Author: clopes
Date: 2012-08-15 15:06:58 -0700 (Wed, 15 Aug 2012)
New Revision: 30202
Added:
csplugins/trunk/toronto/clopes/mcode/src/test/java/org/cytoscape/mcode/internal/AbstractMCODETest.java
csplugins/trunk/toronto/clopes/mcode/src/test/java/org/cytoscape/mcode/internal/util/
csplugins/trunk/toronto/clopes/mcode/src/test/java/org/cytoscape/mcode/internal/util/MCODEUtilTest.java
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/MCODECluster.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
csplugins/trunk/toronto/clopes/mcode/src/test/java/org/cytoscape/mcode/internal/model/MCODEAlgorithmTest.java
Log:
MCODE now deletes and disposes unused subnetworks (including the temporary ones
created during the analysis) and network views.
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
2012-08-15 22:03:16 UTC (rev 30201)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/model/MCODEAlgorithm.java
2012-08-15 22:06:58 UTC (rev 30202)
@@ -208,8 +208,8 @@
* @param inputNetwork The network that will be scored
* @param resultId Title of the result, used as an identifier in
various hash maps
*/
- public void scoreGraph(CyNetwork inputNetwork, int resultId) {
- String callerID = "MCODEAlgorithm.MCODEAlgorithm";
+ public void scoreGraph(final CyNetwork inputNetwork, final int
resultId) {
+ final String callerID = "MCODEAlgorithm.MCODEAlgorithm";
if (inputNetwork == null) {
logger.error("In " + callerID + ": inputNetwork was
null.");
@@ -218,7 +218,7 @@
// Initialize
long msTimeBefore = System.currentTimeMillis();
- Map<Long, NodeInfo> nodeInfoHashMap = new HashMap<Long,
NodeInfo>(inputNetwork.getNodeCount());
+ final Map<Long, NodeInfo> nodeInfoHashMap = new HashMap<Long,
NodeInfo>(inputNetwork.getNodeCount());
// Sort Doubles in descending order
Comparator<Double> scoreComparator = new Comparator<Double>() {
@@ -233,13 +233,12 @@
SortedMap<Double, List<Long>> nodeScoreSortedMap = new
TreeMap<Double, List<Long>>(scoreComparator);
// Iterate over all nodes and calculate MCODE score
- NodeInfo nodeInfo = null;
List<Long> al = null;
int i = 0;
- List<CyNode> nodes = inputNetwork.getNodeList();
+ final List<CyNode> nodes = inputNetwork.getNodeList();
- for (CyNode n : nodes) {
- nodeInfo = calcNodeInfo(inputNetwork, n.getSUID());
+ for (final CyNode n : nodes) {
+ final NodeInfo nodeInfo = calcNodeInfo(inputNetwork,
n.getSUID());
nodeInfoHashMap.put(n.getSUID(), nodeInfo);
double nodeScore = scoreNode(nodeInfo);
@@ -255,9 +254,8 @@
nodeScoreSortedMap.put(nodeScore, al);
}
- if (taskMonitor != null) {
- taskMonitor.setProgress( (++i / (double)
nodes.size()) );
- }
+ if (taskMonitor != null)
+ taskMonitor.setProgress(++i / (double)
nodes.size());
if (cancelled)
break;
@@ -282,9 +280,9 @@
* @param resultSetName Title of the result
* @return An array containing an MCODECluster object for each cluster.
