Help needed to use a tutorial plugin

[R R]

Hi everybody

 

I want to create a plugin for Cytoscape.I went through your tutorials for plugin development.I downloaded the HelloWorld.jar file (plz find in the attachment)from the tutorial page and copied it to the plugins folder of the cytoscape.So  then i tried to start the cytoscape,it not opening at all.But if i delete the HelloWorld.jar file from the folder the cytoscape is loading fine.I tried downloding plugins like BINGO,Agilent Literature Search plugin everything is working perfectly.

 

Please help me to figure out the problem.

 

Thanks

Ms.Ranjan

[piet molenaar]

Hi Ranjan,
I think this has to do with the path to the plugins directory; default this is set as plugins/core
So either try to put the HelloWorld.jar there or add -p plugins to the Cytoscape arguments 
(don't know what IDE you're using...)
Hope this helps,
Piet

--
Piet Molenaar
p.mol...@amc.uva.nl
Department of Human Genetics, M1-131
Academic Medical Center
University of Amsterdam
Meibergdreef 9
1105 AZ Amsterdam
the Netherlands

tel (+31) 20-5666592
fax (+31) 20-6918626

[R R]

Hi Piet

  Thanks for the reply.I am using eclipse IDE.This is the code i tried from the tutorial.Now the cytoscape is loading,but...

 

import

javax.swing.JOptionPane;

import

cytoscape.plugin.CytoscapePlugin;

import

cytoscape.Cytoscape;

public

class NewPlugin extends CytoscapePlugin {

public NewPlugin () {

String message =

"Hello World!";

System.

out.println(message);

// use the CytoscapeDesktop as parent for a Swing dialog

JOptionPane.showMessageDialog( Cytoscape.getDesktop(), message);

}

}

i am getting the following error message.

cytoscape.CytoscapeInit[INFO]: CytoscapeInit static initialization

cytoscape.CytoscapeInit[INFO]: Log information can now be found in the Help->Error Console menu

Exception in thread "main"

java.lang.IllegalArgumentException: name

at sun.misc.URLClassPath$Loader.getResource(Unknown Source)

at sun.misc.URLClassPath.getResource(Unknown Source)

at java.net.URLClassLoader$1.run(Unknown Source)

at java.security.AccessController.doPrivileged(

Native Method)

at java.net.URLClassLoader.findClass(Unknown Source)

at java.lang.ClassLoader.loadClass(Unknown Source)

at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)

at java.lang.ClassLoader.loadClass(Unknown Source)

at java.lang.ClassLoader.loadClassInternal(Unknown Source)

at java.lang.Class.forName0(

Native Method)

at java.lang.Class.forName(Unknown Source)

at cytoscape.plugin.PluginManager.loadResourcePlugins(

PluginManager.java:930)

at cytoscape.plugin.PluginManager.loadPlugins(

PluginManager.java:797)

at cytoscape.CytoscapeInit.init(

CytoscapeInit.java:259)

at cytoscape.CyMain.<init>(

CyMain.java:158)

at cytoscape.CyMain.main(

CyMain.java:122)

I am not able to get the "Java Swing utility class is used to display the message in a dialog window. " as mentioned in the tutorial.In the Run configuration the argument that i gave was

-p  C:\Program Files\Cytoscape_v2.6.1

 

i even have the generated jar file of this java program in the plugins folder of the cytoscape..

 

Did i miss something?

Thanks

Ms.Ranjan

[Peng-Liang Wang]

You may use the sample plugins at http://cytoscape.org/cgi-bin/moin.cgi/plugin_developer_tutorial I think the HelloWorld is very old.

 

Peng

[rex....@syngenta.com]

I tried this a while back.  What seems to happen is that the popup comes up behind the cytoscape splash screen, which demands to be on top of everything until all the plugins are loaded.  If you hit enter, you will dismiss the invisible popup, and cytoscape will come up.   It seems like it might be better for the splash screen to be a little more deferential to the plugins, since it is not inconceivable that they would ask configuration questions as they are loaded.  Of course I am inferring all of this... another plausible explanation is bad feng shui in my workspace.

Rex

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From: cytoscap...@googlegroups.com [mailto:cytoscap...@googlegroups.com] On Behalf Of Peng-Liang Wang
Sent: Friday, December 05, 2008 11:21 AM
To: cytoscap...@googlegroups.com
Subject: [Cytoscape-discuss] Re: Help needed to use a tutorial plugin

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