RelationshipType - a relationship type for an ontology # This class can be used to model various types of relationships (such as "IS_A", "PART_OF", "CONTAINS", "FOUND_IN"). 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.

Mailing Lists
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://bio.perl.org/MailList.html - About the mailing lists

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/ Christian M. Zmasek Email: czmasek@gnf.org or cmzmasek@yahoo.com WWW: http://www.genetics.wustl.edu/eddy/people/zmasek/ Address: Genomics Institute of the Novartis Research Foundation 10675 John Jay Hopkins Drive San Diego, CA 92121 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" ); $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" [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). 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.