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Bio::SearchIO::FastHitUsertContributed PeBio::SearchIO::FastHitEventBuilder(3)

NAME
       Bio::SearchIO::FastHitEventBuilder - Event Handler for SearchIO events.

SYNOPSIS
	 # Do not use this object directly, this object	is part	of the SearchIO
	 # event based parsing system.

	 # to use the FastHitEventBuilder do this

	 use Bio::SearchIO::FastHitEventBuilder;

	 my $searchio =	Bio::SearchIO->new(-format => $format, -file =>	$file);

	 $searchio->attach_EventHandler(Bio::SearchIO::FastHitEventBuilder->new());

	 while(	my $r =	$searchio->next_result ) {
	  while( my $h = $r->next_hit )	{
	   # note that Hits will NOT have HSPs
	  }
	 }

DESCRIPTION
       This object handles Search Events generated by the SearchIO classes and
       build appropriate Bio::Search::*	objects	from them.  This object	is
       intended	for lightweight	parsers	which only want	Hits and not deal with
       the overhead of HSPs.  It is a lot faster than the standard parser
       event handler but of course you are getting less	information and	less
       objects out.

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 _

   new
	Title	: new
	Usage	: my $obj = Bio::SearchIO::FastHitEventBuilder->new();
	Function: Builds a new Bio::SearchIO::FastHitEventBuilder object
	Returns	: Bio::SearchIO::FastHitEventBuilder
	Args	: -hit_factory	  => Bio::Factory::ObjectFactoryI
		  -result_factory => Bio::Factory::ObjectFactoryI

       See Bio::Factory::ObjectFactoryI	for more information

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

   end_result
	Title	: end_result
	Usage	: my @results =	$parser->end_result
	Function: Finishes a result handler cycle Returns : A Bio::Search::Result::ResultI
	Args	: none

   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

   Factory methods
   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 or undef if none registered
	Args	: name of factory class	to retrieve

       See Bio::Factory::ObjectFactoryI	for more information

   inclusion_threshold
       See Bio::SearchIO::blast::inclusion_threshold.

perl v5.24.1			  2017-07Bio::SearchIO::FastHitEventBuilder(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Jason Stajich | APPENDIX

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