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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 =head1 NAME
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20
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21 Bio::EnsEMBL::Compara::DnaFragRegion - dnafrag region on one species
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22
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23 =head1 SYNOPSIS
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24
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25 my $slice = $dnafrag_region->slice;
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26 my $dnafrag = $dnafrag_region->dnafrag;
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27 my $genome_db = $dnafrag_region->genome_db;
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28 my $dnafrag_start = $dnafrag_region->dnafrag_start;
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29 my $dnafrag_end = $dnafrag_region->dnafrag_end;
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30 my $dnafrag_strand = $dnafrag_region->dnafrag_strand;
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31 my $length = $dnafrag_region->length;
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32
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33 =head1 DESCRIPTION
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34
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35 DnaFragRegion are the objects underlying the SyntenyRegion objects. Each synteny is
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36 represented as a Bio::EnsEMBL::Compara::SyntenyRegion object. Each of these objects
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37 contain one Bio::EnsEMBL::Compara::DnaFragRegion object per region which defines the
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38 synteny. For instance, for a syntenic region between human and mouse, there will be
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39 one DnaFragRegion object for the human region and another one for the mouse one.
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40
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41 =head1 OBJECT ATTRIBUTES
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42
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43 =over
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44
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45 =item adaptor
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46
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47 Bio::EnsEMBL::Compara::DBSQL::DnaFragRegionAdaptor object to access DB
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48
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49 =item synteny_region_id
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50
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51 corresponds to dnafrag.synteny_region_id (external ref.)
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52
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53 =item dnafrag_id
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54
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55 corresponds to dnafrag.dnafrag_id (external ref.)
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56
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57 =item dnafrag
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58
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59 Bio::EnsEMBL::Compara::DnaFrag object corresponding to dnafrag_id
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60
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61 =item dnafrag_start
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62
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63 corresponds to dnafrag_region.dnafrag_start
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64
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65 =item dnafrag_end
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66
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67 corresponds to dnafrag_region.dnafrag_end
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68
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69 =item dnafrag_strand
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70
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71 corresponds to dnafrag_region.dnafrag_strand
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72
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73 =back
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74
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75 =head1 APPENDIX
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76
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77 The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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78
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79 =cut
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80
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81
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82 package Bio::EnsEMBL::Compara::DnaFragRegion;
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83
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84 use strict;
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85 use Bio::EnsEMBL::Utils::Argument;
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86 use Bio::EnsEMBL::Utils::Exception;
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87
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88 #use Bio::EnsEMBL::Compara::NestedSet;
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89 #our @ISA = qw(Bio::EnsEMBL::Compara::NestedSet);
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90
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91
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92 =head2 new_fast
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93
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94 Arg : possible keys: ADAPTOR, SYNTENY_REGION_ID, DNAFRAG_ID,
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95 DNAFRAG_START, DNAFRAG_END, DNAFRAG_STRAND
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96 See also parent object: Bio::EnsEMBL::Compara::NestedSet
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97 Example : none
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98 Description : Object constructor.
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99 Returntype : Bio::EnsEMBL::Compara::DnaFragRegion object
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100 Exceptions : none
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101 Caller : general
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102
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103 =cut
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104
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105 sub new {
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106 my ($class, @args) = @_;
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107 # my $self = $class->SUPER::new(@args);
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108 my $self = bless {}, $class;
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109
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110 if (scalar @args) {
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111 #do this explicitly.
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112 my ($adaptor, $synteny_region_id, $dnafrag_id, $dnafrag_start, $dnafrag_end, $dnafrag_strand) = rearrange([qw(ADAPTOR SYNTENY_REGION_ID DNAFRAG_ID DNAFRAG_START DNAFRAG_END DNAFRAG_STRAND)], @args);
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113
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114 $adaptor && $self->adaptor($adaptor);
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115 $synteny_region_id && $self->synteny_region_id($synteny_region_id);
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116 $dnafrag_id && $self->dnafrag_id($dnafrag_id);
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117 $dnafrag_start && $self->dnafrag_start($dnafrag_start);
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118 $dnafrag_end && $self->dnafrag_end($dnafrag_end);
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119 $dnafrag_strand && $self->dnafrag_strand($dnafrag_strand);
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120 }
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121
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122 return $self;
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123 }
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124
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125
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126 =head2 new_fast
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127
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128 Arg 1 : hash reference $hashref
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129 Example : none
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130 Description : This is an ultra fast constructor which requires knowledge of
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131 the objects internals to be used.
