (YoshikoSolution s : result.getSolutions()) {
+ SolutionTab tab = new SolutionTab(s);
+ tabbedPane.add(
+ LocalizationManager.get("solution")+" "+(s.getId()+1),
+ tab
+ ); }
+
+ if (result.getFlags().getIlpGenerated()) {
+ //TODO: Move to MarkerPanel for better codestyle
//Optional Markers
marker = new BasicCollapsiblePanel(LocalizationManager.get("ilpMarker"));
marker.setLayout(new BoxLayout(marker,BoxLayout.Y_AXIS));
- if(result.flags.getOptimal()) {
+ if(result.getFlags().getOptimal()) {
JLabel optimalLabel;
optimalLabel = new JLabel(LocalizationManager.get("optimal"));
optimalLabel.setForeground(GraphicsLoader.yoshikoGreen);
@@ -89,12 +120,12 @@ public class ResultPanel extends JPanel implements CytoPanelComponent{
optimalLabel = new JLabel(LocalizationManager.get("notOptimal"));
optimalLabel.setForeground(Color.RED);
marker.add(optimalLabel);
- marker.add(new JLabel(result.flags.getSolvedInstances()+"/"+result.flags.getReducedInstances()+" "+LocalizationManager.get("redSolved")));
- marker.add(new JLabel(LocalizationManager.get("lastInstanceGap")+" "+(int)(100*result.flags.getLastGap())+"%"));
+ marker.add(new JLabel(result.getFlags().getSolvedInstances()+"/"+result.getFlags().getReducedInstances()+" "+LocalizationManager.get("redSolved")));
+ marker.add(new JLabel(LocalizationManager.get("lastInstanceGap")+" "+(int)(100*result.getFlags().getLastGap())+"%"));
}
- JLabel costLabel = new JLabel(LocalizationManager.get("cost")+" "+result.flags.getTotalCost());
+ JLabel costLabel = new JLabel(LocalizationManager.get("cost")+" "+result.getFlags().getTotalCost());
marker.add(costLabel);
- if (result.flags.getTimedOut()) {
+ if (result.getFlags().getTimedOut()) {
marker.add(new JLabel(LocalizationManager.get("timeoutMarker")));
}
marker.setCollapsed(false);
@@ -111,7 +142,7 @@ public class ResultPanel extends JPanel implements CytoPanelComponent{
});
- SwingUtil.addAll(this,solutionTabs,destroyButton);
+ SwingUtil.addAll(this,invalidLabel,tabbedPane,destroyButton);
//Layout
GroupLayout layout = new GroupLayout(this);
@@ -122,16 +153,18 @@ public class ResultPanel extends JPanel implements CytoPanelComponent{
layout.setHorizontalGroup(horizontalGroup);
layout.setVerticalGroup(verticalGroup);
- if (result.flags.getIlpGenerated()) {
+ if (result.getFlags().getIlpGenerated()) {
horizontalGroup.addComponent(marker,DEFAULT_SIZE,DEFAULT_SIZE,DEFAULT_SIZE);
verticalGroup.addComponent(marker,DEFAULT_SIZE,DEFAULT_SIZE,PREFERRED_SIZE);
}
horizontalGroup
- .addComponent(solutionTabs,DEFAULT_SIZE, DEFAULT_SIZE,Short.MAX_VALUE)
+ .addComponent(invalidLabel,HACKFIX_FIXED_WIDTH, PREFERRED_SIZE,Short.MAX_VALUE)
+ .addComponent(tabbedPane,HACKFIX_FIXED_WIDTH, PREFERRED_SIZE,Short.MAX_VALUE)
.addComponent(destroyButton,DEFAULT_SIZE, DEFAULT_SIZE,DEFAULT_SIZE);
verticalGroup
- .addComponent(solutionTabs,DEFAULT_SIZE, DEFAULT_SIZE,PREFERRED_SIZE)
+ .addComponent(invalidLabel,DEFAULT_SIZE, DEFAULT_SIZE,PREFERRED_SIZE)
+ .addComponent(tabbedPane,DEFAULT_SIZE, DEFAULT_SIZE,PREFERRED_SIZE)
.addComponent(destroyButton,DEFAULT_SIZE, DEFAULT_SIZE,PREFERRED_SIZE);
layout.setAutoCreateGaps(true);
@@ -139,7 +172,17 @@ public class ResultPanel extends JPanel implements CytoPanelComponent{
this.setLayout(layout);
- this.setPreferredSize(new Dimension(this.getPreferredSize().width*2,this.getPreferredSize().height));
+
+ registerAllListeners();
+
+ }
+
+ private void registerAllListeners() {
+ CyCore.registrar.registerService(this, AboutToRemoveEdgesListener.class, new Properties());
+ CyCore.registrar.registerService(this, AboutToRemoveNodesListener.class, new Properties());
+ CyCore.registrar.registerService(this, AddedEdgesListener.class, new Properties());
