Provided by: libbio-perl-perl_1.7.2-2_all bug

NAME

       Bio::Search::Iteration::IterationI - Abstract interface to an iteration from an iterated
       search result, such as PSI-BLAST.

SYNOPSIS

           # Bio::Search::Iteration::IterationI objects cannot be
           # instantiated since this module defines a pure interface.
           # Given an object that implements the
           # Bio::Search::Iteration::IterationI interface,
           # you can do the following things with it:

           # First, open up a SearchIO stream
           use Bio::SearchIO;
           my $file = shift or die "Usage: $0 <BLAST-report-file>\n";
           my $in = Bio::SearchIO->new(-format => 'blast',
                                      -file => $file # comment out this line to read STDIN
                                     );
           # Iterate over all results in the input stream
           while (my $result = $in->next_result) {

               printf "Result #%d: %s\n", $in->result_count, $result->to_string;
               printf "Total Iterations: %d\n", $result->num_iterations();

               # Iterate over all iterations and process old and new hits
               # separately.

               while( my $it = $result->next_iteration) {
                   printf "\nIteration %d\n", $it->number;
                   printf "Converged: %d\n", $it->converged;

                   # Print out the hits not found in previous iteration
                   printf "New hits: %d\n", $it->num_hits_new;
                   while( my $hit = $it->next_hit_new ) {
                       printf "  %s, Expect=%g\n", $hit->name, $hit->expect;
                   }

                   # Print out the hits found in previous iteration
                   printf "Old hits: %d\n", $it->num_hits_old;
                   while( my $hit = $it->next_hit_old ) {
                       printf "  %s, Expect=%g\n", $hit->name, $hit->expect;
                   }
               }
               printf "%s\n\n", '-' x 50;
           }

           printf "Total Reports processed: %d: %s\n", $in->result_count;

           __END__

           # NOTE: The following functionality is just proposed
           # (does not yet exist but might, given sufficient hew and cry):

           # Zero-in on the new hits found in last iteration.
           # By default, iteration() returns the last one.

           my $last_iteration = $result->iteration();
           while( my $hit = $last_iteration->next_hit) {
               # Do something with new hit...
           }

           # Get the first iteration

           my $first_iteration = $result->iteration(1);

DESCRIPTION

       Bio::Search::Result::ResultI objects are data structures containing the results from the
       execution of a search algorithm.  As such, it may contain various algorithm specific
       information as well as details of the execution, but will contain a few fundamental
       elements, including the ability to return Bio::Search::Hit::HitI objects.

   Classification of Hits
       Within a given iteration, the hits can be classified into a number of useful subsets based
       on whether or not the hit appeard in a previous iteration and whether or not the hit is
       below the threshold E-value for inclusion in the score matrix model.

                                  All hits
                                    (A)
                      _______________|_________________
                      |                               |
                   New hits                        Old hits
                     (B)                             (C)
             _________|________                _______|_________
             |                |                |               |
           Below            Above             Below          Above
         threshold        threshold         threshold      threshold
            (D)              (E)              (F)             (G)
                                      _________|___________
                                      |                   |
                                Occurred in a         Occurred in a
                                previous iteration    previous iteration
                                below threshold       above threshold
                                     (H)                  (I)

       Notes: The term threshold in the diagram and descriptions below refer to this inclusion
       threshold. Below threshold actually means at or below threshold.

       The IterationI interface defines a number of methods for extracting these subsets of hits.

       ·   newhits_below_threshold() [subset D]

           Hits that did not appear in a previous iteration and are below threshold in the
           current iteration.

       ·   newhits_not_below_threshold() [subset E]

           Hits that did not appear in a previous iteration and are not below threshold in the
           current iteration.

       ·   newhits() [subset B]

           All newly found hits, below and above the inclusion threshold.  This is the union of
           newhits_below_threshold() + newhits_not_below_threshold() [subset D + subset E].

       ·   oldhits_below_threshold() [subset H]

           Hits that appeared in a previous iteration below threshold and are still below
           threshold in the current iteration.

       ·   oldhits_newly_below_threshold() [subset I]

           Hits that appeared in a previous iteration above threshold but are below threshold in
           the current iteration. (Not applicable to the first iteration.)

