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Bio::Search::IterationUsereContributed PeBio::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 occured 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:

	 http://bugzilla.open-bio.org/

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.

perl v5.14.1			  2011-07Bio::Search::Iteration::IterationI(3)
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