branch-1-6/Bio/Cluster/UniGeneI.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Cluster::UniGeneI.pm
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Andrew Macgregor <andrew at cbbc.murdoch.edu.au>
   8 #
   9 # Copyright Andrew Macgregor, Jo-Ann Stanton, David Green
  10 # Molecular Embryology Group, Anatomy & Structural Biology, University of Otago
  11 # http://anatomy.otago.ac.nz/meg
  12 #
  13 # You may distribute this module under the same terms as perl itself
  14 #
  15 # _history
  16 # April 31, 2002 - Initial implementation by Andrew Macgregor
  17 # POD documentation - main docs before the code
  18
  19 =head1 NAME
  20
  21 Bio::Cluster::UniGeneI - abstract interface of UniGene object
  22
  23 =head1 SYNOPSIS
  24
  25   #
  26
  27 =head1 DESCRIPTION
  28
  29 This is the general interface for a UniGene cluster representation in
  30 Bioperl. You cannot use this module directly, use an implementation
  31 instead.
  32
  33 You can create UniGene cluster objects yourself by instantiating
  34 L<Bio::Cluster::UniGene>. If you read UniGene clusters from a
  35 ClusterIO parser, you will get objects implementing this interface,
  36 most likely instances of said UniGene class.
  37
  38 L<Bio::Cluster::UniGeneI> inherits from L<Bio::ClusterI>, so you can
  39 use it wherever a cluster object is expected.
  40
  41 =head1 FEEDBACK
  42
  43   #
  44
  45 =head2 Mailing Lists
  46
  47 User feedback is an integral part of the evolution of this and other
  48 Bioperl modules. Send your comments and suggestions preferably to one
  49 of the Bioperl mailing lists. Your participation is much appreciated.
  50
  51   bioperl-l@bioperl.org                  - General discussion
  52   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  53
  54 =head2 Support
  55
  56 Please direct usage questions or support issues to the mailing list:
  57
  58 I<bioperl-l@bioperl.org>
  59
  60 rather than to the module maintainer directly. Many experienced and
  61 reponsive experts will be able look at the problem and quickly
  62 address it. Please include a thorough description of the problem
  63 with code and data examples if at all possible.
  64
  65 =head2 Reporting Bugs
  66
  67 Report bugs to the Bioperl bug tracking system to help us keep track
  68 the bugs and their resolution.  Bug reports can be submitted via the
  69 web:
  70
  71   http://bugzilla.open-bio.org/
  72
  73 =head1 AUTHOR - Andrew Macgregor
  74
  75 Email andrew at cbbc.murdoch.edu.au
  76
  77
  78 =head1 APPENDIX
  79
  80
  81 The rest of the documentation details each of the object
  82 methods. Internal methods are usually preceded with a "_".
  83
  84 =cut
  85
  86 # Let the code begin...
  87
  88
  89 package Bio::Cluster::UniGeneI;
  90 use strict;
  91
  92
  93 use base qw(Bio::ClusterI);
  94
  95
  96 =head2 unigene_id
  97
  98  Title   : unigene_id
  99  Usage   : unigene_id();
 100  Function: Returns the unigene_id associated with the object.
 101  Example : $id = $unigene->unigene_id or $unigene->unigene_id($id)
 102  Returns : A string
 103  Args    : None or an id
 104
 105
 106 =cut
 107
 108 sub unigene_id {
 109     my ($self) = @_;
 110     $self->throw_not_implemented;
 111 }
 112
 113
 114
 115 =head2 title
 116
 117  Title   : title
 118  Usage   : title();
 119  Function: Returns the title associated with the object.
 120  Example : $title = $unigene->title or $unigene->title($title)
 121  Returns : A string
 122  Args    : None or a title
 123
 124
 125 =cut
 126
 127 sub title {
 128     my ($self) = @_;
 129     $self->throw_not_implemented;
