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1 #
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2 # Ensembl module for Bio::EnsEMBL::Funcgen::Channel
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3 #
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4 # You may distribute this module under the same terms as Perl itself
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5
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6
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7 =head1 LICENSE
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8
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9 Copyright (c) 1999-2011 The European Bioinformatics Institute and
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10 Genome Research Limited. All rights reserved.
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11
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12 This software is distributed under a modified Apache license.
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13 For license details, please see
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14
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15 http://www.ensembl.org/info/about/code_licence.html
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16
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17 =head1 CONTACT
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18
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19 Please email comments or questions to the public Ensembl
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20 developers list at <ensembl-dev@ebi.ac.uk>.
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21
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22 Questions may also be sent to the Ensembl help desk at
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23 <helpdesk@ensembl.org>.
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24
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25
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26 =head1 NAME
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27
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28 Bio::EnsEMBL::Funcgen::Channel - A module to represent a single channel of an ExperimentalChip
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29
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30 =head1 SYNOPSIS
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31
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32 use Bio::EnsEMBL::Funcgen::Channel;
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33
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34 my $array = Bio::EnsEMBL::Funcgen::Channel->new(
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35 -EXPERIMENTAL_CHIP_ID => $ec_id,
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36 -SAMPLE_ID => $sample_id,
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37 -TYPE => $type,
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38 -DYE => $dye,
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39 );
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40
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41 #-replace TYPE with DENOMINATOR?
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42
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43 my $db_adaptor = Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor->new(...);
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44 my $chan_a = $db_adaptor->get_ChannelAdaptor();
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45 my $chan = $chan_a->fetch_by_type_ExperimentalChip($type, $ExpChip);
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46
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47 =head1 DESCRIPTION
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48
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49 A Channel object represents a single channel on an ExperimentalChip. The data
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50 are stored in the channel table, and associated expermental variables are
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51 stored in the experimental_variable table.
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52
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53 =cut
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54
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55 use strict;
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56 use warnings;
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57
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58
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59 package Bio::EnsEMBL::Funcgen::Channel;
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60
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61
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62 use Bio::EnsEMBL::Utils::Argument qw( rearrange );
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63 use Bio::EnsEMBL::Utils::Exception qw( throw warning );
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64 use Bio::EnsEMBL::Funcgen::Storable;
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65
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66 use vars qw(@ISA);
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67 @ISA = qw(Bio::EnsEMBL::Funcgen::Storable);
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68
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69
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70 =head2 new
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71
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72 Arg [-EXPERIMENTAL_CHIP_ID]: int - the experimental chip dbID
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73
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74
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75
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76 Example : my $array = Bio::EnsEMBL::Funcgen::Channel->new(
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77 -EXPERIMENTAL_CHIP_ID => $ec_id,
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78 -SAMPLE_ID => $sample_id,
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79 -TYPE => $type,
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80 -DYE => $dye,
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81 );
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82 Description: Creates a new Bio::EnsEMBL::Funcgen::Channel object.
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83 Returntype : Bio::EnsEMBL::Funcgen::Channel
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84 Exceptions : None
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85 Caller : General
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86 Status : Medium Risk
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87
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88 =cut
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89
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90 sub new {
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91 my $caller = shift;
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92
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93 my $class = ref($caller) || $caller;
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94
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95 my $self = $class->SUPER::new(@_);
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96
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97 #can we lc these?
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98 my ($ec_id, $sample_id, $type, $dye)
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99 = rearrange( ['EXPERIMENTAL_CHIP_ID', 'SAMPLE_ID', 'TYPE', 'DYE'], @_ );
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100
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101 $self->sample_id($sample_id) if defined $sample_id;
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102 $self->experimental_chip_id($ec_id) if defined $ec_id;
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103 $self->type($type) if defined $type;
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104 $self->dye($dye) if defined $dye;
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105
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106
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107 return $self;
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108 }
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109
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110 =head2 sample_id
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111
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112 Arg [1] : (optional) string - the sample id for this Channel
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113 Example : my $sample_id = $chan->sample_id();
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114 Description: Getter, setter and lazy loader of sample_id attribute.
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115 Returntype : string
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116 Exceptions : None
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117 Caller : General
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118 Status : Medium Risk
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119
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120 =cut
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121
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122 sub sample_id {
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123 my $self = shift;
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124 $self->{'sample_id'} = shift if @_;
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125
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126 if ( ! exists $self->{'sample_id'} && $self->dbID() && $self->adaptor() ) {
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127 $self->adaptor->fetch_attributes($self);
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128 }
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129
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130 return $self->{'sample_id'};
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131 }
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132
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133
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134
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135 =head2 experimental_chip_id
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136
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137 Arg [1] : (optional) int - the experimenta chip dbID
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138 Example : my $ec_id = $chan->experimental_chip_id();
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139 Description: Getter, setter and lazy loader of experimental_chip_id attribute
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140 Returntype : int
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141 Exceptions : None
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142 Caller : General
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143 Status : Medium Risk
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144
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145 =cut
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146
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147 sub experimental_chip_id {
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148 my $self = shift;
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149
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150 $self->{'experimental_chip_id'} = shift if @_;
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151 if ( !exists $self->{'experimental_chip_id'} && $self->dbID() && $self->adaptor() ) {
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152 $self->adaptor->fetch_attributes($self);
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153 }
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154 return $self->{'experimental_chip_id'};
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155 }
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156
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157 =head2 type
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158
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159 Arg [1] : (optional) string - the channel type e.g. EXPERIMENTAL or CONTROL
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160 Example : my $type = $chan->type();
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161 Description: Getter, setter and lazy loader of type attribute
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162 Returntype : string
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163 Exceptions :
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164 Caller : General
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165 Status : Medium Risk
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166
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167 =cut
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168
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169 sub type {
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170 my $self = shift;
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171
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172 $self->{'type'} = shift if @_;
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173
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174 #warn "we need to control EXPERIMENTAL OR CONTROL here or enum on DB";
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175
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176 if ( !exists $self->{'type'} && $self->dbID() && $self->adaptor() ) {
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177 $self->adaptor->fetch_attributes($self);
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178 }
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179 return $self->{'type'};
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180 }
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181
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182 =head2 dye
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183
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184 Arg [1] : (optional) string - the channel type e.g. EXPERIMENTAL or CONTROL
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185 Example : my $dye = $chan->dye();
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186 Description: Getter, setter and lazy loader of dye attribute
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187 Returntype : string
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188 Exceptions :
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189 Caller : General
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190 Status : Medium Risk
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191
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192 =cut
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193
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194 sub dye {
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195 my $self = shift;
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196
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197 $self->{'dye'} = shift if @_;
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198
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199 #if ( !exists $self->{'dye'} && $self->dbID() && $self->adaptor() ) {
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200 # $self->adaptor->fetch_attributes($self);
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201 #}
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202 return $self->{'dye'};
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203 }
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204
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205
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206 1;
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207
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