Author: kono
Date: 2010-01-12 11:38:46 -0800 (Tue, 12 Jan 2010)
New Revision: 18877
Modified:
csplugins/trunk/ucsd/ruschein/DenovoPGNetworkAlignment/src/networks/denovoPGNetworkAlignment/HCSearch2.java
csplugins/trunk/ucsd/ruschein/DenovoPGNetworkAlignment/src/org/cytoscape/DenovoPGNetworkAlignmentPlugin/NestedNetworkCreator.java
csplugins/trunk/ucsd/ruschein/DenovoPGNetworkAlignment/src/org/cytoscape/DenovoPGNetworkAlignmentPlugin/SearchTask.java
Log:
Overview network will be created after search.
Modified:
csplugins/trunk/ucsd/ruschein/DenovoPGNetworkAlignment/src/networks/denovoPGNetworkAlignment/HCSearch2.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/DenovoPGNetworkAlignment/src/networks/denovoPGNetworkAlignment/HCSearch2.java
2010-01-12 19:24:23 UTC (rev 18876)
+++
csplugins/trunk/ucsd/ruschein/DenovoPGNetworkAlignment/src/networks/denovoPGNetworkAlignment/HCSearch2.java
2010-01-12 19:38:46 UTC (rev 18877)
@@ -362,7 +362,7 @@
public static String report(
TypedLinkNetwork<TypedLinkNodeModule<String, BFEdge>,
BFEdge> results) {
-
+
final StringBuilder builder = new StringBuilder();
DoubleVector cscores = new DoubleVector(results.numNodes());
@@ -377,7 +377,6 @@
builder.append("Best cluster score: " + cscores.max(false) +
"\n");
builder.append("Worst cluster score: " + cscores.min(false) +
"\n");
builder.append("Largest cluster size: " + csizes.max(false) +
"\n");
-
DoubleVector escores = new DoubleVector(results.numEdges());
for (TypedLinkEdge<TypedLinkNodeModule<String, BFEdge>, BFEdge>
ed : results
@@ -386,13 +385,13 @@
if (score != -1)
escores.add(score);
}
-
+
builder.append("Best edge score: " + escores.max(false) + "\n");
// csizes.plothist(30);
System.out.println(builder.toString());
-
+
return builder.toString();
}
Modified:
csplugins/trunk/ucsd/ruschein/DenovoPGNetworkAlignment/src/org/cytoscape/DenovoPGNetworkAlignmentPlugin/NestedNetworkCreator.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/DenovoPGNetworkAlignment/src/org/cytoscape/DenovoPGNetworkAlignmentPlugin/NestedNetworkCreator.java
2010-01-12 19:24:23 UTC (rev 18876)
+++
csplugins/trunk/ucsd/ruschein/DenovoPGNetworkAlignment/src/org/cytoscape/DenovoPGNetworkAlignmentPlugin/NestedNetworkCreator.java
2010-01-12 19:38:46 UTC (rev 18877)
@@ -1,52 +1,61 @@
package org.cytoscape.DenovoPGNetworkAlignmentPlugin;
+import java.util.Set;
-import cytoscape.CyEdge;
-import cytoscape.CyNetwork;
-import cytoscape.CyNode;
-import cytoscape.Cytoscape;
-import cytoscape.data.CyAttributes;
-import java.util.Set;
import networks.denovoPGNetworkAlignment.BFEdge;
-import networks.linkedNetworks.TypedLinkEdge;
import networks.linkedNetworks.TypedLinkNetwork;
import networks.linkedNetworks.TypedLinkNode;
import networks.linkedNetworks.TypedLinkNodeModule;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
-
-/** Creates an overview network for the detected complexes and nested networks
for each complex.
+/**
+ * Creates an overview network for the detected complexes and nested networks
+ * for each complex.
*/
class NestedNetworkCreator {
CyNetwork overviewNetwork = null;
-
/**
- * Instantiates an overview network of complexes (modules) and one
nested network for each node in the overview network.
+ * Instantiates an overview network of complexes (modules) and one
nested
+ * network for each node in the overview network.
*/
- NestedNetworkCreator(final TypedLinkNetwork<TypedLinkNodeModule<String,
BFEdge>, BFEdge> networkOfModules) {
+ NestedNetworkCreator(
+ final TypedLinkNetwork<TypedLinkNodeModule<String,
BFEdge>, BFEdge> networkOfModules) {
createOverviewNetwork(networkOfModules.nodes());
}
- CyNetwork getOverviewNetwork() { return overviewNetwork; }
+ CyNetwork getOverviewNetwork() {
+ return overviewNetwork;
+ }
- private void createOverviewNetwork(final
Set<TypedLinkNode<TypedLinkNodeModule<String, BFEdge>, BFEdge>> overviewNodes) {
- overviewNetwork =
Cytoscape.createNetwork(findNextAvailableNetworkName("Complexes"), /*
create_view = */ true);
+ private void createOverviewNetwork(
+ final Set<TypedLinkNode<TypedLinkNodeModule<String,
BFEdge>, BFEdge>> overviewNodes) {
+ overviewNetwork = Cytoscape.createNetwork(
+ findNextAvailableNetworkName("Complex Search
Result: " + new java.util.Date()), /* create_view = */
+ true);
int nodeIndex = 1;
for (final TypedLinkNode<TypedLinkNodeModule<String, BFEdge>,
BFEdge> module : overviewNodes) {
- final String nodeName =
findNextAvailableNodeName("Complex" + nodeIndex);
- final CyNode newNode = Cytoscape.getCyNode(nodeName, /*
create = */ true);
+ final String nodeName =
findNextAvailableNodeName("Complex"
+ + nodeIndex);
+ final CyNode newNode = Cytoscape.getCyNode(nodeName, /*
create = */
+ true);
overviewNetwork.addNode(newNode);
++nodeIndex;
}
}
-
/**
- * Finds an unused network name starting with a first choice. If the
first choice is not available, we will successively try to append -1
- * -2, -3 and so on, until we indentify an unused name.
