[Biojava-l] handling gap symbols

[Andreas Prlic]

Hi Wim,

> I've checked out the latest code from the git repository, but I'm having
> some trouble getting it to compile properly. I hope this is the right place
> to ask more questions.

yes, unfortunately not all modules do compile at the present. I will
delete one or two of the broken modules over the next days, they are
dead code that remained after refactoring... The good news is that due
to the modularization you don;t need all of the modules to compile.
Just to take a look at the alignment module, you will need core and
alignment, which both compile fine....

You could also get the snapshot of the alignment module (and some
others that compile) via Maven from
http://www.biojava.org/download/maven/

Andreas

>
> My first question is whether I really need all of the modules for this
> simple alignment, or whether I can just stick to one of them (sequence?
> alignment?).
>
> The first problem I'm having to build the full package is a test failing in
> structure (testFilterDuplicateAFPs) and in the das module
> (testUniProtServer, testParseSourcesResponse). Skipping those I also found a
> small file encoding bug (a source file is encoded as ISO-8859-1 and the
> compiler is using either the platform encoding or default UTF-8), I've
> attached a small patch for this.
>
> The second problem (after skipping the tests) is apparently a reference
> problem to the core module from DNATools. I keep getting:
> .../sequence/sequence-dna/src/main/java/org/biojava3/seq/dna/DNATools.java:[29,31]
> package org.biojava3.core.symbol does not exist
>
> Indeed, the biojava-3 module doesn't contain that package.
>
> thanks for any help,
> Wim
> --
> Wim De Smet
> http://www.straininfo.net/
>
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>
>



-- 
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Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
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