[Biojava-l] Mass Search Results

[Michael Jones]

It's actually Mr. Jones but I like how evil Dr. Jones sounds.


At 12:24 PM 1/8/2002 +0000, Keith James wrote:
> >>>>> "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?

Yes sounds good. There are some aspects of SeqSimilaritySearchHit like 
score typing that seem a little two specific since different algorithms may 
use different scoring strategies. So I think this is a good strategy in 
general as well as for including MS searches. Do you think it would be a 
good idea to add a getAnnotations() method to the base interface that 
returns a map of values for a result (Both in the SearchResult interface 
and the Hit interface). I am thinking this would be nice since, for 
example, there are lots of MS search algorithms out there and they all 
produce similar results with slight differences. So a getAnnotations() 
method would make it easier to create these different implementations 
without having to have a separate interface for each.


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