From a49f59ebf5a9e8627f5a4dab14da363f9bd9b630 Mon Sep 17 00:00:00 2001
From: Philipp Spohr <spohr.philipp@web.de>
Date: Thu, 14 Dec 2017 14:14:30 +0100
Subject: [PATCH] Fixes to meta-graph bugs introduced recently
---
.../swing/components/SolutionTab.java | 10 ++++++----
.../tasks/CreateClusterViewsTask.java | 7 ++++---
.../tasks/CreateMetaGraphTask.java | 7 +++++--
.../yoshikoWrapper/tasks/GetClustersTask.java | 18 +++++++++++++++++-
.../yoshikoWrapper/tasks/GetSolutionsTask.java | 17 ++++++++++++++---
5 files changed, 46 insertions(+), 13 deletions(-)
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 104d39a..b0c4e99 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
@@ -203,22 +203,24 @@ public class SolutionTab extends JPanel {
layout = new GroupLayout(this);
layout.setHorizontalGroup(layout.createParallelGroup(Alignment.CENTER,true)
+ .addComponent(createClusterView,DEFAULT_SIZE,DEFAULT_SIZE,PREFERRED_SIZE)
+ .addComponent(createMetaGraph,DEFAULT_SIZE,DEFAULT_SIZE,PREFERRED_SIZE)
.addGap(8)
.addComponent(clusterCount,DEFAULT_SIZE,DEFAULT_SIZE,Short.MAX_VALUE)
.addComponent(hideSingles,DEFAULT_SIZE,DEFAULT_SIZE,Short.MAX_VALUE)
.addGap(8)
.addComponent(scrollPane,PREFERRED_SIZE,PREFERRED_SIZE,Short.MAX_VALUE)
- .addComponent(createClusterView,DEFAULT_SIZE,DEFAULT_SIZE,PREFERRED_SIZE)
- .addComponent(createMetaGraph,DEFAULT_SIZE,DEFAULT_SIZE,PREFERRED_SIZE)
+ .addGap(4)
);
layout.setVerticalGroup(layout.createSequentialGroup()
+ .addComponent(createClusterView,DEFAULT_SIZE,DEFAULT_SIZE,DEFAULT_SIZE)
+ .addComponent(createMetaGraph,DEFAULT_SIZE,DEFAULT_SIZE,DEFAULT_SIZE)
.addGap(8)
.addComponent(clusterCount,DEFAULT_SIZE,DEFAULT_SIZE,DEFAULT_SIZE)
.addComponent(hideSingles,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)
+ .addGap(4)
);
this.setLayout(layout);
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateClusterViewsTask.java b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateClusterViewsTask.java
index 72d6270..0531fa7 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateClusterViewsTask.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateClusterViewsTask.java
@@ -22,6 +22,10 @@ public class CreateClusterViewsTask implements Task {
@Tunable
public ArrayList<YoshikoCluster> clusters; //TODO: Make Tunable, reference by ID?
+ /**
+ * Killswitch, used to determine if the algorithm has been terminated.
