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Blixem_X in the ?Method

Dave Matthews matthews at GREENGENES.CIT.CORNELL.EDU
Sat Jun 5 14:34:25 EST 1999


Hi Brian,

> So, this object, whose name is Method, is used for displaying output
> from various
> programs such as BLAST, BLIXEM, GENEFINDER etc. ...
> 
> 1. I get the feeling that I still don't have the entire story on
> ?Method.
> ..., this definition seems to imply that output from
> various programs is being displayed by ACeDB. Presumably,
> that is done by Pick_me_to_call from some other object?
> Or is there a mechanism for xace to display the output?

The Sequence display shows homology bars according the Method specified:

?Sequence Homol DNA_homol ?Sequence ?Method Float Int UNIQUE Int Int UNIQUE Int
                Pep_homol ?Protein ?Method Float Int UNIQUE Int Int UNIQUE Int
                Motif_homol ?Motif ?Method Float Int UNIQUE Int Int UNIQUE Int

The results from external programs must be reformatted and loaded into ACEDB
as Sequence data corresponding to this model.


> 2. At the risk of being impertinent, in my humble opinion,
> it is not a good idea to call an object by the name "Method",
> because the word "method" has a very precise, and important
> meaning in Object-Oriented Programming.

There a number of words that have very different meanings in different
contexts.  In this case I think the sense is that any given sequence
homology will have been determined according to a particular combination of
parameters and source database, the method.  The ?Method tags allow the
Sequence display to show different methods separate from each other, and
in different ways as appropriate.  

- Dave




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