Author: mes
Date: 2011-01-28 15:17:03 -0800 (Fri, 28 Jan 2011)
New Revision: 23823

Added:
   core3/plugin-api/tags/plugin-api-3.0.0-alpha2/
   core3/plugin-api/tags/plugin-api-3.0.0-alpha2/pom.xml
   
core3/plugin-api/tags/plugin-api-3.0.0-alpha2/src/main/java/org/cytoscape/plugin/CyPluginAdapter.java
   
core3/plugin-api/tags/plugin-api-3.0.0-alpha2/src/test/java/org/cytoscape/plugin/CyPluginAdapterTest.java
Removed:
   core3/plugin-api/tags/plugin-api-3.0.0-alpha2/pom.xml
   
core3/plugin-api/tags/plugin-api-3.0.0-alpha2/src/main/java/org/cytoscape/plugin/CyPluginAdapter.java
   
core3/plugin-api/tags/plugin-api-3.0.0-alpha2/src/test/java/org/cytoscape/plugin/CyPluginAdapterTest.java
Log:
[maven-release-plugin]  copy for tag plugin-api-3.0.0-alpha2

Copied: core3/plugin-api/tags/plugin-api-3.0.0-alpha2 (from rev 23568, 
core3/plugin-api/trunk)

Deleted: core3/plugin-api/tags/plugin-api-3.0.0-alpha2/pom.xml
===================================================================
--- core3/plugin-api/trunk/pom.xml      2011-01-24 00:58:13 UTC (rev 23568)
+++ core3/plugin-api/tags/plugin-api-3.0.0-alpha2/pom.xml       2011-01-28 
23:17:03 UTC (rev 23823)
@@ -1,142 +0,0 @@
-<?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>
-    <artifactId>parent</artifactId>
-    <groupId>org.cytoscape</groupId>
-    <version>3.0.0-alpha1</version>
-  </parent>
-
-  <properties>
-    <bundle.symbolicName>org.cytoscape.plugin-api</bundle.symbolicName>
-    <bundle.namespace>org.cytoscape.plugin</bundle.namespace>
-  </properties>
-
-  <modelVersion>4.0.0</modelVersion>
-  <groupId>org.cytoscape</groupId>
-  <artifactId>plugin-api</artifactId>
-  <version>3.0.0-alpha2-SNAPSHOT</version>
-
-  <name>${bundle.symbolicName}</name>
-
-  <packaging>bundle</packaging>
-
-  <scm>
-    
<connection>scm:svn:http://chianti.ucsd.edu/svn/core3/plugin-api/trunk</connection>
-    
<developerConnection>scm:svn:svn+ssh://grenache.ucsd.edu/cellar/common/svn/core3/plugin-api/trunk</developerConnection>
-    <url>http://chianti.ucsd.edu/svn/core3/plugin-api/trunk</url>
-  </scm>
-
-  <repositories>
-      <!-- bootstrap for cytoscape dependencies, namely the parent POM 
snapshots -->
-      <repository>
-          <id>cytoscape_snapshots</id>
-          <snapshots>
-            <enabled>true</enabled>
-          </snapshots>
-          <releases>
-            <enabled>false</enabled>
-          </releases>
-          <name>Cytoscape Snapshots</name>
-          
<url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
-       </repository>
-       <!-- bootstrap for cytoscape dependencies, namely the parent POM 
releases -->
-       <repository>
-          <id>cytoscape_releases</id>
-          <snapshots>
-            <enabled>false</enabled>
-          </snapshots>
-          <releases>
-            <enabled>true</enabled>
-          </releases>
-          <name>Cytoscape Releases</name>
-          
<url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
-       </repository>
-  </repositories>
-
-  <build>
-    <plugins>
-      <plugin>
-        <artifactId>maven-assembly-plugin</artifactId>
-        <version>2.2-beta-5</version>
-        <configuration>
-          <descriptorRefs>
-            <descriptorRef>jar-with-dependencies</descriptorRef>
-          </descriptorRefs>
-                 <!-- 
-                 this confuses the installation and doesn't install 
-                 separate plugin-api and cytoscape-api jars
-          <finalName>cytoscape-api-${version}</finalName>
-          <appendAssemblyId>false</appendAssemblyId>
-                 -->
-        </configuration>
-        <executions>
-          <execution>
-            <id>make-assembly</id>
-            <phase>package</phase>
-            <goals>
-              <goal>single</goal>
-            </goals>
-          </execution>
-        </executions>
-      </plugin>
-      <plugin>
-        <groupId>org.ops4j</groupId>
-        <artifactId>maven-pax-plugin</artifactId>
-        <version>1.4</version>
-        <extensions>true</extensions>
-      </plugin>
-      <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>
-      <plugin>
-        <groupId>org.apache.maven.plugins</groupId>
-        <artifactId>maven-jar-plugin</artifactId>
-        <executions>
-          <execution>
-            <goals>
-              <goal>test-jar</goal>
-            </goals>
-          </execution>
