~+'''How to set up Netbeans to develop Cytoscape plugins'''+~

''Fred Eisele'' (FredEisele)

August 2007

<<TableOfContents>>

== 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.

== 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 [[http://cytoscape.org/manual/Cytoscape2_1Manual.pdf|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]].

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Category: NetbeansAndCytoscapeDevelopment