Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages

  
 
  

home | help
Bio::OntologyIO::HandlUseriContribuoedIPerHaDocumentanterPro_BioSQL_Handler(3)

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 v5.24.1		 Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler(3)

NAME | SYNOPSIS | DESCRIPTION | AUTHOR | Contributors

Want to link to this manual page? Use this URL:
<https://www.freebsd.org/cgi/man.cgi?query=Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler&sektion=3&manpath=FreeBSD+12.1-RELEASE+and+Ports>

home | help