+ CyCore.registrar.registerService(this, AddedNodesListener.class, new Properties());
+ CyCore.registrar.registerService(this, NetworkAboutToBeDestroyedListener.class, new Properties());
}
public void deleteSolution() {
@@ -152,20 +195,29 @@ public class ResultPanel extends JPanel implements CytoPanelComponent{
if (dialogResult != JOptionPane.YES_OPTION) {
return;
}
-
+ result.dispose();
CyCore.registrar.unregisterService(this,CytoPanelComponent.class);
removeAll();
super.setVisible(false);
}
- private void addSolutionTab(YoshikoSolution s) throws Exception {
- SolutionTab tab = new SolutionTab(s);
- solutionTabs.add(
- LocalizationManager.get("solution")+" "+(s.getId()+1),
- tab
- );
+ private void invalidateResult() {
+ invalidLabel.setText(LocalizationManager.get("invalidated"));
+ invalidLabel.setForeground(Color.RED);
+ for (SolutionTab t: solutionTabs) {
+ t.invalidateResult();
+ }
+ }
+
+
+ private void invalidateIfRelevant(AbstractCyEvent<CyNetwork> e) {
+ if (e.getSource() == result.getOriginalGraph()) {
+ invalidateResult();
+ }
}
+ //______________SETTER/GETTER_______________//
+
@Override
public Component getComponent() {
return this;
@@ -190,4 +242,33 @@ public class ResultPanel extends JPanel implements CytoPanelComponent{
return result;
}
+
+ //LISTENER METHODS
+
+ @Override
+ public void handleEvent(NetworkAboutToBeDestroyedEvent e) {
+ if (e.getNetwork() == result.getOriginalGraph()) {
+ invalidate();
+ }
+ }
+ @Override
+ public void handleEvent(AddedNodesEvent e) {
+ invalidateIfRelevant(e);
+ }
+
+ @Override
+ public void handleEvent(AddedEdgesEvent e) {
+ invalidateIfRelevant(e);
+ }
+
+ @Override
+ public void handleEvent(AboutToRemoveNodesEvent e) {
+ invalidateIfRelevant(e);
+ }
+
+ @Override
+ public void handleEvent(AboutToRemoveEdgesEvent e) {
+ invalidateIfRelevant(e);
+ }
+
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/SolutionTab.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/SolutionTab.java
index 6506fe0..6d22d6c 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/SolutionTab.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/SolutionTab.java
@@ -22,15 +22,12 @@
package de.hhu.ba.yoshikoWrapper.swing.components;
import static javax.swing.GroupLayout.DEFAULT_SIZE;
+
import static javax.swing.GroupLayout.PREFERRED_SIZE;
-import java.awt.Dimension;
-import java.awt.ScrollPane;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
-import java.util.Comparator;
-import javax.swing.BoxLayout;
import javax.swing.GroupLayout;
import javax.swing.GroupLayout.Alignment;
import javax.swing.GroupLayout.Group;
@@ -47,68 +44,76 @@ import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoCluster;
import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoSolution;
import de.hhu.ba.yoshikoWrapper.swing.SwingUtil;
+import de.hhu.ba.yoshikoWrapper.tasks.CreateClusterViews;
import de.hhu.ba.yoshikoWrapper.tasks.CreateMetaGraphTask;
-
+/**
+ * Swing Component, that represents one solution of a Yoshiko result and displays it
+ *
+ */
@SuppressWarnings("serial")
public class SolutionTab extends JPanel {
+ //SWING COMPONENTS
+
private final JScrollPane scrollPane;
private final ClusterViewList scrollPaneContent;
private final JLabel clusterCount;
+ private final JButton createClusterView;
private final JButton createMetaGraph;
+ //SWING LAYOUT OBJECTS
+ private final GroupLayout layout;
+ private final GroupLayout scrollLayout;
+ private final Group horizontalGroup_scrollLayout;
+ private final Group verticalGroup_scrollLayout;
+
+ //SYMBOLIC LINKS
+
private final YoshikoSolution solution;
+ /**
+ * Basic constructor, creates a new SolutionTab representing a given YoshikoSolution.
