#
# BioPerl module for Bio::Phenotype::OMIM::OMIMentryAllelicVariant
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Christian M. Zmasek <czmasek-at-burnham.org> or <cmzmasek@yahoo.com>
#
# (c) Christian M. Zmasek, czmasek-at-burnham.org, 2002.
# (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002.
#
# You may distribute this module under the same terms as perl itself.
# Refer to the Perl Artistic License (see the license accompanying this
# software package, or see http://www.perl.com/language/misc/Artistic.html)
# for the terms under which you may use, modify, and redistribute this module.
#
# THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
# WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
# MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Phenotype::OMIM::OMIMentryAllelicVariant - Representation of a allelic
variant of the OMIM database
=head1 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" );
=head1 DESCRIPTION
This class models the allelic variant of the OMIM database.
This class is intended to be used together with a OMIM entry class.
=head1 FEEDBACK
=head2 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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 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/
=head1 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
=head1 APPENDIX
The rest of the documentation details each of the object
methods.
=cut
# Let the code begin...
package Bio::Phenotype::OMIM::OMIMentryAllelicVariant;
use strict;
use base qw(Bio::Root::Root);
=head2 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
=cut
sub new {
my( $class, @args ) = @_;
my $self = $class->SUPER::new( @args );
my ( $number, $title, $symbol, $desc, $ori, $mut, $pos, $am )
= $self->_rearrange( [ qw( NUMBER
TITLE
SYMBOL
DESCRIPTION
AA_ORI
AA_MUT
POSITION
ADDITIONAL_MUTATIONS ) ], @args );
$self->init();
$number && $self->number( $number );
$title && $self->title( $title );
$symbol && $self->symbol( $symbol );
$desc && $self->description( $desc );
$ori && $self->aa_ori( $ori );
$mut && $self->aa_mut( $mut );
$pos && $self->position( $pos );
$am && $self->additional_mutations( $am );
return $self;
} # new
=head2 init
Title : init()
Usage : $av->init();
Function: Initializes this OMIMentryAllelicVariant to all "".
Returns :
Args :
=cut
sub init {
my( $self ) = @_;
$self->number( "" );
$self->title( "" );
$self->symbol( "" );
$self->description( "" );
$self->aa_ori( "" );
$self->aa_mut( "" );
$self->position( "" );
$self->additional_mutations( "" );
} # init
=head2 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).
=cut
sub number {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_number" } = $value;
}
return $self->{ "_number" };
} # number
=head2 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).
=cut
sub title {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_title" } = $value;
}
return $self->{ "_title" };
} # title
=head2 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).
=cut
sub symbol {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_symbol" } = $value;
}
return $self->{ "_symbol" };
} # symbol
=head2 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).
=cut
sub description {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_description" } = $value;
}
return $self->{ "_description" };
} # description
=head2 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).
=cut
sub aa_ori {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_aa_ori" } = $value;
}
return $self->{ "_aa_ori" };
} # aa_ori
=head2 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).
=cut
sub aa_mut {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_aa_mut" } = $value;
}
return $self->{ "_aa_mut" };
} # aa_mut
=head2 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).
=cut
sub position {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_position" } = $value;
}
return $self->{ "_position" };
} # position
=head2 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).
=cut
sub additional_mutations {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_additional_mutations" } = $value;
}
return $self->{ "_additional_mutations" };
} # additional_mutations
=head2 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 :
=cut
sub to_string {
my( $self ) = @_;
my $s = "";
$s .= "-- Number:\n";
$s .= $self->number()."\n";
$s .= "-- Title:\n";
$s .= $self->title()."\n";
$s .= "-- Symbol:\n";
$s .= $self->symbol()."\n";
$s .= "-- Description:\n";
$s .= $self->description()."\n";
$s .= "-- Original AA(s):\n";
$s .= $self->aa_ori()."\n";
$s .= "-- Mutated AA(s):\n";
$s .= $self->aa_mut()."\n";
$s .= "-- Position:\n";
$s .= $self->position()."\n";
$s .= "-- Additional Mutation(s):\n";
$s .= $self->additional_mutations();
return $s;
} # to_string
1;