Bio/SeqFeature/Gene/ExonI.pm

   1 #
   2 # BioPerl module for Bio::SeqFeature::Gene::ExonI
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Hilmar Lapp <hlapp@gmx.net>
   7 #
   8 # Copyright Hilmar Lapp
   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::SeqFeature::Gene::ExonI - Interface for a feature representing an exon
  17
  18 =head1 SYNOPSIS
  19
  20 See documentation of methods.
  21
  22 =head1 DESCRIPTION
  23
  24 A feature representing an exon. An exon in this definition is
  25 transcribed and at least for one particular transcript not spliced out
  26 of the pre-mRNA. However, it does not necessarily code for amino acid.
  27
  28 =head1 FEEDBACK
  29
  30 =head2 Mailing Lists
  31
  32 User feedback is an integral part of the evolution of this
  33 and other Bioperl modules. Send your comments and suggestions preferably
  34  to one of the Bioperl mailing lists.
  35 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 the bugs and their resolution.  Bug reports can be submitted via the
  55 web:
  56
  57   https://github.com/bioperl/bioperl-live/issues
  58
  59 =head1 AUTHOR - Hilmar Lapp
  60
  61 Email hlapp@gmx.net
  62
  63 =head1 APPENDIX
  64
  65 The rest of the documentation details each of the object methods.
  66 Internal methods are usually preceded with a _
  67
  68 =cut
  69
  70
  71 # Let the code begin...
  72
  73
  74 package Bio::SeqFeature::Gene::ExonI;
  75 use strict;
  76
  77 use base qw(Bio::SeqFeatureI);
  78
  79
  80 =head2 is_coding
  81
  82  Title   : is_coding
  83  Usage   : if($exon->is_coding()) {
  84                    # do something
  85            }
  86  Function: Whether or not the exon codes for amino acid.
  87  Returns : TRUE if the object represents a feature translated into protein,
  88            and FALSE otherwise.
  89  Args    :
  90
  91
  92 =cut
  93
  94 sub is_coding {
  95     my ($self) = @_;
  96     $self->throw_not_implemented();
  97 }
  98
  99 =head2 cds
 100
 101  Title   : cds()
 102  Usage   : $cds = $exon->cds();
 103  Function: Get the coding sequence of the exon as a sequence object.
 104
 105            The returned sequence object must be in frame 0, i.e., the first
 106            base starts a codon.
 107
 108            An implementation may return undef, indicating that a coding
 109            sequence does not exist, e.g. for a UTR (untranslated region).
 110
 111  Returns : A L<Bio::PrimarySeqI> implementing object.
 112  Args    :
 113
 114
 115 =cut
 116
 117 sub cds {
 118     my ($self) = @_;
 119     $self->throw_not_implemented();
 120 }
 121
 122 1;