bio::search::hit::hitfactory(3pm) [debian man page]

Bio::Search::Hit::HitFactory(3pm)			User Contributed Perl Documentation			 Bio::Search::Hit::HitFactory(3pm)

NAME

       Bio::Search::Hit::HitFactory - A factory to create Bio::Search::Hit::HitI objects

SYNOPSIS

	   use Bio::Search::Hit::HitFactory;
	   my $factory = Bio::Search::Hit::HitFactory->new();
	   my $resultobj = $factory->create(@args);

DESCRIPTION

       This is a general way of hiding the object creation process so that we can dynamically change the objects that are created by the SearchIO
       parser depending on what format report we are parsing.

       This object is for creating new Hits.

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://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich
       Email jason@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::Search::Hit::HitFactory->new();
	Function: Builds a new Bio::Search::Hit::HitFactory object
	Returns : Bio::Search::Hit::HitFactory
	Args	:

   create
	Title	: create
	Usage	: $factory->create(%args)
	Function: Create a new L<Bio::Search::Hit::HitI> object
	Returns : L<Bio::Search::Hit::HitI>
	Args	: hash of initialization parameters

   type
	Title	: type
	Usage	: $factory->type('Bio::Search::Hit::GenericHit');
	Function: Get/Set the Hit creation type
	Returns : string
	Args	: [optional] string to set

perl v5.14.2							    2012-03-02					 Bio::Search::Hit::HitFactory(3pm)

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://redmine.open-bio.org/projects/bioperl/

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.

perl v5.14.2							    2012-03-02				   Bio::SearchIO::FastHitEventBuilder(3pm)