diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/cytoUtil/GraphAnalyzer.java b/src/main/java/de/hhu/ba/yoshikoWrapper/cytoUtil/GraphAnalyzer.java
new file mode 100644
index 0000000000000000000000000000000000000000..dfc6d39ea6efbcff99994b46f3b760d66d3610ca
--- /dev/null
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/cytoUtil/GraphAnalyzer.java
@@ -0,0 +1,50 @@
+package de.hhu.ba.yoshikoWrapper.cytoUtil;
+
+import java.util.List;
+
+import org.cytoscape.model.CyEdge;
+import org.cytoscape.model.CyNetwork;
+
+public class GraphAnalyzer {
+ public static boolean isMultiGraph(CyNetwork net) {
+ //TODO: Better algorithm?
+
+
+ int n = net.getNodeCount();
+ List<CyEdge> edges = net.getEdgeList();
+
+ //Easiest check: Check if the graph contains more edges than a complete graph
+ if (edges.size() > (n*(n-1))/2) {
+ return true;
+ }
+
+ for (int i = 0; i < edges.size()-1; i++) {
+ for (int j=i+1; j<edges.size();j++) {
+ if (connectSameNodes(edges.get(i),edges.get(j))){
+ return true;
+ }
+ }
+ }
+
+ return false;
+ }
+
+ private static boolean connectSameNodes(CyEdge e1, CyEdge e2) {
+ if (//Treating all edges as undirected here
+ (e1.getSource() == e2.getTarget() && e1.getTarget() == e2.getSource()) ||
+ (e1.getSource() == e2.getSource() && e1.getTarget() == e2.getTarget())
+ ) {
+ return true;
+ }
+ return false;
+ }
+
+ public static boolean isDirected(CyNetwork net) {
+ for (CyEdge e: net.getEdgeList()) {
+ if (e.isDirected()) {
+ return true;
+ }
+ }
+ return false;
+ }
+}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/MainPanel.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/MainPanel.java
index 54063d36c3689abec64f5158236e10d21667b806..77553e9f0d963c906dce5c976e648584f9408a81 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/MainPanel.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/MainPanel.java
@@ -49,6 +49,7 @@ import javax.swing.ScrollPaneConstants;
import org.cytoscape.application.swing.CytoPanelComponent;
import org.cytoscape.application.swing.CytoPanelName;
+import org.cytoscape.model.CyNetwork;
import org.cytoscape.util.swing.BasicCollapsiblePanel;
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.TaskIterator;
@@ -57,6 +58,7 @@ import de.hhu.ba.yoshikoWrapper.core.CyCore;
import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
import de.hhu.ba.yoshikoWrapper.core.ParameterSet;
import de.hhu.ba.yoshikoWrapper.core.YoshikoLoader;
+import de.hhu.ba.yoshikoWrapper.cytoUtil.GraphAnalyzer;
import de.hhu.ba.yoshikoWrapper.swing.AboutDialogFactory;
import de.hhu.ba.yoshikoWrapper.swing.GraphicsLoader;
import de.hhu.ba.yoshikoWrapper.swing.LanguageSwitcherPanelFactory;
@@ -263,6 +265,32 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
@Override
public void actionPerformed(ActionEvent e) {
+ CyNetwork networkToBeProcessed = CyCore.cy.getCurrentNetwork();
+
+ //WARNINGS FOR FEATURES THAT ARE NOT RESEARCHED
+ //TODO: (Obviously) research!
