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 <[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? 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 - [EMAIL PROTECTED] - http://www.sanger.ac.uk/Users/kdj =- >Pathogen Sequencing Unit, Wellcome Trust Sanger Institute, Cambridge, UK >_______________________________________________ >Biojava-l mailing list - [EMAIL PROTECTED] >http://biojava.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
