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 / 
bioperl-1.2.1
/ Bio::Ontology::RelationshipType

NAME

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").

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

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/

AUTHOR

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

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" );
           $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
 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).