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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::SNP
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24
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25 =head1 SYNOPSIS
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26
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27 $snp = new Bio::EnsEMBL::SNP(
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28 -start => 10,
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29 -end => 10,
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30 -strand => 1,
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31 -source => 'The SNP Consortium',
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32 -score => 99, # new meaning
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33 -status => 'suspected', # new
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34 -alleles => 't|c' # new
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35 );
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36
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37 # add it to an annotated sequence
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38
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39 $annseq->add_SeqFeature($feat);
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40
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41 =head1 DESCRIPTION
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42
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43 This class was written because the EnsEMBL::ExternalData::Variation
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44 object is way too slow. There was simply too much chaining to bioperl
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45 methods many, many layers deep. This object behaves like a Variation
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46 but has a much faster constructor, and faster accessors for the relevant
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47 methods needed by the web.
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48
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49 =head1 METHODS
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50
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51 =cut
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52
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53
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54 package Bio::EnsEMBL::SNP;
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55 use vars qw(@ISA);
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56 use strict;
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57
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58
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59 use Bio::EnsEMBL::ExternalData::Variation;
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60 use Scalar::Util qw(weaken isweak);
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61
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62 @ISA = qw( Bio::EnsEMBL::ExternalData::Variation );
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63
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64
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65 sub new_fast {
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66 my $class = shift;
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67 my $hashref = shift;
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68 my $self = bless $hashref, $class;
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69 weaken($self->{adaptor}) if ( ! isweak($self->{adaptor}) );
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70 return $self;
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71 }
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72
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73 sub dbID {
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74 my $self = shift;
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75
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76 if(@_) {
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77 $self->{'dbID'} = shift;
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78 }
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79
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80 return $self->{'dbID'};
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81 }
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82
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83 sub position {
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84 my ($self, $arg) = @_;
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85
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86 if(defined $arg) {
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87 $self->{_gsf_start} = $arg;
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88 $self->{_gsf_end} = $arg;
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89 }
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90
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91 return $self->{_gsf_start};
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92 }
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93
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94 sub start {
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95 my ($self, $arg) = @_;
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96
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97 if(defined $arg) {
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98 $self->{_gsf_start} = $arg;
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99 }
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100
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101 return $self->{_gsf_start};
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102 }
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103
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104 sub end {
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105 my ($self, $arg) = @_;
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106
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107 if(defined $arg) {
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108 $self->{_gsf_end} = $arg;
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109 }
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110
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111 return $self->{_gsf_end};
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112 }
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113
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114
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115 sub source {
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116 my ($self, $arg) = @_;
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117
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118 if(defined $arg) {
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119 $self->{_source} = $arg;
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120 }
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121
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122 return $self->{_source};
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123 }
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124
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125 sub score {
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126 my ($self, $arg) = @_;
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127
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128 if(defined $arg) {
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129 $self->{_gsf_score} = $arg;
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130 }
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131
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132 return $self->{_gsf_score};
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133 }
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134
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135
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136 sub source_tag {
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137 my ($self, $arg) = @_;
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138
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139 if(defined $arg) {
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140 $self->{_source_tag} = $arg;
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141 }
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142
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143 return $self->{_source_tag};
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144 }
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145
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146 sub source_version {
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147 my ($self, $arg) = @_;
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148
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149 if(defined $arg) {
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150 $self->{_source_version} = $arg;
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151 }
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152
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153 return $self->{_source_version};
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154 }
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155
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156
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157 =head2 display_name
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158
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159 Arg [1] : none
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160 Example : print $snp->display_name();
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161 Description: This method returns a string that is considered to be
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162 the 'display' identifier. For snps this is the
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163 returns the same thing as the id method.
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164 Returntype : string
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165 Exceptions : none
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166 Caller : web drawing code
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167
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168 =cut
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169
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170 sub display_name {
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171 my $self = shift;
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172 return $self->id();
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173 }
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174
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175
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176
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177 1;
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