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1 #
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2 # EnsEMBL module for Bio::EnsEMBL::Funcgen::CoordSystem
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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::Funcgen::CoordSystem
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28
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29 =head1 SYNOPSIS
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30
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31 my $db = Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor->new(...);
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32
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33 my $csa = $db->get_CoordSystemAdaptor();
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34
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35 #
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36 # Get default chromosome coord system for the 39_36a DB:
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37 #
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38 my $cs = $csa->fetch_by_name_schema_build_version('chromosome', '39_36a');
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39 my $str = join ':', $cs->name(),$cs->version(),$cs->dbID();
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40 print "$str\n";
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41
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42
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43 =head1 DESCRIPTION
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44
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45 This has been adapted from the core CoordSystem object to accomodate the multi-assembly
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46 aspects of the eFG schema, namely hadnling the schema_build of the referenced core DB.
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47
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48 This is a simple object which contains a few coordinate system attributes:
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49 name, internal identifier, version and schema_build. A coordinate system is
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50 uniquely defined by its name and version and which DB it came from i.e. schema_build.
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51 A version of a coordinate system applies to all sequences within a coordinate system.
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52 This should not be confused with individual sequence versions.
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53
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54 Take for example the Human assembly. The version 'NCBI33' applies to
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55 to all chromosomes in the NCBI33 assembly (that is the entire 'chromosome'
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56 coordinate system). The 'clone' coordinate system in the same database would
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57 have no version however. Although the clone sequences have their own sequence
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58 versions, there is no version which applies to the entire set of clones.
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59
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60 Coordinate system objects are immutable. Their name and version, and other
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61 attributes may not be altered after they are created.
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62
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63 =cut
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64
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65
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66 use strict;
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67 use warnings;
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68
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69 package Bio::EnsEMBL::Funcgen::CoordSystem;
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70
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71 use Bio::EnsEMBL::Storable;
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72
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73 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
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74 use Bio::EnsEMBL::Utils::Exception qw(throw);
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75
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76 use vars qw(@ISA);
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77
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78 @ISA = qw(Bio::EnsEMBL::Storable);
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79
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80 my %warnings;
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81
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82
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83 =head2 new
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84
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85 Arg [..] : List of named arguments:
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86 -NAME - The name of the coordinate system
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87 -VERSION - (optional) The version of the coordinate system.
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88 Note that if the version passed in is undefined,
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89 it will be set to the empty string in the
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90 resulting CoordSystem object.
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91 -RANK - The rank of the coordinate system. The highest
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92 level coordinate system should have rank 1, the
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93 second highest rank 2 and so on. An example of
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94 a high level coordinate system is 'chromosome' an
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95 example of a lower level coordinate system is
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96 'clone'.
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97 -SCHEMA_BUILD - The schema and data build version of the DB of
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98 origin.
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99 -TOP_LEVEL - (optional) Sets whether this is a top-level coord
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100 system. Default = 0. This should only be set to
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101 true if you are creating an artificial toplevel
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102 coordsystem by the name of 'toplevel'
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103 -SEQUENCE_LEVEL - (optional) Sets whether this is a sequence
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104 level coordinate system. Default = 0
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105 -DEFAULT - (optional)
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106 Whether this is the default version of the
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107 coordinate systems of this name. Default = 0
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108 -DBID - (optional) The internal identifier of this
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109 coordinate system
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110 -ADAPTOR - (optional) The adaptor which provides database
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111 interaction for this object
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112 Example : $cs = Bio::EnsEMBL::CoordSystem->new(-NAME => 'chromosome',
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113 -VERSION => 'NCBI33',
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114 -RANK => 1,
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115 -DBID => 1,
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116 -SCHEMA_BUILD => '39_36a',
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117 -ADAPTOR => adaptor,
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118 -DEFAULT => 1,
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119 -SEQUENCE_LEVEL => 0);
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120 Description: Creates a new CoordSystem object representing a coordinate
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121 system.
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122 Returntype : Bio::EnsEMBL::Funcgen::CoordSystem
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123 Exceptions : none
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124 Caller : general
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125 Status : Stable
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126
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127 =cut
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128
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129 sub new {
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130 my $caller = shift;
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131 my $class = ref($caller) || $caller;
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132
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133 my $self = $class->SUPER::new(@_);
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134
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135
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136 #Can we just hadnle schema_build here and call super->new for the rest.
