Bio::Phenotype::OMIM OMIMentryAllelicVariant
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Summary
Bio::Phenotype::OMIM::OMIMentryAllelicVariant - Representation of a allelic
variant of the OMIM database
Package variables
No package variables defined.
Inherit
Bio::Root::Root
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.
Methods
newDescriptionCode
initDescriptionCode
numberDescriptionCode
titleDescriptionCode
symbolDescriptionCode
descriptionDescriptionCode
aa_oriDescriptionCode
aa_mutDescriptionCode
positionDescriptionCode
additional_mutationsDescriptionCode
to_stringDescriptionCode
Methods description
newcode    nextTop
 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
initcodeprevnextTop
 Title   : init()
Usage : $av->init();
Function: Initializes this OMIMentryAllelicVariant to all "".
Returns :
Args :
numbercodeprevnextTop
 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).
titlecodeprevnextTop
 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).
symbolcodeprevnextTop
 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).
descriptioncodeprevnextTop
 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_oricodeprevnextTop
 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_mutcodeprevnextTop
 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).
positioncodeprevnextTop
 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_mutationscodeprevnextTop
 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_stringcodeprevnextTop
 Title   : to_string()
Usage : print $av->to_string();
Function: To string method for OMIMentryAllelicVariant objects.
Returns : A string representations of this OMIMentryAllelicVariant.
Args :
Methods code
newdescriptionprevnextTop
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 
}
initdescriptionprevnextTop
sub init {
    my( $self ) = @_;

    $self->number( "" );
    $self->title( "" );
    $self->symbol( "" );
    $self->description( "" );
    $self->aa_ori( "" );
    $self->aa_mut( "" );
    $self->position( "" );
    $self->additional_mutations( "" );
    
} # init
}
numberdescriptionprevnextTop
sub number {
    my ( $self, $value ) = @_;

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

    return $self->{ "_number" };

} # number
}
titledescriptionprevnextTop
sub title {
    my ( $self, $value ) = @_;

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

    return $self->{ "_title" };

} # title
}
symboldescriptionprevnextTop
sub symbol {
    my ( $self, $value ) = @_;

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

    return $self->{ "_symbol" };

} # symbol
}
descriptiondescriptionprevnextTop
sub description {
    my ( $self, $value ) = @_;

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

    return $self->{ "_description" };

} # description
}
aa_oridescriptionprevnextTop
sub aa_ori {
    my ( $self, $value ) = @_;

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

    return $self->{ "_aa_ori" };

} # aa_ori
}
aa_mutdescriptionprevnextTop
sub aa_mut {
    my ( $self, $value ) = @_;

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

    return $self->{ "_aa_mut" };

} # aa_mut
}
positiondescriptionprevnextTop
sub position {
    my ( $self, $value ) = @_;

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

    return $self->{ "_position" };

} # position
}
additional_mutationsdescriptionprevnextTop
sub additional_mutations {
    my ( $self, $value ) = @_;

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

    return $self->{ "_additional_mutations" };

} # additional_mutations
}
to_stringdescriptionprevnextTop
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;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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/
AUTHORTop
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
APPENDIXTop
The rest of the documentation details each of the object
methods.