Bio::Phenotype::OMIM::OMIMentryAllelicVariant(3pm)	User Contributed Perl Documentation	Bio::Phenotype::OMIM::OMIMentryAllelicVariant(3pm)

NAME

       Bio::Phenotype::OMIM::OMIMentryAllelicVariant - Representation of a allelic variant of the OMIM database

SYNOPSIS

	 use Bio::Phenotype::OMIM::OMIMentryAllelicVariant;

	 $av = Bio::Phenotype::OMIM::OMIMentryAllelicVariant->new( -number		 => ".0001",
								   -title		 => "ALCOHOL INTOLERANCE",
								   -symbol		 => "ALDH2*2",
								   -description 	 => "The ALDH2*2-encoded ...",
								   -aa_ori		 => "GLU",
								   -aa_mut		 => "LYS",
								   -position		 => 487,
								   -additional_mutations => "IVS4DS, G-A, +1" );

DESCRIPTION

       This class models the allelic variant of the OMIM database.  This class is intended to be used together with a OMIM entry class.

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one
       of the Bioperl mailing lists.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution.  Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR

       Christian M. Zmasek

       Email: czmasek-at-burnham.org  or  cmzmasek@yahoo.com

       WWW:   http://monochrome-effect.net/

       Address:

	 Genomics Institute of the Novartis Research Foundation
	 10675 John Jay Hopkins Drive
	 San Diego, CA 92121

APPENDIX

       The rest of the documentation details each of the object methods.

   new
	Title	: new
	Usage	: $av = Bio::Phenotype::OMIM::OMIMentryAllelicVariant->new( -number		  => ".0001",
									    -title		  => "ALCOHOL INTOLERANCE",
									    -symbol		  => "ALDH2*2",
									    -description	  => "The ALDH2*2-encoded ...",
									    -aa_ori		  => "GLU",
									    -aa_mut		  => "LYS",
									    -position		  => 487,
									    -additional_mutations => "IVS4DS, G-A, +1" );
	Function: Creates a new OMIMentryAllelicVariant object.
	Returns : A new OMIMentryAllelicVariant object.
	Args	: -number		=> the OMIM allelic variant number
		  -title		=> the title
		  -symbol		=> a symbol
		  -description		=> a description
		  -aa_ori		=> the original amino acid
		  -aa_mut		=> the mutated amino acid
		  -position		=> the position of the mutation
		  -additional_mutations => free form description of additional mutations

   init
	Title	: init()
	Usage	: $av->init();
	Function: Initializes this OMIMentryAllelicVariant to all "".
	Returns :
	Args	:

   number
	Title	: number
	Usage	: $av->number( ".0001" );
		  or
		  print $av->number();
	Function: Set/get for the OMIM allelic variant number of this
		  OMIMentryAllelicVariant.
	Returns : The OMIM allelic variant number.
	Args	: The OMIM allelic variant number (optional).

   title
	Title	: title
	Usage	: $av->title( "ALCOHOL INTOLERANCE" );
		  or
		  print $av->title();
	Function: Set/get for the title of this OMIMentryAllelicVariant.
	Returns : The title.
	Args	: The title (optional).

   symbol
	Title	: symbol
	Usage	: $av->symbol( "ALDH2*2" );
		  or
		  print $av->symbol();
	Function: Set/get for the symbol of this OMIMentryAllelicVariant.
	Returns : A symbol.
	Args	: A symbol (optional).

   description
	Title	: description
	Usage	: $av->description( "The ALDH2*2-encoded protein has a change ..." );
		  or
		  print $av->description();
	Function: Set/get for the description of this OMIMentryAllelicVariant.
	Returns : A description.
	Args	: A description (optional).

   aa_ori
	Title	: aa_ori
	Usage	: $av->aa_ori( "GLU" );
		  or
		  print $av->aa_ori();
	Function: Set/get for the original amino acid(s).
	Returns : The original amino acid(s).
	Args	: The original amino acid(s) (optional).

   aa_mut
	Title	: aa_mut
	Usage	: $av->aa_mut( "LYS" );
		  or
		  print $av->aa_mut();
	Function: Set/get for the mutated amino acid(s).
	Returns : The mutated amino acid(s).
	Args	: The mutated amino acid(s) (optional).

   position
	Title	: position
	Usage	: $av->position( 487 );
		  or
		  print $av->position();
	Function: Set/get for the position of the mutation.
	Returns : The position of the mutation.
	Args	: The position of the mutation (optional).

   additional_mutations
	Title	: additional_mutations
	Usage	: $av->additional_mutations( "1-BP DEL, 911T" );
		  or
		  print $av->additional_mutations();
	Function: Set/get for free form description of (additional) mutation(s).
	Returns : description of (additional) mutation(s).
	Args	: description of (additional) mutation(s) (optional).

   to_string
	Title	: to_string()
	Usage	: print $av->to_string();
	Function: To string method for OMIMentryAllelicVariant objects.
	Returns : A string representations of this OMIMentryAllelicVariant.
	Args	:

perl v5.14.2							    2012-03-02			Bio::Phenotype::OMIM::OMIMentryAllelicVariant(3pm)