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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::DBEntry -
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24 Object representing an external reference (xref)
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25
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26 =head1 DESCRIPTION
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27
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28 This object holds information about external references (xrefs) to
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29 Ensembl objects.
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30
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31 =head1 METHODS
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32
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33 =cut
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34
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35 package Bio::EnsEMBL::DBEntry;
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36
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37 use strict;
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38 use warnings;
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39 no warnings qw(uninitialized);
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40
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41 use Bio::EnsEMBL::Storable;
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42 use Bio::Annotation::DBLink;
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43
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44 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
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45 use Bio::EnsEMBL::Utils::Exception qw(deprecate);
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46 use Scalar::Util qw(weaken isweak);
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47
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48 our @ISA = qw(Bio::EnsEMBL::Storable Bio::Annotation::DBLink);
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49
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50
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51 =head2 new_fast
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52
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53 Arg [1] : Hashref $hashref - hash reference to bless as new DBEntry object
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54 Description: A very quick constructor that requires internal knowledge of
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55 the class. This is used in speed critical sections of the code
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56 where many objects need to be created quickly.
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57 Returntype : Bio::EnsEMBL::DBEntry
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58 Exceptions : none
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59 Caller : general
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60 Status : Stable
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61
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62 =cut
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63
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64 sub new_fast {
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65 my $class = shift;
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66 my $hashref = shift;
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67 my $self = bless $hashref, $class;
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68 weaken($self->{adaptor}) if ( ! isweak($self->{adaptor}) );
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69 return $self;
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70 }
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71
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72
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73 =head2 new
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74
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75 Args [...] : list of named parameters
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76 Example : my $dbentry = new Bio::EnsEMBL::DBEntry(
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77 -adaptor => $adaptor,
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78 -primary_id => $pid,
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79 -version => $version,
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80 -dbname => $dbname,
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81 -release => $release,
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82 -display_id => $did,
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83 -description => $description,
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84 -priority => $priority,
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85 -db_display_name => $db_display_name,
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86 -info_type => $info_type,
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87 -info_text => $info_text,
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88 -type => $type,
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89 -secondary_db_name => $secondary_db_name,
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90 -secondary_db_table => $secondary_db_table
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91 -linkage_annotation => $object_xref_text);
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92 Description: Creates a new DBEntry object
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93 Returntype : Bio::EnsEMBL::DBEntry
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94 Exceptions : none
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95 Caller : Bio::EnsEMBL::DBEntryAdaptor
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96 Status : At Risk
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97 Due to 'PRIORITY',
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98 'INFO_TYPE', 'INFO_TEXT', ''DB_DISPLAY_NAME', 'TYPE',
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99 'SECONDARY_DB_NAME', 'SECONDARY_DB_TABLE'
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100 being under development - if you don't use any of these the
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101 method can be considered Stable
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102
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103 =cut
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104
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105 sub new {
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106 my ($class, @args) = @_;
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107
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108 my $self = bless {},$class;
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109
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110 my ( $adaptor, $dbID, $primary_id, $version,
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111 $dbname, $release, $display_id, $description,
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112 $priority,
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113 $db_display_name, $info_type, $info_text, $type,
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114 $secondary_db_name, $secondary_db_table, $link_annotation, $analysis) =
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115 rearrange ( ['ADAPTOR','DBID','PRIMARY_ID','VERSION',
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116 'DBNAME','RELEASE','DISPLAY_ID','DESCRIPTION',
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117 'PRIORITY',
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118 'DB_DISPLAY_NAME', 'INFO_TYPE', 'INFO_TEXT', 'TYPE',
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119 'SECONDARY_DB_NAME', 'SECONDARY_DB_TABLE', 'LINKAGE_ANNOTATION', 'ANALYSIS'], @args );
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120
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121 $self->adaptor($adaptor);
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122 $self->{'dbID'} = $dbID;
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123
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124 if( defined $primary_id ) { $self->primary_id( $primary_id ) }
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125 if( defined $version ) { $self->version( $version ) } else
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126 { $self->version( 0 ); }
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127 if( defined $dbname ) { $self->dbname( $dbname ) }
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128 if( defined $release) { $self->release( $release ) }
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129 if( defined $display_id) { $self->display_id( $display_id ) }
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130 if( defined $description) { $self->description($description) }
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131 if( defined $priority) { $self->priority($priority) }
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132 if( defined $db_display_name) { $self->db_display_name($db_display_name) }
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133 if( defined $info_type) { $self->info_type($info_type) }
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134 if( defined $info_text) { $self->info_text($info_text) }
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135 if( defined $type) { $self->type($type) }
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136 if( defined $secondary_db_name) { $self->secondary_db_name($secondary_db_name) }
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137 if( defined $secondary_db_table) { $self->secondary_db_table($secondary_db_table) }
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138
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139 $self->linkage_annotation($link_annotation) if defined $link_annotation;
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140 $self->analysis($analysis) if defined $analysis;
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141
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142
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143 return $self;
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144 }
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145
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146
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147 =head2 primary_id
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148
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149 Arg [1] : (optional) String $arg - value to set
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150 Example : none
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151 Description: Getter/setter for attribute 'primary_id'.
