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BioPerl-1.6.901
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Ontology::RelationshipType

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://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.