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Bio::OntologyIO::HandlUser:ContributedOPerloDyIO::Handlers::InterProHandler(3)

NAME
       Bio::OntologyIO::Handlers::InterProHandler - XML	handler	class for
       InterProParser

SYNOPSIS
	# do not use directly -	used and instantiated by InterProParser

DESCRIPTION
       Handles xml events generated by InterProParser when parsing InterPro
       XML files.

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://github.com/bioperl/bioperl-live/issues

AUTHOR - Peter Dimitrov
       Email dimitrov@gnf.org

CONTRIBUTORS
       Juguang Xiao, juguang@tll.org.sg

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

   new
	Title	: new
	Usage	: $h = Bio::OntologyIO::Handlers::InterProHandler->new;
	Function: Initializes global variables
	Example	:
	Returns	: an InterProHandler object
	Args	:

   ontology_engine
	Title	: ontology_engine
	Usage	: $obj->ontology_engine($newval)
	Function: Get/set ontology engine. Can be initialized only once.
	Example	:
	Returns	: value	of ontology_engine (a scalar)
	Args	: new value (a scalar, optional)

   ontology
	Title	: ontology
	Usage	:
	Function: Get the ontology to add the InterPro terms to.

		  The value is determined automatically	once ontology_engine
		  has been set and if it hasn't	been set before.

	Example	:
	Returns	: A L<Bio::Ontology::OntologyI>	implementing object.
	Args	: On set, a L<Bio::Ontology::OntologyI>	implementing object.

   term_factory
	Title	: term_factory
	Usage	: $obj->term_factory($newval)
	Function: Get/set the ontology term object factory
	Example	:
	Returns	: value	of term_factory	(a Bio::Factory::ObjectFactory instance)
	Args	: on set, new value (a Bio::Factory::ObjectFactory instance
		  or undef, optional)

   _cite_skip
	Title	: _cite_skip
	Usage	: $obj->_cite_skip($newval)
	Function:
	Example	:
	Returns	: value	of _cite_skip (a scalar)
	Args	: new value (a scalar, optional)

   _hash
	Title	: _hash
	Usage	: $obj->_hash($newval)
	Function:
	Example	:
	Returns	: value	of _hash (a scalar)
	Args	: new value (a scalar, optional)

   _stack
	Title	: _stack
	Usage	: $obj->_stack($newval)
	Function:
	Example	:
	Returns	: value	of _stack (a scalar)
	Args	: new value (a scalar, optional)

   _top
	Title	: _top
	Usage	:
	Function:
	Example	:
	Returns	:
	Args	:

   _term
	Title	: _term
	Usage	: $obj->_term($newval)
	Function: Get/set method for the term currently	processed.
	Example	:
	Returns	: value	of term	(a scalar)
	Args	: new value (a scalar, optional)

   _clear_term
	Title	: _clear_term
	Usage	:
	Function: Removes the current term from	the handler
	Example	:
	Returns	:
	Args	:

   _names
	Title	: _names
	Usage	: $obj->_names($newval)
	Function:
	Example	:
	Returns	: value	of _names (a scalar)
	Args	: new value (a scalar, optional)

   _create_relationship
	Title	: _create_relationship
	Usage	:
	Function: Helper function. Adds	relationships to one of	the relationship stores.
	Example	:
	Returns	:
	Args	:

   start_element
	Title	: start_element
	Usage	:
	Function: This is a method that	is derived from	XML::SAX::Base and
		  has to be overridden for processing start of xml element
		  events. Used internally only.

	Example	:
	Returns	:
	Args	:

   _char_storage
	Title	: _char_storage
	Usage	: $obj->_char_storage($newval)
	Function:
	Example	:
	Returns	: value	of _char_storage (a scalar)
	Args	: new value (a scalar, optional)

   characters
	Title	: characters
	Usage	:
	Function: This is a method that	is derived from	XML::SAX::Base and has to be overridden	for processing xml characters events. Used internally only.
	Example	:
	Returns	:
	Args	:

   end_element
	Title	: end_element
	Usage	:
	Function: This is a method that	is derived from	XML::SAX::Base and has to be overridden	for processing end of xml element events. Used internally only.
	Example	:
	Returns	:
	Args	:

   secondary_accessions_map
	Title	: secondary_accessions_map
	Usage	: $obj->secondary_accessions_map($newval)
	Function:
	Example	: $map = $interpro_handler->secondary_accessions_map();
	Returns	: Reference to a hash that maps	InterPro identifier to an
	 array reference of secondary accessions following the InterPro
	xml schema.
	Args	: Empty	hash reference

   _increment_record_count
	Title	: _increment_record_count
	Usage	:
	Function:
	Example	:
	Returns	:
	Args	:

   _increment_processed_count
	Title	: _increment_processed_count
	Usage	:
	Function:
	Example	:
	Returns	:
	Args	:

perl v5.24.1			 Bio::OntologyIO::Handlers::InterProHandler(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Peter Dimitrov | CONTRIBUTORS | APPENDIX

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