Bio::Phenotype
Correlate
Summary
Correlate - Representation of a correlating phenotype in a given species
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
use Bio::Phenotype::Correlate;
$co = Bio::Phenotype::Correlate->new( -name => "4(Tas1r3)",
-description => "mouse correlate of human phenotype MIM 605865",
-species => $mouse,
-type => "homolog",
-comment => "type=homolog is putative" );
print $co->name();
print $co->description();
print $co->species()->binomial();
print $co->type();
print $co->comment();
print $co->to_string();
Description
This class models correlating phenotypes.
Its creation was inspired by the OMIM database where many human phenotypes
have a correlating mouse phenotype. Therefore, this class is intended
to be used together with a phenotype class.
Methods
Methods description
Title : new
Usage : $co = Bio::Phenotype::Correlate->new( -name => "4(Tas1r3)",
-description => "mouse correlate of human phenotype MIM 605865",
-species => $mouse,
-type => "homolog",
-comment => "type=homolog is putative" );
Function: Creates a new Correlate object.
Returns : A new Correlate object.
Args : -name => a name or id
-description => a description
-species => the species of this correlating phenotype [Bio::Species]
-type => the type of correlation
-comment => a comment |
Title : init()
Usage : $co->init();
Function: Initializes this Correlate to all "".
Returns :
Args : |
Title : name
Usage : $co->name( "4(Tas1r3)" );
or
print $co->name();
Function: Set/get for the name or id of this Correlate.
Returns : The name or id of this Correlate.
Args : The name or id of this Correlate (optional). |
Title : description
Usage : $co->description( "mouse correlate of human phenotype MIM 03923" );
or
print $co->description();
Function: Set/get for the description of this Correlate.
Returns : A description of this Correlate.
Args : A description of this Correlate (optional). |
Title : species
Usage : $co->species( $species );
or
$species = $co->species();
Function: Set/get for the species of this Correlate.
Returns : The Bio::Species of this Correlate [Bio::Species].
Args : The Bio::Species of this Correlate [Bio::Species] (optional). |
Title : type
Usage : $co->type( "homolog" );
or
print $co->type();
Function: Set/get for the type of this Correlate.
Returns : The type of this Correlate.
Args : The type of this Correlate (optional). |
Title : comment
Usage : $co->comment( "doubtful" );
or
print $co->comment();
Function: Set/get for an arbitrary comment about this Correlate.
Returns : A comment.
Args : A comment (optional). |
Title : to_string()
Usage : print $co->to_string();
Function: To string method for Correlate objects.
Returns : A string representations of this Correlate.
Args : |
Methods code
sub new
{
my( $class, @args ) = @_;
my $self = $class->SUPER::new( @args );
my ( $name, $desc, $species, $type, $comment )
= $self->_rearrange( [ qw( NAME
DESCRIPTION
SPECIES
TYPE
COMMENT ) ], @args );
$self->init();
$name && $self->name( $name );
$desc && $self->description( $desc );
$species && $self->species( $species );
$type && $self->type( $type );
$comment && $self->comment( $comment );
return $self;
}
} | sub init
{
my( $self ) = @_;
$self->name( "" );
$self->description( "" );
my $species = Bio::Species->new();
$species->classification( qw( species Undetermined ) );
$self->species( $species );
$self->type( "" );
$self->comment( "" );
}
} | sub name
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_name" } = $value;
}
return $self->{ "_name" };
}
} | sub description
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_description" } = $value;
}
return $self->{ "_description" };
}
} | sub species
{
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->_check_ref_type( $value, "Bio::Species" );
$self->{ "_species" } = $value;
}
return $self->{ "_species" };
}
} | sub type
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_type" } = $value;
}
return $self->{ "_type" };
}
} | sub comment
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_comment" } = $value;
}
return $self->{ "_comment" };
}
} | sub to_string
{
my ( $self ) = @_;
my $s = "";
$s .= "-- Name:\n";
$s .= $self->name()."\n";
$s .= "-- Description:\n";
$s .= $self->description()."\n";
$s .= "-- Species:\n";
$s .= $self->species()->binomial()."\n";
$s .= "-- Type of correlation:\n";
$s .= $self->type()."\n";
$s .= "-- Comment:\n";
$s .= $self->comment();
return $s;
}
} | | _check_ref_type | description | prev | next | Top |
sub _check_ref_type
{ my ( $self, $value, $expected_class ) = @_;
if ( ! defined( $value ) ) {
$self->throw( ( caller( 1 ) )[ 3 ] .": Found [undef"
."] where [$expected_class] expected" );
}
elsif ( ! ref( $value ) ) {
$self->throw( ( caller( 1 ) )[ 3 ] .": Found scalar"
." where [$expected_class] expected" );
}
elsif ( ! $value->isa( $expected_class ) ) {
$self->throw( ( caller( 1 ) )[ 3 ] .": Found [". ref( $value )
."] where [$expected_class] expected" );
}
}
} | General documentation
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Report bugs to the Bioperl bug tracking system to help us keep track
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The rest of the documentation details each of the object
methods.