For some reason, I am having trouble adding an AtomicSymbol as an indexed
member of a SimpleAlphabet (i.e I can add it as a member of the alphabet,
but the method I use to add it doesn't create an indice for it).
e.g. I use
SimpleAlphabet() alph = new SimpleAlphabet();
alph.setName("Protein Domains);
....
//iterate over alphabet names ...
AtomicSymbol symb = AlphabetManager.createSymbol(token, name, ann);
alph.addSymbol(symb);
which works fine, however, when I try for some symbol symb1 added to the
alphabet in the step above:
AlphabetIndex alphindex =
AlphabetManager.getAlphabetIndex(alph);
System.out.println(alphindex.indexForSymbol(AtomicSymbol) symb1);
Then at run-time I am told that:
org.biojava.bio.BioError: Assertion Failure: Symbol 110
was not an indexed member of the alphabet Protein Domains despite being in
the alphabet.
As an aside I'm not sure if I would be better of using IntegerAlphabet, as
the names of the members of the alphabet are integers (representing Pfam
protein domains, indexed from 1 to 3600). However, as far as I could
tell, IntegerAlphabet does not have a addSymbol() method, which meant that
I could not use it to construct a new alphabet.
Thanks in advance for any ideas.
Lachlan
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