+ * @param s The solution that is to be displayed by this tab
+ * @throws Exception
+ */
public SolutionTab(YoshikoSolution s) throws Exception {
+ //Save abstract solution object for reference
this.solution = s;
- //init swing components
+ //Declaration of Swing Components
scrollPaneContent = new ClusterViewList();
- //Sort cluster by size, descending
- solution.cluster.sort(new Comparator<YoshikoCluster>() {
-
- @Override
- public int compare(YoshikoCluster o1, YoshikoCluster o2) {
- if (o1.getSize() == o2.getSize()) {
- return 0;
- }
- else if(o1.getSize() < o2.getSize()) {
- return 1;
- }
- return -1;
- }
-
- });
-
- GroupLayout scrollLayout = new GroupLayout(scrollPaneContent);
- scrollLayout.setAutoCreateContainerGaps(true);
- scrollLayout.setAutoCreateGaps(true);
-
- Group horizontalGroup = scrollLayout.createParallelGroup();
- Group verticalGroup = scrollLayout.createSequentialGroup();
-
for (YoshikoCluster c: solution.cluster) {
ClusterView clusterView = new ClusterView(c);
scrollPaneContent.add(clusterView);
- horizontalGroup.addComponent(clusterView);
- verticalGroup.addComponent(clusterView);
}
- scrollLayout.setHorizontalGroup(horizontalGroup);
- scrollLayout.setVerticalGroup(verticalGroup);
+ scrollPane = new JScrollPane(scrollPaneContent);
- scrollPaneContent.setLayout(scrollLayout);
+ clusterCount = new JLabel(LocalizationManager.get("clusterFound")+" "+s.cluster.size());
- scrollPane = new JScrollPane(scrollPaneContent);
+ createClusterView = new JButton(LocalizationManager.get("createClusterView"));
+ createMetaGraph = new JButton(LocalizationManager.get("createMetaGraph"));
+
+ //Configuration of Swing Components
scrollPane.setHorizontalScrollBarPolicy(ScrollPaneConstants.HORIZONTAL_SCROLLBAR_NEVER);
scrollPane.setVerticalScrollBarPolicy(ScrollPaneConstants.VERTICAL_SCROLLBAR_ALWAYS);
- clusterCount = new JLabel(LocalizationManager.get("clusterFound")+" "+s.cluster.size());
+ createClusterView.addActionListener(new ActionListener() {
+
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ CyCore.dialogTaskManager.execute(
+ new TaskIterator(1,
+ new CreateClusterViews(solution.getClusters())
+ )
+ );
+ }
+
+ });
- createMetaGraph = new JButton(LocalizationManager.get("createMetaGraph"));
createMetaGraph.addActionListener(new ActionListener() {
@Override
@@ -121,22 +126,57 @@ public class SolutionTab extends JPanel {
}
});
- SwingUtil.addAll(this,clusterCount,scrollPane,createMetaGraph);
+
+ //Add configured Swing Components to self
+
+ SwingUtil.addAll(this,clusterCount,scrollPane,createClusterView,createMetaGraph);
//Layout
- GroupLayout layout = new GroupLayout(this);
- layout.setHorizontalGroup(layout.createParallelGroup(Alignment.LEADING,true)
+
+ scrollLayout = new GroupLayout(scrollPaneContent);
+
+ horizontalGroup_scrollLayout = scrollLayout.createParallelGroup();
+ verticalGroup_scrollLayout = scrollLayout.createSequentialGroup();
+
+ scrollLayout.setHorizontalGroup(horizontalGroup_scrollLayout);
+ scrollLayout.setVerticalGroup(verticalGroup_scrollLayout);
+
+ scrollLayout.setAutoCreateContainerGaps(true);
+ scrollLayout.setAutoCreateGaps(true);
+
+ for (ClusterView v: scrollPaneContent.getClusterViews()) {
+ horizontalGroup_scrollLayout.addComponent(v);
+ verticalGroup_scrollLayout.addComponent(v);
+ }
+
+ scrollPaneContent.setLayout(scrollLayout);
+
+ layout = new GroupLayout(this);
+
+ layout.setHorizontalGroup(layout.createParallelGroup(Alignment.CENTER,true)
+ .addGap(8)
.addComponent(clusterCount,DEFAULT_SIZE,DEFAULT_SIZE,DEFAULT_SIZE)
+ .addGap(8)
.addComponent(scrollPane,PREFERRED_SIZE,DEFAULT_SIZE,Short.MAX_VALUE)
+ .addComponent(createClusterView,DEFAULT_SIZE,DEFAULT_SIZE,DEFAULT_SIZE)
.addComponent(createMetaGraph,DEFAULT_SIZE,DEFAULT_SIZE,DEFAULT_SIZE)
);
layout.setVerticalGroup(layout.createSequentialGroup()
+ .addGap(8)
.addComponent(clusterCount,DEFAULT_SIZE,DEFAULT_SIZE,DEFAULT_SIZE)
+ .addGap(8)
