Bio/Phenotype/Measure.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Phenotype::Measure
   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::Measure - Representation of context/value(-range)/unit triplets
  26
  27 =head1 SYNOPSIS
  28
  29   use Bio::Phenotype::Measure;
  30
  31   my $measure = Bio::Phenotype::Measure->new( -context     => "length",
  32                                               -description => "reduced length in 4(Tas1r3)",
  33                                               -start       => 0,
  34                                               -end         => 15,
  35                                               -unit        => "mm",
  36                                               -comment     => "see also Miller et al" );
  37
  38   print $measure->context();
  39   print $measure->description();
  40   print $measure->start();
  41   print $measure->end();
  42   print $measure->unit();
  43   print $measure->comment();
  44
  45   print $measure->to_string();
  46
  47 =head1 DESCRIPTION
  48
  49 Measure is for biochemically defined phenotypes or any other types of measures.
  50
  51 =head1 FEEDBACK
  52
  53 =head2 Mailing Lists
  54
  55 User feedback is an integral part of the evolution of this and other
  56 Bioperl modules. Send your comments and suggestions preferably to one
  57 of the Bioperl mailing lists.  Your participation is much appreciated.
  58
  59   bioperl-l@bioperl.org                  - General discussion
  60   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  61
  62 =head2 Reporting Bugs
  63
  64 Report bugs to the Bioperl bug tracking system to help us keep track
  65 the bugs and their resolution.  Bug reports can be submitted via the
  66 web:
  67
  68   http://bugzilla.open-bio.org/
  69
  70 =head1 AUTHOR
  71
  72 Christian M. Zmasek
  73
  74 Email: czmasek@gnf.org  or  cmzmasek@yahoo.com
  75
  76 WWW:   http://www.genetics.wustl.edu/eddy/people/zmasek/
  77
  78 Address:
  79
  80   Genomics Institute of the Novartis Research Foundation
  81   10675 John Jay Hopkins Drive
  82   San Diego, CA 92121
  83
  84 =head1 APPENDIX
  85
  86 The rest of the documentation details each of the object
  87 methods.
  88
  89 =cut
  90
  91
  92 # Let the code begin...
  93
  94 package Bio::Phenotype::Measure;
  95 use strict;
  96
  97 use base qw(Bio::Root::Root);
  98
  99
 100 =head2 new
 101
 102  Title   : new
 103  Usage   : my $me = Bio::Phenotype::Measure->new( -context     => "length",
 104                                                   -description => "reduced length in 4(Tas1r3)",
 105                                                   -start       => 0,
 106                                                   -end         => 15,
 107                                                   -unit        => "mm",
 108                                                   -comment     => "see Miller also et al" );
 109  Function: Creates a new Measure object.
 110  Returns : A new Measure object.
 111  Args    : -context     => the context
 112            -description => a description
 113            -start       => the start value
 114            -end         => the end value
 115            -unit        => the unit
 116            -comment     => a comment
 117
 118 =cut
 119
 120 sub new {
 121     my( $class, @args ) = @_;
 122
 123     my $self = $class->SUPER::new( @args );
 124
 125     my ( $con, $desc, $start, $end, $unit, $comment )
 126     = $self->_rearrange( [ qw( CONTEXT
 127                                DESCRIPTION
 128                                START
 129                                END
 130                                UNIT
 131                                COMMENT ) ], @args );
 132
 133     $self->init();
 134
 135     $con     && $self->context( $con );
 136     $desc    && $self->description( $desc );
 137     $start   && $self->start( $start );
 138     $end     && $self->end( $end );
 139     $unit    && $self->unit( $unit );
 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   : $measure->init();
 153  Function: Initializes this Measure to all "".
 154  Returns :
 155  Args    :
 156
 157 =cut
 158
 159 sub init {
 160     my( $self ) = @_;
 161
 162     $self->context( "" );
 163     $self->description( "" );
 164     $self->start( "" );
 165     $self->end( "" );
 166     $self->unit( "" );
 167     $self->comment( "" );
 168
 169 } # init
 170
 171
 172
 173
 174 =head2 context
 175
 176  Title   : context
 177  Usage   : $measure->context( "Ca-conc" );
 178            or
 179            print $measure->context();
