Raw content of Bio::Phenotype::OMIM::OMIMentryAllelicVariant # $Id: OMIMentryAllelicVariant.pm,v 1.5 2002/12/12 18:27:01 czmasek Exp $ # # BioPerl module for Bio::Phenotype::OMIM::OMIMentryAllelicVariant # # Cared for by Christian M. Zmasek <czmasek@gnf.org> or <cmzmasek@yahoo.com> # # (c) Christian M. Zmasek, czmasek@gnf.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 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://bio.perl.org/MailList.html - About the mailing lists =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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ =head1 AUTHOR Christian M. Zmasek Email: czmasek@gnf.org or cmzmasek@yahoo.com WWW: http://www.genetics.wustl.edu/eddy/people/zmasek/ 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 vars qw( @ISA ); use strict; use Bio::Root::Object; @ISA = 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;