Provided by: libbio-perl-perl_1.6.901-2_all bug

NAME

       Bio::Ontology::SimpleOntologyEngine - Implementation of OntologyEngineI interface

SYNOPSIS

         my $soe = Bio::Ontology::SimpleOntologyEngine->new;

DESCRIPTION

       This is a "simple" implementation of Bio::Ontology::OntologyEngineI.

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 list.  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 of the bugs and their
       resolution. Bug reports can be submitted via the web:

         https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Peter Dimitrov

       Email dimitrov@gnf.org

CONTRIBUTORS

       Hilmar Lapp, hlapp at gmx.net

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

   new
        Title   : new
        Usage   : $soe = Bio::Ontology::SimpleOntologyEngine->new;
        Function: Initializes the ontology engine.
        Example : $soe = Bio::Ontology::SimpleOntologyEngine->new;
        Returns : Object of class SimpleOntologyEngine.
        Args    :

   _instantiated_terms_store
        Title   : _instantiated_terms_store
        Usage   : $obj->_instantiated_terms_store($newval)
        Function:
        Example :
        Returns : hash
        Args    : empty hash

   mark_instantiated
        Title   : mark_instantiated
        Usage   : $self->mark_instantiated(TermI terms): TermI
        Function: Marks TermI objects as fully instantiated,
                  allowing for proper counting of the number of terms in the term store.
                  The TermI objects has to be already stored in the term store in order
                  to be marked.
        Example : $self->mark_instantiated($term);
        Returns : its argument or throws an exception if a term is not
                  in the term store.
        Args    : array of objects of class TermI.

   mark_uninstantiated
        Title   : mark_uninstantiated
        Usage   : $self->mark_uninstantiated(TermI terms): TermI
        Function: Marks TermI objects as not fully instantiated,
        Example : $self->mark_uninstantiated($term);
        Returns : its argument or throws an exception if a term is not
                  in the term store(if the term is not marked it does nothing).
        Args    : array of objects of class TermI.

   _term_store
        Title   : term_store
        Usage   : $obj->_term_store($newval)
        Function:
        Example :
        Returns : reference to an array of Bio::Ontology::TermI objects
        Args    : reference to an array of Bio::Ontology::TermI objects

   add_term
        Title   : add_term
        Usage   : add_term(TermI term): TermI
        Function: Adds TermI object to the ontology engine term store.
        Marks the term fully instantiated by default.
        Example : $soe->add_term($term)
        Returns : its argument.
        Args    : object of class TermI.

   get_term_by_identifier
        Title   : get_term_by_identifier
        Usage   : get_term_by_identifier(String id): TermI
        Function: Retrieves terms from the term store by their identifier
                  field, or an empty list if not there.
        Example : $term = $soe->get_term_by_identifier("IPR000001");
        Returns : An array of zero or more Bio::Ontology::TermI objects.
        Args    : An array of identifier strings

   _get_number_rels
        Title   : get_number_rels
        Usage   :
        Function:
        Example :
        Returns :
        Args    :

   _get_number_terms
        Title   : _get_number_terms
        Usage   :
        Function:
        Example :
        Returns :
        Args    :

   _relationship_store
        Title   : _storerelationship_store
        Usage   : $obj->relationship_store($newval)
        Function:
        Example :
        Returns : reference to an array of Bio::Ontology::TermI objects
        Args    : reference to an array of Bio::Ontology::TermI objects

   _inverted_relationship_store
        Title   : _inverted_relationship_store
        Usage   :
        Function:
        Example :
        Returns : reference to an array of Bio::Ontology::TermI objects
        Args    : reference to an array of Bio::Ontology::TermI objects

   _relationship_type_store
        Title   : _relationship_type_store
        Usage   : $obj->_relationship_type_store($newval)
        Function:
        Example :
        Returns : reference to an array of Bio::Ontology::RelationshipType objects
        Args    : reference to an array of Bio::Ontology::RelationshipType objects

   _add_relationship_simple
        Title   : _add_relationship_simple
        Usage   :
        Function:
        Example :
        Returns :
        Args    :

   add_relationship
        Title   : add_relationship
        Usage   : add_relationship(RelationshipI relationship): RelationshipI
        Function: Adds a relationship object to the ontology engine.
        Example :
        Returns : Its argument.
        Args    : A RelationshipI object.

   get_relationships
        Title   : get_relationships
        Usage   : get_relationships(): RelationshipI
        Function: Retrieves all relationship objects.
        Example :
        Returns : Array of RelationshipI objects
        Args    :

   get_all_relationships
        Title   : get_all_relationships
        Usage   : get_all_relationships(): RelationshipI
        Function: Retrieves all relationship objects.
        Example :
        Returns : Array of RelationshipI objects
        Args    :

   get_predicate_terms
        Title   : get_predicate_terms
        Usage   : get_predicate_terms(): TermI
        Function: Retrives all relationship types stored in the engine
        Example :
        Returns : reference to an array of Bio::Ontology::RelationshipType objects
        Args    :

   _is_rel_type
        Title   : _is_rel_type
        Usage   :
        Function:
        Example :
        Returns :
        Args    :

   _typed_traversal
        Title   : _typed_traversal
        Usage   :
        Function:
        Example :
        Returns :
        Args    :

   get_child_terms
        Title   : get_child_terms
        Usage   : get_child_terms(TermI term, TermI predicate_terms): TermI
                  get_child_terms(TermI term, RelationshipType predicate_terms): TermI
        Function: Retrieves all child terms of a given term, that satisfy a
                  relationship among those that are specified in the second
                  argument or undef otherwise. get_child_terms is a special
                  case of get_descendant_terms, limiting the search to the
                  direct descendants.
        Example :
        Returns : Array of TermI objects.
        Args    : First argument is the term of interest, second is the list of
                  relationship type terms.

   get_descendant_terms
        Title   : get_descendant_terms
        Usage   : get_descendant_terms(TermI term, TermI rel_types): TermI
                  get_child_terms(TermI term, RelationshipType predicate_terms): TermI
        Function: Retrieves all descendant terms of a given term, that
                  satisfy a relationship among those that are specified in
                  the second argument or undef otherwise. Uses
                  _typed_traversal to find all descendants.

