[Biojava-l] Mass Search Results

[Keith James]

>>>>> "Dr. Jones" == Michael Jones <mjones@mpi.com> writes:

[...]

    Dr. Jones> The SeqSimilaritySearchResult has the following
    Dr. Jones> methods.

    Dr. Jones> List getHits(); The List contains
    Dr. Jones> SeqSimilaritySearchHit which has methods to return a
    Dr. Jones> variety of scoring (Score, PValue, EValue) parameters,
    Dr. Jones> SeqSimilaritySearchSubHit to do alignments (Peptide
    Dr. Jones> Hits could be used here). We could add the masses into
    Dr. Jones> the interface or just calculate them on the fly.

    Dr. Jones> It would be nice if SeqSimilaritySearchHit and
    Dr. Jones> SeqSimilaritySearchResult had some sort of map for
    Dr. Jones> miscellaneous results and error messages. Some of the
    Dr. Jones> complex scoring results you discuss above are probably
    Dr. Jones> to specific for any general interface definition but is
    Dr. Jones> something that should be included in the results. These
    Dr. Jones> type of results could be returned within a general
    Dr. Jones> properties map. I would like to try and use
    Dr. Jones> SeqSimilaritySearchResult if possible just to help with
    Dr. Jones> cross talk as the Bio* stuff takes over the world.

I'm not familiar with the requirements for a mass search results
interface. However, it seems from your comments that there is an
overlap with the existing interface for similarity searches. In order
to obtain a better fit for your requirements it may be beneficial if
we rearrange the interfaces in org.biojava.bio.search -

 Factor out methods common to as many different types of "search" as
 possible and place them in a new base interface

 Make SeqSimilaritySearchResult et al extend the base interface with
 methods appropriate for sequence similarity searches (so leaving all
 the current implementations unaffected)

 Create new interface(s) tailored to mass search (or any other search
 with specific requirements), also extending the base interface

For example,

interface SearchResult
        java.util.List  getHits()
        java.util.Map   getSearchParameters() 

interface SeqSimilaritySearchResult extends SearchResult
        SymbolList      getQuerySequence()
        SequenceDB      getSequenceDB()

interface PeptideMassSearchResult
        ... as you see fit

Does this sound like an option?

Keith

-- 

-= Keith James - kdj@sanger.ac.uk - http://www.sanger.ac.uk/Users/kdj =-
Pathogen Sequencing Unit, Wellcome Trust Sanger Institute, Cambridge, UK