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152 This is the object's primary id in the external database.
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153 Returntype : String
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154 Exceptions : none
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155 Caller : general
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156 Status : Stable
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157
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158 =cut
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159
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160 sub primary_id {
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161 my ( $self, $arg ) = @_;
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162 if( defined $arg ) {
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163 $self->{primary_id} = $arg;
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164 }
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165 return $self->{primary_id};
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166 }
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167
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168
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169 =head2 display_id
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170
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171 Arg [1] : (optional) String $arg - value to set
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172 Example : none
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173 Description: Getter/setter for attribute 'display_id'.
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174 The object's preferred display name. This can be the same
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175 as primary_id or ensembl-specific.
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176 Returntype : String
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177 Exceptions : none
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178 Caller : general
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179 Status : Stable
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180
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181 =cut
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182
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183 sub display_id{
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184 my ( $self, $arg ) = @_;
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185 if( defined $arg ) {
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186 $self->{display_id} = $arg;
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187 }
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188 return $self->{display_id};
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189 }
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190
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191
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192 =head2 optional_id
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193
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194 Args : none
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195 Example : none
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196 Description: Additional getter for attribute 'display_id'.
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197 The object's preferred display name.
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198 Only include for BioPerl interface compliance, please use
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199 $self->display_id().
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200 Returntype : String
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201 Exceptions : none
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202 Caller : general
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203 Status : Stable
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204
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205 =cut
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206
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207 sub optional_id {
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208 my $self = shift;
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209 return $self->display_id;
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210 }
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211
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212
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213 =head2 dbname
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214
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215 Arg [1] : (optional) String $arg - value to set
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216 Example : none
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217 Description: Getter/setter for attribute 'dbname'.
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218 The name of the external database.
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219 Returntype : String
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220 Exceptions : none
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221 Caller : general
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222 Status : Stable
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223
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224 =cut
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225
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226 sub dbname {
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227 my ( $self, $arg ) = @_;
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228 if( defined $arg ) {
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229 $self->{dbname} = $arg;
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230 }
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231 return $self->{dbname};
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232 }
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233
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234
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235 =head2 database
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236
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237 Args : none
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238 Example : none
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239 Description: Additional getter for attribute 'dbname'.
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240 The name of the external database.
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241 Only include for BioPerl interface compliance, please use
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242 $self->dbname().
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243 Returntype : String
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244 Exceptions : none
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245 Caller : general
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246 Status : Stable
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247
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248 =cut
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249
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250 sub database {
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251 my $self = shift;
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252 return $self->dbname();
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253 }
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254
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255
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256 =head2 release
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257
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258 Arg [1] : (optional) String $arg - value to set
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259 Example : none
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260 Description: Getter/setter for attribute 'release'.
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261 The external database release name.
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262 Returntype : String
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263 Exceptions : none
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264 Caller : general
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265 Status : Stable
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266
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267 =cut
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268
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269 sub release {
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270 my ( $self, $arg ) = @_;
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271 if( defined $arg ) {
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272 $self->{release} = $arg;
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273 }
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274 return $self->{release};
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275 }
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276
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277
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278 =head2 version
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279
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280 Arg [1] : (optional) String $arg - value to set
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281 Example : none
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282 Description: Getter/setter for attribute 'version'.
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283 The object's version in the external database.
