table of contents
| Bio::SearchIO::FastHitEventBuilder(3pm) | User Contributed Perl Documentation | Bio::SearchIO::FastHitEventBuilder(3pm) |
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.
| 2021-08-15 | perl v5.32.1 |