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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::DensityFeature - A feature representing a density, or
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24 precentage coverage etc. in a given region.
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25
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26 =head1 SYNOPSIS
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27
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28 use Bio::EnsEMBL::DensityFeature;
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29
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30 $feature = Bio::EnsEMBL::DensityFeature->new(
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31 -seq_region => $region,
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32 -start => 1,
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33 -end => 1e6,
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34 -density_type => $dt,
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35 -density_value => 98.5
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36 );
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37
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38 =head1 DESCRIPTION
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39
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40 A density feature represents a count, density, or percentage coverage,
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41 etc. for a given region.
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42
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43 This module is part of the Ensembl project http://www.ensembl.org
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44
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45 =head1 METHODS
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46
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47 =cut
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48
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49
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50 use strict;
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51 use warnings;
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52
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53 package Bio::EnsEMBL::DensityFeature;
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54
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55 use Bio::EnsEMBL::Feature;
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56 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
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57 use Bio::EnsEMBL::Utils::Exception qw(throw);
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58 use Bio::EnsEMBL::DensityType;
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59
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60 use vars qw(@ISA);
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61
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62 @ISA = qw(Bio::EnsEMBL::Feature);
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63
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64
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65 =head2 new
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66
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67 Arg [SEQ_REGION] : the sequence over which the density was calculated.
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68
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69 Arg [START] : start point on the seq at which density was calulated.
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70
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71 Arg [END] : end point on the seq at which density was calulated.
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72
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73 Arg [DENSITY_TYPE] : the type of density calculated.
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74
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75 Arg [DENSITY_VALUE] : the density.
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76
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77 Arg [...] : Named arguments passed to superclass
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78 Example : $feature = Bio::EnsEMBL::DensityFeature->new
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79 (-seq_region => $region,
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80 -start => 1,
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81 -end => 1e6,
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82 -density_type => $dt,
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83 -density_value => 98.5)
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84
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85 Description: Creates a new density feature.
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86 Returntype : Bio::EnsEMBL::DensityFeature
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87 Exceptions : throw if invalid density value type is provided
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88 Caller : general
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89 Status : Stable
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90
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91 =cut
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92
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93 sub new {
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94 my $caller = shift;
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95
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96 #allow constructor to be called as class or object method
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97 my $class = ref($caller) || $caller;
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98
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99 my $self = $class->SUPER::new(@_);
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100
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101 my($seq_region, $start, $end, $dt, $dv) =
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102 rearrange(['SEQ_REGION', 'START', 'END', 'DENSITY_TYPE', 'DENSITY_VALUE'],
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103 @_);
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104
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105 throw("Density value must be >= 0.") if($dv < 0);
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106
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107 if(!defined($dt)){
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108 throw("Density Type is NOT optional.");
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109 }
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110
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111 $self->{'density_type'} = $dt;
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112 $self->{'density_value'} = $dv;
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113
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114 $self->{'slice'} = $seq_region;
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115 $self->{'start'} = $start;
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116 $self->{'end'} = $end;
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117
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118
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119 return $self;
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120 }
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121
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122
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123 =head2 new_fast
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124
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125 Arg [...] : none
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126 Example : $feature = Bio::EnsEMBL::DensityFeature->new_fast();
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127 Description: Creates a new density feature.
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128 Returntype : Bio::EnsEMBL::DensityFeature
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129 Exceptions : none
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130 Caller : general
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131 Status : Stable
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132
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133 =cut
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134
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135 sub new_fast{
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136 my $caller = shift;
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137
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138 #allow constructor to be called as class or object method
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139 my $class = ref($caller) || $caller;
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140
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141 my $self = $class->SUPER::new(@_);
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142
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143 return $self;
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144 }
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145
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146
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147 =head2 strand
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148
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149 Arg [1] : none
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150 Example : $strand = $df->strand();
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151 Description: Getter fot the strand attribute. Density features always have
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152 strand 0 and this attribute is not settable.
