[Bioperl-l] Bio::FeatureHolderI

[Lincoln Stein]

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