Bio::OntologyIO::Handlers::InterProHandler.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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    :