Raw content of Bio::Search::Result::GenericResult # $Id: GenericResult.pm,v 1.15 2002/12/05 13:46:34 heikki Exp $ # # BioPerl module for Bio::Search::Result::GenericResult # # Cared for by Jason Stajich <jason@bioperl.org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Search::Result::GenericResult - Generic Implementation of Bio::Search::Result::ResultI interface applicable to most search results. =head1 SYNOPSIS # typically one gets Results from a SearchIO stream use Bio::SearchIO; my $io = new Bio::SearchIO(-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_hits()) { # 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 = new Bio::Search::Result::GenericResult ( -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; =head1 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. =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 the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/MailList.shtml - About the mailing lists =head2 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/ =head1 AUTHOR - Jason Stajich and Steve Chervitz Email jason@bioperl.org Email sac@bioperl.org =head1 CONTRIBUTORS Additional contributors names and emails here =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::GenericResult; use vars qw(@ISA); use strict; use Bio::Root::Root; use Bio::Search::Result::ResultI; use overload '""' => \&to_string; @ISA = qw(Bio::Root::Root Bio::Search::Result::ResultI); =head2 new Title : new Usage : my $obj = new Bio::Search::Result::GenericResult(); Function: Builds a new Bio::Search::Result::GenericResult object Returns : Bio::Search::Result::GenericResult Args : -query_name => Name of query Sequence -query_accession => Query accession number (if available) -query_description => Description of query sequence -query_length => Length of query sequence -database_name => Name of database -database_letters => Number of residues in database -database_entries => Number of entries in database -parameters => hash ref of search parameters (key => value) -statistics => hash ref of search statistics (key => value) -algorithm => program name (blastx) -algorithm_version => version of the algorithm (2.1.2) -algorithm_reference => literature reference string for this algorithm =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->{'_hits'} = []; $self->{'_hitindex'} = 0; $self->{'_statistics'} = {}; $self->{'_parameters'} = {}; my ($qname,$qacc,$qdesc,$qlen, $dbname,$dblet,$dbent,$params, $stats, $hits, $algo, $algo_v, $prog_ref, $algo_r) = $self->_rearrange([qw(QUERY_NAME QUERY_ACCESSION QUERY_DESCRIPTION QUERY_LENGTH DATABASE_NAME DATABASE_LETTERS DATABASE_ENTRIES PARAMETERS STATISTICS HITS ALGORITHM ALGORITHM_VERSION PROGRAM_REFERENCE ALGORITHM_REFERENCE )],@args); $algo_r ||= $prog_ref; defined $algo && $self->algorithm($algo); defined $algo_v && $self->algorithm_version($algo_v); defined $algo_r && $self->algorithm_reference($algo_r); defined $qname && $self->query_name($qname); defined $qacc && $self->query_accession($qacc); defined $qdesc && $self->query_description($qdesc); defined $qlen && $self->query_length($qlen); defined $dbname && $self->database_name($dbname); defined $dblet && $self->database_letters($dblet); defined $dbent && $self->database_entries($dbent); if( defined $params ) { if( ref($params) !~ /hash/i ) { $self->throw("Must specify a hash reference with the the parameter '-parameters"); } while( my ($key,$value) = each %{$params} ) { $self->add_parameter($key,$value); } } if( defined $stats ) { if( ref($stats) !~ /hash/i ) { $self->throw("Must specify a hash reference with the the parameter '-statistics"); } while( my ($key,$value) = each %{$stats} ) { $self->add_statistic($key,$value); } } if( defined $hits ) { $self->throw("Must define arrayref of Hits when initializing a $class\n") unless ref($hits) =~ /array/i; foreach my $s ( @$hits ) { $self->add_hit($s); } } return $self; } =head2 algorithm Title : algorithm Usage : my $r_type = $hsp->algorithm Function: Obtain the name of the algorithm used to obtain the Result Returns : string (e.g., BLASTP) Args : [optional] scalar string to set value =cut sub algorithm{ my ($self,$value) = @_; my $previous = $self->{'_algorithm'}; if( defined $value || ! defined $previous ) { $value = $previous = '' unless defined $value; $self->{'_algorithm'} = $value; } return $previous; } =head2 algorithm_version Title : algorithm_version Usage : my $r_version = $hsp->algorithm_version Function: Obtain the version of the algorithm used to obtain the Result Returns : string (e.g., 2.1.2) Args : [optional] scalar string to set algorithm version value =cut sub algorithm_version{ my ($self,$value) = @_; my $previous = $self->{'_algorithm_version'}; if( defined $value || ! defined $previous ) { $value = $previous = '' unless defined $value; $self->{'_algorithm_version'} = $value; } return $previous; } =head2 Bio::Search::Result::ResultI interface methods Bio::Search::Result::ResultI implementation =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) = @_; my $index = $self->_nexthitindex; return undef if $index > scalar @{$self->{'_hits'}}; return $self->{'_hits'}->[$index]; } =head2 query_name Title : query_name Usage : $id = $result->query_name(); Function: Get the string identifier of the query used by the algorithm that performed the search. Returns : a string. Args : [optional] new string value for query name =cut sub query_name { my ($self,$value) = @_; my $previous = $self->{'_queryname'}; if( defined $value || ! defined $previous ) { $value = $previous = '' unless defined $value; $self->{'_queryname'} = $value; } return $previous; } =head2 query_accession Title : query_accession Usage : $id = $result->query_accession(); Function: Get the accession (if available) for the query sequence Returns : a string Args : [optional] new string value for accession =cut sub query_accession { my ($self,$value) = @_; my $previous = $self->{'_queryacc'}; if( defined $value || ! defined $previous ) { $value = $previous = '' unless defined $value; $self->{'_queryacc'} = $value; } return $previous; } =head2 query_length Title : query_length Usage : $id = $result->query_length(); Function: Get the length of the query sequence used in the search. Returns : a number Args : [optional] new integer value for query length =cut sub query_length { my ($self,$value) = @_; my $previous = $self->{'_querylength'}; if( defined $value || ! defined $previous ) { $value = $previous = 0 unless defined $value; $self->{'_querylength'} = $value; } return $previous; } =head2 query_description Title : query_description Usage : $id = $result->query_description(); Function: Get the description of the query sequence used in the search. Returns : a string Args : [optional] new string for the query description =cut sub query_description { my ($self,$value) = @_; my $previous = $self->{'_querydesc'}; if( defined $value || ! defined $previous ) { $value = $previous = '' unless defined $value; $self->{'_querydesc'} = $value; } return $previous; } =head2 database_name Title : database_name Usage : $name = $result->database_name() Function: Used to obtain the name of the database that the query was searched against by the algorithm. Returns : a scalar string Args : [optional] new string for the db name =cut sub database_name { my ($self,$value) = @_; my $previous = $self->{'_dbname'}; if( defined $value || ! defined $previous ) { $value = $previous = '' unless defined $value; $self->{'_dbname'} = $value; } return $previous; } =head2 database_letters Title : database_letters Usage : $size = $result->database_letters() Function: Used to obtain the size of database that was searched against. Returns : a scalar integer (units specific to algorithm, but probably the total number of residues in the database, if available) or undef if the information was not available to the Processor object. Args : [optional] new scalar integer for number of letters in db =cut sub database_letters { my ($self,$value) = @_; my $previous = $self->{'_dbletters'}; if( defined $value || ! defined $previous ) { $value = $previous = '' unless defined $value; $self->{'_dbletters'} = $value; } return $previous; } =head2 database_entries Title : database_entries Usage : $num_entries = $result->database_entries() Function: Used to obtain the