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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::MiscFeature - A miscelaneous feature with arbitrary features and
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24 associations.
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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::MiscFeature;
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29 use Bio::EnsEMBL::MiscSet;
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30 use Bio::EnsEMBL::Attribute;
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31
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32 my $mfeat = Bio::EnsEMBL::MiscFeature->new(
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33 -START => 1200,
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34 -END => 100_000,
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35 -STRAND => 1,
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36 -SLICE => $slice
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37 );
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38
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39 # Can add attributes to the misc feature and associate with various
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40 # sets
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41 my $clone_set = Bio::EnsEMBL::MiscSet->new(
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42 -CODE => 'clone',
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43 -NAME => '1MB clone set',
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44 -DESCRIPTION => '1MB CloneSet'
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45 );
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46
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47 my $tiling_path_set = Bio::EnsEMBL::MiscSet->new(
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48 -CODE => 'tilingpath',
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49 -NAME => 'tiling path set'
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50 );
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51
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52 my $attrib1 = Bio::EnsEMBL::Attribute->new(
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53 -VALUE => 'RLX12451',
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54 -CODE => 'name',
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55 -NAME => 'name'
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56 );
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57
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58 my $attrib2 = Bio::EnsEMBL::Attribute->new(
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59 -VALUE => '4',
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60 -CODE => 'version',
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61 -NAME => 'version'
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62 );
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63
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64 my $attrib3 = Bio::EnsEMBL::Attribute->new(
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65 -VALUE => 'AL42131.4',
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66 -CODE => 'synonym',
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67 -NAME => 'synonym'
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68 );
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69
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70 # can associate a misc feature with any number of sets
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71
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72 $mfeat->add_MiscSet($clone_set);
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73 $mfeat->add_MiscSet($tiling_path_set);
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74
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75 # can add arbitrary attributes to a misc feature
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76
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77 $mfeat->add_Attribute($attrib1);
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78 $mfeat->add_Attribute($attrib2);
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79 $mfeat->add_Attribute($attrib3);
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80
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81 my ($name_attrib) = @{ $mfeat->get_all_Attributes('name') };
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82 my @all_attribs = @{ $mfeat->get_all_Attributes() };
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83
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84 my @all_sets = @{ $mfeat->get_all_MiscSets() };
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85 my ($clone_set) = @{ $mfeat->get_all_CloneSets('clone') };
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86
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87
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88 # Can do normal feature operations as well
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89 $mfeat = $mfeat->transform('supercontig');
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90 print $mfeat->slice->seq_region_name, ' ', $mfeat->start, '-',
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91 $mfeat->end;
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92
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93
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94 =head1 DESCRIPTION
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95
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96 MiscFeatures are extremely general features with a location, and an
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97 arbitrary group of attributes. They are grouped with other features of
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98 the same 'type' through the use of MiscSets (see Bio::EnsEMBL::MiscSet).
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99 Attributes are attached in the fom of Bio::EnsEMBL::Attribute objects.
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100 See Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor for ways to fetch or store
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101 MiscFeatures.
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102
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103 =cut
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104
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105
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106 package Bio::EnsEMBL::MiscFeature;
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107
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108 use strict;
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109 use warnings;
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110
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111 use Bio::EnsEMBL::Feature;
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112 use Bio::EnsEMBL::Utils::Exception qw(throw);
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113 use Scalar::Util qw(weaken isweak);
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114
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115 use vars qw(@ISA);
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116
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117 @ISA = qw(Bio::EnsEMBL::Feature);
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118
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119 =head2 new
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120
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121 Arg [-SLICE]: Bio::EnsEMBL::SLice - Represents the sequence that this
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122 feature is on. The coordinates of the created feature are
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123 relative to the start of the slice.
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124 Arg [-START]: The start coordinate of this feature relative to the start
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125 of the slice it is sitting on. Coordinates start at 1 and
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126 are inclusive.
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127 Arg [-END] : The end coordinate of this feature relative to the start of
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128 the slice it is sitting on. Coordinates start at 1 and are
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129 inclusive.
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130 Arg [-STRAND]: The orientation of this feature. Valid values are 1,-1,0.
