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1 #
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2 # Ensembl module for Bio::EnsEMBL::Funcgen::Collection::ResultFeature
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3 #
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4 =head1 LICENSE
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5
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6 Copyright (c) 1999-2011 The European Bioinformatics Institute and
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7 Genome Research Limited. All rights reserved.
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8
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9 This software is distributed under a modified Apache license.
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10 For license details, please see
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11
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12 http://www.ensembl.org/info/about/code_licence.html
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13
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14 =head1 CONTACT
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15
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16 Please email comments or questions to the public Ensembl
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17 developers list at <ensembl-dev@ebi.ac.uk>.
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18
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19 Questions may also be sent to the Ensembl help desk at
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20 <helpdesk@ensembl.org>.
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21
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22
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23 =head1 NAME
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24
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25 Bio::EnsEMBL::Funcgen::Collection::ResultFeature - A module to represent a lightweight ResultFeature collection
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26
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27 =head1 SYNOPSIS
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28
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29 use Bio::EnsEMBL::Funcgen::Collection::ResultFeature;
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30
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31 my $rfeature = Bio::EnsEMBL::Funcgen::Collection::ResultFeature->new_fast({
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32 start => $start,
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33 end => $end,
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34 scores => [ $score ]
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35 });
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36
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37 my @rfeatures = @{$rset->get_displayable_ResultFeatures_by_Slice($slice)};
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38
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39 foreach my $rfeature (@rfeatures){
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40 my $score = $rfeature->score();
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41 my $rf_start = $rfeature->start();
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42 my $rf_end = $rfeature->end();
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43 }
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44
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45 =head1 DESCRIPTION
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46
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47 This is a Collection feature which is designed to store compressed/collected
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48 feature information for a defined window/bin size over a complete seq_region.
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49 Or alternatively a single feature at the natural resolution i.e. window_size == 0.
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50 The complete seq_region collections are cropped to provide a ResultFeature on any
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51 given Slice. ResultFeatures are primarily stored in the result_feature table,
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52 but can also be generated on the fly from unprocessed data in the array result
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53 tables.
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54
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55
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56 =head1 SEE ALSO
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57
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58 Bio::EnsEMBL::Funcgen::DBSQL::ResultFeatureAdaptor
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59 Bio::EnsEMBL::Funcgen::Collector::ResultFeature
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60
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61 =cut
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62
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63
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64 #This is distinct from a normal feature as the collection may have differen attributes and methods from the normal feature
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65 #implementation. For example a Bio::EnsEMBL::Collection::Gene would only have summary information over several genes.
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66 #Altho', unlikely that we'll ever collect genes.
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67
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68 use strict;
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69 use warnings;
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70
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71
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72 package Bio::EnsEMBL::Funcgen::Collection::ResultFeature;
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73 use base ('Bio::EnsEMBL::Feature');#@ISA
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74
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75 #This needs to inherit from Bio::EnsEMBL::Collection
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76 #Which can host some of the below methods
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77
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78 #Reverted to hash implementation as we no longer deal with
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79 #huge amounts of features due to collections.
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80 #This enables use of transform/seq_region_start/end methods
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81 #and enable us to store on slices that do not begin at 1
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82 #Altho need to remove code stipulating this
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83
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84
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85
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86 #To do
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87 #Can we move any of these methods to a base Collection class?
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88 #Should probably now use normal new method with validation?
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89
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90 =head2 new_fast
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91
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92 Args : Array with attributes start, end, strand, scores, probe, result_set_id, window_size, slice IN THAT ORDER.
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93 WARNING: None of these are validated, hence can omit some where not needed
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94 Example : none
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95 Description: Fast and list version of new. Only works if the code is very disciplined.
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96 Returntype : Bio::EnsEMBL::Funcgen::ResultFeature
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97 Exceptions : None
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98 Caller : ResultSetAdaptor
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99 Status : At Risk
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100
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101 =cut
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102
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103 sub new_fast {
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104 #This is agnostic towards to type of reference
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105 return bless ($_[1], $_[0]);
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106
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107 }
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108
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109
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110
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111 =head2 scores
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112
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113 Example : my $score = $rf->score();
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114 Description: Getter of the scores attribute for ResultFeature
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115 objects
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116 Returntype : Arrayref.
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117 Exceptions : None
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118 Caller : General
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119 Status : At Risk
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120
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121 =cut
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122
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123 sub scores {
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124 return $_[0]->{scores};
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125 }
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126
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127
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128
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129 =head2 probe
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130
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131 Example : my $probe = $rf->probe();
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132 Description: Getter of the probe attribute for ResultFeature
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133 objects
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134 Returntype : Bio::EnsEMBL::Funcgen::Probe
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135 Exceptions : None
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136 Caller : General
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137 Status : At Risk - This can only be used for Features with window 0.
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138
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139 =cut
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140
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141 #probe_id is currently not available in the result_feature table, so this would be a result/probe_feature query.
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142
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143 sub probe {
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144 return $_[0]->{probe};
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145 }
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146
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147
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148 sub result_set_id {
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149 return $_[0]->{result_set_id};
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150 }
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151
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152 sub window_size {
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153 return $_[0]->{window_size};
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154 }
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155
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156
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157 sub get_min_max_scores{
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158
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159 if(! defined $_[0]->{'min_max_scores'}){
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160 my @sorted_scores = sort { $a <=> $b } @{$_[0]->{'scores'}};
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161 $_[0]->{'min_max_scores'} = [$sorted_scores[0], $sorted_scores[$#sorted_scores]];
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162 }
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163
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164 return $_[0]->{'min_max_scores'};
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165 }
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166
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167
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168 1;
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169
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