I am thinking about creating some biojava interfaces and implementations for peptide-mass fingerprint and peptide fragment mass searches of sequence databases. I would like to make it general enough so that it could be used to wrap some of the popular search tools. So I need to abstract out things like Scoring schemes.
In general the input would be a set of masses (Protein and peptide or Fragments and Parent peptide), error tolerance and other filters. The output would be a set of proteins or nucleotide sequences along with there associated scores and possibly with the matches as features annotated onto the returned sequences. I have been looking at some of the Interfaces used for FastA searches but I am not sure that they are appropriate for the problem above. For Example the SearchBuilder has as one of its methods SeqSimilaritySearchResult makeSearchResult(). A SeqSimilaritySearchResult has a method getQuerySequence() that is not appropriate for the mass search problem. What do people think. Should I go ahead and use them and just ignore getQuerySequence() or should I create new interfaces? Perhaps I could just extend SeqSimilaritySearchResult and add a getQueryMassSet method or just use the same interface and just put the masses into the SearchParameters Map. Also these interfaces according to the documentation seem to be designed to handle parsing of results but not for algorithm implementations. Is there some other interfaces that may be more appropriate for doing search algorithm implementations? _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