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131 Arg [-SEQNAME] : A seqname to be used instead of the default name of the
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132 of the slice. Useful for features that do not have an
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133 attached slice such as protein features.
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134 Arg [-dbID] : (optional) internal database id
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135 Arg [-ADAPTOR]: (optional) Bio::EnsEMBL::DBSQL::BaseAdaptor
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136 Example : $feature = Bio::EnsEMBL::MiscFeature->new(-start => 1,
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137 -end => 100,
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138 -strand => 1,
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139 -slice => $slice,
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140 -analysis => $analysis);
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141 Description: Constructs a new Bio::EnsEMBL::Feature. Generally subclasses
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142 of this method are instantiated, rather than this class itself.
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143 Returntype : Bio::EnsEMBL::MiscFeature
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144 Exceptions : Thrown on invalid -SLICE, -ANALYSIS, -STRAND ,-ADAPTOR arguments
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145 Caller : general, subclass constructors
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146 Status : Stable
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147
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148 =cut
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149
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150
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151 sub new {
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152 my $class = shift;
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153
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154 my $self = $class->SUPER::new(@_);
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155
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156 $self->{'attributes'} = [];
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157
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158 return $self;
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159 }
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160
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161
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162 =head2 new_fast
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163
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164 Arg [...] : hashref to bless as new MiscFeature
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165 Example : $miscfeature = Bio::EnsEMBL::MiscFeature->new_fast();
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166 Description: Creates a new Miscfeature.
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167 Returntype : Bio::EnsEMBL::MiscFeature
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168 Exceptions : none
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169 Caller : general
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170 Status : Stable
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171
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172 =cut
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173
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174
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175 sub new_fast {
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176 my $class = shift;
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177 my $hashref = shift;
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178
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179 $hashref->{'attributes'} ||= [];
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180
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181 my $self = bless $hashref, $class;
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182 weaken($self->{adaptor}) if ( ! isweak($self->{adaptor}) );
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183 return $self;
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184 }
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185
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186
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187
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188 =head2 add_Attribute
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189
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190 Arg [1] : Bio::EnsEMBL::Attribute $attribute
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191 Example : $misc_feature->add_attribute($attribute);
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192 Description: Adds an attribute to this misc. feature
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193 Returntype : none
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194 Exceptions : throw on wrong argument type
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195 Caller : general
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196 Status : Stable
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197
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198 =cut
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199
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200 sub add_Attribute {
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201 my ($self, $attrib) = @_;
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202
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203 if( ! defined $attrib || ! $attrib->isa( "Bio::EnsEMBL::Attribute" )) {
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204 throw( "You have to provide a Bio::EnsEMBL::Attribute, not a [$attrib]" );
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205 }
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206
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207 $self->{'attributes'} ||= [];
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208 push @{$self->{'attributes'}}, $attrib
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209 }
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210
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211
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212
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213 =head2 add_MiscSet
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214
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215 Arg [1] : Bio::EnsEMBL::MiscSet $set
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216 The set to add
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217 Example : $misc_feature->add_MiscSet(Bio::EnsEMBL::MiscSet->new(...));
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218 Description: Associates this MiscFeature with a given Set.
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219 Returntype : none
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220 Exceptions : throw if the set arg is not provided,
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221 throw if the set to be added does not have a code
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222 Caller : general
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223 Status : Stable
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224
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225 =cut
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226
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227
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228 sub add_MiscSet {
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229 my $self = shift;
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230 my $miscSet = shift;
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231
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232 if(!$miscSet || !ref($miscSet) || !$miscSet->isa('Bio::EnsEMBL::MiscSet')) {
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233 throw('Set argument must be a Bio::EnsEMBL::MiscSet');
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234 }
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235
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236 $self->{'miscSets'} ||= [];
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237
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238 push( @{$self->{'miscSets'}}, $miscSet );
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239 }
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240
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241
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242
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243 =head2 get_all_MiscSets
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244
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245 Arg [1] : optional string $code
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246 The code of the set to retrieve
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247 Example : $set = $misc_feature->get_all_MiscSets($code);
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248 Description: Retrieves a set that this feature is associated with via its
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249 code. Can return empty lists. Usually returns about one elements lists.
