Re: [Jtreeview-users] treeview applet

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Dear Christophe,

I've gotten it to work, you can check it at:

http://miniprep.caltech.edu/~remote/applet/testApplet2.html

My applet tag is as follows:

       <APPLET CODE="edu/stanford/genetics/treeview/applet/ 
ButtonApplet.class"
       archive="TreeViewApplet.jar,nanoxml-2.2.2.jar,plugins/ 
Dendrogram.jar" width=150 height=50
         alt="Your browser understands the &lt;APPLET&gt; tag but  
isn't running the applet, for some reason."
 >
         Your browser is completely ignoring the &lt;APPLET&gt; tag!
         <param name="cdtFile" value="spellman_K_G5_A3.cdt">
         <param name="cdtName" value="spellman K">
         <param name="plugins"  
value="edu.stanford.genetics.treeview.plugin.dendroview.KnnDendrogramFac 
tory">
       </applet>

A variety of other combinations work as well, for instance setting  
the style parameter to kmeans or linked. I am not sure what's going  
wrong on your side; perhaps it is looking for some things in the  
wrong places? Are you sure Dendrogram.jar is in the plugins  
subdirectory? Which distribution are you using?

	-Alok

On Oct 4, 2006, at 12:24 AM, Christophe Klopp wrote:

> Dear Alok,
>
> I tried :
> <param name="plugins"
> value="edu.stanford.genetics.treeview.plugin.dendroview.DendrogramFact 
> ory,edu.stanford.genetics.treeview.plugin.dendroview.KnnDendrogramFact 
> ory">
>
> <param name="plugins"
> value="edu.stanford.genetics.treeview.plugin.dendroview.KnnDendrogramF 
> actory">
>
> <param name="plugins"
> value="edu.stanford.genetics.treeview.plugin.dendroview.KnnDendrogramF 
> actory,edu.stanford.genetics.treeview.plugin.dendroview.alignmentFacto 
> ry">
>
> But non of them worked.
>
> I found this in the code:
> src/edu/stanford/genetics/treeview/app/LinkedViewApp.java:       *
> Usage: java -jar treeview.jar -r <my cdt> -t [auto|classic|kmeans| 
> linked].
>
> And I tried
> <param name="style" value="kmeans">
> to give the parameter but it does not work either.
>
> Thanks'
>
> Christophe
>
>
> Alok Saldanha wrote:
>> Dear Christophe,
>>
>> You may need to add the Knn dendrogram view to the plugins parameter,
>> i.e.
>>
>> <param name="plugins"
>> value="edu.stanford.genetics.treeview.plugin.dendroview.DendrogramFac 
>> tory,edu.stanford.genetics.treeview.plugin.dendroview.KnnDendrogramFa 
>> ctory">
>>
>>
>> There's actually three plugins bundled into Dendrogram.jar,
>> edu.stanford.genetics.treeview.plugin.dendroview.DendrogramFactory
>> edu.stanford.genetics.treeview.plugin.dendroview.KnnDendrogramFactory
>> edu.stanford.genetics.treeview.plugin.dendroview.AlignmentFactory
>>
>> You need to specify which ones this particular applet will need... in
>> your case, you can probably leave off the DendrogramFactory. You can
>> also add more plugin jars to the archive attribute of the applet tag
>> if you need them. Let me know if this helps.
>>
>>     -Alok
>>
>> On Oct 3, 2006, at 8:22 AM, Christophe Klopp wrote:
>>
>>> Hi,
>>>
>>> I hope you are or are able to redirect this question to the suitable
>>> person.
>>>
>>> We want to present Kmeans data in the java treeview applet.
>>> We have 3 files :
>>> - x.cdt
>>> - x.kgg
>>> - x.jtv
>>>
>>> The applet works but does not separate the different kmean blocks
>>> (information from the x.kgg file).
>>> We tried to add the other files and a "kmeans" style to the  
>>> applet HTML
>>> code :
>>>
>>> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.1//EN"
>>> "http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd">
>>> <html>
>>>   <head>
>>>         <meta http-equiv="Content-Type" content="text/html;
>>> charset=iso-8859-1" />
>>>       <title>Java TreeView Access  </title>
>>>         <link rel="SHORTCUT ICON"
>>> href="fileadmin/Sigenae/favicon.ico" />
>>>         <link rel="stylesheet" type="text/css"
>>> href="fileadmin/Sigenae/sigenae.css" />
>>>   </head>
>>>   <body>
>>>       <h1>Java TreeView access for SCRIBE Trout Data</h1>
>>>       <h2>Click on the button hereunder to access the data. </h2>
>>>       <hr>
>>>       <APPLET
>>> CODE="edu/stanford/genetics/treeview/applet/ButtonApplet.class"
>>>
>>> archive="TreeViewApplet.jar,nanoxml-2.2.2.jar,plugins/ 
>>> Dendrogram.jar"
>>> width=250 height=50
>>>         alt="Your browser understands the &lt;APPLET&gt; tag but  
>>> isn't
>>> running the applet, for some reason."
>>>>
>>>         Your browser is completely ignoring the &lt;APPLET&gt; tag!
>>>         <param name="cdtFile" value="1.cdt">
>>>         <param name="kggFile" value="1.kgg">
>>>         <param name="jtvFile" value="1.jtv">
>>>         <param name="cdtName" value="SCRIBE trout data">
>>>                 <param name="plugins"
>>> value="edu.stanford.genetics.treeview.plugin.dendroview.DendrogramFa 
>>> ctory">
>>>
>>>         <param name="style" value="kmeans">
>>>       </applet>
>>>       <hr>
>>>   </body>
>>> </html>
>>>
>>> But we got a Treview frame error 253 : no plugin to display  
>>> (because of
>>> the style).
>>>
>>> Thanks' for any example or  help.
>>>
>>> Christophe
>>>
>>>
>>> -- 
>>> ====================================================================
>>> = Christophe KLOPP BIA    INRA Toulouse 31326 Castanet-Tolosan     =
>>> = Tel: 33 5 61 28 50 36   Email: chr...@to... =
>>> = http://www.sigenae.org/                                          =
>>> ====================================================================
>>>
>>
>
> -- 
> ====================================================================
> = Christophe KLOPP BIA    INRA Toulouse 31326 Castanet-Tolosan     =
> = Tel: 33 5 61 28 50 36   Email: chr...@to... =
> = http://www.sigenae.org/                                          =
> ====================================================================
>