|
0
|
1 # $Id: UniGeneI.pm,v 1.9 2002/10/25 22:49:03 lapp Exp $
|
|
|
2 #
|
|
|
3 # BioPerl module for Bio::Cluster::UniGeneI.pm
|
|
|
4 #
|
|
|
5 # Cared for by Andrew Macgregor <andrew@anatomy.otago.ac.nz>
|
|
|
6 #
|
|
|
7 # Copyright Andrew Macgregor, Jo-Ann Stanton, David Green
|
|
|
8 # Molecular Embryology Group, Anatomy & Structural Biology, University of Otago
|
|
|
9 # http://anatomy.otago.ac.nz/meg
|
|
|
10 #
|
|
|
11 # You may distribute this module under the same terms as perl itself
|
|
|
12 #
|
|
|
13 # _history
|
|
|
14 # April 31, 2002 - Initial implementation by Andrew Macgregor
|
|
|
15 # POD documentation - main docs before the code
|
|
|
16
|
|
|
17 =head1 NAME
|
|
|
18
|
|
|
19 Bio::Cluster::UniGeneI - abstract interface of UniGene object
|
|
|
20
|
|
|
21 =head1 SYNOPSIS
|
|
|
22
|
|
|
23 #
|
|
|
24
|
|
|
25 =head1 DESCRIPTION
|
|
|
26
|
|
|
27 This is the general interface for a UniGene cluster representation in Bioperl. You cannot use this module directly, use an implementation instead.
|
|
|
28
|
|
|
29 You can create UniGene cluster objects yourself by instantiating
|
|
|
30 L<Bio::Cluster::UniGene>. If you read UniGene clusters from a
|
|
|
31 ClusterIO parser, you will get objects implementing this interface,
|
|
|
32 most likely instances of said UniGene class.
|
|
|
33
|
|
|
34 L<Bio::Cluster::UniGeneI> inherits from L<Bio::ClusterI>, so you can
|
|
|
35 use it wherever a cluster object is expected.
|
|
|
36
|
|
|
37 =head1 FEEDBACK
|
|
|
38
|
|
|
39 #
|
|
|
40
|
|
|
41 =head2 Mailing Lists
|
|
|
42
|
|
|
43 User feedback is an integral part of the evolution of this and other
|
|
|
44 Bioperl modules. Send your comments and suggestions preferably to one
|
|
|
45 of the Bioperl mailing lists. Your participation is much appreciated.
|
|
|
46
|
|
|
47 bioperl-l@bioperl.org - General discussion
|
|
|
48 http://bio.perl.org/MailList.html - About the mailing lists
|
|
|
49
|
|
|
50 =head2 Reporting Bugs
|
|
|
51
|
|
|
52 Report bugs to the Bioperl bug tracking system to help us keep track
|
|
|
53 the bugs and their resolution. Bug reports can be submitted via email
|
|
|
54 or the web:
|
|
|
55
|
|
|
56 bioperl-bugs@bioperl.org
|
|
|
57 http://bugzilla.bioperl.org/
|
|
|
58
|
|
|
59 =head1 AUTHOR - Andrew Macgregor
|
|
|
60
|
|
|
61 Email andrew@anatomy.otago.ac.nz
|
|
|
62
|
|
|
63
|
|
|
64 =head1 APPENDIX
|
|
|
65
|
|
|
66
|
|
|
67 The rest of the documentation details each of the object
|
|
|
68 methods. Internal methods are usually preceded with a "_".
|
|
|
69
|
|
|
70 =cut
|
|
|
71
|
|
|
72 # Let the code begin...
|
|
|
73
|
|
|
74
|
|
|
75 package Bio::Cluster::UniGeneI;
|
|
|
76 use vars qw(@ISA $VERSION);
|
|
|
77 use strict;
|
|
|
78
|
|
|
79 use Bio::ClusterI;
|
|
|
80
|
|
|
81 $VERSION = '1.0';
|
|
|
82 @ISA = qw(Bio::ClusterI);
|
|
|
83
|
|
|
84
|
|
|
85 =head2 unigene_id
|
|
|
86
|
|
|
87 Title : unigene_id
|
|
|
88 Usage : unigene_id();
|
|
|
89 Function: Returns the unigene_id associated with the object.
|
|
|
90 Example : $id = $unigene->unigene_id or $unigene->unigene_id($id)
|
|
|
91 Returns : A string
|
|
|
92 Args : None or an id
|
|
|
93
|
|
|
94
|
|
|
95 =cut
|
|
|
96
|
|
|
97 sub unigene_id {
|
|
|
98 my ($self) = @_;
|
|
|
99 $self->throw_not_implemented;
|
|
|
100 }
|
|
|
101
|
|
|
102
|
|
|
103
|
|
|
104 =head2 title
|
|
|
105
|
|
|
106 Title : title
|
|
|
107 Usage : title();
|
|
|
108 Function: Returns the title associated with the object.
|
|
|
109 Example : $title = $unigene->title or $unigene->title($title)
|
|
|
110 Returns : A string
|
|
|
111 Args : None or a title
|
|
|
112
|
|
|
113
|
|
|
114 =cut
|
|
|
115
|
|
|
116 sub title {
|
|
|
117 my ($self) = @_;
|
|
|
118 $self->throw_not_implemented;
|
|
|
119 }
|
|
|
120
|
|
|
121
|
|
|
122 =head2 gene
|
|
|
123
|
|
|
124 Title : gene
|
|
|
125 Usage : gene();
|
|
|
126 Function: Returns the gene associated with the object.
|
|
|
127 Example : $gene = $unigene->gene or $unigene->gene($gene)
|
|
|
128 Returns : A string
|
|
|
129 Args : None or a gene
|
|
|
130
|
|
|
131
|
|
|
132 =cut
|
|
|
133
|
|
|
134 sub gene {
|
|
|
135 my ($self) = @_;
|
|
|
136 $self->throw_not_implemented;
|
|
|
137 }
|
|
|
138
|
|
|
139
|
|
|
140 =head2 cytoband
|
|
|
141
|
|
|
142 Title : cytoband
|
|
|
143 Usage : cytoband();
|
|
|
144 Function: Returns the cytoband associated with the object.
|
|
|
145 Example : $cytoband = $unigene->cytoband or $unigene->cytoband($cytoband)
|
|
|
146 Returns : A string
|
|
|
147 Args : None or a cytoband
|
|
|
148
|
|
|
149
|
|
|
150 =cut
|
|
|
151
|
|
|
152 sub cytoband {
|
|
|
153 my ($self) = @_;
|
|
|
154 $self->throw_not_implemented;
|
|
|
155 }
|
|
|
156
|
|
|
157
|
|
|
158 =head2 mgi
|
|
|
159
|
|
|
160 Title : mgi
|
|
|
161 Usage : mgi();
|
|
|
162 Function: Returns the mgi associated with the object.
|
|
|
163 Example : $mgi = $unigene->mgi or $unigene->mgi($mgi)
|
|
|
164 Returns : A string
|
|
|
165 Args : None or a mgi
|
|
|
166
|
|
|
167
|
|
|
168 =cut
|
|
|
169
|
|
|
170 sub mgi {
|
|
|
171 my ($self) = @_;
|
|
|
172 $self->throw_not_implemented;
|
|
|
173 }
|
|
|
174
|
|
|
175
|
|
|
176 =head2 locuslink
|
|
|
177
|
|
|
178 Title : locuslink
|
|
|
179 Usage : locuslink();
|
|
|
180 Function: Returns or stores a reference to an array containing locuslink data.
|
|
|
181 This should really only be used by ClusterIO, not directly
|
|
|
182 Returns : An array reference
|
|
|
183 Args : None or an array reference
|
|
|
184
|
|
|
185 =cut
|
|
|
186
|
|
|
187 sub locuslink {
|
|
|
188 my ($self) = @_;
|
|
|
189 $self->throw_not_implemented;