-        </executions>
-      </plugin>
-    </plugins>
-  </build>
-
-       <!-- These dependencies are meant to capture the entire public 
Cytoscape API -->
-       <dependencies>
-               <dependency>
-                       <groupId>org.cytoscape</groupId>
-                       <artifactId>session-api</artifactId>
-                       <version>3.0.0-alpha2-SNAPSHOT</version>
-               </dependency>
-               <dependency>
-                       <groupId>org.cytoscape</groupId>
-                       <artifactId>core-task-api</artifactId>
-                       <version>3.0.0-alpha2-SNAPSHOT</version>
-               </dependency>
-               
-               <dependency>
-                       <groupId>junit</groupId>
-                       <artifactId>junit</artifactId>
-                       <version>${junit.version}</version>
-                       <scope>test</scope>
-               </dependency>
-               <dependency>
-                       <groupId>org.mockito</groupId>
-                       <artifactId>mockito-all</artifactId>
-                       <version>1.8.1</version>
-                       <scope>test</scope>
-               </dependency>
-       </dependencies>
-
-</project>

Copied: core3/plugin-api/tags/plugin-api-3.0.0-alpha2/pom.xml (from rev 23822, 
core3/plugin-api/trunk/pom.xml)
===================================================================
--- core3/plugin-api/tags/plugin-api-3.0.0-alpha2/pom.xml                       
        (rev 0)
+++ core3/plugin-api/tags/plugin-api-3.0.0-alpha2/pom.xml       2011-01-28 
23:17:03 UTC (rev 23823)
@@ -0,0 +1,172 @@
+<?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>
+    <artifactId>parent</artifactId>
+    <groupId>org.cytoscape</groupId>
+    <version>3.0.0-alpha4</version>
+  </parent>
+
+  <properties>
+    <bundle.symbolicName>org.cytoscape.plugin-api</bundle.symbolicName>
+    <bundle.namespace>org.cytoscape.plugin</bundle.namespace>
+  </properties>
+
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>org.cytoscape</groupId>
+  <artifactId>plugin-api</artifactId>
+  <version>3.0.0-alpha2</version>
+
+  <name>${bundle.symbolicName}</name>
+
+  <packaging>bundle</packaging>
+
+  <scm>
+    
<connection>scm:svn:http://chianti.ucsd.edu/svn/core3/plugin-api/tags/plugin-api-3.0.0-alpha2</connection>
+    
<developerConnection>scm:svn:svn+ssh://grenache.ucsd.edu/cellar/common/svn/core3/plugin-api/tags/plugin-api-3.0.0-alpha2</developerConnection>
+    
<url>http://chianti.ucsd.edu/svn/core3/plugin-api/tags/plugin-api-3.0.0-alpha2</url>
+  </scm>
+
+  <repositories>
+      <!-- bootstrap for cytoscape dependencies, namely the parent POM 
snapshots -->
+      <repository>
+          <id>cytoscape_snapshots</id>
+          <snapshots>
+            <enabled>true</enabled>
+          </snapshots>
+          <releases>
+            <enabled>false</enabled>
+          </releases>
+          <name>Cytoscape Snapshots</name>
+          
<url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+       </repository>
+       <!-- bootstrap for cytoscape dependencies, namely the parent POM 
releases -->
+       <repository>
+          <id>cytoscape_releases</id>
+          <snapshots>
+            <enabled>false</enabled>
+          </snapshots>
+          <releases>
+            <enabled>true</enabled>
+          </releases>
+          <name>Cytoscape Releases</name>
+          
<url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+       </repository>
+  </repositories>
+
+  <build>
+    <plugins>
+      <plugin>
+        <artifactId>maven-assembly-plugin</artifactId>
+        <version>2.2-beta-5</version>
+        <configuration>
+          <descriptorRefs>
+            <descriptorRef>jar-with-dependencies</descriptorRef>
+          </descriptorRefs>
+                 <!-- 
+                 this confuses the installation and doesn't install 
+                 separate plugin-api and cytoscape-api jars
+          <finalName>cytoscape-api-${version}</finalName>
+          <appendAssemblyId>false</appendAssemblyId>
+                 -->
+        </configuration>
+        <executions>
+          <execution>
+            <id>make-assembly</id>
+            <phase>package</phase>
+            <goals>
+              <goal>single</goal>
+            </goals>
+          </execution>
+        </executions>
+      </plugin>
