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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::DBSQL::BaseAlignFeatureAdaptor - Abstract Base class for
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24 AlignFeatureAdaptors
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25
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26 =head1 SYNOPSIS
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27
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28 Abstract class, should not be instantiated. Implementation of abstract
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29 methods must be performed by subclasses.
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30
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31 =head1 DESCRIPTION
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32
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33 This is a base adaptor for the align feature adaptors
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34 DnaAlignFeatureAdaptor and ProteinAlignFeatureAdaptor.
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35
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36 =head1 METHODS
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37
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38 =cut
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39
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40 package Bio::EnsEMBL::DBSQL::BaseAlignFeatureAdaptor;
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41 use vars qw(@ISA @EXPORT);
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42 use strict;
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43
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44 use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
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45
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46 @ISA = qw(Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor);
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47
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48 @EXPORT = (@{$DBI::EXPORT_TAGS{'sql_types'}});
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49
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50 =head2 fetch_all_by_Slice_and_hcoverage
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51
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52 Arg [1] : Bio::EnsEMBL::Slice $slice
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53 The slice from which to obtain align features.
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54 Arg [2] : (optional) float $hcoverage
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55 A lower bound for the hcoverage of feats to obtain.
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56 Arg [3] : (optional) string $logic_name
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57 The logic name of the type of features to obtain.
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58 Example : @feats = @{
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59 $adaptor->fetch_all_by_Slice_and_hcoverage( $slice,
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60 50.0 ) };
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61 Description: Returns a listref of features created from the
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62 database which are on the Slice $slice and with a
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63 hcoverage greater than $hcoverage. If logic name
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64 is defined, only features with an analysis of type
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65 $logic_name will be returned.
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66 Returntype : listref of Bio::EnsEMBL::BaseAlignFeatures
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67 in Slice coordinates
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68 Exceptions : none
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69 Caller : general
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70 Status : At Risk
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71
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72 =cut
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73
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74 sub fetch_all_by_Slice_and_hcoverage {
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75 my ( $self, $slice, $hcoverage, $logic_name ) = @_;
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76
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77 my $constraint;
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78 if ( defined($hcoverage) ) {
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79 $constraint = "hcoverage > $hcoverage";
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80 }
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81
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82 return
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83 $self->fetch_all_by_Slice_constraint( $slice, $constraint,
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84 $logic_name );
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85 }
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86
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87 =head2 fetch_all_by_Slice_and_external_db
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88
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89 Arg [1] : Bio::EnsEMBL::Slice $slice
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90 The slice from which to obtain align features.
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91 Arg [2] : String $external_db_name
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92 Name of the external DB to which the align features
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93 should be restricted.
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94 Arg [3] : (optional) string $logic_name
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95 The logic name of the type of features to obtain.
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96 Example : @feats = @{
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97 $adaptor->fetch_all_by_Slice_and_external_db( $slice,
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98 'EMBL' ) };
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99 Description: Returns a listref of features created from the
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100 database which are on the Slice $slice and associated
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101 with external DB $external_db_name. If logic name
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102 is defined, only features with an analysis of type
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103 $logic_name will be returned.
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104 Returntype : listref of Bio::EnsEMBL::BaseAlignFeatures
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105 in Slice coordinates
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106 Exceptions : thrown if $external_db_name is not defined or if
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107 the subclass does not return a table alias for the
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108 external_db table from _tables()
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109 Caller : general
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110 Status : At Risk
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111
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112 =cut
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113
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114 sub fetch_all_by_Slice_and_external_db {
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115 my ( $self, $slice, $external_db_name, $logic_name ) = @_;
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116
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117 if ( !defined($external_db_name) ) {
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118 throw("Need name of external DB to restrict to");
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119 }
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120
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121 my @join_tables = $self->_tables();
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122
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123 my $edb_alias;
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124 foreach my $join_table (@join_tables) {
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125 my ( $table, $table_alias ) = @{$join_table};
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126 if ( $table eq 'external_db' ) {
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127 $edb_alias = $table_alias;
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128 last;
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129 }
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130 }
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131
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132 if ( !defined($edb_alias) ) {
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133 throw("Can not find alias for external_db table");
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134 }
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135
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136 my $constraint = sprintf( "%s.db_name = %s",
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137 $edb_alias,
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138 $self->dbc()->db_handle()
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139 ->quote( $external_db_name, SQL_VARCHAR )
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140 );
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141
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142 return
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143 $self->fetch_all_by_Slice_constraint( $slice, $constraint,
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144 $logic_name );
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145 } ## end sub fetch_all_by_Slice_and_external_db
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146
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147 =head2 fetch_all_by_Slice_and_pid
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148
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149 Arg [1] : Bio::EnsEMBL::Slice $slice
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150 The slice from which to obtain align features.
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151 Arg [2] : (optional) float $pid
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152 A lower bound for the percentage identity of features
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153 to obtain.
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154 Arg [3] : (optional) string $logic_name
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155 The logic name of the type of features to obtain.
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156 Example : @feats =
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157 @{ $adaptor->fetch_all_by_Slice_and_pid( $slice, 50.0 ) };
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158 Description: Returns a listref of features created from the
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159 database which are on the Slice $slice and with a
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160 percentage identity greater than $pid. If logic name
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161 is defined, only features with an analysis of type
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162 $logic_name will be returned.
