[Bioperl-l] sequence filtering

[Jason Stajich]

I guess this makes sense - would be very cool if we could add some
speedups so that if we wanted to just parse the feature table in a genome
record we could do this in bioperl w/o having to manage the sequence data
as well.  Again, fixed by doing event based parsing.  Will have to get
that started at some point.

But I guess this is a reasonable stopgap measure.

-jason

On Tue, 8 Oct 2002, Hilmar Lapp wrote:

> Apparently (unfortunately) it didn't ring a lot of bells for many people.
> I'm still looking forward how Biojava does this exactly, even though I've
> now looked through some of their interfaces.
>
> It seems to me what they do is not terribly different from the following
> interface Bio::Factory::ObjectBuilderI that I propose as a solution. There
> would be an implementation Bio::Seq::SeqBuilder.
>
> =head2 want_slot
>
>  Title   : want_slot
>  Usage   :
>  Function: Whether or not the object builder wants to populate the
>            specified slot of the object to be built.
>
>            The slot can be specified either as the name of the
>            respective method, or the initialization parameter that
>            would be otherwise passed to new() of the object to be
>            built.
>
>  Example :
>  Returns : TRUE if the object builder wants to populate the slot, and
>            FALSE otherwise.
>  Args    : the name of the slot (a string)
>
>
> =cut
>
> =head2 add_slot_value
>
>  Title   : add_slot_value
>  Usage   :
>  Function: Adds one or more values to the specified slot of the object
>            to be built.
>
>            Naming the slot is the same as for want_slot().
>
>            The object builder may further filter the content to be
>            set, or even completely ignore the request.
>
>            If this method reports failure, the caller should not add
>            more values to the same slot. In addition, the caller may
>            find it appropriate to abandon the object being built
>            altogether.
>
>  Example :
>  Returns : TRUE on success, and FALSE otherwise
>  Args    : the name of the slot (a string)
>            parameters determining the value to be set
>
>
> =cut
>
> =head2 want_object
>
>  Title   : want_object
>  Usage   :
>  Function: Whether or not the object builder is still interested in
>            continuing with the object being built.
>
>            If this method returns FALSE, the caller should not add any
>            more values to slots, or otherwise risks that the builder
>            throws an exception. In addition, make_object() is likely
>            to return undef after this method returned FALSE.
>
>  Example :
>  Returns : TRUE if the object builder wants to continue building
>            the present object, and FALSE otherwise.
>  Args    : none
>
>
> =cut
>
> =head2 make_object
>
>  Title   : make_object
>  Usage   :
>  Function: Get the built object.
>
>            This method is allowed to return undef if no value has ever
>            been added since the last call to make_object(), or if
>            want_object() returned FALSE (or would have returned FALSE)
>            before calling this method.
>
>  Example :
>  Returns : the object that was built
>  Args    : none
>
>
> =cut
>
> What do people think?
>
> 	-hilmar
>

-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu