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Re: Source code for FigTree available?

Hi Andrew,

On Wed, Feb 02, 2011 at 09:35:46PM +0100, Andrew Rambaut wrote:
> FigTree is available under an open source license (GPL2) from:
> http://code.google.com/p/figtree/

I checked this out and made some progress in building a Debian package
from it for the official Debian GNU/Linux distribution.  However, I
stumbled upon some questions I would like to clarify with your help.

 1. If I just run ant in the build tree I get in addition to figtree.jar
    two files: figtree-pdf.jar and figtree.war.  I found out that
    figtree-pdf.jar just sends PDF content to stdout but I found no
    documentation about the options which might be givven to this
    command line tool.  So I left it out from the distribution as well
    as figtree.war.  I think you are doing the same in the Linux
    binary download.  Could you please confirm that this is OK for you
    or is there some more interesting functionality for users which is
    just hidden for me?

 2. Usage of quaqua.jar: I found some guidelines for Quaqua at
    but I guess I'm doing something wrong:  The interface of FigTree
    just looks uglyish as default Java applications.  This becomes
    specifically important in the output if some strings are rendered
    in a way that they do overlap.  Any hint what I might have done

 3. For a Debian package in the main distribution it is not allowed to
    ship with binary code without source.  Thus when I ship with the
    JAR files in lib/ it means FigTree has to go to the non-free section
    even if your code is perfectly free.  So I tried to iron out those
    JARs but I was not sure whether I really found the correct source:

    freehep.jar: Packaged for Debian - so I hopefully do not need to
             deal with this provided that FigTree works with version
             2.1.1 of this library.
    iText.jar: I found the source at http://itextpdf.com/.
             Can you confirm that the latest version will work?
    jam.jar: I had trouble to find this project.  Any URL to the source?
             this would be really helpful.
    jebl.jar: There are two (competing?) projects:
                http://jebl.sourceforge.net/    and
             The latter claims to be a branch of the former but both
             projects seem to be somehow active.  Which one is the one
             you are including (and thus which one should I prefer) 
	     BTW, this library itself would be an interesting target
             for Debian Med in any case - but which project is "the
             better" choice?
    jwt/*: The Java Web Tolkit also seems to be needed (at least
           jwt-3.1.7pre1.jar and servlet-api-2.5-6.0.2.jar - I can
           leave out commons-*.jar for a successfull build).  I wonder
           for what purpose this is actually needed because I have
           finally not found a functionality in FigTree which might
           need web access - but most probably I'm wrong.  Could you
           please clarify whether this is really needed?

Kind regards and thanks for any help



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