Bio::Search::Result::BlastResult(3pm)			User Contributed Perl Documentation		     Bio::Search::Result::BlastResult(3pm)

NAME

       Bio::Search::Result::BlastResult - Blast-specific subclass of Bio::Search::Result::GenericResult

SYNOPSIS

	   # Working with iterations (PSI-BLAST results)

	   $result->next_iteration();
	   $result->num_iterations();
	   $result->iteration();
	   $result->iterations();

       # See Bio::Search::Result::GenericResult for information about working with Results.

       # See Bio::Search::Iteration::IterationI # for details about working with iterations.

       # TODO: #     * Show how to configure a SearchIO stream so that it generates #	    BlastResult objects.

DESCRIPTION

       This object is a subclass of Bio::Search::Result::GenericResult and provides some operations that facilitate working with BLAST and PSI-
       BLAST results.

       For general information about working with Results, see Bio::Search::Result::GenericResult.

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://redmine.open-bio.org/projects/bioperl/

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::Result::BlastResult->new();
	Function: Builds a new Bio::Search::Result::BlastResult object
	Returns : Bio::Search::Result::BlastResult
	Args	: See Bio::Search::Result::GenericResult();
		  The following parameters are specific to BlastResult:
		    -iterations  => array ref of Bio::Search::Iteration::IterationI objects
		    -inclusion_threshold => e-value threshold for inclusion in the
					    PSI-BLAST score matrix model (blastpgp)

   hits
	Title	: hits
	Usage	: my @hits = $result->hits
	Function: Returns the available hits for this Result
	Returns : Array of L<Bio::Search::Hit::HitI> objects
	Args	: none
	Note	: This method overrides L<Bio::Search::Result::GenericResult::hits> to
		  take into account the possibility of multiple iterations, as occurs
		  in PSI-BLAST reports.
		  If there are multiple iterations, all 'new' hits for all iterations
		  are returned. These are the hits that did not occur in a previous
		  iteration.

		  See Also: L<Bio::Search::Result::GenericResult::hits>

   next_hit
	Title	: next_hit
	Usage	: while( $hit = $result->next_hit()) { ... }
	Function: Returns the next available Hit object, representing potential
		  matches between the query and various entities from the database.
	Returns : a Bio::Search::Hit::HitI object or undef if there are no more.
	Args	: none
	Note	: This method overrides L<Bio::Search::Result::GenericResult::next_hit>
		  to take into account the possibility of multiple iterations, as
		  occurs in PSI-BLAST reports.

		  If there are multiple iterations, calling next_hit() traverses the
		  all of the hits, old and new, for each iteration, calling next_hit()
		  on each iteration.

		  See Also: L<Bio::Search::Iteration::GenericIteration::next_hit>

   num_hits
	Title	: num_hits
	Usage	: my $hitcount= $result->num_hits
	Function: returns the number of hits for this query result
	Returns : integer
	Args	: none
	Note	: This method overrides L<Bio::Search::Result::GenericResult::num_hits>
		  to take into account the possibility of multiple iterations, as
		  occurs in PSI-BLAST reports.

		  If there are multiple iterations, calling num_hits() returns the
		  number of 'new' hits for each iteration. These are the hits that did
		  not occur in a previous iteration.

		  See Also: L<Bio::Search::Result::GenericResult::num_hits>

   add_hit
	Title	: add_hit
	Usage	: $report->add_hit($hit)
	Function: Adds a HitI to the stored list of hits
	Returns : Number of HitI currently stored
	Args	: Bio::Search::Hit::HitI

   add_iteration
	Title	: add_iteration
	Usage	: $report->add_iteration($iteration)
	Function: Adds a IterationI to the stored list of iterations
	Returns : Number of IterationI currently stored
	Args	: Bio::Search::Iteration::IterationI