*/
- public MCODECluster[] findClusters(CyNetwork inputNetwork, int
resultId) {
- SortedMap<Double, List<Long>> nodeScoreSortedMap;
- Map<Long, NodeInfo> nodeInfoHashMap;
+ public MCODECluster[] findClusters(final CyNetwork inputNetwork, int
resultId) {
+ final SortedMap<Double, List<Long>> nodeScoreSortedMap;
+ final Map<Long, NodeInfo> nodeInfoHashMap;
// First we check if the network has been scored under this
result title (i.e. scoring
// was required due to a scoring parameter change). If it
hasn't then we want to use the
@@ -301,7 +299,6 @@
nodeInfoHashMap = nodeInfoResultsMap.get(resultId);
}
- MCODECluster currentCluster;
String callerID = "MCODEAlgorithm.findClusters";
if (inputNetwork == null) {
@@ -338,8 +335,6 @@
currentNode = alNodesWithSameScore.get(j);
if (!nodeSeenHashMap.containsKey(currentNode)) {
- currentCluster = new MCODECluster();
-
currentCluster.setSeedNode(currentNode);//store the current node as the seed
node
// We store the current node seen hash
map for later exploration purposes
Map<Long, Boolean>
nodeSeenHashMapSnapShot = new HashMap<Long, Boolean>(nodeSeenHashMap);
@@ -359,16 +354,17 @@
CySubNetwork clusterNet =
createClusterNetwork(alCluster, inputNetwork);
if (!filterCluster(clusterNet))
{
- if (params.isHaircut())
{
+ if (params.isHaircut())
haircutCluster(clusterNet, alCluster);
- }
- if (params.isFluff()) {
+ if (params.isFluff())
fluffClusterBoundary(alCluster, nodeSeenHashMap, nodeInfoHashMap);
- }
-
currentCluster.setALCluster(alCluster);
clusterNet =
createClusterNetwork(alCluster, inputNetwork);
+
+ MCODECluster
currentCluster = new MCODECluster();
+
currentCluster.setALCluster(alCluster);
+
currentCluster.setSeedNode(currentNode);//store the current node as the seed
node
currentCluster.setNetwork(clusterNet);
currentCluster.setClusterScore(scoreCluster(currentCluster));
currentCluster.setNodeSeenHashMap(nodeSeenHashMapSnapShot);//store the list of
all the nodes that have already been seen and incorporated in other clusters
@@ -416,17 +412,19 @@
}
}
}
+
+ // Dispose clusters that were not selected
+ for (MCODECluster c : alClusters) {
+ if (!selectedALClusters.contains(c))
+ c.dispose();
+ }
alClusters = selectedALClusters;
}
- // Finally convert the arraylist into a fixed array
- MCODECluster[] clusters = new MCODECluster[alClusters.size()];
-
- for (int c = 0; c < clusters.length; c++) {
- clusters[c] = (MCODECluster) alClusters.get(c);
- }
-
+ // Finally convert the list into a fixed array
+ MCODECluster[] clusters = alClusters.toArray(new
MCODECluster[alClusters.size()]);
+
long msTimeAfter = System.currentTimeMillis();
lastFindTime = msTimeAfter - msTimeBefore;
@@ -438,14 +436,14 @@
*
* @param cluster cluster being explored
* @param nodeScoreCutoff slider source value
- * @param inputNetwork network
+ * @param inputNet network
* @param resultId ID of the result set being explored
* @return explored cluster
*/
- public MCODECluster exploreCluster(MCODECluster cluster,
-
double nodeScoreCutoff,
-
CyNetwork inputNetwork,
- int
resultId) {
+ public MCODECluster exploreCluster(final MCODECluster cluster,
+
final double nodeScoreCutoff,
+
final CyNetwork inputNet,
+
final int resultId) {
// This method is similar to the finding method with the
exception of the filtering so that the decrease of the cluster size
// can produce a single node, also the use of the node seen
hash map is differentially applied...
Map<Long, NodeInfo> nodeInfoHashMap =
nodeInfoResultsMap.get(resultId);
@@ -467,40 +465,38 @@
.getMaxDepthFromStart(), nodeInfoHashMap);
// Make sure seed node is part of cluster, if not already in
there
- if (!alCluster.contains(seedNode)) {
+ if (!alCluster.contains(seedNode))
alCluster.add(seedNode);
- }
// Create an input graph for the filter and haircut methods
- CySubNetwork clusterNetwork = createClusterNetwork(alCluster,
inputNetwork);
+ CySubNetwork clusterNet = createClusterNetwork(alCluster,
inputNet);
- if (params.isHaircut()) {
- haircutCluster(clusterNetwork, alCluster);
- }
+ if (params.isHaircut())
+ haircutCluster(clusterNet, alCluster);
