--- name: "Bio::Search::Iteration::GenericIteration" section: "3pm" platform: "linux" package: "libbio-perl-perl" version: "1.7.8-1" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/Bio::Search::Iteration::GenericIteration" --- # Bio::Search::Iteration::GenericIteration(3pm) A generic implementation of the Bio::Search::Iteration::IterationI interface. ## 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. ```