Bio::Search::Iteration::GenericIteration - A generic implementation of the Bio::Search::Iteration::IterationI interface.
use Bio::Search::Iteration::GenericIteration; my $it = new Bio::Search::GenericIteration( -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.
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 Bio::Tools::BPlite::Iteration, except that Bio::Search::Iteration::GenericIteration is a pure container, without any parsing functionality as is in Bio::Tools::BPlite::Iteration.
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
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/
Email sac@bioperl.org
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : my $obj = new Bio::Search::Iteration(%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
See documentation in Bio::Search::Iteration::IterationI.
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
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().
See documentation in Bio::Search::Iteration::IterationI::next_hit_new().
See documentation in Bio::Search::Iteration::IterationI::next_hit_old().
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
See documentation in Bio::Search::Iteration::IterationI::num_hits().
See documentation in Bio::Search::Iteration::IterationI::num_hits_new().
See documentation in Bio::Search::Iteration::IterationI::num_hits_old().
See documentation in Bio::Search::Iteration::IterationI::add_hit().
See Documentation in InterfaceI.
Returns a list containing all newhits in this order:
newhits_below_threshold newhits_not_below_threshold newhits_unclassified
See more documentation in InterfaceI.
See documentation in Bio::Search::Iteration::IterationI::newhits_below_threshold().
See documentation in Bio::Search::Iteration::IterationI::newhits_not_below_threshold().
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
Returns a list containing all oldhits in this order:
oldhits_below_threshold oldhits_newly_below_threshold oldhits_not_below_threshold
See documentation in Bio::Search::Iteration::IterationI::oldhits_below_threshold().
See documentation in Bio::Search::Iteration::IterationI::oldhits_newly_below_threshold().
See documentation in Bio::Search::Iteration::IterationI::oldhits_not_below_threshold().
See documentation in Bio::Search::Iteration::IterationI::hits_below_threshold().
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.
Purpose : Frees up the memory used by the get_hit() functionality. For the memory-conscious.
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.