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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::MiscSet - This is a set representing a classification of
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24 a group of miscellaneuos features.
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25
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26 =head1 SYNOPSIS
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27
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28 use Bio::EnsEMBL::MiscSet;
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29
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30 my $misc_set = Bio::EnsEMBL::MiscSet->new(
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31 1234, $adaptor, 'tilepath',
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32 'Assembly Tiling Path',
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33 'The tiling path of clones', 1e6
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34 );
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35
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36 my $misc_feature->add_set($misc_set);
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37
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38 =head1 DESCRIPTION
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39
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40 MiscSets represent classsifications or groupings of MiscFeatures.
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41 Features are classified into sets essentially to define what they are
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42 and how they may be used. Generally MiscFeatures are retrieved on
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43 the basis of their associated sets. See Bio::EnsEMBL::MiscFeature,
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44 Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor.
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45
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46 Note that MiscSets and MiscFeatures were formerly known as MapSets and
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47 MapFrags
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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 package Bio::EnsEMBL::MiscSet;
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54
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55 use strict;
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56
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57 use Bio::EnsEMBL::Storable;
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58 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
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59
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60 use vars qw(@ISA);
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61
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62 @ISA = qw(Bio::EnsEMBL::Storable);
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63
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64
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65 =head2 new
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66
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67 Arg [1] : int $misc_set_id
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68 The internal identifier for this misc set
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69 Arg [2] : string $code
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70 The unique code which identifies this set type
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71 Arg [3] : string $name
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72 The human readable name of this set
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73 Arg [4] : string $desc
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74 The description of this set
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75 Arg [5] : int $max_len
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76 The maximum length of features of this mapset
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77 Example : $set = new Bio::EnsEMBL::MiscSet(1234, 'tilepath',
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78 'Assembly Tiling Path',
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79 'The tiling path of clones',
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80 1e6);
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81 Description: Instantiates a Bio::EnsEMBL::MiscSet
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82 Returntype : Bio::EnsEMBL::MiscSet
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83 Exceptions : none
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84 Caller : MiscFeatureAdaptor
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85 Status : Stable
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86
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87 =cut
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88
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89 sub new {
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90 my $caller = shift;
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91
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92 my $class = ref($caller) || $caller;
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93
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94 my $self = $class->SUPER::new(@_);
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95
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96 my($code, $name, $desc, $max_len) =
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97 rearrange([qw(CODE NAME DESCRIPTION LONGEST_FEATURE)], @_);
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98
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99 $self->{'code'} = $code;
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100 $self->{'name'} = $name;
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101 $self->{'description'} = $desc;
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102 $self->{'longest_feature'} = $max_len;
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103
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104 return $self;
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105 }
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106
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107 =head2 code
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108
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109 Arg [1] : string $newval (optional)
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110 The new value to set the code attribute to
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111 Example : $code = $obj->code()
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112 Description: Getter/Setter for the code attribute
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113 Returntype : string
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114 Exceptions : none
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115 Caller : general
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116 Status : Stable
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117
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118 =cut
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119
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120 sub code{
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121 my $self = shift;
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122 $self->{'code'} = shift if(@_);
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123 return $self->{'code'};
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124 }
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125
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126
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127 =head2 name
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128
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129 Arg [1] : string $newval (optional)
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130 The new value to set the code attribute to
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131 Example : $name = $obj->name()
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132 Description: Getter/Setter for the name attribute
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133 Returntype : string
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134 Exceptions : none
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135 Caller : general
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136 Status : Stable
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137
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138 =cut
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139
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140 sub name {
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141 my $self = shift;
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142 $self->{'name'} = shift if(@_);
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143 return $self->{'name'};
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144 }
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145
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146
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147 =head2 description
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148
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149 Arg [1] : string $newval (optional)
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150 The new value to set the description attribute to
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151 Example : $description = $obj->description()
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152 Description: Getter/Setter for the description attribute
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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 description{
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161 my $self = shift;
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162 $self->{'description'} = shift if(@_);
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163 return $self->{'description'};
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164 }
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165
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166
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167 =head2 longest_feature
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168
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169 Arg [1] : int $newval (optional)
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170 The new value to set the longest_feature attribute to
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171 Example : $longest_feature = $obj->longest_feature()
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172 Description: Getter/Setter for the longest_feature attribute
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173 Returntype : int
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174 Exceptions : none
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175 Caller : general
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176 Status : Stable
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177
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178 =cut
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179
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180 sub longest_feature{
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181 my $self = shift;
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182 $self->{'longest_feature'} = shift if(@_);
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183 return $self->{'longest_feature'};
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184 }
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185
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186
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187 1;
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