- if (params.isFluff()) {
+ if (params.isFluff())
fluffClusterBoundary(alCluster, nodeSeenHashMap,
nodeInfoHashMap);
- }
+ clusterNet = createClusterNetwork(alCluster, inputNet);
+
+ cluster.setNetwork(clusterNet);
cluster.setALCluster(alCluster);
- clusterNetwork = createClusterNetwork(alCluster, inputNetwork);
- cluster.setNetwork(clusterNetwork);
cluster.setClusterScore(scoreCluster(cluster));
return cluster;
}
- private CySubNetwork createClusterNetwork(List<Long> alCluster,
CyNetwork inputNetwork) {
- Set<CyNode> nodes = new HashSet<CyNode>();
+ private CySubNetwork createClusterNetwork(final List<Long> alCluster,
final CyNetwork inputNet) {
+ final Set<CyNode> nodes = new HashSet<CyNode>();
- for (Long id : alCluster) {
- CyNode n = inputNetwork.getNode(id);
+ for (final Long id : alCluster) {
+ CyNode n = inputNet.getNode(id);
nodes.add(n);
}
- CySubNetwork outputNetwork =
mcodeUtil.createSubNetwork(inputNetwork, nodes, SavePolicy.DO_NOT_SAVE);
+ CySubNetwork outputNet = mcodeUtil.createSubNetwork(inputNet,
nodes, SavePolicy.DO_NOT_SAVE);
- return outputNetwork;
+ return outputNet;
}
/**
@@ -548,11 +544,10 @@
* @param nodeId The SUID of the node in the input network to score
* @return A NodeInfo object containing node information required for
the algorithm
*/
- private NodeInfo calcNodeInfo(CyNetwork inputNetwork, Long nodeId) {
+ private NodeInfo calcNodeInfo(final CyNetwork inputNetwork, final Long
nodeId) {
final Long[] neighborhood;
+ final String callerID = "MCODEAlgorithm.calcNodeInfo";
- String callerID = "MCODEAlgorithm.calcNodeInfo";
-
if (inputNetwork == null) {
logger.error("In " + callerID + ": gpInputGraph was
null.");
return null;
@@ -595,7 +590,7 @@
}
// extract neighborhood subgraph
- CySubNetwork neighborhoodNet =
mcodeUtil.createSubNetwork(inputNetwork, neighbors, SavePolicy.DO_NOT_SAVE);
+ final CySubNetwork neighborhoodNet =
mcodeUtil.createSubNetwork(inputNetwork, neighbors, SavePolicy.DO_NOT_SAVE);
if (neighborhoodNet == null) {
// this shouldn't happen
@@ -604,12 +599,11 @@
}
// Calculate the node information for each node
- NodeInfo nodeInfo = new NodeInfo();
+ final NodeInfo nodeInfo = new NodeInfo();
// Density
- if (neighborhoodNet != null) {
+ if (neighborhoodNet != null)
nodeInfo.density = calcDensity(neighborhoodNet,
params.isIncludeLoops());
- }
nodeInfo.numNodeNeighbors = neighborhood.length;
@@ -622,9 +616,8 @@
// Calculate the core density - amplifies the density of
heavily interconnected regions and attenuates
// that of less connected regions
- if (kCore != null) {
+ if (kCore != null)
nodeInfo.coreDensity = calcDensity(kCore,
params.isIncludeLoops());
- }
// Record neighbor array for later use in cluster detection step
nodeInfo.nodeNeighbors = neighborhood;
@@ -776,10 +769,9 @@
* @param clusterNetwork The cluster to check if it passes the filter
* @return true if cluster should be filtered, false otherwise
*/
- private boolean filterCluster(CySubNetwork clusterNetwork) {
- if (clusterNetwork == null) {
+ private boolean filterCluster(final CySubNetwork clusterNetwork) {
+ if (clusterNetwork == null)
return true;
- }
// filter if the cluster does not satisfy the user specified
k-core
CySubNetwork kCore = getKCore(clusterNetwork,
params.getKCore());
@@ -794,17 +786,17 @@
* @param cluster The cluster node ID list (in the original
graph)
* @return true
*/
- private boolean haircutCluster(CySubNetwork clusterNetwork, List<Long>
cluster) {
+ private boolean haircutCluster(final CySubNetwork clusterNetwork, final
List<Long> cluster) {
// get 2-core
- CySubNetwork kCore = getKCore(clusterNetwork, 2);
+ final CySubNetwork kCore = getKCore(clusterNetwork, 2);
if (kCore != null) {
// clear the cluster and add all 2-core nodes back into
it
cluster.clear();
- // must add back the nodes in a way that preserves
gpInputGraph node indices
- for (CyNode n : kCore.getNodeList()) {
+
+ // must add back the nodes in a way that preserves node
indices
+ for (CyNode n : kCore.getNodeList())
cluster.add(n.getSUID());
- }
}
return true;
@@ -819,7 +811,7 @@
* possible edges.
