NAME

Genetics::Genotype

SYNOPSIS

  $gt = new Genetics::Genotype(name => '1-D12S91',
			       importID => 13,
			       dateCreated => $today,
			       Keywords => [ {name => "Test Data", 
					      dataType => "Boolean", 
					      value => 1}, 
					   ], 
			       isActive => 1,
			       icResult => "Pass",
			       dateCollected => "1993-11-13",
			       Subject => {name => "EAPed20.1", importID => 12},
			       Marker => {name => "D12S91", importID => 1},
			       AssayAttrs => [ {name => "lab",
						dataType=> "string",
						value => "Lab 6"}, 
					       {name => "machineID",
						dataType => "String",
						value => "ABC1234"}
					     ],
			       AlleleCalls => [ {alleleName => 3, 
						 alleleType => "Code", 
						 phase => "Maternal", 
						 AssayAttrs => [ {name => "peakHeight",
								  dataType => "Number",
								  value => 367} ]
						},
						{alleleName => 1, 
						 alleleType => "Code", 
						 phase => "Paternal", 
						 AssayAttrs => [ {name => "peakHeight",
								  dataType => "Number",
								  value => 435} ]
						},
					      ]
			      ) ;

See the GenPerl Tutorial for more information.

DESCRIPTION

A Perl class encapsulating data associated with GNOM Genotype objects. Genotype objects represent the experimentally determined set of alleles that an individual has at a genetic marker.

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

FEEDBACK

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

AUTHOR - Steve Mathias

Email: mathias@genomica.com

Phone: (720) 565-4029

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

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 (_).

Imported Packages

Genetics::Object       Superclass
strict			Just to be anal
vars			Global variables

Public methods

printXML

Function  : Print an XML representation of the object.
Argument  : An XML::Writer object being used to generate the XML.
Returns   : String
Scope     : Public
Comments  : Calls Genetics::Object->printGeneralXML to generate XML elements
            common to all Genetics::Object objects.

asHTML

Function  : Generate an HTML representation of the object.
Argument  : A Genetics::Genotype object and a scalar containing the name 
            of the GenPerl database in which the object is stored. 
Returns   : Scalar containing the HTML text.
Scope     : Public Instance Method
Comments  : Calls Genetics::Object->_generalHTMLParam to generate HTML 
            elements common to all Genetics::Object objects.  An 
            HTML::Template object is used to actually generate the HTML.