Bio::Ontology::RelationshipType.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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.