* @return The density of the network
*/
- public double calcDensity(CySubNetwork network, boolean includeLoops) {
+ private double calcDensity(final CySubNetwork network, final boolean
includeLoops) {
String callerID = "MCODEAlgorithm.calcDensity";
if (network == null) {
@@ -861,65 +853,60 @@
/**
* Find a k-core of a network. A k-core is a subgraph of minimum degree
k
*
- * @param inputNetwork The input network
+ * @param inputNet The input network
* @param k The k of the k-core to find e.g. 4 will find a
4-core
* @return Returns a subgraph with the core, if any was found at given k
*/
- public CySubNetwork getKCore(CySubNetwork inputNetwork, int k) {
+ private CySubNetwork getKCore(final CySubNetwork inputNet, int k) {
String callerID = "MCODEAlgorithm.getKCore";
- if (inputNetwork == null) {
+ if (inputNet == null) {
logger.error("In " + callerID + ": inputNetwork was
null.");
return null;
}
// filter all nodes with degree less than k until convergence
boolean firstLoop = true;
- CySubNetwork outputNetwork = null;
+ CySubNetwork outputNet = inputNet;
while (true && !cancelled) {
int numDeleted = 0;
- List<Long> alCoreNodeIndices = new
ArrayList<Long>(inputNetwork.getNodeCount());
- List<CyNode> nodes = inputNetwork.getNodeList();
+ List<Long> alCoreNodeIndices = new
ArrayList<Long>(outputNet.getNodeCount());
+ List<CyNode> nodes = outputNet.getNodeList();
for (CyNode n : nodes) {
- int degree =
inputNetwork.getAdjacentEdgeList(n, CyEdge.Type.ANY).size();
+ int degree = outputNet.getAdjacentEdgeList(n,
CyEdge.Type.ANY).size();
- if (degree >= k) {
+ if (degree >= k)
alCoreNodeIndices.add(n.getSUID());
//contains all nodes with degree >= k
- } else {
+ else
numDeleted++;
- }
}
if (numDeleted > 0 || firstLoop) {
Set<CyNode> outputNodes = new HashSet<CyNode>();
for (Long index : alCoreNodeIndices) {
- CyNode n = inputNetwork.getNode(index);
+ CyNode n = outputNet.getNode(index);
outputNodes.add(n);
}
- outputNetwork =
mcodeUtil.createSubNetwork(inputNetwork.getRootNetwork(), outputNodes,
- SavePolicy.DO_NOT_SAVE);
+ outputNet =
mcodeUtil.createSubNetwork(outputNet.getRootNetwork(), outputNodes,
SavePolicy.DO_NOT_SAVE);
- if (outputNetwork.getNodeCount() == 0) {
+ if (outputNet.getNodeCount() == 0)
return null;
- }
- // Iterate again, but with a new k-core input
graph
- inputNetwork = outputNetwork;
-
- if (firstLoop) {
+ // Iterate again, but with a new k-core input
graph...
+
+ if (firstLoop)
firstLoop = false;
- }
} else {
// stop the loop
break;
}
}
- return outputNetwork;
+ return outputNet;
}
/**
@@ -930,8 +917,8 @@
* The first object is the highest k value i.e. objectArray[0]
* The second object is the highest k-core as a CyNetwork i.e.
objectArray[1]
*/
- public Object[] getHighestKCore(CySubNetwork network) {
- String callerID = "MCODEAlgorithm.getHighestKCore";
+ private Object[] getHighestKCore(final CySubNetwork network) {
+ final String callerID = "MCODEAlgorithm.getHighestKCore";
if (network == null) {
logger.error("In " + callerID + ": network was null.");
@@ -939,16 +926,15 @@
}
int i = 1;
- CySubNetwork curNet = null, prevNet = null;
+ CySubNetwork curNet = network, prevNet = null;
- while ((curNet = getKCore(network, i)) != null) {
- network = curNet;
+ while ((curNet = getKCore(curNet, i)) != null) {
prevNet = curNet;
i++;
}
-
+
Integer k = i - 1;
- Object[] returnArray = new Object[2];
+ final Object[] returnArray = new Object[2];
returnArray[0] = k;
returnArray[1] = prevNet; //in the last iteration, curNet is
null (loop termination condition)
Modified:
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/model/MCODECluster.java
===================================================================
---
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/model/MCODECluster.java
2012-08-15 22:03:16 UTC (rev 30201)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/model/MCODECluster.java
2012-08-15 22:06:58 UTC (rev 30202)
