branch-1-6/Bio/Phenotype/Correlate.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Phenotype::Correlate
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Christian M. Zmasek <czmasek-at-burnham.org> or <cmzmasek@yahoo.com>
   8 #
   9 # (c) Christian M. Zmasek, czmasek-at-burnham.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::Correlate - Representation of a correlating phenotype in a given species
  28
  29 =head1 SYNOPSIS
  30
  31   use Bio::Phenotype::Correlate;
  32
  33   $co = Bio::Phenotype::Correlate->new( -name        => "4(Tas1r3)",
  34                                         -description => "mouse correlate of human phenotype MIM 605865",
  35                                         -species     => $mouse,
  36                                         -type        => "homolog",
  37                                         -comment     => "type=homolog is putative" );
  38
  39   print $co->name();
  40   print $co->description();
  41   print $co->species()->binomial();
  42   print $co->type();
  43   print $co->comment();
  44
  45   print $co->to_string();
  46
  47 =head1 DESCRIPTION
  48
  49 This class models correlating phenotypes.
  50 Its creation was inspired by the OMIM database where many human phenotypes
  51 have a correlating mouse phenotype. Therefore, this class is intended
  52 to be used together with a phenotype class.
  53
  54
  55 =head1 FEEDBACK
  56
  57 =head2 Mailing Lists
  58
  59 User feedback is an integral part of the evolution of this and other
  60 Bioperl modules. Send your comments and suggestions preferably to one
  61 of the Bioperl mailing lists.  Your participation is much appreciated.
  62
  63   bioperl-l@bioperl.org                  - General discussion
  64   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  65
  66 =head2 Support
  67
  68 Please direct usage questions or support issues to the mailing list:
  69
  70 I<bioperl-l@bioperl.org>
  71
  72 rather than to the module maintainer directly. Many experienced and
  73 reponsive experts will be able look at the problem and quickly
  74 address it. Please include a thorough description of the problem
  75 with code and data examples if at all possible.
  76
  77 =head2 Reporting Bugs
  78
  79 Report bugs to the Bioperl bug tracking system to help us keep track
  80 the bugs and their resolution.  Bug reports can be submitted via the
  81 web:
  82
  83   http://bugzilla.open-bio.org/
  84
  85 =head1 AUTHOR
  86
  87 Christian M. Zmasek
  88
  89 Email: czmasek-at-burnham.org  or  cmzmasek@yahoo.com
  90
  91 WWW:   http://monochrome-effect.net/
  92
  93 Address:
  94
  95   Genomics Institute of the Novartis Research Foundation
  96   10675 John Jay Hopkins Drive
  97   San Diego, CA 92121
  98
  99 =head1 APPENDIX
 100
 101 The rest of the documentation details each of the object
 102 methods.
 103
 104 =cut
 105
 106
 107 # Let the code begin...
 108
 109 package Bio::Phenotype::Correlate;
 110 use strict;
 111 use Bio::Species;
 112
 113 use base qw(Bio::Root::Root);
 114
 115
 116 =head2 new
 117
 118  Title   : new
 119  Usage   : $co = Bio::Phenotype::Correlate->new( -name        => "4(Tas1r3)",
 120                                                  -description => "mouse correlate of human phenotype MIM 605865",
 121                                                  -species     => $mouse,
 122                                                  -type        => "homolog",
 123                                                  -comment     => "type=homolog is putative" );
 124  Function: Creates a new Correlate object.
 125  Returns : A new Correlate object.
 126  Args    : -name        => a name or id
 127            -description => a description
 128            -species     => the species of this correlating phenotype [Bio::Species]
 129            -type        => the type of correlation
 130            -comment     => a comment
 131
 132 =cut
 133
 134 sub new {
 135
 136     my( $class, @args ) = @_;
 137
 138     my $self = $class->SUPER::new( @args );
 139
 140     my ( $name, $desc, $species, $type, $comment )
 141     = $self->_rearrange( [ qw( NAME
 142                                DESCRIPTION
 143                                SPECIES
 144                                TYPE
 145                                COMMENT ) ], @args );
 146
 147     $self->init();
 148
 149     $name    && $self->name( $name );
 150     $desc    && $self->description( $desc );
 151     $species && $self->species( $species );
 152     $type    && $self->type( $type );
 153     $comment && $self->comment( $comment );
 154
 155     return $self;
 156
 157 } # new
 158
 159
 160
 161
 162 =head2 init
 163
 164  Title   : init()
 165  Usage   : $co->init();
 166  Function: Initializes this Correlate to all "".
 167  Returns :
 168  Args    :
 169
 170 =cut
 171
 172 sub init {
 173
 174     my( $self ) = @_;
 175
 176     $self->name( "" );
 177     $self->description( "" );
 178     my $species = Bio::Species->new();
 179     $species->classification( qw( species Undetermined ) );
 180     $self->species( $species );
 181     $self->type( "" );
 182     $self->comment( "" );
 183
 184 } # init
 185
 186
 187
 188
 189 =head2 name
 190
 191  Title   : name
 192  Usage   : $co->name( "4(Tas1r3)" );
 193            or
 194            print $co->name();