+      <plugin>
+        <groupId>org.ops4j</groupId>
+        <artifactId>maven-pax-plugin</artifactId>
+        <version>1.4</version>
+        <extensions>true</extensions>
+      </plugin>
+      <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>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-jar-plugin</artifactId>
+        <executions>
+          <execution>
+            <goals>
+              <goal>test-jar</goal>
+            </goals>
+          </execution>
+        </executions>
+      </plugin>
+    </plugins>
+  </build>
+
+       <!-- These dependencies are meant to capture the entire public 
Cytoscape API -->
+       <dependencies>
+               <dependency>
+                       <groupId>org.cytoscape</groupId>
+                       <artifactId>session-api</artifactId>
+                       <version>3.0.0-alpha2</version>
+               </dependency>
+               <dependency>
+                       <groupId>org.cytoscape</groupId>
+                       <artifactId>core-task-api</artifactId>
+                       <version>3.0.0-alpha2</version>
+               </dependency>
+               <dependency>
+                       <groupId>org.cytoscape</groupId>
+                       <artifactId>swing-application-api</artifactId>
+                       <version>3.0.0-alpha1</version>
+               </dependency>
+               <dependency>
+                       <groupId>org.cytoscape</groupId>
+                       <artifactId>io-api</artifactId>
+                       <version>3.0.0-alpha2</version>
+               </dependency>
+               <dependency>
+                       <groupId>org.cytoscape</groupId>
+                       <artifactId>service-util</artifactId>
+                       <version>3.0.0-alpha1</version>
+               </dependency>
+               <dependency>
+                       <groupId>org.cytoscape</groupId>
+                       <artifactId>work-swing-api</artifactId>
+                       <version>3.0.0-alpha1</version>
+               </dependency>
+               <dependency>
+                       <groupId>org.cytoscape</groupId>
+                       <artifactId>layout-api</artifactId>
+                       <version>3.0.0-alpha1</version>
+               </dependency>
+               <dependency>
+                       <groupId>org.cytoscape</groupId>
+                       <artifactId>property-api</artifactId>
+                       <version>3.0.0-alpha3</version>
+               </dependency>
+               
+               <dependency>
+                       <groupId>junit</groupId>
+                       <artifactId>junit</artifactId>
+                       <version>${junit.version}</version>
+                       <scope>test</scope>
+               </dependency>
+               <dependency>
+                       <groupId>org.mockito</groupId>
+                       <artifactId>mockito-all</artifactId>
+                       <version>1.8.1</version>
+                       <scope>test</scope>
+               </dependency>
+       </dependencies>
+
+</project>

Deleted: 
core3/plugin-api/tags/plugin-api-3.0.0-alpha2/src/main/java/org/cytoscape/plugin/CyPluginAdapter.java
===================================================================
--- 
core3/plugin-api/trunk/src/main/java/org/cytoscape/plugin/CyPluginAdapter.java  
    2011-01-24 00:58:13 UTC (rev 23568)
+++ 
core3/plugin-api/tags/plugin-api-3.0.0-alpha2/src/main/java/org/cytoscape/plugin/CyPluginAdapter.java
       2011-01-28 23:17:03 UTC (rev 23823)
@@ -1,139 +0,0 @@
-package org.cytoscape.plugin;
-
-import org.cytoscape.model.CyNetworkFactory;
-import org.cytoscape.model.CyNetworkManager;
-import org.cytoscape.model.subnetwork.CyRootNetworkFactory;
-import org.cytoscape.model.CyTableFactory;
-import org.cytoscape.event.CyEventHelper;
-import org.cytoscape.view.model.CyNetworkViewFactory;
-import org.cytoscape.view.model.CyNetworkViewManager;
-// TODO once the layout api has stabilized
-//import org.cytoscape.view.layout.CyLayouts;
-import org.cytoscape.view.presentation.RenderingEngineFactory;
-import org.cytoscape.view.vizmap.VisualMappingManager;
-import org.cytoscape.session.CyApplicationManager;
-import org.cytoscape.session.CySessionManager;
-import org.cytoscape.work.TaskManager;
-
-
-/**
- * A Java-only api providing access to Cytoscape functionality.