|
|
|
190 }
|
|
|
191
|
|
|
192
|
|
|
193 =head2 gnm_terminus
|
|
|
194
|
|
|
195 Title : gnm_terminus
|
|
|
196 Usage : gnm_terminus();
|
|
|
197 Function: Returns the gnm_terminus associated with the object.
|
|
|
198 Example : $gnm_terminus = $unigene->gnm_terminus or $unigene->gnm_terminus($gnm_terminus)
|
|
|
199 Returns : A string
|
|
|
200 Args : None or a gnm_terminus
|
|
|
201
|
|
|
202 =cut
|
|
|
203
|
|
|
204 sub gnm_terminus {
|
|
|
205 my ($self) = @_;
|
|
|
206 $self->throw_not_implemented;
|
|
|
207 }
|
|
|
208
|
|
|
209
|
|
|
210 =head2 scount
|
|
|
211
|
|
|
212 Title : scount
|
|
|
213 Usage : scount();
|
|
|
214 Function: Returns the scount associated with the object.
|
|
|
215 Example : $scount = $unigene->scount or $unigene->scount($scount)
|
|
|
216 Returns : A string
|
|
|
217 Args : None or a scount
|
|
|
218
|
|
|
219 =cut
|
|
|
220
|
|
|
221 sub scount {
|
|
|
222 my ($self) = @_;
|
|
|
223 $self->throw_not_implemented;
|
|
|
224 }
|
|
|
225
|
|
|
226
|
|
|
227
|
|
|
228 =head2 express
|
|
|
229
|
|
|
230 Title : express
|
|
|
231 Usage : express();
|
|
|
232 Function: Returns or stores a reference to an array containing tissue expression data.
|
|
|
233 This should really only be used by ClusterIO, not directly
|
|
|
234 Returns : An array reference
|
|
|
235 Args : None or an array reference
|
|
|
236
|
|
|
237 =cut
|
|
|
238
|
|
|
239 sub express {
|
|
|
240 my ($self) = @_;
|
|
|
241 $self->throw_not_implemented;
|
|
|
242 }
|
|
|
243
|
|
|
244
|
|
|
245 =head2 chromosome
|
|
|
246
|
|
|
247 Title : chromosome
|
|
|
248 Usage : chromosome();
|
|
|
249 Function: Returns or stores a reference to an array containing chromosome lines
|
|
|
250 This should really only be used by ClusterIO, not directly
|
|
|
251 Returns : An array reference
|
|
|
252 Args : None or an array reference
|
|
|
253
|
|
|
254 =cut
|
|
|
255
|
|
|
256 sub chromosome {
|
|
|
257 my ($self) = @_;
|
|
|
258 $self->throw_not_implemented;
|
|
|
259 }
|
|
|
260
|
|
|
261
|
|
|
262 =head2 sts
|
|
|
263
|
|
|
264 Title : sts
|
|
|
265 Usage : sts();
|
|
|
266 Function: Returns or stores a reference to an array containing sts lines
|
|
|
267 This should really only be used by ClusterIO, not directly
|
|
|
268 Returns : An array reference
|
|
|
269 Args : None or an array reference
|
|
|
270
|
|
|
271 =cut
|
|
|
272
|
|
|
273 sub sts {
|
|
|
274 my ($self) = @_;
|
|
|
275 $self->throw_not_implemented;
|
|
|
276 }
|
|
|
277
|
|
|
278
|
|
|
279 =head2 txmap
|
|
|
280
|
|
|
281 Title : txmap
|
|
|
282 Usage : txmap();
|
|
|
283 Function: Returns or stores a reference to an array containing txmap lines
|
|
|
284 Returns : An array reference
|
|
|
285 Args : None or an array reference
|
|
|
286
|
|
|
287 =cut
|
|
|
288
|
|
|
289 sub txmap {
|
|
|
290 my ($self) = @_;
|
|
|
291 $self->throw_not_implemented;
|
|
|
292 }
|
|
|
293
|
|
|
294
|
|
|
295 =head2 protsim
|
|
|
296
|
|
|
297 Title : protsim
|
|
|
298 Usage : protsim();
|
|
|
299 Function: Returns or stores a reference to an array containing protsim lines
