Bio::Phenotype::OMIM::OMIMentryAllelicVariant - Representation of a allelic

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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

SYNOPSIS

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  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

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

FEEDBACK

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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

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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

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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    :
BioPerl documentation Contained in the BioPerl distribution. 
#
# 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



# Let the code begin...


package Bio::Phenotype::OMIM::OMIMentryAllelicVariant;
use strict;

use base qw(Bio::Root::Root);


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 





sub init {
    my( $self ) = @_;

    $self->number( "" );
    $self->title( "" );
    $self->symbol( "" );
    $self->description( "" );
    $self->aa_ori( "" );
    $self->aa_mut( "" );
    $self->position( "" );
    $self->additional_mutations( "" );
    
} # init





sub number {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->{ "_number" } = $value;
    }

    return $self->{ "_number" };

} # number




sub title {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->{ "_title" } = $value;
    }

    return $self->{ "_title" };

} # title





sub symbol {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->{ "_symbol" } = $value;
    }

    return $self->{ "_symbol" };

} # symbol





sub description {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->{ "_description" } = $value;
    }

    return $self->{ "_description" };

} # description





sub aa_ori {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->{ "_aa_ori" } = $value;
    }

    return $self->{ "_aa_ori" };

} # aa_ori





sub aa_mut {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->{ "_aa_mut" } = $value;
    }

    return $self->{ "_aa_mut" };

} # aa_mut





sub position {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->{ "_position" } = $value;
    }

    return $self->{ "_position" };

} # position





sub additional_mutations {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->{ "_additional_mutations" } = $value;
    }

    return $self->{ "_additional_mutations" };

} # additional_mutations




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;