Author: clopes
Date: 2012-08-15 09:44:27 -0700 (Wed, 15 Aug 2012)
New Revision: 30197
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/view/MCODEResultsPanel.java
Log:
Fixed MCODE node attributes: It doesn't need to add virtual columns to cluster
networks anymore, since the new DEFAULT table handles it automatically.
Fixed repeated cluster names in "MCODE_Cluster" column.
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 15:02:11 UTC (rev 30196)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/util/MCODEUtil.java
2012-08-15 16:44:27 UTC (rev 30197)
@@ -61,14 +61,12 @@
import org.cytoscape.mcode.internal.model.MCODECurrentParameters;
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.CyIdentifiable;
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.SavePolicy;
import org.cytoscape.model.subnetwork.CyRootNetwork;
import org.cytoscape.model.subnetwork.CyRootNetworkManager;
@@ -515,29 +513,6 @@
view.fitContent();
view.updateView();
}
-
- 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", "rawtypes" })
public VisualStyle getClusterStyle() {
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
2012-08-15 15:02:11 UTC (rev 30196)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/view/MCODEResultsPanel.java
2012-08-15 16:44:27 UTC (rev 30197)
@@ -24,6 +24,7 @@
import java.util.HashMap;
import java.util.Hashtable;
import java.util.Iterator;
+import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
@@ -114,6 +115,10 @@
@SuppressWarnings("serial")
public class MCODEResultsPanel extends JPanel implements CytoPanelComponent {
+ private static final String SCORE_ATTR = "MCODE_Score";
+ private static final String NODE_STATUS_ATTR = "MCODE_Node_Status";
+ private static final String CLUSTER_ATTR = "MCODE_Cluster";
+
// table size parameters
private static final int graphPicSize = 80;
private static final int defaultRowHeight = graphPicSize + 8;
@@ -307,6 +312,7 @@
* @return panel A JPanel with the contents of the explore panel, get's
* added to the explore collapsable panel's content pane
*/
+ @SuppressWarnings("rawtypes")
private JPanel createExploreContent(int selectedRow) {
JPanel panel = new JPanel();
panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS));
@@ -421,41 +427,33 @@
Long rgi = n.getSUID();
CyTable netNodeTbl = network.getDefaultNodeTable();
- if (netNodeTbl.getColumn("MCODE_Cluster") == null)
- netNodeTbl.createListColumn("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);
+ if (netNodeTbl.getColumn(CLUSTER_ATTR) == null)
+ netNodeTbl.createListColumn(CLUSTER_ATTR,
String.class, false);
+ if (netNodeTbl.getColumn(NODE_STATUS_ATTR) == null)
+ netNodeTbl.createColumn(NODE_STATUS_ATTR,
String.class, false);
+ if (netNodeTbl.getColumn(SCORE_ATTR) == null)
+ netNodeTbl.createColumn(SCORE_ATTR,
Double.class, false);
CyRow nodeRow = network.getRow(n);
- nodeRow.set("MCODE_Node_Status", "Unclustered");
- nodeRow.set("MCODE_Score",
alg.getNodeScore(n.getSUID(), resultId));
+ nodeRow.set(NODE_STATUS_ATTR, "Unclustered");
+ nodeRow.set(SCORE_ATTR, alg.getNodeScore(n.getSUID(),
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>();
+ Set<String> clusterNameSet = new
LinkedHashSet<String>();
- if (nodeRow.isSet("MCODE_Cluster")) {
- clusterArrayList =
nodeRow.getList("MCODE_Cluster", String.class);
-
clusterArrayList.add(cluster.getClusterName());
- } else {
-
clusterArrayList.add(cluster.getClusterName());
- }
+ if (nodeRow.isSet(CLUSTER_ATTR))
+
clusterNameSet.addAll(nodeRow.getList(CLUSTER_ATTR, String.class));
- nodeRow.set("MCODE_Cluster",
clusterArrayList);
+
clusterNameSet.add(cluster.getClusterName());
+ nodeRow.set(CLUSTER_ATTR, new
ArrayList<String>(clusterNameSet));
- if (cluster.getSeedNode() == rgi) {
-
nodeRow.set("MCODE_Node_Status", "Seed");
- } else {
-
nodeRow.set("MCODE_Node_Status", "Clustered");
- }
+ if (cluster.getSeedNode() == rgi)
+ nodeRow.set(NODE_STATUS_ATTR,
"Seed");
+ else
+ nodeRow.set(NODE_STATUS_ATTR,
"Clustered");
}
}
}
@@ -477,7 +475,7 @@
}
@Override
- public void actionPerformed(ActionEvent actionEvent) {
+ public void actionPerformed(final ActionEvent evt) {
final NumberFormat nf = NumberFormat.getInstance();
nf.setMaximumFractionDigits(3);
final MCODECluster cluster = clusters[selectedRow];
@@ -492,8 +490,6 @@
CySubNetwork newNetwork =
mcodeUtil.createSubNetwork(clusterNetwork, clusterNetwork.getNodeList(),
SavePolicy.SESSION_FILE);
newNetwork.getRow(newNetwork).set(CyNetwork.NAME, title);
-
- mcodeUtil.addVirtualColumns(newNetwork,
network);
VisualStyle vs =
mcodeUtil.getNetworkViewStyle(networkView);
CyNetworkView newNetworkView =
mcodeUtil.createNetworkView(newNetwork, vs);
@@ -647,6 +643,7 @@
listIt(enumerations);
}
+ @SuppressWarnings("rawtypes")
public void listIt(HashMap<?, ?> enumerations) {
// First we sort the hash map of attributes values and
their occurrences
ArrayList<?> enumerationsSorted = sortMap(enumerations);
@@ -714,7 +711,7 @@
* Has values mapped to keys
* @return outputList of Map.Entries
*/
- @SuppressWarnings("unchecked")
+ @SuppressWarnings({ "unchecked", "rawtypes" })
private ArrayList sortMap(Map map) {
ArrayList outputList = null;
int count = 0;
@@ -760,7 +757,7 @@
this.modelEnumerator = modelEnumerator;
}
- @SuppressWarnings("unchecked")
+ @SuppressWarnings({ "unchecked", "rawtypes" })
public void actionPerformed(ActionEvent e) {
// The key is the attribute value and the value is the
number of times that value appears in the cluster
HashMap<String, Integer> attributeEnumerations = new
HashMap<String, Integer>();
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