+ if (GraphAnalyzer.isMultiGraph(networkToBeProcessed)) {
+ JOptionPane.showMessageDialog(
+ null,
+ LocalizationManager.get("multiGraphWarning"),
+ LocalizationManager.get("optionpane_title"),
+ JOptionPane.WARNING_MESSAGE
+ );
+ }
+
+ //Annotation: Currently Cytoscape is really weird concerning directed/undirected edges
+ //There is an API function isDirected() for edges but all edges are directed
+ //I'll leave this commented out until CS makes sense
+
+// if (GraphAnalyzer.isDirected(networkToBeProcessed)) {
+// JOptionPane.showMessageDialog(
+// null,
+// LocalizationManager.get("directedGraphWarning"),
+// LocalizationManager.get("optionpane_title"),
+// JOptionPane.WARNING_MESSAGE
+// );
+// }
+
//SWING BLACK MAGIC
Window noWindow = null;
JDialog statusWindow = new JDialog(noWindow);
@@ -277,7 +305,7 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
if (YoshikoLoader.isLibraryLoaded()){
AbstractTask yoshiko = new AlgorithmTask(
popupLevel,
- CyCore.cy.getCurrentNetwork(),
+ networkToBeProcessed,
fetchParameter()
);
/**
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 09d41554c356d1f2b3ef86008dc66b80dfa9bc6a..907ea0179d4916e793d840901da5f3136abb5294 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
@@ -32,13 +32,16 @@ import java.util.Properties;
import javax.swing.BoxLayout;
import javax.swing.GroupLayout;
-import javax.swing.GroupLayout.Group;
+import javax.swing.GroupLayout.ParallelGroup;
+import javax.swing.GroupLayout.SequentialGroup;
import javax.swing.Icon;
import javax.swing.JButton;
import javax.swing.JLabel;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JTabbedPane;
+import javax.swing.LayoutStyle;
+import javax.swing.SwingConstants;
import org.cytoscape.application.swing.CytoPanelComponent;
import org.cytoscape.application.swing.CytoPanelName;
@@ -93,6 +96,11 @@ NetworkAboutToBeDestroyedListener
private boolean isValid;
+ //SWING LAYOUT
+
+ private ParallelGroup horizontalGroup;
+ private SequentialGroup verticalGroup;
+
public ResultPanel(YoshikoResult result) throws Exception {
this.result = result;
@@ -101,6 +109,7 @@ NetworkAboutToBeDestroyedListener
//Init subcomponents
invalidLabel = new JLabel();
+ invalidLabel.setHorizontalAlignment(SwingConstants.CENTER);
tabbedPane = new JTabbedPane();
solutionTabs = new ArrayList<SolutionTab>();
@@ -157,8 +166,8 @@ NetworkAboutToBeDestroyedListener
//Layout
GroupLayout layout = new GroupLayout(this);
- Group horizontalGroup = layout.createParallelGroup(Alignment.LEADING,true);
- Group verticalGroup = layout.createSequentialGroup();
+ horizontalGroup = layout.createParallelGroup(Alignment.CENTER,true);
+ verticalGroup = layout.createSequentialGroup();
layout.setHorizontalGroup(horizontalGroup);
layout.setVerticalGroup(verticalGroup);
@@ -169,12 +178,13 @@ NetworkAboutToBeDestroyedListener
}
horizontalGroup
- .addComponent(invalidLabel,HACKFIX_FIXED_WIDTH, PREFERRED_SIZE,Short.MAX_VALUE)
+ .addComponent(invalidLabel,DEFAULT_SIZE, 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(invalidLabel,DEFAULT_SIZE, PREFERRED_SIZE,Short.MAX_VALUE)
+ .addComponent(invalidLabel,DEFAULT_SIZE, DEFAULT_SIZE,DEFAULT_SIZE)
.addComponent(tabbedPane,DEFAULT_SIZE, DEFAULT_SIZE,PREFERRED_SIZE)
+ .addPreferredGap(LayoutStyle.ComponentPlacement.RELATED, DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(destroyButton,DEFAULT_SIZE, DEFAULT_SIZE,PREFERRED_SIZE);
layout.setAutoCreateGaps(true);
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateClusterViews.java b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateClusterViews.java
index a681836cfa8bd4108aa63e6f35d49a69943a4042..28bc3faea2f10eb11808512439dc56ebfdb2088a 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateClusterViews.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateClusterViews.java
@@ -15,19 +15,45 @@ import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoCluster;
public class CreateClusterViews implements Task {
+ //TODO: Merge redundant code with CreateMetaGraphTask
+
private ArrayList<YoshikoCluster> clusters;
+ private boolean isTerminated;
+
+ /**
+ * Used to fall back upon cancellation
+ */
+ private CyNetworkView previousView;
+
+ /**
+ * This internal list is used to track which networks have already been initialized.