- * This class will provide access the various Manager and 
- * Factory interfaces defined in different API jars that are
- * normally made available to plugins as OSGi services. Through
- * these interfaces developers will have access to most management
- * and creational facilities defined in the Cytoscape API.
- * This is a convenience interface intended make plugin development
- * as simple as possible.
- */
-public interface CyPluginAdapter {
-
-       //
-       // model api
-       //
-
-       /**
-        * Returns an instance of {@link CyNetworkFactory}.
-        * @return an instance of {@link CyNetworkFactory}.
-        */
-       CyNetworkFactory getCyNetworkFactory(); 
-
-       /**
-        * Returns an instance of {@link CyTableFactory}.
-        * @return an instance of {@link CyTableFactory}.
-        */
-       CyTableFactory getCyTableFactory(); 
-
-       /**
-        * Returns an instance of {@link CyRootNetworkFactory}.
-        * @return an instance of {@link CyRootNetworkFactory}.
-        */
-       CyRootNetworkFactory getCyRootNetworkFactory(); 
-
-       /**
-        * Returns an instance of {@link CyEventHelper}.
-        * @return an instance of {@link CyEventHelper}.
-        */
-       CyEventHelper getCyEventHelper(); 
-
-       /**
-        * Returns an instance of {@link CyNetworkManager}.
-        * @return an instance of {@link CyNetworkManager}.
-        */
-       CyNetworkManager getCyNetworkManager(); 
-
-       //
-       // viewmodel api
-       //
-
-       /**
-        * Returns an instance of {@link CyNetworkViewFactory}.
-        * @return an instance of {@link CyNetworkViewFactory}.
-        */
-       CyNetworkViewFactory getCyNetworkViewFactory();
-
-       /**
-        * Returns an instance of {@link CyNetworkViewManager}.
-        * @return an instance of {@link CyNetworkViewManager}.
-        */
-       CyNetworkViewManager getCyNetworkViewManager();
-
-       //
-       // session api
-       //
-
-       /**
-        * Returns an instance of {@link CyApplicationManager}.
-        * @return an instance of {@link CyApplicationManager}.
-        */
-       CyApplicationManager getCyApplicationManager();
-
-       /**
-        * Returns an instance of {@link CySessionManager}.
-        * @return an instance of {@link CySessionManager}.
-        */
-       CySessionManager getCySessionManager();
-
-       //
-       // work api
-       //
-
-       /**
-        * Returns an instance of {@link TaskManager}.
-        * @return an instance of {@link TaskManager}.
-        */
-       TaskManager getTaskManager();
-
-       //
-       // presentation api
-       //
-
-       /**
-        * Returns an instance of {@link RenderingEngineFactory}.
-        * @return an instance of {@link RenderingEngineFactory}.
-        */
-       RenderingEngineFactory getPresentationFactory();
-
-       //
-       // vizmap api
-       //
-
-       /**
-        * Returns an instance of {@link VisualMappingManager}.
-        * @return an instance of {@link VisualMappingManager}.
-        */
-       VisualMappingManager getVisualMappingManager();
-
-
-       //
-       // layout api
-       //
-
-// TODO once the layout api has stabilized
-       /**
-        * Returns an instance of {@link CyLayouts}.
-        * @return an instance of {@link CyLayouts}.