@@ -48,7 +48,7 @@
public class MCODECluster {
private List<Long> alCluster;
- private CyNetworkView view; // keeps track of layout so that layout
process doesn't have to be repeated unecessarily
+ private CyNetworkView view; // keeps track of layout so that layout
process doesn't have to be repeated unnecessarily
private CySubNetwork network;
private Long seedNode;
private Map<Long, Boolean> nodeSeenHashMap; // stores the nodes that
have already been included in higher ranking clusters
@@ -72,7 +72,7 @@
return clusterName;
}
- public void setClusterName(String clusterName) {
+ public void setClusterName(final String clusterName) {
this.clusterName = clusterName;
}
@@ -80,7 +80,10 @@
return view;
}
- public void setView(CyNetworkView view) {
+ public void setView(final CyNetworkView view) {
+ if (this.view != null)
+ this.view.dispose();
+
this.view = view;
}
@@ -88,7 +91,11 @@
return network;
}
- public void setNetwork(CySubNetwork network) {
+ public void setNetwork(final CySubNetwork network) {
+ if (view != null && view.getModel().equals(this.network))
+ view.dispose();
+
+ dispose(this.network);
this.network = network;
}
@@ -96,7 +103,7 @@
return clusterScore;
}
- public void setClusterScore(double clusterScore) {
+ public void setClusterScore(final double clusterScore) {
this.clusterScore = clusterScore;
}
@@ -104,7 +111,7 @@
return alCluster;
}
- public void setALCluster(List<Long> alCluster) {
+ public void setALCluster(final List<Long> alCluster) {
this.alCluster = alCluster;
}
@@ -132,4 +139,17 @@
this.rank = rank;
this.clusterName = "Cluster " + (rank + 1);
}
+
+ public void dispose() {
+ if (view != null)
+ view.dispose();
+ dispose(network);
+ }
+
+ private static void dispose(final CySubNetwork net) {
+ if (net != null) {
+ net.getRootNetwork().removeSubNetwork(net);
+ net.dispose();
+ }
+ }
}
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
2012-08-15 22:03:16 UTC (rev 30201)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/task/MCODEAnalyzeTask.java
2012-08-15 22:06:58 UTC (rev 30202)
@@ -149,7 +149,7 @@
} catch (Exception e) {
throw new Exception("Error while executing the MCODE
analysis", e);
} finally {
- mcodeUtil.removeUnusedSubNetworks(network, clusters);
+ mcodeUtil.disposeUnusedSubNetworks(network, clusters);
if (listener != null) {
listener.handleEvent(new
AnalysisCompletedEvent(success, clusters, imageList));
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
2012-08-15 22:03:16 UTC (rev 30201)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/util/MCODEUtil.java
2012-08-15 22:06:58 UTC (rev 30202)
@@ -129,6 +129,7 @@
* * Description: Utilities for MCODE
*/
+// TODO refactor: remove circular dependencies
/**
* Utilities for MCODE
*/
@@ -161,7 +162,7 @@
private int currentResultId;
- private Set<CySubNetwork> subNetworks;
+ private Map<CyRootNetwork, Set<CySubNetwork>> createdSubNetworks;
private static final Logger logger =
LoggerFactory.getLogger(MCODEUtil.class);
@@ -209,26 +210,39 @@
currentParameters = new MCODECurrentParameters();
networkAlgorithms = new HashMap<Long, MCODEAlgorithm>();
networkResults = new HashMap<Long, Set<Integer>>();
- subNetworks = new HashSet<CySubNetwork>();
+ createdSubNetworks = new HashMap<CyRootNetwork,
Set<CySubNetwork>>();
}
- public void removeUnusedSubNetworks(CyNetwork network, MCODECluster[]
clusters) {
- Map<CySubNetwork, Boolean> clusterNetworks = new
HashMap<CySubNetwork, Boolean>();
+ public void disposeUnusedSubNetworks(final CyNetwork network, final
MCODECluster[] clusters) {
+ final Map<CySubNetwork, Boolean> clusterNetworks = new
HashMap<CySubNetwork, Boolean>();
if (clusters != null && clusters.length > 0) {
for (MCODECluster c : clusters)
clusterNetworks.put(c.getNetwork(),
Boolean.TRUE);
}
- CyRootNetwork rootNet = rootNetworkMgr.getRootNetwork(network);
+ final CyRootNetwork rootNet =
rootNetworkMgr.getRootNetwork(network);
