[Biojava-l] (no subject)

[Tim Salmon]

hi biojava'ers,

i have discovered a small potential problem with the biojava 1.10 distribution that i thought you might like to have brought to your attention.
i have biojava installed on an imac running os-x. os-x apparently limits the filename sizes to shorter than those of a number of the files in biojava. this is not critical in all cases as i have successfully run the demo suggested on the web-page. however, when i tested the potential problem by doing a build as suggested i got this.

tim: biojava [3:04:52pm]: java build.Builder all
Running complete build...
Compiling...
/Users/tim/Bioinformatics/biojava/src/org/biojava/bio/dist/OrderNDistributionFactory.java:68: cannot resolve symbol
symbol : class IndexedNthOrderDistribution
location: class org.biojava.bio.dist.OrderNDistributionFactory
return new IndexedNthOrderDistribution(alpha, df);
^
/Users/tim/Bioinformatics/biojava/src/org/biojava/bio/dist/OrderNDistributionFactory.java:70: cannot resolve symbol
symbol : class GeneralNthOrderDistribution
location: class org.biojava.bio.dist.OrderNDistributionFactory
return new GeneralNthOrderDistribution(alpha, df);
^
/Users/tim/Bioinformatics/biojava/src/org/biojava/bio/dist/TranslatedDistribution.java:59: cannot resolve symbol
symbol : class SimpleReversibleTranslationTable
location: class org.biojava.bio.dist.TranslatedDistribution
new SimpleReversibleTranslationTable(
^
src/org/biojava/bio/symbol/AlphabetManager.java:458: cannot resolve symbol
symbol : class InfiniteCrossProductAlphabet
location: class org.biojava.bio.symbol.AlphabetManager
cpa = new InfiniteCrossProductAlphabet(aList);
^
src/org/biojava/bio/symbol/SimpleCrossProductAlphabet.java:143: cannot resolve symbol
symbol : class CrossProductSymbolNameParser
location: class org.biojava.bio.symbol.SimpleCrossProductAlphabet
return new CrossProductSymbolNameParser(this);
^
src/org/biojava/bio/symbol/SparseCrossProductAlphabet.java:104: cannot resolve symbol
symbol : class CrossProductSymbolNameParser
location: class org.biojava.bio.symbol.SparseCrossProductAlphabet
return new CrossProductSymbolNameParser(this);
^
6 errors
Exception in thread "main" java.io.IOException: Couldn't build!
at build.Builder.buildAll(Builder.java:223)
at build.Builder.main(Builder.java:175)

As you can see, the longer file names have caused this to fail.
I hope this is not too much of an issue for you. If I can be of any assisatance with this matter, please let me know.

cheers,
tim


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tim salmon

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