Cytoscape_3/AppDeveloper/SettingUpAnIDE/Eclipse

Introduction

This is an introduction to Cytoscape 3 App 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 Eclipse Plugins From Eclipse Marketplace

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

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

Eclipse Plugins to Install

You need to install some Eclipse plugins to develop Cytoscape 3 apps. 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 an Eclipse plugin to integrate Maven. Now it is a part of Eclipse foundation, so you can skip Marketplace and go direct to m2eclipse configuration.

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

Checkout Cytoscape 3 App 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/app-developer/trunk/ (for core developers, svn+ssh://grenache.ucsd.edu/cellar/common/svn/core3/app-developer/trunk/).

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

Build App 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 app.

Create the App

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

Simple App

1. Select New → Java Project

2. Enter project name. This can be anything. In this example, we use Cy3SimpleApp as a sample app name.

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

4. Right-click src folder and create a class file HelloWorldApp. 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-App: org.cytoscape.sample.HelloWorldApp

     This is your App's main class name. Be sure to include a return at the end of the last line or it may be excluded upon export!

6. Your project directory looks like this:

   • 

7. Write App main class:

   •    1 package org.cytoscape.sample;
        2 
        3 import org.cytoscape.app.AbstractCyApp;
        4 import org.cytoscape.app.CyAppAdapter;
        5 
        6 public class HelloWorldApp extends AbstractCyApp {
        7 
        8         public HelloWorldApp(CyAppAdapter 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 app 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 app jar file exists in the directory you specified above.

Test your app

1. Run Cytoscape from command-line

2. Select Apps>App Manager

3. Select Import Local App tab

4. Click Select button and select the app 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 App

Cytoscape 3 Bundle App

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

Tutorial:Creating an OSGi Bundle Cytoscape 3 App

Questions?

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