Phenotype.pm

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

- printXML
- asHTML

# NAME

Genetics::Phenotype

# SYNOPSIS

      $pt = new Genetics::Phenotype(name => 'JXPed1-1-Age',
                                    importID => 266,
                                    dateCreated => $today,
                                    dateCollected => "1987-03-17",
                                    Keywords => [ {name => "Test Data",
                                                   dataType => "Boolean",
                                                   value => 1},
                                                ],
                                    Subject => {name => "JXPed1-1", importID => 12},
                                    StudyVariable => {name => "Age", importID => 444},
                                    AssayAttrs => [ {name => "Clinic Name",
                                                     dataType => "String",
                                                     value => "Sister of Gracious Mercy and Hope"},
                                                  ],
                                    value => 12,
                                    isActive => 1,
                                   ) ;

    See the GenPerl Tutorial for more information.

# DESCRIPTION

Phenotype objects represent the experimentally determined value an individual has for a trait, affection status, environmental exposure, or drug treatment.

# 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              Print an XML representation of the object

## printXML

      Function  : Print an XML representation of the object.
      Argument  : A Genetics::Genotype object and the 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::Phenotype 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.