Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler(3pm) User Contributed Perl DocumentationBio::OntologyIO::Handlers::InterPro_BioSQL_Handler(3pm)

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.  Interal 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 peristent object with primary key
	Args	: the ontology to persist as a Bio::Ontology::OntologyI
		  compliant object

perl v5.14.2							    2012-03-02		   Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler(3pm)