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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 NAME
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20
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21 Bio::EnsEMBL::Compara::GeneTreeMember
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22
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23 =head1 DESCRIPTION
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24
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25 Currently the GeneTreeMember objects are used to represent the leaves of
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26 the gene trees (whether they contain proteins or non-coding RNas).
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27
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28 Each GeneTreeMember object is simultaneously a tree node (inherits from
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29 GeneTreeNode) and an aligned member (inherits from AlignedMember).
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30
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31 =head1 INHERITANCE TREE
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32
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33 Bio::EnsEMBL::Compara::GeneTreeMember
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34 +- Bio::EnsEMBL::Compara::AlignedMember
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35 `- Bio::EnsEMBL::Compara::GeneTreeNode
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36
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37 =head1 AUTHORSHIP
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38
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39 Ensembl Team. Individual contributions can be found in the CVS log.
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40
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41 =head1 MAINTAINER
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42
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43 $Author: mm14 $
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44
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45 =head VERSION
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46
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47 $Revision: 1.5 $
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48
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49 =head1 APPENDIX
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50
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51 The rest of the documentation details each of the object methods.
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52 Internal methods are usually preceded with an underscore (_)
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53
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54 =cut
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55
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56 package Bio::EnsEMBL::Compara::GeneTreeMember;
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57
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58 use strict;
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59
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60 use base ('Bio::EnsEMBL::Compara::AlignedMember', 'Bio::EnsEMBL::Compara::GeneTreeNode'); # careful with the order; new() is currently inherited from Member-AlignedMember branch
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61
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62
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63 =head2 copy
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64
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65 Arg [1] : none
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66 Example : $copy = $gene_tree_member->copy();
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67 Description : Creates a new GeneTreeMember object from an existing one
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68 Returntype : Bio::EnsEMBL::Compara::GeneTreeMember
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69 Exceptions : none
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70 Caller : general
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71 Status : Stable
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72
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73 =cut
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74
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75 sub copy {
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76 my $self = shift;
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77
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78 my $mycopy = $self->Bio::EnsEMBL::Compara::GeneTreeNode::copy;
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79 $self->Bio::EnsEMBL::Compara::AlignedMember::copy($mycopy); # we could rename this method into topup() as it is not needed by 'AlignedMember' class itself
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80 bless $mycopy, 'Bio::EnsEMBL::Compara::GeneTreeMember';
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81
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82 return $mycopy;
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83 }
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84
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85
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86 =head2 string_node (overrides default method in Bio::EnsEMBL::Compara::NestedSet)
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87
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88 Arg [1] : none
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89 Example : $aligned_member->string_node();
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90 Description : Outputs the info for this GeneTreeMember. First, the node_id, the
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91 left and right indexes are printed, then the species name. If the
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92 gene member can be determined, the methods prints the stable_id,
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93 the display label and location of the gene member, otherwise the
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94 member_id and stable_id of the object are printed.
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95 Returntype : none
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96 Exceptions : none
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97 Caller : general
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98 Status : Stable
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99
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100 =cut
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101
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102 sub string_node {
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103 my $self = shift;
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104 my $str = sprintf("(%s %d,%d)", $self->node_id, $self->left_index, $self->right_index);
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105 if($self->genome_db_id and $self->adaptor) {
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106 my $genome_db = $self->genome_db;
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107 if (!defined($genome_db)) {
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108 $DB::single=1;1;
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109 }
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110 $str .= sprintf(" %s", $genome_db->name)
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111 }
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112 if($self->gene_member) {
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113 $str .= sprintf(" %s %s %s:%d-%d",
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114 $self->gene_member->stable_id, $self->gene_member->display_label || '', $self->gene_member->chr_name,
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115 $self->gene_member->chr_start, $self->gene_member->chr_end);
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116 } elsif($self->stable_id) {
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117 $str .= sprintf(" (%d) %s", $self->member_id, $self->stable_id);
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118 }
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119 $str .= "\n";
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120 }
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121
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122
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123
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124 =head2 name (overrides default method in Bio::EnsEMBL::Compara::Graph::CGObject)
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125
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126 Arg [1] : none
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127 Example : $aligned_member->name();
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128 Description : Returns the stable_id of the object (from the Bio::EnsEMBL::Compara::Member object).
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129 Returntype : string
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130 Exceptions : none
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131 Caller : general
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132 Status : Stable
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133
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134 =cut
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135
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136 sub name {
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137 my $self = shift;
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138 return $self->stable_id(@_);
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139 }
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140
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141 1;
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142
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