[Biojava-l] Re: Biojava-l digest, Vol 1 #44 - 2 msgs

[Aaron Kitzmiller]

I haven't seen this (org.biojava.bio.seq.GappedResidueList ) on the JavaDocs yet, so this may be a moot point, but I'm curious about how you implemented this and if you've created a GappedResidueList interface.  The reason I ask is that I've been investigating the use of GCGs SeqStore for the storage of a number of things, including alignments.  Their implementation uses a gap vector that stores offsets and gap sizes in a single text line.  If you've built this with an interface, I should be able to create a SeqStore-specific implementation that will work with the rest of the code.

Aaron K.

Aaron Kitzmiller
Genetics Institute
35 Cambridge Park Dr.
Cambridge, MA 02140
Phone: (617) 665-6831
Fax: (617) 665-8870
akitzmiller@genetics.com


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Today's Topics:

  1. Gapped sequences (Matthew Pocock)
  2. hello! (C J Whitaker)

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Message: 1
Date: Wed, 15 Mar 2000 17:52:54 +0000
From: Matthew Pocock <mrp@sanger.ac.uk>
Organization: The Sanger Center
To: "biojava-l@biojava.org" <biojava-l@biojava.org>
Subject: [Biojava-l] Gapped sequences

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


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Message: 2
Date: Fri, 17 Mar 2000 14:18:51 +0000
From: C J Whitaker <cjw47@cam.ac.uk>
To: biojava-l@biojava.org 
Subject: [Biojava-l] hello!

Just to say cool new site
Caroline!




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