Bio/Phenotype/Correlate.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Phenotype::Correlate
   4 #
   5 # Cared for by Christian M. Zmasek <czmasek@gnf.org> or <cmzmasek@yahoo.com>
   6 #
   7 # (c) Christian M. Zmasek, czmasek@gnf.org, 2002.
   8 # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002.
   9 #
  10 # You may distribute this module under the same terms as perl itself.
  11 # Refer to the Perl Artistic License (see the license accompanying this
  12 # software package, or see http://www.perl.com/language/misc/Artistic.html)
  13 # for the terms under which you may use, modify, and redistribute this module.
  14 #
  15 # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
  16 # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
  17 # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
  18 #
  19 # You may distribute this module under the same terms as perl itself
  20
  21 # POD documentation - main docs before the code
  22
  23 =head1 NAME
  24
  25 Bio::Phenotype::Correlate - Representation of a correlating phenotype in a given species
  26
  27 =head1 SYNOPSIS
  28
  29   use Bio::Phenotype::Correlate;
  30
  31   $co = Bio::Phenotype::Correlate->new( -name        => "4(Tas1r3)",
  32                                         -description => "mouse correlate of human phenotype MIM 605865",
  33                                         -species     => $mouse,
  34                                         -type        => "homolog",
  35                                         -comment     => "type=homolog is putative" );
  36
  37   print $co->name();
  38   print $co->description();
  39   print $co->species()->binomial();
  40   print $co->type();
  41   print $co->comment();
  42
  43   print $co->to_string();
  44
  45 =head1 DESCRIPTION
  46
  47 This class models correlating phenotypes.
  48 Its creation was inspired by the OMIM database where many human phenotypes
  49 have a correlating mouse phenotype. Therefore, this class is intended
  50 to be used together with a phenotype class.
  51
  52
  53 =head1 FEEDBACK
  54
  55 =head2 Mailing Lists
  56
  57 User feedback is an integral part of the evolution of this and other
  58 Bioperl modules. Send your comments and suggestions preferably to one
  59 of the Bioperl mailing lists.  Your participation is much appreciated.
  60
  61   bioperl-l@bioperl.org                  - General discussion
  62   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  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   http://bugzilla.open-bio.org/
  71
  72 =head1 AUTHOR
  73
  74 Christian M. Zmasek
  75
  76 Email: czmasek@gnf.org  or  cmzmasek@yahoo.com
  77
  78 WWW:   http://www.genetics.wustl.edu/eddy/people/zmasek/
  79
  80 Address:
  81
  82   Genomics Institute of the Novartis Research Foundation
  83   10675 John Jay Hopkins Drive
  84   San Diego, CA 92121
  85
  86 =head1 APPENDIX
  87
  88 The rest of the documentation details each of the object
  89 methods.
  90
  91 =cut
  92
  93
  94 # Let the code begin...
  95
  96 package Bio::Phenotype::Correlate;
  97 use strict;
  98 use Bio::Species;
  99
 100 use base qw(Bio::Root::Root);
 101
 102
 103 =head2 new
 104
 105  Title   : new
 106  Usage   : $co = Bio::Phenotype::Correlate->new( -name        => "4(Tas1r3)",
 107                                                  -description => "mouse correlate of human phenotype MIM 605865",
 108                                                  -species     => $mouse,
 109                                                  -type        => "homolog",
 110                                                  -comment     => "type=homolog is putative" );
 111  Function: Creates a new Correlate object.
 112  Returns : A new Correlate object.
 113  Args    : -name        => a name or id
 114            -description => a description
 115            -species     => the species of this correlating phenotype [Bio::Species]
 116            -type        => the type of correlation
 117            -comment     => a comment
 118
 119 =cut
 120
 121 sub new {
 122
 123     my( $class, @args ) = @_;
 124
 125     my $self = $class->SUPER::new( @args );
 126
 127     my ( $name, $desc, $species, $type, $comment )
 128     = $self->_rearrange( [ qw( NAME
 129                                DESCRIPTION
 130                                SPECIES
 131                                TYPE
 132                                COMMENT ) ], @args );
 133
 134     $self->init();
 135
 136     $name    && $self->name( $name );
 137     $desc    && $self->description( $desc );
 138     $species && $self->species( $species );
 139     $type    && $self->type( $type );
 140     $comment && $self->comment( $comment );
 141
 142     return $self;
 143
 144 } # new
 145
 146
 147
 148
 149 =head2 init
 150
 151  Title   : init()
 152  Usage   : $co->init();
 153  Function: Initializes this Correlate to all "".
 154  Returns :
 155  Args    :
 156
 157 =cut
 158
 159 sub init {
 160
 161     my( $self ) = @_;
 162
 163     $self->name( "" );
 164     $self->description( "" );
 165     my $species = Bio::Species->new();
 166     $species->classification( qw( species Undetermined ) );
 167     $self->species( $species );
 168     $self->type( "" );
 169     $self->comment( "" );
 170
 171 } # init
 172
 173
 174
 175
 176 =head2 name
 177
 178  Title   : name
 179  Usage   : $co->name( "4(Tas1r3)" );
 180            or
 181            print $co->name();
