Bio/Phenotype/Measure.pm

   1 #
   2 # BioPerl module for Bio::Phenotype::Measure
   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::Measure - Representation of context/value(-range)/unit triplets
  27
  28 =head1 SYNOPSIS
  29
  30   use Bio::Phenotype::Measure;
  31
  32   my $measure = Bio::Phenotype::Measure->new( -context     => "length",
  33                                               -description => "reduced length in 4(Tas1r3)",
  34                                               -start       => 0,
  35                                               -end         => 15,
  36                                               -unit        => "mm",
  37                                               -comment     => "see also Miller et al" );
  38
  39   print $measure->context();
  40   print $measure->description();
  41   print $measure->start();
  42   print $measure->end();
  43   print $measure->unit();
  44   print $measure->comment();
  45
  46   print $measure->to_string();
  47
  48 =head1 DESCRIPTION
  49
  50 Measure is for biochemically defined phenotypes or any other types of measures.
  51
  52 =head1 FEEDBACK
  53
  54 =head2 Mailing Lists
  55
  56 User feedback is an integral part of the evolution of this and other
  57 Bioperl modules. Send your comments and suggestions preferably to one
  58 of the Bioperl mailing lists.  Your participation is much appreciated.
  59
  60   bioperl-l@bioperl.org                  - General discussion
  61   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  62
  63 =head2 Support
  64
  65 Please direct usage questions or support issues to the mailing list:
  66
  67 I<bioperl-l@bioperl.org>
  68
  69 rather than to the module maintainer directly. Many experienced and
  70 reponsive experts will be able look at the problem and quickly
  71 address it. Please include a thorough description of the problem
  72 with code and data examples if at all possible.
  73
  74 =head2 Reporting Bugs
  75
  76 Report bugs to the Bioperl bug tracking system to help us keep track
  77 the bugs and their resolution.  Bug reports can be submitted via the
  78 web:
  79
  80   https://github.com/bioperl/bioperl-live/issues
  81
  82 =head1 AUTHOR
  83
  84 Christian M. Zmasek
  85
  86 Email: czmasek-at-burnham.org  or  cmzmasek@yahoo.com
  87
  88 WWW:   http://monochrome-effect.net/
  89
  90 Address:
  91
  92   Genomics Institute of the Novartis Research Foundation
  93   10675 John Jay Hopkins Drive
  94   San Diego, CA 92121
  95
  96 =head1 APPENDIX
  97
  98 The rest of the documentation details each of the object
  99 methods.
 100
 101 =cut
 102
 103
 104 # Let the code begin...
 105
 106 package Bio::Phenotype::Measure;
 107 use strict;
 108
 109 use base qw(Bio::Root::Root);
 110
 111
 112 =head2 new
 113
 114  Title   : new
 115  Usage   : my $me = Bio::Phenotype::Measure->new( -context     => "length",
 116                                                   -description => "reduced length in 4(Tas1r3)",
 117                                                   -start       => 0,
 118                                                   -end         => 15,
 119                                                   -unit        => "mm",
 120                                                   -comment     => "see Miller also et al" );
 121  Function: Creates a new Measure object.
 122  Returns : A new Measure object.
 123  Args    : -context     => the context
 124            -description => a description
 125            -start       => the start value
 126            -end         => the end value
 127            -unit        => the unit
 128            -comment     => a comment
 129
 130 =cut
 131
 132 sub new {
 133     my( $class, @args ) = @_;
 134
 135     my $self = $class->SUPER::new( @args );
 136
 137     my ( $con, $desc, $start, $end, $unit, $comment )
 138     = $self->_rearrange( [ qw( CONTEXT
 139                                DESCRIPTION
 140                                START
 141                                END
 142                                UNIT
 143                                COMMENT ) ], @args );
 144
 145     $self->init();
 146
 147     $con     && $self->context( $con );
 148     $desc    && $self->description( $desc );
 149     $start   && $self->start( $start );
 150     $end     && $self->end( $end );
 151     $unit    && $self->unit( $unit );
 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   : $measure->init();
 165  Function: Initializes this Measure to all "".
 166  Returns :
 167  Args    :
 168
 169 =cut
 170
 171 sub init {
 172     my( $self ) = @_;
 173
 174     $self->context( "" );
 175     $self->description( "" );
 176     $self->start( "" );
 177     $self->end( "" );
 178     $self->unit( "" );
 179     $self->comment( "" );
 180
 181 } # init
 182
 183
 184
 185
 186 =head2 context
 187
 188  Title   : context
 189  Usage   : $measure->context( "Ca-conc" );
 190            or
 191            print $measure->context();