-       CyLayouts getCyLayouts();
-        */
-
-}

Copied: 
core3/plugin-api/tags/plugin-api-3.0.0-alpha2/src/main/java/org/cytoscape/plugin/CyPluginAdapter.java
 (from rev 23819, 
core3/plugin-api/trunk/src/main/java/org/cytoscape/plugin/CyPluginAdapter.java)
===================================================================
--- 
core3/plugin-api/tags/plugin-api-3.0.0-alpha2/src/main/java/org/cytoscape/plugin/CyPluginAdapter.java
                               (rev 0)
+++ 
core3/plugin-api/tags/plugin-api-3.0.0-alpha2/src/main/java/org/cytoscape/plugin/CyPluginAdapter.java
       2011-01-28 23:17:03 UTC (rev 23823)
@@ -0,0 +1,264 @@
+package org.cytoscape.plugin;
+
+import org.cytoscape.application.swing.CySwingApplication;
+import org.cytoscape.event.CyEventHelper;
+import org.cytoscape.model.CyNetworkFactory;
+import org.cytoscape.model.CyNetworkManager;
+import org.cytoscape.model.CyTableManager;
+import org.cytoscape.model.CyTableFactory;
+import org.cytoscape.model.subnetwork.CyRootNetworkFactory;
+import org.cytoscape.session.CyApplicationManager;
+import org.cytoscape.session.CySessionManager;
+import org.cytoscape.view.model.CyNetworkViewFactory;
+import org.cytoscape.view.model.CyNetworkViewManager;
+import org.cytoscape.view.layout.CyLayouts;
+import org.cytoscape.view.presentation.RenderingEngineManager;
+import org.cytoscape.view.vizmap.VisualMappingManager;
+import org.cytoscape.view.vizmap.VisualStyleFactory;
+import org.cytoscape.work.TaskManager;
+import org.cytoscape.work.undo.UndoSupport;
+import org.cytoscape.work.swing.GUITaskManager;
+import org.cytoscape.io.write.CyNetworkViewWriterManager;
+import org.cytoscape.io.write.CySessionWriterManager;
+//import org.cytoscape.io.write.CyTableWriterManager;
+import org.cytoscape.io.write.CyPropertyWriterManager;
+import org.cytoscape.io.write.PresentationWriterManager;
+import org.cytoscape.io.read.CyNetworkViewReaderManager;
+import org.cytoscape.io.read.CySessionReaderManager;
+import org.cytoscape.io.read.CyTableReaderManager;
+import org.cytoscape.io.read.CyPropertyReaderManager;
+import org.cytoscape.property.CyProperty;
+import org.cytoscape.service.util.CyServiceRegistrar;
+
+import java.util.Properties;
+
+/**
+ * A Java-only api providing access to Cytoscape functionality.
+ * This class will provide access the various Manager and 
+ * Factory interfaces defined in different API jars that are
+ * normally made available to plugins as OSGi services. Through
+ * these interfaces developers will have access to most management
+ * and creational facilities defined in the Cytoscape API.
+ * This is a convenience interface intended make plugin development
+ * as simple as possible.
+ */
+public interface CyPluginAdapter {
+
+       //
+       // model api
+       //
+
+       /**
+        * Returns an instance of {@link CyNetworkFactory}.
+        * @return an instance of {@link CyNetworkFactory}.
+        */
+       CyNetworkFactory getCyNetworkFactory(); 
+
+       /**
+        * Returns an instance of {@link CyTableFactory}.
+        * @return an instance of {@link CyTableFactory}.
+        */
+       CyTableFactory getCyTableFactory(); 
+
+       /**
+        * Returns an instance of {@link CyTableManager}.
+        * @return an instance of {@link CyTableManager}.
+        */
+       CyTableManager getCyTableManager();
+
+       /**
+        * Returns an instance of {@link CyRootNetworkFactory}.
+        * @return an instance of {@link CyRootNetworkFactory}.
+        */
+       CyRootNetworkFactory getCyRootNetworkFactory(); 
+
+       /**
+        * Returns an instance of {@link CyEventHelper}.
+        * @return an instance of {@link CyEventHelper}.
+        */
+       CyEventHelper getCyEventHelper(); 
+
+       /**
+        * Returns an instance of {@link CyNetworkManager}.
+        * @return an instance of {@link CyNetworkManager}.
+        */
+       CyNetworkManager getCyNetworkManager(); 
+
+       //
+       // viewmodel api
+       //
+
+       /**
+        * Returns an instance of {@link CyNetworkViewFactory}.
+        * @return an instance of {@link CyNetworkViewFactory}.
+        */
+       CyNetworkViewFactory getCyNetworkViewFactory();
+
+       /**
+        * Returns an instance of {@link CyNetworkViewManager}.
+        * @return an instance of {@link CyNetworkViewManager}.
+        */
+       CyNetworkViewManager getCyNetworkViewManager();
+
+       //
+       // session api
+       //
+
+       /**
+        * Returns an instance of {@link CyApplicationManager}.
+        * @return an instance of {@link CyApplicationManager}.
+        */
+       CyApplicationManager getCyApplicationManager();
+
+       /**
+        * Returns an instance of {@link CySessionManager}.
+        * @return an instance of {@link CySessionManager}.
+        */
+       CySessionManager getCySessionManager();
+
+       //
+       // work api
+       //
+
+       /**
+        * Returns an instance of {@link TaskManager}.
+        * @return an instance of {@link TaskManager}.
