NAME

Bio::SearchIO::EventHandlerI - An abstract Event Handler for Search Result parsing

SYNOPSIS

# do not use this object directly it is an interface # See Bio::SearchIO::SearchResultEventBuilder for an implementation

use Bio::SearchIO::SearchResultEventBuilder;
my $handler = Bio::SearchIO::SearchResultEventBuilder->new();

DESCRIPTION

This interface describes the basic methods needed to handle Events thrown from parsing a Search Result such as FASTA, BLAST, or HMMer.

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 - Jason Stajich

Email jason-at-bioperl.org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

start_result

Title   : start_result
Usage   : $handler->start_result($data)
Function: Begins a result event cycle
Returns : none 
Args    : Type of Result

end_result

Title   : end_result
Usage   : $handler->end_result($data)
Function: Ends a result event cycle
Returns : Bio::Search::Result::ResultI object
Args    : none

start_hsp

Title   : start_hsp
Usage   : $handler->start_hsp($data)
Function: Start a HSP event cycle
Returns : none
Args    : type of element
          associated hashref

end_hsp

Title   : end_hsp
Usage   : $handler->end_hsp()
Function: Ends a HSP event cycle
Returns : Bio::Search::HSP::HSPI object
Args    : type of event and associated hashref

start_hit

Title   : start_hit
Usage   : $handler->start_hit()
Function: Starts a Hit event cycle
Returns : none
Args    : type of event and associated hashref

end_hit

Title   : end_hit
Usage   : $handler->end_hit()
Function: Ends a Hit event cycle
Returns : Bio::Search::Hit::HitI object
Args    : type of event and associated hashref

start_iteration

Title   : start_iteration
Usage   : $handler->start_iteration()
Function: Starts an Iteration event cycle
Returns : none
Args    : type of event and associated hashref

end_iteration

Title   : end_iteration
Usage   : $handler->end_iteration()
Function: Ends an Iterationevent cycle
Returns : Bio::Search::Iteration::IterationI object
Args    : type of event and associated hashref

register_factory

Title   : register_factory
Usage   : $handler->register_factory('TYPE',$factory);
Function: Register a specific factory for a object type class
Returns : none
Args    : string representing the class and
          Bio::Factory::ObjectFactoryI

See Bio::Factory::ObjectFactoryI for more information

factory

Title   : factory
Usage   : my $f = $handler->factory('TYPE');
Function: Retrieves the associated factory for requested 'TYPE'
Returns : a Bio::Factory::ObjectFactoryI
Throws  : Bio::Root::BadParameter if none registered for the supplied type
Args    : name of factory class to retrieve