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284 Returntype : String
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285 Exceptions : none
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286 Caller : general
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287 Status : Stable
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288
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289 =cut
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290
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291 sub version {
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292 my ( $self, $arg ) = @_;
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293 if( defined $arg ) {
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294 $self->{version} = $arg;
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295 }
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296 return $self->{version};
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297 }
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298
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299
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300 =head2 description
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301
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302 Arg [1] : (optional) String $arg - value to set
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303 Example : none
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304 Description: Getter/setter for attribute 'description'.
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305 The object's description, from the xref table
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306 Returntype : String
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307 Exceptions : none
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308 Caller : general
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309 Status : Stable
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310
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311 =cut
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312
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313 sub description {
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314 my ( $self, $arg ) = @_;
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315
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316 if ( defined($arg) ) { $self->{'description'} = $arg }
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317
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318 return $self->{description};
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319 }
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320
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321 =head2 analysis
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322
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323 Arg [1] : Bio::EnsEMBL::Analysis $analysis
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324 Example : none
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325 Description: get/set for attribute analysis
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326 Returntype : Bio::EnsEMBL::Analysis
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327 Exceptions : none
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328 Caller : general
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329 Status : Stable
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330
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331 =cut
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332
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333 sub analysis {
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334 my $self = shift;
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335 $self->{analysis} = shift if( @_ );
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336 return $self->{analysis};
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337 }
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338
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339 =head2 comment
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340
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341 Args : none
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342 Example : none
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343 Description: Additional getter for attribute 'description'.
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344 The object's description.
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345 Only include for BioPerl interface compliance, please use
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346 $self->description().
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347 Returntype : String
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348 Exceptions : none
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349 Caller : general
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350 Status : Stable
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351
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352 =cut
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353
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354 sub comment {
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355 my $self = shift;
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356 return $self->description();
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357 }
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358
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359
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360 =head2 priority
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361
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362 Arg [1] : int $priority
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363 Example : none
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364 Priority : Getter/setter for attribute 'priority'. Note this
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365 is the priority from the external_db table.
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366 Returntype : String
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367 Exceptions : none
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368 Caller : general
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369 Status : At Risk
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370 : due to it being under development
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371
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372 =cut
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373
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374 sub priority {
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375 my ( $self, $arg ) = @_;
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376 if( defined $arg ) {
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377 $self->{priority} = $arg;
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378 }
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379 return $self->{priority};
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380 }
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381
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382
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383 =head2 db_display_name
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384
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385 Arg [1] : String $db_display_name
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386 Example : none
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387 Description: Getter/setter for attribute 'db_display_name'.
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388 The preferred display name for the external database. Has
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389 "Projected " prepended if info_type='PROJECTION'.
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390 Returntype : String
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391 Exceptions : none
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392 Caller : general
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393
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394 =cut
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395
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396 sub db_display_name {
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397 my ( $self, $arg ) = @_;
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398 if( defined $arg ) {
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399 $self->{db_display_name} = $arg;
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400 }
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401
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402 my $name;
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403 if ($self->{info_type} && $self->{info_type} eq "PROJECTION") {
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404 $name = "Projected " . $self->{db_display_name};
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405 } else {
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406 $name = $self->{db_display_name};
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407 }
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408
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409 return $name;
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410 }
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411
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412
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413 =head2 info_type
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414
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415 Arg [1] : String $info_type
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416 Example : none
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417 Description: Getter/setter for attribute 'info_type'.
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418 Returntype : String
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419 Exceptions : none
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420 Caller : general
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421
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422 =cut
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423
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424 sub info_type {
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425 my ( $self, $arg ) = @_;
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426 if( defined $arg ) {
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427 $self->{info_type} = $arg;
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428 }
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429 return $self->{info_type};
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430 }
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431
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432
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433 =head2 info_text
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434
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435 Arg [1] : String $info_text
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436 Example : none
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437 Description: Getter/setter for attribute 'info_text'.
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438 Returntype : String
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439 Exceptions : none
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440 Caller : general
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441
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442 =cut
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443
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444 sub info_text {
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445 my ( $self, $arg ) = @_;
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446 if( defined $arg ) {
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447 $self->{info_text} = $arg;
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448 }
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449 return $self->{info_text};
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450 }
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451
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452 =head2 linkage_annotation
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453
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454 Arg [1] : String $object_xref_text
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455 Example : none
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456 Description: Getter/setter for attribute 'linkage_annotation'.
