Genotype.pm

- NAME
- SYNOPSIS
- DESCRIPTION
- LICENSE
- FEEDBACK
- AUTHOR - Steve Mathias
- DETAILS
- Imported Packages
- Public methods

- printXML
- asHTML

# 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.