|
|
|
300 This should really only be used by ClusterIO, not directly
|
|
|
301 Returns : An array reference
|
|
|
302 Args : None or an array reference
|
|
|
303
|
|
|
304 =cut
|
|
|
305
|
|
|
306 sub protsim {
|
|
|
307 my ($self) = @_;
|
|
|
308 $self->throw_not_implemented;
|
|
|
309 }
|
|
|
310
|
|
|
311
|
|
|
312 =head2 sequence
|
|
|
313
|
|
|
314 Title : sequence
|
|
|
315 Usage : sequence();
|
|
|
316 Function: Returns or stores a reference to an array containing sequence data
|
|
|
317 This should really only be used by ClusterIO, not directly
|
|
|
318 Returns : An array reference
|
|
|
319 Args : None or an array reference
|
|
|
320
|
|
|
321 =cut
|
|
|
322
|
|
|
323 sub sequence {
|
|
|
324 my ($self) = @_;
|
|
|
325 $self->throw_not_implemented;
|
|
|
326 }
|
|
|
327
|
|
|
328 =head2 species
|
|
|
329
|
|
|
330 Title : species
|
|
|
331 Usage : $obj->species($newval)
|
|
|
332 Function: Get the species object for this Unigene cluster.
|
|
|
333 Example :
|
|
|
334 Returns : value of species (a L<Bio::Species> object)
|
|
|
335 Args :
|
|
|
336
|
|
|
337
|
|
|
338 =cut
|
|
|
339
|
|
|
340 sub species{
|
|
|
341 shift->throw_not_implemented();
|
|
|
342 }
|
|
|
343
|
|
|
344 =head1 Methods inherited from L<Bio::ClusterI>
|
|
|
345
|
|
|
346 =cut
|
|
|
347
|
|
|
348 =head2 display_id
|
|
|
349
|
|
|
350 Title : display_id
|
|
|
351 Usage :
|
|
|
352 Function: Get/set the display name or identifier for the cluster
|
|
|
353 Returns : a string
|
|
|
354 Args : optional, on set the display ID ( a string)
|
|
|
355
|
|
|
356 =cut
|
|
|
357
|
|
|
358 =head2 description
|
|
|
359
|
|
|
360 Title : description
|
|
|
361 Usage : Bio::ClusterI->description("POLYUBIQUITIN")
|
|
|
362 Function: get/set for the consensus description of the cluster
|
|
|
363 Returns : the description string
|
|
|
364 Args : Optional the description string
|
|
|
365
|
|
|
366 =cut
|
|
|
367
|
|
|
368 =head2 size
|
|
|
369
|
|
|
370 Title : size
|
|
|
371 Usage : Bio::ClusterI->size();
|
|
|
372 Function: get/set for the size of the family,
|
|
|
373 calculated from the number of members
|
|
|
374 Returns : the size of the family
|
|
|
375 Args :
|
|
|
376
|
|
|
377 =cut
|
|
|
378
|
|
|
379 =head2 cluster_score
|
|
|
380
|
|
|
381 Title : cluster_score
|
|
|
382 Usage : $cluster ->cluster_score(100);
|
|
|
383 Function: get/set for cluster_score which
|
|
|
384 represent the score in which the clustering
|
|
|
385 algorithm assigns to this cluster.
|
|
|
386 Returns : a number
|
|
|
387
|
|
|
388 =cut
|
|
|
389
|
|
|
390 =head2 get_members
|
|
|
391
|
|
|
392 Title : get_members
|
|
|
393 Usage : Bio::ClusterI->get_members(($seq1, $seq2));
|
|
|
394 Function: retrieve the members of the family by some criteria, for
|
|
|
395 example :
|
|
|
396 $cluster->get_members(-species => 'homo sapiens');
|
|
|
397
|
|
|
398 Will return all members if no criteria are provided.
|
|
|
399
|
|
|
400 Returns : the array of members
|
|
|
401 Args :
|
|
|
402
|
|
|
403 =cut
|
|
|
404
|
|
|
405 1;
|