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132 Returntype : Bio::EnsEMBL::Compara::DnaFragRegion object
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133 Exceptions : none
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134 Caller : general
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135
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136 =cut
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137
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138 sub new_fast {
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139 my ($class, $hashref) = @_;
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140
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141 return bless $hashref, $class;
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142 }
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143
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144
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145 =head2 synteny_region_id
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146
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147 Arg 1 : (optional) integer $synteny_region_id
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148 Example : my $synteny_region_id = $dnafrag->synteny_region_id;
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149 Description : Getter/setter for the synteny_region_id attribute
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150 Returntype : integer
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151 Exceptions : none
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152 Caller : general
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153
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154 =cut
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155
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156 sub synteny_region_id {
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157 my $obj = shift;
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158
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159 if (@_) {
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160 my $value = shift;
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161 $obj->{'synteny_region_id'} = $value;
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162 }
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163
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164 return $obj->{'synteny_region_id'};
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165 }
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166
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167
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168 =head2 dnafrag_id
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169
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170 Arg 1 : (optional) integer $dnafrag_id
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171 Example : my $dnafrag_id = $dnafrag->dnafrag_id;
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172 Description : Getter/setter for the dnafrag_id attribute
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173 Returntype : integer
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174 Exceptions : none
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175 Caller : general
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176
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177 =cut
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178
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179 sub dnafrag_id {
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180 my $obj = shift;
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181
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182 if (@_) {
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183 my $value = shift;
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184 $obj->{'dnafrag_id'} = $value;
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185 }
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186
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187 return $obj->{'dnafrag_id'};
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188 }
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189
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190
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191 =head2 dnafrag_start
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192
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193 Arg 1 : (optional) integer $dnafrag_start
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194 Example : my $dnafrag_start = $dnafrag->dnafrag_start;
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195 Description : Getter/setter for the dnafrag_start attribute
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196 Returntype : integer
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197 Exceptions : none
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198 Caller : general
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199
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200 =cut
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201
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202 sub dnafrag_start {
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203 my $obj = shift;
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204
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205 if (@_) {
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206 my $value = shift;
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207 $obj->{'dnafrag_start'} = $value;
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208 }
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209
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210 return $obj->{'dnafrag_start'};
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211 }
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212
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213
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214 =head2 dnafrag_end
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215
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216 Arg 1 : (optional) integer $dnafrag_end
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217 Example : my $dnafrag_end = $dnafrag->dnafrag_end;
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218 Description : Getter/setter for the dnafrag_end attribute
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219 Returntype : integer
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220 Exceptions : none
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221 Caller : general
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222
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223 =cut
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224
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225 sub dnafrag_end {
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226 my $obj = shift;
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227
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228 if (@_) {
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229 my $value = shift;
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230 $obj->{'dnafrag_end'} = $value;
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231 }
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232
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233 return $obj->{'dnafrag_end'};
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234 }
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235
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236
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237 =head2 dnafrag_strand
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238
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239 Arg 1 : (optional) integer $dnafrag_strand
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240 Example : my $dnafrag_strand = $dnafrag->dnafrag_strand;
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241 Description : Getter/setter for the dnafrag_strand attribute
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242 Returntype : integer (1 or -1)
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243 Exceptions : none
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244 Caller : general
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245
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246 =cut
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247
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248 sub dnafrag_strand {
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249 my $obj = shift;
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250
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251 if (@_) {
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252 my $value = shift;
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253 $obj->{'dnafrag_strand'} = $value;
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254 }
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255
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256 return $obj->{'dnafrag_strand'};
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257 }
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258
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259
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260 =head2 adaptor
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261
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262 Arg 1 : (optional) Bio::EnsEMBL::Compara::DBSQL::DnaFragRegioAdaptor $adaptor
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263 Example : my $adaptor = $dnafrag->adaptor;
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264 Description : Getter/setter for the corresponding
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265 Bio::EnsEMBL::Compara::DBSQL::DnaFragRegioAdaptor object
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266 Returntype : Bio::EnsEMBL::Compara::DBSQL::DnaFragRegioAdaptor object
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267 Exceptions : none
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268 Caller : general
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269
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270 =cut
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271
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272 sub adaptor {
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273 my $obj = shift;
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274
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275 if (@_) {
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276 my $value = shift;
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277 $obj->{'adaptor'} = $value;
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278 }
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279
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280 return $obj->{'adaptor'};
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281 }
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282
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283
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284 =head2 dnafrag
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285
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286 Arg 1 : (optional) Bio::EnsEMBL::Compara::DnaFrag object
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287 Example : $dnafrag = $dnafragregion->dnafrag;
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288 Description : Getter/setter for the Bio::EnsEMBL::Compara::DnaFrag object corresponding to this
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289 Bio::EnsEMBL::Compara::DnaFragRegion object.
