Bio/Phenotype/Phenotype.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Phenotype::Phenotype
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Christian M. Zmasek <czmasek@gnf.org> or <cmzmasek@yahoo.com>
   8 #
   9 # (c) Christian M. Zmasek, czmasek@gnf.org, 2002.
  10 # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002.
  11 #
  12 # You may distribute this module under the same terms as perl itself.
  13 # Refer to the Perl Artistic License (see the license accompanying this
  14 # software package, or see http://www.perl.com/language/misc/Artistic.html)
  15 # for the terms under which you may use, modify, and redistribute this module.
  16 #
  17 # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
  18 # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
  19 # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
  20 #
  21 # You may distribute this module under the same terms as perl itself
  22
  23 # POD documentation - main docs before the code
  24
  25 =head1 NAME
  26
  27 Bio::Phenotype::Phenotype - A class for modeling phenotypes
  28
  29 =head1 SYNOPSIS
  30
  31   #get Bio::Phenotype::PhenotypeI somehow
  32
  33   print $phenotype->name(), "\n";
  34   print $phenotype->description(), "\n";
  35
  36   my @keywords = ( "achondroplasia", "dwarfism" );
  37   $phenotype->add_keywords( @keywords );
  38   foreach my $keyword ( $phenotype->each_keyword() ) {
  39        print $keyword, "\n";
  40   }
  41   $phenotype->remove_keywords();
  42
  43
  44   foreach my $gene_symbol ( $phenotype->each_gene_symbol() ) {
  45        print $gene_symbol, "\n";
  46   }
  47
  48   foreach my $corr ( $phenotype->each_Correlate() ) {
  49        # Do something with $corr
  50   }
  51
  52   foreach my $var ( $phenotype->each_Variant() ) {
  53        # Do something with $var (mutation)
  54   }
  55
  56   foreach my $measure ( $phenotype->each_Measure() ) {
  57        # Do something with $measure
  58   }
  59
  60
  61 =head1 DESCRIPTION
  62
  63 This superclass implements common methods for classes modelling phenotypes.
  64 Bio::Phenotype::OMIM::OMIMentry is an example of an instantiable phenotype
  65 class (the design of this interface was partially guided by the need
  66 to model OMIM entries).
  67 Please note. This class provides methods to associate mutations
  68 (methods "each_Variant", ...) and genotypes (methods "each_Genotype", ...)
  69 with phenotypes. Yet, these aspects might need some future enhancements,
  70 especially since there is no "genotype" class yet.
  71
  72 =head1 FEEDBACK
  73
  74 =head2 Mailing Lists
  75
  76 User feedback is an integral part of the evolution of this and other
  77 Bioperl modules. Send your comments and suggestions preferably to the
  78 Bioperl mailing lists  Your participation is much appreciated.
  79
  80   bioperl-l@bioperl.org                  - General discussion
  81   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  82
  83 =head2 Support
  84
  85 Please direct usage questions or support issues to the mailing list:
  86
  87 L<bioperl-l@bioperl.org>
  88
  89 rather than to the module maintainer directly. Many experienced and
  90 reponsive experts will be able look at the problem and quickly
  91 address it. Please include a thorough description of the problem
  92 with code and data examples if at all possible.
  93
  94 =head2 Reporting Bugs
  95
  96 report bugs to the Bioperl bug tracking system to help us keep track
  97 the bugs and their resolution.  Bug reports can be submitted via the
  98 web:
  99
 100   http://bugzilla.open-bio.org/
 101
 102 =head1 AUTHOR
 103
 104 Christian M. Zmasek
 105
 106 Email: czmasek@gnf.org  or  cmzmasek@yahoo.com
 107
 108 WWW:   http://www.genetics.wustl.edu/eddy/people/zmasek/
 109
 110 Address:
 111
 112   Genomics Institute of the Novartis Research Foundation
 113   10675 John Jay Hopkins Drive
 114   San Diego, CA 92121
 115
 116 =head1 APPENDIX
 117
 118 The rest of the documentation details each of the object
 119 methods. Internal methods are usually preceded with a _
 120
 121 =cut
 122
 123
 124 # Let the code begin...
