Cytoscape WikiHow to set up Netbeans to develop Cytoscape plugins
Fred Eisele (FredEisele)
August 2007
Introduction
This document is an introduction on how to set up Netbeans to develop Cytoscape plugins. It is assumed that you have Netbeans installed and running.
Setting up a project
- Create a java class library project
File->New->Project... then select Java Class Library
Name the project, selecting working directories etc.
- Edit the projects properties
right click the new created project in the Package Explorer and select Properties
Add the cytoscape libraries, cytoscape.jar from the main Cytoscape folder and all the .jar files from the lib/ folder inside the main Cytoscape folder.
select Libraries from the tree in the left panel
add the cytoscape specific Add JAR/Folder
- Prepare to run cytoscape
select Run from the left panel
set the "Main class" to 'cytoscape.CyMain'
- (optional) set the "Arguments"
- to pick up standard plugins use '-p "C:\Program Files\Cytoscape_v2.5.0\plugins"' (or whatever the plugin directory is), this option can be repeated
preload your network, node/edge atributes, expression data, etc. See the Cytoscape's manual for more information on the available command line options.
Apply your changes
Cytoscape needs to know that your plugin exists
Netbeans takes care of including the plugin library in the class path but it does not notify Cytoscape of its existance. This can be done in one of two ways. The preferred way is to "install" the plugin. This has the added benefit of making it possible to uninstall and reinstall without restarting Cytoscape.
The easiest way to cause Cytoscape to recognize the plugin is to place a "dummy" jar file in one of the plugin directories. All that is needed is a jar file containing a class with a default constructor. This is not executed at runtime as the actual libraries will be found first.
You can find help at the Developer_Homepage and Cytoscape_Plugin_Tutorial.
Category: NetbeansAndCytoscapeDevelopment