[Biojava-dev] Counting gaps

[Schreiber, Mark]

Hi -

In DistributionTools I have a method that generates a Distribution[]
from an Alignment. Originally I wanted to make it so that it could
optionally include the counts of the Gaps at any position in the
Alignment when determining the weights in the Distribution. Of course
there is no way for the Distribution to add counts of the Gap symbol so
the method gives the same result no matter what.

What would be the best way to include the Gaps during training?
Ultimately Alignments should really be implementations of MarkovModel
and GappedSequence should be a Markov chain (maybe for BioJava 2)

- Mark

Mark Schreiber PhD
Bioinformatics
AgResearch Invermay
PO Box 50034
Mosgiel
New Zealand
 
PH:   +64 3 489 9175
FAX:  +64 3 489 3739

=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================