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137 #We will also have to handle the top/default levels issues with multiple DBs
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138
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139
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140 #my ($name, $version, $sbuild, $top_level, $sequence_level, $default, $rank) =
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141 # rearrange(['NAME','VERSION', 'SCHEMA_BUILD','TOP_LEVEL', 'SEQUENCE_LEVEL',
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142 # 'DEFAULT', 'RANK'], @_);
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143
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144 my ($name, $version) = rearrange(['NAME','VERSION'], @_);
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145
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146
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147 throw('A name argument is required') if(! $name);
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148
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149
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150 $version = '' if(!defined($version));
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151
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152
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153 #$top_level = ($top_level) ? 1 : 0;
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154 #$sequence_level = ($sequence_level) ? 1 : 0;
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155 #$default = ($default) ? 1 : 0;
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156 #$rank ||= 0;
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157
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158 #if($top_level) {
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159 # if($rank) {
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160 # throw('RANK argument must be 0 if TOP_LEVEL is 1');
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161 # }
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162
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163 # if($name) {
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164 # if($name ne 'toplevel') {
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165 # throw('The NAME argument must be "toplevel" if TOP_LEVEL is 1')
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166 # }
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167 # } else {
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168 # $name = 'toplevel';
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169 # }
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170
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171 # if($sequence_level) {
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172 # throw("SEQUENCE_LEVEL argument must be 0 if TOP_LEVEL is 1");
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173 # }
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174
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175 # $default = 0;
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176
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177 # } else {
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178 # if(!$rank) {
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179 # throw("RANK argument must be non-zero if not toplevel CoordSystem");
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180 # }
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181 # if($name eq 'toplevel') {
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182 # throw("Cannot name coord system 'toplevel' unless TOP_LEVEL is 1");
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183 # }
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184 # }
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185
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186 # if($rank !~ /^\d+$/) {
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187 # throw('The RANK argument must be a positive integer');
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188 # }
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189
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190
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191 $self->{'core_cache'} = {};
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192 $self->{'version'} = $version;
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193 $self->{'name'} = $name;
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194 #$self->{'schema_build'} = $sbuild;
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195 #$self->{'top_level'} = $top_level;
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196 #$self->{'sequence_level'} = $sequence_level;
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197 #$self->{'default'} = $default;
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198 #$self->{'rank'} = $rank;
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199
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200
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201
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202
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203 return $self;
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204 }
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205
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206
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207 =head2 add_core_coord_system_info
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208
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209 Arg [1] : mandatory hash:
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210
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211 -RANK => $rank,
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212 -SEQUENCE_LEVEL => $seq_lvl,
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213 -DEFAULT => $default,
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214 -SCHEMA_BUILD => $sbuild,
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215 -CORE_COORD_SYSTEM_ID => $ccs_id,
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216 -IS_STORED => $stored_status,
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217
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218 Example : $cs->add_core_coord_system_info(
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219 -RANK => $rank,
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220 -SEQUENCE_LEVEL => $seq_lvl,
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221 -DEFAULT => $default,
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222 -SCHEMA_BUILD => $sbuild,
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223 -CORE_COORD_SYSTEM_ID => $ccs_id,
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224 -IS_STORED => 1,
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225 );
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226
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227 Description: Setter for core coord system information
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228 Returntype : none
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229 Exceptions : throws if:
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230 rank not 0 when toplevel
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231 name not 'TOPLEVEL" when toplevel
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232 sequence level and top level
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233 no schema_build defined
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234 no rank
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235 rank 0 when not toplevel
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236 name 'TOPLEVEL' when not toplevel
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237
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238 Caller : Bio::EnsEMBL::Funcgen::DBSQL::CoordSystemAdaptor and ?
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239 Status : at risk - replace with add_core_CoordSystem? implement top level?
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240
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241 #this does not check name and version!
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242
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243
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244 =cut
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245
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246 sub add_core_coord_system_info {
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247 my ($self) = shift;
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248
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249 my ($sbuild, $top_level, $sequence_level, $default, $rank, $stored, $ccs_id) =
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250 rearrange(['SCHEMA_BUILD','TOP_LEVEL', 'SEQUENCE_LEVEL',
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251 'DEFAULT', 'RANK', 'IS_STORED', 'CORE_COORD_SYSTEM_ID'], @_);
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252
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253
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254 throw('Must provide a schema_build') if ! $sbuild;
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255 throw('Must provide a core_coord_system_id') if ! $ccs_id;
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256
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257
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258 #$top_level = ($top_level) ? 1 : 0;
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259 $sequence_level = ($sequence_level) ? 1 : 0;
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260 $default = ($default) ? 1 : 0;
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261 $stored ||=0;
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262
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263 $rank ||= 0;
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264
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265 if($top_level) {
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266 if($rank) {
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267 throw('RANK argument must be 0 if TOP_LEVEL is 1');
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268 }
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269
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270 if($self->name()) {
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271 if($self->name() ne 'toplevel') {
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272 throw('The NAME argument must be "toplevel" if TOP_LEVEL is 1')
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273 }
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274 } else {
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275 throw('toplevel not yet implemented');
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276 #$name = 'toplevel';
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277 }
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278
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279 if($sequence_level) {
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280 throw("SEQUENCE_LEVEL argument must be 0 if TOP_LEVEL is 1");
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281 }
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282
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283 $default = 0;
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284
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285 } else {
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286 if(!$rank) {
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287 throw("RANK argument must be non-zero if not toplevel CoordSystem");
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288 }
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289 if($self->name() eq 'toplevel') {
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290 throw("Cannot name coord system 'toplevel' unless TOP_LEVEL is 1");
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291 }
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292 }
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293
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294 if($rank !~ /^\d+$/) {
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295 throw('The RANK argument must be a positive integer');
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296 }
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297
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298
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299 #We can add unstored coord systems here
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300 #But will these ever have valid entries in the seq_region cache
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301 #Initialising this cache key turning off the warning in equals about
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302 #Using the nearest coord_system
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303
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304 $self->{'core_cache'}{$sbuild} = {(
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305 RANK => $rank,
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306 SEQUENCE_LEVEL => $sequence_level,
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307 DEFAULT => $default,
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308 CORE_COORD_SYSTEM_ID => $ccs_id,
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309 IS_STORED => $stored,
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310 )};
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311
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312
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313
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314
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315 return;
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316 }
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317
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318
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319 #remove all but schema_buil and equals?
