|
0
|
1 #
|
|
|
2 # Ensembl module for Bio::EnsEMBL::Funcgen::ResultFeature
|
|
|
3 #
|
|
|
4
|
|
|
5 =head1 LICENSE
|
|
|
6
|
|
|
7 Copyright (c) 1999-2011 The European Bioinformatics Institute and
|
|
|
8 Genome Research Limited. All rights reserved.
|
|
|
9
|
|
|
10 This software is distributed under a modified Apache license.
|
|
|
11 For license details, please see
|
|
|
12
|
|
|
13 http://www.ensembl.org/info/about/code_licence.html
|
|
|
14
|
|
|
15 =head1 CONTACT
|
|
|
16
|
|
|
17 Please email comments or questions to the public Ensembl
|
|
|
18 developers list at <ensembl-dev@ebi.ac.uk>.
|
|
|
19
|
|
|
20 Questions may also be sent to the Ensembl help desk at
|
|
|
21 <helpdesk@ensembl.org>.
|
|
|
22
|
|
|
23
|
|
|
24 =head1 NAME
|
|
|
25
|
|
|
26 Bio::EnsEMBL::Funcgen::ResultFeature - A module to represent a lightweight ResultFeature object
|
|
|
27
|
|
|
28 =head1 SYNOPSIS
|
|
|
29
|
|
|
30 use Bio::EnsEMBL::Funcgen::ResultFeature;
|
|
|
31
|
|
|
32 my $rfeature = Bio::EnsEMBL::Funcgen::ResultFeature->new_fast([$start, $end, $score ]);
|
|
|
33
|
|
|
34 my @rfeatures = @{$rset->get_displayable_ResultFeature_by_Slice($slice)};
|
|
|
35
|
|
|
36 foreach my $rfeature (@rfeatures){
|
|
|
37 my $score = $rfeature->score();
|
|
|
38 my $rf_start = $rfeature->start();
|
|
|
39 my $rf_end = $rfeature->end();
|
|
|
40 }
|
|
|
41
|
|
|
42 =head1 DESCRIPTION
|
|
|
43
|
|
|
44 This is a very sparse class designed to be as lightweight as possible to enable fast rendering in the web browser.
|
|
|
45 As such only the information absolutely required is contained. Any a piori information is omitted e.g. seq_region_id,
|
|
|
46 this will already be known as ResultFeatures are retrieved via a Slice method in ResultSet via the ResultSetAdaptor,
|
|
|
47 likewise with analysis and experimental_chip information. ResultFeatures are transient objects, in that they are not
|
|
|
48 stored in the DB, but are a very small subset of information from the result and oligo_feature tables. ResultFeatures
|
|
|
49 should only be generated by the ResultSetAdaptor as there is no parameter checking in place.
|
|
|
50
|
|
|
51 =cut
|
|
|
52
|
|
|
53 use strict;
|
|
|
54 use warnings;
|
|
|
55
|
|
|
56 #Could set global named vars here for element names. Would take more memory
|
|
|
57
|
|
|
58 package Bio::EnsEMBL::Funcgen::ResultFeature;
|
|
|
59
|
|
|
60 use base ('Bio::EnsEMBL::Feature');
|
|
|
61
|
|
|
62 =head2 new_fast
|
|
|
63
|
|
|
64 Args : Array with attributes start, end, strand, score, probe, result_set_id, winow_size IN THAT ORDER.
|
|
|
65 WARNING: None of these are validated, hence can omit some where not needed
|
|
|
66 Example : none
|
|
|
67 Description: Fast and list version of new. Only works if the code is very disciplined.
|
|
|
68 Returntype : Bio::EnsEMBL::Funcgen::ResultFeature
|
|
|
69 Exceptions : None
|
|
|
70 Caller : ResultSetAdaptor
|
|
|
71 Status : At Risk
|
|
|
72
|
|
|
73 =cut
|
|
|
74
|
|
|
75 sub new_fast {
|
|
|
76 my ($class, @args) = @_;
|
|
|
77 #return bless ($arrayref, $class);
|
|
|
78
|
|
|
79 #Passing arrayref here may cause problems with changing vars after obj creation
|
|
|
80
|
|
|
81 #warn "in new fast with @args";
|
|
|
82
|
|
|
83 bless \@args, $class;
|
|
|
84 }
|
|
|
85
|
|
|
86
|
|
|
87
|
|
|
88
|
|
|
89 =head2 start
|
|
|
90
|
|
|
91 Example : my $start = $rf->start();
|
|
|
92 Description: Getter of the start attribute for ResultFeature
|
|
|
93 objects.
|
|
|
94 Returntype : int
|
|
|
95 Exceptions : None
|
|
|
96 Caller : General
|
|
|
97 Status : At Risk - Now also sets to enable projection
|
|
|
98
|
|
|
99 =cut
|
|
|
100
|
|
|
101 sub start {
|
|
|
102 $_[0]->[0] = $_[1] if $_[1];
|
|
|
103 $_[0]->[0];
|
|
|
104 }
|
|
|
105
|
|
|
106
|
|
|
107 =head2 end
|
|
|
108
|
|
|
109 Example : my $start = $rf->end();
|
|
|
110 Description: Getter of the end attribute for ResultFeature
|
|
|
111 objects.
