fix #1

bug fix, code clean, added license header

.gitignore

@@ -0,0 +1,3 @@
+/bin/
+/build/
+/dist/

META-INF/MANIFEST.MF

@@ -2,12 +2,16 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: FindYourInteraction
 Bundle-SymbolicName: org.pathvisio.findyourinteraction
-Bundle-Version: 1.0.0
+Bundle-Version: 1.0.1
 Bundle-Activator: org.pathvisio.findyourinteraction.Activator
 Import-Package: org.osgi.framework
 Require-Bundle: org.pathvisio.desktop,
  org.pathvisio.core,
  org.pathvisio.gui,
  org.bridgedb
+Bundle-License: http://www.apache.org/licenses/LICENSE-2.0
+Bundle-DocURL: https://github.com/PathVisio/FindYourInteraction
+Bundle-Description: PathVisio plugin to load metabolic reactions from Rhea
+Bundle-Copyright: 2016-2018 BiGCaT Bioinformatics
 
 

build.xml

@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <project name="org.pathvisio.findyourinteraction" default="install" basedir=".">
 
-  <property name="pathvisio.dir" value="../../../trunk"/>
+  <property name="pathvisio.dir" value="../pathvisio"/>
 	<property name="bundle.dest" value="dist"/>
 	<property name="jar.name" value="org.pathvisio.findyourinteraction.jar"/>
 

src/org/pathvisio/findyourinteraction/Activator.java

@@ -1,24 +1,24 @@
-// FindYourInteraction Plugin for PathVisio,
-// a tool for data visualization and analysis using Biological Pathways
-// Copyright 2006-2015 BiGCaT Bioinformatics
+//  FindYourInteraction Plugin for PathVisio
+//	Find metabolic reaction from Rhea
+//	Copyright 2016-2018 BiGCaT, Maastricht University
 //
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
+//   Licensed under the Apache License, Version 2.0 (the "License");
+//   you may not use this file except in compliance with the License.
+//   You may obtain a copy of the License at
 //
-// http://www.apache.org/licenses/LICENSE-2.0
-//
-// Unless required by applicable law or agreed to in writing, software
-// distributed under the License is distributed on an "AS IS" BASIS,
-// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-// See the License for the specific language governing permissions and
-// limitations under the License.
+//       http://www.apache.org/licenses/LICENSE-2.0
 //
+//   Unless required by applicable law or agreed to in writing, software
+//   distributed under the License is distributed on an "AS IS" BASIS,
+//   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+//   See the License for the specific language governing permissions and
+//   limitations under the License.
 
 package org.pathvisio.findyourinteraction;
 
 /**
- * @author anwesha, jonathan
+ * OSGI activator of the plugin
+ * @author anwesha, jonathan, mkutmon
  */
 import org.osgi.framework.BundleActivator;
 import org.osgi.framework.BundleContext;

src/org/pathvisio/findyourinteraction/FindYourInteractionPlugin.java

@@ -1,3 +1,19 @@
+//  FindYourInteraction Plugin for PathVisio
+//	Find metabolic reaction from Rhea
+//	Copyright 2016-2018 BiGCaT, Maastricht University
+//
+//   Licensed under the Apache License, Version 2.0 (the "License");
+//   you may not use this file except in compliance with the License.
+//   You may obtain a copy of the License at
+//
+//       http://www.apache.org/licenses/LICENSE-2.0
+//
+//   Unless required by applicable law or agreed to in writing, software
+//   distributed under the License is distributed on an "AS IS" BASIS,
+//   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+//   See the License for the specific language governing permissions and
+//   limitations under the License.
+
 package org.pathvisio.findyourinteraction;
 
 import javax.swing.JPopupMenu;
@@ -7,41 +23,43 @@
 import org.pathvisio.desktop.plugin.Plugin;
 import org.pathvisio.gui.PathwayElementMenuListener.PathwayElementMenuHook;
 
+/**
+ * PathVisio plugin class
+ * Registering menu items and actions
+ * @author anwesha, jonathan, mkutmon
+ *
+ */
 public class FindYourInteractionPlugin implements Plugin{
 	private PvDesktop desktop;
+	private PathwayElementMenuHook menuHook;
 
 	@Override
 	public void init(final PvDesktop desktop) {
-		// TODO Auto-generated method stub
 		this.desktop = desktop;
-		desktop.addPathwayElementMenuHook(new PathwayElementMenuHook(){
-                  /**
+
+		menuHook = new PathwayElementMenuHook() {	
+			@Override
+			public void pathwayElementMenuHook(VPathwayElement e, JPopupMenu menu) {
+				SearchInteractionAction showInfoAction = new SearchInteractionAction(desktop, e);
+				menu.add (showInfoAction);
+			}
+		};
+		desktop.addPathwayElementMenuHook(new PathwayElementMenuHook() {
+                  /** 
                    * This method is called whenever the user right-clicks
                    * on an element in the Pathway.
                    * VPathwayElement contains the object that was clicked on.
                    */
 				@Override
-				public void pathwayElementMenuHook(VPathwayElement e,
-						JPopupMenu menu) {
-					// TODO Auto-generated method stub
-					// We instantiate an Action
-					SearchInteractionAction showInfoAction = new SearchInteractionAction(desktop);
-
-                    // pass the clicked element to the action object
-                    showInfoAction.setElement(e);
-//                    desktop.getSwingEngine().getEngine().getActivePathway().get
-                    // Insert action into the menu.
-                    // NB: this is optional, we can choose e.g.
-                    // to insert only when the clicked element is a certain type.
+				public void pathwayElementMenuHook(VPathwayElement e, JPopupMenu menu) {
+					SearchInteractionAction showInfoAction = new SearchInteractionAction(desktop, e);
                     menu.add (showInfoAction);
 				}
           });
 	}
 
 	@Override
 	public void done() {
-		// TODO Auto-generated method stub
-//		desktop.dispose();;
+		desktop.getSwingEngine().getApplicationPanel().getPathwayElementMenuListener().removePathwayElementMenuHook(menuHook);
 	}
-
 }