> Hi Victoria,
> Yes this is possible by creating a separate project for your plugin: it's
> documented at wiki here:http://www.cytoscape.org/cgi-bin/moin.cgi/SettingUpEclipseForPluginDe...
> Hope this helps, if not just ask!
> Piet

> On Mon, May 26, 2008 at 7:53 PM, Victoria Mui <vickee...@gmail.com> wrote:

> > Hi,

> > I'm wondering if there is a way to dynamically debug a plugin in
> > Eclipse when the Cytoscape program is executed from within Eclipse.

> > Thanks,
> > Victoria

> --
> Piet Molenaar
> p.molen...@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

> Hi Victoria,
> The trick is mentioned in the last paragraph of the wiki docs on the
> subject:

> "*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."

> I think putting the jar of your plugin into the cytoscape plugins dir will
> solve your problems.
> Hope this helps,
> Cheers,
> Piet

> On Tue, May 27, 2008 at 6:43 PM, Victoria Mui <vickee...@gmail.com> wrote:

> > Thanks Piet!

> > I've followed the instructions listed on that page.  However, I've
> > encountered the following problems:

> > 1) If I run my plugin without specifying the Program Arguments in the
> > Run Dialog under (x) = Arguments, my HelloWorld plugin gets executed,
> > but execution just stops after that (so the rest of the Cytoscape
> > program is not executed)

> > 2) If I run my plugin with the Cytoscape plugins folder path specified
> > in Program Arguments, Cytoscape runs, but fails to load my HelloWorld
> > plugin.

> > I've also noticed that in both of these cases, the Filters and Editor
> > tabs on the left hand side are also not generated.

> > Do you happen to know of a solution to these problems?

> > Thanks,
> > Victoria

> > On May 27, 3:35 am, "piet molenaar" <piet....@gmail.com> wrote:
> > > Hi Victoria,
> > > Yes this is possible by creating a separate project for your plugin: it's
> > > documented at wiki here:
> >http://www.cytoscape.org/cgi-bin/moin.cgi/SettingUpEclipseForPluginDe...
> > > Hope this helps, if not just ask!
> > > Piet

> > > On Mon, May 26, 2008 at 7:53 PM, Victoria Mui <vickee...@gmail.com>
> > wrote:

> > > > Hi,

> > > > I'm wondering if there is a way to dynamically debug a plugin in
> > > > Eclipse when the Cytoscape program is executed from within Eclipse.

> > > > Thanks,
> > > > Victoria

> > > --
> > > Piet Molenaar
> > > p.molen...@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

> --
> Piet Molenaar
> p.molen...@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

> Hi Victoria,
> I've reproduced your errors and I think they're due to the fact that the
> paths described in the sample are not windows specific and that currently
> the plugins in the default cytoscape svn configuration are in the
> plugins/core directory. So in my configuration (where both the helloworld
> plugin project and the cytoscape project are in the same level directory) I
> had to set the plugins path as ../Cytoscape_2_6/plugins/core
> I put the helloworld jar from the tutorial in that directory and it worked
> for me.

> However, in order to see your code changes you'll have to rebuild the jar...
> A better way might be to create a directory called plugins in your plugin
> project and than set the path for plugins to that (ie: -p plugins); copy the
> plugins from the cytoscape/plugins/core dir over to that plugins dir and
> have eclipse build a jar from your plugin each time you build your project
> (this can be done through the export dialog; see eclipse help :'creating jar
> file'). In this way the eclipse debugger will stop in your plugin code.

> If this works for you I'll adapt the existing wiki.
> Cheers,
> Piet

> On Wed, May 28, 2008 at 3:17 PM, Victoria Mui <vickee...@gmail.com> wrote:

> > Hi Piet,

> > I actually created a JAR file consisting of the HelloWorld.class file
> > and the manifest file with the following contents:

> > Manifest-Version: 1.0

> > Created-By: 0.92-gcc

> > And I've placed this JAR file in the cytoscape plugins folder.  I've
> > copied this manifest file from the HelloWorld.jar file that was
> > provided to us in one of the Cytoscape plugin tutorials I've read.

