[Bioperl-l] Bio::FeatureHolderI

[Hilmar Lapp]

Yes, that's one way. An alternative is to define an interface an 
implementation of which must be passed in. Cleaner (and I think 
that's how BioJava does it), but maybe unnecessarily complicated in 
bioperl. I'm leaning towards your shortcut for simplicity reasons.

If simple filtering by matching attribute values is to be 
implemented by the FeatureHolderI itself like you suggest, I'd vote 
for having those args match the parameter names you supply to new(). 
I.e., for filtering by tag this would mean -primary and -source, 
depending on which attribute you want to filter (which BTW exposes 
another annoying inconsistency we have: parameter names should be 
the same as the method names [with a hyphen preprended]).

Votes/comments/suggestions solicited ...

	-hilmar

On Monday, November 18, 2002, at 12:03 AM, Lincoln Stein wrote:

> The Bio::Das and Bio::DB::GFF get_SeqFeatures methods both support 
> filters, so
> I am happy if you formalize this.
>
> I suggest two ways to filter, to start with:
>
> 	(-tag => \@tag_list)
>
> Filter on the basis of a list of primary tags.  The returned 
> features are a
> union or ORing the tags.
>
> 	(-filter => \&filter)
>
> Pass each feature to the filter subroutine.  Return features for 
> which the
> subroutine returns true.
>
> Lincoln
>
> On Sunday 17 November 2002 06:55 am, Hilmar Lapp wrote:
>> I'd suggest adding this alongside AnnotatableI. The benefit is not
>> new functionality, but rather imposing a more rigorous and fostering
>> a more consistent API structure on those classes that have features.
>>
>> I have the module ready to commit, and I'd adjust Bio::Seq and
>> SeqFeature::Generic to implement this (clearly not very difficult).
>> What do people thing? Core guys? This should be very similar to the
>> biojava model, but I haven't checked that for a while.
>>
>> =head2 get_SeqFeatures
>>
>>   Title   : get_SeqFeatures
>>   Usage   :
>>   Function: Get the feature objects held by this feature holder.
>>   Example :
>>   Returns : an array of Bio::SeqFeatureI implementing objects
>>   Args    : none
>>
>> At some day we may want to expand this method to allow for a feature
>> filter to be passed in.
>>
>> =cut
>>
>> =head2 feature_count
>>
>>   Title   : feature_count
>>   Usage   : $obj->feature_count()
>>   Function: Return the number of SeqFeatures attached to a feature
>> holder.
>>
>>             This is before flattening a possible sub-feature tree.
>>
>>             We provide a default implementation here that just counts
>>             the number of objects returned by get_SeqFeatures().
>>             Implementors may want to override this with a more
>>             efficient implementation.
>>
>>   Returns : integer representing the number of SeqFeatures
>>   Args    : None
>>
>> At some day we may want to expand this method to allow for a feature
>> filter to be passed in.
>>
>> Our default implementation allows for any number of additional
>> arguments and will pass them on get_SeqFeatures(). I.e., in order to
>> support filter arguments, just support them in get_SeqFeatures().
>>
>> =cut
>>
>> =head2 get_all_SeqFeatures
>>
>>   Title   : get_all_SeqFeatures
>>   Usage   :
>>   Function: Get the flattened tree of feature objects held by this
>>             feature holder. The difference to get_SeqFeatures is that
>>             the entire tree of sub-features will be flattened out.
>>
>>             We provide a default implementation here, so implementors
>>             don''t necessarily need to implement this method.
>>
>>   Example :
>>   Returns : an array of Bio::SeqFeatureI implementing objects
>>   Args    : none
>>
>> At some day we may want to expand this method to allow for a feature
>> filter to be passed in.
>>
>> Our default implementation allows for any number of additional
>> arguments and will pass them on to any invocation of
>> get_SeqFeatures(), wherever a component of the tree implements
>> FeatureHolderI. I.e., in order to support filter arguments, just
>> support them in get_SeqFeatures().
>>
>> =cut
>>
--
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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