 192  Function: Set/get for the context of this Measure.
 193  Returns : The context.
 194  Args    : The context (optional).
 195
 196 =cut
 197
 198 sub context {
 199     my ( $self, $value ) = @_;
 200
 201     if ( defined $value ) {
 202         $self->{ "_context" } = $value;
 203     }
 204
 205     return $self->{ "_context" };
 206
 207 } # context
 208
 209
 210
 211
 212 =head2 description
 213
 214  Title   : description
 215  Usage   : $measure->description( "reduced in 4(Tas1r3)" );
 216            or
 217            print $measure->description();
 218  Function: Set/get for the description of this Measure.
 219  Returns : A description.
 220  Args    : A description (optional).
 221
 222 =cut
 223
 224 sub description {
 225     my ( $self, $value ) = @_;
 226
 227     if ( defined $value ) {
 228         $self->{ "_description" } = $value;
 229     }
 230
 231     return $self->{ "_description" };
 232
 233 } # description
 234
 235
 236
 237
 238 =head2 start
 239
 240  Title   : start
 241  Usage   : $measure->start( 330 );
 242            or
 243            print $measure->start();
 244  Function: Set/get for the start value of this Measure.
 245  Returns : The start value.
 246  Args    : The start value (optional).
 247
 248 =cut
 249
 250 sub start {
 251     my ( $self, $value ) = @_;
 252
 253     if ( defined $value ) {
 254         $self->{ "_start" } = $value;
 255     }
 256
 257     return $self->{ "_start" };
 258
 259 } #  start
 260
 261
 262
 263
 264 =head2 end
 265
 266  Title   : end
 267  Usage   : $measure->end( 459 );
 268            or
 269            print $measure->end();
 270  Function: Set/get for the end value of this Measure.
 271  Returns : The end value.
 272  Args    : The end value (optional).
 273
 274 =cut
 275
 276 sub end {
 277     my ( $self, $value ) = @_;
 278
 279     if ( defined $value ) {
 280         $self->{ "_end" } = $value;
 281     }
 282
 283     return $self->{ "_end" };
 284
 285 } # end
 286
 287
 288
 289
 290 =head2 unit
 291
 292  Title   : unit
 293  Usage   : $measure->unit( "mM" );
 294            or
 295            print $measure->unit();
 296  Function: Set/get for the unit of this Measure.
 297  Returns : The unit.
 298  Args    : The unit (optional).
 299
 300 =cut
 301
 302 sub unit {
 303     my ( $self, $value ) = @_;
 304
 305     if ( defined $value ) {
 306         $self->{ "_unit" } = $value;
 307     }
 308
 309     return $self->{ "_unit" };
 310
 311 } # unit
 312
 313
 314
 315
 316 =head2 comment
 317
 318  Title   : comment
 319  Usage   : $measure->comment( "see also Miller et al" );
 320            or
 321            print $measure->comment();
 322  Function: Set/get for an arbitrary comment about this Measure.
 323  Returns : A comment.
 324  Args    : A comment (optional).
 325
 326 =cut
 327
 328 sub comment {
 329     my ( $self, $value ) = @_;
 330
 331     if ( defined $value ) {
 332         $self->{ "_comment" } = $value;
 333     }
 334
 335     return $self->{ "_comment" };
 336
 337 } # comment
 338
 339
 340
 341
 342 =head2 to_string
 343
 344  Title   : to_string()
 345  Usage   : print $measure->to_string();
 346  Function: To string method for Measure objects.
 347  Returns : A string representations of this Measure.
 348  Args    :
 349
 350 =cut
 351
 352 sub to_string {
 353     my ( $self ) = @_;
 354
 355     my $s = "";
 356
 357     $s .= "-- Context:\n";
 358     $s .= $self->context()."\n";
 359     $s .= "-- Description:\n";
 360     $s .= $self->description()."\n";
 361     $s .= "-- Start:\n";
 362     $s .= $self->start()."\n";
 363     $s .= "-- End:\n";
 364     $s .= $self->end()."\n";
 365     $s .= "-- Unit:\n";
 366     $s .= $self->unit()."\n";
 367     $s .= "-- Comment:\n";
 368     $s .= $self->comment();
 369
 370     return $s;
 371
 372 } # to_string
 373
 374
 375
 376 1;