       ·   oldhits_not_below_threshold() [subset G]

           Hits that appeared in a previous iteration not below threshold and are still not below
           threshold in the current iteration.

       ·   oldhits()  [subset C]

           All hits that occurred in a previous iteration, whether below or above threshold in
           the current iteration. Union of oldhits_below_threshold() +
           oldhits_newly_below_threshold() + oldhits_not_below_threshold() [subset H + subset I +
           subset G]. (Not applicable to the first iteration.)

       ·   hits_below_threshold() [subset D + subset F]

           All hits, old and new, that are below the inclusion threshold in this iteration. This
           is the union of newhits_below_threshold() + oldhits_below_threshold() +
           oldhits_newly_below_threshold() [subset D + subset H + subset I].

       ·   hits() [subset A]

           The union of newhits() and oldhits() [subset B + subset C].

       For the first iteration, the methods oldhits, oldhits_below_threshold,
       oldhits_newly_below_threshold, and oldhits_not_below_threshold() will return empty lists.

       Iterator and numbers-of-hit methods are provided for subsets A, B, and C:

       ·   next_hit_new(), num_hits_new() [subset B]

       ·   next_hit_old(), num_hits_old() [subset C]

       ·   next_hit(), num_hits() [subset A]

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 one of the Bioperl mailing lists.  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 the bugs and their
       resolution.  Bug reports can be submitted via the web:

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

AUTHOR

       Steve Chervitz <sac@bioperl.org>

       See the FEEDBACK section  for where to send bug reports and comments.

COPYRIGHT

       Copyright (c) 2003 Steve Chervitz. All Rights Reserved.

DISCLAIMER

       This software is provided "as is" without warranty of any kind.

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are
       usually preceded with a _

   number
        Title   : number
        Usage   : $it_number = $iteration->number();
        Purpose : returns the number of the iteration (a.k.a "round")
                  within the Result.
        Returns : integer
        Args    : [optional] integer to set the number of the iteration

   converged
        Title   : converged
        Usage   : $it_converged = $iteration->converged();
        Purpose : Indicates whether or not the iteration has converged
        Returns : boolean
        Args    : [optional] boolean value to set the converged of the iteration

   next_hit
        Title   : next_hit
        Usage   : while( $hit = $iteration->next_hit( [$found_again]) ) { ... }
        Purpose : Iterates through all of the HitI objects
                  including new hits and old hits found in a previous iteration
                  and both below and above the inclusion threshold.
                  Corresponds to subset A in the "Classification of Hits"
                  documentation section of this module.
        Returns : A Bio::Search::Hit::HitI object or undef if there are no more.
                  Hits will be returned in the order in which they occur in the report
                  unless otherwise specified.
        Args    : none

       See Also: hits, "Classification of Hits"

       next_hit() iterates through all hits, including the new ones for this iteration and those
       found in previous iterations.  You can interrogate each hit using
       Bio::Search::Hit::HitI::found_again to determine whether it is new or old.

       To get just the new hits, use next_hit_new.  To get just the old hits, use next_hit_old.

   next_hit_new
        Title   : next_hit_new
        Usage   : while( $hit = $iteration->next_hit_new() ) { ... }
        Purpose : Iterates through all newly found hits (did not occur in a
                  previous iteration) and are either below or above the inclusion threshold.
                  Corresponds to subset B in the "Classification of Hits"
                  documentation section of this module.
        Returns : A Bio::Search::Hit::HitI object or undef if there are no more.
                  Hits will be returned in the order in which they occur in the report
                  unless otherwise specified.
        Args    : none

       See Also: next_hit, next_hit_old, newhits, "Classification of Hits"

   next_hit_old
        Title   : next_hit_old
        Usage   : while( $hit = $iteration->next_hit_old() ) { ... }
        Purpose : Iterates through the Hit objects representing just the
                  hits that have been found in a previous iteration, whether
                  below or above the inclusion threshold.
                  Corresponds to subset C in the "Classification of Hits"
                  documentation section of this module.
        Returns : A Bio::Search::Hit::HitI object or undef if there are no more.
                  Hits will be returned in the order in which they occur in the report
                  unless otherwise specified.
        Args    : none