 125
 126
 127 package Bio::Phenotype::Phenotype;
 128 use strict;
 129
 130 use Bio::Species;
 131 use Bio::Variation::VariantI;
 132 use Bio::Annotation::DBLink;
 133 use Bio::Annotation::Reference;
 134 use Bio::Phenotype::Measure;
 135 use Bio::Phenotype::Correlate;
 136 use Bio::Map::CytoPosition;
 137 use Bio::Range;
 138
 139
 140 use base qw(Bio::Root::Root Bio::Phenotype::PhenotypeI);
 141
 142
 143
 144
 145 =head2 new
 146
 147  Title   : new
 148  Usage   : $obj = Bio::Phenotype::Phenotype->new( -name         => "XY",
 149                                                   -description  => "This is ..." );
 150  Function: Creates a new Phenotype object.
 151  Returns : A new Phenotype object.
 152  Args    : -name                           => the name
 153            -description                    => the description of this phenotype
 154            -species                        => ref to the the species
 155            -comment                        => a comment
 156
 157 =cut
 158
 159 sub new {
 160
 161     my( $class,@args ) = @_;
 162
 163     my $self = $class->SUPER::new( @args );
 164
 165     my ( $name,
 166          $description,
 167          $species,
 168          $comment )
 169     = $self->_rearrange( [ qw( NAME
 170                                DESCRIPTION
 171                                SPECIES
 172                                COMMENT ) ], @args );
 173
 174     $self->init();
 175
 176     $name                           && $self->name( $name );
 177     $description                    && $self->description( $description );
 178     $species                        && $self->species( $species );
 179     $comment                        && $self->comment( $comment );
 180
 181     return $self;
 182
 183 } # new
 184
 185
 186 =head2 init
 187
 188  Title   : init()
 189  Usage   : $obj->init();
 190  Function: Initializes this OMIMentry to all "" and empty lists.
 191  Returns :
 192  Args    :
 193
 194 =cut
 195
 196 sub init {
 197
 198     my( $self ) = @_;
 199
 200
 201     $self->name( "" );
 202     $self->description( "" );
 203     my $species = Bio::Species->new();
 204     $species->classification( qw( sapiens Homo ) );
 205     $self->species( $species );
 206     $self->comment( "" );
 207     $self->remove_Correlates();
 208     $self->remove_References();
 209     $self->remove_CytoPositions();
 210     $self->remove_gene_symbols();
 211     $self->remove_Genotypes();
 212     $self->remove_DBLinks();
 213     $self->remove_keywords();
 214     $self->remove_Variants();
 215     $self->remove_Measures();
 216
 217 } # init
 218
 219
 220 =head2 name
 221
 222  Title   : name
 223  Usage   : $obj->name( "r1" );
 224            or
 225            print $obj->name();
 226  Function: Set/get for the name or id of this phenotype.
 227  Returns : A name or id [scalar].
 228  Args    : A name or id [scalar] (optional).
 229
 230 =cut
 231
 232 sub name {
 233     my ( $self, $value ) = @_;
 234
 235     if ( defined $value ) {
 236         $self->{ "_name" } = $value;
 237     }
 238
 239     return $self->{ "_name" };
 240
 241 } # name
 242
 243
 244 =head2 description
 245
 246  Title   : description
 247  Usage   : $obj->description( "This is ..." );
 248            or
 249            print $obj->description();
 250  Function: Set/get for the description of this phenotype.
 251  Returns : A description [scalar].
 252  Args    : A description [scalar] (optional).
 253
 254 =cut
 255
 256 sub description {
 257     my $self = shift;
 258     return $self->{ "_description" } = shift if(@_);
 259     return $self->{ "_description" };
 260 }
 261
 262 =head2 species
 263
 264  Title   : species
 265  Usage   : $obj->species( $species );
 266            or
 267            $species = $obj->species();
