Bio/LiveSeq/Exon.pm

   1 # $Id$
   2 #
   3 # bioperl module for Bio::LiveSeq::Exon
   4 #
   5 # Cared for by Joseph Insana <insana@ebi.ac.uk> <jinsana@gmx.net>
   6 #
   7 # Copyright Joseph Insana
   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::LiveSeq::Exon - Range abstract class for LiveSeq
  16
  17 =head1 SYNOPSIS
  18
  19   # documentation needed
  20
  21 =head1 DESCRIPTION
  22
  23 Class for EXON objects. They consist of a beginlabel, an endlabel (both
  24 referring to a LiveSeq DNA object) and a strand.
  25 The strand could be 1 (forward strand, default), -1 (reverse strand).
  26
  27 =head1 AUTHOR - Joseph A.L. Insana
  28
  29 Email:  Insana@ebi.ac.uk, jinsana@gmx.net
  30
  31 =head1 APPENDIX
  32
  33 The rest of the documentation details each of the object
  34 methods. Internal methods are usually preceded with a _
  35
  36 =cut
  37
  38 # Let the code begin...
  39
  40 package Bio::LiveSeq::Exon;
  41
  42 use strict;
  43 use base qw(Bio::LiveSeq::Range);
  44
  45 =head2 new
  46
  47   Title   : new
  48   Usage   : $exon1 = Bio::LiveSeq::Exon-> new(-seq => $objref,
  49                                               -start => $startlabel,
  50                                               -end => $endlabel, -strand => 1);
  51
  52   Function: generates a new Bio::LiveSeq::Exon
  53   Returns : reference to a new object of class Exon
  54   Errorcode -1
  55   Args    : two labels and an integer
  56
  57 =cut
  58
  59 =head2 get_Transcript
  60
  61   Title   : get_Transcript
  62   Usage   : $transcript = $obj->get_Transcript()
  63   Function: retrieves the reference to the object of class Transcript (if any)
  64             attached to a LiveSeq object
  65   Returns : object reference
  66   Args    : none
  67   Note    : only Exons that compose a Transcript (i.e. those created out of
  68             a CDS Entry-Feature) will have an attached Transcript
  69
  70 =cut
  71
  72 sub get_Transcript {
  73   my $self=shift;
  74   return ($self->{'transcript'}); # this is set on all Exons a Transcript is made of when Transcript->new is called
  75 }
  76
  77 # this checks if the attached Transcript has a Gene object attached
  78 sub gene {
  79   my ($self,$value) = @_;
  80   if (defined $value) {
  81     $self->{'gene'} = $value;
  82   }
  83   unless (exists $self->{'gene'}) {
  84     unless (exists $self->get_Transcript->{'gene'}) {
  85       return (0);
  86     } else {
  87       return ($self->get_Transcript->{'gene'});
  88     }
  89   } else {
  90     return $self->{'gene'};
  91   }
  92 }
  93
  94 1;