InterProHandler - XML handler class for InterProParser # do not use directly - used and instantiated by InterProParser Handles xml events generated by InterProParser when parsing InterPro xml files.

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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 email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ Email dimitrov@gnf.org Juguang Xiao, juguang@tll.org.sg Additional contributors names and emails here 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 :