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320 #depends on how we handle levels
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321
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322 =head2 name
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323
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324 Arg [1] : (optional) string $name
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325 Example : print $coord_system->name();
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326 Description: Getter for the name of this coordinate system
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327 Returntype : string
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328 Exceptions : none
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329 Caller : general
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330 Status : Stable
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331
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332 =cut
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333
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334 sub name {
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335 my $self = shift;
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336 return $self->{'name'};
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337 }
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338
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339
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340 =head2 get_latest_schema_build
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341
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342 Example : my $db_schema_build = $coord_system->get_latest_schema_build();
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343 Description: Getter for the most recent schema_build of this coordinate system
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344 Returntype : string
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345 Exceptions : none
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346 Caller : general
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347 Status : at risk
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348
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349 =cut
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350
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351 sub get_latest_schema_build {
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352 my $self = shift;
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353
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354 return (sort (keys %{$self->{'core_cache'}}))[0];
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355 }
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356
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357
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358 =head2 contains_schema_build
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359
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360 Example : if ($coord_system->contains_schema_build('43_36e')){..do some coord system things ..};
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361 Description: Returns true is the CoordSystem maps to the corresponding core CoordSystem
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362 Returntype : Boolean
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363 Exceptions : throws if schema_build not defined
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364 Caller : general
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365 Status : at risk
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366
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367 =cut
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368
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369 sub contains_schema_build {
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370 my ($self, $schema_build) = @_;
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371
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372 throw('Must pass a schema_build') if ! $schema_build;
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373
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374 return (exists $self->{'core_cache'}{$schema_build}) ? 1 : 0;
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375 }
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376
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377 =head2 version
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378
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379 Arg [1] : none
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380 Example : print $coord->version();
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381 Description: Getter/Setter for the version of this coordinate system. This
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382 will return an empty string if no version is defined for this
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383 coordinate system.
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384 Returntype : string
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385 Exceptions : none
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386 Caller : general
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387 Status : Stable
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388
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389 =cut
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390
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391 sub version {
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392 my $self = shift;
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393
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394 return $self->{'version'};
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395 }
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396
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397
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398
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399
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400 =head2 equals
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401
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402 Arg [1] : Bio::EnsEMBL::Funcgen::CoordSystem $cs
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403 The coord system to compare to for equality.
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404 Example : if($coord_sys->equals($other_coord_sys)) { ... }
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405 Description: Compares 2 coordinate systems and returns true if they are
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406 equivalent. The definition of equivalent is sharing the same
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407 name and version.
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408 Returntype : string
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409 Exceptions : none
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410 Caller : general
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411 Status : At risk
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412
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413 =cut
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414
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415 sub equals {
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416 my $self = shift;
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417 my $cs = shift;
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418
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419 if(!$cs || !ref($cs) ||
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420 (! $cs->isa('Bio::EnsEMBL::Funcgen::CoordSystem') &&
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421 ! $cs->isa('Bio::EnsEMBL::CoordSystem'))){
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422 throw('Argument must be a Bio::EnsEMBL::Funcgen::CoordSystem');
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423 }
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424
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425
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426 #need to add check on schema_build here
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427 #all schema_builds should have been added by BaseFeatureAdaptor during import
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428 #fails if we are using two different versions with the same cs's
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429
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430 if(($self->version() eq $cs->version()) &&
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431 ($self->name() eq $cs->name())){
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432
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433 #we need to make sure these are default CS, otherwise we can get into trouble with
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434 #re-used or mismatched seq_region_ids between DB wih different default assemblies
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435
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436 if (! $self->contains_schema_build($self->adaptor->db->_get_schema_build($cs->adaptor()))) {
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437
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438 #Only warn first time this is seen
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439 my $warning_key = $self->adaptor->db->_get_schema_build($cs->adaptor()).':'.$self->name().':'.$self->version;
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440
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441 if(! exists $warnings{$warning_key}){
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442 warn 'You are using a schema_build('.$self->adaptor->db->_get_schema_build($cs->adaptor()).') which has no CoordSystem stored for '.$cs->version.". Defaulting to closest name version match.\n";
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443 $warnings{$warning_key} = 1;
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444 }
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445 }
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446 return 1;
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447 }
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448
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449 return 0;
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450 }
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451
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452
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453
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454
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455 =head2 is_top_level
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456
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457 Arg [1] : none
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458 Example : if($coord_sys->is_top_level()) { ... }
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459 Description: Returns true if this is the toplevel pseudo coordinate system.
