[Biojava-l] Mass Search Results

[Michael Jones]

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?