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457 Returntype : String
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458 Exceptions : none
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459 Caller : general
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460
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461 =cut
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462
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463 sub linkage_annotation {
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464 my ( $self, $arg ) = @_;
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465
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466 $self->{linkage_annotation} = $arg if defined $arg;
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467
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468 return $self->{linkage_annotation};
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469 }
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470
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471
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472 =head2 type
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473
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474 Arg [1] : String $type
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475 Example : none
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476 Description: Getter/setter for attribute 'type'.
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477 Returntype : String
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478 Exceptions : none
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479 Caller : general
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480
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481 =cut
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482
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483 sub type {
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484 my ( $self, $arg ) = @_;
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485 if( defined $arg ) {
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486 $self->{type} = $arg;
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487 }
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488 return $self->{type};
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489 }
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490
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491 =head2 secondary_db_name
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492
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493 Arg [1] : String $secondary_db_name
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494 Description: Getter/setter for attribute 'secondary_db_name'.
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495 Returntype : String
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496 Exceptions : none
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497 Caller : general
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498
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499 =cut
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500
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501 sub secondary_db_name {
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502 my ( $self, $arg ) = @_;
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503 if( defined $arg ) {
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504 $self->{secondary_db_name} = $arg;
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505 }
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506 return $self->{secondary_db_name};
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507 }
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508
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509
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510 =head2 secondary_db_table
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511
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512 Arg [1] : String $secondary_db_table
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513 Description: Getter/setter for attribute 'secondary_db_table'.
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514 Returns : String
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515 Exceptions : none
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516 Caller : general
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517
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518 =cut
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519
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520 sub secondary_db_table {
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521 my ( $self, $arg ) = @_;
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522 if( defined $arg ) {
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523 $self->{secondary_db_table} = $arg;
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524 }
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525 return $self->{secondary_db_table};
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526 }
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527
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528
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529 =head2 add_synonym
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530
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531 Arg [1] : String $arg - synonym to add
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532 Description: Add a synonym for the external object.
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533 Returntype : none
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534 Exceptions : none
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535 Caller : general
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536 Status : Stable
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537
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538 =cut
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539
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540
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541 sub add_synonym {
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542 my ( $self, $arg ) = @_;
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543 if( defined $arg ) {
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544 push( @{$self->{synonyms}}, $arg );
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545 }
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546 }
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547
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548
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549 =head2 get_all_synonyms
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550
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551 Args : none
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552 Example : my @synonyms = @{ $db_entry->get_all_synonyms };
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553 Description: Get a list of synonyms known for this object.
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554 Synonyms are lazy-loaded if required.
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555 Returntype : listref of strings. May be empty.
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556 Exceptions : none
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557 Caller : general
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558 Status : Stable
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559
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560 =cut
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561
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562 sub get_all_synonyms {
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563
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564 my $self = shift;
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565
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566 # lazy-load synonyms if required
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567 if (!$self->{synonyms} && $self->adaptor()) {
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568 $self->{synonyms} = $self->adaptor()->fetch_all_synonyms($self->dbID());
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569 }
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570
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571 return $self->{synonyms};
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572 }
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573
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574
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575 =head2 get_all_dependents
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576
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577 Args[1] : (optional) Bio::EnsEMBL::Gene, Transcript or Translation object
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578 Example : my @dependents = @{ $db_entry->get_all_dependents };
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579 Description: Get a list of DBEntrys that are depenednet on the DBEntry.
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580 if an ensembl gene transcript or translation is given then only
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581 the ones on that object will be given
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582 Returntype : listref of DBEntrys. May be empty.
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583 Exceptions : none
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584 Caller : general
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585 Status : UnStable
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586
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587 =cut
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588
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589 sub get_all_dependents {
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590 my $self = shift;
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591 my $ensembl_object = shift;
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592
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593 return $self->adaptor()->get_all_dependents($self->dbID(), $ensembl_object);
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594 }
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595
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596 =head2 get_all_masters
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597
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598 Args[1] : (optional) Bio::EnsEMBL::Gene, Transcript or Translation object
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599 Example : my @masters = @{ $db_entry->get_all_masters };
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600 Description: Get a list of DBEntrys that are the masters of the DBEntry.
