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

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.