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1 #
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2 # Ensembl module for Bio::EnsEMBL::Funcgen::ExternalFeature
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3 #
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4
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5
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6 =head1 LICENSE
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7
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8 Copyright (c) 1999-2011 The European Bioinformatics Institute and
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9 Genome Research Limited. All rights reserved.
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10
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11 This software is distributed under a modified Apache license.
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12 For license details, please see
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13
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14 http://www.ensembl.org/info/about/code_licence.html
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15
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16 =head1 CONTACT
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17
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18 Please email comments or questions to the public Ensembl
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19 developers list at <ensembl-dev@ebi.ac.uk>.
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20
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21 Questions may also be sent to the Ensembl help desk at
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22 <helpdesk@ensembl.org>.
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23
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24
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25 =head1 NAME
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26
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27 Bio::EnsEMBL::ExternalFeature - A module to represent an externally curated feature
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28 mapping from an external_db.
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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::ExternalFeature;
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33
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34 my $feature = Bio::EnsEMBL::Funcgen::ExternalFeature->new(
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35 -SLICE => $chr_1_slice,
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36 -START => 1_000_000,
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37 -END => 1_000_024,
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38 -STRAND => -1,
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39 -DISPLAY_LABEL => $text,
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40 -FEATURE_SET => $fset,
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41 -FEATURE_TYPE => $ftype,
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42 );
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43
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44
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45
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46 =head1 DESCRIPTION
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47
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48 An ExternalFeature object represents the genomic placement of an externally curated
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49 feature from and DB external to Ensembl.
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50
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51 =cut
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52
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53 use strict;
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54 use warnings;
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55
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56 package Bio::EnsEMBL::Funcgen::ExternalFeature;
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57
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58 use Bio::EnsEMBL::Utils::Argument qw( rearrange );
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59 use Bio::EnsEMBL::Utils::Exception qw( throw );
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60 use Bio::EnsEMBL::Funcgen::SetFeature;
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61 use Bio::EnsEMBL::Funcgen::FeatureType;
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62
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63 use vars qw(@ISA);
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64 @ISA = qw(Bio::EnsEMBL::Funcgen::SetFeature);
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65
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66
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67 =head2 new
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68
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69
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70 Arg [-FEATURE_SET] : Bio::EnsEMBL::Funcgen::FeatureSet
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71 Arg [-FEATURE_TYPE] : Bio::EnsEMBL::Funcgen::FeatureType
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72 Arg [-ANALYSIS] : Bio::EnsEMBL::Analysis
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73 Arg [-SLICE] : Bio::EnsEMBL::Slice - The slice on which this feature is.
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74 Arg [-START] : int - The start coordinate of this feature relative to the start of the slice
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75 it is sitting on. Coordinates start at 1 and are inclusive.
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76 Arg [-END] : int -The end coordinate of this feature relative to the start of the slice
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77 it is sitting on. Coordinates start at 1 and are inclusive.
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78 Arg [-DISPLAY_LABEL]: string - Display label for this feature
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79 Arg [-STRAND] : int - The orientation of this feature. Valid values are 1, -1 and 0.
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80 Arg [-dbID] : (optional) int - Internal database ID.
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81 Arg [-ADAPTOR] : (optional) Bio::EnsEMBL::DBSQL::BaseAdaptor - Database adaptor.
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82 Example : my $feature = Bio::EnsEMBL::Funcgen::ExternalFeature->new(
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83 -SLICE => $chr_1_slice,
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84 -START => 1_000_000,
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85 -END => 1_000_024,
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86 -STRAND => -1,
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87 -DISPLAY_LABEL => $text,
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88 -FEATURE_SET => $fset,
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89 -FEATURE_TYPE => $ftpe,
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90 );
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91
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92
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93 Description: Constructor for ExternalFeature objects.
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94 Returntype : Bio::EnsEMBL::Funcgen::ExternalFeature
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95 Exceptions : None
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96 Caller : General
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97 Status : At Risk
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98
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99 =cut
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100
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101 sub new {
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102 my $caller = shift;
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103
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104 my $class = ref($caller) || $caller;
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105 my $self = $class->SUPER::new(@_);
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106
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107 #Remove this method if we interdb_stable_id to SetFeature
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108 ($self->{'interdb_stable_id'}) = rearrange(['INTERDB_STABLE_ID'], @_);
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109
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110 return $self;
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111 }
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112
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113 =head2 interdb_stable_id
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114
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115 Arg [1] : (optional) int - stable_id e.g 1
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116 Example : my $idb_sid = $feature->interdb_stable_id();
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117 Description: Getter for the interdb_stable_id attribute for this feature.
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118 This is simply to avoid using internal db IDs for inter DB linking
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119 Returntype : int
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120 Exceptions : None
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121 Caller : General
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122 Status : At Risk
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123
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124 =cut
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125
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126 sub interdb_stable_id {
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127 return $_[0]->{'interdb_stable_id'};
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128 }
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129
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130
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131
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132
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133 =head2 display_label
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134
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135 Example : my $label = $feature->display_label();
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136 Description: Getter for the display label of this feature.
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137 Returntype : String
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138 Exceptions : None
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139 Caller : General
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140 Status : Medium risk
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141
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142 =cut
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143
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144 sub display_label {
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145 my $self = shift;
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146
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147 if(! $self->{'display_label'} && $self->adaptor){
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148
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149 $self->{'display_label'} = $self->feature_set->feature_type->name().' - ';
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150 $self->{'display_label'} .= $self->cell_type->name() if $self->cell_type();
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151 $self->{'display_label'} .= $self->feature_type->name() if(defined $self->{'feature_type'});
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152 }
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153
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154 return $self->{'display_label'};
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155 }
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156
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157
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158
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159 1;
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160
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