[Biojava-dev] Pairwise Alignment methods

[Mark Schreiber]

Hi Felipe -

I agree this is a barrier to ease of use. Even if Sequences are
required internally for some obscure reason there is no reason why
dummy Sequences cannot be made inside the aligner.  These sequences
could be given names like 'query' and 'subject' or even 'seq1' and
'seq2'.

I will take a look at adding some methods.

Best regards,

- Mark

On Jan 23, 2008 2:58 PM, Felipe Albrecht <felipe.albrecht at gmail.com> wrote:
> Hello all,
>
> I have a simple question about pairwise alignment classes (SmithWaterman and
> NeedlemanWunsch):
> Why it is necessary two Sequence for alignment and not two SymbolList?
>
> Example, I have a SymbolList collection to align between then,
> by this way I need to create some "dummies"  Sequence for to do the
> alignment.
>
> Reading the source, I saw that the unique field that is exclusive to
> Sequence is the name, for the alignment output,
> but if I need only the alignment result, it is useless.
>
> It is not possible to override the pairwiseAlignment to accept SymbolList or
> may be a new method that the parameters are 2 SymbolList and returns the
> alignment score?
>
> Thank you
>
> Felipe Albrecht
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