 268  Function: Set/get for the species of this phenotype.
 269  Returns : A species [Bio::Species].
 270  Args    : A species [Bio::Species] (optional).
 271
 272 =cut
 273
 274 sub species {
 275     my ( $self, $value ) = @_;
 276
 277     if ( defined $value ) {
 278         $self->_check_ref_type( $value, "Bio::Species" );
 279         $self->{ "_species" } = $value;
 280     }
 281
 282     return $self->{ "_species" };
 283
 284 } # species
 285
 286 =head2 comment
 287
 288  Title   : comment
 289  Usage   : $obj->comment( "putative" );
 290            or
 291            print $obj->comment();
 292  Function: Set/get for a comment about this phenotype.
 293  Returns : A comment [scalar].
 294  Args    : A comment [scalar] (optional).
 295
 296 =cut
 297
 298 sub comment {
 299     my $self = shift;
 300     return $self->{ "_comment" } = shift if(@_);
 301     return $self->{ "_comment" };
 302 } # comment
 303
 304
 305 =head2 each_gene_symbol
 306
 307  Title   : each_gene_symbol()
 308  Usage   : @gs = $obj->each_gene_symbol();
 309  Function: Returns a list of gene symbols [scalars, most likely Strings]
 310            associated with this phenotype.
 311  Returns : A list of scalars.
 312  Args    :
 313
 314 =cut
 315
 316 sub each_gene_symbol {
 317     my ( $self ) = @_;
 318
 319     return @{$self->{"_gene_symbols"}} if exists($self->{"_gene_symbols"});
 320     return ();
 321 } # each_gene_symbol
 322
 323
 324 =head2 add_gene_symbols
 325
 326  Title   : add_gene_symbols
 327  Usage   : $obj->add_gene_symbols( @gs );
 328            or
 329            $obj->add_gene_symbols( $gs );
 330  Function: Pushes one or more gene symbols [scalars, most likely Strings]
 331            into the list of gene symbols.
 332  Returns :
 333  Args    : scalar(s).
 334
 335 =cut
 336
 337 sub add_gene_symbols {
 338     my ( $self, @values ) = @_;
 339
 340     return unless( @values );
 341
 342     push( @{ $self->{ "_gene_symbols" } }, @values );
 343
 344 } # add_gene_symbols
 345
 346
 347 =head2 remove_gene_symbols
 348
 349  Usage   : $obj->remove_gene_symbols();
 350  Function: Deletes (and returns) the list of gene symbols [scalars,
 351            most likely Strings] associated with this phenotype.
 352  Returns : A list of scalars.
 353  Args    :
 354
 355 =cut
 356
 357 sub remove_gene_symbols {
 358     my ( $self ) = @_;
 359
 360     my @a = $self->each_gene_symbol();
 361     $self->{ "_gene_symbols" } = [];
 362     return @a;
 363
 364 } # remove_gene_symbols
 365
 366
 367
 368
 369 =head2 each_Variant
 370
 371  Title   : each_Variant()
 372  Usage   : @vs = $obj->each_Variant();
 373  Function: Returns a list of Bio::Variation::VariantI implementing objects
 374            associated with this phenotype.
 375            This is for representing the actual mutation(s) causing this
 376            phenotype.
 377            {* The "variants" data member and its methods will/might need to be
 378            changed/improved in one way or another, CZ 09/06/02 *}
 379  Returns : A list of Bio::Variation::VariantI implementing objects.
 380  Args    :
 381
 382 =cut
 383
 384 sub each_Variant {
 385      my ( $self ) = @_;
 386
 387      return @{ $self->{ "_variants" } } if exists($self->{ "_variants" });
 388      return ();
 389 } # each_Variant
 390
 391
 392 =head2 add_Variants
 393
 394  Usage   : $obj->add_Variants( @vs );
 395            or
 396            $obj->add_Variants( $v );
 397  Function: Pushes one or more Bio::Variation::VariantI implementing objects
 398            into the list of Variants.