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163 Returntype : listref of Bio::EnsEMBL::BaseAlignFeatures
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164 in Slice coordinates
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165 Exceptions : none
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166 Caller : general
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167 Status : Stable
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168
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169 =cut
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170
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171 sub fetch_all_by_Slice_and_pid {
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172 my ( $self, $slice, $pid, $logic_name ) = @_;
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173
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174 # #get the primary table alias
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175 # my @tabs = $self->_tables;
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176 # my $alias = $tabs[0]->[1];
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177
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178 # if(defined $pid) {
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179 # $constraint = "${alias}.perc_ident > $pid";
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180 # }
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181
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182 my $constraint;
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183 if ( defined($pid) ) {
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184 $constraint = sprintf( "perc_ident > %s",
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185 $self->dbc()->db_handle()
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186 ->quote( $pid, SQL_FLOAT ) );
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187 }
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188
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189 return
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190 $self->fetch_all_by_Slice_constraint( $slice, $constraint,
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191 $logic_name );
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192 }
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193
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194
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195 =head2 fetch_all_by_hit_name
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196
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197 Arg [1] : string $hit_name
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198 The hit_name of the features to obtain
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199 Arg [2] : (optional) string $logic_name
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200 The analysis logic name of the type of features to
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201 obtain.
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202 Example : @feats =
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203 @{ $adaptor->fetch_all_by_hit_name( $name,
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204 $logic_name ); }
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205 Description: Returns a listref of features created from the
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206 database which correspond to the given hit_name. If
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207 logic name is defined, only features with an analysis
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208 of type $logic_name will be returned.
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209 Returntype : listref of Bio::EnsEMBL::BaseAlignFeatures
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210 Exceptions : thrown if hit_name is not defined
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211 Caller : general
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212 Status : Stable
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213
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214 =cut
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215
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216 sub fetch_all_by_hit_name {
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217 my ( $self, $hit_name, $logic_name ) = @_;
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218
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219 if ( !defined($hit_name) ) {
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220 throw("hit_name argument is required");
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221 }
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222
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223 # Construct a constraint like 't1.hit_name = "123"'
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224 my @tabs = $self->_tables();
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225 my ( $name, $syn ) = @{ $tabs[0] };
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226
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227 my $constraint = sprintf( "%s.hit_name = %s",
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228 $syn,
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229 $self->dbc()->db_handle()->quote( $hit_name, SQL_VARCHAR ) );
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230
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231 if ( defined($logic_name) ) {
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232 # Add the $logic_name constraint
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233 $constraint =
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234 $self->_logic_name_to_constraint( $constraint, $logic_name );
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235 }
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236
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237 return $self->generic_fetch($constraint);
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238 }
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239
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240
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241 =head2 fetch_all_by_hit_name_unversioned
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242
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243 Arg [1] : string $hit_name
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244 The beginning of the hit_name of the features to
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245 obtain, e.g. AA768786 would retrieve AA768786.1,
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246 AA768786.2 etc.
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247 Arg [2] : (optional) string $logic_name
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248 The analysis logic name of the type of features to
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249 obtain.
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250 Example : @feats =
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251 @{ $adaptor->fetch_all_by_hit_name( $name,
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252 $logic_name ) };
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253 Description: Returns a listref of features created from the
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254 database which start with the given hit_name. If
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255 logic name is defined, only features with an analysis
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256 of type $logic_name will be returned.
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257 Returntype : listref of Bio::EnsEMBL::BaseAlignFeatures
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258 Exceptions : thrown if hit_name is not defined
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259 Caller : general
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260 Status : At risk
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261
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262 =cut
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263
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264 sub fetch_all_by_hit_name_unversioned {
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265 my ( $self, $hit_name, $logic_name ) = @_;
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266
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267 if ( !defined($hit_name) ) {
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268 throw("hit_name argument is required");
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269 }
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270 $hit_name =~ s/_/\\_/;
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271
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272 #construct a constraint like 't1.hit_name = "123"'
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273 my @tabs = $self->_tables;
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274 my ( $name, $syn ) = @{ $tabs[0] };
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275
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276 my $constraint = sprintf( "%s.hit_name LIKE %s",
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277 $syn,
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278 $self->dbc()->db_handle()->quote( $hit_name . '.%', SQL_VARCHAR ) );
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279
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280 if ( defined($logic_name) ) {
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281 # Add the $logic_name constraint
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282 $constraint =
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283 $self->_logic_name_to_constraint( $constraint, $logic_name );
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284 }
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285
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286 return $self->generic_fetch($constraint);
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287 }
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288
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289
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290
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291 =head2 fetch_all_by_RawContig_and_pid
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292
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293 Description: DEPRECATED use fetch_all_by_Slice_and_pid instead
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294
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295 =cut
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296
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297 sub fetch_all_by_RawContig_and_pid {
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298 my($self, $contig, $pid, $logic_name) = @_;
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299
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300 my $constraint;
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301
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302 #get the primary table alias
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303 my @tabs = $self->_tables;
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304 my $alias = $tabs[0]->[1];
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305
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306 if(defined $pid) {
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307 $constraint = "${alias}.perc_ident > $pid";
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308 }
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309
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310 return $self->fetch_all_by_RawContig_constraint($contig,
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311 $constraint,
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312 $logic_name);
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313 }
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314
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315
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316
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317
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318 ##implemented by subclasses:
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319 # store
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320 # _tables
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321 # _columns
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322 # _obj_from_hashref
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323
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324
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325
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326 1;
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