Author: mes
Date: 2012-01-20 13:05:16 -0800 (Fri, 20 Jan 2012)
New Revision: 28069
Added:
csplugins/trunk/ucsd/mes/SubNetworkCreatorTest/
csplugins/trunk/ucsd/mes/SubNetworkCreatorTest/pom.xml
csplugins/trunk/ucsd/mes/SubNetworkCreatorTest/src/
csplugins/trunk/ucsd/mes/SubNetworkCreatorTest/src/main/
csplugins/trunk/ucsd/mes/SubNetworkCreatorTest/src/main/java/
csplugins/trunk/ucsd/mes/SubNetworkCreatorTest/src/main/java/org/
csplugins/trunk/ucsd/mes/SubNetworkCreatorTest/src/main/java/org/cytoscape/
csplugins/trunk/ucsd/mes/SubNetworkCreatorTest/src/main/java/org/cytoscape/internal/
csplugins/trunk/ucsd/mes/SubNetworkCreatorTest/src/main/java/org/cytoscape/internal/test/
csplugins/trunk/ucsd/mes/SubNetworkCreatorTest/src/main/java/org/cytoscape/internal/test/CyActivator.java
csplugins/trunk/ucsd/mes/SubNetworkCreatorTest/src/main/java/org/cytoscape/internal/test/InfiniteTask.java
csplugins/trunk/ucsd/mes/SubNetworkCreatorTest/src/main/java/org/cytoscape/internal/test/InfiniteTaskFactory.java
Log:
adding some tests for cy3
Added: csplugins/trunk/ucsd/mes/SubNetworkCreatorTest/pom.xml
===================================================================
--- csplugins/trunk/ucsd/mes/SubNetworkCreatorTest/pom.xml
(rev 0)
+++ csplugins/trunk/ucsd/mes/SubNetworkCreatorTest/pom.xml 2012-01-20
21:05:16 UTC (rev 28069)
@@ -0,0 +1,98 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0";
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
http://maven.apache.org/maven-v4_0_0.xsd";>
+ <parent>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>support-parent</artifactId>
+ <version>3.0.0-alpha7-SNAPSHOT</version>
+ </parent>
+
+ <properties>
+
<bundle.symbolicName>org.cytoscape.subnetorktask-testing-impl</bundle.symbolicName>
+ <bundle.namespace>org.cytoscape.internal</bundle.namespace>
+ </properties>
+
+ <modelVersion>4.0.0</modelVersion>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>subnetorktask-testing-impl</artifactId>
+ <name>Subnetwork Tasks for Testing</name>
+ <packaging>bundle</packaging>
+
+ <build>
+ <resources>
+ <resource>
+ <directory>src/main/resources</directory>
+ </resource>
+ </resources>
+ <plugins>
+ <plugin>
+ <groupId>org.apache.felix</groupId>
+ <artifactId>maven-bundle-plugin</artifactId>
+
<version>${maven-bundle-plugin.version}</version>
+ <extensions>true</extensions>
+ <configuration>
+ <instructions>
+
<Bundle-SymbolicName>${bundle.symbolicName}</Bundle-SymbolicName>
+
<Bundle-Version>${project.version}</Bundle-Version>
+
<Bundle-Activator>org.cytoscape.internal.test.CyActivator</Bundle-Activator>
+ </instructions>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+
+ <repositories>
+ <!-- bootstrap for cytoscape dependencies, namely the parent
POM snapshots -->
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+
<url>http://code.cytoscape.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <!-- bootstrap for cytoscape dependencies, namely the parent
POM releases -->
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+
<url>http://code.cytoscape.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+
+ <dependencies>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>model-api</artifactId>
+ <version>${cytoscape.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>work-api</artifactId>
+ <version>${cytoscape.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>core-task-api</artifactId>
+ <version>${cytoscape.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>service-api</artifactId>
+ <version>${cytoscape.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.osgi</groupId>
+ <artifactId>org.osgi.core</artifactId>
+ <version>${osgi.api.version}</version>
+ </dependency>
+ </dependencies>
+</project>
Added:
