--- name: "Bio::Search::Result::CrossMatchResult" section: "3pm" platform: "linux" package: "libbio-perl-perl" version: "1.7.8-1" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/Bio::Search::Result::CrossMatchResult" --- # Bio::Search::Result::CrossMatchResult(3pm) CrossMatch-specific subclass of Bio::Search::Result::GenericResult ## 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 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 ```