Bio::Ontology::RelationshipType(3pm) User Contributed Perl Documentation Bio::Ontology::RelationshipType(3pm)
NAME
Bio::Ontology::RelationshipType - a relationship type for an ontology
SYNOPSIS
#
DESCRIPTION
This class can be used to model various types of relationships (such as "IS_A", "PART_OF", "CONTAINS", "FOUND_IN", "RELATED_TO").
This class extends Bio::Ontology::Term, so it essentially is-a Bio::Ontology::TermI. In addition, all methods are overridden such as to
make the object immutable.
FEEDBACK
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bioperl-l@bioperl.org - General discussion
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Support
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 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 the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR
Christian M. Zmasek
Email: czmasek-at-burnham.org or cmzmasek@yahoo.com
WWW: http://monochrome-effect.net/
Address:
Genomics Institute of the Novartis Research Foundation
10675 John Jay Hopkins Drive
San Diego, CA 92121
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
get_instance
Title : get_instance
Usage : $IS_A = Bio::Ontology::RelationshipType->get_instance( "IS_A" );
$PART_OF = Bio::Ontology::RelationshipType->get_instance( "PART_OF" );
$RELATED_TO = Bio::Ontology::RelationshipType->get_instance( "RELATED_TO" );
$CONTAINS = Bio::Ontology::RelationshipType->get_instance( "CONTAINS" );
$FOUND_IN = Bio::Ontology::RelationshipType->get_instance( "FOUND_IN" );
Function: Factory method to create instances of RelationshipType
Returns : [Bio::Ontology::RelationshipType]
Args : "IS_A" or "PART_OF" or "CONTAINS" or "FOUND_IN" or
"RELATED_TO" [scalar]
the ontology [Bio::Ontology::OntologyI] (optional)
init
Title : init()
Usage : $type->init();
Function: Initializes this to all undef and empty lists.
Returns :
Args :
equals
Title : equals
Usage : if ( $type->equals( $other_type ) ) { ...
Function: Compares this type to another one, based on string "eq" of
the "identifier" field, if at least one of the two types has
the identifier set, or string eq of the name otherwise.
Returns : true or false
Args : [Bio::Ontology::RelationshipType]
identifier
Title : identifier
Usage : $term->identifier( "IS_A" );
or
print $term->identifier();
Function: Set/get for the immutable identifier of this Type.
Returns : The identifier [scalar].
Args : The identifier [scalar] (optional).
name
Title : name
Usage : $term->name( "is a type" );
or
print $term->name();
Function: Set/get for the immutable name of this Type.
Returns : The name [scalar].
Args : The name [scalar] (optional).
definition
Title : definition
Usage : $term->definition( "" );
or
print $term->definition();
Function: Set/get for the immutable definition of this Type.
Returns : The definition [scalar].
Args : The definition [scalar] (optional).
ontology
Title : ontology
Usage : $term->ontology( $top );
or
$top = $term->ontology();
Function: Set/get for the ontology this relationship type lives in.
Returns : The ontology [Bio::Ontology::OntologyI].
Args : On set, the ontology [Bio::Ontology::OntologyI] (optional).
version
Title : version
Usage : $term->version( "1.00" );
or
print $term->version();
Function: Set/get for immutable version information.
Returns : The version [scalar].
Args : The version [scalar] (optional).
is_obsolete
Title : is_obsolete
Usage : $term->is_obsolete( 1 );
or
if ( $term->is_obsolete() )
Function: Set/get for the immutable obsoleteness of this Type.
Returns : the obsoleteness [0 or 1].
Args : the obsoleteness [0 or 1] (optional).
comment
Title : comment
Usage : $term->comment( "..." );
or
print $term->comment();
Function: Set/get for an arbitrary immutable comment about this Type.
Returns : A comment.
Args : A comment (optional).
Private methods
May be overridden in a derived class, but should never be called from outside.
veto_change
Title : veto_change
Usage :
Function: Called if an attribute is changed. Setting an attribute is
considered a change if it had a value before and the attempt
to set it would change the value.
This method returns the message to be printed in the exception.
Example :
Returns : A string
Args : The name of the attribute that was attempted to change.
Optionally, the old value and the new value for reporting
purposes only.
perl v5.14.2 2012-03-02 Bio::Ontology::RelationshipType(3pm)