comparison variant_effect_predictor/Bio/EnsEMBL/DensityFeature.pm @ 0:1f6dce3d34e0

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author mahtabm
date Thu, 11 Apr 2013 02:01:53 -0400
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1 =head1 LICENSE
2
3 Copyright (c) 1999-2012 The European Bioinformatics Institute and
4 Genome Research Limited. All rights reserved.
5
6 This software is distributed under a modified Apache license.
7 For license details, please see
8
9 http://www.ensembl.org/info/about/code_licence.html
10
11 =head1 CONTACT
12
13 Please email comments or questions to the public Ensembl
14 developers list at <dev@ensembl.org>.
15
16 Questions may also be sent to the Ensembl help desk at
17 <helpdesk@ensembl.org>.
18
19 =cut
20
21 =head1 NAME
22
23 Bio::EnsEMBL::DensityFeature - A feature representing a density, or
24 precentage coverage etc. in a given region.
25
26 =head1 SYNOPSIS
27
28 use Bio::EnsEMBL::DensityFeature;
29
30 $feature = Bio::EnsEMBL::DensityFeature->new(
31 -seq_region => $region,
32 -start => 1,
33 -end => 1e6,
34 -density_type => $dt,
35 -density_value => 98.5
36 );
37
38 =head1 DESCRIPTION
39
40 A density feature represents a count, density, or percentage coverage,
41 etc. for a given region.
42
43 This module is part of the Ensembl project http://www.ensembl.org
44
45 =head1 METHODS
46
47 =cut
48
49
50 use strict;
51 use warnings;
52
53 package Bio::EnsEMBL::DensityFeature;
54
55 use Bio::EnsEMBL::Feature;
56 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
57 use Bio::EnsEMBL::Utils::Exception qw(throw);
58 use Bio::EnsEMBL::DensityType;
59
60 use vars qw(@ISA);
61
62 @ISA = qw(Bio::EnsEMBL::Feature);
63
64
65 =head2 new
66
67 Arg [SEQ_REGION] : the sequence over which the density was calculated.
68
69 Arg [START] : start point on the seq at which density was calulated.
70
71 Arg [END] : end point on the seq at which density was calulated.
72
73 Arg [DENSITY_TYPE] : the type of density calculated.
74
75 Arg [DENSITY_VALUE] : the density.
76
77 Arg [...] : Named arguments passed to superclass
78 Example : $feature = Bio::EnsEMBL::DensityFeature->new
79 (-seq_region => $region,
80 -start => 1,
81 -end => 1e6,
82 -density_type => $dt,
83 -density_value => 98.5)
84
85 Description: Creates a new density feature.
86 Returntype : Bio::EnsEMBL::DensityFeature
87 Exceptions : throw if invalid density value type is provided
88 Caller : general
89 Status : Stable
90
91 =cut
92
93 sub new {
94 my $caller = shift;
95
96 #allow constructor to be called as class or object method
97 my $class = ref($caller) || $caller;
98
99 my $self = $class->SUPER::new(@_);
100
101 my($seq_region, $start, $end, $dt, $dv) =
102 rearrange(['SEQ_REGION', 'START', 'END', 'DENSITY_TYPE', 'DENSITY_VALUE'],
103 @_);
104
105 throw("Density value must be >= 0.") if($dv < 0);
106
107 if(!defined($dt)){
108 throw("Density Type is NOT optional.");
109 }
110
111 $self->{'density_type'} = $dt;
112 $self->{'density_value'} = $dv;
113
114 $self->{'slice'} = $seq_region;
115 $self->{'start'} = $start;
116 $self->{'end'} = $end;
117
118
119 return $self;
120 }
121
122
123 =head2 new_fast
124
125 Arg [...] : none
126 Example : $feature = Bio::EnsEMBL::DensityFeature->new_fast();
127 Description: Creates a new density feature.
128 Returntype : Bio::EnsEMBL::DensityFeature
129 Exceptions : none
130 Caller : general
131 Status : Stable
132
133 =cut
134
135 sub new_fast{
136 my $caller = shift;
137
138 #allow constructor to be called as class or object method
139 my $class = ref($caller) || $caller;
140
141 my $self = $class->SUPER::new(@_);
142
143 return $self;
144 }
145
146
147 =head2 strand
148
149 Arg [1] : none
150 Example : $strand = $df->strand();
151 Description: Getter fot the strand attribute. Density features always have
152 strand 0 and this attribute is not settable.
