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    :

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq