Bio::Search::Iteration::GenericIteration man page on Pidora

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Bio::Search::IterationUsernContribuBio::Search::Iteration::GenericIteration(3)

NAME
       Bio::Search::Iteration::GenericIteration - A generic implementation of
       the Bio::Search::Iteration::IterationI interface.

SYNOPSIS
	   use Bio::Search::Iteration::GenericIteration;
	   my $it = Bio::Search::GenericIteration->new(
				     -number => 1,
				     -converged => 0,
				     -newhits_unclassified => [@newhits_unclass],
				     -newhits_below => [@newhits_below_threshold],
				     -newhits_not_below => [@newhits_not_below_threshold],
				     -oldhits_below => [@oldhits_below_threshold],
				     -oldhits_newly_below => [@oldhits_newly_below_threshold],
				     -oldhits_not_below => [@oldhits_not_below_threshold],
					       );

       # TODO: Describe how to configure a SearchIO stream so that it
       generates #	 GenericIteration objects.

DESCRIPTION
       This module acts as a container for Bio::Search::Hit::HitI objects,
       allowing a Search::Result::ResultI object to partition its hits based
       on which iteration the hit occurred in (e.g., a PSI-BLAST round).

       Unless you're writing a parser, you won't ever need to create a
       GenericIteration or any other IterationI-implementing object. If you
       use the SearchIO system, IterationI objects are created automatically
       from a SearchIO stream which returns Bio::Search::Result::ResultI
       objects and you get the IterationI objects via the ResultI API.

       For documentation on what you can do with GenericIteration (and other
       IterationI objects), please see the API documentation in
       Bio::Search::Iteration::IterationI.

       Bio::Search::Iteration::GenericIteration is similar in spirit to the
       deprecated Bio::Tools::BPlite::Iteration modules in bioperl releases
       prior to 1.6, except that Bio::Search::Iteration::GenericIteration is a
       pure container, without any parsing functionality as is in
       Bio::Tools::BPlite::Iteration.

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 - Steve Chervitz
       Email sac@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::Iteration->new(%args);
	Function: Builds a new Bio::Search::Iteration object
	Returns : Bio::Search::Iteration::GenericIteration object
	Args	: -number => integer for the number of this iteration (required)
		  -converged => boolean value whether or not the iteration converged
		  -newhits_unclassified => array reference to hits that were not found
			      in a previous iteration for the iteration and have not been
			      classified with regard to the inclusion threshold

		  # The following are only used for PSI-BLAST reports:

		  -newhits_below => array reference to hits were not found in a
			       previous iteration and are below the inclusion threshold.
		  -newhits_not_below => array reference to hits that were not found in a
			       previous iteration below threshold that and are not below
			       the inclusion threshold threshold.
		  -oldhits_below => array reference to hits that were found
			       in a previous iteration below inclusion threshold and are
			       still below threshold in the current iteration.
		  -oldhits_newly_below => array reference to hits that were found
			       in a previous iteration above threshold but are below
			       threshold in the current iteration.
		  -oldhits_not_below => array reference to hits that were found in a
			       previous iteration above threshold that and are still above
			       the inclusion threshold threshold.

		  -hit_factory => Bio::Factory::ObjectFactoryI capable of making
			       Bio::Search::Hit::HitI objects

   number
       See documentation in Bio::Search::Iteration::IterationI.

   converged
       See documentation in Bio::Search::Iteration::IterationI.

   hit_factory
	Title	: hit_factory
	Usage	: $hit->hit_factory($hit_factory)
	Function: Get/set the factory used to build HitI objects if necessary.
	Returns : Bio::Factory::ObjectFactoryI
	Args	: Bio::Factory::ObjectFactoryI

   next_hit
       This iterates through all old hits as returned by oldhits followed by
       all new hits as returned by newhits.

       For more documentation see
       Bio::Search::Iteration::IterationI::next_hit().

   next_hit_new
       See documentation in
       Bio::Search::Iteration::IterationI::next_hit_new().

   next_hit_old
       See documentation in
       Bio::Search::Iteration::IterationI::next_hit_old().

   rewind
	Title	: rewind
	Usage	: $iteration->rewind;
	Function: Allow one to reset the Hit iterators to the beginning
		  Since this is an in-memory implementation
	Returns : none
	Args	: none

   num_hits
       See documentation in Bio::Search::Iteration::IterationI::num_hits().

   num_hits_new
       See documentation in
       Bio::Search::Iteration::IterationI::num_hits_new().

   num_hits_old
       See documentation in
       Bio::Search::Iteration::IterationI::num_hits_old().

   add_hit
       See documentation in Bio::Search::Iteration::IterationI::add_hit().

   hits
       See Documentation in InterfaceI.

   newhits
       Returns a list containing all newhits in this order:

       newhits_below_threshold newhits_not_below_threshold
       newhits_unclassified

       See more documentation in InterfaceI.

   newhits_below_threshold
       See documentation in
       Bio::Search::Iteration::IterationI::newhits_below_threshold().

   newhits_not_below_threshold
       See documentation in
       Bio::Search::Iteration::IterationI::newhits_not_below_threshold().

   newhits_unclassified
	Title	: newhits_unclassified
	Usage	: foreach( $iteration->hits_unclassified ) {...}
	Function: Gets all newhits that have not been partitioned into
		  sets relative to the inclusion threshold.
	Returns : Array of Bio::Search::Hit::HitI objects.
	Args	: none

   oldhits
       Returns a list containing all oldhits in this order:

       oldhits_below_threshold oldhits_newly_below_threshold
       oldhits_not_below_threshold

       See more documentation in InterfaceI.

   oldhits_below_threshold
       See documentation in
       Bio::Search::Iteration::IterationI::oldhits_below_threshold().

   oldhits_newly_below_threshold
       See documentation in
       Bio::Search::Iteration::IterationI::oldhits_newly_below_threshold().

   oldhits_not_below_threshold
       See documentation in
       Bio::Search::Iteration::IterationI::oldhits_not_below_threshold().

   hits_below_threshold
       See documentation in
       Bio::Search::Iteration::IterationI::hits_below_threshold().

   get_hit
       See documentation in Bio::Search::Iteration::IterationI::get_hit().

       To free up the memory used by the get_hit() functionality, call
       free_hit_lookup().

       This functionality might be useful at the Result level, too.
       BlastResult::get_hit() would return a list of HitI objects for hits
       that occur in multiple iterations.

   free_hit_lookup
	Purpose : Frees up the memory used by the get_hit() functionality.
		  For the memory-conscious.

perl v5.14.1			  2Bio::Search::Iteration::GenericIteration(3)
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