Bio/Phenotype/PhenotypeI.pm

   1 #
   2 # BioPerl module for Bio::Phenotype::PhenotypeI
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Christian M. Zmasek <czmasek-at-burnham.org> or <cmzmasek@yahoo.com>
   7 #
   8 # (c) Christian M. Zmasek, czmasek-at-burnham.org, 2002.
   9 # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002.
  10 #
  11 # You may distribute this module under the same terms as perl itself.
  12 # Refer to the Perl Artistic License (see the license accompanying this
  13 # software package, or see http://www.perl.com/language/misc/Artistic.html)
  14 # for the terms under which you may use, modify, and redistribute this module.
  15 #
  16 # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
  17 # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
  18 # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
  19 #
  20 # You may distribute this module under the same terms as perl itself
  21
  22 # POD documentation - main docs before the code
  23
  24 =head1 NAME
  25
  26 Bio::Phenotype::PhenotypeI - An interface for classes modeling phenotypes
  27
  28 =head1 SYNOPSIS
  29
  30   #get Bio::Phenotype::PhenotypeI somehow
  31
  32   print $phenotype->name(), "\n";
  33   print $phenotype->description(), "\n";
  34
  35   my @keywords = ( "achondroplasia", "dwarfism" );
  36   $phenotype->add_keywords( @keywords );
  37   foreach my $keyword ( $phenotype->each_keyword() ) {
  38        print $keyword, "\n";
  39   }
  40   $phenotype->remove_keywords();
  41
  42
  43   foreach my $gene_symbol ( $phenotype->each_gene_symbol() ) {
  44        print $gene_symbol, "\n";
  45   }
  46
  47   foreach my $corr ( $phenotype->each_Correlate() ) {
  48        # Do something with $corr
  49   }
  50
  51   foreach my $var ( $phenotype->each_Variant() ) {
  52        # Do something with $var (mutation)
  53   }
  54
  55   foreach my $measure ( $phenotype->each_Measure() ) {
  56        # Do something with $measure
  57   }
  58
  59
  60 =head1 DESCRIPTION
  61
  62 This superclass defines common methods for classes modelling phenotypes.
  63 Bio::Phenotype::OMIM::OMIMentry is an example of an instantiable phenotype
  64 class (the design of this interface was partially guided by the need
  65 to model OMIM entries).
  66 Please note. This interface provides methods to associate mutations
  67 (methods "each_Variant", ...) and genotypes (methods "each_Genotype", ...)
  68 with phenotypes. Yet, these aspects might need some future enhancements,
  69 especially since there is no "genotype" class yet.
  70
  71 =head1 FEEDBACK
  72
  73 =head2 Mailing Lists
  74
  75 User feedback is an integral part of the evolution of this and other
  76 Bioperl modules. Send your comments and suggestions preferably to the
  77 Bioperl mailing lists  Your participation is much appreciated.
  78
  79   bioperl-l@bioperl.org                  - General discussion
  80   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  81
  82 =head2 Support
  83
  84 Please direct usage questions or support issues to the mailing list:
  85
  86 I<bioperl-l@bioperl.org>
  87
  88 rather than to the module maintainer directly. Many experienced and
  89 reponsive experts will be able look at the problem and quickly
  90 address it. Please include a thorough description of the problem
  91 with code and data examples if at all possible.
  92
  93 =head2 Reporting Bugs
  94
  95 report bugs to the Bioperl bug tracking system to help us keep track
  96 the bugs and their resolution.  Bug reports can be submitted via the
  97 web:
  98
  99   https://redmine.open-bio.org/projects/bioperl/
 100
 101 =head1 AUTHOR
 102
 103 Christian M. Zmasek
 104
 105 Email: czmasek-at-burnham.org  or  cmzmasek@yahoo.com
 106
 107 WWW:   http://monochrome-effect.net/
 108
 109 Address:
 110
 111   Genomics Institute of the Novartis Research Foundation
 112   10675 John Jay Hopkins Drive
 113   San Diego, CA 92121
 114
 115 =head1 APPENDIX
 116
 117 The rest of the documentation details each of the object
 118 methods. Internal methods are usually preceded with a _
 119
 120 =cut
 121
 122
 123 # Let the code begin...
