Bio/Phenotype/Correlate.pm

   1 #
   2 # BioPerl module for Bio::Phenotype::Correlate
   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::Correlate - Representation of a correlating phenotype in a given species
  27
  28 =head1 SYNOPSIS
  29
  30   use Bio::Phenotype::Correlate;
  31
  32   $co = Bio::Phenotype::Correlate->new( -name        => "4(Tas1r3)",
  33                                         -description => "mouse correlate of human phenotype MIM 605865",
  34                                         -species     => $mouse,
  35                                         -type        => "homolog",
  36                                         -comment     => "type=homolog is putative" );
  37
  38   print $co->name();
  39   print $co->description();
  40   print $co->species()->binomial();
  41   print $co->type();
  42   print $co->comment();
  43
  44   print $co->to_string();
  45
  46 =head1 DESCRIPTION
  47
  48 This class models correlating phenotypes.
  49 Its creation was inspired by the OMIM database where many human phenotypes
  50 have a correlating mouse phenotype. Therefore, this class is intended
  51 to be used together with a phenotype class.
  52
  53
  54 =head1 FEEDBACK
  55
  56 =head2 Mailing Lists
  57
  58 User feedback is an integral part of the evolution of this and other
  59 Bioperl modules. Send your comments and suggestions preferably to one
  60 of the Bioperl mailing lists.  Your participation is much appreciated.
  61
  62   bioperl-l@bioperl.org                  - General discussion
  63   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  64
  65 =head2 Support
  66
  67 Please direct usage questions or support issues to the mailing list:
  68
  69 I<bioperl-l@bioperl.org>
  70
  71 rather than to the module maintainer directly. Many experienced and
  72 reponsive experts will be able look at the problem and quickly
  73 address it. Please include a thorough description of the problem
  74 with code and data examples if at all possible.
  75
  76 =head2 Reporting Bugs
  77
  78 Report bugs to the Bioperl bug tracking system to help us keep track
  79 the bugs and their resolution.  Bug reports can be submitted via the
  80 web:
  81
  82   https://redmine.open-bio.org/projects/bioperl/
  83
  84 =head1 AUTHOR
  85
  86 Christian M. Zmasek
  87
  88 Email: czmasek-at-burnham.org  or  cmzmasek@yahoo.com
  89
  90 WWW:   http://monochrome-effect.net/
  91
  92 Address:
  93
  94   Genomics Institute of the Novartis Research Foundation
  95   10675 John Jay Hopkins Drive
  96   San Diego, CA 92121
  97
  98 =head1 APPENDIX
  99
 100 The rest of the documentation details each of the object
 101 methods.
 102
 103 =cut
 104
 105
 106 # Let the code begin...
 107
 108 package Bio::Phenotype::Correlate;
 109 use strict;
 110 use Bio::Species;
 111
 112 use base qw(Bio::Root::Root);
 113
 114
 115 =head2 new
 116
 117  Title   : new
 118  Usage   : $co = Bio::Phenotype::Correlate->new( -name        => "4(Tas1r3)",
 119                                                  -description => "mouse correlate of human phenotype MIM 605865",
 120                                                  -species     => $mouse,
 121                                                  -type        => "homolog",
 122                                                  -comment     => "type=homolog is putative" );
 123  Function: Creates a new Correlate object.
 124  Returns : A new Correlate object.
 125  Args    : -name        => a name or id
 126            -description => a description
 127            -species     => the species of this correlating phenotype [Bio::Species]
 128            -type        => the type of correlation
 129            -comment     => a comment
 130
 131 =cut
 132
 133 sub new {
 134
 135     my( $class, @args ) = @_;
 136
 137     my $self = $class->SUPER::new( @args );
 138
 139     my ( $name, $desc, $species, $type, $comment )
 140     = $self->_rearrange( [ qw( NAME
 141                                DESCRIPTION
 142                                SPECIES
 143                                TYPE
 144                                COMMENT ) ], @args );
 145
 146     $self->init();
 147
 148     $name    && $self->name( $name );
 149     $desc    && $self->description( $desc );
 150     $species && $self->species( $species );
 151     $type    && $self->type( $type );
 152     $comment && $self->comment( $comment );
 153
 154     return $self;
 155
 156 } # new
 157
 158
 159
 160
 161 =head2 init
 162
 163  Title   : init()
 164  Usage   : $co->init();
 165  Function: Initializes this Correlate to all "".
 166  Returns :
 167  Args    :
 168
 169 =cut
 170
 171 sub init {
 172
 173     my( $self ) = @_;
 174
 175     $self->name( "" );
 176     $self->description( "" );
 177     my $species = Bio::Species->new();
 178     $species->classification( qw( species Undetermined ) );
 179     $self->species( $species );
 180     $self->type( "" );
 181     $self->comment( "" );
 182
 183 } # init
 184
 185
 186
 187
 188 =head2 name
 189
 190  Title   : name
 191  Usage   : $co->name( "4(Tas1r3)" );
 192            or
 193            print $co->name();
