lib/Bio/Cluster/UniGeneI.pm

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