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geraore · Jun 14, 2013 · d21fa5b · d21fa5b
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diff --git a/UseNestedNetwork/pom.xml b/UseNestedNetwork/pom.xml
@@ -0,0 +1,133 @@
+<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/xsd/maven-4.0.0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+
+	<properties>
+		<bundle.symbolicName>UseNestedNetwork</bundle.symbolicName>
+		<bundle.namespace>org.cytoscape.sample.internal</bundle.namespace>
+		<cytoscape.api.version>3.0.1</cytoscape.api.version>
+
+		<maven-bundle-plugin.version>2.3.4</maven-bundle-plugin.version>
+		<osgi.api.version>4.2.0</osgi.api.version>
+	</properties>
+
+	<groupId>org.cytoscape.sample</groupId>
+	<artifactId>UseNestedNetwork</artifactId>
+	<packaging>bundle</packaging>
+	<name>${bundle.symbolicName}</name>
+
+	<version>0.0.1-SNAPSHOT</version>
+
+	<build>
+		<plugins>
+			<plugin>
+				<inherited>true</inherited>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-compiler-plugin</artifactId>
+				<version>3.0</version>
+				<configuration>
+					<source>1.6</source>
+					<target>1.6</target>
+					<optimize>true</optimize>
+					<showWarnings>true</showWarnings>
+					<showDeprecation>true</showDeprecation>
+					<compilerArguments>
+						<Xmaxwarns>10000</Xmaxwarns>
+						<Xmaxerrs>10000</Xmaxerrs>
+					</compilerArguments>
+				</configuration>
+			</plugin>
+			<plugin>
+				<groupId>org.apache.felix</groupId>
+				<artifactId>maven-bundle-plugin</artifactId>
+				<version>${maven-bundle-plugin.version}</version>
+				<extensions>true</extensions>
+				<configuration>
+					<instructions>
+						<Bundle-SymbolicName>${bundle.symbolicName}</Bundle-SymbolicName>
+						<Bundle-Version>${project.version}</Bundle-Version>
+						<Export-Package>!${bundle.namespace}.*</Export-Package>
+						<Private-Package>${bundle.namespace}.*</Private-Package>
+						<Bundle-Activator>${bundle.namespace}.CyActivator</Bundle-Activator>
+					</instructions>
+				</configuration>
+			</plugin>
+		</plugins>
+	</build>
+
+	<!-- Links to the Cytoscape Maven repositories. -->
+	<repositories>
+		<repository>
+			<id>cytoscape_snapshots</id>
+			<snapshots>
+				<enabled>true</enabled>
+			</snapshots>
+			<releases>
+				<enabled>false</enabled>
+			</releases>
+			<name>Cytoscape Snapshots</name>
+			<url>http://code.cytoscape.org/nexus/content/repositories/snapshots/</url>
+		</repository>
+		<repository>
+			<id>cytoscape_releases</id>
+			<snapshots>
+				<enabled>false</enabled>
+			</snapshots>
+			<releases>
+				<enabled>true</enabled>
+			</releases>
+			<name>Cytoscape Releases</name>
+			<url>http://code.cytoscape.org/nexus/content/repositories/releases/</url>
+		</repository>
+	</repositories>
+
+	<dependencies>
+		<dependency>
+			<groupId>org.cytoscape</groupId>
+			<artifactId>swing-application-api</artifactId>
+			<version>${cytoscape.api.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>org.cytoscape</groupId>
+			<artifactId>work-api</artifactId>
+			<version>${cytoscape.api.version}</version>
+		</dependency>
+
+		<dependency>
+			<groupId>org.cytoscape</groupId>
+			<artifactId>swing-app-api</artifactId>
+			<version>${cytoscape.api.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>org.cytoscape</groupId>
+			<artifactId>app-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>${osgi.api.version}</version>
+		</dependency>
+
+
+		<dependency>
+			<groupId>org.ops4j.pax.logging</groupId>
