Provided by: libbio-perl-perl_1.7.2-3_all bug

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:

         https://github.com/bioperl/bioperl-live/issues

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 v5.28.0                                2018-10-Bio::Search::Iteration::GenericIteration(3pm)