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460 The toplevel coordinate system is not a real coordinate system
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461 which is stored in the database, but it is a placeholder that
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462 can be used to request transformations or retrievals to/from
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463 the highest defined coordinate system in a given region.
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464 Returntype : 0 or 1
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465 Exceptions : none
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466 Caller : general
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467 Status : at risk - not implemented yet
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468
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469 =cut
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470
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471 sub is_top_level {
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472 my $self = shift;
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473
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474 throw('Not yet implmented, need to test against the core cache using dnadb/schema_build');
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475
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476 return $self->{'top_level'};
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477 }
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478
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479
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480 #These attribute methods are largely redundant
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481 #is_default is used by Feature Adaptors to restrict features to
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482 #current default assembly for non slice based methods
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483 #Especially redundant now we have implemented this in fetch_all
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484
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485 =head2 is_sequence_level
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486
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487 Arg [1] : Bio::EnsEMBL::DBSQL::DBAdaptor
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488 Example : if($coord_sys->is_sequence_level($dnadb)) { ... }
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489 Description: Returns true if this is a sequence level coordinate system
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490 for a given dnadb
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491 Returntype : 0 or 1
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492 Exceptions : none
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493 Caller : general
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494 Status : at risk
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495
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496 =cut
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497
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498 sub is_sequence_level {
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499 my ($self, $dnadb) = @_;
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500
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501 return $self->get_coord_system_attribute('sequence_level', $dnadb);
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502 }
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503
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504
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505 =head2 is_default
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506
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507 Arg [1] : Bio::EnsEMBL::DBSQL::DBAdaptor
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508 Example : if($coord_sys->is_default($dnadb)) { ... }
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509 Description: Returns true if this coordinate system is the default
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510 version of the coordinate system of this name for a given dnadb.
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511 Returntype : 0 or 1
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512 Exceptions : none
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513 Caller : general - Used
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514 Status : at risk
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515
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516 =cut
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517
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518 sub is_default {
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519 my ($self, $dnadb) = @_;
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520
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521 return $self->get_coord_system_attribute('default', $dnadb);
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522 }
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523
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524 sub get_coord_system_attribute{
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525 my($self, $attr_name, $dnadb) = @_;
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526
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527 if(! ($dnadb && ref($dnadb) && $dnadb->isa('Bio::EnsEMBL::DBSQL::DBAdaptor'))){
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528 throw("You must pass a dnadb to access the CoordSystem attribute:\t $attr_name");
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529 }
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530
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531 my $schema_build = $self->adaptor->db->_get_schema_build($dnadb);
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532
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533 if(! $self->contains_schema_build($schema_build)){
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534 throw("CoordSystem does not contain the schema_build:\t$schema_build");
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535 }
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536
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537 return $self->{'core_cache'}{$schema_build}{uc($attr_name)};
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538
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539 }
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540
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541
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542 =head2 rank
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543
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544 Arg [1] : Bio::EnsEMBL::DBSQL::DBAdaptor
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545 Example : if($cs1->rank($dnadb) < $cs2->rank($dnadb)) {
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546 print $cs1->name(), " is a higher level coord system than",
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547 $cs2->name(), "\n";
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548 }
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549 Description: Returns the rank of this coordinate system for a given dnadb.
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550 A lower number is a higher coordinate system. The highest level coordinate
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551 system has a rank of 1 (e.g. 'chromosome'). The toplevel
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552 pseudo coordinate system has a rank of 0.
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553 Returntype : int
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554 Exceptions : none
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555 Caller : general
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556 Status : at risk - not yet implemented
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557
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558 =cut
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559
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560 sub rank {
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|
561 my ($self, $dnadb) = @_;
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|
562 return $self->get_coord_system_attribute('rank', $dnadb);
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563
|
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|
564 }
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565
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566 1;
|
