Cytoscape WikiHow to set up Netbeans to develop Cytoscape plugins (draft)
Fred Eisele (FredEisele)
August 2007
Introduction
This document is an introduction on how to set up [http://www.netbeans.org Netbeans] to develop Cytoscape plugins. It is assumed that you have Netbeans installed and running.
Creating a project
Go to File->New->Project... then select Java Project.
On the next dialog, put a name for your project and click Finish.
Right click the new created project in the Package Explorer and select Properties
Then select Java Build Path on the left panel and Libraries in the tabs on the right panel, then choose Add External JARs...
Add cytoscape.jar from the main Cytoscape folder and all the .jar files from the lib/ folder inside the main Cytoscape folder. (you need 2 steps to do this, one for cytoscape.jar and another for the other .jar's)
Apply your changes
- Now, create your plugin! You can find some help at the ["Developer_Homepage"].
Running the plugin
To Run your plugin, select Run->Run... in Netbeans and click New (at the bottom-left part of the dialog) to create the settings to run your plugin .
Put a Name for the Run Target and choose cytoscape.CyMain as the Main class.
On the next tab ((x)= Arguments) put the path to your Cytoscape's plugins folder as program arguments (you can add other arguments here, like preload your network, node/edge atributes, expression data, etc. See the Cytoscape's [http://cytoscape.org/manual/Cytoscape2_1Manual.pdf manual] for more information on the available command line options.
- Now you can run your plugin!
Debugging
The plugin can be debugged in two modes. One mode is typical and involves restarting Cytoscape each time. The other mode provides for attaching the plugin to a running version of Cytoscape.
Category: NetbeansAndCytoscapeDevelopment