[Biojava-dev] Pairwise Alignment methods

[Felipe Albrecht]

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