#27 command line option for GTR file


Please add command line option for specifying .gtr file.
The content of .gtr file should be consistent with .cdt file, similar to the way it is used now. My understanding is that JTV currently looks for the .gtr file in the same directory where the .cdt file is specified. If the .gtr file is missing, JTV will display the tree without interconnecting branches. This will work fine in almost most cases except the following:

I am trying to open a CDT file in the web client browser connected to a ASP.NET web server. The only way to do this is to use "Response.Redirect(filename.cdt)" function to redirect the web page to the client machine. The brower then makes a local copy of the .CDT file in the "Temporary Internet files" folder in the client machine, and the JTV is lauched with "-r" option to open this local copy. Since there is no .GTR file in the same directory where the .CDT file is, and there is no way to force the JTV to look elsewhere for the original GTR file, there is no tree branches in my display.

(You will NOT see this problem if you just browse to the file and open it manually from the web browser).


  • lee

    lee - 2007-03-29

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    After more thinking, I have a better idea for solving this problem.
    The information contained in CDT and GTR files can easily be respresented in one single file in XML format.
    The tree-like structure of XML documents matches exactly the JTV tree data.
    The spectrum information contained in the CDT file can be stored as attributes for the leaf nodes (genes).
    The correlation value between two nodes/genes can be stored in their common parents.
    The only things that needs to be changed in JTV is to add a XML file reader.

  • Alok Saldanha

    Alok Saldanha - 2007-07-13

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    It is probably a good idea in general to add arguments for the .gtr and .atr files, and it should be quick to do.

    The idea to use XML is a good one, and in fact I already use it with the .jtv document level config file. We could actually stuff all the data in the same file, and have a single file, although I am not sure how to do it efficiently. should the data be stored as a tab separated list in a single attribute, or should there be a separate attribute for each column?
    Perhaps a middle ground would be to have separate attributes for the additional columns in an extended GTR file, but to have only a single "data" attribute for the spectrum information.
    The XML idea will take more time.


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