/ 
Genetics-0.03
River stage zero No dependents
/ Genetics::Marker

NAME

Genetics::Marker

SYNOPSIS

  $marker = new Genetics::Marker(name => 'D12S91',
				 importID => 1,
				 dateCreated => $today,
				 comment => "Marker in EA critical region",
				 NameAliases => [ {name => "d12s6666"}
						], 
				 Contact => {name => "Jean Weissenbach",
					     organization => "Genethon"}, 
				 DBXReferences => [ {accessionNumber => "NT_009758.3",
						     databaseName => "GenBank"}
						  ],
				 Keywords => [ {name => "Test Data", 
						dataType => "Boolean", 
						value => 1},
					     ], 
				 chromosome => "12", 
				 malePloidy => 2,
				 femalePloidy => 2,
				 polymorphismType => "Repeat", 
				 polymorphismIndex1 => 7, 
				 polymorphismIndex2 => 11, 
				 repeatSequence => "CA",
				 Organism => {genusSpecies => "Homo sapiens"},
				 Alleles => [ {name => 1, type => "Code"}, 
					      {name => 2, type => "Code"},
					      {name => 3, type => "Code"},
					      {name => 4, type => "Code"},
					      {name => 5, type => "Code"},
					      {name => 6, type => "Code"} ],
				 ISCNMapLocations => [ {chrNumber => "12", 
							chrArm => "p", 
							band => "12.2.1", 
							bandingMethod => "Geimsa"}, ],
				 Sequence => {lengthUnits => "bp",
					      length => 17,
					      sequence => "ACGTUMRCACAWSYKVHDBXN"},
				) ;

See the GenPerl Tutorial for more information.

DESCRIPTION

Marker objects represent polymorphic genetic markers.

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  : 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::Marker 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.