Author: kono
Date: 2010-01-12 13:11:26 -0800 (Tue, 12 Jan 2010)
New Revision: 18880
Modified:
csplugins/trunk/ucsd/ruschein/DenovoPGNetworkAlignment/src/org/cytoscape/DenovoPGNetworkAlignmentPlugin/NestedNetworkCreator.java
csplugins/trunk/ucsd/ruschein/DenovoPGNetworkAlignment/src/org/cytoscape/DenovoPGNetworkAlignmentPlugin/SearchTask.java
Log:
Minor changes only.
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 20:53:43 UTC (rev 18879)
+++
csplugins/trunk/ucsd/ruschein/DenovoPGNetworkAlignment/src/org/cytoscape/DenovoPGNetworkAlignmentPlugin/NestedNetworkCreator.java
2010-01-12 21:11:26 UTC (rev 18880)
@@ -1,6 +1,5 @@
package org.cytoscape.DenovoPGNetworkAlignmentPlugin;
-
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@@ -17,7 +16,6 @@
import cytoscape.data.CyAttributes;
import cytoscape.data.Semantics;
-
/**
* Creates an overview network for the detected complexes and nested networks
* for each complex.
@@ -26,64 +24,69 @@
private CyNetwork overviewNetwork = null;
private Map<Integer, String> nodeIndexToNodeNameMap;
-
/**
* 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,
- final List<EdgeProperties> edgeProperties)
- {
+ NestedNetworkCreator(
+ final TypedLinkNetwork<TypedLinkNodeModule<String,
BFEdge>, BFEdge> networkOfModules) {
nodeIndexToNodeNameMap = new HashMap<Integer, String>();
createOverviewNetworkNodes(networkOfModules.nodes());
- createOverviewNetworkEdges(edgeProperties);
+ //createOverviewNetworkEdges(edgeProperties);
}
-
CyNetwork getOverviewNetwork() {
return overviewNetwork;
}
+ private void createOverviewNetworkNodes(
+ final Set<TypedLinkNode<TypedLinkNodeModule<String,
BFEdge>, BFEdge>> overviewNodes) {
+ overviewNetwork = Cytoscape.createNetwork(
+ findNextAvailableNetworkName("Complex Search
Result: "
+ + new java.util.Date()),
+ /* create_view = */true);
- private void createOverviewNetworkNodes(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 String nodeName =
findNextAvailableNodeName("Complex"
+ + nodeIndex);
nodeIndexToNodeNameMap.put(nodeIndex, nodeName);
- final CyNode newNode = Cytoscape.getCyNode(nodeName, /*
create = */ true);
+ final CyNode newNode = Cytoscape.getCyNode(nodeName, /*
create = */
+ true);
overviewNetwork.addNode(newNode);
++nodeIndex;
}
}
-
- private void createOverviewNetworkEdges(final List<EdgeProperties>
edgeProperties) {
+ private void createOverviewNetworkEdges(
+ final List<EdgeProperties> edgeProperties) {
final CyAttributes edgeAttribs = Cytoscape.getEdgeAttributes();
for (final EdgeProperties edgeProps : edgeProperties) {
- final String sourceNodeName =
nodeIndexToNodeNameMap.get(Integer.valueOf(edgeProps.getSourceNodeIndex()));
+ final String sourceNodeName =
nodeIndexToNodeNameMap.get(Integer
+
.valueOf(edgeProps.getSourceNodeIndex()));
if (sourceNodeName == null)
- throw new IllegalStateException("this should be
impossible: can't find source node name!");
+ throw new IllegalStateException(
+ "this should be impossible:
can't find source node name!");
- final String targetNodeName =
nodeIndexToNodeNameMap.get(Integer.valueOf(edgeProps.getTargetNodeIndex()));
+ final String targetNodeName =
nodeIndexToNodeNameMap.get(Integer
+
.valueOf(edgeProps.getTargetNodeIndex()));
if (targetNodeName == null)
- throw new IllegalStateException("this should be
impossible: can't find target node name!");
+ throw new IllegalStateException(
+ "this should be impossible:
can't find target node name!");
final CyNode sourceNode =
Cytoscape.getCyNode(sourceNodeName);
final CyNode targetNode =
Cytoscape.getCyNode(targetNodeName);
- final CyEdge newEdge = Cytoscape.getCyEdge(sourceNode,
targetNode, Semantics.INTERACTION, "complex-complex",
- /* create =
*/ true);
-
+ final CyEdge newEdge = Cytoscape.getCyEdge(sourceNode,
targetNode,
+ Semantics.INTERACTION,
"complex-complex",
+ /* create = */true);
- edgeAttribs.setAttribute(newEdge.getIdentifier(), "edge
score", Double.valueOf(edgeProps.getEdgeScore()));
+ edgeAttribs.setAttribute(newEdge.getIdentifier(), "edge
score",
+
Double.valueOf(edgeProps.getEdgeScore()));
}
}
-
/**
* 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
@@ -107,7 +110,6 @@
}
}
-
/**
* 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
@@ -132,7 +134,6 @@
}
}
-
/**
* Returns the first network with title "networkTitle" or null, if
there is
* no network w/ this title.
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 20:53:43 UTC (rev 18879)
+++
csplugins/trunk/ucsd/ruschein/DenovoPGNetworkAlignment/src/org/cytoscape/DenovoPGNetworkAlignmentPlugin/SearchTask.java
2010-01-12 21:11:26 UTC (rev 18880)
@@ -1,13 +1,17 @@
package org.cytoscape.DenovoPGNetworkAlignmentPlugin;
+import java.util.ArrayList;
+
import networks.denovoPGNetworkAlignment.BFEdge;
import networks.denovoPGNetworkAlignment.HCScoringFunction;
import networks.denovoPGNetworkAlignment.HCSearch2;
import networks.denovoPGNetworkAlignment.SouravScore;
+import networks.linkedNetworks.TypedLinkEdge;
import networks.linkedNetworks.TypedLinkNetwork;
import networks.linkedNetworks.TypedLinkNodeModule;
import cytoscape.task.Task;
import cytoscape.task.TaskMonitor;
+import data.StringTable;
public class SearchTask implements Task {
private TaskMonitor taskMonitor = null;
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