[Biojava-dev] ScoringMatrix interface/implementations

[mark.schreiber at group.novartis.com]

Hi Rahul -

I like this approach. The only minor problem is what to do with 
ambiguities that are not found in the matrix. Currently you through an 
exception which is fine although you might also want another 
implementation that more gracefully averages the match values of all the 
possible sub-symbols of the ambiguity.

Looking forward to seeing the rest.

Mark





Rahul Karnik <rahul at genebrew.com>
Sent by: biojava-dev-bounces at portal.open-bio.org
10/07/2004 12:44 PM

 
        To:     BioJava Dev <biojava-dev at biojava.org>
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-dev] ScoringMatrix interface/implementations


As a first step in the building of a framework for sequence alignment, I
have attached:

- a ScoringMatrix interface
- two simple implementations
- a matrix reader
- a junit test case and a test file

Please let me know if and how I should integrate this ScoringMatrix
design with the existing WeightMatrix used with the HMM code. Of course,
any other comments and suggestions are welcome too.

Thanks,
Rahul







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[ Attachment ''SCORINGMATRIX.JAVA'' removed by Mark Schreiber ]
[ Attachment ''SIMPLESCORINGMATRIX.JAVA'' removed by Mark Schreiber ]
[ Attachment ''SYMMETRICSCORINGMATRIX.JAVA'' removed by Mark Schreiber ]
[ Attachment ''SCORINGMATRIXREADER.JAVA'' removed by Mark Schreiber ]
[ Attachment ''SCORINGMATRIXREADERTEST.JAVA'' removed by Mark Schreiber ]
[ Attachment ''BLOSUM50.MATRIX'' removed by Mark Schreiber ]