+        */
+       TaskManager getTaskManager();
+
+       /**
+        * Returns an instance of {@link UndoSupport}.
+        * @return an instance of {@link UndoSupport}.
+        */
+       UndoSupport getUndoSupport();
+       
+       //
+       // work swing api
+       //
+
+       /**
+        * Returns an instance of {@link GUITaskManager}.
+        * @return an instance of {@link GUITaskManager}.
+        */
+       GUITaskManager getGUITaskManager();
+
+       //
+       // presentation api
+       //
+
+       /**
+        * Returns an instance of {@link RenderingEngineManager}.
+        * @return an instance of {@link RenderingEngineManager}.
+        */
+       RenderingEngineManager getRenderingEngineManager();
+
+       //
+       // vizmap api
+       //
+
+       /**
+        * Returns an instance of {@link VisualMappingManager}.
+        * @return an instance of {@link VisualMappingManager}.
+        */
+       VisualMappingManager getVisualMappingManager();
+       
+       /**
+        * Returns an instance of {@link VisualStyleFactory}.
+        * @return an instance of {@link VisualStyleFactory}.
+        */
+       VisualStyleFactory getVisualStyleFactory();
+
+       //
+       // layout api
+       //
+       /**
+        * Returns an instance of {@link CyLayouts}.
+        * @return an instance of {@link CyLayouts}.
+        */
+       CyLayouts getCyLayouts();
+
+       //
+       // swing application api
+       //
+
+       /**
+        * Returns an instance of {@link CySwingApplication}.
+        * @return an instance of {@link CySwingApplication}.
+        */
+       CySwingApplication getCySwingApplication();
+
+       //
+       // property api
+       //
+       /**
+        * Returns an instance of {@link CyProperty<Properties>}.
+        * @return an instance of {@link CyProperty<Properties>}.
+        */
+       CyProperty<Properties> getCoreProperties();
+
+       //
+       // io api
+       //
+       /**
+        * Returns an instance of {@link CyNetworkViewReaderManager}.
+        * @return an instance of {@link CyNetworkViewReaderManager}.
+        */
+       CyNetworkViewReaderManager getCyNetworkViewReaderManager();
+
+       /**
+        * Returns an instance of {@link CyPropertyReaderManager}.
+        * @return an instance of {@link CyPropertyReaderManager}.
+        */
+       CyPropertyReaderManager getCyPropertyReaderManager();
+
+       /**
+        * Returns an instance of {@link CySessionReaderManager}.
+        * @return an instance of {@link CySessionReaderManager}.
+        */
+       CySessionReaderManager getCySessionReaderManager();
+
+       /**
+        * Returns an instance of {@link CyTableReaderManager}.
+        * @return an instance of {@link CyTableReaderManager}.
+        */
+       CyTableReaderManager getCyTableReaderManager();
+
+       /**
+        * Returns an instance of {@link CyNetworkViewWriterManager}.
+        * @return an instance of {@link CyNetworkViewWriterManager}.
+        */
+       CyNetworkViewWriterManager getCyNetworkViewWriterManager();
+
+       /**
+        * Returns an instance of {@link CyPropertyWriterManager}.
+        * @return an instance of {@link CyPropertyWriterManager}.
+        */
+       CyPropertyWriterManager getCyPropertyWriterManager();
+
+       /**
+        * Returns an instance of {@link CySessionWriterManager}.
+        * @return an instance of {@link CySessionWriterManager}.
+        */
+       CySessionWriterManager getCySessionWriterManager();
+
+       /**
+        * Returns an instance of {@link CyTableWriterManager}.
+        * @return an instance of {@link CyTableWriterManager}.
+       CyTableWriterManager getCyTableWriterManager();
+        */
+
+       /**
+        * Returns an instance of {@link PresentationWriterManager}.
+        * @return an instance of {@link PresentationWriterManager}.
+        */
+       PresentationWriterManager getPresentationWriterManager();
+
+       //
+       // service util
+       //
+       /**
+        * Returns an instance of {@link CyServiceRegistrar}.
+        * @return an instance of {@link CyServiceRegistrar}.
