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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 package Bio::EnsEMBL::RepeatConsensus;
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22
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23 use strict;
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24
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25 use Bio::EnsEMBL::Storable;
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26 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
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27 use Scalar::Util qw(weaken isweak);
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28
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29 use vars qw(@ISA);
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30 @ISA = qw(Bio::EnsEMBL::Storable);
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31
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32
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33 =head2 new
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34
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35 Arg [NAME] : string (optional)
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36 The name of this repeat consensus
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37 Arg [LENGTH]: int (optional)
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38 The length of the repeat consensus sequence
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39 Arg [REPEAT_CLASS]: string (optional)
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40 The type of repeat consensus
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41 Arg [REPEAT_CONSENSUS]: string (optional)
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42 The sequence of this repeat consensus
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43 Arg [REPEAT_TYPE]: string
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44 Its like class only more general
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45 Arg [...]: Named arguments to superclass constructor
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46 (see Bio::EnsEMBL::Storable)
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47 Example : $rc = Bio::EnsEMBL::RepeatConsensus->new
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48 (-REPEAT_CONSENSUS => 'AATG'
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49 -NAME => '(AATG)n',
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50 -REPEAT_CLASS => 'Simple_repeat',
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51 -LENGTH => '4',
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52 -DBID => 1023,
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53 -ADAPTOR => $rc_adaptor);
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54 Description: Creates a new Bio::EnsEMBL::RepeatConsensus object
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55 Returntype : Bio::EnsEMBL::RepeatConsensus
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56 Exceptions : none
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57 Caller : RepeatFeatureAdaptors
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58 Status : Stable
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59
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60 =cut
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61
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62 sub new {
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63 my $caller = shift;
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64
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65 my $class = ref($caller) || $caller;
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66
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67 my $self = $class->SUPER::new(@_);
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68
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69 my ($name, $length, $repeat_class, $repeat_consensus, $repeat_type ) =
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70 rearrange(['NAME', 'LENGTH', 'REPEAT_CLASS', 'REPEAT_CONSENSUS', 'REPEAT_TYPE'], @_);
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71
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72 $self->{'name'} = $name;
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73 $self->{'length'} = $length;
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74 $self->{'repeat_class'} = $repeat_class;
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75 $self->{'repeat_consensus'} = $repeat_consensus;
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76 $self->{'repeat_type'} = $repeat_type;
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77
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78 return $self;
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79 }
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80
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81
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82 =head2 new_fast
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83
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84 Arg [1] : hashref to bless as a new RepeatConsensus
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85
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86 Description: Creates a new Bio::EnsEMBL::RepeatConsensus object
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87 Returntype : Bio::EnsEMBL::RepeatConsensus
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88 Exceptions : none
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89 Caller : internal
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90 Status : Stable
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91
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92 =cut
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93
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94 sub new_fast {
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95 my $class = shift;
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96 my $hashref = shift;
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97 my $self = bless $hashref, $class;
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98 weaken($self->{adaptor}) if ( ! isweak($self->{adaptor}) );
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99 return $self;
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100 }
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101
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102
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103 =head2 name
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104
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105 Arg [1] : string $name (optional)
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106 Example : $name = $repeat_consensus->name()
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107 Description: Getter/Setter for the name of this repeat_consensus
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108 Returntype : string
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109 Exceptions : none
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110 Caller : general
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111 Status : Stable
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112
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113 =cut
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114
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115 sub name {
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116 my $self = shift;
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117 $self->{'name'} = shift if(@_);
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118 return $self->{'name'};
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119 }
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120
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121
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122 =head2 length
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123
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124 Arg [1] : int $length (optional)
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125 Example : $length = $repeat_consensus->length()
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126 Description: Getter/Setter for the length of this repeat_consensus
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127 Returntype : int
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128 Exceptions : none
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129 Caller : general
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130 Status : Stable
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131
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132 =cut
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133
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134 sub length {
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135 my $self = shift;
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136 $self->{'length'} = shift if(@_);
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137 return $self->{'length'};
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138 }
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139
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140
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141 =head2 repeat_class
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142
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143 Arg [1] : string $class (optional)
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144 The class of
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145 Example : $class = $repeat_consensus->repeat_class()
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146 Description: Getter/Setter for the class of this repeat_consensus
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147 Returntype : string
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148 Exceptions : none
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149 Caller : general
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150 Status : Stable
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151
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152 =cut
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153
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154 sub repeat_class {
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155 my $self = shift;
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156 $self->{'repeat_class'} = shift if(@_);
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157 return $self->{'repeat_class'};
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158 }
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159
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160 =head2 repeat_type
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161
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162 Arg [1] : string $type (optional)
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163 The type of the consensus
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164 Example : $type = $repeat_consensus->repeat_type()
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165 Description: Getter/Setter for the type of this repeat_consensus
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166 Returntype : string
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167 Exceptions : none
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168 Caller : general
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169
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170 =cut
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171
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172 sub repeat_type {
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173 my $self = shift;
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174 $self->{'repeat_type'} = shift if(@_);
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175 return $self->{'repeat_type'};
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176 }
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177
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178
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179 =head2 desc
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180
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181 Arg [1] : none
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182 Example : $desc = $repeat_consensus->desc()
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183 Description: Getter for the description of this repeat consensus as extracted
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184 from the repeat_class. This method is probably useless.
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185 Returntype : string
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186 Exceptions : none
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187 Caller : general
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188 Status : Medium risk
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189
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190 =cut
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191
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192 sub desc {
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193 my $self = shift;
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194 my $class = $self->repeat_class or return;
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195 return "class=$class";
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196 }
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197
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198
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199
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200 =head2 repeat_consensus
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201
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202 Arg [1] : string $consensus_seq (optional)
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203 The sequence of this repeat consensus
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204 Example : $consensus = $repeat_consensus->repeat_consensus();
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205 Description: Getter/Setter for the sequence of this repeat_consensus.
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206 Returntype : string
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207 Exceptions : none
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208 Caller : general
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209
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210 =cut
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211
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212 sub repeat_consensus {
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213 my $self = shift;
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214 $self->{'repeat_consensus'} = shift if(@_);
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215 return $self->{'repeat_consensus'};
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216 }
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217
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218
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219
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220 =head2 seq
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221
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222 Arg [1] : none
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223 Example : none
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224 Description: Returns the repeat consensus. This method is useless - Use
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225 repeat_consensus() instead.
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226 Returntype : string
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227 Exceptions : none
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228 Caller : general
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229 Status : Stable
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230
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231 =cut
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232
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233 sub seq {
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234 my( $self ) = @_;
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235 return $self->repeat_consensus;
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236 }
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237
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238 1;
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239
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240 __END__
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241
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242 =head1 NAME - Bio::EnsEMBL::RepeatConsensus
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243
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244 =head1 DESCRIPTION
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245
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246 This object represents an entry in the
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247 repeat_consensus table.
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248
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249 It can contain the consensus sequence for a
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250 repeat such as a particular Alu, or "cag" for a
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251 simple triplet repeat.
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252
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253 =head1 AUTHOR
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254
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255 James Gilbert B<email> jgrg@sanger.ac.uk
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256
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