 399  Returns :
 400  Args    : Bio::Variation::VariantI implementing object(s).
 401
 402 =cut
 403
 404 sub add_Variants {
 405     my ( $self, @values ) = @_;
 406
 407     return unless( @values );
 408
 409     foreach my $value ( @values ) {
 410         $self->_check_ref_type( $value, "Bio::Variation::VariantI" );
 411     }
 412
 413     push( @{ $self->{ "_variants" } }, @values );
 414
 415 } # add_Variants
 416
 417
 418 =head2 remove_Variants
 419
 420  Title   : remove_Variants
 421  Usage   : $obj->remove_Variants();
 422  Function: Deletes (and returns) the list of Bio::Variation::VariantI implementing
 423            objects associated with this phenotype.
 424  Returns : A list of Bio::Variation::VariantI implementing objects.
 425  Args    :
 426
 427 =cut
 428
 429 sub remove_Variants {
 430     my ( $self ) = @_;
 431
 432     my @a = $self->each_Variant();
 433     $self->{ "_variants" } = [];
 434     return @a;
 435
 436 } # remove_Variants
 437
 438
 439
 440
 441 =head2 each_Reference
 442
 443  Title   : each_Reference()
 444  Usage   : @refs = $obj->each_Reference();
 445  Function: Returns a list of Bio::Annotation::Reference objects
 446            associated with this phenotype.
 447  Returns : A list of Bio::Annotation::Reference objects.
 448  Args    :
 449
 450 =cut
 451
 452 sub each_Reference {
 453     my ( $self ) = @_;
 454
 455     return @{ $self->{ "_references" } } if exists($self->{ "_references" });
 456     return ();
 457 } # each_Reference
 458
 459
 460 =head2 add_References
 461
 462  Title   : add_References
 463  Usage   : $obj->add_References( @refs );
 464            or
 465            $obj->add_References( $ref );
 466  Function: Pushes one or more Bio::Annotation::Reference objects
 467            into the list of References.
 468  Returns :
 469  Args    : Bio::Annotation::Reference object(s).
 470
 471 =cut
 472
 473 sub add_References {
 474     my ( $self, @values ) = @_;
 475
 476     return unless( @values );
 477
 478     foreach my $value ( @values ) {
 479         $self->_check_ref_type( $value, "Bio::Annotation::Reference" );
 480     }
 481
 482     push( @{ $self->{ "_references" } }, @values );
 483
 484 } # add_References
 485
 486
 487 =head2 remove_References
 488
 489  Title   : remove_References()
 490  Usage   : $obj->remove_References();
 491  Function: Deletes (and returns) the list of Bio::Annotation::Reference objects
 492            associated with this phenotype.
 493  Returns : A list of Bio::Annotation::Reference objects.
 494  Args    :
 495
 496 =cut
 497
 498 sub remove_References {
 499     my ( $self ) = @_;
 500
 501     my @a = $self->each_Reference();
 502     $self->{ "_references" } = [];
 503     return @a;
 504
 505 } # remove_References
 506
 507
 508
 509
 510 =head2 each_CytoPosition
 511
 512  Title   : each_CytoPosition()
 513  Usage   : @cps = $obj->each_CytoPosition();
 514  Function: Returns a list of Bio::Map::CytoPosition objects
 515            associated with this phenotype.
 516  Returns : A list of Bio::Map::CytoPosition objects.
 517  Args    :
 518
 519 =cut
 520
 521 sub each_CytoPosition {
 522     my ( $self ) = @_;
 523
 524     return @{$self->{"_cyto_positions"}} if exists($self->{"_cyto_positions"});
 525     return ();
 526 } # each_CytoPosition
 527
 528
 529 =head2 add_CytoPositions
 530
 531  Title   : add_CytoPositions
 532  Usage   : $obj->add_CytoPositions( @cps );
 533            or
 534            $obj->add_CytoPositions( $cp );
 535  Function: Pushes one or more Bio::Map::CytoPosition objects
 536            into the list of CytoPositions.
