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Genetics-0.03
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/ Genetics::Subject

NAME

Genetics::Subject

SYNOPSIS

  $subject = new Genetics::Subject(name => 'JXPed1-1',
                                   importID => 12,
                                   dateCreated => $today,
                                   NameAliases => [ {name => "jb2002", 
                                                     contactName => "Gregor Mendel"}
                                                  ], 
                                   Contact => {name => "J.P. Morgan, II", 
                                               comment => "Referring physican"}, 
                                   DBXReferences => [ {accessionNumber => "abc123",
                                                       databaseName => "Clinical Land",
                                                       schemaName => "Master",
                                                       comment => "Internal Clinical DB"}
                                                    ],
                                   Keywords => [ {name => "Study Population", 
                                                  dataType => "String", 
                                                  description => "Internal study identifier.", 
                                                  value => "Test"},
                                                 {name => "Foo", 
                                                  dataType => "String", 
                                                  description => "Crap", 
                                                  value => "Bar"},
                                                 {name => "Test Data", 
                                                  dataType => "Boolean", 
                                                  value => 1}, 
                                               ], 
                                   gender => "Male",
                                   dateOfBirth => "1937-08-18", 
                                   dateOfDeath => "1997-02-15",
                                   isProband => 1,
                                   Mother => {name => "JXPed1-2", importID => 32}, 
                                   Father => {name => "JXPed1-3", importID => 22}, 
                                   Kindred => {name => "JXPed1", importID => 264}, 
                                   Organism => {genusSpecies => "Homo sapiens"},
                                  ) ;

See the GenPerl Tutorial for more information.

DESCRIPTION

Subject objects represent the individuals in genetic studies.

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

hasParents

  Function  : Find out if a Subject has parents.
  Argument  : N/A
  Returns   : 1 if a Subject has both a Mother and Father, 0 otherwise.
  Scope     : Public
  Comments  : Only checks for references in the Mother and Father fields; 
              does not check whether or not these references point to valid 
              Subjects.

getMotherName

  Function  : Get a Subject's Mother's name.
  Argument  : N/A
  Returns   : String
  Scope     : Public
  Comments  :

getFatherName

  Function  : Get a Subject's Father's name.
  Argument  : N/A
  Returns   : String
  Scope     : Public
  Comments  :

printXML

  Function  : Print an XML representation of the object.
  Argument  : A Genetics::Subject object and the XML::Writer object being used 
              to generate the XML.
  Returns   : N/A
  Scope     : Public Instance Method
  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::Subject 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.