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 :