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Manual Reference Pages  -  BIO::SEARCHIO::FASTHITEVENTBUILDER (3)

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NAME

Bio::SearchIO::FastHitEventBuilder - Event Handler for SearchIO events.

CONTENTS

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.
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perl v5.20.3 BIO::SEARCHIO::FASTHITEVENTBUILDER (3) 2016-04-05

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