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250 Returntype : listref of Bio::EnsEMBL::MiscSet
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251 Exceptions : throw if the code arg is not provided
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252 Caller : general
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253 Status : Stable
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254
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255 =cut
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256
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257
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258 sub get_all_MiscSets {
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259 my $self = shift;
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260 my $code = shift;
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261
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262 $self->{'miscSets'} ||= [];
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263 if( defined $code ) {
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264 my @results = grep { uc($_->code())eq uc( $code ) } @{$self->{'miscSets'}};
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265 return \@results;
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266 } else {
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267 return $self->{'miscSets'};
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268 }
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269 }
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270
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271
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272 =head2 get_all_Attributes
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273
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274 Arg [1] : optional string $code
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275 The code of the Attribute objects to retrieve
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276 Example : @attributes = @{ $misc_feature->get_all_Attributes('name') };
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277 Description: Retrieves a list of Attribute objects for given code or all
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278 of the associated Attributes.
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279 Returntype : listref of Bio::EnsEMBL::Attribute
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280 Exceptions :
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281 Caller : general
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282 Status : Stable
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283
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284 =cut
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285
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286 sub get_all_Attributes {
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287 my $self = shift;
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288 my $code = shift;
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289
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290 my @results;
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291 my $result;
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292
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293 if( defined $code ) {
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294 @results = grep { uc( $_->code() ) eq uc( $code )} @{$self->{'attributes'}};
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295 return \@results;
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296 } else {
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297 return $self->{'attributes'};
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298 }
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299 }
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300
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301 =head2 get_all_attribute_values
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302
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303 Arg [1] : string $code
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304 The code of the Attribute object values to retrieve
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305 Example : @attributes_vals = @{$misc_feature->get_all_attribute_values('name')};
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306 Description: Retrieves a list of Attribute object values for given code or all
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307 of the associated Attributes.
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308 Returntype : listref of values
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309 Exceptions :
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310 Caller : general
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311 Status : Stable
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312
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313 =cut
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314
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315 sub get_all_attribute_values {
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316 my $self = shift;
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317 my $code = shift;
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318 my @results = map { uc( $_->code() ) eq uc( $code ) ? $_->value : () }
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319 @{$self->{'attributes'}};
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320 return \@results;
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321 }
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322
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323 =head2 get_scalar_attribute
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324
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325 Arg [1] : string $code
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326 The code of the Attribute object values to retrieve
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327 Example : $vals = $misc_feature->get_scalar_attribute('name');
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328 Description: Retrieves a value for given code or all
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329 of the associated Attributes.
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330 Returntype : scalar value
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331 Exceptions :
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332 Caller : general
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333 Status : Stable
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334
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335
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336 =cut
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337
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338
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339 sub get_scalar_attribute {
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340 my $self = shift;
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341 my $code = shift;
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342 my @results = grep { uc( $_->code() ) eq uc( $code )} @{$self->{'attributes'}};
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343 return @results ? $results[0]->value() : '';
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344 }
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345
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346 sub get_first_scalar_attribute {
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347 my $self = shift;
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348 foreach my $code ( @_ ) {
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349 my @results = grep { uc( $_->code() ) eq uc( $code )} @{$self->{'attributes'}};
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350 return $results[0]->value() if @results;
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351 }
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352 return '';
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353 }
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354 =head2 display_id
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355
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356 Arg [1] : none
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357 Example : print $kb->display_id();
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358 Description: This method returns a string that is considered to be
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359 the 'display' identifier. For misc_features this is the first
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360 name or synonym attribute or '' if neither are defined.
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361 Returntype : string
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362 Exceptions : none
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363 Caller : web drawing code
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364 Status : Stable
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365
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366 =cut
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367
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368 sub display_id {
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369 my $self = shift;
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370 my ($attrib) = @{$self->get_all_Attributes('name')};
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371 ($attrib) = @{$self->get_all_Attributes('synonym')} if(!$attrib);
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372 if( defined $attrib ) {
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373 return $attrib->value();
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374 } else {
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375 return '';
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376 }
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377 }
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378
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379
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380
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381
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382 1;
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