- * @param initialPreference The network name we'd like to use, if it
is available. If not we use it as a prefix instead.
+ * Finds an unused network name starting with a first choice. If the
first
+ * choice is not available, we will successively try to append -1 -2,
-3 and
+ * so on, until we indentify an unused name.
+ *
+ * @param initialPreference
+ * The network name we'd like to use, if it is available. If
not
+ * we use it as a prefix instead.
*/
private String findNextAvailableNetworkName(final String
initialPreference) {
// Try the preferred choice first:
@@ -62,35 +71,40 @@
}
}
-
/**
- * Finds an unused node name starting with a first choice. If the
first choice is not available, we will successively try to append -1
- * -2, -3 and so on, until we indentify an unused name.
- * @param initialPreference The node name we'd like to use, if it is
available. If not we use it as a prefix instead.
+ * Finds an unused node name starting with a first choice. If the first
+ * choice is not available, we will successively try to append -1 -2,
-3 and
+ * so on, until we indentify an unused name.
+ *
+ * @param initialPreference
+ * The node name we'd like to use, if it is available. If
not we
+ * use it as a prefix instead.
*/
private String findNextAvailableNodeName(final String
initialPreference) {
// Try the preferred choice first:
- CyNode node = Cytoscape.getCyNode(initialPreference, /* create
= */ false);
+ CyNode node = Cytoscape
+ .getCyNode(initialPreference, /* create =
*/false);
if (node == null)
return initialPreference;
for (int suffix = 1; true; ++suffix) {
final String titleCandidate = initialPreference + "-" +
suffix;
- node = Cytoscape.getCyNode(titleCandidate, /* create =
*/ false);
+ node = Cytoscape.getCyNode(titleCandidate, /* create =
*/false);
if (node == null)
return titleCandidate;
}
}
+ /**
+ * Returns the first network with title "networkTitle" or null, if
there is
+ * no network w/ this title.
+ */
+ private CyNetwork getNetworkByTitle(final String networkTitle) {
+ for (final CyNetwork network : Cytoscape.getNetworkSet()) {
+ if (network.getTitle().equals(networkTitle))
+ return network;
+ }
- /** Returns the first network with title "networkTitle" or null, if
there is no network w/ this title.
- */
- private CyNetwork getNetworkByTitle(final String networkTitle) {
- for (final CyNetwork network : Cytoscape.getNetworkSet()) {
- if (network.getTitle().equals(networkTitle))
- return network;
- }
-
- return null;
- }
+ return null;
+ }
}
Modified:
csplugins/trunk/ucsd/ruschein/DenovoPGNetworkAlignment/src/org/cytoscape/DenovoPGNetworkAlignmentPlugin/SearchTask.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/DenovoPGNetworkAlignment/src/org/cytoscape/DenovoPGNetworkAlignmentPlugin/SearchTask.java
2010-01-12 19:24:23 UTC (rev 18876)
+++
csplugins/trunk/ucsd/ruschein/DenovoPGNetworkAlignment/src/org/cytoscape/DenovoPGNetworkAlignmentPlugin/SearchTask.java
2010-01-12 19:38:46 UTC (rev 18877)
@@ -35,10 +35,15 @@
hcScoringFunction.Initialize(converter.getPhysicalNetwork(),
converter
.getGeneticNetwork());
final TypedLinkNetwork<TypedLinkNodeModule<String, BFEdge>,
BFEdge> results = HCSearch2
- .search(converter.getPhysicalNetwork(),
converter.getGeneticNetwork(), hcScoringFunction);
-
- setStatus("Search finished!\n\n" + HCSearch2.report(results));
-
+ .search(converter.getPhysicalNetwork(),
converter
+ .getGeneticNetwork(),
hcScoringFunction);
+
+ final NestedNetworkCreator nnCreator = new
NestedNetworkCreator(results);
+
+ setStatus("Search finished!\n\n" + "Number of Complexes = "
+ + nnCreator.getOverviewNetwork().getNodeCount()
+ "\n\n"
+ + HCSearch2.report(results));
+
setPercentCompleted(100);
}
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