+ * This is used to remove those views upon cancellation.
+ */
+ private ArrayList<CySubNetwork> initializedSubNetworks;
+
public CreateClusterViews(ArrayList<YoshikoCluster> clusters) {
this.clusters = clusters;
+
+ this.previousView = CyCore.cy.getCurrentNetworkView();
+ this.isTerminated = false;
+ this.initializedSubNetworks = new ArrayList<CySubNetwork>();
}
@Override
public void run(TaskMonitor taskMonitor) throws Exception {
+
+ taskMonitor.setTitle(LocalizationManager.get("task_ccv"));
+
CyLayoutAlgorithm layout = CyCore.layoutAlgorithmManager.getDefaultLayout();
for (YoshikoCluster c : clusters) {
+ if (this.isTerminated) {
+ throw new Exception("Terminated by user!"); //TODO: Localize
+ }
CySubNetwork subnet = c.getSubNetwork();
+ initializedSubNetworks.add(subnet);
taskMonitor.setStatusMessage(LocalizationManager.get("status_createCV")+" "+(c.getID()+1));
- CyCore.networkManager.addNetwork(subnet);
+ CyCore.networkManager.addNetwork(subnet,false);
//Create network view and register it
CyNetworkView subnetView = CyCore.networkViewFactory.createNetworkView(subnet);
//layout cluster
@@ -47,6 +73,13 @@ public class CreateClusterViews implements Task {
}
@Override
- public void cancel() {}
+ public void cancel() {
+ this.isTerminated = true;
+ //Remove generated ClusterViews
+ for (CySubNetwork v: initializedSubNetworks) {
+ CyCore.networkManager.destroyNetwork(v);
+ }
+ CyCore.cy.setCurrentNetworkView(previousView);
+ }
}
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 b5fd244dac47e3ddd763bd5913998d8131332f7c..caa8663bee3816c97e8d836b2585bf9e2145e443 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateMetaGraphTask.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateMetaGraphTask.java
@@ -1,5 +1,6 @@
package de.hhu.ba.yoshikoWrapper.tasks;
+import java.util.ArrayList;
import java.util.HashMap;
import org.cytoscape.model.CyEdge;
@@ -24,12 +25,26 @@ public class CreateMetaGraphTask extends AbstractTask {
private final YoshikoSolution solution;
+ private boolean isTerminated;
+
+ /**
+ * This internal list is used to track which networks have already been initialized.
+ * This is used to remove those views upon cancellation.
+ */
+ private ArrayList<CySubNetwork> initializedSubNetworks;
+
public CreateMetaGraphTask(YoshikoSolution s) {
this.solution = s;
+
+ this.isTerminated = false;
+ this.initializedSubNetworks = new ArrayList<CySubNetwork>();
}
@Override
public void run(TaskMonitor taskMonitor) throws Exception {
+
+ taskMonitor.setTitle(LocalizationManager.get("task_cmg"));
+
CyNetwork metaGraph = CyCore.networkFactory.createNetwork();
metaGraph.getRow(metaGraph).set(CyNetwork.NAME, LocalizationManager.get("metaGraph"));
@@ -44,14 +59,21 @@ public class CreateMetaGraphTask extends AbstractTask {
HashMap<YoshikoCluster,CyNode> map = new HashMap<YoshikoCluster,CyNode>();
+
//Add nodes
for (YoshikoCluster c: solution.getClusters()) {
+ if(isTerminated) {
+ throw new Exception("Terminated by user!");
+ }
+
CyNode clusterNode = metaGraph.addNode();
CySubNetwork subnet = c.getSubNetwork();
+ //Store reference
+ this.initializedSubNetworks.add(subnet);
taskMonitor.setStatusMessage(LocalizationManager.get("status_createCV")+" "+(c.getID()+1));
- CyCore.networkManager.addNetwork(subnet);
+ CyCore.networkManager.addNetwork(subnet,false);
//Create network view and register it
CyNetworkView subnetView = CyCore.networkViewFactory.createNetworkView(subnet);