 124
 125
 126 package Bio::Phenotype::PhenotypeI;
 127 use base qw(Bio::Root::RootI);
 128
 129
 130
 131 =head2 name
 132
 133  Title   : name
 134  Usage   : $obj->name( "r1" );
 135            or
 136            print $obj->name();
 137  Function: Set/get for the name or id of this phenotype.
 138  Returns : A name or id [scalar].
 139  Args    : A name or id [scalar] (optional).
 140
 141 =cut
 142
 143 sub name {
 144     my ( $self ) = @_;
 145
 146     $self->throw_not_implemented();
 147
 148 } # name
 149
 150
 151
 152
 153 =head2 description
 154
 155  Title   : description
 156  Usage   : $obj->description( "This is ..." );
 157            or
 158            print $obj->description();
 159  Function: Set/get for the description of this phenotype.
 160  Returns : A description [scalar].
 161  Args    : A description [scalar] (optional).
 162
 163 =cut
 164
 165 sub description {
 166      my ( $self ) = @_;
 167
 168     $self->throw_not_implemented();
 169
 170 } # description
 171
 172
 173
 174
 175 =head2 species
 176
 177  Title   : species
 178  Usage   : $obj->species( $species );
 179            or
 180            $species = $obj->species();
 181  Function: Set/get for the species of this phenotype.
 182  Returns : A species [Bio::Species].
 183  Args    : A species [Bio::Species] (optional).
 184
 185 =cut
 186
 187 sub species {
 188     my ( $self ) = @_;
 189
 190     $self->throw_not_implemented();
 191
 192 } # species
 193
 194
 195
 196
 197 =head2 comment
 198
 199  Title   : comment
 200  Usage   : $obj->comment( "putative" );
 201            or
 202            print $obj->comment();
 203  Function: Set/get for a comment about this phenotype.
 204  Returns : A comment [scalar].
 205  Args    : A comment [scalar] (optional).
 206
 207 =cut
 208
 209 sub comment {
 210     my ( $self ) = @_;
 211
 212     $self->throw_not_implemented();
 213
 214 } # comment
 215
 216
 217
 218
 219 =head2 each_gene_symbol
 220
 221  Title   : each_gene_symbol()
 222  Usage   : @gs = $obj->each_gene_symbol();
 223  Function: Returns a list of gene symbols [scalars, most likely Strings]
 224            associated with this phenotype.
 225  Returns : A list of scalars.
 226  Args    :
 227
 228 =cut
 229
 230 sub each_gene_symbol {
 231     my ( $self ) = @_;
 232
 233     $self->throw_not_implemented();
 234
 235 } # each_gene_symbol
 236
 237
 238 =head2 add_gene_symbols
 239
 240  Title   : add_gene_symbols
 241  Usage   : $obj->add_gene_symbols( @gs );
 242            or
 243            $obj->add_gene_symbols( $gs );
 244  Function: Pushes one or more gene symbols [scalars, most likely Strings]
 245            into the list of gene symbols.
 246  Returns :
 247  Args    : scalar(s).
 248
 249 =cut
 250
 251 sub add_gene_symbols {
 252     my ( $self ) = @_;
 253
 254     $self->throw_not_implemented();
 255
 256 } # add_gene_symbols
 257
 258
 259 =head2 remove_gene_symbols
 260
 261  Usage   : $obj->remove_gene_symbols();
 262  Function: Deletes (and returns) the list of gene symbols [scalars,
 263            most likely Strings] associated with this phenotype.
 264  Returns : A list of scalars.
 265  Args    :
 266
 267 =cut
 268
 269 sub remove_gene_symbols {
 270     my ( $self ) = @_;
 271
 272     $self->throw_not_implemented();
 273
 274 } # remove_gene_symbols
 275
 276
 277
 278
 279 =head2 each_Variant
 280
 281  Title   : each_Variant()
 282  Usage   : @vs = $obj->each_Variant();
 283  Function: Returns a list of Bio::Variation::VariantI implementing objects
 284            associated with this phenotype.
 285            This is for representing the actual mutation(s) causing this
 286            phenotype.
 287            {* The "variants" data member and its methods will/might need to be
 288            changed/improved in one way or another, CZ 09/06/02 *}
 289  Returns : A list of Bio::Variation::VariantI implementing objects.
 290  Args    :
 291
 292 =cut
 293
 294 sub each_Variant {
 295     my ( $self ) = @_;
 296
 297     $self->throw_not_implemented();
 298
 299 } # each_Variant
 300
 301
 302 =head2 add_Variants
 303
 304  Usage   : $obj->add_Variants( @vs );
 305            or
 306            $obj->add_Variants( $v );
 307  Function: Pushes one or more Bio::Variation::VariantI implementing objects
 308            into the list of Variants.
