Author: clopes
Date: 2012-01-12 15:10:02 -0800 (Thu, 12 Jan 2012)
New Revision: 28005
Removed:
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/model/MCODEGraph.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/util/MCODEUtil.java
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/view/MCODEResultsPanel.java
Log:
Deleted the MCODEGraph--it uses CySubNetworks again.
Fixed MCODE sub-network attributes + MCODE style/vizmappers
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
2012-01-12 22:55:52 UTC (rev 28004)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/model/MCODEAlgorithm.java
2012-01-12 23:10:02 UTC (rev 28005)
@@ -16,6 +16,7 @@
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
+import org.cytoscape.model.subnetwork.CySubNetwork;
import org.cytoscape.work.TaskMonitor;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -353,11 +354,11 @@
}
// Create an input graph for
the filter and haircut methods
- MCODEGraph clusterGraph =
createClusterGraph(alCluster, inputNetwork);
+ CySubNetwork clusterNet =
createClusterNetwork(alCluster, inputNetwork);
- if
(!filterCluster(clusterGraph)) {
+ if (!filterCluster(clusterNet))
{
if (params.isHaircut())
{
-
haircutCluster(clusterGraph, alCluster);
+
haircutCluster(clusterNet, alCluster);
}
if (params.isFluff()) {
@@ -365,8 +366,8 @@
}
currentCluster.setALCluster(alCluster);
- clusterGraph =
createClusterGraph(alCluster, inputNetwork);
-
currentCluster.setGraph(clusterGraph);
+ clusterNet =
createClusterNetwork(alCluster, inputNetwork);
+
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
currentCluster.setResultId(resultId);
@@ -471,7 +472,7 @@
}
// Create an input graph for the filter and haircut methods
- MCODEGraph clusterNetwork = createClusterGraph(alCluster,
inputNetwork);
+ CySubNetwork clusterNetwork = createClusterNetwork(alCluster,
inputNetwork);
if (params.isHaircut()) {
haircutCluster(clusterNetwork, alCluster);
@@ -482,14 +483,14 @@
}
cluster.setALCluster(alCluster);
- clusterNetwork = createClusterGraph(alCluster, inputNetwork);
- cluster.setGraph(clusterNetwork);
+ clusterNetwork = createClusterNetwork(alCluster, inputNetwork);
+ cluster.setNetwork(clusterNetwork);
cluster.setClusterScore(scoreCluster(cluster));
return cluster;
}
- private MCODEGraph createClusterGraph(List<Integer> alCluster,
CyNetwork inputNetwork) {
+ private CySubNetwork createClusterNetwork(List<Integer> alCluster,
CyNetwork inputNetwork) {
Set<CyNode> nodes = new HashSet<CyNode>();
for (int index : alCluster) {
@@ -497,9 +498,9 @@
nodes.add(n);
}
- MCODEGraph clusterGraph = mcodeUtil.createGraph(inputNetwork,
nodes);
+ CySubNetwork outputNetwork =
mcodeUtil.createSubNetwork(inputNetwork, nodes);
- return clusterGraph;
+ return outputNetwork;
}
/**
@@ -531,8 +532,8 @@
int numNodes = 0;
double density = 0.0, score = 0.0;
- numNodes = cluster.getGraph().getNodeCount();
- density = calcDensity(cluster.getGraph(), true);
+ numNodes = cluster.getNetwork().getNodeCount();
+ density = calcDensity(cluster.getNetwork(), true);
score = density * numNodes;
return score;
@@ -594,9 +595,9 @@
}
// extract neighborhood subgraph
- MCODEGraph neighborhoodGraph =
mcodeUtil.createGraph(inputNetwork, neighbors);
+ CySubNetwork neighborhoodNet =
mcodeUtil.createSubNetwork(inputNetwork, neighbors);
- if (neighborhoodGraph == null) {
+ if (neighborhoodNet == null) {
// this shouldn't happen
logger.error("In " + callerID + ": gpNodeNeighborhood
was null.");
return null;