+ * We can use this to cancel at a given point (so we don't need to finish the entire task)
+ */
private boolean isTerminated;
/**
@@ -77,11 +81,8 @@ public class CreateClusterViewsTask implements Task {
StyleManager.style(subnetView,CyCore.visualMappingManager.getCurrentVisualStyle());
CyCore.networkViewManager.addNetworkView(subnetView);
}
-
}
);
-
-
}
}
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 1f24dea..cf0ffb6 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateMetaGraphTask.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateMetaGraphTask.java
@@ -94,7 +94,7 @@ public class CreateMetaGraphTask extends AbstractTask{
//Link clusters 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("clusters")+" "+c.getID());
+ metaGraph.getRow(clusterNode).set("name", LocalizationManager.get("clusters")+" "+(c.getID()+1));
metaGraph.getRow(clusterNode).set(StyleManager.CLUSTERSIZE_COLUMN_NAME,c.getSize());
map.put(c, clusterNode);
}
@@ -105,12 +105,13 @@ public class CreateMetaGraphTask extends AbstractTask{
taskMonitor.setStatusMessage(LocalizationManager.get("metaGraph_edges"));
Iterator<YoshikoCluster> it1 = solution.getClusters().iterator();
- Iterator<YoshikoCluster> it2 = solution.getClusters().iterator();
while (it1.hasNext()) {
YoshikoCluster c1 = it1.next();
+ Iterator<YoshikoCluster> it2 = solution.getClusters().iterator();
while(it2.hasNext()) {
YoshikoCluster c2 = it2.next();
+ System.out.println("Debug: Processing edges between cluster "+c1.getID()+" and "+c2.getID());
if(isTerminated) {
throw new Exception("Terminated by user!");
@@ -126,7 +127,9 @@ public class CreateMetaGraphTask extends AbstractTask{
for (CyNode c1n : c1.getSubNetwork().getNodeList()) {
for (CyNode c2n : c2.getSubNetwork().getNodeList()) {
if (solution.getOriginalGraph().containsEdge(c1n, c2n) || solution.getOriginalGraph().containsEdge(c2n, c1n)) {
+ System.out.println("Debug: Found relevant edge from "+c1n.getSUID()+ " to "+c2n.getSUID());
if (!metaGraph.containsEdge(map.get(c1), map.get(c2))){
+ System.out.println("We create a new edge for it");
CyEdge edge = metaGraph.addEdge(map.get(c1), map.get(c2), false);
metaGraph.getRow(edge).set(StyleManager.EDGESTRENGTH_COLUMN_NAME,1);
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/GetClustersTask.java b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/GetClustersTask.java
index 0afa05e..6a49b1e 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/GetClustersTask.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/GetClustersTask.java
@@ -9,16 +9,32 @@ import org.cytoscape.work.Tunable;
import de.hhu.ba.yoshikoWrapper.core.ResultList;
import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoCluster;
import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoResult;
-import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoSolution;
+/**
+ * A task that retrieves the clusters associated with a given solution in a given result. This is meant to be used via CyRest / command line functionality exclusively
+ *
+ * @author Philipp Spohr, Dec 12, 2017
+ *
+ */
public class GetClustersTask implements ObservableTask {
+
+ /**
+ * The ID of the result for which the clusters are to be retrieved
+ */
@Tunable(description="The result ID for which the solutions should be displayed", context="nogui")
public int resultID = -1;
+ /**
+ * The ID of the solution for which the clusters are to be retrieved
+ */
@Tunable(description="The solution ID for which the solutions should be displayed", context="nogui")
public long solutionID = -1;
+
+ /**
+ * The clusters as a collection when they are retrieved
+ */
private Collection<YoshikoCluster> clusters;
@Override
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/GetSolutionsTask.java b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/GetSolutionsTask.java
index b36ef96..b4d60d6 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/GetSolutionsTask.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/GetSolutionsTask.java
@@ -10,11 +10,23 @@ import de.hhu.ba.yoshikoWrapper.core.ResultList;
import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoResult;
import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoSolution;
+/**
+ * Basic task that retrieves solutions associated with a run (result)
+ * This is meant to be invoked from cmd / CyRest exclusively to receive solution IDs
+ * @author Philipp Spohr, Dec 12, 2017
+ *
+ */
public class GetSolutionsTask implements ObservableTask {
+ /**
+ * The result ID for the result/run for which the solutions are to be retrieved
+ */
@Tunable(description="The result ID for which the solutions should be displayed", context="nogui")
public int resultID = -1;
+ /**
+ * The solutions as a collection in case the task was successful
+ */
private Collection<YoshikoSolution> solutions;
@Override
@@ -27,9 +39,7 @@ public class GetSolutionsTask implements ObservableTask {
}
@Override
- public void cancel() {
- // TODO Auto-generated method stub
- }
+ public void cancel() {} //There is nothing here that remains in an instable state as we are simply reading / retrieving data
@SuppressWarnings("unchecked")
@Override
@@ -44,4 +54,5 @@ public class GetSolutionsTask implements ObservableTask {
return null;
}
+
}
--
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