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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::StableIdEvent- object representing a stable ID mapping event
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24
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25 =head1 SYNOPSIS
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26
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27 my $old_id = Bio::EnsEMBL::ArchiveStableId->new(
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28 -stable_id => 'ENSG001',
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29 -version => 1,
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30 -type => 'Gene',
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31 );
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32
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33 my $new_id = Bio::EnsEMBL::ArchiveStableId->new(
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34 -stable_id => 'ENSG001',
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35 -version => 2,
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36 -type => 'Gene',
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37 );
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38
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39 my $event = Bio::EnsEMBL::StableIdEvent->new(
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40 -old_id => $old_id,
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41 -new_id => $new_id,
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42 -score => 0.997
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43 );
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44
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45 # directly access attributes in old and new ArchiveStableId
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46 my $old_stable_id = $event->get_attribute( 'old', 'stable_id' );
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47
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48 =head1 DESCRIPTION
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49
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50 This object represents a stable ID mapping event. Such an event links two
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51 ArchiveStableIds with a mapping score.
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52
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53 =head1 METHODS
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54
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55 new
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56 old_ArchiveStableId
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57 new_ArchiveStableId
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58 score
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59 get_attribute
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60 ident_string
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61
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62 =head1 RELATED MODULES
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63
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64 Bio::EnsEMBL::ArchiveStableId
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65 Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor
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66 Bio::EnsEMBL::StableIdHistoryTree
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67
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68 =cut
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69
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70 package Bio::EnsEMBL::StableIdEvent;
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71
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72 use strict;
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73 use warnings;
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74 no warnings 'uninitialized';
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75
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76 use Bio::EnsEMBL::Utils::Exception qw(throw warning);
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77 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
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78
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79
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80 =head2 new
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81
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82 Arg[1] : Bio::EnsEMBL::ArchiveStableId $old_id
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83 The old ArchiveStableId in the mapping event
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84 Arg[2] : Bio::EnsEMBL::ArchiveStableId $new_id
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85 The new ArchiveStableId in the mapping event
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86 Arg[3] : (optional) float $score - score of this mapping event
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87 Example : my $event = Bio::EnsEMBL::StableIdEvent->new(
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88 $arch_id1, $arch_id2, 0.977);
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89 Description : object constructor
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90 Return type : Bio::EnsEMBL::StableIdEvent
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91 Exceptions : thrown on wrong argument types
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92 Caller : Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor::fetch_history_tree_by_stable_id, general
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93 Status : At Risk
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94 : under development
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95
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96 =cut
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97
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98 sub new {
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99 my $caller = shift;
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100 my $class = ref($caller) || $caller;
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101
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102 my ($old_id, $new_id, $score) = rearrange([qw(OLD_ID NEW_ID SCORE)], @_);
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103
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104 throw("Need old or new Bio::EnsEMBL::ArchiveStableId to create StableIdEvent")
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105 unless ($old_id || $new_id);
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106
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107 my $self = {};
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108 bless $self, $class;
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109
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110 # initialise object
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111 $self->old_ArchiveStableId($old_id);
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112 $self->new_ArchiveStableId($new_id);
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113 $self->score($score);
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114
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115 return $self;
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116 }
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117
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118
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119 =head2 old_ArchiveStableId
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120
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121 Arg[1] : (optional) Bio::EnsEMBL::ArchiveStableId $archive_id, or undef
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122 The old ArchiveStableId to set for this mapping event
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123 Example : # getter
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124 my $archive_id = $event->old_ArchiveStableId;
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125
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126 # setter
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127 $event->old_ArchiveStableId($archive_id);
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128 Description : Getter/setter for old ArchiveStableId in this mapping event.
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129 Return type : Bio::EnsEMBL::ArchiveStableId
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130 Exceptions : thrown on wrong argument type
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131 Caller : general
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132 Status : At Risk
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133 : under development
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134
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135 =cut
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136
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137 sub old_ArchiveStableId {
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138 my $self = shift;
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139
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140 # setter
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141 if (@_) {
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142 my $archive_id = shift;
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143
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144 # if argument is defined, check type. undef is also legal as an argument.
