annotate variant_effect_predictor/Bio/EnsEMBL/Compara/SyntenyRegion.pm @ 1:d6778b5d8382 draft default tip

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author willmclaren
date Fri, 03 Aug 2012 10:05:43 -0400
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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::SyntenyRegion - Synteny region
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22
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23 =head1 SYNOPSIS
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24
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25 print $this_synteny_region->dbID;
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26
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27 print $this_synteny_region->method_link_species_set_id;
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28
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29 my $these_dnafrag_regions = $this_synteny_region->get_all_DnaFragRegions();
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30 foreach my $this_dnafrag_region (@$these_dnafrag_regions) {
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31 print $this_dnafrag_region->genome_db->name, ": ", $this_dnafrag_region->slice->name, "\n";
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32 }
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33
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34 =head1 DESCRIPTION
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35
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36 A Bio::EnsEMBL::Compara::SyntenyRegion object is a container of Bio::EnsEMBL::Compara::DnaFragRegion
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37 objects. Each Bio::EnsEMBL::Compara::DnaFragRegion represent a genomic region which is in synteny
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38 with the other regions represented in the Bio::EnsEMBL::Compara::SyntenyRegion object.
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39
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40 Also, the Bio::EnsEMBL::Compara::SyntenyRegion object implicitly contains a
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41 Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object which defines the type of synteny.
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42
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43 =head1 OBJECT ATTRIBUTES
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44
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45 =over
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46
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47 =item dbID
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48
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49 corresponds to synteny_region.synteny_region_id
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50
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51 =item adaptor
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52
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53 Bio::EnsEMBL::Compara::DBSQL::SyntenyRegionAdaptor object to access DB
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54
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55 =item method_link_species_set_id
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56
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57 corresponds to synteny_region.method_link_species_set_id
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58
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59 =back
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60
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61 =head1 APPENDIX
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62
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63 The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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64
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65 =cut
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66
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67
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68 # Let the code begin...
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69
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70
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71 package Bio::EnsEMBL::Compara::SyntenyRegion;
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72
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73 use strict;
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74 use Bio::EnsEMBL::Utils::Argument;
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75 use Bio::EnsEMBL::Utils::Exception;
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76
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77 #use Bio::EnsEMBL::Compara::NestedSet;
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78 #our @ISA = qw(Bio::EnsEMBL::Compara::NestedSet);
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79
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80 =head2 new_fast
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81
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82 Arg [-DBID] : integer $dbID
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83 Arg [-METHOD_LINK_SPECIES_SET_ID]
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84 : integer $method_link_species_set_id
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85 Arg [-ADAPTOR]
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86 : Bio::EnsEMBL::Compara::DBSQL::SyntenyRegionAdaptor $adaptor
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87 Example : none
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88 Description : This is the default constructor
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89 Returntype : Bio::EnsEMBL::Compara::SyntenyRegion object
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90 Exceptions : none
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91 Caller :
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92 Status : Stable
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93
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94 =cut
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95
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96 sub new {
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97 my ($class, @args) = @_;
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98
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99 # my $self = $class->SUPER::new(@args);
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100
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101 my $self = bless {}, $class;
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102
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103 if (scalar @args) {
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104 #do this explicitly.
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105 my ($dbid, $method_link_species_set_id, $adaptor, $regions) =
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106 rearrange([qw(DBID METHOD_LINK_SPECIES_SET_ID ADAPTOR REGIONS)], @args);
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107
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108 $dbid && $self->dbID($dbid);
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109 $regions && $self->regions($regions);
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110 $method_link_species_set_id && $self->method_link_species_set_id($method_link_species_set_id);
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111 $adaptor && $self->adaptor($adaptor);
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112 }
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113
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114 return $self;
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115 }
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116
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117
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118 =head2 new_fast
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119
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120 Arg [1] : hash reference $hashref
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121 Example : none
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122 Description : This is an ultra fast constructor which requires knowledge of
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123 the objects internals to be used.
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124 Returntype : Bio::EnsEMBL::Compara::SyntenyRegion object
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125 Exceptions : none
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126 Caller :
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127 Status : Stable
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128
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129 =cut
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130
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131 sub new_fast {
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132 my ($class, $hashref) = @_;
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133
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134 return bless $hashref, $class;
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135 }
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136
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137
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138 =head2 stable_id
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139
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140 DEPRECATED: SyntenyRegions don't have any stable id.
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141
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142 =cut
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143
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144 sub stable_id {
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145 my $obj = shift;
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146
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147 deprecate("SyntenyRegions don't have any stable id.");
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148
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149 if( @_ ) {
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150 my $value = shift;
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151 $obj->{'stable_id'} = $value;
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152 }
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153
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154 return $obj->{'stable_id'};
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155 }
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156
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157
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158 =head2 method_link_species_set_id
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159
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160 Arg [1] : (optional) integer $method_link_species_set_id
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161 Example : none
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162 Description : Getter/setter for the method_link_species_set_id value.
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163 Returntype : integer
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164 Exceptions : none
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165 Caller : general
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166 Status : Stable
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167
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168 =cut
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169
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170 sub method_link_species_set_id {
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171 my $obj = shift;
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172 if( @_ ) {
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173 my $value = shift;
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174 $obj->{'method_link_species_set_id'} = $value;
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175 }
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176 return $obj->{'method_link_species_set_id'};
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177 }
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178
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179
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180 =head2 dbID
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181
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182 Arg [1] : (optional) integer $dbID
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183 Example : none
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184 Description : Getter/setter for the dbID value. This corresponds to
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185 synteny_region.synteny_region_id
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186 Returntype : integer
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187 Exceptions : none
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188 Caller : general
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189 Status : Stable
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190
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191 =cut
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192
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193 sub dbID {
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194 my $obj = shift;
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195
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196 if (@_) {
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197 my $value = shift;
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198 $obj->{'dbID'} = $value;
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199 }
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200
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201 return $obj->{'dbID'};
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202 }
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203
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204
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205 =head2 adaptor
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206
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207 Arg [1] : (optional) Bio::EnsEMBL::Compara::DBSQL::SyntenyRegionAdaptor $adaptor
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208 Example : none
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209 Description : Getter/setter for the adaptor
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210 Returntype : Bio::EnsEMBL::Compara::DBSQL::SyntenyRegionAdaptor object
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211 Exceptions : none
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212 Caller : general
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213 Status : Stable
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214
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215 =cut
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216
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217 sub adaptor {
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218 my $obj = shift;
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219
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220 if (@_) {
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221 my $value = shift;
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222 $obj->{'adaptor'} = $value;
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223 }
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224
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225 return $obj->{'adaptor'};
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226 }
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227
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228
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229 =head2 get_all_DnaFragRegions
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230
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231 Arg 1 : -none-
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232 Example : my $all_dnafrag_regions = $obj->get_all_DnaFragRegions();
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233 Description: returns all the DnaFragRegion objects for this syntenic
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234 region. This method is an alias for children(), see
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235 Bio::EnsEMBL::Compara::NestedSet for more details.
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236 Returntype : a ref. to an array of Bio::EnsEMBL::Compara::DnaFragRegion
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237 objects
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238 Exception :
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239 Caller : general
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240 Status : Stable
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241
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242 =cut
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243
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244 sub get_all_DnaFragRegions {
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245 my $obj = shift;
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246
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247 return $obj->regions();
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248 # return $obj->children();
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249 }
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250
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251 sub regions {
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252 my ($obj, $value) = @_;
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253
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254 if (defined $value) {
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255 $obj->{'regions'} = $value;
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256 }
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257
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258 return $obj->{'regions'};
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259 }
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260
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261 1;