 537  Returns :
 538  Args    : Bio::Map::CytoPosition object(s).
 539
 540 =cut
 541
 542 sub add_CytoPositions {
 543     my ( $self, @values ) = @_;
 544
 545     return unless( @values );
 546
 547     foreach my $value ( @values ) {
 548         $self->_check_ref_type( $value, "Bio::Map::CytoPosition" );
 549     }
 550
 551     push( @{ $self->{ "_cyto_positions" } }, @values );
 552
 553 } # add_CytoPositions
 554
 555
 556 =head2 remove_CytoPositions
 557
 558  Title   : remove_CytoPositions
 559  Usage   : $obj->remove_CytoPositions();
 560  Function: Deletes (and returns) the list o fBio::Map::CytoPosition objects
 561            associated with this phenotype.
 562  Returns : A list of Bio::Map::CytoPosition objects.
 563  Args    :
 564
 565 =cut
 566
 567 sub remove_CytoPositions {
 568     my ( $self ) = @_;
 569
 570     my @a = $self->each_CytoPosition();
 571     $self->{ "_cyto_positions" } = [];
 572     return @a;
 573
 574 } # remove_CytoPositions
 575
 576
 577
 578
 579 =head2 each_Correlate
 580
 581  Title   : each_Correlate()
 582  Usage   : @corrs = $obj->each_Correlate();
 583  Function: Returns a list of Bio::Phenotype::Correlate objects
 584            associated with this phenotype.
 585            (Correlates are correlating phenotypes in different species;
 586            inspired by mouse correlates of human phenotypes in the OMIM
 587            database.)
 588  Returns : A list of Bio::Phenotype::Correlate objects.
 589  Args    :
 590
 591 =cut
 592
 593 sub each_Correlate {
 594     my ( $self ) = @_;
 595
 596     return @{ $self->{ "_correlates" } } if exists($self->{ "_correlates" });
 597     return ();
 598 } # each_Correlate
 599
 600
 601
 602
 603 =head2 add_Correlates
 604
 605  Title   : add_Correlates
 606  Usage   : $obj->add_Correlates( @corrs );
 607            or
 608            $obj->add_Correlates( $corr );
 609  Function: Pushes one or more Bio::Phenotype::Correlate objects
 610            into the list of Correlates.
 611  Returns :
 612  Args    : Bio::Phenotype::Correlate object(s).
 613
 614 =cut
 615
 616 sub add_Correlates {
 617     my ( $self, @values ) = @_;
 618
 619     return unless( @values );
 620
 621     foreach my $value ( @values ) {
 622         $self->_check_ref_type( $value, "Bio::Phenotype::Correlate" );
 623     }
 624
 625     push( @{ $self->{ "_correlates" } }, @values );
 626
 627 } # add_Correlates
 628
 629
 630 =head2 remove_Correlates
 631
 632  Title   : remove_Correlates
 633  Usage   : $obj->remove_Correlates();
 634  Function: Deletes (and returns) the list of Bio::Phenotype::Correlate objects
 635            associated with this phenotype.
 636  Returns : A list of Bio::Phenotype::Correlate objects.
 637  Args    :
 638
 639 =cut
 640
 641 sub remove_Correlates {
 642     my ( $self ) = @_;
 643
 644     my @a = $self->each_Correlate();
 645     $self->{ "_correlates" } = [];
 646     return @a;
 647
 648 } # remove_Correlates
 649
 650
 651
 652
 653 =head2 each_Measure
 654
 655  Title   : each_Measure()
 656  Usage   : @ms = $obj->each_Measure();
 657  Function: Returns a list of Bio::Phenotype::Measure objects
 658            associated with this phenotype.
 659            (Measure is for biochemically defined phenotypes
 660            or any other types of measures.)
 661  Returns : A list of Bio::Phenotype::Measure objects.
 662  Args    :
 663
 664 =cut
 665
 666 sub each_Measure {
 667     my ( $self ) = @_;
 668
 669     return @{ $self->{ "_measures" } } if exists($self->{ "_measures" });
 670     return ();
 671 } # each_Measure
 672
 673
 674 =head2 add_Measures
 675
 676  Title   : add_Measures
 677  Usage   : $obj->add_Measures( @ms );
 678            or
 679            $obj->add_Measures( $m );
 680  Function: Pushes one or more Bio::Phenotype::Measure objects
 681            into the list of Measures.
