Bio::Search::Iteration::IterationI(3)

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.