 309  Returns :
 310  Args    : Bio::Variation::VariantI implementing object(s).
 311
 312 =cut
 313
 314 sub add_Variants {
 315     my ( $self ) = @_;
 316
 317     $self->throw_not_implemented();
 318
 319 } # add_Variants
 320
 321
 322 =head2 remove_Variants
 323
 324  Title   : remove_Variants
 325  Usage   : $obj->remove_Variants();
 326  Function: Deletes (and returns) the list of Bio::Variation::VariantI implementing
 327            objects associated with this phenotype.
 328  Returns : A list of Bio::Variation::VariantI implementing objects.
 329  Args    :
 330
 331 =cut
 332
 333 sub remove_Variants {
 334     my ( $self ) = @_;
 335
 336     $self->throw_not_implemented();
 337
 338 } # remove_Variants
 339
 340
 341
 342
 343 =head2 each_Reference
 344
 345  Title   : each_Reference()
 346  Usage   : @refs = $obj->each_Reference();
 347  Function: Returns a list of Bio::Annotation::Reference objects
 348            associated with this phenotype.
 349  Returns : A list of Bio::Annotation::Reference objects.
 350  Args    :
 351
 352 =cut
 353
 354 sub each_Reference {
 355     my ( $self ) = @_;
 356
 357     $self->throw_not_implemented();
 358
 359 } # each_Reference
 360
 361
 362 =head2 add_References
 363
 364  Title   : add_References
 365  Usage   : $obj->add_References( @refs );
 366            or
 367            $obj->add_References( $ref );
 368  Function: Pushes one or more Bio::Annotation::Reference objects
 369            into the list of References.
 370  Returns :
 371  Args    : Bio::Annotation::Reference object(s).
 372
 373 =cut
 374
 375 sub add_References {
 376     my ( $self ) = @_;
 377
 378     $self->throw_not_implemented();
 379
 380 } # add_References
 381
 382
 383 =head2 remove_References
 384
 385  Title   : remove_References()
 386  Usage   : $obj->remove_References();
 387  Function: Deletes (and returns) the list of Bio::Annotation::Reference objects
 388            associated with this phenotype.
 389  Returns : A list of Bio::Annotation::Reference objects.
 390  Args    :
 391
 392 =cut
 393
 394 sub remove_References {
 395     my ( $self ) = @_;
 396
 397     $self->throw_not_implemented();
 398
 399 } # remove_References
 400
 401
 402
 403
 404 =head2 each_CytoPosition
 405
 406  Title   : each_CytoPosition()
 407  Usage   : @cps = $obj->each_CytoPosition();
 408  Function: Returns a list of Bio::Map::CytoPosition objects
 409            associated with this phenotype.
 410  Returns : A list of Bio::Map::CytoPosition objects.
 411  Args    :
 412
 413 =cut
 414
 415 sub each_CytoPosition {
 416     my ( $self ) = @_;
 417
 418     $self->throw_not_implemented();
 419
 420 } # each_CytoPosition
 421
 422
 423 =head2 add_CytoPositions
 424
 425  Title   : add_CytoPositions
 426  Usage   : $obj->add_CytoPositions( @cps );
 427            or
 428            $obj->add_CytoPositions( $cp );
 429  Function: Pushes one or more Bio::Map::CytoPosition objects
 430            into the list of CytoPositions.
 431  Returns :
 432  Args    : Bio::Map::CytoPosition object(s).
 433
 434 =cut
 435
 436 sub add_CytoPositions {
 437     my ( $self ) = @_;
 438
 439     $self->throw_not_implemented();
 440
 441 } # add_CytoPositions
 442
 443
 444 =head2 remove_CytoPositions
 445
 446  Title   : remove_CytoPositions
 447  Usage   : $obj->remove_CytoPositions();
 448  Function: Deletes (and returns) the list o fBio::Map::CytoPosition objects
 449            associated with this phenotype.
