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Bio::SearchIO::SearchRUsertContributedoPerearchIO::SearchResultEventBuilder(3)

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

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

DESCRIPTION
       This object handles Search Events generated by the SearchIO classes and
       build appropriate Bio::Search::*	objects	from them.

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

CONTRIBUTORS
       Sendu Bala, bix@sendu.me.uk

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::SearchResultEventBuilder->new();
	Function: Builds a new Bio::SearchIO::SearchResultEventBuilder object
	Returns	: Bio::SearchIO::SearchResultEventBuilder
	Args	: -hsp_factory	  => Bio::Factory::ObjectFactoryI
		  -hit_factory	  => Bio::Factory::ObjectFactoryI
		  -result_factory => Bio::Factory::ObjectFactoryI
		  -inclusion_threshold => e-value threshold for	inclusion in the
					  PSI-BLAST score matrix model (blastpgp)
		  -signif      => float	or scientific notation number to be used
				  as a P- or Expect value cutoff
		  -score       => integer or scientific	notation number	to be used
				  as a blast score value cutoff
		  -bits	       => integer or scientific	notation number	to be used
				  as a bit score value cutoff
		  -hit_filter  => reference to a function to be	used for
				  filtering hits based on arbitrary criteria.

       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_hsp
	Title	: start_hsp
	Usage	: $handler->start_hsp($name,$data)
	Function: Begins processing a HSP event
	Returns	: none
	Args	: type of element
		  associated data (hashref)

   end_hsp
	Title	: end_hsp
	Usage	: $handler->end_hsp()
	Function: Finish processing a HSP event
	Returns	: none
	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

   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
	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

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

   max_significance
	Usage	  : $obj->max_significance();
	Purpose	  : Set/Get the	P or Expect value used as significance screening cutoff.
		    This is the	value of the -signif parameter supplied	to new().
		    Hits with P	or E-value at HIT level	above this are skipped.
	Returns	  : Scientific notation	number with this format: 1.0e-05.
	Argument  : Number (sci	notation, float, integer) (when	setting)
	Throws	  : Bio::Root::BadParameter exception if the supplied argument is
		  : not	a valid	number.
	Comments  : Screening of significant hits uses the data	provided on the
		  : description	line. For NCBI BLAST1 and WU-BLAST, this data
		  : is P-value.	for NCBI BLAST2	it is an Expect	value.

   signif
       Synonym for max_significance()

   min_score
	Usage	  : $obj->min_score();
	Purpose	  : Gets the Blast score used as screening cutoff.
		    This is the	value of the -score parameter supplied to new().
		    Hits with scores at	HIT level below	this are skipped.
	Returns	  : Integer (or	undef if not set)
	Argument  : Integer (when setting)
	Throws	  : Bio::Root::BadParameter exception if the supplied argument is
		  : not	a valid	number.
	Comments  : Screening of significant hits uses the data	provided on the
		  : description	line.

   min_bits
	Usage	  : $obj->min_bits();
	Purpose	  : Gets the Blast bit score used as screening cutoff.
		    This is the	value of the -bits parameter supplied to new().
		    Hits with bits score at HIT	level below this are skipped.
	Returns	  : Integer (or	undef if not set)
	Argument  : Integer (when setting)
	Throws	  : Bio::Root::BadParameter exception if the supplied argument is
		  : not	a valid	number.
	Comments  : Screening of significant hits uses the data	provided on the
		  : description	line.

   hit_filter
	Usage	  : $obj->hit_filter();
	Purpose	  : Set/Get a function reference used for filtering out	hits.
		    This is the	value of the -hit_filter parameter supplied to new().
		    Hits that fail to pass the filter at HIT level are skipped.
	Returns	  : Function ref (or undef if not set)
	Argument  : Function ref (when setting)
	Throws	  : Bio::Root::BadParameter exception if the supplied argument is
		  : not	a function reference.

perl v5.24.1			  20Bio::SearchIO::SearchResultEventBuilder(3)

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

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