 130 }
 131
 132
 133 =head2 gene
 134
 135  Title   : gene
 136  Usage   : gene();
 137  Function: Returns the gene associated with the object.
 138  Example : $gene = $unigene->gene or $unigene->gene($gene)
 139  Returns : A string
 140  Args    : None or a gene
 141
 142
 143 =cut
 144
 145 sub gene {
 146     my ($self) = @_;
 147     $self->throw_not_implemented;
 148 }
 149
 150
 151 =head2 cytoband
 152
 153  Title   : cytoband
 154  Usage   : cytoband();
 155  Function: Returns the cytoband associated with the object.
 156  Example : $cytoband = $unigene->cytoband or $unigene->cytoband($cytoband)
 157  Returns : A string
 158  Args    : None or a cytoband
 159
 160
 161 =cut
 162
 163 sub cytoband {
 164     my ($self) = @_;
 165     $self->throw_not_implemented;
 166 }
 167
 168
 169 =head2 mgi
 170
 171  Title   : mgi
 172  Usage   : mgi();
 173  Function: Returns the mgi associated with the object.
 174  Example : $mgi = $unigene->mgi or $unigene->mgi($mgi)
 175  Returns : A string
 176  Args    : None or a mgi
 177
 178
 179 =cut
 180
 181 sub mgi {
 182     my ($self) = @_;
 183     $self->throw_not_implemented;
 184 }
 185
 186
 187 =head2 locuslink
 188
 189  Title   : locuslink
 190  Usage   : locuslink();
 191  Function: Returns or stores a reference to an array containing locuslink data.
 192            This should really only be used by ClusterIO, not directly
 193  Returns : An array reference
 194  Args    : None or an array reference
 195
 196 =cut
 197
 198 sub locuslink {
 199     my ($self) = @_;
 200     $self->throw_not_implemented;
 201 }
 202
 203
 204 =head2 homol
 205
 206  Title   : homol
 207  Usage   : homol();
 208  Function: Returns the homol entry associated with the object.
 209  Example : $homol = $unigene->homol or $unigene->homol($homol)
 210  Returns : A string
 211  Args    : None or a homol entry
 212
 213 =cut
 214
 215 sub homol {
 216     my ($self) = @_;
 217     $self->throw_not_implemented;
 218 }
 219
 220
 221 =head2 restr_expr
 222
 223  Title   : restr_expr
 224  Usage   : restr_expr();
 225  Function: Returns the restr_expr entry associated with the object.
 226  Example : $restr_expr = $unigene->restr_expr or $unigene->restr_expr($restr_expr)
 227  Returns : A string
 228  Args    : None or a restr_expr entry
 229
 230 =cut
 231
 232 sub restr_expr {
 233     my ($self) = @_;
 234     $self->throw_not_implemented;
 235 }
 236
 237
 238 =head2 gnm_terminus
 239
 240  Title   : gnm_terminus
 241  Usage   : gnm_terminus();
 242  Function: Returns the gnm_terminus associated with the object.
 243  Example : $gnm_terminus = $unigene->gnm_terminus or $unigene->gnm_terminus($gnm_terminus)
 244  Returns : A string
 245  Args    : None or a gnm_terminus
 246
 247 =cut
 248
 249 sub gnm_terminus {
 250     my ($self) = @_;
 251     $self->throw_not_implemented;
 252 }
 253
 254
 255 =head2 scount
 256
 257  Title   : scount
 258  Usage   : scount();
 259  Function: Returns the scount associated with the object.
 260  Example : $scount = $unigene->scount or $unigene->scount($scount)
 261  Returns : A string
 262  Args    : None or a scount
 263
 264 =cut
 265
 266 sub scount {
 267     my ($self) = @_;
 268     $self->throw_not_implemented;
