>>>>> "Dr. Jones" == Michael Jones <[EMAIL PROTECTED]> 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 - [EMAIL PROTECTED] - http://www.sanger.ac.uk/Users/kdj =-
Pathogen Sequencing Unit, Wellcome Trust Sanger Institute, Cambridge, UK
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