[Biojava-l] Gap Problem

[Emig, Robin]

Is there any reason why the following line should return false if the
current symbol is the 
gap symbol?

((sl.symbolAt(i) == sl.getAlphabet().getGapSymbol()) 

I tried this simple code and s=AlphabetManager$GapSymbol, but
sl1.getAlphabet.getGapSymbol()== a simple basis symbol. What gives, why did
the parser put a AlphabetManager$GapSymbol in the symbol list and not its
appropriate alphabet.getGapSymbol?

       SymbolParser tp;
       tp=(ProteinTools.getTAlphabet()).getParser("token");
       SymbolList sl1=tp.parse("-");
        Symbol s;
       for (Iterator it=sl1.iterator();it.hasNext();) {
        s=(Symbol)it.next();

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