Author: mes
Date: 2012-01-25 14:58:39 -0800 (Wed, 25 Jan 2012)
New Revision: 28111
Modified:
core3/impl/trunk/io-impl/performance/src/main/java/org/cytoscape/io/read/sif/PerfTest.java
Log:
now creating subnetworks as well
Modified:
core3/impl/trunk/io-impl/performance/src/main/java/org/cytoscape/io/read/sif/PerfTest.java
===================================================================
---
core3/impl/trunk/io-impl/performance/src/main/java/org/cytoscape/io/read/sif/PerfTest.java
2012-01-25 22:57:20 UTC (rev 28110)
+++
core3/impl/trunk/io-impl/performance/src/main/java/org/cytoscape/io/read/sif/PerfTest.java
2012-01-25 22:58:39 UTC (rev 28111)
@@ -8,6 +8,8 @@
import java.io.InputStream;
import java.util.List;
import java.util.Properties;
+import java.util.Set;
+import java.util.HashSet;
import org.cytoscape.ding.NetworkViewTestSupport;
import org.cytoscape.event.CyEventHelper;
@@ -25,6 +27,8 @@
import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewFactory;
+import org.cytoscape.model.subnetwork.CyRootNetwork;
+import org.cytoscape.model.subnetwork.CyRootNetworkManager;
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.TaskIterator;
import org.cytoscape.work.TaskMonitor;
@@ -43,6 +47,7 @@
protected CyNetworkViewFactory viewFactory;
protected ReadUtils readUtil;
protected CyLayoutAlgorithmManager layouts;
+ protected CyRootNetworkManager rootMgr;
private Properties properties;
@@ -57,6 +62,7 @@
NetworkTestSupport nts = new NetworkTestSupport();
netFactory = nts.getNetworkFactory();
+ rootMgr = nts.getRootNetworkFactory();
properties = new Properties();
CyProperty<Properties> cyProperties = new
SimpleCyProperty("Test", properties, DO_NOT_SAVE);
@@ -160,6 +166,21 @@
}
end = System.currentTimeMillis();
System.out.println("Getting all neighbor nodes: " + (end -
start));
+
+ // create subnetworks
+ CyRootNetwork root = rootMgr.getRootNetwork(net);
+ int i = 0;
+ for ( CyNode n : net.getNodeList() ) {
+ if ( i++ > 1000 ) break;
+ List<CyNode> nl = net.getNeighborList(n,CyEdge.Type.ANY);
+ Set<CyEdge> es = new HashSet<CyEdge>();
+ for ( CyNode nn : nl ) {
+ List<CyEdge> ee =
net.getConnectingEdgeList(n,nn,CyEdge.Type.ANY);
+ es.addAll(ee);
+ }
+ root.addSubNetwork(nl,es);
+ }
+
}
}
--
You received this message because you are subscribed to the Google Groups
"cytoscape-cvs" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/cytoscape-cvs?hl=en.