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601 if an ensembl gene transcript or translation is given then only
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602 the ones on that object will be given.
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603 Returntype : listref of DBEntrys. May be empty.
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604 Exceptions : none
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605 Caller : general
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606 Status : UnStable
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607
|
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608 =cut
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|
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609
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610 sub get_all_masters {
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611 my $self = shift;
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612 my $ensembl_object = shift;
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613
|
|
|
614 return $self->adaptor()->get_all_masters($self->dbID(), $ensembl_object);
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|
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615 }
|
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616
|
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617
|
|
|
618 =head2 flush_synonyms
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|
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619
|
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620 Args : none
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|
621 Description: Remove all synonyms from this object.
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|
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622 Returntype : none
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|
623 Exceptions : none
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|
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624 Caller : general
|
|
|
625 Status : Stable
|
|
|
626
|
|
|
627 =cut
|
|
|
628
|
|
|
629 sub flush_synonyms {
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|
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630 my $self = shift;
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|
|
631 $self->{synonyms} = [];
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|
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632 }
|
|
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633
|
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634
|
|
|
635 =head2 status
|
|
|
636
|
|
|
637 Arg [1] : (optional) String $arg - value to set
|
|
|
638 Description: Getter/setter for attribute 'status'.
|
|
|
639 Returntype : String
|
|
|
640 Exceptions : none
|
|
|
641 Caller : general
|
|
|
642 Status : Stable
|
|
|
643
|
|
|
644 =cut
|
|
|
645
|
|
|
646
|
|
|
647 sub status{
|
|
|
648 my ( $self, $arg ) = @_;
|
|
|
649 if( defined $arg ) {
|
|
|
650 $self->{status} = $arg;
|
|
|
651 }
|
|
|
652 return $self->{status};
|
|
|
653 }
|
|
|
654
|
|
|
655 =head2 ensembl_object_type
|
|
|
656
|
|
|
657 Arg [1] : (optional) String $arg - value to set
|
|
|
658 Description: Getter/setter for attribute ensembl_object_type.
|
|
|
659 Returntype : String
|
|
|
660 Exceptions : none
|
|
|
661 Caller : general
|
|
|
662 Status : Stable
|
|
|
663
|
|
|
664 =cut
|
|
|
665
|
|
|
666
|
|
|
667 sub ensembl_object_type{
|
|
|
668 my ( $self, $arg ) = @_;
|
|
|
669 if( defined $arg ) {
|
|
|
670 $self->{ensembl_object_type} = $arg;
|
|
|
671 }
|
|
|
672 return $self->{ensembl_object_type};
|
|
|
673 }
|
|
|
674
|
|
|
675 =head2 ensembl_id
|
|
|
676
|
|
|
677 Arg [1] : (optional) String $arg - value to set
|
|
|
678 Description: Getter/setter for attribute ensembl_id.
|
|
|
679 Returntype : String
|
|
|
680 Exceptions : none
|
|
|
681 Caller : general
|
|
|
682 Status : Stable
|
|
|
683
|
|
|
684 =cut
|
|
|
685
|
|
|
686
|
|
|
687 sub ensembl_id{
|
|
|
688 my ( $self, $arg ) = @_;
|
|
|
689 if( defined $arg ) {
|
|
|
690 $self->{ensembl_id} = $arg;
|
|
|
691 }
|
|
|
692 return $self->{ensembl_id};
|
|
|
693 }
|
|
|
694
|
|
|
695
|
|
|
696
|
|
|
697 =head1 DEPRECATED METHODS
|
|
|
698
|
|
|
699 =cut
|
|
|
700
|
|
|
701 =head2 get_synonyms
|
|
|
702
|
|
|
703 DEPRECATED use get_all_synonyms instead
|
|
|
704
|
|
|
705 =cut
|
|
|
706
|
|
|
707 sub get_synonyms {
|
|
|
708 my $self = shift;
|
|
|
709
|
|
|
710 deprecate("get_synonyms has been renamed get_all_synonyms.");
|
|
|
711 return $self->get_all_synonyms;
|
|
|
712 }
|
|
|
713
|
|
|
714 1;
|
|
|
715
|
