Dear Anna,

I'm not sure I fully understand, but there is an "index" attribute that you can set on the "UrlExtractor" and "ArrayUrlExtractor" tags that will specify which header column, or in the case of arrays row to use. For example,

<ArrayUrlExtractor index="0" urlTemplate='$url2' isEnabled='1'/>

Should tell it to use the "AID" row instead of the "GID" row. Sorry about the delay.


On Thu, Mar 18, 2010 at 2:06 PM, Anna Ratner <> wrote:
Hi Alok,

Changing my jtv file to what you suggested i.e.:
<UrlExtractor urlTemplate='$url1' isEnabled='1'/>
<ArrayUrlExtractor urlTemplate='$url2' isEnabled='1'/>
instead of the previous:
  <Preset name='Gene' template='$url1' header='*' enabled='true'/>
  <Preset name='Sample' template='$url2' header='*' enabled='true'/>
works and my .jtv file loads the url settings. The only problem now is that it inserts the "AID" values into the HEADER field instead of "GID" for the ArrayUrl template, so I still have to manually change the selection in the drop-down for url settings -> array. How do I specify which values to use here in my .jtv file.
Thank you,

From: Alok Saldanha <>
To: Anna Ratner <>
Sent: Thu, March 18, 2010 5:57:49 AM

Subject: Re: [Jtreeview-users] How to load a .jtv url settings file into TreeViewApplet?

Dear Anna,

Most likely the jtv file is being recognized, you can be sure of it by changing your color (Settings->Pixel Settings, although I just noticed the Color label is misaligned). There seems to be something funky going on with the URL Settings, namely they don't seem to be actually written to disk. I won't have time to look into this further until the weekend, alas Java Treeview is on the backburner for the time being, warts and all. For now the best workaround is to close java treeview and manually open the .jtv file in  a text editor. You need to add "urlTemplate" and "isEnabled" attributes to the UrlExtractor tag which should be a child of DocumentConfig, which is the root tag of the document. Here is an example to link to google:

<UrlExtractor urlTemplate="" isEnabled="1" />

If this doesn't help send me a link to the site with a non-working applet and I'll take a look.


On Wed, Mar 17, 2010 at 9:58 PM, Anna Ratner <> wrote:
I am using the Jave TreeViewApplet on a web page (thank you for this software!) and the problem that I am running into is that it doesn't want to take my .jtv file for url settings. I found a previous issue in the archive where someone was having a similar problem, but that was eventually fixed according to the emails. I write the .jtv file into the same directory as the .cdt, .atr, and .gtr files.
      <APPLET code="edu/stanford/genetics/treeview/applet/ButtonApplet.class"
              width='250' height='50'>
        <PARAM name="cdtFile" value="$tmp_url/cluster$$.cdt">
        <PARAM name="cdtName" value="with Java TreeView">
        <PARAM name="styleName" value="linked">
        <PARAM name="plugins" value="edu.stanford.genetics.treeview.plugin.dendroview.DendrogramFactory">
Also, where can I find the documentation for how to specify url settings for applets?
Any help would be appreciated.
Thank you very much,

Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
Jtreeview-users mailing list