[Biojava-l] Mass Search Results

[William.Old@UCHSC.edu]

> -----Original Message-----
> From: Michael Jones [mailto:mjones@mpi.com]
> Sent: Tuesday, January 08, 2002 8:36 AM
> To: Keith James; BioJava List
> Subject: Re: [Biojava-l] Mass Search Results
> 
> 
>> >  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.

I agree with creating a new base interface to capture the common elements of
searches and extending it for the specific requirements of the searches.
Using a generalized method to return annotations for searches, results, and
hits is also a good idea. Even though each search algorithm returns similar
types of results, they can be very different, and over time the data types
returned will change. 

What about an interface for the storage/retrieval of search results/hits in
a database schema? An example of using a database to store mass spec search
results was recently published in Proteomics: (Proteomics 2001, 1 ,
1489-1494). 

Will