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Bio::Search::Result::CUserMContributedBPo::Search::Result::CrossMatchResult(3)

NAME
       Bio::Search::Result::CrossMatchResult - CrossMatch-specific subclass of
       Bio::Search::Result::GenericResult

SYNOPSIS
	   # Working with iterations (CrossMatch 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 #	 CrossMatchResult objects.

DESCRIPTION
       This object is a	subclass of Bio::Search::Result::GenericResult and
       provides	some operations	that facilitate	working	with CrossMatch	and
       CrossMatch 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://github.com/bioperl/bioperl-live/issues

AUTHOR - Shin Leong
       Email sleong@watson.wustl.edu

CONTRIBUTORS
       Additional contributors names and emails	here

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

   hits
       This method overrides Bio::Search::Result::GenericResult::hits to take
       into account the	possibility of multiple	iterations, as occurs in
       CrossMatch 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: Bio::Search::Result::GenericResult::hits

   next_hit
       This method overrides Bio::Search::Result::GenericResult::next_hit to
       take into account the possibility of multiple iterations, as occurs in
       CrossMatch 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: Bio::Search::Iteration::GenericIteration::next_hit

   num_hits
       This method overrides Bio::Search::Result::GenericResult::num_hits to
       take into account the possibility of multiple iterations, as occurs in
       CrossMatch 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: Bio::Search::Result::GenericResult::num_hits

   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 CrossMatch 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 (CrossMatch).
	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 (CrossMatch).
	Returns	  : Total number of iterations in the report
	Argument  : none (read-only)

   number_of_iterations
       Same as num_iterations.

   round
       Same as 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

   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 (CrossMatch)
		    If iteration number	is not specified and this is a CrossMatch 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 (CrossMatch)

   _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 CrossMatch
		  score	matrix model (blastpgp)	that was used for generating the report
		  being	parsed.
	Returns	: number (real)	or undef if not	a CrossMatch report.
	Args	: none

perl v5.24.1			  2017Bio::Search::Result::CrossMatchResult(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Shin Leong | CONTRIBUTORS | APPENDIX

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