Raw content of Bio::Das::FeatureTypeI
<![CDATA[# $Id: FeatureTypeI.pm,v 1.3 2002/11/11 18:16:30 lapp Exp $
#
# BioPerl module for Bio::Das::FeatureTypeI
#
# Cared for by Lincoln Stein <lstein@cshl.org>
#
# Copyright Lincoln Stein
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Das::FeatureTypeI - Simple interface to Sequence Ontology feature types
=head1 SYNOPSIS
# Get a Bio::Das::FeatureTypeI object from somewhere
$term = $db->fetch....
# Get the name of the term
$definition = $term->name;
# Get the accession of the term
$accession = $term->accession;
# Get the definition of the term
$definition = $term->definition;
# Get the parents of the term, optionally filtered by relationship
@parents = $term->parents($relationship);
# Get the children of the term, optionally filtered by relationship
@children = $term->children($relationship);
# Given a parent and child, returns their relationship, or undef if
# not directly related
$relationship = $parent->relationship($child);
# Return true if two terms are identical
$match = $term1->equals($term2);
# Return true if $term2 is a descendent of $term1, optionally
# filtering by relationship ("isa" assumed)
$match = $term1->is_descendent($term2,$relationship);
# Return true if $term2 is a parent of $term1, optionally
# filtering by relationship ("isa" assumed)
$match = $term1->is_parent($term2,$relationship);
# Return true if $term2 is equal to $term1 or if $term2 descends
# from term 1 via the "isa" relationship
$match = $term1->match($term2);
# Create a new term de novo
$term = Bio::Das::FeatureTypeI->new(-name => $name,
-accession => $accession,
-definition => $definition);
# Add a child to a term
$term1->add_child($term2,$relationship);
# Delete a child from a term
$term1->delete_child($term2);
=head1 DESCRIPTION
Bio::Das::FeatureTypeI is an interface to the Gene Ontology
Consortium's Sequence Ontology (SO). The SO, like other ontologies,
is a directed acyclic graph in which a child node may have multiple
parents. The relationship between parent and child is one of a list
of relationships. The SO currently recognizes two relationships "isa"
and "partof".
The intent of this interface is to interoperate with older software
that uses bare strings to represent feature types. For this reason,
the interface overloads the stringify ("") and string equals (eq)
operations.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this
and other Bioperl modules. Send your comments and suggestions preferably
to one of the Bioperl mailing lists.
Your participation is much appreciated.
bioperl-l@bio.perl.org
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.
Bug reports can be submitted via email or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Lincoln Stein
Email lstein@cshl.org
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
#'
# Let the code begin...
package Bio::Das::FeatureTypeI;
use strict;
use vars qw(@ISA);
use Bio::Root::RootI;
use overload '""' => 'name',
eq => 'match',
fallback => 1;
# Object preamble - inherits from Bio::Root::RootI;
@ISA = qw(Bio::Root::RootI);
=head2 name
Title : name
Usage : $string = $term->name
Function: return the term for the type
Returns : a string
Args : none
Status : Public
=cut
sub name { shift->throw_not_implemented }
=head2 accession
Title : accession
Usage : $string = $term->accession
Function: return the accession number for the term
Returns : a string
Args : none
Status : Public
=cut
sub accession { shift->throw_not_implemented }
=head2 definition
Title : definition
Usage : $string = $term->definition
Function: return the human-readable definition for the term
Returns : a string
Args : none
Status : Public
=cut
sub definition { shift->throw_not_implemented }
=head2 parents
Title : parents
Usage : @terms = $term->parents($relationship)
Function: return parent terms
Returns : list of Bio::Das::FeatureTypeI
Args : none
Status : Public
Returns the parents for the current term, empty if there are none. An
optional relationship argument will return those parents
that are related via the specified relationship type.
The relationship is one of "isa" or "partof".
=cut
sub parents { shift->throw_not_implemented; }
=head2 children
Title : children
Usage : @terms = $term->children($relationship)
Function: return children terms
Returns : list of Bio::Das::FeatureTypeI
Args : none
Status : Public
Returns the children for the current term, empty if there are none. An
optional relationship argument will return those children
that are related via the specified relationship type.
The relationship is one of "isa" or "partof".
