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NAME

       Bio::FeatureHolderI - the base interface an object with features must
       implement

SYNOPSIS

           use Bio::SeqIO;
           # get a feature-holding object somehow: for example, Bio::SeqI objects
           # have features
           my $seqio = Bio::SeqIO->new(-fh => \*STDIN, -format => 'genbank');
           while (my $seq = $seqio->next_seq()) {
               # $seq is-a Bio::FeatureHolderI, hence:
               my @feas = $seq->get_SeqFeatures();
               # each element is-a Bio::SeqFeatureI
               foreach my $fea (@feas) {
                   # do something with the feature objects
               }
           }

DESCRIPTION

       This is the base interface that all feature-holding objects must
       implement.

       Popular feature-holders are for instance Bio::Seq objects. Since
       Bio::SeqFeatureI defines a sub_SeqFeature() method, most
       Bio::SeqFeatureI implementations like Bio::SeqFeature::Generic will
       implement the feature holder interface as well.

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other
       Bioperl modules. Send your comments and suggestions preferably to the
       Bioperl mailing list.  Your participation is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and
       reponsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the problem with code and
       data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of
       the bugs and their resolution. Bug reports can be submitted via the
       web:

         https://github.com/bioperl/bioperl-live/issues

AUTHOR - Hilmar Lapp

       Email hlapp at gmx.net

CONTRIBUTORS

       Steffen Grossmann [SG], grossman-at-molgen.mpg.de Mark A. Jensen, maj
       -at- fortinbras -dot- us

APPENDIX

       The rest of the documentation details each of the object methods.
       Internal methods are usually preceded with a _

   get_SeqFeatures()
        Usage   : @feats = $obj->get_SeqFeatures()
        Function: Get the feature objects held by this feature holder.
        Example :
        Returns : an array of Bio::SeqFeatureI implementing objects
                  if tag specified, return features having that tag
        Args    : [optional] scalar string (feature tag)

   add_SeqFeature()
        Usage   : $feat->add_SeqFeature($subfeat);
                  $feat->add_SeqFeature($subfeat,'EXPAND')
        Function: Add a SeqFeature into the subSeqFeature array.
                  with no 'EXPAND' qualifer, subfeat will be tested
                  as to whether it lies inside the parent, and throw
                  an exception if not.

                  If EXPAND is used and the object implements Bio::RangeI
                  (which is not guaranteed), the parent''s start/end/strand
                  will be extended so that the new subFeature can be accomodated.
        Example :
        Returns : nothing
        Args    : a Bio::SeqFeatureI object

   remove_SeqFeatures()
        Usage   : $obj->remove_SeqFeatures
        Function: Removes all sub SeqFeatures.  If you want to remove only a subset,
                  remove that subset from the returned array, and add back the rest.
        Returns : The array of Bio::SeqFeatureI implementing sub-features that was
                  deleted from this feature.
        Args    : none

   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 to get_SeqFeatures(). I.e., in order to
       support filter arguments, just support them in get_SeqFeatures().

   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().



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