/ 
BioPerl-1.7.8
River stage two • 61 direct dependents • 66 total dependents
/ Bio::SearchIO::FastHitEventBuilder

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.

[email protected]                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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.