Bio/UpdateableSeqI.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::UpdateableSeqI
   4 #
   5 # Cared for by David Block <dblock@gene.pbi.nrc.ca>
   6 #
   7 # Copyright David Block
   8 #
   9 # You may distribute this module under the same terms as perl itself
  10
  11 # POD documentation - main docs before the code
  12
  13 =head1 NAME
  14
  15 Bio::UpdateableSeqI - Descendant of Bio::SeqI that allows updates
  16
  17 =head1 SYNOPSIS
  18
  19 See Bio::SeqI for most of the documentation.
  20 See the documentation of the methods for further details.
  21
  22 =head1 DESCRIPTION
  23
  24 Bio::UpdateableSeqI is an interface for Sequence objects which are
  25 expected to allow users to perform basic editing functions (update/delete)
  26 on their component SeqFeatures.
  27
  28 =head1 FEEDBACK
  29
  30 =head2 Mailing Lists
  31
  32 User feedback is an integral part of the evolution of this and other
  33 Bioperl modules. Send your comments and suggestions preferably to
  34 the Bioperl mailing list.  Your participation is much appreciated.
  35
  36   bioperl-l@bioperl.org                  - General discussion
  37   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  38
  39 =head2 Reporting Bugs
  40
  41 Report bugs to the Bioperl bug tracking system to help us keep track
  42 of the bugs and their resolution. Bug reports can be submitted via the
  43 web:
  44
  45   http://bugzilla.open-bio.org/
  46
  47 =head1 AUTHOR - David Block
  48
  49 Email dblock@gene.pbi.nrc.ca
  50
  51 =head1 CONTRIBUTORS
  52
  53 Ewan Birney forced me to this...
  54
  55 =head1 APPENDIX
  56
  57 The rest of the documentation details each of the object methods.
  58 Internal methods are usually preceded with a _
  59
  60 =cut
  61
  62
  63 # Let the code begin...
  64
  65
  66 package Bio::UpdateableSeqI;
  67 use strict;
  68 use Carp;
  69
  70 # Object preamble - inherits from Bio::Root::Root
  71
  72
  73
  74 use base qw(Bio::SeqI);
  75
  76
  77 =head2 delete_feature
  78
  79  Title   : delete_feature
  80  Usage   : my $orphanlist=$self->delete_feature($feature,$transcript,$gene);
  81  Function: deletes the specified $feature from the given transcript, if $transcript is sent and exists and $feature is a feature of $transcript,
  82            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
  83            of the $gene object that may be left as orphans and returns them as a listref.
  84  Example : I want to delete transcript 'abc' of gene 'def', with three exons, leaving only transcript 'ghi' with two exons.
  85            This will leave exons 1 and 3 part of 'ghi', but exon 2 will become an orphan.
  86            my $orphanlist=$seq->delete_feature($transcript{'abc'},undef,$gene{'def'});
  87            $orphanlist is a reference to a list containing $exon{'2'};
  88  Returns : a listref of orphaned features after the deletion of $feature (optional)
  89  Args    : $feature - the feature to be deleted
  90            $transcript - the transcript containing the $feature, so that a $feature can be removed from only one transcript when there are multiple
  91                          transcripts in a gene.
  92            $gene - the gene containing the $transcript and/or the $feature
  93
  94
  95 =cut
  96
  97 sub delete_feature{
  98    my ($self,$feature,$transcript,$gene) = @_;
  99
 100    $self->throw_not_implemented();
 101 }
 102
 103
 104 1;