Bio::Ontology
Path
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Summary
Path - a path for an ontology term graph
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
$path = Bio::Ontology::Path->new( -identifier => "16847",
-subject_term => $subj,
-object_term => $obj,
-predicate_term => $pred,
-distance => 3 );
Description
This is a basic implementation of Bio::Ontology::PathI.
Essiantially this is a very thin extension of
Bio::Ontology::Relationship. It basically adds a method distance().
Methods
Methods description
Title : distance
Usage : $obj->distance($newval)
Function: Get/set the distance between the two terms connected
by this path.
Note that modifying the distance may not be meaningful. The
implementation here is not connected to any graph engine,
so changing an existing value may simply render the
attribute's value wrong.
Example :
Returns : value of distance (a scalar)
Args : on set, new value (a scalar or undef, optional) |
Title : init()
Usage : $rel->init();
Function: Initializes this Path to all undef.
Returns :
Args : |
Title : new
Usage : $rel = Bio::Ontology::Path->new(-identifier => "16847",
-subject_term => $subject,
-object_term => $object,
-predicate_term => $type );
-distance => 3 );
Function: Creates a new Bio::Ontology::Path.
Returns : A new Bio::Ontology::Path object.
Args : -identifier => the identifier of this relationship [scalar]
-subject_term => the subject term [Bio::Ontology::TermI]
-object_term => the object term [Bio::Ontology::TermI]
-predicate_term => the predicate term [Bio::Ontology::TermI]
-distance => the distance between subject and object |
Title : to_string()
Usage : print $rel->to_string();
Function: to_string method for Path.
Returns : A string representation of this Path.
Args : |
Methods code
sub distance
{ my $self = shift;
return $self->{'_distance'} = shift if @_;
return $self->{'_distance'};} | sub init
{ my $self = shift;
$self->SUPER::init(@_);
$self->{ "_distance" } = undef;
}
} | sub new
{
my( $class, @args ) = @_;
my $self = $class->SUPER::new( @args );
my ( $distance ) =
$self->_rearrange( [qw( DISTANCE)
], @args );
$distance && $self->distance($distance);
return $self;
}
} | sub to_string
{ my( $self ) = @_;
my $s = $self->SUPER::to_string();
$s .= "-- Distance:\n";
$s .= $self->distance() if defined($self->distance());
$s .= "\n";
return $s;
}
1;} | General documentation
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The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _