Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm

   1 #
   2 # BioPerl module for Bio::Phenotype::OMIM::OMIMentryAllelicVariant
   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::OMIM::OMIMentryAllelicVariant - Representation of a allelic
  27 variant of the OMIM database
  28
  29 =head1 SYNOPSIS
  30
  31   use Bio::Phenotype::OMIM::OMIMentryAllelicVariant;
  32
  33   $av = Bio::Phenotype::OMIM::OMIMentryAllelicVariant->new( -number               => ".0001",
  34                                                             -title                => "ALCOHOL INTOLERANCE",
  35                                                             -symbol               => "ALDH2*2",
  36                                                             -description          => "The ALDH2*2-encoded ...",
  37                                                             -aa_ori               => "GLU",
  38                                                             -aa_mut               => "LYS",
  39                                                             -position             => 487,
  40                                                             -additional_mutations => "IVS4DS, G-A, +1" );
  41
  42 =head1 DESCRIPTION
  43
  44 This class models the allelic variant of the OMIM database.
  45 This class is intended to be used together with a OMIM entry class.
  46
  47
  48 =head1 FEEDBACK
  49
  50 =head2 Mailing Lists
  51
  52 User feedback is an integral part of the evolution of this and other
  53 Bioperl modules. Send your comments and suggestions preferably to one
  54 of the Bioperl mailing lists.  Your participation is much appreciated.
  55
  56   bioperl-l@bioperl.org                  - General discussion
  57   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  58
  59 =head2 Support
  60
  61 Please direct usage questions or support issues to the mailing list:
  62
  63 I<bioperl-l@bioperl.org>
  64
  65 rather than to the module maintainer directly. Many experienced and
  66 reponsive experts will be able look at the problem and quickly
  67 address it. Please include a thorough description of the problem
  68 with code and data examples if at all possible.
  69
  70 =head2 Reporting Bugs
  71
  72 Report bugs to the Bioperl bug tracking system to help us keep track
  73 the bugs and their resolution.  Bug reports can be submitted via the
  74 web:
  75
  76   https://github.com/bioperl/bioperl-live/issues
  77
  78 =head1 AUTHOR
  79
  80 Christian M. Zmasek
  81
  82 Email: czmasek-at-burnham.org  or  cmzmasek@yahoo.com
  83
  84 WWW:   http://monochrome-effect.net/
  85
  86 Address:
  87
  88   Genomics Institute of the Novartis Research Foundation
  89   10675 John Jay Hopkins Drive
  90   San Diego, CA 92121
  91
  92 =head1 APPENDIX
  93
  94 The rest of the documentation details each of the object
  95 methods.
  96
  97 =cut
  98
  99
 100 # Let the code begin...
 101
 102
 103 package Bio::Phenotype::OMIM::OMIMentryAllelicVariant;
 104 use strict;
 105
 106 use base qw(Bio::Root::Root);
 107
 108 =head2 new
 109
 110  Title   : new
 111  Usage   : $av = Bio::Phenotype::OMIM::OMIMentryAllelicVariant->new( -number               => ".0001",
 112                                                                      -title                => "ALCOHOL INTOLERANCE",
 113                                                                      -symbol               => "ALDH2*2",
 114                                                                      -description          => "The ALDH2*2-encoded ...",
 115                                                                      -aa_ori               => "GLU",
 116                                                                      -aa_mut               => "LYS",
 117                                                                      -position             => 487,
 118                                                                      -additional_mutations => "IVS4DS, G-A, +1" );
