|
0
|
1
|
|
|
2 #
|
|
|
3 # Ensembl module for Bio::EnsEMBL::Funcgen::Set
|
|
|
4 #
|
|
|
5
|
|
|
6 =head1 LICENSE
|
|
|
7
|
|
|
8 Copyright (c) 1999-2011 The European Bioinformatics Institute and
|
|
|
9 Genome Research Limited. All rights reserved.
|
|
|
10
|
|
|
11 This software is distributed under a modified Apache license.
|
|
|
12 For license details, please see
|
|
|
13
|
|
|
14 http://www.ensembl.org/info/about/code_licence.html
|
|
|
15
|
|
|
16 =head1 CONTACT
|
|
|
17
|
|
|
18 Please email comments or questions to the public Ensembl
|
|
|
19 developers list at <ensembl-dev@ebi.ac.uk>.
|
|
|
20
|
|
|
21 Questions may also be sent to the Ensembl help desk at
|
|
|
22 <helpdesk@ensembl.org>.
|
|
|
23
|
|
|
24
|
|
|
25 =head1 NAME
|
|
|
26
|
|
|
27 Bio::EnsEMBL::Funcgen::Set - A module to represent a base Set object.
|
|
|
28
|
|
|
29
|
|
|
30 =head1 SYNOPSIS
|
|
|
31
|
|
|
32 use Bio::EnsEMBL::Funcgen::Set;
|
|
|
33
|
|
|
34 @INC = qw (Bio::EnsEMBL::Funcgen::Set)
|
|
|
35
|
|
|
36 sub new {
|
|
|
37 my $caller = shift;
|
|
|
38
|
|
|
39 my $class = ref($caller) || $caller;
|
|
|
40
|
|
|
41 my $self = $class->SUPER::new(@_);
|
|
|
42
|
|
|
43
|
|
|
44 }
|
|
|
45
|
|
|
46 =head1 DESCRIPTION
|
|
|
47
|
|
|
48 A base Set object which provides access common methods available across all Funcgen Set classes.
|
|
|
49
|
|
|
50
|
|
|
51 =cut
|
|
|
52
|
|
|
53 use strict;
|
|
|
54 use warnings;
|
|
|
55
|
|
|
56 package Bio::EnsEMBL::Funcgen::Set;
|
|
|
57
|
|
|
58 use Bio::EnsEMBL::Utils::Argument qw( rearrange );
|
|
|
59 use Bio::EnsEMBL::Utils::Exception qw( throw warning deprecate);
|
|
|
60 use Bio::EnsEMBL::Funcgen::Storable;
|
|
|
61
|
|
|
62 use vars qw(@ISA);
|
|
|
63 @ISA = qw(Bio::EnsEMBL::Funcgen::Storable);
|
|
|
64
|
|
|
65
|
|
|
66 =head2 new
|
|
|
67
|
|
|
68 Example : my $self = $class->SUPER::new(@_);
|
|
|
69 Description: Constructor for Set objects.
|
|
|
70 Returntype : Bio::EnsEMBL::Funcgen::Set
|
|
|
71 Exceptions : None
|
|
|
72 Caller : General
|
|
|
73 Status : At risk
|
|
|
74
|
|
|
75 =cut
|
|
|
76
|
|
|
77 sub new {
|
|
|
78 my $caller = shift;
|
|
|
79
|
|
|
80 my $class = ref($caller) || $caller;
|
|
|
81
|
|
|
82 my $self = $class->SUPER::new(@_);
|
|
|
83
|
|
|
84 #TYPE was never parsed here?
|
|
|
85 #Only in inheritants that used it i.e. FeatureSet
|
|
|
86
|
|
|
87 my ($name, $anal, $ftype, $ctype, $set_type, $fclass, $type)
|
|
|
88 = rearrange(['NAME', 'ANALYSIS', 'FEATURE_TYPE', 'CELL_TYPE', 'SET_TYPE', 'FEATURE_CLASS', 'TYPE'], @_);
|
|
|
89
|
|
|
90 throw('Need to specify a name') if ! defined $name;
|
|
|
91
|
|
|
92 $self->set_type($set_type);
|
|
|
93 $self->feature_class($fclass);
|
|
|
94 $self->feature_class($type) if $type;#Remove this when fully implemented
|
|
|
95 $self->{'name'} = $name;
|
|
|
96 $self->cell_type($ctype) if $ctype;
|
|
|
97 $self->feature_type($ftype) if $ftype;
|
|
|
98
|
|
|
99 if(defined $anal){
|
|
|
100 $self->analysis($anal);
|
|
|
101 }elsif($self->set_type ne 'input'){
|
|
|
102 #Could move this to child Sets and just set analysis here
|
|
|
103 #As with ftype
|
|
|
104 throw('Must pass a valid -analysis parameter for a '.ref($self));
|
|
|
105 }
|
|
|
106
|
|
|
107 return $self;
|
|
|
108 }
|
|
|
109
|
|
|
110
|
|
|
111
|
|
|
112
|
|
|
113
|
|
|
114
|
|
|
115 =head2 name
|
|
|
116
|
|
|
117 Example : my $set->name('SET1');
|
|
|
118 Description: Getter/Setter for the name of this Set.
|
|
|
119 Returntype : string
|
|
|
120 Exceptions : None
|
|
|
121 Caller : General
|
|
|
122 Status : At Risk
|
|
|
123
|
|
|
124 =cut
|
|
|
125
|
|
|
126 sub name {
|
|
|
127 my $self = shift;
|
|
|
128
|
|
|
129 return $self->{'name'};
|
|
|
130 }
|
|
|
131
|
|
|
132 =head2 cell_type
|
|
|
133
|
|
|
134 Example : my $dset_ctype_name = $dset->cell_type->name();
|
|
|
135 Description: Getter for the cell_type for this DataSet.
|
|
|
136 Returntype : Bio::EnsEMBL::Funcgen::CellType
|
|
|
137 Exceptions : throws if arg not valid
|
|
|
138 Caller : General
|
|
|
139 Status : At Risk
|
|
|
140
|
|
|
141 =cut
|
|
|
142
|
|
|
143 sub cell_type {
|
|
|
144 my ($self, $ctype) = @_;
|
|
|
145
|
|
|
146 if(defined $ctype){
|
|
|
147
|
|
|
148 if(! (ref($ctype) eq 'Bio::EnsEMBL::Funcgen::CellType'
|
|
|
149 && $ctype->dbID())){
|
|
|
150 throw('Must pass a valid stored Bio::EnsEMBL::Funcgen::CellType');
|
|
|
151 }
|
|
|
152 $self->{'cell_type'} = $ctype;
|
|
|
153 }
|
|
|
154
|
|
|
155 return $self->{'cell_type'};
|
|
|
156 }
|
|
|
157
|
|
|
158 =head2 feature_type
|
|
|
159
|
|
|
160 Example : my $dset_ftype_name = $dset->feature_type->name();
|
|
|
161 Description: Getter for the feature_type for this DataSet.
|
|
|
162 Returntype : Bio::EnsEMBL::Funcgen::FeatureType
|
|
|
163 Exceptions : Throws if arg not valid
|
|
|
164 Caller : General
|
|
|
165 Status : At Risk
|
|
|
166
|
|
|
167 =cut
|
|
|
168
|
|
|
169 sub feature_type {
|
|
|
170 my ($self, $ftype) = @_;
|
|
|
171
|
|
|
172 if(defined $ftype){
|
|
|
173
|
|
|
174 if(! (ref($ftype) eq 'Bio::EnsEMBL::Funcgen::FeatureType'
|
|
|
175 && $ftype->dbID())){
|
|
|
176 throw('Must pass a valid stored Bio::EnsEMBL::Funcgen::FeatureType');
|
|
|
177 }
|
|
|
178 $self->{'feature_type'} = $ftype;
|
|
|
179 }
|
|
|
180
|
|
|
181
|
|
|
182 return $self->{'feature_type'};
|
|
|
183 }
|
|
|
184
|
|
|
185
|
|
|
186 =head2 feature_class
|
|
|
187
|
|
|
188 Arg[0] : string - feature class e.g. result, annotated, regulatory or external.
|
|
|
189 Example : my $fclass = $dset->feature_class;
|
|
|
190 Description: Getter for the feature_type for this Set.
|
|
|
191 Returntype : string
|
|
|
192 Exceptions : None
|
|
|
193 Caller : General
|
|
|
194 Status : At Risk
|
|
|
195
|
|
|
196 =cut
|
|
|
197
|
|
|
198 #Supercededs type method in FeatureSet
|
|
|
199
|
|
|
200 sub feature_class {
|
|
|
201 my ($self, $fclass) = @_;
|
|
|
202
|
|
|
203 if(defined $fclass){
|
|
|
204
|
|
|
205 #Leave this an implement in inheritants
|
|
|
206 #if(! grep /^${fclass}$/, ('annotated', 'result', 'external', 'regulatory')){
|
|
|
207 # throw("You have no supplied a valid feature class:\t$fclass");
|
|
|
208 #}
|
|
|
209
|
|
|
210 $self->{'feature_class'} = $fclass;
|
|
|
211 }
|
|
|
212
|
|
|
213 return $self->{'feature_class'};
