Bio::SearchIO::SearchResultEventBuilder(3pm) User Contributed Perl Documentation Bio::SearchIO::SearchResultEventBuilder(3pm)
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://redmine.open-bio.org/projects/bioperl/
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
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.
perl v5.14.2 2012-03-02 Bio::SearchIO::SearchResultEventBuilder(3pm)