+ final Set<CySubNetwork> snSet = createdSubNetworks.get(rootNet);
- for (CySubNetwork sn : subNetworks) {
- // Only remove the subnetwork if it is not registered
- if (!clusterNetworks.containsKey(sn) &&
!networkMgr.networkExists(sn.getSUID()))
- rootNet.removeSubNetwork(sn);
+ if (snSet != null) {
+ final Set<CySubNetwork> disposedSet = new
HashSet<CySubNetwork>();
+
+ for (final CySubNetwork sn : snSet) {
+ // Only remove the subnetwork if it is not
registered
+ if (!clusterNetworks.containsKey(sn) &&
!networkMgr.networkExists(sn.getSUID())) {
+ try {
+ if
(rootNet.containsNetwork(sn)) {
+ dispose(sn);
+ disposedSet.add(sn);
+ }
+ } catch (Exception e) {
+ logger.error("Error disposing:
" + sn);
+ }
+ }
+ }
+
+ snSet.removeAll(disposedSet);
}
-
- subNetworks.clear();
}
public MCODECurrentParameters getCurrentParameters() {
@@ -274,34 +288,28 @@
public boolean removeNetworkResult(final int resultId) {
boolean removed = false;
- Long networkToRemove = null;
+ Long networkId = null;
for (Entry<Long, Set<Integer>> entries :
networkResults.entrySet()) {
Set<Integer> ids = entries.getValue();
if (ids.remove(resultId)) {
- if (ids.isEmpty()) {
- networkToRemove = entries.getKey();
- }
+ if (ids.isEmpty())
+ networkId = entries.getKey();
removed = true;
break;
}
}
- if (networkToRemove != null) {
- removeNetworkResults(networkToRemove);
- }
+ if (networkId != null)
+ networkResults.remove(networkId);
this.getCurrentParameters().removeResultParams(resultId);
return removed;
}
- public Set<Integer> removeNetworkResults(final long suid) {
- return networkResults.remove(suid);
- }
-
/**
* Convert a network to an image. This is used by the
MCODEResultsPanel.
*
@@ -491,8 +499,17 @@
}
final CySubNetwork subNet = root.addSubNetwork(nodes, edges,
policy);
- subNetworks.add(subNet);
+ // Save it for later disposal
+ Set<CySubNetwork> snSet = createdSubNetworks.get(root);
+
+ if (snSet == null) {
+ snSet = new HashSet<CySubNetwork>();
+ createdSubNetworks.put(root, snSet);
+ }
+
+ snSet.add(subNet);
+
return subNet;
}
@@ -807,4 +824,13 @@
return props;
}
+
+ public static void dispose(final CyNetwork net) {
+ if (net != null) {
+ if (net instanceof CySubNetwork)
+ ((CySubNetwork)
net).getRootNetwork().removeSubNetwork((CySubNetwork) net);
+
+ net.dispose();
+ }
+ }
}
Added:
csplugins/trunk/toronto/clopes/mcode/src/test/java/org/cytoscape/mcode/internal/AbstractMCODETest.java
===================================================================
---
csplugins/trunk/toronto/clopes/mcode/src/test/java/org/cytoscape/mcode/internal/AbstractMCODETest.java
(rev 0)
+++
csplugins/trunk/toronto/clopes/mcode/src/test/java/org/cytoscape/mcode/internal/AbstractMCODETest.java
2012-08-15 22:06:58 UTC (rev 30202)
@@ -0,0 +1,62 @@
+package org.cytoscape.mcode.internal;
+
+import static org.junit.Assert.assertEquals;
+
+import java.util.List;
+
+import org.cytoscape.ding.NetworkViewTestSupport;
+import org.cytoscape.mcode.internal.model.MCODEAlgorithm;
+import org.cytoscape.mcode.internal.model.MCODECluster;
+import org.cytoscape.mcode.internal.model.MCODEParameterSet;
+import org.cytoscape.mcode.internal.util.MCODEUtil;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNode;
+
+public abstract class AbstractMCODETest {
+
+ protected MCODEAlgorithm alg;
+ protected MCODEUtil mcodeUtil;
+ protected final NetworkViewTestSupport netViewTestSupport;
+
+ public AbstractMCODETest() {
+ netViewTestSupport = new NetworkViewTestSupport();
+ }
+
+ protected MCODECluster[] findClusters(CyNetwork net, int resultId) {
+ return findClusters(net, resultId, new MCODEParameterSet());
+ }
+
+ protected MCODECluster[] findClusters(CyNetwork net, int resultId,
MCODEParameterSet params) {
+ mcodeUtil.getCurrentParameters().setParams(params, resultId,
net.getSUID());
+ alg = new MCODEAlgorithm(net.getSUID(), mcodeUtil);
+ alg.scoreGraph(net, resultId);
+
+ return alg.findClusters(net, resultId);
+ }
+
+ protected CyNetwork createCompleteGraph(int totalNodes) {
