[Biojava-l] Gapped sequences

[Matthew Pocock]

Dear all,

I have just commited org.biojava.bio.seq.GappedResidueList which lets
you view any
underlying ResidueList and add/remove gaps. There is a demo under
biojava-live/demos/seq that shows you how the api works by adding and
removing gaps.

Gaps can be added in the view's frame-of-reference, or by using the
coordinates of the underlying sequence. Gaps are always removed using
the view's coordinates (it seemed easier that way).

I guess the next things are:

1) Make DP spit out GappedResidueLists in the StatePaths when gaps are
emitted or dot-states are used.

2) Write GappedAlignment that lets you add/remove gaps in an alignment
by column & for each sequence.

If you have tried to use the DP code recently, you may have noticed it
playing up. We found some bugs in it, and the API was getting messy, so
it is all up in the air at the moment. I will tell you all as soon as it
is working again (and hopefuly include some nifty demos!).

Matthew