GO::OntologyProvider - abstract base class providing API for the provision on Gene Ontology information

GO-TermFinder documentation Contained in the GO-TermFinder distribution.

Index

Code Index:

NAME

Top

GO::OntologyProvider - abstract base class providing API for the provision on Gene Ontology information

DESCRIPTION

Top

GO::OntologyProvider is an abstract class that defines an interface that should be implemented by specific subclasses, which may read ontology information from databases, flatfiles, XML files etc.

All of the methods return either one or many GO::Node(s), and any concrete subclass is expected to fully flesh out the such Node objects with all the parents, children and paths to the root, such that any node should return a true value when the isValid method is invoked on it.

Constructor

Top

Because this is an abstract class, there is no constructor. A constructor must be implemented by concrete subclasses.

Public instance methods

Top

All of these public instance methods must be implemented by concrete subclasses.

allNodes

This method returns an array of all the GO::Nodes that have been created.

Usage:

    my @nodes = $ontologyProvider->allNodes;

rootNode

This method returns the root node in the ontology.

Usage:

	my $rootNode = $ontologyProvider->rootNode;

nodeFromId

This method returns a GO::Node corresponding to the provided GOID, should one exist. Otherwise it returns undef.

Usage:

	my $node = $ontologyProvider->nodeFromId("GO:0003673");

numNodes

This method returns the number of nodes that exist within the ontology.

Usage:

	my $numNodes = $ontologyProvider->numNodes;

AUTHOR

Top

Gavin Sherlock, sherlock@genome.stanford.edu

GO-TermFinder documentation Contained in the GO-TermFinder distribution. 
package GO::OntologyProvider;

# File         : OntologyProvider.pm
# Author       : Gavin Sherlock
# Date Begun   : September 23rd 2002

# $Id: OntologyProvider.pm,v 1.7 2004/05/05 22:12:33 sherlock Exp $

# License information (the MIT license)

# Copyright (c) 2003 Gavin Sherlock; Stanford University

# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated documentation files
# (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, copy, modify, merge,
# publish, distribute, sublicense, and/or sell copies of the Software,
# and to permit persons to whom the Software is furnished to do so,
# subject to the following conditions:

# The above copyright notice and this permission notice shall be
# included in all copies or substantial portions of the Software.

# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
# NONINFRINGEMENT.  IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
# BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
# ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.


use strict;
use warnings;
use diagnostics;

use vars qw ($VERSION);

$VERSION = 0.12;

############################################################################
sub allNodes{
############################################################################

############################################################################

    $_[0]->__complainStubMethod;

}

############################################################################
sub rootNode{
############################################################################

############################################################################

    $_[0]->__complainStubMethod;

}

############################################################################
sub nodeFromId{
############################################################################

############################################################################

    $_[0]->__complainStubMethod;

}

############################################################################
sub numNodes{
############################################################################

############################################################################

    $_[0]->__complainStubMethod;

}

############################################################################
sub __complainStubMethod{
############################################################################

    my ($self) = @_;

    my $subroutine = (caller(1))[3];

    $subroutine =~ s/.+:://;

    my $package = ref $self;

    die "The package $package has not implemented the required method $subroutine().\n";

}

1; # to keep Perl happy