Provided by: libbio-perl-perl_1.7.6-3_all bug

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

   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://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   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://github.com/bioperl/bioperl-live/issues

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.