 180  Function: Set/get for the context of this Measure.
 181  Returns : The context.
 182  Args    : The context (optional).
 183
 184 =cut
 185
 186 sub context {
 187     my ( $self, $value ) = @_;
 188
 189     if ( defined $value ) {
 190         $self->{ "_context" } = $value;
 191     }
 192
 193     return $self->{ "_context" };
 194
 195 } # context
 196
 197
 198
 199
 200 =head2 description
 201
 202  Title   : description
 203  Usage   : $measure->description( "reduced in 4(Tas1r3)" );
 204            or
 205            print $measure->description();
 206  Function: Set/get for the description of this Measure.
 207  Returns : A description.
 208  Args    : A description (optional).
 209
 210 =cut
 211
 212 sub description {
 213     my ( $self, $value ) = @_;
 214
 215     if ( defined $value ) {
 216         $self->{ "_description" } = $value;
 217     }
 218
 219     return $self->{ "_description" };
 220
 221 } # description
 222
 223
 224
 225
 226 =head2 start
 227
 228  Title   : start
 229  Usage   : $measure->start( 330 );
 230            or
 231            print $measure->start();
 232  Function: Set/get for the start value of this Measure.
 233  Returns : The start value.
 234  Args    : The start value (optional).
 235
 236 =cut
 237
 238 sub start {
 239     my ( $self, $value ) = @_;
 240
 241     if ( defined $value ) {
 242         $self->{ "_start" } = $value;
 243     }
 244
 245     return $self->{ "_start" };
 246
 247 } #  start
 248
 249
 250
 251
 252 =head2 end
 253
 254  Title   : end
 255  Usage   : $measure->end( 459 );
 256            or
 257            print $measure->end();
 258  Function: Set/get for the end value of this Measure.
 259  Returns : The end value.
 260  Args    : The end value (optional).
 261
 262 =cut
 263
 264 sub end {
 265     my ( $self, $value ) = @_;
 266
 267     if ( defined $value ) {
 268         $self->{ "_end" } = $value;
 269     }
 270
 271     return $self->{ "_end" };
 272
 273 } # end
 274
 275
 276
 277
 278 =head2 unit
 279
 280  Title   : unit
 281  Usage   : $measure->unit( "mM" );
 282            or
 283            print $measure->unit();
 284  Function: Set/get for the unit of this Measure.
 285  Returns : The unit.
 286  Args    : The unit (optional).
 287
 288 =cut
 289
 290 sub unit {
 291     my ( $self, $value ) = @_;
 292
 293     if ( defined $value ) {
 294         $self->{ "_unit" } = $value;
 295     }
 296
 297     return $self->{ "_unit" };
 298
 299 } # unit
 300
 301
 302
 303
 304 =head2 comment
 305
 306  Title   : comment
 307  Usage   : $measure->comment( "see also Miller et al" );
 308            or
 309            print $measure->comment();
 310  Function: Set/get for an arbitrary comment about this Measure.
 311  Returns : A comment.
 312  Args    : A comment (optional).
 313
 314 =cut
 315
 316 sub comment {
 317     my ( $self, $value ) = @_;
 318
 319     if ( defined $value ) {
 320         $self->{ "_comment" } = $value;
 321     }
 322
 323     return $self->{ "_comment" };
 324
 325 } # comment
 326
 327
 328
 329
 330 =head2 to_string
 331
 332  Title   : to_string()
 333  Usage   : print $measure->to_string();
 334  Function: To string method for Measure objects.
 335  Returns : A string representations of this Measure.
 336  Args    :
 337
 338 =cut
 339
 340 sub to_string {
 341     my ( $self ) = @_;
 342
 343     my $s = "";
 344
 345     $s .= "-- Context:\n";
 346     $s .= $self->context()."\n";
 347     $s .= "-- Description:\n";
 348     $s .= $self->description()."\n";
 349     $s .= "-- Start:\n";
 350     $s .= $self->start()."\n";
 351     $s .= "-- End:\n";
 352     $s .= $self->end()."\n";
 353     $s .= "-- Unit:\n";
 354     $s .= $self->unit()."\n";
 355     $s .= "-- Comment:\n";
 356     $s .= $self->comment();
 357
 358     return $s;
 359
 360 } # to_string
 361
 362
 363
 364 1;