Bio::Phenotype::OMIM
OMIMentryAllelicVariant
Summary
OMIMentryAllelicVariant - Representation of a allelic variant of the OMIM database
Package variables
No package variables defined.
Included modules
Inherit
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
Methods description
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 |
Title : init()
Usage : $av->init();
Function: Initializes this OMIMentryAllelicVariant to all "".
Returns :
Args : |
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
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). |
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). |
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). |
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). |
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). |
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). |
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). |
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
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;
}
} | sub init
{ my( $self ) = @_;
$self->number( "" );
$self->title( "" );
$self->symbol( "" );
$self->description( "" );
$self->aa_ori( "" );
$self->aa_mut( "" );
$self->position( "" );
$self->additional_mutations( "" );
}
} | sub number
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_number" } = $value;
}
return $self->{ "_number" };
}
} | sub title
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_title" } = $value;
}
return $self->{ "_title" };
}
} | sub symbol
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_symbol" } = $value;
}
return $self->{ "_symbol" };
}
} | sub description
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_description" } = $value;
}
return $self->{ "_description" };
}
} | sub aa_ori
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_aa_ori" } = $value;
}
return $self->{ "_aa_ori" };
}
} | sub aa_mut
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_aa_mut" } = $value;
}
return $self->{ "_aa_mut" };
}
} | sub position
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_position" } = $value;
}
return $self->{ "_position" };
}
} | sub additional_mutations
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_additional_mutations" } = $value;
}
return $self->{ "_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;
}
} | General documentation
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The rest of the documentation details each of the object
methods.