Bio/UpdateableSeqI.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::UpdateableSeqI
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by David Block <dblock@gene.pbi.nrc.ca>
   8 #
   9 # Copyright David Block
  10 #
  11 # You may distribute this module under the same terms as perl itself
  12
  13 # POD documentation - main docs before the code
  14
  15 =head1 NAME
  16
  17 Bio::UpdateableSeqI - Descendant of Bio::SeqI that allows updates
  18
  19 =head1 SYNOPSIS
  20
  21 See Bio::SeqI for most of the documentation.
  22 See the documentation of the methods for further details.
  23
  24 =head1 DESCRIPTION
  25
  26 Bio::UpdateableSeqI is an interface for Sequence objects which are
  27 expected to allow users to perform basic editing functions (update/delete)
  28 on their component SeqFeatures.
  29
  30 =head1 FEEDBACK
  31
  32 =head2 Mailing Lists
  33
  34 User feedback is an integral part of the evolution of this and other
  35 Bioperl modules. Send your comments and suggestions preferably to
  36 the Bioperl mailing list.  Your participation is much appreciated.
  37
  38   bioperl-l@bioperl.org                  - General discussion
  39   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  40
  41 =head2 Support
  42
  43 Please direct usage questions or support issues to the mailing list:
  44
  45 I<bioperl-l@bioperl.org>
  46
  47 rather than to the module maintainer directly. Many experienced and
  48 reponsive experts will be able look at the problem and quickly
  49 address it. Please include a thorough description of the problem
  50 with code and data examples if at all possible.
  51
  52 =head2 Reporting Bugs
  53
  54 Report bugs to the Bioperl bug tracking system to help us keep track
  55 of the bugs and their resolution. Bug reports can be submitted via the
  56 web:
  57
  58   http://bugzilla.open-bio.org/
  59
  60 =head1 AUTHOR - David Block
  61
  62 Email dblock@gene.pbi.nrc.ca
  63
  64 =head1 CONTRIBUTORS
  65
  66 Ewan Birney forced me to this...
  67
  68 =head1 APPENDIX
  69
  70 The rest of the documentation details each of the object methods.
  71 Internal methods are usually preceded with a _
  72
  73 =cut
  74
  75
  76 # Let the code begin...
  77
  78
  79 package Bio::UpdateableSeqI;
  80 use strict;
  81 use Carp;
  82
  83 # Object preamble - inherits from Bio::Root::Root
  84
  85
  86
  87 use base qw(Bio::SeqI);
  88
  89
  90 =head2 delete_feature
  91
  92  Title   : delete_feature
  93  Usage   : my $orphanlist=$self->delete_feature($feature,$transcript,$gene);
  94  Function: deletes the specified $feature from the given transcript, if $transcript is sent and exists and $feature is a feature of $transcript,
  95            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
  96            of the $gene object that may be left as orphans and returns them as a listref.
  97  Example : I want to delete transcript 'abc' of gene 'def', with three exons, leaving only transcript 'ghi' with two exons.
  98            This will leave exons 1 and 3 part of 'ghi', but exon 2 will become an orphan.
  99            my $orphanlist=$seq->delete_feature($transcript{'abc'},undef,$gene{'def'});
 100            $orphanlist is a reference to a list containing $exon{'2'};
 101  Returns : a listref of orphaned features after the deletion of $feature (optional)
 102  Args    : $feature - the feature to be deleted
 103            $transcript - the transcript containing the $feature, so that a $feature can be removed from only one transcript when there are multiple
 104                          transcripts in a gene.
 105            $gene - the gene containing the $transcript and/or the $feature
 106
 107
 108 =cut
 109
 110 sub delete_feature{
 111    my ($self,$feature,$transcript,$gene) = @_;
 112
 113    $self->throw_not_implemented();
 114 }
 115
 116
 117 1;