 450  Returns : A list of Bio::Map::CytoPosition objects.
 451  Args    :
 452
 453 =cut
 454
 455 sub remove_CytoPositions {
 456     my ( $self ) = @_;
 457
 458     $self->throw_not_implemented();
 459
 460 } # remove_CytoPositions
 461
 462
 463
 464
 465 =head2 each_Correlate
 466
 467  Title   : each_Correlate()
 468  Usage   : @corrs = $obj->each_Correlate();
 469  Function: Returns a list of Bio::Phenotype::Correlate objects
 470            associated with this phenotype.
 471            (Correlates are correlating phenotypes in different species;
 472            inspired by mouse correlates of human phenotypes in the OMIM
 473            database.)
 474  Returns : A list of Bio::Phenotype::Correlate objects.
 475  Args    :
 476
 477 =cut
 478
 479 sub each_Correlate {
 480     my ( $self ) = @_;
 481
 482     $self->throw_not_implemented();
 483
 484 } # each_Correlate
 485
 486
 487
 488
 489 =head2 add_Correlates
 490
 491  Title   : add_Correlates
 492  Usage   : $obj->add_Correlates( @corrs );
 493            or
 494            $obj->add_Correlates( $corr );
 495  Function: Pushes one or more Bio::Phenotype::Correlate objects
 496            into the list of Correlates.
 497  Returns :
 498  Args    : Bio::Phenotype::Correlate object(s).
 499
 500 =cut
 501
 502 sub add_Correlates {
 503     my ( $self ) = @_;
 504
 505     $self->throw_not_implemented();
 506
 507 } # add_Correlates
 508
 509
 510 =head2 remove_Correlates
 511
 512  Title   : remove_Correlates
 513  Usage   : $obj->remove_Correlates();
 514  Function: Deletes (and returns) the list of Bio::Phenotype::Correlate objects
 515            associated with this phenotype.
 516  Returns : A list of Bio::Phenotype::Correlate objects.
 517  Args    :
 518
 519 =cut
 520
 521 sub remove_Correlates {
 522     my ( $self ) = @_;
 523
 524     $self->throw_not_implemented();
 525
 526 } # remove_Correlates
 527
 528
 529
 530
 531 =head2 each_Measure
 532
 533  Title   : each_Measure()
 534  Usage   : @ms = $obj->each_Measure();
 535  Function: Returns a list of Bio::Phenotype::Measure objects
 536            associated with this phenotype.
 537            (Measure is for biochemically defined phenotypes
 538            or any other types of measures.)
 539  Returns : A list of Bio::Phenotype::Measure objects.
 540  Args    :
 541
 542 =cut
 543
 544 sub each_Measure {
 545     my ( $self ) = @_;
 546
 547     $self->throw_not_implemented();
 548
 549 } # each_Measure
 550
 551
 552 =head2 add_Measures
 553
 554  Title   : add_Measures
 555  Usage   : $obj->add_Measures( @ms );
 556            or
 557            $obj->add_Measures( $m );
 558  Function: Pushes one or more Bio::Phenotype::Measure objects
 559            into the list of Measures.
 560  Returns :
 561  Args    : Bio::Phenotype::Measure object(s).
 562
 563 =cut
 564
 565 sub add_Measures {
 566     my ( $self ) = @_;
 567
 568     $self->throw_not_implemented();
 569
 570 } # add_Measures
 571
 572
 573 =head2 remove_Measures
 574
 575  Title   : remove_Measures
 576  Usage   : $obj->remove_Measures();
 577  Function: Deletes (and returns) the list of Bio::Phenotype::Measure objects
 578            associated with this phenotype.
 579  Returns : A list of Bio::Phenotype::Measure objects.
 580  Args    :
 581
 582 =cut
 583
 584 sub remove_Measures {
 585     my ( $self ) = @_;
 586
 587     $self->throw_not_implemented();
 588
 589 } # remove_Measures
 590
 591
 592
 593
 594 =head2 each_keyword
 595
 596  Title   : each_keyword()
 597  Usage   : @kws = $obj->each_keyword();
 598  Function: Returns a list of key words [scalars, most likely Strings]
 599            associated with this phenotype.
 600  Returns : A list of scalars.
 601  Args    :
 602
 603 =cut
 604
 605 sub each_keyword {
 606     my ( $self ) = @_;
 607
 608     $self->throw_not_implemented();
 609
 610 } # each_keyword
 611
 612
 613 =head2 add_keywords
 614
 615  Title   : add_keywords
 616  Usage   : $obj->add_keywords( @kws );
 617            or
 618            $obj->add_keywords( $kw );
 619  Function: Pushes one or more keywords [scalars, most likely Strings]
 620            into the list of key words.