|
|
|
214 }
|
|
|
215
|
|
|
216
|
|
|
217
|
|
|
218 =head2 analysis
|
|
|
219
|
|
|
220 Example : my $anal_name = $set->analysis->logic_name();
|
|
|
221 Description: Getter for the analysis attribute for this Set.
|
|
|
222 Returntype : Bio::EnsEMBL::Analysis
|
|
|
223 Exceptions : None
|
|
|
224 Caller : General
|
|
|
225 Status : At Risk
|
|
|
226
|
|
|
227 =cut
|
|
|
228
|
|
|
229 sub analysis {
|
|
|
230 my $self = shift;
|
|
|
231
|
|
|
232 if(@_){
|
|
|
233 throw('Must pass a valid stored Analysis') if (! (ref($_[0]) eq 'Bio::EnsEMBL::Analysis'
|
|
|
234 && $_[0]->dbID()));
|
|
|
235 $self->{'analysis'} = shift;
|
|
|
236 }
|
|
|
237
|
|
|
238
|
|
|
239 return $self->{'analysis'};
|
|
|
240 }
|
|
|
241
|
|
|
242 =head2 display_label
|
|
|
243
|
|
|
244 Example : print $set->display_label();
|
|
|
245 Description: Getter for the display_label attribute for this Set.
|
|
|
246 This is more appropriate for teh predicted_features of the set.
|
|
|
247 Use the individual display_labels for each raw result set.
|
|
|
248 Returntype : str
|
|
|
249 Exceptions : None
|
|
|
250 Caller : General
|
|
|
251 Status : At Risk
|
|
|
252
|
|
|
253 =cut
|
|
|
254
|
|
|
255 sub display_label {
|
|
|
256 my $self = shift;
|
|
|
257
|
|
|
258
|
|
|
259 #Add display label in table?
|
|
|
260 #Can we aborc ResultSet method into this?
|
|
|
261
|
|
|
262 if(! $self->{'display_label'}){
|
|
|
263
|
|
|
264 #if($self->product_FeatureSet->feature_type->class() eq 'Regulatory Feature'){
|
|
|
265 # $self->{'display_label'} = 'Regulatory Features';
|
|
|
266 #}
|
|
|
267 #else{
|
|
|
268
|
|
|
269 #This only works for annotated/regulatory_feature sets and result sets
|
|
|
270 #Move to other Set classes?
|
|
|
271
|
|
|
272 $self->{'display_label'} = $self->feature_type->name()." -";
|
|
|
273 $self->{'display_label'} .= " ".($self->cell_type->display_label() ||
|
|
|
274 $self->cell_type->description() ||
|
|
|
275 $self->cell_type()->name());
|
|
|
276
|
|
|
277
|
|
|
278 if($self->set_type eq 'result'){
|
|
|
279 $self->{'display_label'} .= " signal";
|
|
|
280 }
|
|
|
281 else{
|
|
|
282 $self->{'display_label'} .= " enriched sites";
|
|
|
283 }
|
|
|
284 }
|
|
|
285
|
|
|
286 return $self->{'display_label'};
|
|
|
287 }
|
|
|
288
|
|
|
289
|
|
|
290
|
|
|
291 =head2 set_type
|
|
|
292
|
|
|
293 Example : my $set_type = $set->set_type;
|
|
|
294 Description: Getter for the Set type for this Set.
|
|
|
295 Returntype : string e.g. result, feature, data, input
|
|
|
296 Exceptions : None
|
|
|
297 Caller : General
|
|
|
298 Status : At Risk
|
|
|
299
|
|
|
300 =cut
|
|
|
301
|
|
|
302 sub set_type {
|
|
|
303 my ($self, $set_type) = @_;
|
|
|
304
|
|
|
305 if(defined $set_type){
|
|
|
306 $self->{'_set_type'} = $set_type;
|
|
|
307 }
|
|
|
308 elsif(! defined $self->{'_set_type'}){
|
|
|
309 my @namespace = split/\:\:/, ref($self);
|
|
|
310 ($self->{'_set_type'} = lc($namespace[$#namespace])) =~ s/set//;
|
|
|
311
|
|
|
312 }
|
|
|
313
|
|
|
314 return $self->{'_set_type'};
|
|
|
315 }
|
|
|
316
|
|
|
317 =head2 type
|
|
|
318
|
|
|
319 Example : my $type = $set->type;
|
|
|
320 Description: Getter for the type for this Set.
|
|
|
321 e.g. annotated, external, regulatory for FeatureSets
|
|
|
322 or
|
|
|
323 array, sequencing for InputSets
|
|
|
324 Currently not applicable to DataSets or ResultSets
|
|
|
325 Exceptions : None
|
|
|
326 Returntype : string
|
|
|
327 Exceptions : None
|
|
|
328 Caller : General
|
|
|
329 Status : At Risk
|
|
|
330
|
|
|
331 =cut
|
|
|
332
|
|
|
333 sub type {
|
|
|
334 my $self = shift;
|
|
|
335
|
|
|
336 deprecate("Please use feature_class instead");
|
|
|
337
|
|
|
338 return $self->feature_class(@_);
|
|
|
339
|
|
|
340 #$self->{'feature_class'} = shift if @_;
|
|
|
341
|
|
|
342 #return $self->{'feature_class'};
|
|
|
343 }
|
|
|
344
|
|
|
345
|
|
|
346
|
|
|
347 1;
|
|
|
348
|
