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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::DBSQL::MetaCoordContainer;
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22
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23 use strict;
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24 use warnings;
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25
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26 use vars qw(@ISA);
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27 use strict;
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28
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29 use Bio::EnsEMBL::DBSQL::BaseAdaptor;
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30 use Bio::EnsEMBL::Utils::Exception;
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31
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32 @ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
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33
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34 sub new {
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35 my $class = shift;
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36
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37 my $self = $class->SUPER::new(@_);
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38
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39 #
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40 # Retrieve the list of the coordinate systems that features are stored
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41 # in and cache them.
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42 #
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43
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44 my @coord_systems =
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45 @{ $self->db()->dnadb()->get_CoordSystemAdaptor->fetch_all() };
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46
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47 my @cs_ids;
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48 foreach my $cs (@coord_systems) { push( @cs_ids, $cs->dbID() ) }
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49
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50 my $sth = $self->prepare(
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51 'SELECT mc.table_name, mc.coord_system_id, mc.max_length '
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52 . 'FROM meta_coord mc '
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53 . 'WHERE mc.coord_system_id in ('
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54 . join( ',', @cs_ids )
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55 . ')' );
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56
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57 $sth->execute();
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58
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59 while ( my ( $table_name, $cs_id, $max_length ) =
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60 $sth->fetchrow_array() )
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61 {
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62 $table_name = lc($table_name);
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63
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64 $self->{'_feature_cache'}->{$table_name} ||= [];
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65
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66 push( @{ $self->{'_feature_cache'}->{$table_name} }, $cs_id );
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67 $self->{'_max_len_cache'}->{$cs_id}->{$table_name} = $max_length;
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68 }
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69 $sth->finish();
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70
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71 return $self;
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72 } ## end sub new
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73
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74
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75
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76
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77 =head2 fetch_all_CoordSystems_by_feature_type
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78
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79 Arg [1] : string $table - the name of the table to retrieve coord systems
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80 for. E.g. 'gene', 'exon', 'dna_align_feature'
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81 Example : @css = @{$mcc->fetch_all_CoordSystems_by_feature_type('gene')};
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82 Description: This retrieves the list of coordinate systems that features
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83 in a particular table are stored. It is used internally by
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84 the API to perform queries to these tables and to ensure that
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85 features are only stored in appropriate coordinate systems.
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86 Returntype : listref of Bio::EnsEMBL::CoordSystem objects
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87 Exceptions : throw if name argument not provided
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88 Caller : BaseFeatureAdaptor
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89 Status : Stable
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90
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91 =cut
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92
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93 sub fetch_all_CoordSystems_by_feature_type {
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94 my $self = shift;
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95 my $table = lc(shift); #case insensitive matching
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96
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97 throw('Name argument is required') unless $table;
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98
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99 if(!$self->{'_feature_cache'}->{$table}) {
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100 return [];
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101 }
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102
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103 my @cs_ids = @{$self->{'_feature_cache'}->{$table}};
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104 my @coord_systems;
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105
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106 my $csa = $self->db->get_CoordSystemAdaptor();
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107
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108 foreach my $cs_id (@cs_ids) {
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109 my $cs = $csa->fetch_by_dbID($cs_id);
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110
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111 if(!$cs) {
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112 throw("meta_coord table refers to non-existant coord_system $cs_id");
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113 }
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114
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115 push @coord_systems, $cs;
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116 }
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117
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118 return \@coord_systems;
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119 }
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120
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121
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122
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123 =head2 fetch_max_length_by_CoordSystem_feature_type
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124
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125 Arg [1] : Bio::EnsEMBL::CoordSystem $cs
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126 Arg [2] : string $table
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127 Example : $max_len = $mcc->fetch_max_length_by_CoordSystem_feature_type($cs,'gene');
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128 Description: Returns the maximum length of features of a given type in
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129 a given coordinate system.
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130 Returntype : int or undef
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131 Exceptions : throw on incorrect argument
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132 Caller : BaseFeatureAdaptor
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133 Status : Stable
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134
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135 =cut
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136
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137
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138 sub fetch_max_length_by_CoordSystem_feature_type {
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139 my $self = shift;
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140 my $cs = shift;
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141 my $table = shift;
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142
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143 if(!ref($cs) || !$cs->isa('Bio::EnsEMBL::CoordSystem')) {
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144 throw('Bio::EnsEMBL::CoordSystem argument expected');
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145 }
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146
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147 throw("Table name argument is required") unless $table;
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148
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149 return $self->{'_max_len_cache'}->{$cs->dbID()}->{lc($table)};
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150 }
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151
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152
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153
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154 =head2 add_feature_type
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155
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156 Arg [1] : Bio::EnsEMBL::CoordSystem $cs
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157 The coordinate system to associate with a feature table
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158 Arg [2] : string $table - the name of the table in which features of
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159 a given coordinate system will be stored in
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160 Arg [3] : int $length
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161 This length is used to update the max_length in the database
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162 and the internal cache.
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163 Example : $csa->add_feature_table($chr_coord_system, 'gene');
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164 Description: This function tells the coordinate system adaptor that
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165 features from a specified table will be stored in a certain
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166 coordinate system. If this information is not already stored
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167 in the database it will be added.
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168 Returntype : none
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169 Exceptions : none
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170 Caller : BaseFeatureAdaptor
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171 Status : Stable
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172
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173 =cut
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174
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175
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176 sub add_feature_type {
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177 my $self = shift;
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178 my $cs = shift;
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179 my $table = lc(shift);
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180 my $length = shift;
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181 if(!ref($cs) || !$cs->isa('Bio::EnsEMBL::CoordSystem')) {
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182 throw('CoordSystem argument is required.');
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183 }
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184
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185 if(!$table) {
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186 throw('Table argument is required.');
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187 }
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188
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189 my $cs_ids = $self->{'_feature_cache'}->{$table} || [];
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190
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191 my ($exists) = grep {$cs->dbID() == $_} @$cs_ids;
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192 if( $exists ) {
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193 if( !$self->{'_max_len_cache'}->{$cs->dbID()}->{$table} ||
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194 $self->{'_max_len_cache'}->{$cs->dbID()}->{$table} < $length ) {
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195 my $sth = $self->prepare('UPDATE meta_coord ' .
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196 "SET max_length = $length " .
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197 'WHERE coord_system_id = ? ' .
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198 'AND table_name = ? '.
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199 "AND (max_length<$length ".
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200 "OR max_length is null)");
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201 $sth->execute( $cs->dbID(), $table );
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202 $self->{'_max_len_cache'}->{$cs->dbID()}->{$table} = $length;
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203 }
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204 return;
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205 }
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206
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207 #store the new tablename -> coord system relationship in the db
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208 #ignore failures b/c during the pipeline multiple processes may try
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209 #to update this table and only the first will be successful
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210 my $sth = $self->prepare('INSERT IGNORE INTO meta_coord ' .
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211 'SET coord_system_id = ?, ' .
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212 'table_name = ?, ' .
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213 'max_length = ? '
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214 );
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215
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216 $sth->execute($cs->dbID, $table, $length );
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217
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218 #update the internal cache
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219 $self->{'_feature_cache'}->{$table} ||= [];
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220 push @{$self->{'_feature_cache'}->{$table}}, $cs->dbID();
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221 $self->{'_max_len_cache'}->{$cs->dbID()}->{$table} = $length;
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222
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223 return;
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224 }
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225
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226
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227 1;
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