.addComponent(scrollPane,DEFAULT_SIZE,DEFAULT_SIZE,DEFAULT_SIZE)
+ .addComponent(createClusterView,DEFAULT_SIZE,DEFAULT_SIZE,DEFAULT_SIZE)
.addComponent(createMetaGraph,DEFAULT_SIZE,DEFAULT_SIZE,DEFAULT_SIZE)
);
this.setLayout(layout);
}
+ public void invalidateResult() {
+ createClusterView.setEnabled(false);
+ createMetaGraph.setEnabled(false);
+ }
+
+
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/AlgorithmTask.java b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/AlgorithmTask.java
index 787ee1c..fbe450f 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/AlgorithmTask.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/AlgorithmTask.java
@@ -143,17 +143,17 @@ public class AlgorithmTask extends AbstractTask {
long numberOfSolutions = result.getNumberOfSolutions();
- taskMonitor.setStatusMessage("Found: "+numberOfSolutions+" solutions!"); //TODO localize
-
- YoshikoResult yoshikoResult = new YoshikoResult();
- yoshikoResult.flags = result.getFlags();
+ taskMonitor.setStatusMessage("Found: "+numberOfSolutions+" solutions!"); //TODO: Localize
+ YoshikoResult yoshikoResult = new YoshikoResult(net,result.getFlags());
//Loop over (multiple) solutions
for (long i=0;i<numberOfSolutions;i++) {
taskMonitor.setStatusMessage("Processing solution "+(i+1)+" of "+numberOfSolutions);
- YoshikoSolution solution = new YoshikoSolution(net,i);
+
+ YoshikoSolution solution = new YoshikoSolution(yoshikoResult,i);
+
String columnName = SOLUTION_COLUMN_PREFIX+(i+1);
net.getDefaultNodeTable().deleteColumn(columnName);
@@ -165,7 +165,7 @@ public class AlgorithmTask extends AbstractTask {
//Loop over cluster
for (long k=0;k<numberOfClusters;k++) {
//Create java instance
- YoshikoCluster cluster = new YoshikoCluster(k,net);
+ YoshikoCluster cluster = new YoshikoCluster(solution,k);
taskMonitor.setStatusMessage("Processing cluster "+(k+1)+" of "+numberOfClusters);
@@ -181,12 +181,13 @@ public class AlgorithmTask extends AbstractTask {
net.getRow(node).set(columnName, ""+(k+1)); //Add Cluster ID in table (Remove in final version?)
}
- cluster.createSubNetwork();
//Register cluster with solution for further reference
solution.cluster.add(cluster);
}
+ //Sort clusters by size, descending as the biggest clusters are usually the most relevant
+ solution.cluster.sort(YoshikoCluster.lessThanComparator);
//Register solution with result for further reference
- yoshikoResult.solutions.add(solution);
+ yoshikoResult.addSolution(solution);
}
taskMonitor.setProgress(0.99);
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateClusterViews.java b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateClusterViews.java
new file mode 100644
index 0000000..a681836
--- /dev/null
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateClusterViews.java
@@ -0,0 +1,52 @@
+package de.hhu.ba.yoshikoWrapper.tasks;
+
+import java.util.ArrayList;
+
+import org.cytoscape.model.subnetwork.CySubNetwork;
+import org.cytoscape.view.layout.CyLayoutAlgorithm;
+import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.work.Task;
+import org.cytoscape.work.TaskMonitor;
+
+import de.hhu.ba.yoshikoWrapper.core.CyCore;
+import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
+import de.hhu.ba.yoshikoWrapper.cytoUtil.StyleManager;
+import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoCluster;
+
+public class CreateClusterViews implements Task {
+
+ private ArrayList<YoshikoCluster> clusters;
+
+ public CreateClusterViews(ArrayList<YoshikoCluster> clusters) {
+ this.clusters = clusters;
+ }
+
+ @Override
+ public void run(TaskMonitor taskMonitor) throws Exception {
+ CyLayoutAlgorithm layout = CyCore.layoutAlgorithmManager.getDefaultLayout();
+ for (YoshikoCluster c : clusters) {
+ CySubNetwork subnet = c.getSubNetwork();
+ taskMonitor.setStatusMessage(LocalizationManager.get("status_createCV")+" "+(c.getID()+1));
+ CyCore.networkManager.addNetwork(subnet);
