Global Settings for applet

Help
uma
2008-03-04
2013-05-15
  • uma
    uma
    2008-03-04

    Hi,

    I am using stand alone Java TreeView, I dont have problem in configuring the URL and colour settings. But I am not able to use the same settings when I view the same files from an applet ( I am transfering the files from Vista to Linux and I am not able to preserve the settings) I tried playing around with .jtv file  . I dont find "Settings->Edit persistent value.."  in the version I am using. Your reply will be of great help.

    Also, Is it possible to give a link to a specifc gene from a normal Html file to the JavaTree View (basically directly opening Zoomed in to the node where the corresponding gene is? (without using the search option)

    Thanks
    Uma

     
    • Alok Saldanha
      Alok Saldanha
      2008-03-05

      Dear Uma,

      I am not sure why you are having difficulties getting the settings to persist - you should be able to just put the .jtv file in the same directory as the .cdt, no playing around required. "Edit persistent value" must be some obsolete documentation- the url and color settings are stored in the jtv automatically. Is is possible that Vista is hiding line endings from you? Are you able to put some example files online somewhere?

      It is not currently possible to link to a specific gene, although it would not be particularly hard to add. Please add it to the Feature Requests

      https://sourceforge.net/tracker/?group_id=84593&atid=573301

      and it will get done eventually.

      Best wishes,
      Alok

       
    • uma
      uma
      2008-03-05

      Dear Alok,

      Thank you for the reply, I tried putting the .jvt file in the same folder as .cdt folder. No luck! There is jtview.xml file in my home directory in vista but i dont see the corresponding file in linux, may be thats the reason? does applet use this file ?

      thank you
      Uma

       
    • Alok Saldanha
      Alok Saldanha
      2008-03-06

      are you able to put an example .cdt and .jtv online somewhere?

      Thanks,
      Alok

       
    • uma
      uma
      2008-03-06

      Here it is,

      http://www.biologie.ens.fr/diatomics/test/test.php

      as you open the applet you can see one dark page,  the pixel is actually set to 0.001 but its loading with the default setting.

      I have also linked data file (as a tar)

      Thank you very much for the help.

      Uma

       
    • Alok Saldanha
      Alok Saldanha
      2008-03-09

      Dear Uma,

      I had some to look at your issue in detail, and I found a bug in the applet code. You can see the fixed code here:

      http://jtreeview.sourceforge.net/examples/AppletJtv/test.php

      To fix the code on your site, you should take the following steps:

      1) Download the new applet code from

        http://jtreeview.sourceforge.net/examples/AppletJtv/TreeViewApplet.jar

      2) Add the following param tag inside your applet tag:

        <param name="styleName" value="linked">

      The second step should not be necessary, but it is good form to include.

      Please let me know if this helps. The fixes will be included in the next version.

      Best wishes,
      Alok

       
    • uma
      uma
      2008-03-10

      Thank you very much Alok, I am able to see the right colors now. But still have problem with the URL. I see the modified URL (customized to my data) stored and selected in my URL settings but still goes to Yeast site itself. Does this depend on .xml file stored in the home directorey?

      Thanks agin for the help
      Uma

       
    • Alok Saldanha
      Alok Saldanha
      2008-03-17

      Dear Uma,

      It turns out that the applet was ignoring the user-specified URL settings and instead always using the default one. I have revised the code so that it now uses the document-specific one if it is present. The updated code is posted at the same location:

      http://jtreeview.sourceforge.net/examples/AppletJtv/TreeViewApplet.jar

      As you suspected, it should have been possible to work around the issue by placing the global .xml file in a web accessible location and setting the globalSettings param in the applet tag. For reasons that I do not have time to look into right now, this does not work. I apologize, but the applet version was never fully tested. I will probably rethink the logic of how the various document specific, global and default url settings should work- the reason it is so complex is that you can actually have multiple text annotation columns (via settings->annotations and selecting multiple columns), and have clicking on each one link to a different url (by setting the "Header" attribute in the Settings->Presets->Gene URL Presets dialog). This sets up an ambiguity between which URL to use- the document specific one, or the global one that matches a particular column. This is a moot point for your applet, as it only has a document specific one, but it is the historical backdrop in which the bug happened. Probably the whole system should be made more uniform and comprehensible for the next version, but until then please try and make do with the version posted above.

       
    • uma
      uma
      2008-03-17

      Dear Alok,

      Thanks a lot for your help. I am not sure if i have downloaded the right files, The above link points to a .jar file, but I am downloading a zip file from the above link, which dont have a .jar file . I tried adding the files from the zip file, but still didnt work. I dont know if its because i changed the URL from test server to the actual host.

      I have already added this in the actual database; http://www.biologie.ens.fr/diatomics/EST3/exp.php , people are finding it very useful, correct link will be great!

      Thanks again,
      Uma

       
    • Alok Saldanha
      Alok Saldanha
      2008-03-19

      jar files have a similar format to zip files, I bet the browser is getting confused. You should be able to download it by right clicking on the link and selecting "save to disk". In case that doesn't work, here's a zipped jar file:

      http://jtreeview.sourceforge.net/examples/AppletJtv/TreeViewApplet.zip

       
    • uma
      uma
      2008-04-16

      Dear Alok,

      Sorry for getting back very late, we made a release of the database, the tree view with the new code still gives error, its not taking to yeast data anymore but still its a dead link. Is there any other updates available

      Added the tree view in the below database link.

      http://www.biologie.ens.fr/diatomics/EST3/exp.php

      Thanks for your help
      Uma

       
      • Alok Saldanha
        Alok Saldanha
        2008-04-16

        Dear Uma,

        one problem is that your URLs do not begin with http://. If you add this, it seems to work. The full template should be something like:

        http://www.biologie.ens.fr/diatomics/EST3/bar.php?contig=HEADER

        Incidentally, you may have noticed that the menus don't appear in firefox. This is because in old version of java, if I made them appear on the window in firefox they would appear in the wrong place in mac os X. I believe this is no longer the case, and after I fix that and some other bugs I plan to release the next version.

            -Alok

         
        • uma
          uma
          2008-04-16

          Thank you Alok,

          It works! Its very useful for the people using the database.

          thanks again
          Uma