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153 Returntype : int (always 0)
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154 Exceptions : warning if an attempt is made to set the strand
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155 Caller : general
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156 Status : Stable
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157
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158 =cut
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159
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160 sub strand {
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161 my $self = shift;
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162 warning("DensityFeature strand is not settable") if(@_);
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163 return 0;
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164 }
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165
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166
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167
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168 =head2 density_value
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169
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170 Arg [1] : (optional) float $density_value
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171 Example : $dv = $density_feature->density_value();
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172 Description: Getter/Setter for the density value of this DensityFeature.
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173 The density value may be a count, a percentage, or a coverage
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174 of a feature type in the area defined by this feature.
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175 Returntype : float
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176 Exceptions : throw if a negative density value is provided
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177 Caller : general
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178 Status : Stable
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179
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180 =cut
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181
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182 sub density_value {
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183 my $self = shift;
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184
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185 if(@_) {
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186 my $density_value = shift;
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187 throw("Density value must be >= 0.") if($density_value < 0);
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188 $self->{'density_value'} = $density_value;
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189 }
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190
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191 return $self->{'density_value'};
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192 }
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193
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194
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195
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196 =head2 analysis
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197
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198 Arg [1] : (optional) Bio::EnsEMBL::Analysis $analysis
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199 New value for the analysis of the attached DensityType
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200 Example : print $df->analysis()->logic_name();
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201 Description: Overridden superclass analysis method, to chain to analysis
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202 method on attached DensityType.
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203 Returntype : Bio::EnsEMBL::Analysis
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204 Exceptions : none
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205 Caller : general
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206 Status : Stable
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207
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208 =cut
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209
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210 sub analysis {
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211 my $self = shift;
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212
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213 my $dt = $self->density_type();
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214
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215 return undef if(!$dt);
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216
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217 return $dt->analysis(@_);
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218 }
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219
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220
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221
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222 =head2 density_type
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223
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224 Arg [1] : string $newval (optional)
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225 The new value to set the density_value_type attribute to
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226 Example : $density_value_type = $obj->density_value_type()
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227 Description: Getter/Setter for the density_value_type attribute
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228 Returntype : Bio::EnsEMBL::DensityType
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229 Exceptions : if object passed is not of type DensityType
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230 Caller : general
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231 Status : Stable
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232
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233 =cut
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234
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235 sub density_type{
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236 my $self = shift;
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237 if(@_) {
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238 my $type = shift;
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239 if( !ref $type || !$type->isa("Bio::EnsEMBL::DensityType")){
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240 throw("object passed must be an ensembl DensityType ".
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241 "not a [".ref($type)."]");
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242 }
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243 else{
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244 $self->{'density_type'}=$type;
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245 }
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246 }
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247 return $self->{'density_type'};
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248 }
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249
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250
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251 ###BG########
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252
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253 =head2 scaledvalue
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254
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255 Title : scaledvalue
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256 Usage : $obj->scaledvalue($newval)
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257 Function:
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258 Returns : scalar - object's scaled value
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259 Args : newvalue (optional)
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260 Status : Stable
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261
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262 =cut
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263
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264 sub scaledvalue{
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265 my $obj = shift;
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266 if( @_ ) {
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267 my $scaledvalue = shift;
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268 $obj->{'scaledvalue'} = $scaledvalue;
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269 }
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270 return $obj->{'scaledvalue'};
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271 }
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272
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273
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274
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275 =head2 url
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276
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277 Title : url
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278 Usage : $obj->url($newval)
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279 Function:
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280 Returns : String containing this object's url
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281 Args : newvalue (optional)
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282 Status : Stable
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283
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284
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285 =cut
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286
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287 sub url{
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288 my $obj = shift;
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289 if( @_ ) {
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290 my $url = shift;
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291 $obj->{'url'} = $url;
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292 }
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293 return $obj->{'url'};
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294
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295 }
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296
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297
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298 1;
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