Marker.pm

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

- printXML
- asHTML

# 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.