~+'''How to set up Eclipse to develop Cytoscape plugins (draft)'''+~

''Márcio Rosa da Silva'' (MarcioSilva)

June 2005

<<TableOfContents>>


'''Warning: This page and all Cytoscape 2.x plugins are now out of support. Please see the [[http://wiki.cytoscape.org/Cytoscape_3/AppDeveloper/Cytoscape_App_Ladder|developer page for Cytoscape 3.x apps]]. '''

== Introduction ==
This document is an introduction on how to set up [[http://www.eclipse.org|Eclipse]] to develop Cytoscape plugins. It is assumed that you have Eclipse installed and running.

== Creating the project ==
 * Go to {{{File->New->Project...}}} then select {{{Java Project}}}.
 * On the next dialog, put a name for your project and click {{{Finish}}}.
[[http://csresources.sourceforge.net/docs/images/eclipse1.png]]

 * 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)
[[http://csresources.sourceforge.net/docs/images/eclipse2.png]]

[[http://csresources.sourceforge.net/docs/images/eclipse3.png]]

 * {{{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->Open Run Dialog...}}} in Eclipse 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}}}.
[[http://csresources.sourceforge.net/docs/images/eclipse4.png]]

 * 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.
[[http://csresources.sourceforge.net/docs/images/eclipse5.png]]

 * Now you can run your plugin!
'''Note:''' Before running the plugin for the first time, you may need to put a {{{.jar}}} of the plugin in some place Cytoscape will search for plugins (e.g. the {{{plugins/}}} folder inside the Cytoscape installarion folder). Otherwise, Cytoscape will not find your plugin. You don't need to generate the {{{.jar}}} for every run, only the first time. Cytoscape only needs to know your plugin is there, but the actual code will be run from the files in your Eclipse project.

----
Category: EclipseAndCytoscapeDevelopment

## moin code generated by txt2tags 2.0 (http://txt2tags.sf.net)
## cmdline: txt2tags -t moin eclipse.t2t