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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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : $h = Bio::OntologyIO::Handlers::InterProHandler->new; Function: Initializes global variables Example : Returns : an InterProHandler object Args :
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)
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.
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)
Title : _cite_skip Usage : $obj->_cite_skip($newval) Function: Example : Returns : value of _cite_skip (a scalar) Args : new value (a scalar, optional)
Title : _hash Usage : $obj->_hash($newval) Function: Example : Returns : value of _hash (a scalar) Args : new value (a scalar, optional)
Title : _stack Usage : $obj->_stack($newval) Function: Example : Returns : value of _stack (a scalar) Args : new value (a scalar, optional)
Title : _top Usage : Function: Example : Returns : Args :
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)
Title : _clear_term Usage : Function: Removes the current term from the handler Example : Returns : Args :
Title : _names Usage : $obj->_names($newval) Function: Example : Returns : value of _names (a scalar) Args : new value (a scalar, optional)
Title : _create_relationship Usage : Function: Helper function. Adds relationships to one of the relationship stores. Example : Returns : Args :
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 :
Title : _char_storage Usage : $obj->_char_storage($newval) Function: Example : Returns : value of _char_storage (a scalar) Args : new value (a scalar, optional)
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 :
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 :
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
Title : _increment_record_count Usage : Function: Example : Returns : Args :
Title : _increment_processed_count Usage : Function: Example : Returns : Args :
To install LocalConfig, copy and paste the appropriate command in to your terminal.
cpanm
cpanm LocalConfig
CPAN shell
perl -MCPAN -e shell install LocalConfig
For more information on module installation, please visit the detailed CPAN module installation guide.