+			<artifactId>pax-logging-api</artifactId>
+			<version>1.5.2</version>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.cytoscape</groupId>
+			<artifactId>service-api</artifactId>
+			<version>${cytoscape.api.version}</version>
+			<type>test-jar</type>
+			<scope>test</scope>
+		</dependency>
+	</dependencies>
+
+</project>
diff --git a/UseNestedNetwork/src/main/java/org/cytoscape/sample/internal/CyActivator.java b/UseNestedNetwork/src/main/java/org/cytoscape/sample/internal/CyActivator.java
@@ -0,0 +1,33 @@
+package org.cytoscape.sample.internal;
+
+import org.cytoscape.application.swing.CySwingApplication;
+import org.cytoscape.sample.internal.MyNestedNetworkAction;
+import org.cytoscape.application.swing.CyAction;
+import org.osgi.framework.BundleContext;
+import org.cytoscape.service.util.AbstractCyActivator;
+import java.util.Properties;
+import org.cytoscape.app.swing.CySwingAppAdapter;;
+
+
+
+public class CyActivator extends AbstractCyActivator {
+	public CyActivator() {
+		super();
+	}
+
+
+	public void start(BundleContext bc) {
+
+		//CySwingApplication cytoscapeDesktopService = getService(bc,CySwingApplication.class);
+
+		CySwingAppAdapter adapter = getService(bc,CySwingAppAdapter.class);
+
+//		MyCytoPanel myCytoPanel = new MyCytoPanel();
+		MyNestedNetworkAction nestedNetworkAction = new MyNestedNetworkAction(adapter);
+
+//		registerService(bc,myCytoPanel,CytoPanelComponent.class, new Properties());
+		registerService(bc,nestedNetworkAction,CyAction.class, new Properties());
+
+	}
+}
+
diff --git a/UseNestedNetwork/src/main/java/org/cytoscape/sample/internal/MyNestedNetworkAction.java b/UseNestedNetwork/src/main/java/org/cytoscape/sample/internal/MyNestedNetworkAction.java
@@ -0,0 +1,55 @@
+package org.cytoscape.sample.internal;
+
+import java.awt.event.ActionEvent;
+import org.cytoscape.app.swing.CySwingAppAdapter;
+import org.cytoscape.application.swing.AbstractCyAction;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNode;
+import org.cytoscape.model.subnetwork.CyRootNetwork;
+
+
+public class MyNestedNetworkAction extends AbstractCyAction {
+
+	private final CySwingAppAdapter adapter;
+
+	public MyNestedNetworkAction(CySwingAppAdapter adapter){
+		// Add a menu item
+		super("Create nested network");
+		setPreferredMenu("Apps");
+
+		this.adapter = adapter;		
+	}
+
+	/**
+	 *  DOCUMENT ME!
+	 *
+	 * @param e DOCUMENT ME!
+	 */
+	public void actionPerformed(ActionEvent e) {
+
+		//1. create an overview network for two nested network
+		CyNetwork overview = this.adapter.getCyNetworkFactory().createNetwork();
+		overview.getRow(overview).set("name", "Overview network");
+
+		CyNode node1 = overview.addNode();
+		CyNode node2 = overview.addNode();
+		this.adapter.getCyNetworkManager().addNetwork(overview);
+
+		//2. create two networks in the same network collection		
+		CyNetwork network1 = this.adapter.getCyNetworkFactory().createNetwork();
+		network1.getRow(network1).set("name", "Network 1");
+		network1.addNode(); // add one node
+		this.adapter.getCyNetworkManager().addNetwork(network1);
+
+		CyRootNetwork rootNetwork = this.adapter.getCyRootNetworkManager().getRootNetwork(network1);
+
+		CyNetwork network2 = rootNetwork.addSubNetwork();
+		network2.getRow(network2).set("name", "Network 2");
+		network2.addNode(); // add one node
+		this.adapter.getCyNetworkManager().addNetwork(network2);
+
+		// 3. set the two network as nested network of the overview network
+		node1.setNetworkPointer(network1);
+		node2.setNetworkPointer(network2);
+	}
+}