Author: mes
Date: 2012-01-20 10:22:35 -0800 (Fri, 20 Jan 2012)
New Revision: 28066
Modified:
core3/impl/trunk/model-impl/performance-debug/src/main/java/org/cytoscape/model/PerfTest.java
Log:
tweaked test to create subnetworks
Modified:
core3/impl/trunk/model-impl/performance-debug/src/main/java/org/cytoscape/model/PerfTest.java
===================================================================
---
core3/impl/trunk/model-impl/performance-debug/src/main/java/org/cytoscape/model/PerfTest.java
2012-01-20 18:20:24 UTC (rev 28065)
+++
core3/impl/trunk/model-impl/performance-debug/src/main/java/org/cytoscape/model/PerfTest.java
2012-01-20 18:22:35 UTC (rev 28066)
@@ -12,16 +12,21 @@
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyTable;
import org.cytoscape.model.NetworkTestSupport;
+import org.cytoscape.model.subnetwork.CyRootNetwork;
+import org.cytoscape.model.subnetwork.CyRootNetworkManager;
import org.cytoscape.service.util.CyServiceRegistrar;
import java.util.ArrayList;
import java.util.List;
import java.util.Random;
+import java.util.HashSet;
+import java.util.Set;
public class PerfTest {
private final CyNetworkFactory netFactory;
+ private final CyRootNetworkManager rootMgr;
public static void main(String[] args) {
new PerfTest().runTestLoop();
@@ -30,70 +35,57 @@
public PerfTest() {
NetworkTestSupport testSupport = new NetworkTestSupport();
netFactory = testSupport.getNetworkFactory();
+ rootMgr = testSupport.getRootNetworkFactory();
}
public void runTestLoop() {
- final int EFFECTIVE_LOOP_COUNT = 5;
- for (int i = 0; i <= EFFECTIVE_LOOP_COUNT; ++i) {
+ final int EFFECTIVE_LOOP_COUNT = 1;
+ for (int i = 0; i < EFFECTIVE_LOOP_COUNT; i++) {
final long startTime = System.currentTimeMillis();
testMiscNodeAndEdgeOps();
final long endTime = System.currentTimeMillis();
- final long startTime2 = System.currentTimeMillis();
- testMiscNodeAndEdgeOpsBuilder();
- final long endTime2 = System.currentTimeMillis();
-
- long noBuilder = (endTime-startTime);
- long withBuilder = (endTime2-startTime2);
+ long createNet = (endTime-startTime);
- long diff = noBuilder - withBuilder;
- double per =
((double)diff)/((double)(endTime-startTime));
- System.out.println("difference: " + diff + " no
builder: " + noBuilder + " builder: " + withBuilder);
+ System.out.println("createNetwork && subs: " +
createNet);
}
}
private void testMiscNodeAndEdgeOps() {
- final CyNetwork network = netFactory.getInstance();
+ final CyNetwork network = netFactory.createNetwork();
+ // create nodes
final int NODE_COUNT = 50000;
final List<CyNode> nodes = new ArrayList<CyNode>(NODE_COUNT);
- for (int i = 0; i < NODE_COUNT; ++i) {
+ for (int i = 0; i < NODE_COUNT; i++) {
nodes.add(network.addNode());
}
boolean isDirected = true;
final Random rand = new Random(1234L);
+ // create edges
final int EDGE_COUNT = 100000;
final List<CyEdge> edges = new ArrayList<CyEdge>(EDGE_COUNT);
- for (int i = 0; i < EDGE_COUNT; ++i) {
+ for (int i = 0; i < EDGE_COUNT; i++) {
final CyNode source =
nodes.get(rand.nextInt(NODE_COUNT));
final CyNode target =
nodes.get(rand.nextInt(NODE_COUNT));
edges.add(network.addEdge(source, target, isDirected));
isDirected = !isDirected;
}
- }
- private void testMiscNodeAndEdgeOpsBuilder() {
- CyNetworkBuilder netBuilder = new CyNetworkBuilder();
-
- final int NODE_COUNT = 50000;
- final List<CyNodeBuilder> nodes = new
ArrayList<CyNodeBuilder>(NODE_COUNT);
- for (int i = 0; i < NODE_COUNT; ++i) {
- nodes.add(netBuilder.addNode());
+ // create subnetworks
+ CyRootNetwork root = rootMgr.getRootNetwork(network);
+ int i = 0;
+ for ( CyNode n : network.getNodeList() ) {
+ if ( i++ > 1000 ) break;
+ List<CyNode> nl =
network.getNeighborList(n,CyEdge.Type.ANY);
+ Set<CyEdge> es = new HashSet<CyEdge>();
+ for ( CyNode nn : nl ) {
+ List<CyEdge> ee =
network.getConnectingEdgeList(n,nn,CyEdge.Type.ANY);
+ es.addAll(ee);
+ }
+ root.addSubNetwork(nl,es);
}
-
- boolean isDirected = true;
- final Random rand = new Random(1234L);
-
- final int EDGE_COUNT = 100000;
- final List<CyEdgeBuilder> edges = new
ArrayList<CyEdgeBuilder>(EDGE_COUNT);
- for (int i = 0; i < EDGE_COUNT; ++i) {
- final CyNodeBuilder source =
nodes.get(rand.nextInt(NODE_COUNT));
- final CyNodeBuilder target =
nodes.get(rand.nextInt(NODE_COUNT));
- edges.add(netBuilder.addEdge(source, target,
isDirected));
- isDirected = !isDirected;
- }
- final CyNetwork network = netFactory.getInstance();
}
}
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