Bio::Search::Result::ResultI - Abstract interface to Search Result objects # Bio::Search::Result::ResultI objects cannot be instantiated since this # module defines a pure interface. # Given an object that implements the Bio::Search::Result::ResultI interface, # you can do the following things with it: use Bio::SearchIO; my $io = new Bio::SearchIO(-format => 'blast', -file => 't/data/HUMBETGLOA.tblastx'); my $result = $io->next_result; while( $hit = $result->next_hit()) { # enter code here for hit processing } my $id = $result->query_name(); my $desc = $result->query_description(); my $dbname = $result->database_name(); my $size = $result->database_letters(); my $num_entries = $result->database_entries(); my $gap_ext = $result->get_parameter('gapext'); my @params = $result->available_parameters; my $kappa = $result->get_statistic('kappa'); my @statnames = $result->available_statistics; Bio::Search::Result::ResultI objects are data structures containing the results from the execution of a search algorithm. As such, it may contain various algorithm specific information as well as details of the execution, but will contain a few fundamental elements, including the ability to return Bio::Search::Hit::HitI objects.

Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bio.perl.org/MailList.html - About the mailing lists

Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Aaron Mackey <amackey@virginia.edu> (original author) Steve Chervitz <sac@bioperl.org> See the FEEDBACK section for where to send bug reports and comments. Copyright (c) 1999-2001 Aaron Mackey, Steve Chervitz. All Rights Reserved. This software is provided "as is" without warranty of any kind. The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

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 : none

query_accession
Title : query_accession Usage : $id = $result->query_accession(); Function: Get the accession (if available) for the query sequence Returns : a string 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 : none

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 : none

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 : none

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 : none

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 : none

get_parameter
Title : get_parameter Usage : my $gap_ext = $result->get_parameter('gapext') Function: Returns the value for a specific parameter used when running this result Returns : string Args : name of parameter (string)

available_parameters
Title : available_parameters Usage : my @params = $result->available_parameters Function: Returns the names of the available parameters Returns : Return list of available parameters used for this result Args : none

get_statistic
Title : get_statistic Usage : my $gap_ext = $result->get_statistic('kappa') Function: Returns the value for a specific statistic available from this result Returns : string Args : name of statistic (string)

available_statistics
Title : available_statistics Usage : my @statnames = $result->available_statistics Function: Returns the names of the available statistics Returns : Return list of available statistics used for this result Args : none

algorithm
Title : algorithm Usage : my $r_type = $result->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 = $result->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

algorithm_reference
Title : algorithm_reference Usage : $obj->algorithm_reference($newval) Function: Returns : value of the literature reference for the algorithm Args : newvalue (optional) Comments: The default implementation in ResultI returns an empty string rather than throwing a NotImplemented exception, since the ref may not always be available and is not critical.

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 HitI objects contained within this Result Returns : Array of Bio::Search::Hit::HitI objects Args : none See Also: Bio::Search::Hit::HitI

no_hits_found
Usage : $nohits = $blast->no_hits_found(); 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 : none

set_no_hits_found
Usage : $blast->set_no_hits_found(); Purpose : Set boolean indicator indicating whether or not any hits were present in the report. Returns : n/a Argument : none