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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 =head1 AUTHORSHIP
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20
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21 Ensembl Team. Individual contributions can be found in the CVS log.
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22
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23 =cut
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24
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25 =head1 NAME
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26
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27 MemberDomain - DESCRIPTION of Object
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28
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29 =head1 DESCRIPTION
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30
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31 A subclass of Member which extends it to store a domain (start / end)
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32 within the sequence
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33
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34 =head1 INHERITANCE TREE
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35
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36 Bio::EnsEMBL::Compara::MemberDomain
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37 +- Bio::EnsEMBL::Compara::Member
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38
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39 =head1 METHODS
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40
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41 =cut
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42
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43 package Bio::EnsEMBL::Compara::MemberDomain;
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44
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45 use strict;
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46 use Bio::EnsEMBL::Utils::Exception;
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47 use Bio::EnsEMBL::Compara::Member;
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48
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49 use base ('Bio::EnsEMBL::Compara::Member');
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50
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51
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52 ##################################
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53 # overriden superclass methods
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54 ##################################
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55
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56 =head2 copy
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57
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58 Arg [1] : none
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59 Example : $copy = $aligned_member->copy();
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60 Description : Creates a new MemberDomain object from an existing one
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61 Returntype : Bio::EnsEMBL::Compara::MemberDomain
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62 Exceptions : none
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63 Caller : general
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64 Status : Stable
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65
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66 =cut
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67
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68 sub copy {
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69 my $self = shift;
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70
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71 my $mycopy = @_ ? shift : {}; # extending or from scratch?
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72 $self->SUPER::copy($mycopy);
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73 bless $mycopy, 'Bio::EnsEMBL::Compara::MemberDomain';
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74
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75 # The following does not Work if the initial object is only a Member
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76 if (UNIVERSAL::isa($self, 'Bio::EnsEMBL::Compara::MemberDomain')) {
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77 $mycopy->member_start($self->member_start);
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78 $mycopy->member_end($self->member_end);
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79 }
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80
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81 return $mycopy;
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82 }
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83
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84
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85 =head2 member_start
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86
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87 Arg [1] : (optional) $member_start
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88 Example : $object->member_start($member_start);
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89 Example : $member_start = $object->member_start();
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90 Description : Getter/setter for the member_start attribute. For non-global
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91 alignments, this represent the starting point of the local
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92 alignment.
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93 Currently the data provided as MemberDomains (leaves of the
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94 GeneTree) are obtained using global alignments and the
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95 member_start is always undefined.
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96 Returntype : integer
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97 Exceptions : none
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98 Caller : general
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99 Status : Stable
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100
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101 =cut
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102
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103 sub member_start {
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104 my $self = shift;
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105 $self->{'_member_start'} = shift if(@_);
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106 return $self->{'_member_start'};
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107 }
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108
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109
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110 =head2 member_end
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111
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112 Arg [1] : (optional) $member_end
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113 Example : $object->member_end($member_end);
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114 Example : $member_end = $object->member_end();
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115 Description : Getter/setter for the member_end attribute. For non-global
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116 alignments, this represent the ending point of the local
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117 alignment.
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118 Currently the data provided as MemberDomains (leaves of the
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119 GeneTree) are obtained using global alignments and the
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120 member_end is always undefined.
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121 Returntype : integer
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122 Exceptions : none
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123 Caller : general
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124 Status : Stable
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125
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126 =cut
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127
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128 sub member_end {
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129 my $self = shift;
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130 $self->{'_member_end'} = shift if(@_);
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131 return $self->{'_member_end'};
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132 }
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133
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134
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135
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136 1;
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