> > It seems very strange because in both cases (mentioned in my last
> > post), it seems to load the Cytoscape program half way and fails to
> > load the layouts, the Data Panel, the Filters and Editor tabs.

> > Could it be that my JAR file is missing something?  Because it seems
> > to me that once it finishes my "HelloWorld" plugin, the program
> > doesn't know how to continue the rest of the program execution.

> > If some program execution output will help, the following is the
> > Eclipse output when I run my plugin (the (1) and (2) correspond to the
> > cases in my last post):

> > (1)
> > Hello World!
> > cytoscape[INFO]: starting delete action
> > cytoscape[INFO]: ending delete action
> > cytoscape[INFO]: PreferenceAction()...
> > cytoscape[INFO]: BookmarkAction()...
> > cytoscape[INFO]: CytoscapeInit static initialization
> > Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
> >        at cytoscape.Cytoscape.exit(Cytoscape.java:431)
> >        at cytoscape.view.CytoscapeDesktop
> > $1.windowClosing(CytoscapeDesktop.java:346)
> >        at
> > java.awt.AWTEventMulticaster.windowClosing(AWTEventMulticaster.java:
> > 332)
> >        at
> > java.awt.AWTEventMulticaster.windowClosing(AWTEventMulticaster.java:
> > 332)
> >        at java.awt.Window.processWindowEvent(Window.java:1827)
> >        at javax.swing.JFrame.processWindowEvent(JFrame.java:279)
> >        at java.awt.Window.processEvent(Window.java:1785)
> >        at java.awt.Component.dispatchEventImpl(Component.java:4413)
> >        at java.awt.Container.dispatchEventImpl(Container.java:2116)
> >        at java.awt.Window.dispatchEventImpl(Window.java:2440)
> >        at java.awt.Component.dispatchEvent(Component.java:4243)
> >        at java.awt.EventQueue.dispatchEvent(EventQueue.java:599)
> >        at

> > java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.jav a:
> > 273)
> >        at
> > java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:
> > 183)
> >        at

> > java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.jav a:
> > 173)
> >        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:
> > 168)
> >        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:
> > 160)
> >        at java.awt.EventDispatchThread.run(EventDispatchThread.java:121)

> > * Note: The NullPointerException occurred when I tried to close the
> > Cytoscape program by using the "X" on the upper right corner of the
> > program. *

