Author: kono
Date: 2011-05-12 16:17:39 -0700 (Thu, 12 May 2011)
New Revision: 25043
Added:
csplugins/trunk/ucsd/kono/cyaction-plugin/osgi.bnd
csplugins/trunk/ucsd/kono/cyaction-plugin/pom.xml
csplugins/trunk/ucsd/kono/cyaction-plugin/src/
csplugins/trunk/ucsd/kono/cyaction-plugin/src/main/
csplugins/trunk/ucsd/kono/cyaction-plugin/src/main/java/
csplugins/trunk/ucsd/kono/cyaction-plugin/src/main/java/org/
csplugins/trunk/ucsd/kono/cyaction-plugin/src/main/java/org/cytoscape/
csplugins/trunk/ucsd/kono/cyaction-plugin/src/main/java/org/cytoscape/myplugin/
csplugins/trunk/ucsd/kono/cyaction-plugin/src/main/java/org/cytoscape/myplugin/internal/
csplugins/trunk/ucsd/kono/cyaction-plugin/src/main/java/org/cytoscape/myplugin/internal/MenuAction.java
csplugins/trunk/ucsd/kono/cyaction-plugin/src/main/resources/
csplugins/trunk/ucsd/kono/cyaction-plugin/src/main/resources/META-INF/
csplugins/trunk/ucsd/kono/cyaction-plugin/src/main/resources/META-INF/spring/
csplugins/trunk/ucsd/kono/cyaction-plugin/src/main/resources/META-INF/spring/bundle-context-osgi.xml
csplugins/trunk/ucsd/kono/cyaction-plugin/src/main/resources/META-INF/spring/bundle-context.xml
Log:
New sample for Cy3 tutorial.
Added: csplugins/trunk/ucsd/kono/cyaction-plugin/osgi.bnd
===================================================================
--- csplugins/trunk/ucsd/kono/cyaction-plugin/osgi.bnd
(rev 0)
+++ csplugins/trunk/ucsd/kono/cyaction-plugin/osgi.bnd 2011-05-12 23:17:39 UTC
(rev 25043)
@@ -0,0 +1,7 @@
+#-----------------------------------------------------------------
+# Use this file to add customized Bnd instructions for the bundle
+#-----------------------------------------------------------------
+
+Import-Package: *
+Private-Package: ${bundle.namespace}.internal.*
+Export-Package: ${bundle.namespace}
Added: csplugins/trunk/ucsd/kono/cyaction-plugin/pom.xml
===================================================================
--- csplugins/trunk/ucsd/kono/cyaction-plugin/pom.xml
(rev 0)
+++ csplugins/trunk/ucsd/kono/cyaction-plugin/pom.xml 2011-05-12 23:17:39 UTC
(rev 25043)
@@ -0,0 +1,130 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0";
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
http://maven.apache.org/maven-v4_0_0.xsd";>
+
+ <properties>
+
<bundle.symbolicName>org.cytoscape.myplugin.cyaction-plugin</bundle.symbolicName>
+ <bundle.namespace>org.cytoscape.myplugin</bundle.namespace>
+ </properties>
+
+ <modelVersion>4.0.0</modelVersion>
+ <groupId>org.cytoscape.myplugin</groupId>
+ <artifactId>cyaction-plugin</artifactId>
+ <version>0.0.1-SNAPSHOT</version>
+
+ <name>${bundle.symbolicName} [${bundle.namespace}]</name>
+
+ <packaging>bundle</packaging>
+
+ <build>
+ <resources>
+ <resource>
+ <directory>src/main/resources</directory>
+ </resource>
+ </resources>
+ <!-- Cytoscape requires Java 1.6 -->
+ <plugins>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-compiler-plugin</artifactId>
+ <configuration>
+ <source>1.6</source>
+ <target>1.6</target>
+ <optimize>true</optimize>
+ <showWarnings>true</showWarnings>
+ <showDeprecation>true</showDeprecation>
+ <compilerArguments>
+ <Xmaxwarns>10000</Xmaxwarns>
+ <Xmaxerrs>10000</Xmaxerrs>
+ </compilerArguments>
+ </configuration>
+ </plugin>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-surefire-plugin</artifactId>
+ <configuration>
+
<redirectTestOutputToFile>true</redirectTestOutputToFile>
+ </configuration>
+ </plugin>
+ <plugin>
+ <groupId>org.ops4j</groupId>
+ <artifactId>maven-pax-plugin</artifactId>
+ <version>1.5-SNAPSHOT</version>
+ <extensions>true</extensions>
+ </plugin>
+ <!-- Generates the OSGi metadata based on the osgi.bnd
file. -->
+ <plugin>
+ <groupId>org.apache.felix</groupId>
+ <artifactId>maven-bundle-plugin</artifactId>
+ <version>1.4.3</version>
+ <configuration>
+ <instructions>
+
<Bundle-SymbolicName>${bundle.symbolicName}</Bundle-SymbolicName>
+
<Bundle-Version>${pom.version}</Bundle-Version>
+ <_include>-osgi.bnd</_include>
+ </instructions>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+
+ <!-- Links to the Cytoscape Maven repositories. -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+
<url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ </releases>
+ <name>Cytoscape Releases</name>
+
<url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+ <!-- Dependencies needed to compile this project. -->
+ <dependencies>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>swing-application-api</artifactId>
+ <version>3.0.0-alpha2-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>session-api</artifactId>
+ <version>3.0.0-alpha3-SNAPSHOT</version>
+ </dependency>
+
+ <!-- Logging -->
+ <dependency>
+ <groupId>org.ops4j.pax.logging</groupId>
+ <artifactId>pax-logging-api</artifactId>
