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

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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 email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ Email sac@bioperl.org Additional contributors names and emails here The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : my $obj = new Bio::Search::Result::BlastResult(); 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
This method overrides 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: 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 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: 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 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: 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 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
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

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