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145 if (defined($archive_id)) {
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146 throw("Need a Bio::EnsEMBL::ArchiveStableId.") unless
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147 (ref($archive_id) && $archive_id->isa('Bio::EnsEMBL::ArchiveStableId'));
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148 }
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149
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150 $self->{'old_id'} = $archive_id;
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151 }
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152
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153 # getter
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154 return $self->{'old_id'};
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155 }
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156
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157
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158 =head2 new_ArchiveStableId
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159
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160 Arg[1] : (optional) Bio::EnsEMBL::ArchiveStableId $archive_id, or undef
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161 The new ArchiveStableId to set for this mapping event
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162 Example : # getter
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163 my $archive_id = $event->new_ArchiveStableId;
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164
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165 # setter
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166 $event->new_ArchiveStableId($archive_id);
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167 Description : Getter/setter for new ArchiveStableId in this mapping event.
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168 Return type : Bio::EnsEMBL::ArchiveStableId
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169 Exceptions : thrown on wrong argument type
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170 Caller : general
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171 Status : At Risk
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172 : under development
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173
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174 =cut
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175
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176 sub new_ArchiveStableId {
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177 my $self = shift;
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178
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179 # setter
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180 if (@_) {
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181 my $archive_id = shift;
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182
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183 # if argument is defined, check type. undef is also legal as an argument.
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184 if (defined($archive_id)) {
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185 throw("Need a Bio::EnsEMBL::ArchiveStableId.") unless
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186 (ref($archive_id) && $archive_id->isa('Bio::EnsEMBL::ArchiveStableId'));
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187 }
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188
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189 $self->{'new_id'} = $archive_id;
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190 }
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191
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192 # getter
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193 return $self->{'new_id'};
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194 }
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195
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196
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197 =head2 score
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198
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199 Arg[1] : (optional) float $score - the score to set
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200 Example : my $score = $event->score;
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201 Description : Getter/setter for mapping event score.
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202 Return type : float or undef
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203 Exceptions : none
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204 Caller : general
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205 Status : At Risk
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206 : under development
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207
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208 =cut
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209
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210 sub score {
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211 my $self = shift;
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212 $self->{'score'} = shift if (@_);
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213 return $self->{'score'};
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214 }
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215
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216
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217 =head2 get_attribute
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218
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219 Arg[1] : String $type - determines whether to get attribute from 'old'
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220 or 'new' ArchiveStableId
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221 Arg[2] : String $attr - ArchiveStableId attribute to fetch
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222 Example : my $old_stable_id = $event->get_attribute('old', 'stable_id');
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223 Description : Accessor to attributes of the ArchiveStableIds attached to this
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224 event. Convenience method that does the check for undef old
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225 and/or new ArchiveStableId for you.
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226 Return type : same as respective method in Bio::EnsEMBL::ArchiveStableId, or
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227 undef
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228 Exceptions : thrown on wrong arguments
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229 Caller : general
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230 Status : At Risk
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231 : under development
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232
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233 =cut
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234
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235 sub get_attribute {
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236 my ($self, $type, $attr) = @_;
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237
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238 throw("First argument passed to this function has to be 'old' or 'new'.")
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239 unless ($type eq 'old' or $type eq 'new');
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240
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241 my %allowed_attribs = map { $_ => 1 }
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242 qw(stable_id version db_name release assembly);
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243
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244 throw("Attribute $attr not allowed.") unless $allowed_attribs{$attr};
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245
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246 my $call = $type.'_ArchiveStableId';
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247
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248 if (my $id = $self->$call) {
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249 return $id->$attr;
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250 } else {
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251 return undef;
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252 }
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253 }
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254
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255
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256 =head2 ident_string
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257
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258 Example : print $event->ident_string, "\n";
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259 Description : Returns a string that can be used to identify your StableIdEvent.
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260 Useful in debug warnings.
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261 Return type : String
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262 Exceptions : none
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263 Caller : general
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264 Status : At Risk
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265 : under development
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266
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267 =cut
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268
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269 sub ident_string {
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270 my $self = shift;
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271
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272 my $old_id = $self->old_ArchiveStableId;
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273 my $new_id = $self->new_ArchiveStableId;
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274
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275 my $str;
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276
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277 if ($old_id) {
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278 $str = $old_id->stable_id.'.'.$old_id->version.' ('.
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279 $old_id->release.')';
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280 } else {
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281 $str = 'null';
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282 }
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283
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284 $str .= ' -> ';
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285
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286 if ($new_id) {
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287 $str .= $new_id->stable_id.'.'.$new_id->version.' ('.
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288 $new_id->release.')';
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289 } else {
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290 $str .= 'null';
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291 }
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292
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293 $str .= ' ['.$self->score.']';
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294
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295 return $str;
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296 }
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297
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298
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299 1;
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300
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