csplugins/trunk/ucsd/mes/SubNetworkCreatorTest/src/main/java/org/cytoscape/internal/test/CyActivator.java
===================================================================
---
csplugins/trunk/ucsd/mes/SubNetworkCreatorTest/src/main/java/org/cytoscape/internal/test/CyActivator.java
(rev 0)
+++
csplugins/trunk/ucsd/mes/SubNetworkCreatorTest/src/main/java/org/cytoscape/internal/test/CyActivator.java
2012-01-20 21:05:16 UTC (rev 28069)
@@ -0,0 +1,40 @@
+
+
+
+
+package org.cytoscape.internal.test;
+
+import org.cytoscape.work.TaskManager;
+
+import org.cytoscape.work.TaskFactory;
+import org.cytoscape.task.NetworkTaskFactory;
+import org.cytoscape.model.subnetwork.CyRootNetworkManager;
+
+
+import org.osgi.framework.BundleContext;
+
+import org.cytoscape.service.util.AbstractCyActivator;
+
+import java.util.Properties;
+
+
+
+public class CyActivator extends AbstractCyActivator {
+ public CyActivator() {
+ super();
+ }
+
+
+ public void start(BundleContext bc) {
+
+ CyRootNetworkManager rootNetworkManagerServiceRef =
getService(bc,CyRootNetworkManager.class);
+
+ InfiniteTaskFactory infiniteTaskFactory = new
InfiniteTaskFactory(rootNetworkManagerServiceRef);
+
+ Properties infiniteTaskFactoryProps = new Properties();
+ infiniteTaskFactoryProps.setProperty("preferredMenu","Help");
+ infiniteTaskFactoryProps.setProperty("title","Subnetwork
Test...");
+
registerService(bc,infiniteTaskFactory,NetworkTaskFactory.class,
infiniteTaskFactoryProps);
+ }
+}
+
Added:
csplugins/trunk/ucsd/mes/SubNetworkCreatorTest/src/main/java/org/cytoscape/internal/test/InfiniteTask.java
===================================================================
---
csplugins/trunk/ucsd/mes/SubNetworkCreatorTest/src/main/java/org/cytoscape/internal/test/InfiniteTask.java
(rev 0)
+++
csplugins/trunk/ucsd/mes/SubNetworkCreatorTest/src/main/java/org/cytoscape/internal/test/InfiniteTask.java
2012-01-20 21:05:16 UTC (rev 28069)
@@ -0,0 +1,38 @@
+
+package org.cytoscape.internal.test;
+
+
+import org.cytoscape.work.*;
+import org.cytoscape.model.*;
+import org.cytoscape.model.subnetwork.*;
+import java.util.*;
+
+
+public class InfiniteTask extends AbstractTask {
+
+ private CyNetwork net;
+ private CyRootNetworkManager rootMgr;
+ public InfiniteTask(CyNetwork net, CyRootNetworkManager rootMgr) {
+ this.net = net;
+ this.rootMgr = rootMgr;
+ }
+
+ public void run(final TaskMonitor taskMonitor) throws Exception {
+ CyRootNetwork root = rootMgr.getRootNetwork(net);
+ int numNodes = net.getNodeList().size();
+ int i = 0;
+ for ( CyNode n : net.getNodeList() ) {
+ if ( cancelled )
+ return;
+ 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);
+ taskMonitor.setProgress( (double)i++/(double)numNodes);
+ }
+ }
+}
Added:
csplugins/trunk/ucsd/mes/SubNetworkCreatorTest/src/main/java/org/cytoscape/internal/test/InfiniteTaskFactory.java
===================================================================
---
csplugins/trunk/ucsd/mes/SubNetworkCreatorTest/src/main/java/org/cytoscape/internal/test/InfiniteTaskFactory.java
(rev 0)
+++
csplugins/trunk/ucsd/mes/SubNetworkCreatorTest/src/main/java/org/cytoscape/internal/test/InfiniteTaskFactory.java
2012-01-20 21:05:16 UTC (rev 28069)
@@ -0,0 +1,19 @@
+
+package org.cytoscape.internal.test;
+
+import org.cytoscape.work.TaskIterator;
+import org.cytoscape.work.TaskFactory;
+import org.cytoscape.task.AbstractNetworkTaskFactory;
+import org.cytoscape.model.subnetwork.*;
+
+
+public class InfiniteTaskFactory extends AbstractNetworkTaskFactory {
+ CyRootNetworkManager rootMgr;
+ public InfiniteTaskFactory(CyRootNetworkManager rootMgr) {
+ this.rootMgr = rootMgr;
+ }
+
+ public TaskIterator createTaskIterator() {
+ return new TaskIterator(new InfiniteTask(network,rootMgr));
+ }
+}
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