diff variant_effect_predictor/Bio/UpdateableSeqI.pm @ 0:1f6dce3d34e0

Uploaded

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+++ b/variant_effect_predictor/Bio/UpdateableSeqI.pm	Thu Apr 11 02:01:53 2013 -0400
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+# $Id: UpdateableSeqI.pm,v 1.4 2002/10/22 07:45:09 lapp Exp $
+#
+# BioPerl module for Bio::UpdateableSeqI
+#
+# Cared for by David Block <[e-mail]>
+#
+# Copyright David Block
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::UpdateableSeqI - Descendant of Bio::SeqI that allows updates
+
+=head1 SYNOPSIS
+
+See Bio::SeqI for most of the documentation.
+See the documentation of the methods for further details.
+
+=head1 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.
+
+=head1 FEEDBACK
+
+=head2 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.
+
+  [e-mail]              - General discussion
+  http://bioperl.org/MailList.shtml  - About the mailing lists
+
+=head2 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
+email or the web:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - David Block
+
+Email [e-mail]
+
+=head1 CONTRIBUTORS
+
+Ewan Birney forced me to this...
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods.
+Internal methods are usually preceded with a _
+
+=cut
+
+
+# Let the code begin...
+
+
+package Bio::UpdateableSeqI;
+use vars qw(@ISA);
+use strict;
+use Carp;
+
+# Object preamble - inherits from Bio::Root::Root
+
+use Bio::SeqI;
+
+
+@ISA = qw(Bio::SeqI);
+
+
+=head2 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 $feature
+
+
+=cut
+
+sub delete_feature{
+   my ($self,$feature,$transcript,$gene) = @_;
+
+   $self->throw_not_implemented();
+}
+
+
+1;