Thanks Matthew,
To produce a pair-wise alignment from two un-aligned sequences and
introduce gaps I have used the sample at "BioJava In Anger" and it runs
successfully.
Now I need an alignment of two sequences where one of them already have
gaps before I align.
I mean that the DP class don´t accept GappedSequence, it´s right?
[]s
Guedes
Matthew Pocock escreveu:
If I understand you correctly, one of the two sequences you are aligning
contains a gap before you align them? Or do you want to produce a pair-wise
alignment from two un-aligned sequences and introduce gaps?
If it is the former, you want a state that emits a gap in one sequence and a
symbol in the other, and also advances {1,1}. I think that is easy enough to
set up, but can't remember the exact code. If the worst comes to the worst,
you can construct the distribution over {gap,Protein} using the classes
in .dist and then set up a SimpleState, providing the advance and alphabet in
the constructor.
Matthew
--
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:: Dickson S. Guedes (guedes at unisul dot br)
::
:: UNISUL - Universidade do Sul de Santa Catarina
:: ATI - Assessoria de Tecnologia da Informação
:: (0xx48) 621-3200 - http://www.unisul.br
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