Bio::OntologyIO::Handlers::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 :