Bio/Phenotype/OMIM/MiniMIMentry.pm

   1 #
   2 # BioPerl module for Bio::Phenotype::OMIM::MiniMIMentry
   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::MiniMIMentry - Representation of a Mini MIM entry
  27
  28 =head1 SYNOPSIS
  29
  30   use Bio::Phenotype::OMIM::MiniMIMentry;
  31
  32   $mm = Bio::Phenotype::OMIM::MiniMIMentry->new( -description  => "The central form of ...",
  33                                                  -created      => "Victor A. McKusick: 6/4/1986",
  34                                                  -contributors => "Kelly A. Przylepa - revised: 03/18/2002",
  35                                                  -edited       => "alopez: 06/03/1997" );
  36
  37
  38 =head1 DESCRIPTION
  39
  40 This class representats of Mini MIM entries.
  41 This class is intended to be used together with a OMIM entry class.
  42
  43
  44 =head1 FEEDBACK
  45
  46 =head2 Mailing Lists
  47
  48 User feedback is an integral part of the evolution of this and other
  49 Bioperl modules. Send your comments and suggestions preferably to one
  50 of the Bioperl mailing lists.  Your participation is much appreciated.
  51
  52   bioperl-l@bioperl.org                  - General discussion
  53   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  54
  55 =head2 Support
  56
  57 Please direct usage questions or support issues to the mailing list:
  58
  59 I<bioperl-l@bioperl.org>
  60
  61 rather than to the module maintainer directly. Many experienced and
  62 reponsive experts will be able look at the problem and quickly
  63 address it. Please include a thorough description of the problem
  64 with code and data examples if at all possible.
  65
  66 =head2 Reporting Bugs
  67
  68 Report bugs to the Bioperl bug tracking system to help us keep track
  69 the bugs and their resolution.  Bug reports can be submitted via the
  70 web:
  71
  72   https://github.com/bioperl/bioperl-live/issues
  73
  74 =head1 AUTHOR
  75
  76 Christian M. Zmasek
  77
  78 Email: czmasek-at-burnham.org  or  cmzmasek@yahoo.com
  79
  80 WWW:   http://monochrome-effect.net/
  81
  82 Address:
  83
  84   Genomics Institute of the Novartis Research Foundation
  85   10675 John Jay Hopkins Drive
  86   San Diego, CA 92121
  87
  88 =head1 APPENDIX
  89
  90 The rest of the documentation details each of the object
  91 methods.
  92
  93 =cut
  94
  95
  96 # Let the code begin...
  97
  98 package Bio::Phenotype::OMIM::MiniMIMentry;
  99 use strict;
 100
 101 use base qw(Bio::Root::Root);
 102
 103 =head2 new
 104
 105  Title   : new
 106  Usage   : $mm = Bio::Phenotype::OMIM::MiniMIMentry->new( -description  => "The central form of ...",
 107                                                           -created      => "Victor A. McKusick: 6/4/1986",
 108                                                           -contributors => "Kelly A. Przylepa - revised: 03/18/2002",
 109                                                           -edited       => "alopez: 06/03/1997" );
 110
 111  Function: Creates a new MiniMIMentry object.
 112  Returns : A new MiniMIMentry object.
 113  Args    : -description  => a description
 114            -created      => name(s) and date(s) (free form)
 115            -contributors => name(s) and date(s) (free form)
 116            -edited       => name(s) and date(s) (free form)
 117
 118 =cut
 119
 120 sub new {
 121
 122     my( $class, @args ) = @_;
 123
 124     my $self = $class->SUPER::new( @args );
 125
 126     my ( $desc, $created, $contributors, $edited )
 127     = $self->_rearrange( [ qw( DESCRIPTION
 128                                CREATED
 129                                CONTRIBUTORS
 130                                EDITED ) ], @args );
 131
 132     $self->init();
 133
 134     $desc         && $self->description( $desc );
 135     $created      && $self->created( $created );
 136     $contributors && $self->contributors( $contributors );
 137     $edited       && $self->edited( $edited );
 138
 139     return $self;