@@ -606,17 +607,17 @@
NodeInfo nodeInfo = new NodeInfo();
// Density
- if (neighborhoodGraph != null) {
- nodeInfo.density = calcDensity(neighborhoodGraph,
params.isIncludeLoops());
+ if (neighborhoodNet != null) {
+ nodeInfo.density = calcDensity(neighborhoodNet,
params.isIncludeLoops());
}
nodeInfo.numNodeNeighbors = neighborhood.length;
// Calculate the highest k-core
Integer k = null;
- Object[] returnArray = getHighestKCore(neighborhoodGraph);
+ Object[] returnArray = getHighestKCore(neighborhoodNet);
k = (Integer) returnArray[0];
- MCODEGraph kCore = (MCODEGraph) returnArray[1];
+ CySubNetwork kCore = (CySubNetwork) returnArray[1];
nodeInfo.coreLevel = k.intValue();
// Calculate the core density - amplifies the density of
heavily interconnected regions and attenuates
@@ -772,16 +773,16 @@
/**
* Checks if the cluster needs to be filtered according to heuristics
in this method
*
- * @param clusterGraph The cluster to check if it passes the filter
+ * @param clusterNetwork The cluster to check if it passes the filter
* @return true if cluster should be filtered, false otherwise
*/
- private boolean filterCluster(MCODEGraph clusterGraph) {
- if (clusterGraph == null) {
+ private boolean filterCluster(CySubNetwork clusterNetwork) {
+ if (clusterNetwork == null) {
return true;
}
// filter if the cluster does not satisfy the user specified
k-core
- MCODEGraph kCore = getKCore(clusterGraph, params.getKCore());
+ CySubNetwork kCore = getKCore(clusterNetwork,
params.getKCore());
return kCore == null;
}
@@ -789,13 +790,13 @@
/**
* Gives the cluster a haircut (removed singly connected nodes by
taking a 2-core)
*
- * @param clusterGraph The cluster graph
+ * @param clusterNetwork The cluster network
* @param cluster The cluster node ID list (in the original
graph)
* @return true
*/
- private boolean haircutCluster(MCODEGraph clusterGraph, List<Integer>
cluster) {
+ private boolean haircutCluster(CySubNetwork clusterNetwork,
List<Integer> cluster) {
// get 2-core
- MCODEGraph kCore = getKCore(clusterGraph, 2);
+ CySubNetwork kCore = getKCore(clusterNetwork, 2);
if (kCore != null) {
// clear the cluster and add all 2-core nodes back into
it
@@ -818,7 +819,7 @@
* possible edges.
* @return The density of the network
*/
- public double calcDensity(MCODEGraph network, boolean includeLoops) {
+ public double calcDensity(CySubNetwork network, boolean includeLoops) {
int possibleEdgeNum = 0, actualEdgeNum = 0, loopCount = 0;
double density = 0;
@@ -863,7 +864,7 @@
* @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 MCODEGraph getKCore(MCODEGraph inputNetwork, int k) {
+ public CySubNetwork getKCore(CySubNetwork inputNetwork, int k) {
String callerID = "MCODEAlgorithm.getKCore";
if (inputNetwork == null) {
@@ -873,7 +874,7 @@
// filter all nodes with degree less than k until convergence
boolean firstLoop = true;
- MCODEGraph outputNetwork = null;
+ CySubNetwork outputNetwork = null;
while (true) {
int numDeleted = 0;
@@ -898,7 +899,7 @@
outputNodes.add(n);
}
- outputNetwork =
mcodeUtil.createGraph(inputNetwork.getRootNetwork(), outputNodes);
+ outputNetwork =
mcodeUtil.createSubNetwork(inputNetwork.getRootNetwork(), outputNodes);
if (outputNetwork.getNodeCount() == 0) {
return null;
@@ -920,14 +921,14 @@
}
/**
- * Find the highest k-core in the input graph.
+ * Find the highest k-core in the input network.
*
* @param network The input network
* @return Returns the k-value and the core as an Object array.
