cytoscape-discuss Google Group

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2009-11-20T20:18:14Z

Xxx Sexy hot lady’s aviation us Indian Pakistani Chinese USA
Indonesian Malaysian Singapore Russian photos
[link]

Re: Problems adding plugin as a jar

2009-11-19T15:56:15Z

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

2009-11-19T08:12:33Z

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

2009-11-18T21:01:52Z

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

2009-11-17T12:23:25Z

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

2009-11-17T12:17:42Z

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

2009-11-16T19:46:43Z

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?

2009-11-16T15:44:37Z

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?

2009-11-16T15:03:15Z

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

2009-11-16T14:56:06Z

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

2009-11-16T11:07:57Z

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

2009-11-16T09:14:58Z

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

2009-11-16T03:03:41Z

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

2009-11-15T10:29:49Z

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

2009-11-14T14:38:20Z

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,