Author: clopes
Date: 2012-01-13 14:49:33 -0800 (Fri, 13 Jan 2012)
New Revision: 28017
Modified:
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/model/MCODEAlgorithm.java
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/task/MCODEAnalyzeTask.java
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/util/MCODEUtil.java
Log:
Fixed analyzeTask.cancel(). Fixed the task monitor. Destroying the
sub-networks that are created during the analysis and not used in the results.
Modified:
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/model/MCODEAlgorithm.java
===================================================================
---
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/model/MCODEAlgorithm.java
2012-01-13 22:31:48 UTC (rev 28016)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/model/MCODEAlgorithm.java
2012-01-13 22:49:33 UTC (rev 28017)
@@ -62,8 +62,8 @@
*/
public class MCODEAlgorithm {
- private boolean cancelled = false;
- private TaskMonitor taskMonitor = null;
+ private boolean cancelled;
+ private TaskMonitor taskMonitor;
private static final Logger logger =
LoggerFactory.getLogger(MCODEAlgorithm.class);
@@ -228,6 +228,7 @@
return d2.compareTo(d1);
}
};
+
// Will store Doubles (score) as the key, Lists of node indexes
as values
SortedMap<Double, List<Integer>> nodeScoreSortedMap = new
TreeMap<Double, List<Integer>>(scoreComparator);
@@ -236,7 +237,7 @@
List<Integer> al = null;
int i = 0;
List<CyNode> nodes = inputNetwork.getNodeList();
-
+
for (CyNode n : nodes) {
nodeInfo = calcNodeInfo(inputNetwork, n.getIndex());
nodeInfoHashMap.put(n.getIndex(), nodeInfo);
@@ -255,11 +256,13 @@
}
if (taskMonitor != null) {
- i++;
- taskMonitor.setProgress((i * 100) / (double)
nodes.size());
+ taskMonitor.setProgress( (++i / (double)
nodes.size()) );
}
+
+ if (cancelled)
+ break;
}
-
+
nodeScoreResultsMap.put(resultId, nodeScoreSortedMap);
nodeInfoResultsMap.put(resultId, nodeInfoHashMap);
@@ -316,8 +319,8 @@
long msTimeBefore = System.currentTimeMillis();
HashMap<Integer, Boolean> nodeSeenHashMap = new
HashMap<Integer, Boolean>(); //key is node ID
int currentNode = -1;
- int findingProgress = 0;
- int findingTotal = 0;
+ double findingProgress = 0;
+ double findingTotal = 0;
Collection<List<Integer>> values = nodeScoreSortedMap.values();
//returns a Collection sorted by key order (descending)
// In order to track the progress without significant lags (for
times when many nodes have the same score
@@ -378,13 +381,11 @@
}
if (taskMonitor != null) {
- findingProgress++;
// We want to be sure that only
progress changes are reported and not
// miniscule decimal increments so that
the taskMonitor isn't overwhelmed
- int newProgress = (findingProgress *
100) / findingTotal;
- int oldProgress = ((findingProgress -
1) * 100) / findingTotal;
+ double newProgress = ++findingProgress
/ findingTotal;
- if (newProgress != oldProgress) {
+ if ( Math.round(newProgress * 100) !=
Math.round((newProgress - 0.01) * 100) ) {
taskMonitor.setProgress(newProgress);
}
}
@@ -486,7 +487,7 @@
clusterNetwork = createClusterNetwork(alCluster, inputNetwork);
cluster.setNetwork(clusterNetwork);
cluster.setClusterScore(scoreCluster(cluster));
-
+
return cluster;
}
@@ -806,7 +807,7 @@
cluster.add(n.getIndex());
}
}
-
+
return true;
}
@@ -876,7 +877,7 @@
boolean firstLoop = true;
CySubNetwork outputNetwork = null;
- while (true) {
+ while (true && !cancelled) {
int numDeleted = 0;
List<Integer> alCoreNodeIndices = new
ArrayList<Integer>(inputNetwork.getNodeCount());
List<CyNode> nodes = inputNetwork.getNodeList();
Modified:
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/task/MCODEAnalyzeTask.java
===================================================================
---
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/task/MCODEAnalyzeTask.java
2012-01-13 22:31:48 UTC (rev 28016)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/task/MCODEAnalyzeTask.java
2012-01-13 22:49:33 UTC (rev 28017)
@@ -107,7 +107,8 @@
// Only (re)score the graph if the scoring parameters
have been changed
if (analyze == MCODEAnalyzeAction.RESCORE) {
- taskMonitor.setProgress(0);
+ taskMonitor.setProgress(0.001);
+ taskMonitor.setTitle("MCODE Analysis");
taskMonitor.setStatusMessage("Scoring Network
(Step 1 of 3)");
alg.scoreGraph(network, resultId);
@@ -115,10 +116,10 @@
return;
}
- logger.error("Network was scored in " +