//layout cluster
@@ -66,8 +88,9 @@ public class CreateMetaGraphTask extends AbstractTask {
StyleManager.style(subnetView,CyCore.visualMappingManager.getCurrentVisualStyle());
- CyCore.networkViewManager.addNetworkView(subnetView);
+ CyCore.networkViewManager.addNetworkView(subnetView,false);
+ //Link cluster node in meta graph and subnet graph to use Cytoscape Nested Network feature
clusterNode.setNetworkPointer(subnet);
//Set node attributes
metaGraph.getRow(clusterNode).set("name", LocalizationManager.get("cluster")+" "+c.getID());
@@ -78,6 +101,11 @@ public class CreateMetaGraphTask extends AbstractTask {
//Add edges (O(|C|^2*|V|^2) can maybe be improved? //TODO
for (YoshikoCluster c1:solution.getClusters()) {
for (YoshikoCluster c2:solution.getClusters()) {
+
+ if(isTerminated) {
+ throw new Exception("Terminated by user!");
+ }
+
if (
metaGraph.containsEdge(map.get(c1),map.get(c2))
|| c1 == c2
@@ -130,7 +158,7 @@ public class CreateMetaGraphTask extends AbstractTask {
it
);
- CyCore.networkManager.addNetwork(metaGraph);
+ CyCore.networkManager.addNetwork(metaGraph,false);
CyCore.networkViewManager.addNetworkView(
view
);
@@ -140,4 +168,14 @@ public class CreateMetaGraphTask extends AbstractTask {
CyCore.cy.setCurrentNetworkView(view);
}
+ @Override
+ public void cancel() {
+ //Set killswitch
+ isTerminated = true;
+ //Remove generated ClusterViews
+ for (CySubNetwork v: initializedSubNetworks) {
+ CyCore.networkManager.destroyNetwork(v);
+ }
+ }
+
}
diff --git a/src/main/resources/YoshikoStrings.properties b/src/main/resources/YoshikoStrings.properties
index 75d34207e234662c01ba1b1a8cad786a651f99e1..a5051e928a1c17aa405e3c1af3b03317e4d76e94 100644
--- a/src/main/resources/YoshikoStrings.properties
+++ b/src/main/resources/YoshikoStrings.properties
@@ -19,6 +19,10 @@
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
#-------------------------------------------------------------------------------
+
+
+#TODO: Give more meaningful names to keys, sort
+
about = INSERT SOME AMAZING INFO ABOUT THIS APPLICATION,\n THE AUTHOR AND WHERE TO FIND MORE INFO HERE\n <a href=\"www.hhu.de\" >LINK</a>
aboutButton = About Yoshiko
aboutTitle = Yoshiko Plugin Info
@@ -33,6 +37,7 @@ currentGap = [ILP] Current Instance Gap
defaultDeletion = Default deletion cost:
defaultInsertion = Default insertion cost:
deleteSolution = Do you really want to delete this solution?
+directedGraphWarning = This algorithm works on undirected graphs. Directed edges are \n treated as undirected edges.
disableMultiThreading = Disable Multithreading
discardSolution = Discard
editingCostPanel = Editing Costs
@@ -51,6 +56,7 @@ libraryPanel = Library
metaGraph = Meta Graph
metaGraph_edges = Fetching edges and calculating edge strengths
multFactor = Multiplicative Factor for SNR:
+multiGraphWarning = This graph is a multigraph. This algorithms behavior on multigraphs is not yet researched.
noFeasible = No feasible solution found!
noLibMessage = There is no Yoshiko Library currently loaded! You might have to specify its location.
noLibTitle = Library not loaded!
@@ -85,6 +91,10 @@ status_reductionSN = Applying "Similar-Neighborhood" reduction rule
status_solvingILP = Solving ILP
switchLanguage = Plugin language
+
+task_ccv = Yoshiko: Create Cluster Views
+task_cmg = Yoshiko: Create Meta Graph
+
timeLimitILP = Use time limit for ILP (s):
timedOutMessage = The ILP exceeded the time-limit!
timedOutTitle = Timeout