+ <version>1.5.2</version>
+ <scope>provided</scope>
+ </dependency>
+
+ <!-- dependencies specifically for unit testing -->
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <version>4.8.2</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>test-support</artifactId>
+ <version>3.0.0-alpha2-SNAPSHOT</version>
+ <scope>test</scope>
+ </dependency>
+ </dependencies>
+
+</project>
Added:
csplugins/trunk/ucsd/kono/cyaction-plugin/src/main/java/org/cytoscape/myplugin/internal/MenuAction.java
===================================================================
---
csplugins/trunk/ucsd/kono/cyaction-plugin/src/main/java/org/cytoscape/myplugin/internal/MenuAction.java
(rev 0)
+++
csplugins/trunk/ucsd/kono/cyaction-plugin/src/main/java/org/cytoscape/myplugin/internal/MenuAction.java
2011-05-12 23:17:39 UTC (rev 25043)
@@ -0,0 +1,43 @@
+package org.cytoscape.myplugin.internal;
+
+import java.awt.event.ActionEvent;
+
+import org.cytoscape.application.swing.AbstractCyAction;
+import org.cytoscape.model.CyEdge;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNode;
+import org.cytoscape.session.CyApplicationManager;
+import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.view.presentation.property.MinimalVisualLexicon;
+
+/**
+ * Creates a new menu item under Plugins menu section.
+ *
+ */
+public class MenuAction extends AbstractCyAction {
+
+ public MenuAction(final CyApplicationManager applicationManager,
+ final String menuTitle) {
+ super(menuTitle, applicationManager);
+ setPreferredMenu("Plugins");
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ final CyNetworkView currentNetworkView = applicationManager
+ .getCurrentNetworkView();
+ if (currentNetworkView == null)
+ return;
+
+ // View is always associated with its model.
+ final CyNetwork network = currentNetworkView.getModel();
+
+ for (CyNode node : network.getNodeList()) {
+ if (network.getNeighborList(node,
CyEdge.Type.ANY).isEmpty())
+
currentNetworkView.getNodeView(node).setVisualProperty(
+
MinimalVisualLexicon.NODE_VISIBLE, false);
+ }
+
+ currentNetworkView.updateView();
+
+ }
+}
Added:
csplugins/trunk/ucsd/kono/cyaction-plugin/src/main/resources/META-INF/spring/bundle-context-osgi.xml
===================================================================
---
csplugins/trunk/ucsd/kono/cyaction-plugin/src/main/resources/META-INF/spring/bundle-context-osgi.xml
(rev 0)
+++
csplugins/trunk/ucsd/kono/cyaction-plugin/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2011-05-12 23:17:39 UTC (rev 25043)
@@ -0,0 +1,26 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans xmlns="http://www.springframework.org/schema/beans";
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
xmlns:osgi="http://www.springframework.org/schema/osgi";
+ xsi:schemaLocation="
+ http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans-2.5.xsd
+ http://www.springframework.org/schema/osgi
+ http://www.springframework.org/schema/osgi/spring-osgi-1.0.xsd";
+ default-lazy-init="false">
+
+
+ <!-- ================= Import =========================== -->
+
+ <!-- Import OSGi service from service registry -->
+ <osgi:reference id="cyApplicationManagerServiceRef"
+ interface="org.cytoscape.session.CyApplicationManager" />
+
+
+ <!-- ================= Export =========================== -->
+
+ <!-- Export the instance as an OSGi service -->
+ <osgi:service id="menuActionService" ref="menuAction"
+ interface="org.cytoscape.application.swing.CyAction" />
+
+
+</beans>
Added:
csplugins/trunk/ucsd/kono/cyaction-plugin/src/main/resources/META-INF/spring/bundle-context.xml
===================================================================
---
csplugins/trunk/ucsd/kono/cyaction-plugin/src/main/resources/META-INF/spring/bundle-context.xml
(rev 0)
+++
csplugins/trunk/ucsd/kono/cyaction-plugin/src/main/resources/META-INF/spring/bundle-context.xml
2011-05-12 23:17:39 UTC (rev 25043)
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans xmlns="http://www.springframework.org/schema/beans";
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
+ xmlns:context="http://www.springframework.org/schema/context";
+ xsi:schemaLocation="
+ http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans-2.5.xsd
+ http://www.springframework.org/schema/context
+
http://www.springframework.org/schema/context/spring-context-2.5.xsd";>
+
+ <!-- Create an instance (bean) of the class -->
+ <bean id="menuAction"
class="org.cytoscape.myplugin.internal.MenuAction">
+ <!-- Inject an OSGi service as a constructor argument -->
+ <constructor-arg ref="cyApplicationManagerServiceRef" />
+ <constructor-arg value="Hide uncennected nodes (OSGi bundle
version)" />
+ </bean>
+
+</beans>
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