Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages

  
 
  

home | help
Bio::SearchIO::EventHaUserrContributed Perl DocBio::SearchIO::EventHandlerI(3)

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

       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.

perl v5.24.1			  2017-07-08   Bio::SearchIO::EventHandlerI(3)

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

Want to link to this manual page? Use this URL:
<https://www.freebsd.org/cgi/man.cgi?query=Bio::SearchIO::EventHandlerI&sektion=3&manpath=FreeBSD+12.1-RELEASE+and+Ports>

home | help