Bio/LiveSeq/Exon.pm

   1 #
   2 # bioperl module for Bio::LiveSeq::Exon
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Joseph Insana <insana@ebi.ac.uk> <jinsana@gmx.net>
   7 #
   8 # Copyright Joseph Insana
   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::LiveSeq::Exon - Range abstract class for LiveSeq
  17
  18 =head1 SYNOPSIS
  19
  20   # documentation needed
  21
  22 =head1 DESCRIPTION
  23
  24 Class for EXON objects. They consist of a beginlabel, an endlabel (both
  25 referring to a LiveSeq DNA object) and a strand.
  26 The strand could be 1 (forward strand, default), -1 (reverse strand).
  27
  28 =head1 AUTHOR - Joseph A.L. Insana
  29
  30 Email:  Insana@ebi.ac.uk, jinsana@gmx.net
  31
  32 =head1 APPENDIX
  33
  34 The rest of the documentation details each of the object
  35 methods. Internal methods are usually preceded with a _
  36
  37 =cut
  38
  39 # Let the code begin...
  40
  41 package Bio::LiveSeq::Exon;
  42
  43 use strict;
  44 use base qw(Bio::LiveSeq::Range);
  45
  46 =head2 new
  47
  48   Title   : new
  49   Usage   : $exon1 = Bio::LiveSeq::Exon-> new(-seq => $objref,
  50                                               -start => $startlabel,
  51                                               -end => $endlabel, -strand => 1);
  52
  53   Function: generates a new Bio::LiveSeq::Exon
  54   Returns : reference to a new object of class Exon
  55   Errorcode -1
  56   Args    : two labels and an integer
  57
  58 =cut
  59
  60 =head2 get_Transcript
  61
  62   Title   : get_Transcript
  63   Usage   : $transcript = $obj->get_Transcript()
  64   Function: retrieves the reference to the object of class Transcript (if any)
  65             attached to a LiveSeq object
  66   Returns : object reference
  67   Args    : none
  68   Note    : only Exons that compose a Transcript (i.e. those created out of
  69             a CDS Entry-Feature) will have an attached Transcript
  70
  71 =cut
  72
  73 sub get_Transcript {
  74   my $self=shift;
  75   return ($self->{'transcript'}); # this is set on all Exons a Transcript is made of when Transcript->new is called
  76 }
  77
  78 # this checks if the attached Transcript has a Gene object attached
  79 sub gene {
  80   my ($self,$value) = @_;
  81   if (defined $value) {
  82     $self->{'gene'} = $value;
  83   }
  84   unless (exists $self->{'gene'}) {
  85     unless (exists $self->get_Transcript->{'gene'}) {
  86       return (0);
  87     } else {
  88       return ($self->get_Transcript->{'gene'});
  89     }
  90   } else {
  91     return $self->{'gene'};
  92   }
  93 }
  94
  95 1;