153 Returntype : int (always 0)
154 Exceptions : warning if an attempt is made to set the strand
155 Caller : general
156 Status : Stable
157
158 =cut
159
160 sub strand {
161 my $self = shift;
162 warning("DensityFeature strand is not settable") if(@_);
163 return 0;
164 }
165
166
167
168 =head2 density_value
169
170 Arg [1] : (optional) float $density_value
171 Example : $dv = $density_feature->density_value();
172 Description: Getter/Setter for the density value of this DensityFeature.
173 The density value may be a count, a percentage, or a coverage
174 of a feature type in the area defined by this feature.
175 Returntype : float
176 Exceptions : throw if a negative density value is provided
177 Caller : general
178 Status : Stable
179
180 =cut
181
182 sub density_value {
183 my $self = shift;
184
185 if(@_) {
186 my $density_value = shift;
187 throw("Density value must be >= 0.") if($density_value < 0);
188 $self->{'density_value'} = $density_value;
189 }
190
191 return $self->{'density_value'};
192 }
193
194
195
196 =head2 analysis
197
198 Arg [1] : (optional) Bio::EnsEMBL::Analysis $analysis
199 New value for the analysis of the attached DensityType
200 Example : print $df->analysis()->logic_name();
201 Description: Overridden superclass analysis method, to chain to analysis
202 method on attached DensityType.
203 Returntype : Bio::EnsEMBL::Analysis
204 Exceptions : none
205 Caller : general
206 Status : Stable
207
208 =cut
209
210 sub analysis {
211 my $self = shift;
212
213 my $dt = $self->density_type();
214
215 return undef if(!$dt);
216
217 return $dt->analysis(@_);
218 }
219
220
221
222 =head2 density_type
223
224 Arg [1] : string $newval (optional)
225 The new value to set the density_value_type attribute to
226 Example : $density_value_type = $obj->density_value_type()
227 Description: Getter/Setter for the density_value_type attribute
228 Returntype : Bio::EnsEMBL::DensityType
229 Exceptions : if object passed is not of type DensityType
230 Caller : general
231 Status : Stable
232
233 =cut
234
235 sub density_type{
236 my $self = shift;
237 if(@_) {
238 my $type = shift;
239 if( !ref $type || !$type->isa("Bio::EnsEMBL::DensityType")){
240 throw("object passed must be an ensembl DensityType ".
241 "not a [".ref($type)."]");
242 }
243 else{
244 $self->{'density_type'}=$type;
245 }
246 }
247 return $self->{'density_type'};
248 }
249
250
251 ###BG########
252
253 =head2 scaledvalue
254
255 Title : scaledvalue
256 Usage : $obj->scaledvalue($newval)
257 Function:
258 Returns : scalar - object's scaled value
259 Args : newvalue (optional)
260 Status : Stable
261
262 =cut
263
264 sub scaledvalue{
265 my $obj = shift;
266 if( @_ ) {
267 my $scaledvalue = shift;
268 $obj->{'scaledvalue'} = $scaledvalue;
269 }
270 return $obj->{'scaledvalue'};
271 }
272
273
274
275 =head2 url
276
277 Title : url
278 Usage : $obj->url($newval)
279 Function:
280 Returns : String containing this object's url
281 Args : newvalue (optional)
282 Status : Stable
283
284
285 =cut
286
287 sub url{
288 my $obj = shift;
289 if( @_ ) {
290 my $url = shift;
291 $obj->{'url'} = $url;
292 }
293 return $obj->{'url'};
294
295 }
296
297
298 1;
299
300
301