+ //Create network view and register it
+ CyNetworkView subnetView = CyCore.networkViewFactory.createNetworkView(subnet);
+ //layout cluster
+ CyCore.dialogTaskManager.execute(
+ layout.createTaskIterator(
+ subnetView,
+ layout.getDefaultLayoutContext(),
+ CyLayoutAlgorithm.ALL_NODE_VIEWS,
+ null
+ )
+ );
+
+ StyleManager.style(subnetView,CyCore.visualMappingManager.getCurrentVisualStyle());
+
+ CyCore.networkViewManager.addNetworkView(subnetView);
+ }
+ }
+
+ @Override
+ public void cancel() {}
+
+}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateMetaGraphTask.java b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateMetaGraphTask.java
index 0eb0e0e..b5fd244 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateMetaGraphTask.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateMetaGraphTask.java
@@ -45,10 +45,12 @@ public class CreateMetaGraphTask extends AbstractTask {
//Add nodes
- for (YoshikoCluster c: solution.getCluster()) {
+ for (YoshikoCluster c: solution.getClusters()) {
CyNode clusterNode = metaGraph.addNode();
CySubNetwork subnet = c.getSubNetwork();
+
+ taskMonitor.setStatusMessage(LocalizationManager.get("status_createCV")+" "+(c.getID()+1));
CyCore.networkManager.addNetwork(subnet);
//Create network view and register it
CyNetworkView subnetView = CyCore.networkViewFactory.createNetworkView(subnet);
@@ -72,10 +74,10 @@ public class CreateMetaGraphTask extends AbstractTask {
metaGraph.getRow(clusterNode).set(StyleManager.CLUSTERSIZE_COLUMN_NAME,c.getSize());
map.put(c, clusterNode);
}
-
+ taskMonitor.setStatusMessage(LocalizationManager.get("metaGraph_edges"));
//Add edges (O(|C|^2*|V|^2) can maybe be improved? //TODO
- for (YoshikoCluster c1:solution.getCluster()) {
- for (YoshikoCluster c2:solution.getCluster()) {
+ for (YoshikoCluster c1:solution.getClusters()) {
+ for (YoshikoCluster c2:solution.getClusters()) {
if (
metaGraph.containsEdge(map.get(c1),map.get(c2))
|| c1 == c2
diff --git a/src/main/resources/YoshikoStrings.properties b/src/main/resources/YoshikoStrings.properties
index df0759a..e21c072 100644
--- a/src/main/resources/YoshikoStrings.properties
+++ b/src/main/resources/YoshikoStrings.properties
@@ -28,6 +28,7 @@ clusterSize = Cluster Size:
continueTimeout = The ILP has exceeded the given time limit. Do you want to continue? (This may take a long time)
cost = Editing Cost:
createMetaGraph = Create Meta-Graph
+createClusterView = Create Cluster Views
currentGap = [ILP] Current Instance Gap
defaultDeletion = Default deletion cost:
defaultInsertion = Default insertion cost:
@@ -35,6 +36,7 @@ deleteSolution = Do you really want to delete this solution?
disableMultiThreading = Disable Multithreading
discardSolution = Discard
editingCostPanel = Editing Costs
+exportSelectedClusters = Export selected clusters
firstStart = Thanks for using the Yoshiko Clustering Tool!\nIt appears, that this is your first time using this tool.\nIf you want an in-depth explanation of the algorithm please refer to: [INSERT COOL LINK HERE]
gap = Gap
getYoshiko = Get Yoshiko Library
@@ -46,6 +48,7 @@ lastInstanceGap = Gap (Current Instance):
libFail = Failed to load library! Make sure you got the right file. The required version for this version of the wrapper is:
libraryPanel = Library
metaGraph = Meta Graph
+metaGraph_edges = Fetching edges and calculating edge strengths
multFactor = Multiplicative Factor for SNR:
noFeasible = No feasible solution found!
noLibMessage = There is no Yoshiko Library currently loaded! You might have to specify its location.
@@ -66,6 +69,8 @@ run = Perform Algorithm
showAdvanced = Show advanced options
solution = Solution
+status_createCV = Creating cluster view for cluster:
+
status_reductionAC = Applying "Almost-Clique" reduction rule
status_reductionCR = Applying "Clique" reduction rule
status_reductionCC = Applying "Critical-Clique" reduction rule
--
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