+ CyNetwork net = netViewTestSupport.getNetwork();
+
+ for (int i = 0; i < totalNodes; i++) {
+ net.addNode();
+ }
+
+ List<CyNode> nodes = net.getNodeList();
+
+ for (int i = 0; i < totalNodes; i++) {
+ CyNode src = nodes.get(i);
+
+ for (int j = 0; j < totalNodes; j++) {
+ CyNode tgt = nodes.get(j);
+
+ if (src != tgt && !net.containsEdge(src, tgt))
+ net.addEdge(src, tgt, false);
+ }
+ }
+
+ assertEquals((totalNodes*(totalNodes-1))/2, net.getEdgeCount());
+
+ return net;
+ }
+
+}
\ No newline at end of file
Modified:
csplugins/trunk/toronto/clopes/mcode/src/test/java/org/cytoscape/mcode/internal/model/MCODEAlgorithmTest.java
===================================================================
---
csplugins/trunk/toronto/clopes/mcode/src/test/java/org/cytoscape/mcode/internal/model/MCODEAlgorithmTest.java
2012-08-15 22:03:16 UTC (rev 30201)
+++
csplugins/trunk/toronto/clopes/mcode/src/test/java/org/cytoscape/mcode/internal/model/MCODEAlgorithmTest.java
2012-08-15 22:06:58 UTC (rev 30202)
@@ -1,13 +1,13 @@
package org.cytoscape.mcode.internal.model;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
-import java.util.List;
-
import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.application.swing.CySwingApplication;
import org.cytoscape.ding.NetworkViewTestSupport;
import org.cytoscape.event.CyEventHelper;
+import org.cytoscape.mcode.internal.AbstractMCODETest;
import org.cytoscape.mcode.internal.util.MCODEUtil;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkManager;
@@ -65,15 +65,14 @@
/**
* Test for the MCODE algorithm
*/
-public class MCODEAlgorithmTest {
+public class MCODEAlgorithmTest extends AbstractMCODETest {
- MCODEAlgorithm alg;
CyNetwork networkSmall;
- MCODEUtil mcodeUtil;
@Mock RenderingEngineFactory<CyNetwork> rendererFactory;
@Mock CyRootNetworkManager rootNetMgr;
@Mock CyApplicationManager appMgr;
+ @Mock CyNetworkManager netMgr;
@Mock CyNetworkViewManager netViewMgr;
@Mock VisualMappingManager vmMgr;
@Mock VisualStyleFactory styleFactory;
@@ -83,7 +82,7 @@
@Mock FileUtil fileUtil;
NetworkViewTestSupport netViewTestSupport;
- CyNetworkManager netMgr;
+
CyNetworkViewFactory netViewFactory;
@Before
@@ -159,46 +158,9 @@
assertNotNull(c.getSeedNode());
// TODO: fix
- // check scores of the nodes
+ // check scores of all nodes
// for (CyNode n : cn.getNodeList()) {
// assertEquals(13.345, alg.getNodeScore(n.getSUID(),
resultId), 0.001);
// }
}
-
- private MCODECluster[] findClusters(CyNetwork net, int resultId) {
- return findClusters(net, resultId, new MCODEParameterSet());
- }
-
- private MCODECluster[] findClusters(CyNetwork net, int resultId,
MCODEParameterSet params) {
- mcodeUtil.getCurrentParameters().setParams(params, resultId,
net.getSUID());
- alg = new MCODEAlgorithm(net.getSUID(), mcodeUtil);
- alg.scoreGraph(net, resultId);
-
- return alg.findClusters(net, resultId);
- }
-
- private CyNetwork createCompleteGraph(int totalNodes) {
- CyNetwork net = netViewTestSupport.getNetwork();
-
- for (int i = 0; i < totalNodes; i++) {
- net.addNode();
- }
-
- List<CyNode> nodes = net.getNodeList();
-
- for (int i = 0; i < totalNodes; i++) {
- CyNode src = nodes.get(i);
-
- for (int j = 0; j < totalNodes; j++) {
- CyNode tgt = nodes.get(j);
-
- if (src != tgt && !net.containsEdge(src, tgt))
- net.addEdge(src, tgt, false);
- }
- }
-
- assertEquals((totalNodes*(totalNodes-1))/2, net.getEdgeCount());
-
- return net;
- }
}
Added:
csplugins/trunk/toronto/clopes/mcode/src/test/java/org/cytoscape/mcode/internal/util/MCODEUtilTest.java
===================================================================
---
csplugins/trunk/toronto/clopes/mcode/src/test/java/org/cytoscape/mcode/internal/util/MCODEUtilTest.java
(rev 0)
+++
csplugins/trunk/toronto/clopes/mcode/src/test/java/org/cytoscape/mcode/internal/util/MCODEUtilTest.java
2012-08-15 22:06:58 UTC (rev 30202)
@@ -0,0 +1,105 @@
+package org.cytoscape.mcode.internal.util;
