cytoscape-discuss Google Group

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[link]

Re: Problems adding plugin as a jar

fengbo....@gmail.com (Fengbo Xie) — Thu, 19 Nov 2009 15:56:15 UT

You're welcome.
The cytoscape window will start automatically when you invoke one of
the methods that require Cytoscape desktop, such as loading plugins.

I've post a thread that describes how to avoid the GUI:
[link]

--
Fengbo Xie Ph.D candidate

Re: Problems adding plugin as a jar

francescomusacc...@gmail.com (Franktwis) — Thu, 19 Nov 2009 08:12:33 UT

Hi Fengbo,
I've resolved the problem. It was in the manifest file and in my
compression tree folder created by winrar. Now it works. And,
unbelievably, it works also without opening Cytoscape... I have only
to compile with Eclipse and a new instance of Cytoscape object is
created showing me the program window!

cytoscape wiki

msm...@ucsd.edu (Mike Smoot) — Wed, 18 Nov 2009 21:01:52 UT

Hi Everyone,

Just a quick note that the Cytoscape Wiki is back in action. You can follow
the various links on the home page, or go directly to the root of the wiki
here: [link] If you notice any links still
pointing to the old installation just drop me a line and I will fix them.

Re: Problems adding plugin as a jar

fengbo....@gmail.com (Fengbo Xie) — Tue, 17 Nov 2009 12:23:25 UT

Not finished in the previous message.

In the MAINFEST.MF, you should provide FQCN (Full Qualified Class
Name, class name with package) as Cytoscape-Plugin, such as:
Cytoscape-Plugin: cytoscape.plugin.GraphCreator

Download a plugin's source code from the subversion and have a look at
its Ant build.xml file.

Re: Problems adding plugin as a jar

fengbo....@gmail.com (Fengbo Xie) — Tue, 17 Nov 2009 12:17:42 UT

Do you have a package declaration on top of the GraphCreator.java
source?
It seems you have namespace problem. In Java, it's package.
You should declare GraphCreator in package cytoscape.plugin and put
GraphCreator.class in directory cytoscape/plugin/
And in the MAINFEST.MF

Re: [Cytoscape-discuss] Re: Problems adding plugin as a jar

plw...@bioeng.ucsd.edu (Peng-Liang Wang) — Mon, 16 Nov 2009 19:46:43 UT

It seems to me you have problem in your MANIFEST file. You can unjar a core
plugin and look at how the MANiFEST looks like. In the MANIFEST file, you
need to specify which class is the entry point of your plugin.

Peng

Re: [Cytoscape-discuss] Re: Server down?

ostue...@gmail.com (Oliver Stueker) — Mon, 16 Nov 2009 15:44:37 UT

Hi,

have you specified the plugins main class in the Jar's Manifest?
For details, see section "creating a Jar file" in
Cytoscape_Plugin_Tutorial (I've posted the page in the Google cache
last week).

Kei already posted, that they are aware of the problem and working on it.
Unfortunately I can't tell you more.

Re: Server down?

tjmcg...@gmail.com (mcgrew) — Mon, 16 Nov 2009 15:03:15 UT

Oliver,

That source code will help, but the layout of the .jar files is also
giving me a problem. The plugin seems to load fine as long as I put
everything in the root directory of the jar, but if I try to create
some kind of directory structure it fails to find the main class. I
had hoped to use the example jars to sort out what my problem is.

Re: Problems adding plugin as a jar

francescomusacc...@gmail.com (Franktwis) — Mon, 16 Nov 2009 14:56:06 UT

I downloaded another time Cytoscape and now when I insert this plugin
I have this error:
The class name is GraphCreator.class and is in the directory:
cytoscape/plugin/GraphCreator

java.lang.NoClassDefFoundError : GraphCreator/GraphCreator (wrong name:
GraphCreator)
at java.lang.ClassLoader.defineCl ass1(Native Method)

Problems adding plugin as a jar

francescomusacc...@gmail.com (Franktwis) — Mon, 16 Nov 2009 11:07:57 UT

Hi all,
I'm so sorry to have to write so much times on this forum, but I have
to complete a work for the end of my stage and I found that your
answers are speeding up my work deleting all problems with my
inexperience with Cytoscape.
Well, I finally complete a first part of my work creating a Graph from

Re: Display graph (net) in a window to visualize it with Eclipse

francescomusacc...@gmail.com (Franktwis) — Mon, 16 Nov 2009 09:14:58 UT

thanks Gang... I would know also if my coding is correct when I said:

The only thing I need is to write these two lines in the main of my
class? then it will work?
thanks for your answers
Franktwis

Re: [Cytoscape-discuss] Display graph (net) in a window to visualize it with Eclipse

paladinj...@gmail.com (Gang Su) — Mon, 16 Nov 2009 03:03:41 UT

Hi Franktwis,

Eclipse is only an IDE for development. In order to visualize the
graph you need to run the plugin in Cytoscape.

Gang

Display graph (net) in a window to visualize it with Eclipse

francescomusacc...@gmail.com (Franktwis) — Sun, 15 Nov 2009 10:29:49 UT

Hi all,
I'm new of this forum and for Cytoscape programming.
I'm developing a plugin that create a net and visualize it using datas
taken from an excel file.
The code open excel files and use functions like:
Cytoscape.getCyNode("yellow", true); cyNetwork.addNode(node0); to
build the net.
Now, I followed instructions to add a Visual Style including in my

How to export network graph as image using cytoscape without GUI

fengbo....@gmail.com (fengbo.xie@gmail.com) — Sat, 14 Nov 2009 14:38:20 UT

Cytoscape 2.6 has a headless mode but does not really support it. Cytoscape
3.0 is promised to support this way but the exporter is not implemented yet
(from the subversion revision 18418) , I just can't wait. (And 3.0 is
somehow complicated). After hours of deeping into the source of cytoscape,