        Example :
        Returns : Array of TermI objects.
        Args    : First argument is the term of interest, second is the list of
                  relationship type terms.

   get_parent_terms
        Title   : get_parent_terms
        Usage   : get_parent_terms(TermI term, TermI predicate_terms): TermI
                  get_child_terms(TermI term, RelationshipType predicate_terms): TermI
        Function: Retrieves all parent terms of a given term, that satisfy a
                  relationship among those that are specified in the second
                  argument or undef otherwise. get_parent_terms is a special
                  case of get_ancestor_terms, limiting the search to the
                  direct ancestors.

        Example :
        Returns : Array of TermI objects.
        Args    : First argument is the term of interest, second is the list of relationship type terms.

   get_ancestor_terms
        Title   : get_ancestor_terms
        Usage   : get_ancestor_terms(TermI term, TermI predicate_terms): TermI
                  get_child_terms(TermI term, RelationshipType predicate_terms): TermI
        Function: Retrieves all ancestor terms of a given term, that satisfy
                  a relationship among those that are specified in the second
                  argument or undef otherwise. Uses _typed_traversal to find
                  all ancestors.

        Example :
        Returns : Array of TermI objects.
        Args    : First argument is the term of interest, second is the list
                  of relationship type terms.

   get_leaf_terms
        Title   : get_leaf_terms
        Usage   : get_leaf_terms(): TermI
        Function: Retrieves all leaf terms from the ontology. Leaf term is a term w/o descendants.
        Example : @leaf_terms = $obj->get_leaf_terms()
        Returns : Array of TermI objects.
        Args    :

   get_root_terms
        Title   : get_root_terms
        Usage   : get_root_terms(): TermI
        Function: Retrieves all root terms from the ontology. Root term is a term w/o descendants.
        Example : @root_terms = $obj->get_root_terms()
        Returns : Array of TermI objects.
        Args    :

   _filter_repeated
        Title   : _filter_repeated
        Usage   : @lst = $self->_filter_repeated(@old_lst);
        Function: Removes repeated terms
        Example :
        Returns : List of unique TermI objects
        Args    : List of TermI objects

   get_all_terms
        Title   : get_all_terms
        Usage   : get_all_terms(): TermI
        Function: Retrieves all terms currently stored in the ontology.
        Example : @all_terms = $obj->get_all_terms()
        Returns : Array of TermI objects.
        Args    :

   find_terms
        Title   : find_terms
        Usage   : ($term) = $oe->find_terms(-identifier => "SO:0000263");
        Function: Find term instances matching queries for their attributes.

                  This implementation can efficiently resolve queries by
                  identifier.

        Example :
        Returns : an array of zero or more Bio::Ontology::TermI objects
        Args    : Named parameters. The following parameters should be recognized
                  by any implementations:

                     -identifier    query by the given identifier
                     -name          query by the given name

   relationship_factory
        Title   : relationship_factory
        Usage   : $fact = $obj->relationship_factory()
        Function: Get/set the object factory to be used when relationship
                  objects are created by the implementation on-the-fly.

        Example :
        Returns : value of relationship_factory (a Bio::Factory::ObjectFactoryI
                  compliant object)
        Args    : on set, a Bio::Factory::ObjectFactoryI compliant object

   term_factory
        Title   : term_factory
        Usage   : $fact = $obj->term_factory()
        Function: Get/set the object factory to be used when term objects are
                  created by the implementation on-the-fly.

                  Note that this ontology engine implementation does not
                  create term objects on the fly, and therefore setting this
                  attribute is meaningless.

        Example :
        Returns : value of term_factory (a Bio::Factory::ObjectFactoryI
                  compliant object)
        Args    : on set, a Bio::Factory::ObjectFactoryI compliant object

   _filter_unmarked
        Title   : _filter_unmarked
        Usage   : _filter_unmarked(TermI terms): TermI
        Function: Removes the uninstantiated terms from the list of terms
        Example :
        Returns : array of fully instantiated TermI objects
        Args    : array of TermI objects

   remove_term_by_id
        Title   : remove_term_by_id
        Usage   : remove_term_by_id(String id): TermI
        Function: Removes TermI object from the ontology engine using the
                  string id as an identifier. Current implementation does not
                  enforce consistency of the relationships using that term.
        Example : $term = $soe->remove_term_by_id($id);
        Returns : Object of class TermI or undef if not found.
        Args    : The string identifier of a term.

   to_string
        Title   : to_string
        Usage   : print $sv->to_string();
        Function: Currently returns formatted string containing the number of
                  terms and number of relationships from the ontology engine.
        Example : print $sv->to_string();
        Returns :
        Args    :

   _unique_termid
        Title   : _unique_termid
        Usage   :
        Function: Returns a string that can be used as ID using fail-over
                  approaches.

                  If the identifier attribute is not set, it uses the
                  combination of name and ontology name, provided both are
                  set. If they are not, it returns the name alone.

                  Note that this is a private method. Call from inheriting
                  classes but not from outside.

        Example :
        Returns : a string
        Args    : a Bio::Ontology::TermI compliant object