+        */
+       CyServiceRegistrar getCyServiceRegistrar();
+}

Deleted: 
core3/plugin-api/tags/plugin-api-3.0.0-alpha2/src/test/java/org/cytoscape/plugin/CyPluginAdapterTest.java
===================================================================
--- 
core3/plugin-api/trunk/src/test/java/org/cytoscape/plugin/CyPluginAdapterTest.java
  2011-01-24 00:58:13 UTC (rev 23568)
+++ 
core3/plugin-api/tags/plugin-api-3.0.0-alpha2/src/test/java/org/cytoscape/plugin/CyPluginAdapterTest.java
   2011-01-28 23:17:03 UTC (rev 23823)
@@ -1,76 +0,0 @@
-package org.cytoscape.plugin;
-
-
-import org.junit.Test;
-import static org.junit.Assert.*;
-
-
-public abstract class CyPluginAdapterTest {
-       protected CyPluginAdapter adapter;
-       
-       @Test
-       public void testGetCyTableFactory() { 
-               assertNotNull("dataTable exists", adapter.getCyTableFactory());
-       }
-       
-       @Test
-       public void testGetCyEventHelper() { 
-               assertNotNull("dataTable exists", adapter.getCyEventHelper());
-       } 
-
-// TODO once layout api has stabilized
-//     @Test
-//     public void testGetCyLayouts() { 
-//             assertNotNull("CyLayouts exists", adapter.getCyLayouts());
-//     } 
-
-       @Test
-       public void testGetCyNetworkFactory() { 
-               assertNotNull("CyNetworkFactory exists", 
adapter.getCyNetworkFactory());
-       }
-
-       @Test
-       public void testGetCyNetworkManager() { 
-               assertNotNull("CyNetworkManager exists", 
adapter.getCyNetworkManager());
-       } 
-
-       @Test
-       public void testGetCyNetworkViewFactory() {
-               assertNotNull("CyNetworkViewFactory exists", 
adapter.getCyNetworkViewFactory());
-       }
-
-       @Test
-       public void testGetCyRootNetworkFactory() {
-               assertNotNull("CyRootNetworkFactory exists", 
adapter.getCyRootNetworkFactory());
-       } 
-
-       @Test
-       public void testGetCySessionManager() { 
-               assertNotNull("CySessionManager exists", 
adapter.getCySessionManager());
-       } 
-
-       @Test
-       public void testGetPresentationFactory() { 
-               assertNotNull("PresentationFactory exists", 
adapter.getPresentationFactory());
-       }
-
-       @Test
-       public void testGetTaskManager() { 
-               assertNotNull("TaskManager exists", adapter.getTaskManager());
-       }
-
-       @Test
-       public void testGetVisualMappingManager() { 
-               assertNotNull("VisualMappingManager exists", 
adapter.getVisualMappingManager());
-       } 
-
-       @Test
-       public void testGetCyNetworkViewManager() { 
-               assertNotNull("NetworkViewManager exists", 
adapter.getCyNetworkViewManager());
-       } 
-
-       @Test
-       public void testGetCyApplicationManager() { 
-               assertNotNull("CyApplicationManager exists", 
adapter.getCyApplicationManager());
-       } 
-}

Copied: 
core3/plugin-api/tags/plugin-api-3.0.0-alpha2/src/test/java/org/cytoscape/plugin/CyPluginAdapterTest.java
 (from rev 23819, 
core3/plugin-api/trunk/src/test/java/org/cytoscape/plugin/CyPluginAdapterTest.java)
===================================================================
--- 
core3/plugin-api/tags/plugin-api-3.0.0-alpha2/src/test/java/org/cytoscape/plugin/CyPluginAdapterTest.java
                           (rev 0)
+++ 
core3/plugin-api/tags/plugin-api-3.0.0-alpha2/src/test/java/org/cytoscape/plugin/CyPluginAdapterTest.java
   2011-01-28 23:17:03 UTC (rev 23823)
@@ -0,0 +1,158 @@
+package org.cytoscape.plugin;
+
+
+import org.junit.Test;
+import static org.junit.Assert.*;
+
+
+public abstract class CyPluginAdapterTest {
+       protected CyPluginAdapter adapter;
+       
+       @Test
+       public void testGetCyTableFactory() { 
+               assertNotNull("dataTable exists", adapter.getCyTableFactory());
+       }
+       
+       @Test
+       public void testGetCyEventHelper() { 
+               assertNotNull("dataTable exists", adapter.getCyEventHelper());
+       } 
+
+       @Test
+       public void testGetCyLayouts() { 
+               assertNotNull("CyLayouts exists", adapter.getCyLayouts());
+       } 
+
+       @Test
+       public void testGetCyNetworkFactory() { 
+               assertNotNull("CyNetworkFactory exists", 
adapter.getCyNetworkFactory());
+       }
+
+       @Test