 269 }
 270
 271
 272
 273 =head2 express
 274
 275  Title   : express
 276  Usage   : express();
 277  Function: Returns or stores a reference to an array containing tissue expression data.
 278            This should really only be used by ClusterIO, not directly
 279  Returns : An array reference
 280  Args    : None or an array reference
 281
 282 =cut
 283
 284 sub express {
 285     my ($self) = @_;
 286     $self->throw_not_implemented;
 287 }
 288
 289
 290 =head2 chromosome
 291
 292  Title   : chromosome
 293  Usage   : chromosome();
 294  Function: Returns or stores a reference to an array containing chromosome lines
 295            This should really only be used by ClusterIO, not directly
 296  Returns : An array reference
 297  Args    : None or an array reference
 298
 299 =cut
 300
 301 sub chromosome {
 302     my ($self) = @_;
 303     $self->throw_not_implemented;
 304 }
 305
 306
 307 =head2 sts
 308
 309  Title   : sts
 310  Usage   : sts();
 311  Function: Returns or stores a reference to an array containing sts lines
 312            This should really only be used by ClusterIO, not directly
 313  Returns : An array reference
 314  Args    : None or an array reference
 315
 316 =cut
 317
 318 sub sts {
 319     my ($self) = @_;
 320     $self->throw_not_implemented;
 321 }
 322
 323
 324 =head2 txmap
 325
 326  Title   : txmap
 327  Usage   : txmap();
 328  Function: Returns or stores a reference to an array containing txmap lines
 329  Returns : An array reference
 330  Args    : None or an array reference
 331
 332 =cut
 333
 334 sub txmap {
 335     my ($self) = @_;
 336     $self->throw_not_implemented;
 337 }
 338
 339
 340 =head2 protsim
 341
 342  Title   : protsim
 343  Usage   : protsim();
 344  Function: Returns or stores a reference to an array containing protsim lines
 345            This should really only be used by ClusterIO, not directly
 346  Returns : An array reference
 347  Args    : None or an array reference
 348
 349 =cut
 350
 351 sub protsim {
 352     my ($self) = @_;
 353     $self->throw_not_implemented;
 354 }
 355
 356
 357 =head2 sequence
 358
 359  Title   : sequence
 360  Usage   : sequence();
 361  Function: Returns or stores a reference to an array containing sequence data
 362            This should really only be used by ClusterIO, not directly
 363  Returns : An array reference
 364  Args    : None or an array reference
 365
 366 =cut
 367
 368 sub sequence {
 369     my ($self) = @_;
 370     $self->throw_not_implemented;
 371 }
 372
 373 =head2 species
 374
 375  Title   : species
 376  Usage   : $obj->species($newval)
 377  Function: Get the species object for this Unigene cluster.
 378  Example :
 379  Returns : value of species (a L<Bio::Species> object)
 380  Args    :
 381
 382
 383 =cut
 384
 385 sub species{
 386     shift->throw_not_implemented();
 387 }
 388
 389 =head1 Methods inherited from L<Bio::ClusterI>
 390
 391 =cut
 392
 393 =head2 display_id
 394
 395  Title   : display_id
 396  Usage   :
 397  Function: Get/set the display name or identifier for the cluster
 398  Returns : a string
 399  Args    : optional, on set the display ID ( a string)
 400
 401 =cut
 402
 403 =head2 description
 404
 405  Title   : description
 406  Usage   : Bio::ClusterI->description("POLYUBIQUITIN")
 407  Function: get/set for the consensus description of the cluster
 408  Returns : the description string
 409  Args    : Optional the description string
 410
 411 =cut
 412
 413 =head2 size
 414
 415  Title   : size
 416  Usage   : Bio::ClusterI->size();
 417  Function: get/set for the size of the family,
 418            calculated from the number of members
 419  Returns : the size of the family
 420  Args    :
 421
 422 =cut
 423
 424 =head2 cluster_score
 425
 426  Title   : cluster_score
 427  Usage   : $cluster ->cluster_score(100);
 428  Function: get/set for cluster_score which
 429            represent the score in which the clustering
 430            algorithm assigns to this cluster.
 431  Returns : a number
 432
 433 =cut
 434
 435 =head2 get_members
 436
 437  Title   : get_members
 438  Usage   : Bio::ClusterI->get_members(($seq1, $seq2));
 439  Function: retrieve the members of the family by some criteria, for
 440            example :
 441            $cluster->get_members(-species => 'homo sapiens');
 442
 443            Will return all members if no criteria are provided.
 444
 445  Returns : the array of members
 446  Args    :
 447
 448 =cut
 449
 450 1;