 682  Returns :
 683  Args    : Bio::Phenotype::Measure object(s).
 684
 685 =cut
 686
 687 sub add_Measures {
 688     my ( $self, @values ) = @_;
 689
 690     return unless( @values );
 691
 692     foreach my $value ( @values ) {
 693         $self->_check_ref_type( $value, "Bio::Phenotype::Measure" );
 694     }
 695
 696     push( @{ $self->{ "_measures" } }, @values );
 697
 698 } # add_Measures
 699
 700
 701 =head2 remove_Measures
 702
 703  Title   : remove_Measures
 704  Usage   : $obj->remove_Measures();
 705  Function: Deletes (and returns) the list of Bio::Phenotype::Measure objects
 706            associated with this phenotype.
 707  Returns : A list of Bio::Phenotype::Measure objects.
 708  Args    :
 709
 710 =cut
 711
 712 sub remove_Measures {
 713     my ( $self ) = @_;
 714
 715     my @a = $self->each_Measure();
 716     $self->{ "_measures" } = [];
 717     return @a;
 718
 719 } # remove_Measures
 720
 721
 722
 723
 724 =head2 each_keyword
 725
 726  Title   : each_keyword()
 727  Usage   : @kws = $obj->each_keyword();
 728  Function: Returns a list of key words [scalars, most likely Strings]
 729            associated with this phenotype.
 730  Returns : A list of scalars.
 731  Args    :
 732
 733 =cut
 734
 735 sub each_keyword {
 736     my ( $self ) = @_;
 737
 738     return @{ $self->{ "_keywords" } } if exists($self->{ "_keywords" });
 739     return ();
 740 } # each_keyword
 741
 742
 743 =head2 add_keywords
 744
 745  Title   : add_keywords
 746  Usage   : $obj->add_keywords( @kws );
 747            or
 748            $obj->add_keywords( $kw );
 749  Function: Pushes one or more keywords [scalars, most likely Strings]
 750            into the list of key words.
 751  Returns :
 752  Args    : scalar(s).
 753
 754 =cut
 755
 756 sub add_keywords {
 757     my ( $self, @values ) = @_;
 758
 759     return unless( @values );
 760
 761     push( @{ $self->{ "_keywords" } }, @values );
 762
 763 } # add_keywords
 764
 765
 766 =head2 remove_keywords
 767
 768  Title   : remove_keywords
 769  Usage   : $obj->remove_keywords();
 770  Function: Deletes (and returns) the list of key words [scalars,
 771            most likely Strings] associated with this phenotype.
 772  Returns : A list of scalars.
 773  Args    :
 774
 775 =cut
 776
 777 sub remove_keywords {
 778     my ( $self ) = @_;
 779
 780     my @a = $self->each_keyword();
 781     $self->{ "_keywords" } = [];
 782     return @a;
 783
 784 } # remove_keywords
 785
 786
 787
 788
 789 =head2 each_DBLink
 790
 791  Title   : each_DBLink()
 792  Usage   : @dbls = $obj->each_DBLink();
 793  Function: Returns a list of Bio::Annotation::DBLink objects
 794            associated with this phenotype.
 795  Returns : A list of Bio::Annotation::DBLink objects.
 796  Args    :
 797
 798 =cut
 799
 800 sub each_DBLink {
 801     my ( $self ) = @_;
 802
 803     return @{ $self->{ "_db_links" } } if exists($self->{ "_db_links" });
 804     return ();
 805 }
 806
 807
 808 =head2 add_DBLinks
 809
 810  Title   : add_DBLinks
 811  Usage   : $obj->add_DBLinks( @dbls );
 812            or
 813            $obj->add_DBLinks( $dbl );
 814  Function: Pushes one or more Bio::Annotation::DBLink objects
 815            into the list of DBLinks.
