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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::Mapper::Coordinate
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24
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25 =head1 SYNOPSIS
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26
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27 =head1 DESCRIPTION
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28
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29 Representation of a mapped region in a sequence; returned from Mapper.pm
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30 when the target region maps on to valid sequence.
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31
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32 =head1 METHODS
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33
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34 =cut
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35
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36 package Bio::EnsEMBL::Mapper::Coordinate;
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37
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38 use strict;
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39
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40 =head2 new
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41
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42 Arg [1] char|int id of object in mapped region
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43 Arg [2] int start of region
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44 Arg [3] int end of region
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45 Arg [4] int strand if region
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46 Arg [5] Bio::EnsEMBL::CoordSystem coordsytem of the region
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47 Function creates a new Coordinate object
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48 Returntype Bio::EnsEMBL::Mapper::Coordinate
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49 Exceptions none
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50 Status Stable
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51
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52 =cut
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53
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54 sub new {
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55 my ( $proto, $id, $start, $end, $strand, $coord_system, $rank ) = @_;
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56
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57 my $class = ref($proto) || $proto;
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58
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59 return
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60 bless( { 'id' => $id,
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61 'start' => $start,
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62 'end' => $end,
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63 'strand' => $strand,
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64 'coord_system' => $coord_system,
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65 'rank' => $rank || 0
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66 },
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67 $class );
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68 }
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69
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70
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71 =head2 start
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72
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73 Arg 1 int $start
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74 start coordinate of object in mapped region
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75 Function getter/setter method
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76 Returntype int
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77 Exceptions none
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78 Caller Bio::EnsEMBL::Mapper::Coordinate
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79 Status Stable
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80
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81 =cut
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82
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83 sub start {
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84 my ( $self, $value ) = @_;
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85
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86 if ( defined($value) ) {
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87 $self->{'start'} = $value;
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88 }
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89
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90 return $self->{'start'};
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91 }
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92
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93
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94 =head2 end
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95
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96 Arg 1 int $end
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97 end coordinate of object in mapped region
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98 Function getter/setter method
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99 Returntype int
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100 Exceptions none
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101 Caller Bio::EnsEMBL::Mapper::Coordinate
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102 Status Stable
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103
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104 =cut
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105
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106 sub end {
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107 my ( $self, $value ) = @_;
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108
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109 if ( defined($value) ) {
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110 $self->{'end'} = $value;
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111 }
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112
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113 return $self->{'end'};
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114 }
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115
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116 =head2 strand
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117
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118 Arg 1 int $strand
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119 strand of object in mapped region
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120 Function getter/setter method
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121 Returntype int
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122 Exceptions none
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123 Caller Bio::EnsEMBL::Mapper::Coordinate
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124 Status Stable
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125
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126 =cut
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127
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128 sub strand {
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129 my ( $self, $value ) = @_;
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130
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131 if ( defined($value) ) {
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132 $self->{'strand'} = $value;
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133 }
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134
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135 return $self->{'strand'};
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136 }
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137
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138 =head2 id
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139
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140 Arg 1 char|int $id
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141 id of object in mapped region
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142 e.g. seq_region_id / seq_region_name
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143 Function getter/setter method
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144 Returntype char|int
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145 Exceptions none
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146 Caller Bio::EnsEMBL::Mapper::Coordinate
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147 Status Stable
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148
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149 =cut
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150
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151 sub id {
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152 my ( $self, $value ) = @_;
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153
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154 if ( defined($value) ) {
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155 $self->{'id'} = $value;
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156 }
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157
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158 return $self->{'id'};
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159 }
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160
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161 =head2 coord_system
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162
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163 Arg 1 Bio::EnsEMBL::CoordSystem
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164 Function getter/setter method
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165 Returntype Bio::EnsEMBL::CoordSystem
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166 Exceptions none
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167 Caller Bio::EnsEMBL::Mapper::Coordinate
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168 Status Stable
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169
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170 =cut
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171
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172 sub coord_system {
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173 my ( $self, $value ) = @_;
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174
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175 if ( defined($value) ) {
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176 $self->{'coord_system'} = $value;
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177 }
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178
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179 return $self->{'coord_system'};
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180 }
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181
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182 =head2 length
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183
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184 Function getter method
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185 Returntype int
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186 Exceptions none
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187 Caller ?
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188 Status Stable
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189
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190 =cut
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191
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192 sub length {
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193 my ($self) = @_;
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194
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195 return $self->{'end'} - $self->{'start'} + 1;
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196 }
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197
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198 sub rank {
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199 my ( $self, $value ) = @_;
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200
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201 if ( defined($value) ) {
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202 $self->{'rank'} = $value;
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203 }
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204
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205 return $self->{'rank'};
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206 }
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207
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208 1;
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