--- name: "Bio::Search::Result::GenericResult" 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::GenericResult" --- # Bio::Search::Result::GenericResult(3pm) Generic Implementation of Bio::Search::Result::ResultI interface applicable to most search results. ## NAME Bio::Search::Result::GenericResult - Generic Implementation of Bio::Search::Result::ResultI interface applicable to most search results. ## SYNOPSIS ``` # typically one gets Results from a SearchIO stream use Bio::SearchIO; my $io = Bio::SearchIO->new(-format => 'blast', -file => 't/data/HUMBETGLOA.tblastx'); while( my $result = $io->next_result ) { # process all search results within the input stream while( my $hit = $result->next_hit ) { # insert code here for hit processing } } use Bio::Search::Result::GenericResult; my @hits = (); # would be a list of Bio::Search::Hit::HitI objects # typically these are created from a Bio::SearchIO stream my $result = Bio::Search::Result::GenericResult->new ( -query_name => 'HUMBETGLOA', -query_accession => '' -query_description => 'Human haplotype C4 beta-globin gene, complete cds.' -query_length => 3002 -database_name => 'ecoli.aa' -database_letters => 4662239, -database_entries => 400, -parameters => { 'e' => '0.001' }, -statistics => { 'kappa' => 0.731 }, -algorithm => 'blastp', -algorithm_version => '2.1.2', ); my $id = $result->query_name(); my $desc = $result->query_description(); my $name = $result->database_name(); my $size = $result->database_letters(); my $num_entries = $result->database_entries(); my $gap_ext = $result->get_parameter('e'); my @params = $result->available_parameters; my $kappa = $result->get_statistic('kappa'); my @statnames = $result->available_statistics; ``` \# TODO: Show how to configure a SearchIO stream so that it generates # GenericResult objects. ## DESCRIPTION This object is an implementation of the Bio::Search::Result::ResultI interface and provides a generic place to store results from a sequence database search. Unless you're writing a parser, you won't ever need to create a GenericResult or any other ResultI-implementing object. If you use the SearchIO system, ResultI objects are created automatically from a SearchIO stream which returns Bio::Search::Result::ResultI objects. For documentation on what you can do with GenericResult (and other ResultI objects), please see the API documentation in Bio::Search::Result::ResultI. ## 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 - Jason Stajich and Steve Chervitz Email jason@bioperl.org Email sac@bioperl.org ## CONTRIBUTORS Sendu Bala, bix@sendu.me.uk ## 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::GenericResult->new(); Function: Builds a new Bio::Search::Result::GenericResult object Returns : Bio::Search::Result::GenericResult Args : -query_name => Name of query Sequence -query_accession => Query accession number (if available) -query_description => Description of query sequence -query_length => Length of query sequence -database_name => Name of database -database_letters => Number of residues in database -database_entries => Number of entries in database -hits => array ref of Bio::Search::Hit::HitI objects -parameters => hash ref of search parameters (key => value) -statistics => hash ref of search statistics (key => value) -algorithm => program name (blastx) -algorithm_version => version of the algorithm (2.1.2) -algorithm_reference => literature reference string for this algorithm -rid => value of the BLAST Request ID (eg. RID: ZABJ4EA7014) -hit_factory => Bio::Factory::ObjectFactoryI capable of making Bio::Search::Hit::HitI objects ``` ### algorithm ``` Title : algorithm Usage : my $r_type = $hsp->algorithm Function: Obtain the name of the algorithm used to obtain the Result Returns : string (e.g., BLASTP) Args : [optional] scalar string to set value ``` ### algorithm\_version ``` Title : algorithm_version Usage : my $r_version = $hsp->algorithm_version Function: Obtain the version of the algorithm used to obtain the Result Returns : string (e.g., 2.1.2) Args : [optional] scalar string to set algorithm version value ``` ### Bio::Search::Result::ResultI interface methods Bio::Search::Result::ResultI implementation ### 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 ``` ### query\_name ``` Title : query_name Usage : $id = $result->query_name(); Function: Get the string identifier of the query used by the algorithm that performed the search. Returns : a string. Args : [optional] new string value for query name ``` ### query\_accession ``` Title : query_accession Usage : $id = $result->query_accession(); Function: Get the accession (if available) for the query sequence Returns : a string Args : [optional] new string value for accession ``` ### query\_gi ``` Title : query_gi Usage : $acc = $hit->query_gi(); Function: Retrieve the NCBI Unique ID (aka the GI #), if available, for the query Returns : a scalar string (empty string if not set) Args : none ``` ### query\_length ``` Title : query_length Usage : $id = $result->query_length(); Function: Get the length of the query sequence used in the search. Returns : a number Args : [optional] new integer value for query length ``` ### query\_description ``` Title : query_description Usage : $id = $result->query_description(); Function: Get the description of the query sequence used in the search. Returns : a string Args : [optional] new string for the query description ``` ### database\_name ``` Title : database_name Usage : $name = $result->database_name() Function: Used to obtain the name of the database that the query was searched against by the algorithm. Returns : a scalar string Args : [optional] new string for the db name ``` ### database\_letters ``` Title : database_letters Usage : $size = $result->database_letters() Function: Used to obtain the size of database that was searched against. Returns : a scalar integer (units specific to algorithm, but probably the total number of residues in the database, if available) or undef if the information was not available to the Processor object. Args : [optional] new scalar integer for number of letters in db ``` ### database\_entries ``` Title : database_entries Usage : $num_entries = $result->database_entries() Function: Used to obtain the number of entries contained in the database. Returns : a scalar integer representing the number of entities in the database or undef if the information was not available. Args : [optional] new integer for the number of sequence entries in the db ``` ### get\_parameter ``` Title : get_parameter Usage : my $gap_ext = $report->get_parameter('gapext') Function: Returns the value for a specific parameter used when running this report Returns : string Args : name of parameter (string) ``` ### available\_parameters ``` Title : available_parameters Usage : my @params = $report->available_paramters Function: Returns the names of the available parameters Returns : Return list of available parameters used for this report Args : none ``` ### get\_statistic ``` Title : get_statistic Usage : my $gap_ext = $report->get_statistic('kappa') Function: Returns the value for a specific statistic available from this report Returns : string Args : name of statistic (string) ``` ### available\_statistics ``` Title : available_statistics Usage : my @statnames = $report->available_statistics Function: Returns the names of the available statistics Returns : Return list of available statistics used for this report Args : none ``` ### Bio::Search::Report Bio::Search::Result::GenericResult specific methods ### 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 ``` ### hit\_factory ``` Title : hit_factory Usage : $hit->hit_factory($hit_factory) Function: Get/set the factory used to build HitI objects if necessary. Returns : Bio::Factory::ObjectFactoryI Args : Bio::Factory::ObjectFactoryI ``` ### rewind ``` Title : rewind Usage : $result->rewind; Function: Allow one to reset the Hit iterator to the beginning Since this is an in-memory implementation Returns : none Args : none ``` ### \_nexthitindex ``` Title : _nexthitindex Usage : private ``` ### add\_parameter ``` Title : add_parameter Usage : $report->add_parameter('gapext', 11); Function: Adds a parameter Returns : none Args : key - key value name for this parama value - value for this parameter ``` ### add\_statistic ``` Title : add_statistic Usage : $report->add_statistic('lambda', 2.3); Function: Adds a parameter Returns : none Args : key - key value name for this parama value - value for this parameter ``` ### 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 ``` ### hits ``` Title : hits Usage : my @hits = $result->hits Function: Returns the available hits for this Result Returns : Array of L objects Args : none ``` ### algorithm\_reference ``` Title : algorithm_reference Usage : $obj->algorithm_reference($newval) Function: Returns : string containing literature reference for the algorithm Args : newvalue string (optional) Comments: Formerly named program_reference(), which is still supported for backwards compatibility. ``` ### program\_reference ``` Title : program_reference Usage : $obj->program_reference() Function: Returns : string containing literature reference for the algorithm Args : Comments: Deprecated - use algorithm_reference() instead. ``` ### rid ``` Title : rid Usage : $obj->rid($newval) Function: Returns : value of the BLAST Request ID (eg. RID: ZABJ4EA7014) Args : newvalue (optional) Comments: The default implementation in ResultI returns an empty string rather than throwing a NotImplemented exception, since the RID may not always be available and is not critical. See: (1) https://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/BLAST/rid.html (2) https://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node63.html ``` ### no\_hits\_found See documentation in **Bio::Search::Result::ResultI::no\_hits\_found()** ### set\_no\_hits\_found See documentation in **Bio::Search::Result::ResultI::set\_no\_hits\_found()** ### to\_string ``` Title : to_string Usage : print $blast->to_string; Function: Returns a string representation for the Blast result. Primarily intended for debugging purposes. Example : see usage Returns : A string of the form: [GenericResult] query= db=