Cytoscape_3/AppDeveloper/SettingUpAnIDE/Eclipse

Introduction

This is an introduction to Cytoscape 3 Plugin development for Eclipse users.

Prerequisites

You need to know basics of Eclipse and Maven.

Install JDK

To develop Cytoscape 3, you need Java 6 or 7. If you find problems on Java 7, please let us know.

Setting up Eclipse

This procedure had been tested with latest version of Eclipse, Indigo. You can use any version of Eclipse distribution, but we recommend to use Eclipse for RCP and RAP Developers or Eclipse IDE for Java Developers.

Installing Plugin From Eclipse Marketplace

Eclipse Indigo supports plugin store called Eclipse Marketplace. All of the following plugins are available from the Marketplace. To install plugins, open the Marketplace dialog (Help → Eclipse Marketplace), type plugin name in the search box, and click install button.

Usually, you will be asked to restart Eclipse after installing plugins.

Plugins to install

You need to install some plugins to develop Cytoscape 3 plugins. All of the following are required to develop Cytoscape 3 (or any Java applications using Maven and Spring).

Subclipse

To access our Subversion repository from Eclipse, you need to install Subversion client software for Eclipse. In this tutorial, we use Subclipse plugin.

m2eclipse

M2Eclipse is a plugin to integrate Maven to Eclipse. ow it is a part of Eclipse foundation

Many useful documents are available from the project and we recommend to read them.

Spring IDE

Spring IDE helps you to debug/refactor Spring setting files on Eclipse. This is not required to build your plugin, but we strongly recommend to use this if you create Cytoscape 3 Native plugins.

Checkout Cytoscape 3 Plugin Developer's Template Project

1. Select File→New→Other→Maven→Checkout Maven Projects from SCM

2. Select Source Code Management (SCM) system type to svn

3. Make sure the URL is set to http://chianti.ucsd.edu/svn/core3/plugin-developer/trunk/ (for core developers, svn+ssh://grenache.ucsd.edu/cellar/common/svn/core3/plugin-developer/trunk/).

4. Click 'finish' and you'll end up with something like this:

Build Plugin Developer's Template Project

1. Right-click cytoscape project top folder

2. Select Run As → Maven Build

3. Type clean install in the Goals text box

4. Click Run button

Now you can see the following directory structure under target directory:

Run Cytoscape 3

1. Open command-line terminal.

2. Go into target directory you've just created with m2eclipse plugin

3. Execute cytoscape.sh (for unix/mac) or cytoscape.bat (windows)

If you can run Cytoscape, now you are ready to code your plugin.

Create Plugin

There are two types of plugins for Cytoscape 3 and you can use Eclipse for both of them.

Simple Plugin

1. Select New → Java Project

2. Enter project name. This can be anything. In this example, we use Cy3SimplePlugin as a sample plugin name.

3. Add cytoscape-plugin-api jar file as a library

4. Right-click src folder and create a class file HelloWorldPlugin. Use org.cytoscape.sample as its package name

5. Create Manifest file. It's just a text file named MANIFEST.MF. The only entry you need to write in this file is the following:

   • Manifest-Version: 1.0
     Cytoscape-Plugin: org.cytoscape.sample.HelloWorldPlugin

     This is your Plugin's main class name.
6. Your project directory looks like this:

   • 

7. Write Plugin main class:

   •    1 package org.cytoscape.sample;
        2 
        3 import org.cytoscape.plugin.CyPlugin;
        4 import org.cytoscape.plugin.CyPluginAdapter;
        5 
        6 public class HelloWorldPlugin extends CyPlugin {
        7 
        8         public HelloWorldPlugin(CyPluginAdapter adapter) {
        9                 super(adapter);
       10                 
       11                 System.out.println("Hello Cytoscape 3!");
       12         }
       13 }
       14 
     

8. Select File>Export

9. Select JAR FIle and click Next

10. Uncheck MANIFEST.MF file. Otherwise, two manifest files will be created in the JAR!

    • 

11. Type plugin jar file name and click Next

12. Leave all settings as-is and click Next

13. Select Use existing manifest from workspace and specify the one you've just created

    • 

14. Click Finish. Make sure the plugin jar file exists in the directory you specified above.

Test your plugin

1. Run Cytoscape from command-line

2. Select Plugins>Plugin Manager

3. Select Import Local Plugin tab

4. Click Select button and select the plugin jar file you've created

5. You can see Hello Cytoscape 3! in the console

For more realistic example, please try this tutorial:

Tutorial:Creating a Simple Cytoscape 3 Plugin

Cytoscape 3 Bundle Plugin

If you want to create Cytoscape 3 Native bundle plugin, please try the following tutorial:

Tutorial:Creating an OSGi Bundle Cytoscape 3 Plugin

Questions?

If you find problems or have questions, please let us know.