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://redmine.open-bio.org/projects/bioperl/
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
See Bio::Factory::ObjectFactoryI for more information
Bio::Event::EventHandlerI methods¶
will_handle¶
Title : will_handle
Usage : if( $handler->will_handle($event_type) ) { ... }
Function: Tests if this event builder knows how to process a specific event
Returns : boolean
Args : event type name
SAX methods¶
See Bio::Event::EventHandlerI for the additional SAX methods.