[Biojava-l] biojava and Xcode

mark.schreiber at group.novartis.com mark.schreiber at group.novartis.com
Tue Nov 9 23:05:32 EST 2004

Just to add to this.

One of the best ways to debug serious problems is to follow the stack 
trace. If your bug causing exceptions then you can find the class and line 
responsible in the stack trace. If the bug is more subtle then logging and 
or assertions are the preferable way to go. It's also a good discipline.

- Mark

Francois Pepin <fpepin at cs.mcgill.ca>
Sent by: biojava-l-bounces at portal.open-bio.org
11/10/2004 12:00 PM

        To:     Koen van der Drift <kvddrift at earthlink.net>
        cc:     biojava-list <biojava-l at biojava.org>, (bcc: Mark Schreiber/GP/Novartis)
        Subject:        Re: [Biojava-l] biojava and Xcode

Hi Koen,

I've never tried it, but would it be able to follow the biojava code if
you had both the source and the class files in the jar?

Another way would be to compile biojava without making the jar file and
put the class files with yours. Then there would be no reason why the
debugger can't follow it out.

I never use a debugger so I'm not quite sure why it couldn't follow it.
I'm mostly a fan of log4j (I guess the 1.4 logging system would work
fine too) and of using bean shell to go step-by-step.


On Tue, 2004-11-09 at 19:17, Koen van der Drift wrote:
> Hi,
> I have been able to build biojava using Apple's Xcode 1.5. I also was 
> able to make a separate small Xcode project and run some code that
> uses biojava. What I would like to be able to do is, is to debug my 
> code including the code it uses from biojava. I can step through my own 
> code, but as soon as the debugger steps into a biojava function, it 
> treats that as a black box, and I cannot see what happens 'under the 
> hood'. Is there any way to accomplish this, either with Xcode, or 
> another OS X or X11 app? I understand that this is impossible when I 
> only have a jar file, but now I also have all the source code from 
> biojava.
> Maybe I need to create another target in the same project that contains 
> the biojava source, but so far I have not been able to get this to 
> work.
> thanks,
> - Koen.
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