 119  Function: Creates a new OMIMentryAllelicVariant object.
 120  Returns : A new OMIMentryAllelicVariant object.
 121  Args    : -number               => the OMIM allelic variant number
 122            -title                => the title
 123            -symbol               => a symbol
 124            -description          => a description
 125            -aa_ori               => the original amino acid
 126            -aa_mut               => the mutated amino acid
 127            -position             => the position of the mutation
 128            -additional_mutations => free form description of additional mutations
 129
 130 =cut
 131
 132 sub new {
 133
 134     my( $class, @args ) = @_;
 135
 136     my $self = $class->SUPER::new( @args );
 137
 138     my ( $number, $title, $symbol, $desc, $ori, $mut, $pos, $am )
 139     = $self->_rearrange( [ qw( NUMBER
 140                                TITLE
 141                                SYMBOL
 142                                DESCRIPTION
 143                                AA_ORI
 144                                AA_MUT
 145                                POSITION
 146                                ADDITIONAL_MUTATIONS ) ], @args );
 147
 148     $self->init();
 149
 150     $number && $self->number( $number );
 151     $title  && $self->title( $title );
 152     $symbol && $self->symbol( $symbol );
 153     $desc   && $self->description( $desc );
 154     $ori    && $self->aa_ori( $ori );
 155     $mut    && $self->aa_mut( $mut );
 156     $pos    && $self->position( $pos );
 157     $am     && $self->additional_mutations( $am );
 158
 159     return $self;
 160
 161 } # new
 162
 163
 164
 165
 166 =head2 init
 167
 168  Title   : init()
 169  Usage   : $av->init();
 170  Function: Initializes this OMIMentryAllelicVariant to all "".
 171  Returns :
 172  Args    :
 173
 174 =cut
 175
 176 sub init {
 177     my( $self ) = @_;
 178
 179     $self->number( "" );
 180     $self->title( "" );
 181     $self->symbol( "" );
 182     $self->description( "" );
 183     $self->aa_ori( "" );
 184     $self->aa_mut( "" );
 185     $self->position( "" );
 186     $self->additional_mutations( "" );
 187
 188 } # init
 189
 190
 191
 192
 193 =head2 number
 194
 195  Title   : number
 196  Usage   : $av->number( ".0001" );
 197            or
 198            print $av->number();
 199  Function: Set/get for the OMIM allelic variant number of this
 200            OMIMentryAllelicVariant.
 201  Returns : The OMIM allelic variant number.
 202  Args    : The OMIM allelic variant number (optional).
 203
 204 =cut
 205
 206 sub number {
 207     my ( $self, $value ) = @_;
 208
 209     if ( defined $value ) {
 210         $self->{ "_number" } = $value;
 211     }
 212
 213     return $self->{ "_number" };
 214
 215 } # number
 216
 217
 218
 219 =head2 title
 220
 221  Title   : title
 222  Usage   : $av->title( "ALCOHOL INTOLERANCE" );
 223            or
 224            print $av->title();
 225  Function: Set/get for the title of this OMIMentryAllelicVariant.
 226  Returns : The title.
 227  Args    : The title (optional).
 228
 229 =cut
 230
 231 sub title {
 232     my ( $self, $value ) = @_;
 233
 234     if ( defined $value ) {
 235         $self->{ "_title" } = $value;
 236     }
 237
 238     return $self->{ "_title" };
 239
 240 } # title
 241
 242
 243
 244
 245 =head2 symbol
 246
 247  Title   : symbol
 248  Usage   : $av->symbol( "ALDH2*2" );
 249            or
 250            print $av->symbol();
 251  Function: Set/get for the symbol of this OMIMentryAllelicVariant.
 252  Returns : A symbol.
 253  Args    : A symbol (optional).
 254
 255 =cut
 256
 257 sub symbol {
 258     my ( $self, $value ) = @_;
 259
 260     if ( defined $value ) {
 261         $self->{ "_symbol" } = $value;
 262     }
 263
 264     return $self->{ "_symbol" };
 265
 266 } # symbol
 267
 268
 269
 270
 271 =head2 description
 272
 273  Title   : description
 274  Usage   : $av->description( "The ALDH2*2-encoded protein has a change ..." );
 275            or
 276            print $av->description();