=cut
sub children { shift->throw_not_implemented; }
=head2 relationship
Title : relationship
Usage : $relationship = $parent->relationship($child)
Function: return the relationship between a parent and a child
Returns : one of "isa" or "partof"
Args : none
Status : Public
This method returns the relationship between a parent and one of its
immediate descendents. It can return "isa", "partof", or undef if
there is not a direct parent/child relationship (kissing cousins are
*not* recognized).
=cut
sub relationship { shift->throw_not_implemented }
=head2 equals
Title : equals
Usage : $boolean = $term1->equals($term2)
Function: return true if $term1 and $term2 are the same
Returns : boolean
Args : second term
Status : Public
The two terms must be identical. In practice, this means that if
term2 is a Bio::Das::FeatureI object, then its accession number must
match the first term's accession number. Otherwise, if term2 is a
bare string, then it must equal (in a case insensitive manner)
the name of term1.
NOTE TO IMPLEMENTORS: This method is defined in terms of other
methods, so does not need to be implemented.
=cut
#'
sub equals {
my $self = shift;
my $term2 = shift;
if ($term2->isa('Bio::Das::FeatureTypeI')) {
return $self->accession eq $term2->accession;
} else {
return lc $self->name eq lc $term2;
}
}
=head2 is_descendent
Title : is_descendent
Usage : $boolean = $term1->is_descendent($term2 [,$relationship])
Function: return true of $term2 is a descendent of $term1
Returns : boolean
Args : second term
Status : Public
This method returns true if $term2 descends from $term1. The
operation traverses the tree. The traversal can be limited to the
relationship type ("isa" or "partof") if desired. $term2 can be a
bare string, in which case the term names will be used as the basis
for term matching (see equals()).
NOTE TO IMPLEMENTORS: this method is defined as the inverse of
is_parent(). Do not implement it directly, but do implement
is_parent().
=cut
sub is_descendent {
my $self = shift;
my ($term,$relationship) = @_;
$self->throw("$term is not a Bio::Das::FeatureTypeI")
unless $term->isa('Bio::Das::FeatureTypeI');
$term->is_parent($self,$relationship);
}
=head2 is_parent
Title : is_parent
Usage : $boolean = $term1->is_parent($term2 [,$relationship])
Function: return true of $term2 is a parent of $term1
Returns : boolean
Args : second term
Status : Public
This method returns true if $term2 is a parent of $term1. The
operation traverses the tree. The traversal can be limited to the
relationship type ("isa" or "partof") if desired. $term2 can be a
bare string, in which case the term names will be used as the basis
for term matching (see equals()).
NOTE TO IMPLEMENTORS: Implementing this method will also implement
is_descendent().
=cut
sub is_parent { shift->throw_not_implemented }
=head2 match
Title : match
Usage : $boolean = $term1->match($term2)
Function: return true if $term1 equals $term2 or if $term2 is an "isa" descendent
Returns : boolean
Args : second term
Status : Public
This method combines equals() and is_descendent() in such a way that
the two terms will match if they are the same or if the second term is
an instance of the first one. This is also the basis of the operator
overloading of eq.
NOTE TO IMPLEMENTORS: This method is defined in terms of other methods
and does not need to be implemented.
=cut
sub match {
my $self = shift;
my $term2 = shift;
return 1 if $self->equals($term2);
return $self->is_descendent($term2,'isa');
}
=head2 new
Title : new
Usage : $term = Bio::Das::FeatureTypeI->new(@args)
Function: create a new term
Returns : new term
Args : see below
Status : Public
This method creates a new Bio::Das::FeatureTypeI. Arguments:
Argument Description
-------- ------------
-name Name of this term
-accession Accession number for the term
-definition Definition of the term
=cut
sub new { shift->throw_not_implemented }
=head2 add_child
Title : add_child
Usage : $boolean = $term->add_child($term2,$relationship)
Function: add a child to a term
Returns : a boolean indicating success
Args : new child
Throws : a "cycle detected" exception
Status : Public
This method adds a new child to the indicated node. It may detect a
cycle in the DAG and throw a "cycle detected" exception.
=cut
sub add_child { shift->throw_not_implemented }
=head2 delete_child
Title : delete_child
Usage : $boolean = $term->delete_child($term2);
Function: delete a child of the term
Returns : a boolean indicating success
Args : child to be deleted
Throws : a "not a child" exception
Status : Public
This method deletes a new child from the indicated node. It will
throw an exception if the indicated child is not a direct descendent.
=cut
sub delete_child { shift->throw_not_implemented }
1;
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