#----------------------------------------------------------------- # $Id: ResultI.pm 16123 2009-09-17 12:57:27Z cjfields $ # # BioPerl module Bio::Search::Result::ResultI # # Please direct questions and support issues to # # Cared for by Steve Chervitz # # Originally created by Aaron Mackey # # You may distribute this module under the same terms as perl itself #----------------------------------------------------------------- # POD documentation - main docs before the code =head1 NAME Bio::Search::Result::ResultI - Abstract interface to Search Result objects =head1 SYNOPSIS # 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 = Bio::SearchIO->new(-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; =head1 DESCRIPTION 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. =head1 FEEDBACK =head2 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://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I 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. =head2 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 the web: http://bugzilla.open-bio.org/ =head1 AUTHOR Aaron Mackey Eamackey@virginia.eduE (original author) Steve Chervitz Esac@bioperl.orgE See L for where to send bug reports and comments. =head1 COPYRIGHT Copyright (c) 1999-2001 Aaron Mackey, Steve Chervitz. All Rights Reserved. =head1 DISCLAIMER This software is provided "as is" without warranty of any kind. =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut #' # Let the code begin... package Bio::Search::Result::ResultI; use strict; use base qw(Bio::AnalysisResultI); =head2 next_hit Title : next_hit Usage : while( $hit = $result->next_hit()) { ... } Function: Returns the next available Hit object, representing potential matches between the query and various entities from the database. Returns : a Bio::Search::Hit::HitI object or undef if there are no more. Args : none =cut sub next_hit { my ($self,@args) = @_; $self->throw_not_implemented; } =head2 sort_hits Title : sort_hits Usage : $result->sort_hits(\&sort_function) Function : Sorts the available hit objects by a user-supplied function. Defaults to sort by descending score. Returns : n/a Args : A coderef for the sort function. See the documentation on the Perl sort() function for guidelines on writing sort functions. Note : To access the special variables $a and $b used by the Perl sort() function the user function must access Bio::Search::Result::ResultI namespace. For example, use : $result->sort_hits( sub{$Bio::Search::Result::ResultI::a->length <=> $Bio::Search::Result::ResultI::b->length}); NOT $result->sort_hits($a->length <=>$b->length); =cut sub sort_hits { my ($self, $coderef) = @_; my @sorted_hits; if ($coderef) { $self->throw('sort_hits requires a sort function passed as a subroutine reference') unless (ref($coderef) eq 'CODE'); } else { $coderef = \&_default_sort_hits; # throw a warning? } my @hits = $self->hits(); eval {@sorted_hits = sort $coderef @hits }; if ($@) { $self->throw("Unable to sort hits: $@"); } else { $self->{'_hits'} = \@sorted_hits; $self->{'_no_iterations'} = 1; # to bypass iteration checking in hits() method 1; } } =head2 _default sort_hits Title : _default_sort_hits Usage : Do not call directly. Function: Sort hits in descending order by score Args : None Returns: 1 on success Note : Used by $result->sort_hits() =cut sub _default_sort_hits { $Bio::Search::Result::ResultI::b->score <=> $Bio::Search::Result::ResultI::a->score; } =head2 query_name Title : query_name Usage : $id = $result->query_name(); Function: Get the string identifier of the query used by the algorithm that performed the search. Returns : a string. Args : none =cut sub query_name { my ($self,@args) = @_; $self->throw_not_implemented; } =head2 query_accession Title : query_accession Usage : $id = $result->query_accession(); Function: Get the accession (if available) for the query sequence Returns : a string Args : none =cut sub query_accession { my ($self,@args) = @_; $self->throw_not_implemented; } =head2 query_length Title : query_length Usage : $id = $result->query_length(); Function: Get the length of the query sequence used in the search. Returns : a number Args : none =cut sub query_length { my ($self,@args) = @_; $self->throw_not_implemented; } =head2 query_description Title : query_description Usage : $id = $result->query_description(); Function: Get the description of the query sequence used in the search. Returns : a string Args : none =cut sub query_description { my ($self,@args) = @_; $self->throw_not_implemented; } =head2 database_name Title : database_name Usage : $name = $result->database_name() Function: Used to obtain the name of the database that the query was searched against by the algorithm. Returns : a scalar string Args : none =cut sub database_name { my ($self,@args) = @_; $self->throw_not_implemented; } =head2 database_letters Title : database_letters Usage : $size = $result->database_letters() Function: Used to obtain the size of database that was searched against. Returns : a scalar integer (units specific to algorithm, but probably the total number of residues in the database, if available) or undef if the information was not available to the Processor object. Args : none =cut sub database_letters { my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 database_entries Title : database_entries Usage : $num_entries = $result->database_entries() Function: Used to obtain the number of entries contained in the database. Returns : a scalar integer representing the number of entities in the database or undef if the information was not available. Args : none =cut sub database_entries { my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 get_parameter Title : get_parameter Usage : my $gap_ext = $result->get_parameter('gapext') Function: Returns the value for a specific parameter used when running this result Returns : string Args : name of parameter (string) =cut sub get_parameter{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 available_parameters Title : available_parameters Usage : my @params = $result->available_parameters Function: Returns the names of the available parameters Returns : Return list of available parameters used for this result Args : none =cut sub available_parameters{ my ($self) = @_; $self->throw_not_implemented(); } =head2 get_statistic Title : get_statistic Usage : my $gap_ext = $result->get_statistic('kappa') Function: Returns the value for a specific statistic available from this result Returns : string Args : name of statistic (string) =cut sub get_statistic{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 available_statistics Title : available_statistics Usage : my @statnames = $result->available_statistics Function: Returns the names of the available statistics Returns : Return list of available statistics used for this result Args : none =cut sub available_statistics{ my ($self) = @_; $self->throw_not_implemented(); } =head2 algorithm Title : algorithm Usage : my $r_type = $result->algorithm Function: Obtain the name of the algorithm used to obtain the Result Returns : string (e.g., BLASTP) Args : [optional] scalar string to set value =cut sub algorithm{ my ($self) = @_; $self->throw_not_implemented(); } =head2 algorithm_version Title : algorithm_version Usage : my $r_version = $result->algorithm_version Function: Obtain the version of the algorithm used to obtain the Result Returns : string (e.g., 2.1.2) Args : [optional] scalar string to set algorithm version value =cut sub algorithm_version{ my ($self) = @_; $self->throw_not_implemented(); } =head2 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. =cut sub algorithm_reference{ my ($self) = @_; return ''; } =head2 num_hits Title : num_hits Usage : my $hitcount= $result->num_hits Function: returns the number of hits for this query result Returns : integer Args : none =cut sub num_hits{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 hits Title : hits Usage : my @hits = $result->hits Function: Returns the HitI objects contained within this Result Returns : Array of Bio::Search::Hit::HitI objects Args : none See Also: L =cut sub hits{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 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 =cut #----------- sub no_hits_found { shift->throw_not_implemented } =head2 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 =cut sub set_no_hits_found { shift->throw_not_implemented } 1;