bio::mage::tools::mgedontologyhelper(3pm) [debian man page]

MAGE::Tools::MGEDOntologyHelper(3pm)			User Contributed Perl Documentation		      MAGE::Tools::MGEDOntologyHelper(3pm)

Bio::MAGE::Tools::MGEDOntologyHelper
   SYNOPSIS
	 my $mo_helper = Bio::MAGE::Tools::MGEDOntologyHelper->new(
			      sourceFile=>'MGEDOntology.owl',
			      databaseIdentifier=>'MO',
			      );

   DESCRIPTION
BUGS

       Please send bug reports to the project mailing list: (mged-mage 'at' lists 'dot' sf 'dot' net)

AUTHOR

       Eric W. Deutsch (edeutsch 'at' systemsbiology 'dot' org) followup work by Jason E. Stewart (jasons 'at' cpan 'dot' org)

SEE ALSO

       perl(1).

perl v5.10.1							    2006-08-23				      MAGE::Tools::MGEDOntologyHelper(3pm)

MAGE::Association(3pm)					User Contributed Perl Documentation				    MAGE::Association(3pm)

Bio::MAGE::Association
   SYNOPSIS
	 use Bio::MAGE::Association qw(:CARD);

	 # creating an empty instance
	 my $association = Bio::MAGE::Association->new();

	 # populating the instance in the constructor
	 my $association = Bio::MAGE::Association->new(self=>$assoc_end1,
							      other=>$assoc_end2);

	 # setting and retrieving the association ends
	 my $self_end = $association->self();
	 $association->self($value);

	 my $other_end = $association->other();
	 $association->other($value);

   DESCRIPTION
       This class holds the two association ends for each UML association. "self" is the end nearest the class of interest, while "other" is the
       end furthest away. The ends are of type "Bio::MAGE::Association::End".

   CARDINALITY
       Associations in UML have a "cardinality" that determines how many objects can be associated. In the "Bio::MAGE::Association" modulte,
       "cardinality" has two primary dimensions: optional or required, and single or list. So there are four combinations of the two dimensions:

       o   0..1

	   This is an optional single association, meaning it can have one object associated, but it is optional.

       o   1

	   This is a required single association, meaning it must have exactly one object associated.

       o   0..N

	   This is an optional list association, meaning it can have many objects associated.

       o   1..N

	   This is an required list association, meaning it must have at least one object, but it may have many.

       There are four constants defined in this module for handling the cardinalities, and they can be imported into an application using the CARD
       import tag:

	 use Bio::MAGE::Association qw(:CARD);

       The four constants are: CARD_0_OR_1, CARD_1, CARD_0_TO_N, and CARD_1_TO_N.

Bio::MAGE::Association::End
   SYNOPSIS
	 use Bio::MAGE::Association qw(:CARD);

	 # creating an empty instance
	 my $assoc_end = Bio::MAGE::Association::End->new();

	 # populating the instance in the constructor
	 my $assoc_end = Bio::MAGE::Association::End->new(
						       name=>$name,
						       is_ref=>$bool,
						       cardinality=>CARD_0_TO_N,
						       class_name=>$class_name,
						       documentation=>$doc_string,
						       rank=>$rank,
						       ordered=>$bool,
						      );

	 # setting and retrieving object attributes
	 my $name = $assoc_end->name();
	 $assoc_end->name($value);

	 my $is_ref = $assoc_end->is_ref();
	 $assoc_end->is_ref($value);

	 my $cardinality = $assoc_end->cardinality();
	 $assoc_end->cardinality($value);

	 my $class_name = $assoc_end->class_name();
	 $assoc_end->class_name($value);

	 my $documentation = $assoc_end->documentation();
	 $assoc_end->documentation($value);

	 my $rank = $assoc_end->rank();
	 $assoc_end->rank($value);

	 my $ordered = $assoc_end->ordered();
	 $assoc_end->ordered($value);

	 #
	 # Utility methods
	 #

	 # does this end of list cardinality (0..N or 1..N)
	 my $bool = $assoc_end->is_list();

   DESCRIPTION
       This class stores the information in a single UML association end.

perl v5.10.1							    2007-05-14						    MAGE::Association(3pm)