Provided by: libbio-perl-perl_1.7.2-3_all bug

NAME

       Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler - parse an InterPro XML file and
       persist the resulting terms to a Biosql database

SYNOPSIS

          # see load_interpro.pl in bioperl-db/scripts/biosql/

DESCRIPTION

       This module is for parsing an InterPro XML file and persist the resulting terms to a
       Biosql database as soon as the term is complete as signaled by the appropriate xml tag.
       This parser takes advantage of SAX, a stream-based XML parser technology, to keep the used
       memory as small as possible. The alternative parser for InterPro, module InterProHandler,
       builds up the entire ontology in memory, which given the size of the latest InterPro
       releases requires a huge amount of memory.

       This module takes the following non-standard arguments upon instantiation.

          -db           the adaptor factory as returned by a call to
                        Bio::DB::BioDB->new()
          -version      the InterPro version (not available as property!)
          -term_factory the object factory to use for creating terms

       Note that there are two alternatives for how to persist the terms and relationships to the
       database. The default is using the adaptor factory passed as -db or set as a property to
       create persistent objects and store them in the database. The alternative is to specify a
       term persistence and a relationship persistence handler; if one or both have been set, the
       respective handler will be called with each term and relationship that is to be stored.
       See properties persist_term_handler and persist_relationship_handler.

AUTHOR

       Juguang Xiao, juguang@tll.org.sg

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 _

   term_factory
        Title   : term_factory
        Usage   : $obj->term_factory($newval)
        Function: Get/set the ontology term factory to use.

                  As a user of this module it is not necessary to call this
                  method as there will be default. In order to change the
                  default, the easiest way is to instantiate
                  L<Bio::Ontology::TermFactory> with the proper -type
                  argument. Most if not all parsers will actually use this
                  very implementation, so even easier than the aforementioned
                  way is to simply call
                  $ontio->term_factory->type("Bio::Ontology::MyTerm").

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

   db
        Title   : db
        Usage   : $obj->db($newval)
        Function: Sets or retrieves the database adaptor factory.

                  The adaptor factory is a Bio::DB::DBAdaptorI compliant
                  object and will be used to obtain the persistence adaptors
                  necessary to serialize terms and relationships to the
                  database.

                  Usually, you will obtain such an object from a call to
                  Bio::DB::BioDB. You *must* set this property before
                  starting the parse.

                  Note that this property is immutable once set, except that
                  you may set it to undef. Therefore, be careful not to set
                  to undef before setting the desired real value.

        Example :
        Returns : value of db (a Bio::DB::DBAdaptorI compliant object)
        Args    : on set, new value (a Bio::DB::DBAdaptorI compliant object
                  or undef, optional)

   persist_term_handler
        Title   : persist_term_handler
        Usage   : $obj->persist_term_handler($handler,@args)
        Function: Sets or retrieves the persistence handler for terms along
                  with the constant set of arguments to be passed to the
                  handler.

                  If set, the first argument will be treated as a closure and
                  be called for each term to persist to the database. The
                  term will be passed as a named parameter (-term), followed
                  by the other arguments passed to this setter. Note that
                  this allows one to pass an arbitrary configuration to the
                  handler.

                  If not set, terms will be persisted along with their
                  relationships using the respective persistence adaptor
                  returned by the adaptor factory (see property db).

        Example :
        Returns : an array reference with the values passed on set, or an empty
                  array if never set
        Args    : On set, an array of values. The first value is the handler
                  as a closure; all other values will be passed to the handler
                  as constant argument.

   persist_relationship_handler
        Title   : persist_relationship_handler
        Usage   : $obj->persist_relationship_handler($handler,@args)
        Function: Sets or retrieves the persistence handler for relationships
                  along with the constant set of arguments to be passed to
                  the handler.

                  If set, the first argument will be treated as a closure and
                  be called for each relationship to persist to the database. The
                  relationship will be passed as a named parameter (-rel), followed
                  by the other arguments passed to this setter. Note that
                  this allows one to pass an arbitrary configuration to the
                  handler.

                  If not set, relationships will be persisted along with their
                  relationships using the respective persistence adaptor
                  returned by the adaptor factory (see property db).

        Example :
        Returns : an array reference with the values passed on set, or an empty
                  array if never set
        Args    : On set, an array of values. The first value is the handler
                  as a closure; all other values will be passed to the handler
                  as constant argument.

   _persist_term
        Title   : _persist_term
        Usage   :
        Function: Persists a term to the database, using either a previously
                  set persistence handler, or the adaptor factory directly.
        Example :
        Returns :
        Args    : the ontology term to persist

   _persist_relationship
        Title   : _persist_relationship
        Usage   :
        Function: Persists a relationship to the database, using either a
                  previously set persistence handler, or the adaptor factory
                  directly.

        Example :
        Returns :
        Args    : the term relationship to persist

   _persist_ontology
        Title   : _persist_ontology
        Usage   :
        Function: Perists the ontology itself to the database, by either
                  inserting or updating it.

                  Note that this will only create or update the ontology as
                  an entity, not any of its terms, relationships, or
                  relationship types.

        Example :
        Returns : the ontology as a persistent object with primary key
        Args    : the ontology to persist as a Bio::Ontology::OntologyI
                  compliant object

perl v5.28.0                              Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler(3pm)