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Bio::SearchIO::SearchResultEventBuilder.3pm
Langue: en
Version: 2009-03-10 (debian - 07/07/09)
Section: 3 (Bibliothèques de fonctions)
Sommaire
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
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:http://bugzilla.open-bio.org/
AUTHOR - Jason Stajich
Email jason-at-bioperl.orgCONTRIBUTORS
Sendu Bala, bix@sendu.me.ukAPPENDIX
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
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.Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre