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://redmine.open-bio.org/projects/bioperl/

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 v5.18.2                                2014-0Bio::OntologyIO::Handlers::InterProHandler(3pm)