 182  Function: Set/get for the name or id of this Correlate.
 183  Returns : The name or id of this Correlate.
 184  Args    : The name or id of this Correlate (optional).
 185
 186 =cut
 187
 188 sub name {
 189     my ( $self, $value ) = @_;
 190
 191     if ( defined $value ) {
 192         $self->{ "_name" } = $value;
 193     }
 194
 195     return $self->{ "_name" };
 196
 197 } # name
 198
 199
 200
 201
 202 =head2 description
 203
 204  Title   : description
 205  Usage   : $co->description( "mouse correlate of human phenotype MIM 03923" );
 206            or
 207            print $co->description();
 208  Function: Set/get for the description of this Correlate.
 209  Returns : A description of this Correlate.
 210  Args    : A description of this Correlate (optional).
 211
 212 =cut
 213
 214 sub description {
 215     my ( $self, $value ) = @_;
 216
 217     if ( defined $value ) {
 218         $self->{ "_description" } = $value;
 219     }
 220
 221     return $self->{ "_description" };
 222
 223 } # description
 224
 225
 226
 227
 228 =head2 species
 229
 230  Title   : species
 231  Usage   : $co->species( $species );
 232            or
 233            $species = $co->species();
 234  Function: Set/get for the species of this Correlate.
 235  Returns : The Bio::Species of this Correlate [Bio::Species].
 236  Args    : The Bio::Species of this Correlate [Bio::Species] (optional).
 237
 238 =cut
 239
 240 sub species {
 241
 242     my ( $self, $value )  = @_;
 243
 244     if ( defined $value ) {
 245         $self->_check_ref_type( $value, "Bio::Species" );
 246         $self->{ "_species" } = $value;
 247     }
 248
 249     return $self->{ "_species" };
 250
 251 } # species
 252
 253
 254
 255
 256 =head2 type
 257
 258  Title   : type
 259  Usage   : $co->type( "homolog" );
 260            or
 261            print $co->type();
 262  Function: Set/get for the type of this Correlate.
 263  Returns : The type of this Correlate.
 264  Args    : The type of this Correlate (optional).
 265
 266 =cut
 267
 268 sub type {
 269     my ( $self, $value ) = @_;
 270
 271     if ( defined $value ) {
 272         $self->{ "_type" } = $value;
 273     }
 274
 275     return $self->{ "_type" };
 276
 277 } # type
 278
 279
 280
 281
 282 =head2 comment
 283
 284  Title   : comment
 285  Usage   : $co->comment( "doubtful" );
 286            or
 287            print $co->comment();
 288  Function: Set/get for an arbitrary comment about this Correlate.
 289  Returns : A comment.
 290  Args    : A comment (optional).
 291
 292 =cut
 293
 294 sub comment {
 295     my ( $self, $value ) = @_;
 296
 297     if ( defined $value ) {
 298         $self->{ "_comment" } = $value;
 299     }
 300
 301     return $self->{ "_comment" };
 302
 303 } # comment
 304
 305
 306
 307 =head2 to_string
 308
 309  Title   : to_string()
 310  Usage   : print $co->to_string();
 311  Function: To string method for Correlate objects.
 312  Returns : A string representations of this Correlate.
 313  Args    :
 314
 315 =cut
 316
 317 sub to_string {
 318
 319     my ( $self ) = @_;
 320
 321     my $s = "";
 322
 323     $s .= "-- Name:\n";
 324     $s .= $self->name()."\n";
 325     $s .= "-- Description:\n";
 326     $s .= $self->description()."\n";
 327     $s .= "-- Species:\n";
 328     $s .= $self->species()->binomial()."\n";
 329     $s .= "-- Type of correlation:\n";
 330     $s .= $self->type()."\n";
 331     $s .= "-- Comment:\n";
 332     $s .= $self->comment();
 333
 334     return $s;
 335
 336 } # to_string
 337
 338
 339
 340
 341 # Title   : _check_ref_type
 342 # Function: Checks for the correct type.
 343 # Returns :
 344 # Args    : The value to be checked, the expected class.
 345 sub _check_ref_type {
 346     my ( $self, $value, $expected_class ) = @_;
 347
 348     if ( ! defined( $value ) ) {
 349         $self->throw( ( caller( 1 ) )[ 3 ] .": Found [undef"
 350         ."] where [$expected_class] expected" );
 351     }
 352     elsif ( ! ref( $value ) ) {
 353         $self->throw( ( caller( 1 ) )[ 3 ] .": Found scalar"
 354         ." where [$expected_class] expected" );
 355     }
 356     elsif ( ! $value->isa( $expected_class ) ) {
 357         $self->throw( ( caller( 1 ) )[ 3 ] .": Found [". ref( $value )
 358         ."] where [$expected_class] expected" );
 359     }
 360 } # _check_ref_type
 361
 362
 363
 364 1;