Cytoscape Plugin Dev Environment

Materials:

After struggling for a couple of hours, I finally got Netbeans setup to do the work!
Netbeans IDE, Cytoscape Source

Setup:
1. Install Netbeans IDE
2. Install Cytoscape
3. Create a custom plugin folder (for example: c:/cytoscape/plugins/dev/)
4. Create a Netbeans java project
5. Add Cytoscape libs to the project. Specifically, cytoscape.jar and all the /libs/ folder
6. Edit the project properties by right click on the project name. Under 'Run' item,
enter (not by browsing) cytoscape.CyMain; in the arguments, add -p 'your plugin folder'
7. Go to the project folder in the file system, in nbproject folder, edit project.properties, change value of dist.jar to your full file path with the jar name.
For example: dist.jar=C:/Program Files (x86)/Cytoscape_v2.6.0/plugins/dev/HelloWorld.jar, note you should not use any quotes!

Now you are done. You can debug your Cytoscape plugin, you set break points, watch...
it's just nice and easy!
------------------------------------------------------------------------------------
Update: you can directly load a sif file:
-N – Load a .sif file
-n – Load node attributes
-e – Load edge attributes

Thanks for help from Maital Ashkenazi

Super Annoying Eclipse Bug

All Eclipsed Based IDEs, will have menu/dialog item missing/malfunction bugs on windows xp64 system. It seems the bug was fixed, then either a java update or eclipse update or something else just restored the bug.

I spent the whole weekend trying to figure this out, no luck.
-------------------------------------------------------------
Updates. It turned out the fix to this bug is nothing related to Java or Eclipse. It's because of the video card driver and ultramon, a software that provides finer control of multi-panel displays.

The funny thing is that by googling, many of the developers who is using a windows xp 64 system also use multi-display, and also use ultramon. So, we all ran into the same issue. And naturally, most of us think it's a problem from Eclipse. For me it's more complicated: I thought it's a problem from Flex Builder when i tried to import Flare libraries into the IDE; then I thought it was a problem from Eclipse, and by upgrading 3.3 to 3.3.1 i unplugged a monitor (it's this coincidence) and fixed the issue, then i thought it was an issue from eclipse because the upgrade solved the problem. then when eclipse upgraded from 3.3.1 to 3.3.2 it's just natural to think that it's the new fix that restored the bug. Then i went back to 3.3.1, the issue was still there, meanwhile i noticed there was an upgrade in JRE, so i thought was an issue from either Java or Eclipse upgrade remainders...

Eventually, it was just a glitch in the Ultramon and Video driver. Uninstall ultramon, just solved the problem, nice and easy.

This reminds me of the biological experiments: it's not easy to establish causal relationships. Given computers and softwares are becoming more and more sophisticated, the incomparability issue simply can arise from anywhere..