alg.getLastScoreTime() + " ms.");
+ logger.info("Network was scored in " +
alg.getLastScoreTime() + " ms.");
}
- taskMonitor.setProgress(0);
+ taskMonitor.setProgress(0.001);
taskMonitor.setStatusMessage("Finding Clusters (Step 2
of 3)");
clusters = alg.findClusters(network, resultId);
@@ -127,7 +128,7 @@
return;
}
- taskMonitor.setProgress(0);
+ taskMonitor.setProgress(0.001);
taskMonitor.setStatusMessage("Drawing Results (Step 3
of 3)");
// Also create all the images here for the clusters,
since it can be a time consuming operation
@@ -141,13 +142,15 @@
}
imageList[i] =
mcodeUtil.createClusterImage(clusters[i], imageSize, imageSize, null, true,
null);
- taskMonitor.setProgress((i * 100) / (double)
clusters.length);
+ taskMonitor.setProgress((i+1) / (double)
clusters.length);
}
success = true;
} catch (Exception e) {
throw new Exception("Error while executing the MCODE
analysis", e);
} finally {
+ mcodeUtil.removeUnusedSubNetworks(network, clusters);
+
if (listener != null) {
listener.handleEvent(new
AnalysisCompletedEvent(success, clusters, imageList));
}
@@ -158,6 +161,8 @@
public void cancel() {
this.interrupted = true;
alg.setCancelled(true);
+ mcodeUtil.removeNetworkResult(resultId);
+ mcodeUtil.removeNetworkAlgorithm(network.getSUID());
}
/**
Modified:
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/util/MCODEUtil.java
===================================================================
---
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/util/MCODEUtil.java
2012-01-13 22:31:48 UTC (rev 28016)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/util/MCODEUtil.java
2012-01-13 22:49:33 UTC (rev 28017)
@@ -145,6 +145,8 @@
private int currentResultId;
+ private Set<CySubNetwork> subNetworks;
+
private static final Logger logger =
LoggerFactory.getLogger(MCODEUtil.class);
public MCODEUtil(final RenderingEngineFactory<CyNetwork>
renderingEngineFactory,
@@ -191,6 +193,27 @@
currentParameters = new MCODECurrentParameters();
networkAlgorithms = new HashMap<Long, MCODEAlgorithm>();
networkResults = new HashMap<Long, Set<Integer>>();
+ subNetworks = new HashSet<CySubNetwork>();
+ }
+
+ public void removeUnusedSubNetworks(CyNetwork network, MCODECluster[]
clusters) {
+ Set<CySubNetwork> clusterNetworks = new HashSet<CySubNetwork>();
+
+ if (clusters != null && clusters.length > 0) {
+ for (MCODECluster c : clusters) {
+ clusterNetworks.add(c.getNetwork());
+ }
+ }
+
+ CyRootNetwork rootNet = rootNetworkMgr.getRootNetwork(network);
+
+ for (CySubNetwork subNet : subNetworks) {
+ if (!clusterNetworks.contains(subNet)) {
+ rootNet.removeSubNetwork(subNet);
+ }
+ }
+
+ subNetworks.clear();
}
public MCODECurrentParameters getCurrentParameters() {
@@ -208,6 +231,10 @@
public void addNetworkAlgorithm(final long suid, final MCODEAlgorithm
alg) {
networkAlgorithms.put(suid, alg);
}
+
+ public void removeNetworkAlgorithm(final long suid) {
+ networkAlgorithms.remove(suid);
+ }
public boolean containsNetworkResult(final long suid) {
return networkResults.containsKey(suid);
@@ -434,11 +461,11 @@
return image;
}
-private int subNetCount; // TODO: delete
+
public CySubNetwork createSubNetwork(final CyNetwork net,
Collection<CyNode> nodes) {
final CyRootNetwork root = rootNetworkMgr.getRootNetwork(net);
final Set<CyEdge> edges = new HashSet<CyEdge>();
-System.out.println(">> MCODE: Creating sub-network: " + (++subNetCount)); //
TODO: delete
+
for (CyNode n : nodes) {
Set<CyEdge> adjacentEdges = new
HashSet<CyEdge>(net.getAdjacentEdgeList(n, CyEdge.Type.ANY));
@@ -449,9 +476,10 @@
}
}
}
-
+System.out.println(">> MCODE: Creating sub-network..."); // TODO: delete
final CySubNetwork subNet = root.addSubNetwork(nodes, edges);
-
+ subNetworks.add(subNet);
+System.out.println(">> MCODE: [ sub-network created! ]"); // TODO: delete
return subNet;
}
@@ -473,13 +501,6 @@
view.updateView();
}
- public void destroyNetworkViewAndModel(CyNetworkView view) {
- if (view != null) {
- networkViewMgr.destroyNetworkView(view);
- networkMgr.destroyNetwork(view.getModel());
- }
- }
-
public void addVirtualColumns(CySubNetwork subNetwork, CyNetwork
parent) {
CyTable tbl = subNetwork.getDefaultNodeTable();
CyTable parentTbl = parent.getDefaultNodeTable();
@@ -777,7 +798,7 @@
return false;
}
-
+
private static Properties loadProperties(String name) {
Properties props = new Properties();
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