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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:

   http://bugzilla.open-bio.org/
 
 

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.