 140
 141 } # new
 142
 143
 144
 145
 146 =head2 init
 147
 148  Title   : init()
 149  Usage   : $mm->init();
 150  Function: Initializes this MiniMIMentry to all "".
 151  Returns :
 152  Args    :
 153
 154 =cut
 155
 156 sub init {
 157
 158     my( $self ) = @_;
 159
 160     $self->description( "" );
 161     $self->created( "" );
 162     $self->contributors( "" );
 163     $self->edited( "" );
 164
 165
 166 } # init
 167
 168
 169
 170
 171 =head2 description
 172
 173  Title   : description
 174  Usage   : $mm->description( "The central form of ..." );
 175            or
 176            print $mm->description();
 177  Function: Set/get for the description field of the Mini MIM database.
 178  Returns : The description.
 179  Args    : The description (optional).
 180
 181 =cut
 182
 183 sub description {
 184     my ( $self, $value ) = @_;
 185
 186     if ( defined $value ) {
 187         $self->{ "_description" } = $value;
 188     }
 189
 190     return $self->{ "_description" };
 191
 192 } # description
 193
 194
 195
 196
 197 =head2 created
 198
 199  Title   : created
 200  Usage   : $mm->created( "Victor A. McKusick: 6/4/1986" );
 201            or
 202            print $mm->created();
 203  Function: Set/get for the created field of the Mini MIM database.
 204  Returns : Name(s) and date(s) [scalar - free form].
 205  Args    : Name(s) and date(s) [scalar - free form] (optional).
 206
 207 =cut
 208
 209 sub created {
 210     my ( $self, $value ) = @_;
 211
 212     if ( defined $value ) {
 213         $self->{ "_created" } = $value;
 214     }
 215
 216     return $self->{ "_created" };
 217
 218 } # created
 219
 220
 221
 222
 223 =head2 contributors
 224
 225  Title   : contributors
 226  Usage   : $mm->contributors( "Kelly A. Przylepa - revised: 03/18/2002" );
 227            or
 228            print $mm->contributors();
 229  Function: Set/get for the contributors field of the Mini MIM database.
 230  Returns : Name(s) and date(s) [scalar - free form].
 231  Args    : Name(s) and date(s) [scalar - free form] (optional).
 232
 233 =cut
 234
 235 sub contributors {
 236     my ( $self, $value ) = @_;
 237
 238     if ( defined $value ) {
 239         $self->{ "_contributors" } = $value;
 240     }
 241
 242     return $self->{ "_contributors" };
 243
 244 } # contributors
 245
 246
 247
 248
 249 =head2 edited
 250
 251  Title   : edited
 252  Usage   : $mm->edited( "alopez: 06/03/1997" );
 253            or
 254            print $mm->edited();
 255  Function: Set/get for the edited field of the Mini MIM database.
 256  Returns : Name(s) and date(s) [scalar - free form].
 257  Args    : Name(s) and date(s) [scalar - free form] (optional).
 258
 259 =cut
 260
 261 sub edited {
 262     my ( $self, $value ) = @_;
 263
 264     if ( defined $value ) {
 265         $self->{ "_edited" } = $value;
 266     }
 267
 268     return $self->{ "_edited" };
 269
 270 } # edited
 271
 272
 273
 274
 275 =head2 to_string
 276
 277  Title   : to_string()
 278  Usage   : print $mm->to_string();
 279  Function: To string method for MiniMIMentry objects.
 280  Returns : A string representations of this MiniMIMentry.
 281  Args    :
 282
 283 =cut
 284
 285 sub to_string {
 286     my ( $self ) = @_;
 287
 288     my $s = "";
 289
 290     $s .= "-- Description:\n";
 291     $s .= $self->description()."\n";
 292     $s .= "-- Created:\n";
 293     $s .= $self->created()."\n";
 294     $s .= "-- Contributors:\n";
 295     $s .= $self->contributors()."\n";
 296     $s .= "-- Edited:\n";
 297     $s .= $self->edited();
 298
 299     return $s;
 300
 301 } # to_string
 302
 303
 304 1;