* 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(MCODEGraph network) {
+ public Object[] getHighestKCore(CySubNetwork network) {
String callerID = "MCODEAlgorithm.getHighestKCore";
if (network == null) {
@@ -936,7 +937,7 @@
}
int i = 1;
- MCODEGraph curNet = null, prevNet = null;
+ CySubNetwork curNet = null, prevNet = null;
while ((curNet = getKCore(network, i)) != null) {
network = curNet;
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
2012-01-12 22:55:52 UTC (rev 28004)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/model/MCODECluster.java
2012-01-12 23:10:02 UTC (rev 28005)
@@ -3,7 +3,7 @@
import java.util.List;
import java.util.Map;
-import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.subnetwork.CySubNetwork;
import org.cytoscape.view.model.CyNetworkView;
/**
@@ -49,7 +49,7 @@
private List<Integer> alCluster;
private CyNetworkView view; // keeps track of layout so that layout
process doesn't have to be repeated unecessarily
- private MCODEGraph graph;
+ private CySubNetwork network;
private int seedNode;
private Map<Integer, Boolean> nodeSeenHashMap; // stores the nodes that
have already been included in higher ranking clusters
private double clusterScore;
@@ -84,18 +84,14 @@
this.view = view;
}
- public MCODEGraph getGraph() {
- return graph;
+ public CySubNetwork getNetwork() {
+ return network;
}
- public void setGraph(MCODEGraph graph) {
- this.graph = graph;
+ public void setNetwork(CySubNetwork network) {
+ this.network = network;
}
- public CyNetwork getNetwork() {
- return graph != null ? graph.getSubNetwork() : null;
- }
-
public double getClusterScore() {
return clusterScore;
}
Deleted:
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/model/MCODEGraph.java
===================================================================
---
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/model/MCODEGraph.java
2012-01-12 22:55:52 UTC (rev 28004)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/model/MCODEGraph.java
2012-01-12 23:10:02 UTC (rev 28005)
@@ -1,139 +0,0 @@
-package org.cytoscape.mcode.internal.model;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.cytoscape.model.CyEdge;
-import org.cytoscape.model.CyEdge.Type;
-import org.cytoscape.model.CyNode;
-import org.cytoscape.model.subnetwork.CyRootNetwork;
-import org.cytoscape.model.subnetwork.CySubNetwork;
-
-public class MCODEGraph {
-
- private final CyRootNetwork rootNetwork;
- private final Set<CyNode> nodes;
- private final Set<CyEdge> edges;
- private final Map<Integer, CyNode> nodeMap;
- private final Map<Integer, CyEdge> edgeMap;
-
- private CySubNetwork subNetwork;
-
- public MCODEGraph(final CyRootNetwork rootNetwork, final
Collection<CyNode> nodes, final Collection<CyEdge> edges) {
- if (rootNetwork == null)
- throw new NullPointerException("rootNetwork is null!");
- if (nodes == null)
- throw new NullPointerException("nodes is null!");
- if (edges == null)
- throw new NullPointerException("edges is null!");
-
- this.rootNetwork = rootNetwork;
- this.nodes = new HashSet<CyNode>(nodes.size());
- this.edges = new HashSet<CyEdge>(edges.size());
- this.nodeMap = new HashMap<Integer, CyNode>(nodes.size());
- this.edgeMap = new HashMap<Integer, CyEdge>(edges.size());
-
- for (CyNode n : nodes) addNode(n);
- for (CyEdge e : edges) addEdge(e);
- }
-
- public boolean addNode(CyNode node) {
- if (nodes.contains(node)) return false;
- node = rootNetwork.getNode(node.getIndex());
-
- if (nodes.add(node)) {
- nodeMap.put(node.getIndex(), node);
- return true;
- }
-
- return false;
- }
-
- public boolean addEdge(CyEdge edge) {
- if (edges.contains(edge)) return false;
-
- if (nodes.contains(edge.getSource()) &&
nodes.contains(edge.getTarget())) {
- edge = rootNetwork.getEdge(edge.getIndex());
-
- if (edges.add(edge)) {
- edgeMap.put(edge.getIndex(), edge);
- return true;
- }
- }
-
- return false;
- }
-
- public int getNodeCount() {
- return nodes.size();
- }
-
- public int getEdgeCount() {
- return edges.size();
- }
-
- public List<CyNode> getNodeList() {
- return new ArrayList<CyNode>(nodes);
- }
-
- public List<CyEdge> getEdgeList() {
- return new ArrayList<CyEdge>(edges);
- }
-
- public boolean containsNode(CyNode node) {
- return nodes.contains(node);