 277  Function: Set/get for the description of this OMIMentryAllelicVariant.
 278  Returns : A description.
 279  Args    : A description (optional).
 280
 281 =cut
 282
 283 sub description {
 284     my ( $self, $value ) = @_;
 285
 286     if ( defined $value ) {
 287         $self->{ "_description" } = $value;
 288     }
 289
 290     return $self->{ "_description" };
 291
 292 } # description
 293
 294
 295
 296
 297 =head2 aa_ori
 298
 299  Title   : aa_ori
 300  Usage   : $av->aa_ori( "GLU" );
 301            or
 302            print $av->aa_ori();
 303  Function: Set/get for the original amino acid(s).
 304  Returns : The original amino acid(s).
 305  Args    : The original amino acid(s) (optional).
 306
 307 =cut
 308
 309 sub aa_ori {
 310     my ( $self, $value ) = @_;
 311
 312     if ( defined $value ) {
 313         $self->{ "_aa_ori" } = $value;
 314     }
 315
 316     return $self->{ "_aa_ori" };
 317
 318 } # aa_ori
 319
 320
 321
 322
 323 =head2 aa_mut
 324
 325  Title   : aa_mut
 326  Usage   : $av->aa_mut( "LYS" );
 327            or
 328            print $av->aa_mut();
 329  Function: Set/get for the mutated amino acid(s).
 330  Returns : The mutated amino acid(s).
 331  Args    : The mutated amino acid(s) (optional).
 332
 333 =cut
 334
 335 sub aa_mut {
 336     my ( $self, $value ) = @_;
 337
 338     if ( defined $value ) {
 339         $self->{ "_aa_mut" } = $value;
 340     }
 341
 342     return $self->{ "_aa_mut" };
 343
 344 } # aa_mut
 345
 346
 347
 348
 349 =head2 position
 350
 351  Title   : position
 352  Usage   : $av->position( 487 );
 353            or
 354            print $av->position();
 355  Function: Set/get for the position of the mutation.
 356  Returns : The position of the mutation.
 357  Args    : The position of the mutation (optional).
 358
 359 =cut
 360
 361 sub position {
 362     my ( $self, $value ) = @_;
 363
 364     if ( defined $value ) {
 365         $self->{ "_position" } = $value;
 366     }
 367
 368     return $self->{ "_position" };
 369
 370 } # position
 371
 372
 373
 374
 375 =head2 additional_mutations
 376
 377  Title   : additional_mutations
 378  Usage   : $av->additional_mutations( "1-BP DEL, 911T" );
 379            or
 380            print $av->additional_mutations();
 381  Function: Set/get for free form description of (additional) mutation(s).
 382  Returns : description of (additional) mutation(s).
 383  Args    : description of (additional) mutation(s) (optional).
 384
 385 =cut
 386
 387 sub additional_mutations {
 388     my ( $self, $value ) = @_;
 389
 390     if ( defined $value ) {
 391         $self->{ "_additional_mutations" } = $value;
 392     }
 393
 394     return $self->{ "_additional_mutations" };
 395
 396 } # additional_mutations
 397
 398
 399
 400 =head2 to_string
 401
 402  Title   : to_string()
 403  Usage   : print $av->to_string();
 404  Function: To string method for OMIMentryAllelicVariant objects.
 405  Returns : A string representations of this OMIMentryAllelicVariant.
 406  Args    :
 407
 408 =cut
 409
 410 sub to_string {
 411     my( $self ) = @_;
 412
 413     my $s = "";
 414
 415     $s .= "-- Number:\n";
 416     $s .= $self->number()."\n";
 417     $s .= "-- Title:\n";
 418     $s .= $self->title()."\n";
 419     $s .= "-- Symbol:\n";
 420     $s .= $self->symbol()."\n";
 421     $s .= "-- Description:\n";
 422     $s .= $self->description()."\n";
 423     $s .= "-- Original AA(s):\n";
 424     $s .= $self->aa_ori()."\n";
 425     $s .= "-- Mutated AA(s):\n";
 426     $s .= $self->aa_mut()."\n";
 427     $s .= "-- Position:\n";
 428     $s .= $self->position()."\n";
 429     $s .= "-- Additional Mutation(s):\n";
 430     $s .= $self->additional_mutations();
 431
 432     return $s;
 433
 434 } # to_string
 435
 436
 437
 438
 439 1;