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1 # $Id: Exon.pm,v 1.8 2001/06/18 08:27:53 heikki Exp $
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2 #
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3 # bioperl module for Bio::LiveSeq::Exon
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4 #
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5 # Cared for by Joseph Insana <insana@ebi.ac.uk> <jinsana@gmx.net>
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6 #
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7 # Copyright Joseph Insana
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8 #
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9 # You may distribute this module under the same terms as perl itself
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10 #
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11 # POD documentation - main docs before the code
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12
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13 =head1 NAME
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14
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15 Bio::LiveSeq::Exon - Range abstract class for LiveSeq
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16
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17 =head1 SYNOPSIS
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18
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19 # documentation needed
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20
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21 =head1 DESCRIPTION
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22
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23 Class for EXON objects. They consist of a beginlabel, an endlabel (both
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24 referring to a LiveSeq DNA object) and a strand.
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25 The strand could be 1 (forward strand, default), -1 (reverse strand).
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26
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27 =head1 AUTHOR - Joseph A.L. Insana
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28
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29 Email: Insana@ebi.ac.uk, jinsana@gmx.net
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30
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31 Address:
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32
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33 EMBL Outstation, European Bioinformatics Institute
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34 Wellcome Trust Genome Campus, Hinxton
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35 Cambs. CB10 1SD, United Kingdom
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36
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37 =head1 APPENDIX
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38
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39 The rest of the documentation details each of the object
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40 methods. Internal methods are usually preceded with a _
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41
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42 =cut
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43
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44 # Let the code begin...
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45
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46 package Bio::LiveSeq::Exon;
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47 $VERSION=1.1;
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48
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49 # Version history:
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50 # Mon Mar 20 22:26:13 GMT 2000 v 1.0 begun
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51 # Wed Apr 12 12:42:56 BST 2000 v 1.1 get_Transcript added
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52
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53 use strict;
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54 use vars qw($VERSION @ISA);
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55 use Bio::LiveSeq::Range 1.2; # uses Range, inherits from it
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56 @ISA=qw(Bio::LiveSeq::Range);
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57
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58 =head2 new
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59
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60 Title : new
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61 Usage : $exon1 = Bio::LiveSeq::Exon-> new(-seq => $objref,
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62 -start => $startlabel,
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63 -end => $endlabel, -strand => 1);
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64
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65 Function: generates a new Bio::LiveSeq::Exon
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66 Returns : reference to a new object of class Exon
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67 Errorcode -1
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68 Args : two labels and an integer
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69
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70 =cut
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71
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72 =head2 get_Transcript
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73
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74 Title : get_Transcript
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75 Usage : $transcript = $obj->get_Transcript()
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76 Function: retrieves the reference to the object of class Transcript (if any)
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77 attached to a LiveSeq object
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78 Returns : object reference
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79 Args : none
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80 Note : only Exons that compose a Transcript (i.e. those created out of
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81 a CDS Entry-Feature) will have an attached Transcript
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82
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83 =cut
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84
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85 sub get_Transcript {
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86 my $self=shift;
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87 return ($self->{'transcript'}); # this is set on all Exons a Transcript is made of when Transcript->new is called
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88 }
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89
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90 # this checks if the attached Transcript has a Gene object attached
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91 sub gene {
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92 my ($self,$value) = @_;
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93 if (defined $value) {
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94 $self->{'gene'} = $value;
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95 }
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96 unless (exists $self->{'gene'}) {
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97 unless (exists $self->get_Transcript->{'gene'}) {
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98 return (0);
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99 } else {
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100 return ($self->get_Transcript->{'gene'});
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101 }
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102 } else {
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103 return $self->{'gene'};
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104 }
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105 }
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106
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107 1;
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