 195  Function: Set/get for the name or id of this Correlate.
 196  Returns : The name or id of this Correlate.
 197  Args    : The name or id of this Correlate (optional).
 198
 199 =cut
 200
 201 sub name {
 202     my ( $self, $value ) = @_;
 203
 204     if ( defined $value ) {
 205         $self->{ "_name" } = $value;
 206     }
 207
 208     return $self->{ "_name" };
 209
 210 } # name
 211
 212
 213
 214
 215 =head2 description
 216
 217  Title   : description
 218  Usage   : $co->description( "mouse correlate of human phenotype MIM 03923" );
 219            or
 220            print $co->description();
 221  Function: Set/get for the description of this Correlate.
 222  Returns : A description of this Correlate.
 223  Args    : A description of this Correlate (optional).
 224
 225 =cut
 226
 227 sub description {
 228     my ( $self, $value ) = @_;
 229
 230     if ( defined $value ) {
 231         $self->{ "_description" } = $value;
 232     }
 233
 234     return $self->{ "_description" };
 235
 236 } # description
 237
 238
 239
 240
 241 =head2 species
 242
 243  Title   : species
 244  Usage   : $co->species( $species );
 245            or
 246            $species = $co->species();
 247  Function: Set/get for the species of this Correlate.
 248  Returns : The Bio::Species of this Correlate [Bio::Species].
 249  Args    : The Bio::Species of this Correlate [Bio::Species] (optional).
 250
 251 =cut
 252
 253 sub species {
 254
 255     my ( $self, $value )  = @_;
 256
 257     if ( defined $value ) {
 258         $self->_check_ref_type( $value, "Bio::Species" );
 259         $self->{ "_species" } = $value;
 260     }
 261
 262     return $self->{ "_species" };
 263
 264 } # species
 265
 266
 267
 268
 269 =head2 type
 270
 271  Title   : type
 272  Usage   : $co->type( "homolog" );
 273            or
 274            print $co->type();
 275  Function: Set/get for the type of this Correlate.
 276  Returns : The type of this Correlate.
 277  Args    : The type of this Correlate (optional).
 278
 279 =cut
 280
 281 sub type {
 282     my ( $self, $value ) = @_;
 283
 284     if ( defined $value ) {
 285         $self->{ "_type" } = $value;
 286     }
 287
 288     return $self->{ "_type" };
 289
 290 } # type
 291
 292
 293
 294
 295 =head2 comment
 296
 297  Title   : comment
 298  Usage   : $co->comment( "doubtful" );
 299            or
 300            print $co->comment();
 301  Function: Set/get for an arbitrary comment about this Correlate.
 302  Returns : A comment.
 303  Args    : A comment (optional).
 304
 305 =cut
 306
 307 sub comment {
 308     my ( $self, $value ) = @_;
 309
 310     if ( defined $value ) {
 311         $self->{ "_comment" } = $value;
 312     }
 313
 314     return $self->{ "_comment" };
 315
 316 } # comment
 317
 318
 319
 320 =head2 to_string
 321
 322  Title   : to_string()
 323  Usage   : print $co->to_string();
 324  Function: To string method for Correlate objects.
 325  Returns : A string representations of this Correlate.
 326  Args    :
 327
 328 =cut
 329
 330 sub to_string {
 331
 332     my ( $self ) = @_;
 333
 334     my $s = "";
 335
 336     $s .= "-- Name:\n";
 337     $s .= $self->name()."\n";
 338     $s .= "-- Description:\n";
 339     $s .= $self->description()."\n";
 340     $s .= "-- Species:\n";
 341     $s .= $self->species()->binomial()."\n";
 342     $s .= "-- Type of correlation:\n";
 343     $s .= $self->type()."\n";
 344     $s .= "-- Comment:\n";
 345     $s .= $self->comment();
 346
 347     return $s;
 348
 349 } # to_string
 350
 351
 352
 353
 354 # Title   : _check_ref_type
 355 # Function: Checks for the correct type.
 356 # Returns :
 357 # Args    : The value to be checked, the expected class.
 358 sub _check_ref_type {
 359     my ( $self, $value, $expected_class ) = @_;
 360
 361     if ( ! defined( $value ) ) {
 362         $self->throw( ( caller( 1 ) )[ 3 ] .": Found [undef"
 363         ."] where [$expected_class] expected" );
 364     }
 365     elsif ( ! ref( $value ) ) {
 366         $self->throw( ( caller( 1 ) )[ 3 ] .": Found scalar"
 367         ." where [$expected_class] expected" );
 368     }
 369     elsif ( ! $value->isa( $expected_class ) ) {
 370         $self->throw( ( caller( 1 ) )[ 3 ] .": Found [". ref( $value )
 371         ."] where [$expected_class] expected" );
 372     }
 373 } # _check_ref_type
 374
 375
 376
 377 1;