+
+import static org.junit.Assert.assertEquals;
+
+import org.cytoscape.application.CyApplicationManager;
+import org.cytoscape.application.swing.CySwingApplication;
+import org.cytoscape.event.CyEventHelper;
+import org.cytoscape.mcode.internal.AbstractMCODETest;
+import org.cytoscape.mcode.internal.model.MCODECluster;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNetworkManager;
+import org.cytoscape.model.subnetwork.CyRootNetwork;
+import org.cytoscape.model.subnetwork.CyRootNetworkManager;
+import org.cytoscape.util.swing.FileUtil;
+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;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mock;
+import org.mockito.MockitoAnnotations;
+
+/**
+ * Copyright (c) 2004 Memorial Sloan-Kettering Cancer Center
+ * *
+ * * Code written by: Gary Bader
+ * * Authors: Gary Bader, Ethan Cerami, Chris Sander
+ * *
+ * * This library is free software; you can redistribute it and/or modify it
+ * * under the terms of the GNU Lesser General Public License as published
+ * * by the Free Software Foundation; either version 2.1 of the License, or
+ * * any later version.
+ * *
+ * * This library is distributed in the hope that it will be useful, but
+ * * WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ * * MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ * * documentation provided hereunder is on an "as is" basis, and
+ * * Memorial Sloan-Kettering Cancer Center
+ * * has no obligations to provide maintenance, support,
+ * * updates, enhancements or modifications. In no event shall the
+ * * Memorial Sloan-Kettering Cancer Center
+ * * be liable to any party for direct, indirect, special,
+ * * incidental or consequential damages, including lost profits, arising
+ * * out of the use of this software and its documentation, even if
+ * * Memorial Sloan-Kettering Cancer Center
+ * * has been advised of the possibility of such damage. See
+ * * the GNU Lesser General Public License for more details.
+ * *
+ * * You should have received a copy of the GNU Lesser General Public License
+ * * along with this library; if not, write to the Free Software Foundation,
+ * * Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ * *
+ * * User: Gary Bader
+ * * Date: Jul 9, 2004
+ * * Time: 11:57:55 AM
+ * * Description JUnit testing for MCODE
+ */
+
+/**
+ * Test for the MCODE algorithm
+ */
+public class MCODEUtilTest extends AbstractMCODETest {
+
+ CyNetwork networkSmall;
+ @Mock RenderingEngineFactory<CyNetwork> rendererFactory;
+ @Mock CyRootNetworkManager rootNetMgr;
+ @Mock CyApplicationManager appMgr;
+ @Mock CyNetworkManager netMgr;
+ @Mock CyNetworkViewManager netViewMgr;
+ @Mock VisualMappingManager vmMgr;
+ @Mock VisualStyleFactory styleFactory;
+ @Mock VisualMappingFunctionFactory vmfFactory;
+ @Mock CySwingApplication swingApp;
+ @Mock CyEventHelper evtHelper;
+ @Mock FileUtil fileUtil;
+
+ CyNetworkViewFactory netViewFactory;
+
+ @Before
+ public void setUp() throws Exception {
+ MockitoAnnotations.initMocks(this);
+ rootNetMgr = netViewTestSupport.getRootNetworkFactory();
+ netViewFactory = netViewTestSupport.getNetworkViewFactory();
+
+ mcodeUtil = new MCODEUtil(rendererFactory, netViewFactory,
rootNetMgr, appMgr, netMgr, netViewMgr,
+ styleFactory, vmMgr, swingApp, evtHelper,
vmfFactory, vmfFactory, fileUtil);
+ }
+
+ @Test
+ public void testDisposeUnnusedNetworks() {
+ final CyNetwork net = createCompleteGraph(16);
+ final CyRootNetwork rn =
netViewTestSupport.getRootNetworkFactory().getRootNetwork(net);
+ int originalNetCount = rn.getSubNetworkList().size();
+ int resultId = 1;
+ MCODECluster[] clusters = findClusters(net, resultId);
+ assertEquals(1, clusters.length);
+
+ mcodeUtil.disposeUnusedSubNetworks(net, clusters);
+
+ assertEquals(originalNetCount + clusters.length,
rn.getSubNetworkList().size());
+ }
+}
--
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