 816  Returns :
 817  Args    : Bio::Annotation::DBLink object(s).
 818
 819 =cut
 820
 821 sub add_DBLinks {
 822     my ( $self, @values ) = @_;
 823
 824     return unless( @values );
 825
 826     foreach my $value ( @values ) {
 827         $self->_check_ref_type( $value, "Bio::Annotation::DBLink" );
 828     }
 829
 830     push( @{ $self->{ "_db_links" } }, @values );
 831
 832 } # add_DBLinks
 833
 834
 835 =head2 remove_DBLinks
 836
 837  Title   : remove_DBLinks
 838  Usage   : $obj->remove_DBLinks();
 839  Function: Deletes (and returns) the list of Bio::Annotation::DBLink objects
 840            associated with this phenotype.
 841  Returns : A list of Bio::Annotation::DBLink objects.
 842  Args    :
 843
 844 =cut
 845
 846 sub remove_DBLinks {
 847     my ( $self ) = @_;
 848
 849     my @a = $self->each_DBLink();
 850     $self->{ "_db_links" } = [];
 851     return @a;
 852
 853 } # remove_DBLinks
 854
 855
 856
 857
 858 =head2 each_Genotype
 859
 860  Title   : each_Reference()
 861  Usage   : @gts = $obj->each_Reference();
 862  Function: Returns a list of "Genotype" objects
 863            associated with this phenotype.
 864            {* the "genotypes" data member and its methods certainly will/needs to be
 865            changed/improved in one way or another since there is
 866            no "Genotype" class yet, CZ 09/06/02 *}
 867  Returns : A list of "Genotype" objects.
 868  Args    :
 869
 870 =cut
 871
 872 sub each_Genotype {
 873     my ( $self ) = @_;
 874
 875     return @{ $self->{ "_genotypes" } } if exists($self->{ "_genotypes" });
 876     return ();
 877 } # each_Genotype
 878
 879
 880 =head2 add_Genotypes
 881
 882  Title   : add_Genotypes
 883  Usage   : $obj->add_Genotypes( @gts );
 884            or
 885            $obj->add_Genotypes( $gt );
 886  Function: Pushes one or more "Genotypes"
 887            into the list of "Genotypes".
 888  Returns :
 889  Args    : "Genotypes(s)".
 890
 891 =cut
 892
 893 sub add_Genotypes {
 894     my ( $self, @values ) = @_;
 895
 896     return unless( @values );
 897
 898     #foreach my $value ( @values ) {
 899     #    $self->_check_ref_type( $value, "Bio::GenotypeI" );
 900     #}
 901
 902     push( @{ $self->{ "_genotypes" } }, @values );
 903
 904 } # add_Genotypes
 905
 906
 907 =head2 remove_Genotypes
 908
 909  Title   : remove_Genotypes
 910  Usage   : $obj->remove_Genotypes();
 911  Function: Deletes (and returns) the list of "Genotype" objects
 912            associated with this phenotype.
 913  Returns : A list of "Genotype" objects.
 914  Args    :
 915
 916 =cut
 917
 918 sub remove_Genotypes {
 919     my ( $self ) = @_;
 920
 921     my @a = $self->each_Genotype();
 922     $self->{ "_genotypes" } = [];
 923     return @a;
 924
 925 } # remove_Genotypes
 926
 927
 928 =head2 _check_ref_type
 929
 930  Title   : _check_ref_type
 931  Usage   : $self->_check_ref_type( $value, "Bio::Annotation::DBLink" );
 932  Function: Checks for the correct type.
 933  Returns :
 934  Args    : The value to be checked, the expected class.
 935
 936 =cut
 937
 938 sub _check_ref_type {
 939     my ( $self, $value, $expected_class ) = @_;
 940
 941     if ( ! defined( $value ) ) {
 942         $self->throw( ( caller( 1 ) )[ 3 ] .": Found [undef"
 943         ."] where [$expected_class] expected" );
 944     }
 945     elsif ( ! ref( $value ) ) {
 946         $self->throw( ( caller( 1 ) )[ 3 ] .": Found scalar"
 947         ." where [$expected_class] expected" );
 948     }
 949     elsif ( ! $value->isa( $expected_class ) ) {
 950         $self->throw( ( caller( 1 ) )[ 3 ] .": Found [". ref( $value )
 951         ."] where [$expected_class] expected" );
 952     }
 953 } # _check_ref_type
 954
 955
 956
 957 1;