- }
-
- public boolean containsEdge(CyEdge edge) {
- return edges.contains(edge);
- }
-
- public CyNode getNode(int index) {
- return nodeMap.get(index);
- }
-
- public CyEdge getEdge(int index) {
- return edgeMap.get(index);
- }
-
- public List<CyEdge> getAdjacentEdgeList(CyNode node, Type edgeType) {
- List<CyEdge> rootList = rootNetwork.getAdjacentEdgeList(node,
edgeType);
- List<CyEdge> list = new ArrayList<CyEdge>(rootList.size());
-
- for (CyEdge e : rootList) {
- if (containsEdge(e))
- list.add(e);
- }
-
- return list;
- }
-
- public List<CyEdge> getConnectingEdgeList(CyNode source, CyNode target,
Type edgeType) {
- List<CyEdge> rootList =
rootNetwork.getConnectingEdgeList(source, target, edgeType);
- List<CyEdge> list = new ArrayList<CyEdge>(rootList.size());
-
- for (CyEdge e : rootList) {
- if (containsEdge(e))
- list.add(e);
- }
-
- return list;
- }
-
- public CyRootNetwork getRootNetwork() {
- return rootNetwork;
- }
-
- public CySubNetwork getSubNetwork() {
- if (subNetwork == null) {
- subNetwork = rootNetwork.addSubNetwork(nodes, edges);
- }
-
- return subNetwork;
- }
-}
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
2012-01-12 22:55:52 UTC (rev 28004)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/util/MCODEUtil.java
2012-01-12 23:10:02 UTC (rev 28005)
@@ -40,14 +40,15 @@
import org.cytoscape.mcode.internal.model.MCODEAlgorithm;
import org.cytoscape.mcode.internal.model.MCODECluster;
import org.cytoscape.mcode.internal.model.MCODECurrentParameters;
-import org.cytoscape.mcode.internal.model.MCODEGraph;
import org.cytoscape.mcode.internal.util.layout.SpringEmbeddedLayouter;
import org.cytoscape.mcode.internal.view.MCODELoader;
+import org.cytoscape.model.CyColumn;
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyRow;
+import org.cytoscape.model.CyTable;
import org.cytoscape.model.CyTableEntry;
import org.cytoscape.model.subnetwork.CyRootNetwork;
import org.cytoscape.model.subnetwork.CyRootNetworkManager;
@@ -433,11 +434,11 @@
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));
@@ -453,26 +454,6 @@
return subNet;
}
-
- public MCODEGraph createGraph(final CyNetwork net, Collection<CyNode>
nodes) {
- final CyRootNetwork root = rootNetworkMgr.getRootNetwork(net);
- final Set<CyEdge> edges = new HashSet<CyEdge>();
-
- for (CyNode n : nodes) {
- Set<CyEdge> adjacentEdges = new
HashSet<CyEdge>(net.getAdjacentEdgeList(n, CyEdge.Type.ANY));
-
- // Get only the edges that connect nodes that belong to
the subnetwork:
- for (CyEdge e : adjacentEdges) {
- if (nodes.contains(e.getSource()) &&
nodes.contains(e.getTarget())) {
- edges.add(e);
- }
- }
- }
-
- final MCODEGraph graph = new MCODEGraph(root, nodes, edges);
-
- return graph;
- }
public CyNetworkView createNetworkView(final CyNetwork net, VisualStyle
vs) {
final CyNetworkView view =
networkViewFactory.createNetworkView(net, false);
@@ -499,6 +480,29 @@
}
}
+ public void addVirtualColumns(CySubNetwork subNetwork, CyNetwork
parent) {
+ CyTable tbl = subNetwork.getDefaultNodeTable();
+ CyTable parentTbl = parent.getDefaultNodeTable();
+
+ // Add virtual columns for all of the parent network columns
(only nodes):
+ final Collection<CyColumn> columns = parentTbl.getColumns();
+
+ for (CyColumn col : columns) {
+ final String colName = col.getName();
+
+ if (tbl.getColumn(colName) == null)
+ tbl.addVirtualColumn(colName, colName,
parentTbl, CyNode.SUID, false);
+ }
+
+ // Add MCODE columns
+ if (tbl.getColumn("MCODE_Cluster") == null)
+ tbl.addVirtualColumn("MCODE_Cluster", "MCODE_Cluster",
parentTbl, CyNetwork.SUID, false);
+ if (tbl.getColumn("MCODE_Node_Status") == null)
+ tbl.addVirtualColumn("MCODE_Node_Status",
"MCODE_Node_Status", parentTbl, CyNetwork.SUID, false);
+ if (tbl.getColumn("MCODE_Score") == null)
+ tbl.addVirtualColumn("MCODE_Score", "MCODE_Score",
parentTbl, CyNetwork.SUID, false);
+ }
+
@SuppressWarnings("unchecked")
public VisualStyle getClusterStyle() {
if (clusterStyle == null) {
Modified:
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/view/MCODEResultsPanel.java
===================================================================
---
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/view/MCODEResultsPanel.java