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290 Returntype : Bio::EnsEMBL::Compara::Dnafrag object
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291 Exceptions : warns when the corresponding Bio::EnsEMBL::Compara::GenomeDB,
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292 coord_system_name, name or Bio::EnsEMBL::DBSQL::DBAdaptor
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293 cannot be retrieved and returns undef.
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294 Caller : $object->methodname
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295
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296 =cut
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297
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298 sub dnafrag {
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299 my ($self) = shift @_;
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300
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301 if (@_) {
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302 $self->{'_dnafrag'} = shift @_;
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303 } elsif (!defined $self->{'_dnafrag'}) {
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304 if (!defined($self->dnafrag_id)) {
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305 warn "Cannot get the Bio::EnsEMBL::Compara::DnaFrag object without dbID";
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306 return undef;
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307 }
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308 my $dfa = $self->adaptor->db->get_DnaFragAdaptor;
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309 if (!defined($dfa)) {
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310 warn "Cannot get the Bio::EnsEMBL::Compara::DBSQL::DnaFragAdaptor";
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311 return undef;
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312 }
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313 $self->{'_dnafrag'} = $dfa->fetch_by_dbID($self->dnafrag_id);
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314 }
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315 return $self->{'_dnafrag'};
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316 }
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317
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318
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319 =head2 slice
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320
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321 Arg 1 : -none-
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322 Example : $slice = $dnafragregion->slice;
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323 Description : Returns the Bio::EnsEMBL::Slice object corresponding to this
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324 Bio::EnsEMBL::Compara::DnaFrag object.
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325 Returntype : Bio::EnsEMBL::Slice object
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326 Exceptions : warns when the corresponding Bio::EnsEMBL::Compara::GenomeDB,
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327 coord_system_name, name or Bio::EnsEMBL::DBSQL::DBAdaptor
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328 cannot be retrieved and returns undef.
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329 Caller : $object->methodname
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330
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331 =cut
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332
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333 sub slice {
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334 my ($self) = @_;
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335
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336 unless (defined $self->{'_slice'}) {
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337 if (!defined($self->dnafrag->genome_db)) {
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338 warn "Cannot get the Bio::EnsEMBL::Compara::GenomeDB object corresponding to [".$self."]";
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339 return undef;
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340 }
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341 if (!defined($self->dnafrag->coord_system_name)) {
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342 warn "Cannot get the coord_system_name corresponding to [".$self."]";
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343 return undef;
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344 }
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345 if (!defined($self->dnafrag->name)) {
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346 warn "Cannot get the name corresponding to [".$self."]";
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347 return undef;
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348 }
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349 my $dba = $self->dnafrag->genome_db->db_adaptor;
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350 if (!defined($dba)) {
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351 warn "Cannot get the Bio::EnsEMBL::DBSQL::DBAdaptor corresponding to [".$self->dnafrag->genome_db."]";
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352 return undef;
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353 }
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354 $self->{'_slice'} = $dba->get_SliceAdaptor->fetch_by_region($self->dnafrag->coord_system_name, $self->dnafrag->name,$self->dnafrag_start, $self->dnafrag_end, $self->dnafrag_strand);
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355 }
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356
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357 return $self->{'_slice'};
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358 }
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359
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360
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361 =head2 genome_db
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362
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363 Arg 1 : -none-
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364 Example : $genome_db = $dnafragregion->genome_db;
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365 Description : Returns the Bio::EnsEMBL::Compara::GenomeDB object corresponding to this
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366 Bio::EnsEMBL::Compara::DnaFragRegion object. This method is a shortcut
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367 for $dnafragregion->dnafrag->genome_db
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368 Returntype : Bio::EnsEMBL::Compara::GenomeDB object
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369 Exceptions : return undef if no dnafrag can be found for this DnaFragRegion object.
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370 See dnafrag method elsewhere in this document.
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371 Caller : $object->methodname
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372
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373 =cut
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374
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375 sub genome_db {
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376 my ($self) = @_;
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377
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378 if ($self->dnafrag) {
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379 return $self->dnafrag->genome_db;
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380 }
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381
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382 return undef;
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383 }
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384
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385
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386 =head2 length
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387
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388 Arg 1 : -none-
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389 Example : $length = $dnafragregion->length;
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390 Description : Returns the lenght of this DnaFragRegion
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391 Returntype : integer
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392 Exceptions :
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393 Caller : $object->methodname
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394
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395 =cut
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396
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397 sub length {
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398 my ($self) = @_;
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399
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400 return $self->dnafrag_end - $self->dnafrag_start + 1;
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401 }
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402
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403 1;
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