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# GenPerl module 
#

# POD documentation - main docs before the code

=head1 NAME

Genetics::StudyVariable

=head1 SYNOPSIS

  $sv = new Genetics::StudyVariable(name => 'EA Aff Stat',
				    importID => 445,
				    dateCreated => $today,
				    Keywords => [ {name => "Test Data", 
						   dataType => "Boolean", 
						   value => 1}, 
						], 
				    description => "EA Trait Locus", 
				    category => "AffectionStatus", 
				    format => "Code", 
				    isXLinked => 0, 
				    Codes => [ {code => 0,
						description => "Unknown EA Status"},
					       {code => 1,
						description => "EA Unaffected"},
					       {code => 2,
						description => "EA Affected"},
					     ], 
				    AffStatDef => {name => 'EA',
						   diseaseAlleleFreq => 0.001,
						   pen11 => 0.0,
						   pen12 => 0.0,
						   pen22 => 1.0,
						   AffStatElements => [ {code => 0,
									 type => "Unknown",
									 formula => "'EA Aff Stat' = 0"}, 
									{code => 1,
									 type => "Unaffected",
									 formula => "'EA Aff Stat' = 1"}, 
									{code => 2,
									 type => "Affected",
									 formula => "'EA Aff Stat' = 2"}, 
								      ],
						  },
				    LCDef => {name => 'EA Default LC',
					      LiabilityClasses => [ {code => 0,
								     description => "Unknown Age",
								     pen11 => 0.0,
								     pen12 => 0.0,
								     pen22 => 1.0,
								     formula => "'Age' = ''"}, 
								    {code => 1,
								     description => "Age less than 40",
								     pen11 => 0.0,
								     pen12 => 0.2,
								     pen22 => 1.0,
								     formula => "'Age' < 40"}, 
								    {code => 2,
								     description => "Age less than 50",
								     pen11 => 0.0,
								     pen12 => 0.3,
								     pen22 => 1.0,
								     formula => "'Age' < 50"}, 
								    {code => 3,
								     description => "Age grater than or equal to 60",
								     pen11 => 0.0,
								     pen12 => 0.4,
								     pen22 => 1.0,
								     formula => "'Age' >= 60"}, 
								  ],
					     },
				   ) ;
  
See the GenPerl Tutorial for more information.

=head1 DESCRIPTION

StudyVariable objects represent definitions of physical traits, affection 
status loci, environmental exposure, or drug treatments.

=head1 LICENSE

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA

=head1 FEEDBACK

Currently, all feedback should be sent directly to the author.

=head1 AUTHOR - Steve Mathias

Email: mathias@genomica.com

Phone: (720) 565-4029

Address: Genomica Corporation 
         1745 38th Street
         Boulder, CO 80301

=head1 DETAILS

The rest of the documentation describes each of the object variables and 
methods. The names of internal variables and methods are preceded with an
underscore (_).

=cut

##################
#                #
# Begin the code #
#                #
##################

package Genetics::StudyVariable ;

BEGIN {
  $ID = "Genetics::StudyVariable" ;
  #$DEBUG = $main::DEBUG ;