2012-01-12 22:55:52 UTC (rev 28004)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/view/MCODEResultsPanel.java
2012-01-12 23:10:02 UTC (rev 28005)
@@ -61,6 +61,8 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyRow;
+import org.cytoscape.model.CyTable;
+import org.cytoscape.model.subnetwork.CySubNetwork;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.View;
import org.cytoscape.view.presentation.property.MinimalVisualLexicon;
@@ -302,7 +304,6 @@
* @return panel A JPanel with the contents of the explore panel, get's
* added to the explore collapsable panel's content pane
*/
- @SuppressWarnings("unchecked")
private JPanel createExploreContent(int selectedRow) {
JPanel panel = new JPanel();
panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS));
@@ -413,44 +414,47 @@
* used for scoring at the time
*/
public double setNodeAttributesAndGetMaxScore() {
- network.getDefaultNodeTable().deleteColumn("MCODE_Cluster");
- network.getDefaultNodeTable().deleteColumn("MCODE_Node_Status");
- network.getDefaultNodeTable().deleteColumn("MCODE_Score");
-
- network.getDefaultNodeTable().createListColumn("MCODE_Cluster",
String.class, false);
- network.getDefaultNodeTable().createColumn("MCODE_Node_Status",
String.class, false);
- network.getDefaultNodeTable().createColumn("MCODE_Score",
Double.class, false);
-
for (CyNode n : network.getNodeList()) {
int rgi = n.getIndex();
+ CyTable netNodeTbl = network.getDefaultNodeTable();
+
+ if (netNodeTbl.getColumn("MCODE_Cluster") == null)
+ netNodeTbl.createColumn("MCODE_Cluster",
String.class, false);
+ if (netNodeTbl.getColumn("MCODE_Node_Status") == null)
+ netNodeTbl.createColumn("MCODE_Node_Status",
String.class, false);
+ if (netNodeTbl.getColumn("MCODE_Score") == null)
+ netNodeTbl.createColumn("MCODE_Score",
Double.class, false);
- CyRow row = network.getRow(n);
- row.set("MCODE_Node_Status", "Unclustered");
+ CyRow nodeRow = network.getRow(n);
+ nodeRow.set("MCODE_Node_Status", "Unclustered");
+ nodeRow.set("MCODE_Score",
alg.getNodeScore(n.getIndex(), resultId));
for (int c = 0; c < clusters.length; c++) {
MCODECluster cluster = clusters[c];
-
+ CySubNetwork clusterNet = cluster.getNetwork();
+
+ // TODO: encapsulate it with sub-net creation
+ mcodeUtil.addVirtualColumns(clusterNet,
network);
+
if (cluster.getALCluster().contains(rgi)) {
List<String> clusterArrayList = new
ArrayList<String>();
- if (row.isSet("MCODE_Cluster")) {
- clusterArrayList =
row.getList("MCODE_Cluster", String.class);
+ if (nodeRow.isSet("MCODE_Cluster")) {
+ clusterArrayList =
nodeRow.getList("MCODE_Cluster", String.class);
clusterArrayList.add(cluster.getClusterName());
} else {
clusterArrayList.add(cluster.getClusterName());
}
- row.set("MCODE_Cluster",
clusterArrayList);
+ nodeRow.set("MCODE_Cluster",
clusterArrayList);
if (cluster.getSeedNode() == rgi) {
- row.set("MCODE_Node_Status",
"Seed");
+
nodeRow.set("MCODE_Node_Status", "Seed");
} else {
- row.set("MCODE_Node_Status",
"Clustered");
+
nodeRow.set("MCODE_Node_Status", "Clustered");
}
}
}
-
- row.set("MCODE_Score", alg.getNodeScore(n.getIndex(),
resultId));
}
return alg.getMaxScore(resultId);
@@ -482,9 +486,11 @@
@Override
protected CyNetworkView doInBackground() throws
Exception {
- CyNetwork newNetwork =
mcodeUtil.createSubNetwork(clusterNetwork, clusterNetwork.getNodeList());
+ CySubNetwork newNetwork =
mcodeUtil.createSubNetwork(clusterNetwork, clusterNetwork.getNodeList());
newNetwork.getRow(newNetwork).set(CyNetwork.NAME, title);
+ mcodeUtil.addVirtualColumns(newNetwork,
network);
+
VisualStyle vs =
mcodeUtil.getNetworkViewStyle(networkView);
CyNetworkView newNetworkView =
mcodeUtil.createNetworkView(newNetwork, vs);
@@ -637,7 +643,6 @@
listIt(enumerations);
}
- @SuppressWarnings("unchecked")
public void listIt(HashMap<?, ?> enumerations) {
// First we sort the hash map of attributes values and
their occurrences
ArrayList<?> enumerationsSorted = sortMap(enumerations);
@@ -739,8 +744,7 @@
}
/**
- * Handles the selection of all available node attributes for the
- * enumeration within the cluster
+ * Handles the selection of all available node attributes for the
enumeration within the cluster
*/
private class enumerateAction extends AbstractAction {
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