Bio::Ontology Path
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Summary
Bio::Ontology::Path - a path for an ontology term graph
Package variables
No package variables defined.
Inherit
Bio::Ontology::PathI Bio::Ontology::Relationship
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
newDescriptionCode
initDescriptionCode
distanceDescriptionCode
to_stringDescriptionCode
Methods description
newcode    nextTop
 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
initcodeprevnextTop
 Title   : init()
Usage : $rel->init();
Function: Initializes this Path to all undef.
Returns :
Args :
distancecodeprevnextTop
 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)
to_stringcodeprevnextTop
 Title   : to_string()
Usage : print $rel->to_string();
Function: to_string method for Path.
Returns : A string representation of this Path.
Args :
Methods code
newdescriptionprevnextTop
sub new {
    my( $class, @args ) = @_;
    
    my $self = $class->SUPER::new( @args );
   
    my ( $distance ) = 
	$self->_rearrange( [qw( DISTANCE)
			    ], @args );
   
    $distance      && $self->distance($distance);
                                                    
    return $self;
    
} # new
}
initdescriptionprevnextTop
sub init {
    my $self = shift;
    
    $self->SUPER::init(@_);
    $self->{ "_distance" } = undef;
   
} # init
}
distancedescriptionprevnextTop
sub distance {
    my $self = shift;

    return $self->{'_distance'} = shift if @_;
    return $self->{'_distance'};
}
to_stringdescriptionprevnextTop
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;
    
} # 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 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
 Hilmar Lapp <hlapp@gmx.net>
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _