Bio::Phenotype::OMIM
OMIMentryAllelicVariant
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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 : 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 : 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 : 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 : 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 : init() Usage : $av->init(); Function: Initializes this OMIMentryAllelicVariant to all "". Returns : Args : |
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 : 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 : 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 : 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 : 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 : 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 aa_mut
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_aa_mut" } = $value;
}
return $self->{ "_aa_mut" };
}
} |
sub aa_ori
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_aa_ori" } = $value;
}
return $self->{ "_aa_ori" };
}
} |
sub additional_mutations
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_additional_mutations" } = $value;
}
return $self->{ "_additional_mutations" };
}
} |
sub description
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_description" } = $value;
}
return $self->{ "_description" };
}
} |
sub init
{ my( $self ) = @_;
$self->number( "" );
$self->title( "" );
$self->symbol( "" );
$self->description( "" );
$self->aa_ori( "" );
$self->aa_mut( "" );
$self->position( "" );
$self->additional_mutations( "" );
}
} |
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 number
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_number" } = $value;
}
return $self->{ "_number" };
}
} |
sub position
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_position" } = $value;
}
return $self->{ "_position" };
}
} |
sub symbol
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_symbol" } = $value;
}
return $self->{ "_symbol" };
}
} |
sub title
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_title" } = $value;
}
return $self->{ "_title" };
}
} |
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;
}
1; } |
General documentation
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The rest of the documentation details each of the object
methods.