Hello all,
I've been trying to figure out how to determine the location of gap
symbols in an alignment, but I keep running into trouble determining
what is a gap symbol. Apparently there are two different possible gap
symbols and they can both appear in the same alignment?
An example might make it clearer, suppose I perform the following
alignment (matrix is the EDNA matrix):
SequenceAlignment aligner = new NeedlemanWunsch((short) 0, (short) 3,
(short) 10, (short) 10, (short) 1, matrix);
Sequence first = DNATools.createDNASequence("ACT", "query");
Sequence second = DNATools.createDNASequence("AACTA", "target");
Alignment alignment = aligner.getAlignment(first, second);
And Obtain the symbollist for "query", which should look like "-ACT-", I
get the following Symbols:
AlphabetManager$GapSymbol
AlphabetManager$WellKnownAtomicSymbol
AlphabetManager$WellKnownAtomicSymbol
AlphabetManager$WellKnownAtomicSymbol
AlphabetManager$WellKnownGapSymbol
AlphabetManager.getGapSymbol() returns AlphabetManager$GapSymbol, while
symbolList.getAlphabet().getGapSymbol() returns
AlphabetManager$WellKnownGapSymbol. Am I supposed to test against both
or is there a bug here somewhere? I'm using biojava 1.7.1.
regards,
Wim
--
Wim De Smet
http://www.straininfo.net/
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