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1 =head1 LICENSE
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2
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3 Copyright (c) 1999-2012 The European Bioinformatics Institute and
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4 Genome Research Limited. All rights reserved.
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5
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6 This software is distributed under a modified Apache license.
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7 For license details, please see
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8
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9 http://www.ensembl.org/info/about/code_licence.html
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10
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11 =head1 CONTACT
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12
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13 Please email comments or questions to the public Ensembl
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14 developers list at <dev@ensembl.org>.
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15
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16 Questions may also be sent to the Ensembl help desk at
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17 <helpdesk@ensembl.org>.
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18
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19 =cut
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20
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21 =head1 NAME
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22
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23 Bio::EnsEMBL::SplicingTranscriptPair - Object representing an alternative splicing transcript pair
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24
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25 =head1 SYNOPSIS
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26
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27 my $ase = Bio::EnsEMBL::SplicingTranscriptPair->new(
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28 -START => 123,
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29 -END => 1045,
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30 -TRANSCRIPT_ID_1 => $tran1->dbID,
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31 -TRANSCRIPT_ID_2 => %tran2->dbID
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32 );
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33
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34 =head1 DESCRIPTION
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35
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36 A representation of an Alternative Splicing Transcrript Pair within the Ensembl system.
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37
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38 =head1 METHODS
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39
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40 =cut
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41
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42 package Bio::EnsEMBL::SplicingTranscriptPair;
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43
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44 use strict;
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45
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46 use POSIX;
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47 use Bio::EnsEMBL::Feature;
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48 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
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49 use Bio::EnsEMBL::Utils::Exception qw(throw warning deprecate);
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50
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51 use vars qw(@ISA);
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52 @ISA = qw(Bio::EnsEMBL::Feature);
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53
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54
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55
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56
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57 sub transcript_id_1{
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58 my $self = shift;
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59 $self->{'transcript_id_1'} = shift if (@_);
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60
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61 if (defined $self->{'transcript_id_1'}) {
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62 return $self->{'transcript_id_1'};
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63 }
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64
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65 return undef;
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66 }
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67
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68 sub transcript_id_2{
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69 my $self = shift;
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70 $self->{'transcript_id_2'} = shift if (@_);
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71
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72 if (defined $self->{'transcript_id_2'}) {
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73 return $self->{'transcript_id_2'};
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74 }
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75
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76 return undef;
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77 }
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78
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79
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80 sub start{
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81 my $self = shift;
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82 $self->{'start'} = shift if (@_);
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83
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84 if (defined $self->{'start'}) {
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85 return $self->{'start'};
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86 }
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87
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88 return undef;
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89 }
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90
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91 sub end{
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92 my $self = shift;
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93 $self->{'end'} = shift if (@_);
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94
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95 if (defined $self->{'end'}) {
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96 return $self->{'end'};
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97 }
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98
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99 return undef;
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100 }
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101
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102
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103
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104
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105
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106 1;
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