NAME

       Bio::UpdateableSeqI - Descendant of Bio::SeqI that allows updates

SYNOPSIS

       See Bio::SeqI for most of the documentation.  See the documentation of the methods for
       further details.

DESCRIPTION

       Bio::UpdateableSeqI is an interface for Sequence objects which are expected to allow users
       to perform basic editing functions (update/delete) on their component SeqFeatures.

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://redmine.open-bio.org/projects/bioperl/

AUTHOR - David Block

       Email dblock@gene.pbi.nrc.ca

CONTRIBUTORS

       Ewan Birney forced me to this...

APPENDIX

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

   delete_feature
        Title   : delete_feature
        Usage   : my $orphanlist=$self->delete_feature($feature,$transcript,$gene);
        Function: deletes the specified $feature from the given transcript, if $transcript is sent and exists and $feature is a feature of $transcript,
                  or from $gene if the $feature is a feature of $gene, or from $self if $transcript and $gene are not sent.  Keeps track of the features
                  of the $gene object that may be left as orphans and returns them as a listref.
        Example : I want to delete transcript 'abc' of gene 'def', with three exons, leaving only transcript 'ghi' with two exons.
                  This will leave exons 1 and 3 part of 'ghi', but exon 2 will become an orphan.
                  my $orphanlist=$seq->delete_feature($transcript{'abc'},undef,$gene{'def'});
                  $orphanlist is a reference to a list containing $exon{'2'};
        Returns : a listref of orphaned features after the deletion of $feature (optional)
        Args    : $feature - the feature to be deleted
                  $transcript - the transcript containing the $feature, so that a $feature can be removed from only one transcript when there are multiple
                                transcripts in a gene.
                  $gene - the gene containing the $transcript and/or the $feature