       See Also: next_hit, next_hit_old, oldhits, "Classification of Hits"

   num_hits
        Title   : num_hits
        Usage   : my $hitcount_total = $iteration->num_hits
        Purpose : Returns the total number of hits for this query result, including new and old
                  below and above inclusion threshold.
        Returns : integer
        Args    : none

       See Also: num_hits_new, num_hits_old, "Classification of Hits"

   num_hits_new
        Title   : num_hits_new
        Usage   : my $hitcount_new = $result->num_hits_new;
                : my $hitcount_new_below_thresh = $result->num_hits_new( 1 );
        Purpose : Returns the number of new hits in this iteration that were not
                  found in a previous iteration and are either below or above the
                  the inclusion threshold.
                  Corresponds to subset B in the "Classification of Hits"
                  documentation section of this module.
        Returns : integer
        Args    : (optional) boolean, true if you want to get a count of just the new hits
                  that are below the inclusion threshold.

       See Also: num_hits, num_hits_old, "Classification of Hits"

   num_hits_old
        Title   : num_hits_old
        Usage   : my $hitcount_old = $result->num_hits_old;
                : my $hitcount_old_below_thresh = $result->num_hits_old( 1 );
        Purpose : Returns the number of new hits in this iteration that were
                  found in a previous iteration and are either below or above the
                  the inclusion threshold.
                  Corresponds to subset C in the "Classification of Hits"
                  documentation section of this module.
        Returns : integer
        Args    : (optional) boolean, true if you want to get a count of just the old hits
                  that are below the inclusion threshold.

       See Also: num_hits, num_hits_new, "Classification of Hits"

   hits
        Title    : hits
        Usage    : foreach( $obj->hits() ) { ... };
        Purpose  : Provides access to all hits, both new and old, and either
                   below or above the inclusion threshold.
                   Corresponds to subset A in the "Classification of Hits"
                   documentation section of this module.
        Returns  : An array containing all HitI objects.
                   Hits will be ordered according to their occurrence in the report
                   unless otherwise specified.
        Args     : none

       See Also: newhits, oldhits, "Classification of Hits"

   newhits
        Title    : newhits
        Usage    : foreach( $obj->newhits() ) { ... };
        Purpose  : Provides access to hits that were not found in a previous iteration
                   and may be either below or above the inclusion threshold.
                   Corresponds to subset B in the "Classification of Hits"
                   documentation section of this module.
        Returns  : An array containing Bio::Search::Hit::HitI objects.
                   Hits will be ordered according to their occurrence in the report
                   unless otherwise specified.
        Args     : none

       See Also: hits, oldhits, newhits_below_threshold + newhits_not_below_threshold,
       "Classification of Hits"

   oldhits
        Title    : oldhits
        Usage    : foreach( $obj->oldhits() ) { ... };
        Purpose  : Provides access to hits that were found in a previous iteration
                   and are either below or above the inclusion threshold in the current iteration.
                   Corresponds to subset C in the "Classification of Hits"
                   documentation section of this module.
        Returns  : An array containing Bio::Search::Hit::HitI objects.
                   Hits will be ordered according to their occurrence in the report
                   unless otherwise specified.
        Args     : none

       See Also: hits, newhits, oldhits_below_threshold, oldhits_newly_below_threshold,
       oldhits_not_below_threshold, "Classification of Hits"

   newhits_below_threshold
        Title   : newhits_below_threshold
        Usage   : foreach( $obj->newhits_below_threshold() ) { ... };
        Purpose : Provides access to hits that did not appear in a
                  previous iteration and are below threshold.
                  Corresponds to subset D in the "Classification of Hits"
                  documentation section of this module.
        Returns : An array containing Bio::Search::Hit::HitI objects.
                  Hits will be returned in the order in which they occur in the report
                  unless otherwise specified.
        Args    : none

       See Also: newhits_not_below_threshold, oldhits_newly_below_threshold, newhits,
       "Classification of Hits"

   oldhits_below_threshold
        Title   : oldhits_below_threshold
        Usage   : foreach( $obj->oldhits_below_threshold() ) { ... };
        Purpose : Provides access to hits that appeared in a
                  previous iteration below inclusion threshold and are still below threshold.
                  Corresponds to subset H in the "Classification of Hits"
                  documentation section of this module.
        Returns : An array containing Bio::Search::Hit::HitI objects.
                  Hits will be returned in the order in which they occur in the report
                  unless otherwise specified.
        Args    : none

