Bio::SearchIO::FastHitEventBuilder(3)

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.