Bio/UpdateableSeqI.pm

   1 #
   2 # BioPerl module for Bio::UpdateableSeqI
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by David Block <dblock@gene.pbi.nrc.ca>
   7 #
   8 # Copyright David Block
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11
  12 # POD documentation - main docs before the code
  13
  14 =head1 NAME
  15
  16 Bio::UpdateableSeqI - Descendant of Bio::SeqI that allows updates
  17
  18 =head1 SYNOPSIS
  19
  20 See Bio::SeqI for most of the documentation.
  21 See the documentation of the methods for further details.
  22
  23 =head1 DESCRIPTION
  24
  25 Bio::UpdateableSeqI is an interface for Sequence objects which are
  26 expected to allow users to perform basic editing functions (update/delete)
  27 on their component SeqFeatures.
  28
  29 =head1 FEEDBACK
  30
  31 =head2 Mailing Lists
  32
  33 User feedback is an integral part of the evolution of this and other
  34 Bioperl modules. Send your comments and suggestions preferably to
  35 the Bioperl mailing list.  Your participation is much appreciated.
  36
  37   bioperl-l@bioperl.org                  - General discussion
  38   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  39
  40 =head2 Support
  41
  42 Please direct usage questions or support issues to the mailing list:
  43
  44 I<bioperl-l@bioperl.org>
  45
  46 rather than to the module maintainer directly. Many experienced and
  47 reponsive experts will be able look at the problem and quickly
  48 address it. Please include a thorough description of the problem
  49 with code and data examples if at all possible.
  50
  51 =head2 Reporting Bugs
  52
  53 Report bugs to the Bioperl bug tracking system to help us keep track
  54 of the bugs and their resolution. Bug reports can be submitted via the
  55 web:
  56
  57   https://redmine.open-bio.org/projects/bioperl/
  58
  59 =head1 AUTHOR - David Block
  60
  61 Email dblock@gene.pbi.nrc.ca
  62
  63 =head1 CONTRIBUTORS
  64
  65 Ewan Birney forced me to this...
  66
  67 =head1 APPENDIX
  68
  69 The rest of the documentation details each of the object methods.
  70 Internal methods are usually preceded with a _
  71
  72 =cut
  73
  74
  75 # Let the code begin...
  76
  77
  78 package Bio::UpdateableSeqI;
  79 use strict;
  80 use Carp;
  81
  82 # Object preamble - inherits from Bio::Root::Root
  83
  84
  85
  86 use base qw(Bio::SeqI);
  87
  88
  89 =head2 delete_feature
  90
  91  Title   : delete_feature
  92  Usage   : my $orphanlist=$self->delete_feature($feature,$transcript,$gene);
  93  Function: deletes the specified $feature from the given transcript, if $transcript is sent and exists and $feature is a feature of $transcript,
  94            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
  95            of the $gene object that may be left as orphans and returns them as a listref.
  96  Example : I want to delete transcript 'abc' of gene 'def', with three exons, leaving only transcript 'ghi' with two exons.
  97            This will leave exons 1 and 3 part of 'ghi', but exon 2 will become an orphan.
  98            my $orphanlist=$seq->delete_feature($transcript{'abc'},undef,$gene{'def'});
  99            $orphanlist is a reference to a list containing $exon{'2'};
 100  Returns : a listref of orphaned features after the deletion of $feature (optional)
 101  Args    : $feature - the feature to be deleted
 102            $transcript - the transcript containing the $feature, so that a $feature can be removed from only one transcript when there are multiple
 103                          transcripts in a gene.
 104            $gene - the gene containing the $transcript and/or the $feature
 105
 106
 107 =cut
 108
 109 sub delete_feature{
 110    my ($self,$feature,$transcript,$gene) = @_;
 111
 112    $self->throw_not_implemented();
 113 }
 114
 115
 116 1;