+       public void testGetCyNetworkManager() { 
+               assertNotNull("CyNetworkManager exists", 
adapter.getCyNetworkManager());
+       } 
+
+       @Test
+       public void testGetCyNetworkViewFactory() {
+               assertNotNull("CyNetworkViewFactory exists", 
adapter.getCyNetworkViewFactory());
+       }
+
+       @Test
+       public void testGetCyRootNetworkFactory() {
+               assertNotNull("CyRootNetworkFactory exists", 
adapter.getCyRootNetworkFactory());
+       } 
+
+       @Test
+       public void testGetCySessionManager() { 
+               assertNotNull("CySessionManager exists", 
adapter.getCySessionManager());
+       } 
+
+       @Test
+       public void testGetTaskManager() { 
+               assertNotNull("TaskManager exists", adapter.getTaskManager());
+       }
+
+       @Test
+       public void testGetVisualMappingManager() { 
+               assertNotNull("VisualMappingManager exists", 
adapter.getVisualMappingManager());
+       } 
+
+       @Test
+       public void testGetCyNetworkViewManager() { 
+               assertNotNull("NetworkViewManager exists", 
adapter.getCyNetworkViewManager());
+       } 
+
+       @Test
+       public void testGetCyApplicationManager() { 
+               assertNotNull("CyApplicationManager exists", 
adapter.getCyApplicationManager());
+       } 
+
+       @Test
+       public void testGetCySwingApplication() { 
+               assertNotNull("CySwingApplication exists", 
adapter.getCySwingApplication());
+       } 
+
+       @Test
+       public void testCyTableManager() { 
+               assertNotNull("CyTableManager exists", 
adapter.getCyTableManager());
+       } 
+
+       @Test
+       public void testUndoSupport() { 
+               assertNotNull("UndoSupport exists", adapter.getUndoSupport());
+       } 
+
+       @Test
+       public void testGUITaskManager() { 
+               assertNotNull("GUITaskManager exists", 
adapter.getGUITaskManager());
+       } 
+
+       @Test
+       public void testGetRenderingEngineManager() { 
+               assertNotNull("RenderingEngineManager exists", 
adapter.getRenderingEngineManager());
+       } 
+
+       @Test
+       public void testVisualStyleFactory() { 
+               assertNotNull("VisualStyleFactory exists", 
adapter.getVisualStyleFactory());
+       } 
+
+       @Test
+       public void testCyPropertyProperties() { 
+               assertNotNull("CyProperty<Properties> exists", 
adapter.getCoreProperties());
+       } 
+
+       @Test
+       public void testCyNetworkViewReaderManager() { 
+               assertNotNull("CyNetworkViewReaderManager exists", 
adapter.getCyNetworkViewReaderManager());
+       } 
+
+       @Test
+       public void testCyPropertyReaderManager() { 
+               assertNotNull("CyPropertyReaderManager exists", 
adapter.getCyPropertyReaderManager());
+       } 
+
+       @Test
+       public void testCySessionReaderManager() { 
+               assertNotNull("CySessionReaderManager exists", 
adapter.getCySessionReaderManager());
+       } 
+
+       @Test
+       public void testCyTableReaderManager() { 
+               assertNotNull("CyTableReaderManager exists", 
adapter.getCyTableReaderManager());
+       } 
+
+       @Test
+       public void testCyNetworkViewWriterManager() { 
+               assertNotNull("CyNetworkViewWriterManager exists", 
adapter.getCyNetworkViewWriterManager());
+       } 
+
+       @Test
+       public void testCyPropertyWriterManager() { 
+               assertNotNull("CyPropertyWriterManager exists", 
adapter.getCyPropertyWriterManager());
+       } 
+
+       @Test
+       public void testCySessionWriterManager() { 
+               assertNotNull("CySessionWriterManager exists", 
adapter.getCySessionWriterManager());
+       } 
+
+/*
+       @Test
+       public void testCyTableWriterManager() { 
+               assertNotNull("CyTableWriterManager exists", 
adapter.getCyTableWriterManager());
+       } 
+       */
+
+       @Test
+       public void testPresentationWriterManager() { 
+               assertNotNull("PresentationWriterManager exists", 
adapter.getPresentationWriterManager());
+       } 
+
+       @Test
+       public void testCyServiceRegistrar() { 
+               assertNotNull("CyServiceRegistrar exists", 
adapter.getCyServiceRegistrar());
+       } 
+
+}

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