   next_iteration
	Title	: next_iteration
	Usage	: while( $it = $result->next_iteration()) { ... }
	Function: Returns the next Iteration object, representing all hits
		  found within a given PSI-Blast iteration.
	Returns : a Bio::Search::Iteration::IterationI object or undef if there are no more.
	Args	: none

   iteration
	Usage	  : $iteration = $blast->iteration( $number );
	Purpose   : Get an IterationI object for the specified iteration
		    in the search result (PSI-BLAST).
	Returns   : Bio::Search::Iteration::IterationI object
	Throws	  : Bio::Root::NoSuchThing exception if $number is not within
		    range of the number of iterations in this report.
	Argument  : integer (optional, if not specified get the last iteration)
		    First iteration = 1

   num_iterations
	Usage	  : $num_iterations = $blast->num_iterations;
	Purpose   : Get the number of iterations in the search result (PSI-BLAST).
	Returns   : Total number of iterations in the report
	Argument  : none (read-only)

   number_of_iterations
	Usage	  : $num_iterations = $blast->number_of_iterations;
	Purpose   : Get the number of iterations in the search result (PSI-BLAST).
	Returns   : Total number of iterations in the report
	Argument  : none (read-only)
	Note	  : Alias of L<num_iterations>.

   round
	Usage	  : $round = $blast->round( $number );
	Purpose   : Get an IterationI object for the specified iteration
		    in the search result (PSI-BLAST).
	Returns   : Bio::Search::Iteration::IterationI object
	Throws	  : Bio::Root::NoSuchThing exception if $number is not within
		    range of the number of iterations in this report.
	Argument  : integer (optional, if not specified get the last iteration)
		    First iteration = 1
	Note	  : Alias of L<iteration>.

   iterations
	Title	: iterations
	Usage	: my @iterations = $result->iterations
	Function: Returns the IterationI objects contained within this Result
	Returns : Array of L<Bio::Search::Iteration::IterationI> objects
	Args	: none

   psiblast
	Usage	  : if( $blast->psiblast ) { ... }
	Purpose   : Set/get a boolean indicator whether or not the report
		    is a PSI-BLAST report.
	Returns   : 1 if PSI-BLAST, undef if not.
	Argument  : 1 (when setting)

   no_hits_found
	Usage	  : $nohits = $blast->no_hits_found( $iteration_number );
	Purpose   : Get boolean indicator indicating whether or not any hits
		    were present in the report.

		    This is NOT the same as determining the number of hits via
		    the hits() method, which will return zero hits if there were no
		    hits in the report or if all hits were filtered out during the parse.

		    Thus, this method can be used to distinguish these possibilities
		    for hitless reports generated when filtering.

	Returns   : Boolean
	Argument  : (optional) integer indicating the iteration number (PSI-BLAST)
		    If iteration number is not specified and this is a PSI-BLAST result,
		    then this method will return true only if all iterations had
		    no hits found.

   set_no_hits_found
	Usage	  : $blast->set_no_hits_found( $iteration_number );
	Purpose   : Set boolean indicator indicating whether or not any hits
		    were present in the report.
	Returns   : n/a
	Argument  : (optional) integer indicating the iteration number (PSI-BLAST)

   _next_iteration_index
	Title	: _next_iteration_index
	Usage	: private

   rewind
	Title	: rewind
	Usage	: $result->rewind;
	Function: Allow one to reset the Iteration iterator to the beginning
		  Since this is an in-memory implementation
	Returns : none
	Args	: none

   inclusion_threshold
	Title	: inclusion_threshold
	Usage	: my $incl_thresh = $result->inclusion_threshold; (read-only)
	Function: Gets the e-value threshold for inclusion in the PSI-BLAST
		  score matrix model (blastpgp) that was used for generating the report
		  being parsed.
	Returns : number (real) or undef if not a PSI-BLAST report.
	Args	: none

perl v5.14.2							    2012-03-02				     Bio::Search::Result::BlastResult(3pm)