       See Also: oldhits_not_below_threshold, oldhits_newly_below_threshold, oldhits,
       "Classification of Hits"

   oldhits_newly_below_threshold
        Title   : oldhits_newly_below_threshold
        Usage   : foreach( $obj->oldhits_newly_below_threshold() ) { ... };
        Purpose : Provides access to hits that appeared in a previous
                  iteration above threshold but are below threshold in the
                  current iteration. Not applicable to the first iteration.
                  Corresponds to subset I in the "Classification of Hits"
                  documentation section of this module.
        Returns : An array containing Bio::Search::Hit::HitI objects.
                  Hits will be returned in the order in which they occur in the report
                  unless otherwise specified.
        Args    : none

       See Also: newhits_below_threshold, oldhits, "Classification of Hits"

   oldhits_not_below_threshold
        Title   : oldhits_not_below_threshold
        Usage   : foreach( $obj->oldhits_not_below_threshold() ) { ... };
        Purpose : Provides access to hits that appeared in a previous iteration
                  not below threshold and are still not below threshold.
                  Corresponds to subset G in the "Classification of Hits"
                  documentation section of this module.
        Returns : An array containing Bio::Search::Hit::HitI objects.
                  Hits will be returned in the order in which they occur in the report
                  unless otherwise specified.
        Args    : none

       See Also: oldhits_below_threshold, oldhits, "Classification of Hits"

   newhits_not_below_threshold
        Title   : newhits_not_below_threshold
        Usage   : foreach( $obj->newhits_not_below_threshold() ) { ... };
        Purpose : Provides access to hits that did not appear in a
                  previous iteration and are not below threshold
                  in the current iteration.
                  Corresponds to subset E in the "Classification of Hits"
                  documentation section of this module.
        Returns : An array containing Bio::Search::Hit::HitI objects.
                  Hits will be returned in the order in which they occur in the report
                  unless otherwise specified.
        Args    : none

       See Also: newhits_below_threshold, newhits, "Classification of Hits"

   hits_below_threshold
        Title   : hits_below_threshold
        Usage   : foreach( $obj->hits_below_threshold() ) { ... };
        Purpose : Provides access to all hits, old and new, that are below the inclusion threshold.
                  Corresponds to the union of subset D and subset F in the
                  "Classification of Hits" documentation section of this module.
        Returns : An array containing Bio::Search::Hit::HitI objects.
                  Hits will be returned in the order in which they occur in the report
                  unless otherwise specified.
        Args    : none

       See Also: newhits_below_threshold, oldhits_newly_below_threshold, oldhits_below_threshold,
       "Classification of Hits"

   add_hit
        Title   : add_hit
        Usage   : $report->add_hit(-hit             =>$hit_obj,
                                   -old             =>$boolean,
                                   -below_threshold =>$boolean,
                                   -newly_below     =>$boolean )
        Purpose : Adds a HitI to the stored list of hits
        Returns : Number of HitI currently stored for the class of the added hit.
        Args    : Tagged values, the only required one is -hit. All others are used
                  only for PSI-BLAST reports.
                  -hit => Bio::Search::Hit::HitI object
                  -old => boolean, true indicates that the hit was found
                          in a previous iteration. Default=false.
                  -below_threshold => boolean, true indicates that the hit is below
                          the inclusion threshold.
                  -newly_below => boolean, true indicates that the hit is below
                          the inclusion threshold in this iteration but was above
                          the inclusion threshold in a previous iteration.
                          Only appropriate for old hits. Default=false.
        Throws  : Bio::Root::BadParameter if the hit is not a
                  Bio::Search::Hit::HitI.
                  Bio::Root::BadParameter if -old=>false and -newly_below=>true.

   get_hit
        Title   : get_hit
        Usage   : $hit = $report->get_hit( $hit_name )
        Purpose : Gets a HitI object given its name
                  if a hit with this name exists within this Iteration.
        Returns : Bio::Search::Hit::HitI object or undef if there is no such hit.
        Args    : $hit_name = string containing name of the hit
        Throws  : n/a

       The name string must be the same as that returned by Bio::Search::Hit::HitI::name().

       The lookup should be case-insensitive.