 621  Returns :
 622  Args    : scalar(s).
 623
 624 =cut
 625
 626 sub add_keywords {
 627     my ( $self ) = @_;
 628
 629     $self->throw_not_implemented();
 630
 631 } # add_keywords
 632
 633
 634 =head2 remove_keywords
 635
 636  Title   : remove_keywords
 637  Usage   : $obj->remove_keywords();
 638  Function: Deletes (and returns) the list of key words [scalars,
 639            most likely Strings] associated with this phenotype.
 640  Returns : A list of scalars.
 641  Args    :
 642
 643 =cut
 644
 645 sub remove_keywords {
 646     my ( $self ) = @_;
 647
 648     $self->throw_not_implemented();
 649
 650 } # remove_keywords
 651
 652
 653
 654
 655 =head2 each_DBLink
 656
 657  Title   : each_DBLink()
 658  Usage   : @dbls = $obj->each_DBLink();
 659  Function: Returns a list of Bio::Annotation::DBLink objects
 660            associated with this phenotype.
 661  Returns : A list of Bio::Annotation::DBLink objects.
 662  Args    :
 663
 664 =cut
 665
 666 sub each_DBLink {
 667     my ( $self ) = @_;
 668
 669     $self->throw_not_implemented();
 670
 671 }
 672
 673
 674 =head2 add_DBLinks
 675
 676  Title   : add_DBLinks
 677  Usage   : $obj->add_DBLinks( @dbls );
 678            or
 679            $obj->add_DBLinks( $dbl );
 680  Function: Pushes one or more Bio::Annotation::DBLink objects
 681            into the list of DBLinks.
 682  Returns :
 683  Args    : Bio::Annotation::DBLink object(s).
 684
 685 =cut
 686
 687 sub add_DBLinks {
 688     my ( $self ) = @_;
 689
 690     $self->throw_not_implemented();
 691
 692 } # add_DBLinks
 693
 694
 695 =head2 remove_DBLinks
 696
 697  Title   : remove_DBLinks
 698  Usage   : $obj->remove_DBLinks();
 699  Function: Deletes (and returns) the list of Bio::Annotation::DBLink objects
 700            associated with this phenotype.
 701  Returns : A list of Bio::Annotation::DBLink objects.
 702  Args    :
 703
 704 =cut
 705
 706 sub remove_DBLinks {
 707     my ( $self ) = @_;
 708
 709     $self->throw_not_implemented();
 710
 711 } # remove_DBLinks
 712
 713
 714
 715
 716 =head2 each_Genotype
 717
 718  Title   : each_Reference()
 719  Usage   : @gts = $obj->each_Reference();
 720  Function: Returns a list of "Genotype" objects
 721            associated with this phenotype.
 722            {* the "genotypes" data member and its methods certainly will/needs to be
 723            changed/improved in one way or another since there is
 724            no "Genotype" class yet, CZ 09/06/02 *}
 725  Returns : A list of "Genotype" objects.
 726  Args    :
 727
 728 =cut
 729
 730 sub each_Genotype {
 731     my ( $self ) = @_;
 732
 733     $self->throw_not_implemented();
 734
 735 } # each_Genotype
 736
 737
 738 =head2 add_Genotypes
 739
 740  Title   : add_Genotypes
 741  Usage   : $obj->add_Genotypes( @gts );
 742            or
 743            $obj->add_Genotypes( $gt );
 744  Function: Pushes one or more "Genotypes"
 745            into the list of "Genotypes".
 746  Returns :
 747  Args    : "Genotypes(s)".
 748
 749 =cut
 750
 751 sub add_Genotypes {
 752     my ( $self ) = @_;
 753
 754     $self->throw_not_implemented();
 755
 756 } # add_Genotypes
 757
 758
 759 =head2 remove_Genotypes
 760
 761  Title   : remove_Genotypes
 762  Usage   : $obj->remove_Genotypes();
 763  Function: Deletes (and returns) the list of "Genotype" objects
 764            associated with this phenotype.
 765  Returns : A list of "Genotype" objects.
 766  Args    :
 767
 768 =cut
 769
 770 sub remove_Genotypes {
 771     my ( $self ) = @_;
 772
 773     $self->throw_not_implemented();
 774
 775 } # remove_Genotypes
 776
 777
 778
 779
 780
 781 1;