> > (2)
> > cytoscape[INFO]: CytoscapeInit static initialization
> > cytoscape[INFO]: init mode: 1
> > cytoscape[INFO]: Updating plugins...
> > cytoscape[INFO]: loading plugins....
> > cytoscape.plugin.PluginManager[INFO]:  - file: /etc/Cytoscape_v2.6.0/
> > plugins/biopax.jar
> > cytoscape.plugin.PluginManager[INFO]: attempting to load plugin url:
> > jar:file:/etc/Cytoscape_v2.6.0/plugins/biopax.jar!/
> > cytoscape.plugin.PluginManager[INFO]: Loading from manifest
> > org.mskcc.biopax_plugin.plugin.BioPaxPlugIn[INFO]: Plugin successfully
> > loaded
> > cytoscape.plugin.PluginManager[INFO]: Registering
> > org.mskcc.biopax_plugin.plugin.BioPaxPlugIn@109da93
> > cytoscape.plugin.PluginManager[INFO]:      Registering
> > org.mskcc.biopax_plugin.plugin.BioPaxPlugIn
> > cytoscape.plugin.PluginManager[INFO]: Track plugin: true
> > cytoscape.plugin.PluginTracker[INFO]: Removing plugin/theme QuickFind
> > status CURRENT
> > cytoscape.plugin.PluginTracker[INFO]: Removing plugin/theme cPath
> > status CURRENT
> > cytoscape.plugin.PluginTracker[INFO]: Removing plugin/theme yFiles
> > Layouts status CURRENT
> > cytoscape.plugin.PluginTracker[INFO]: Removing plugin/theme LinkOut
> > status CURRENT
> > cytoscape.plugin.PluginTracker[INFO]: Removing plugin/theme Browser
> > status CURRENT
> > cytoscape.plugin.PluginTracker[INFO]: Removing plugin/theme
> > AutomaticLayout status CURRENT
> > cytoscape.plugin.PluginTracker[INFO]: Removing plugin/theme Filters
> > status CURRENT
> > cytoscape.plugin.PluginTracker[INFO]: Removing plugin/theme Old
> > Filters status CURRENT
> > cytoscape.plugin.PluginTracker[INFO]: Removing plugin/theme
> > ManualLayout status CURRENT
> > cytoscape.plugin.PluginTracker[INFO]: Removing plugin/theme
> > CytoscapeEditor status CURRENT
> > cytoscape.plugin.PluginTracker[INFO]: Removing plugin/theme Table
> > Import status CURRENT
> > cytoscape.plugin.PluginTracker[INFO]: Removing plugin/theme PSI-MI
> > status CURRENT
> > cytoscape.plugin.PluginTracker[INFO]: Removing plugin/theme SBML
> > Reader status CURRENT
> > cytoscape.plugin.PluginTracker[INFO]: Removing plugin/theme GraphMerge
> > status CURRENT
> > cytoscape[INFO]: loading session...
> > cytoscape[INFO]: Got VMM Change event.  Cur VS in VMM: Sample1
> > cytoscape[INFO]: Creating Default Image for Sample1
> > cytoscape[INFO]: Got VMM Change event.  Cur VS in VMM: Solid
> > cytoscape[INFO]: Creating Default Image for Solid
> > cytoscape[INFO]: Got VMM Change event.  Cur VS in VMM: Universe
> > cytoscape[INFO]: Creating Default Image for Universe
> > cytoscape[INFO]: Got VMM Change event.  Cur VS in VMM: default
> > cytoscape[INFO]: Creating Default Image for default
> > cytoscape[INFO]: VS Switched --> default, Last = null
> > cytoscape[INFO]: loading networks...
> > cytoscape[INFO]: loading attributes...
> > cytoscape[INFO]: loading expression files...
> > cytoscape[INFO]:
> > Cytoscape initialized successfully in: 5848 ms
> > cytoscape[INFO]: VS Switched --> default, Last = null
> > cytoscape[INFO]: Cytoscape Exiting....

> > Thanks,
> > Victoria

> > On May 28, 6:39 am, "piet molenaar" <piet....@gmail.com> wrote:
> > > Hi Victoria,
> > > The trick is mentioned in the last paragraph of the wiki docs on the
> > > subject:

> > > "*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."

> > > I think putting the jar of your plugin into the cytoscape plugins dir
> > will
> > > solve your problems.
> > > Hope this helps,
> > > Cheers,
> > > Piet

> > > On Tue, May 27, 2008 at 6:43 PM, Victoria Mui <vickee...@gmail.com>
> > wrote:

> > > > Thanks Piet!

> > > > I've followed the instructions listed on that page.  However, I've
> > > > encountered the following problems:

> > > > 1) If I run my plugin without specifying the Program Arguments in the
> > > > Run Dialog under (x) = Arguments, my HelloWorld plugin gets executed,
> > > > but execution just stops after that (so the rest of the Cytoscape
> > > > program is not executed)

> > > > 2) If I run my plugin with the Cytoscape plugins folder path specified
> > > > in Program Arguments, Cytoscape runs, but fails to load my HelloWorld
> > > > plugin.

> > > > I've also noticed that in both of these cases, the Filters and Editor
> > > > tabs on the left hand side are