[Bioperl-l] Bio::FeatureHolderI

[Hilmar Lapp]

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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