 194  Function: Set/get for the name or id of this Correlate.
 195  Returns : The name or id of this Correlate.
 196  Args    : The name or id of this Correlate (optional).
 197
 198 =cut
 199
 200 sub name {
 201     my ( $self, $value ) = @_;
 202
 203     if ( defined $value ) {
 204         $self->{ "_name" } = $value;
 205     }
 206
 207     return $self->{ "_name" };
 208
 209 } # name
 210
 211
 212
 213
 214 =head2 description
 215
 216  Title   : description
 217  Usage   : $co->description( "mouse correlate of human phenotype MIM 03923" );
 218            or
 219            print $co->description();
 220  Function: Set/get for the description of this Correlate.
 221  Returns : A description of this Correlate.
 222  Args    : A description of this Correlate (optional).
 223
 224 =cut
 225
 226 sub description {
 227     my ( $self, $value ) = @_;
 228
 229     if ( defined $value ) {
 230         $self->{ "_description" } = $value;
 231     }
 232
 233     return $self->{ "_description" };
 234
 235 } # description
 236
 237
 238
 239
 240 =head2 species
 241
 242  Title   : species
 243  Usage   : $co->species( $species );
 244            or
 245            $species = $co->species();
 246  Function: Set/get for the species of this Correlate.
 247  Returns : The Bio::Species of this Correlate [Bio::Species].
 248  Args    : The Bio::Species of this Correlate [Bio::Species] (optional).
 249
 250 =cut
 251
 252 sub species {
 253
 254     my ( $self, $value )  = @_;
 255
 256     if ( defined $value ) {
 257         $self->_check_ref_type( $value, "Bio::Species" );
 258         $self->{ "_species" } = $value;
 259     }
 260
 261     return $self->{ "_species" };
 262
 263 } # species
 264
 265
 266
 267
 268 =head2 type
 269
 270  Title   : type
 271  Usage   : $co->type( "homolog" );
 272            or
 273            print $co->type();
 274  Function: Set/get for the type of this Correlate.
 275  Returns : The type of this Correlate.
 276  Args    : The type of this Correlate (optional).
 277
 278 =cut
 279
 280 sub type {
 281     my ( $self, $value ) = @_;
 282
 283     if ( defined $value ) {
 284         $self->{ "_type" } = $value;
 285     }
 286
 287     return $self->{ "_type" };
 288
 289 } # type
 290
 291
 292
 293
 294 =head2 comment
 295
 296  Title   : comment
 297  Usage   : $co->comment( "doubtful" );
 298            or
 299            print $co->comment();
 300  Function: Set/get for an arbitrary comment about this Correlate.
 301  Returns : A comment.
 302  Args    : A comment (optional).
 303
 304 =cut
 305
 306 sub comment {
 307     my ( $self, $value ) = @_;
 308
 309     if ( defined $value ) {
 310         $self->{ "_comment" } = $value;
 311     }
 312
 313     return $self->{ "_comment" };
 314
 315 } # comment
 316
 317
 318
 319 =head2 to_string
 320
 321  Title   : to_string()
 322  Usage   : print $co->to_string();
 323  Function: To string method for Correlate objects.
 324  Returns : A string representations of this Correlate.
 325  Args    :
 326
 327 =cut
 328
 329 sub to_string {
 330
 331     my ( $self ) = @_;
 332
 333     my $s = "";
 334
 335     $s .= "-- Name:\n";
 336     $s .= $self->name()."\n";
 337     $s .= "-- Description:\n";
 338     $s .= $self->description()."\n";
 339     $s .= "-- Species:\n";
 340     $s .= $self->species()->binomial()."\n";
 341     $s .= "-- Type of correlation:\n";
 342     $s .= $self->type()."\n";
 343     $s .= "-- Comment:\n";
 344     $s .= $self->comment();
 345
 346     return $s;
 347
 348 } # to_string
 349
 350
 351
 352
 353 # Title   : _check_ref_type
 354 # Function: Checks for the correct type.
 355 # Returns :
 356 # Args    : The value to be checked, the expected class.
 357 sub _check_ref_type {
 358     my ( $self, $value, $expected_class ) = @_;
 359
 360     if ( ! defined( $value ) ) {
 361         $self->throw( ( caller( 1 ) )[ 3 ] .": Found [undef"
 362         ."] where [$expected_class] expected" );
 363     }
 364     elsif ( ! ref( $value ) ) {
 365         $self->throw( ( caller( 1 ) )[ 3 ] .": Found scalar"
 366         ." where [$expected_class] expected" );
 367     }
 368     elsif ( ! $value->isa( $expected_class ) ) {
 369         $self->throw( ( caller( 1 ) )[ 3 ] .": Found [". ref( $value )
 370         ."] where [$expected_class] expected" );
 371     }
 372 } # _check_ref_type
 373
 374
 375
 376 1;