|
|
|
112 Returntype : int
|
|
|
113 Exceptions : None
|
|
|
114 Caller : General
|
|
|
115 Status : At Risk - Now also sets to enable projection
|
|
|
116
|
|
|
117 =cut
|
|
|
118
|
|
|
119 sub end {
|
|
|
120 $_[0]->[1] = $_[1] if $_[1];
|
|
|
121 $_[0]->[1];
|
|
|
122 }
|
|
|
123
|
|
|
124
|
|
|
125 #Do we need to chacnge this to strand and have slice strand context, as with start and end
|
|
|
126
|
|
|
127 sub strand { $_[0]->[2];}
|
|
|
128
|
|
|
129 =head2 score
|
|
|
130
|
|
|
131 Example : my $score = $rf->score();
|
|
|
132 Description: Getter of the score attribute for ResultFeature
|
|
|
133 objects
|
|
|
134 Returntype : string/float/double?
|
|
|
135 Exceptions : None
|
|
|
136 Caller : General
|
|
|
137 Status : At Risk
|
|
|
138
|
|
|
139 =cut
|
|
|
140
|
|
|
141 sub score { $_[0]->[3];}
|
|
|
142
|
|
|
143
|
|
|
144 =head2 probe
|
|
|
145
|
|
|
146 Example : my $probe = $rf->probe();
|
|
|
147 Description: Getter of the probe attribute for ResultFeature
|
|
|
148 objects
|
|
|
149 Returntype : Bio::EnsEMBL::Funcgen::Probe
|
|
|
150 Exceptions : None
|
|
|
151 Caller : General
|
|
|
152 Status : At Risk - This can only be used for Features with window 0.
|
|
|
153
|
|
|
154 =cut
|
|
|
155
|
|
|
156 #probe_id is currently not available in the result_feature table, so this would be a result/probe_feature query.
|
|
|
157
|
|
|
158 sub probe { $_[0]->[4];}
|
|
|
159
|
|
|
160
|
|
|
161 #The following are only used for storage and retrieval, hence why they are not included in new_fast which is streamlined
|
|
|
162 #for performance
|
|
|
163 #These have no validation so all thi smust be done in the caller/storer i.e. the adaptor
|
|
|
164
|
|
|
165 sub result_set_id { $_[0]->[5];}
|
|
|
166 sub window_size { $_[0]->[6];}
|
|
|
167
|
|
|
168 #May not ever need this
|
|
|
169 #We pass the slice to store
|
|
|
170 #Don't normally want to remap, so don't need furing fetch
|
|
|
171 #Now also sets for to enable projection
|
|
|
172
|
|
|
173 sub slice {
|
|
|
174 $_[0]->[7] = $_[1] if $_[1];
|
|
|
175 $_[0]->[7];
|
|
|
176 }
|
|
|
177
|
|
|
178
|
|
|
179 #Had to reimplement these as they used direct hash calls rather than acessor
|
|
|
180 #redefined to use accessors to array
|
|
|
181
|
|
|
182 sub length {
|
|
|
183 my $self = shift;
|
|
|
184 return $self->end - $self->start + 1;
|
|
|
185 }
|
|
|
186
|
|
|
187 =head2 move
|
|
|
188
|
|
|
189 Arg [1] : int start
|
|
|
190 Arg [2] : int end
|
|
|
191 Arg [3] : (optional) int strand
|
|
|
192 Example : None
|
|
|
193 Description: Sets the start, end and strand in one call rather than in
|
|
|
194 3 seperate calls to the start(), end() and strand() methods.
|
|
|
195 This is for convenience and for speed when this needs to be
|
|
|
196 done within a tight loop.
|
|
|
197 Returntype : none
|
|
|
198 Exceptions : Thrown is invalid arguments are provided
|
|
|
199 Caller : general
|
|
|
200 Status : Stable
|
|
|
201
|
|
|
202 =cut
|
|
|
203
|
|
|
204 sub move {
|
|
|
205 my $self = shift;
|
|
|
206
|
|
|
207 throw('start and end arguments are required') if(@_ < 2);
|
|
|
208
|
|
|
209 my $start = shift;
|
|
|
210 my $end = shift;
|
|
|
211 my $strand = shift;
|
|
|
212
|
|
|
213 if(defined($start) && defined($end) && $end < $start) {
|
|
|
214 throw('start must be less than or equal to end');
|
|
|
215 }
|
|
|
216 if(defined($strand) && $strand != 0 && $strand != -1 && $strand != 1) {
|
|
|
217 throw('strand must be 0, -1 or 1');
|
|
|
218 }
|
|
|
219
|
|
|
220 $self->[0] = $start;
|
|
|
221 $self->[1] = $end;
|
|
|
222 $self->[2] = $strand if(defined($strand));
|
|
|
223 }
|
|
|
224
|
|
|
225
|
|
|
226
|
|
|
227 =head2 feature_Slice
|
|
|
228
|
|
|
229 Args : none
|
|
|
230 Example : $slice = $feature->feature_Slice()
|
|
|
231 Description: Reimplementation of Bio::EnsEMBL::Feature method to enable
|
|
|
232 assembly mapping
|
|
|
233 Returntype : Bio::EnsEMBL::Slice or undef if this feature has no attached
|
|
|
234 Slice.
|
|
|
235 Exceptions : warning if Feature does not have attached slice.
|
|
|
236 Caller : web drawing code
|
|
|
237 Status : Stable
|
|
|
238
|
|
|
239 =cut
|
|
|
240
|
|
|
241
|
|
|
242 sub feature_Slice {
|
|
|
243 my ($self) = @_;
|
|
|
244
|
|
|
245 my $slice = $self->[7];
|
|
|
246
|
|
|
247 if(!$slice) {
|
|
|
248 warning('Cannot obtain Feature_Slice for feature without attached slice');
|
|
|
249 return undef;
|
|
|
250 }
|
|
|
251
|
|
|
252 return $slice->sub_Slice($self->[0], $self->[1]);
|
|
|
253 }
|
|
|
254
|
|
|
255
|
|
|
256
|
|
|
257 1;
|
|
|
258
|