number of entries contained in the database. Returns : a scalar integer representing the number of entities in the database or undef if the information was not available. Args : [optional] new integer for the number of sequence entries in the db =cut sub database_entries { my ($self,$value) = @_; my $previous = $self->{'_dbentries'}; if( defined $value || ! defined $previous ) { $value = $previous = '' unless defined $value; $self->{'_dbentries'} = $value; } return $previous; } =head2 get_parameter Title : get_parameter Usage : my $gap_ext = $report->get_parameter('gapext') Function: Returns the value for a specific parameter used when running this report Returns : string Args : name of parameter (string) =cut sub get_parameter{ my ($self,$name) = @_; return $self->{'_parameters'}->{$name}; } =head2 available_parameters Title : available_parameters Usage : my @params = $report->available_paramters Function: Returns the names of the available parameters Returns : Return list of available parameters used for this report Args : none =cut sub available_parameters{ my ($self) = @_; return keys %{$self->{'_parameters'}}; } =head2 get_statistic Title : get_statistic Usage : my $gap_ext = $report->get_statistic('kappa') Function: Returns the value for a specific statistic available from this report Returns : string Args : name of statistic (string) =cut sub get_statistic{ my ($self,$key) = @_; return $self->{'_statistics'}->{$key}; } =head2 available_statistics Title : available_statistics Usage : my @statnames = $report->available_statistics Function: Returns the names of the available statistics Returns : Return list of available statistics used for this report Args : none =cut sub available_statistics{ my ($self) = @_; return keys %{$self->{'_statistics'}}; } =head2 Bio::Search::Report Bio::Search::Result::GenericResult specific methods =head2 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 =cut sub add_hit { my ($self,$s) = @_; if( $s->isa('Bio::Search::Hit::HitI') ) { push @{$self->{'_hits'}}, $s; } else { $self->warn("Passed in " .ref($s). " as a Hit which is not a Bio::Search::HitI... skipping"); } return scalar @{$self->{'_hits'}}; } =head2 rewind Title : rewind Usage : $result->rewind; Function: Allow one to reset the Hit iteration to the beginning Since this is an in-memory implementation Returns : none Args : none =cut sub rewind{ my ($self) = @_; $self->{'_hitindex'} = 0; } =head2 _nexthitindex Title : _nexthitindex Usage : private =cut sub _nexthitindex{ my ($self,@args) = @_; return $self->{'_hitindex'}++; } =head2 add_parameter Title : add_parameter Usage : $report->add_parameter('gapext', 11); Function: Adds a parameter Returns : none Args : key - key value name for this parama value - value for this parameter =cut sub add_parameter{ my ($self,$key,$value) = @_; $self->{'_parameters'}->{$key} = $value; } =head2 add_statistic Title : add_statistic Usage : $report->add_statistic('lambda', 2.3); Function: Adds a parameter Returns : none Args : key - key value name for this parama value - value for this parameter =cut sub add_statistic { my ($self,$key,$value) = @_; $self->{'_statistics'}->{$key} = $value; 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) = shift; if (not defined $self->{'_hits'}) { $self->throw("Can't get Hits: data not collected."); } return scalar(@{$self->{'_hits'}}); } =head2 hits Title : hits Usage : my @hits = $result->hits Function: Returns the available hits for this Result Returns : Array of L<Bio::Search::Hit::HitI> objects Args : none =cut sub hits{ my ($self) = shift; my @hits = (); if( ref $self->{'_hits'}) { @hits = @{$self->{'_hits'}}; } return @hits; } =head2 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. =cut sub algorithm_reference{ my ($self,$value) = @_; if( defined $value) { $self->{'algorithm_reference'} = $value; } return $self->{'algorithm_reference'}; } sub program_reference { shift->algorithm_reference(@_); } =head2 no_hits_found See documentation in L<Bio::Search::Result::ResultI::no_hits_found()|Bio::Search::Result::ResultI> =cut #----------- sub no_hits_found { #----------- my ($self, $round) = @_; my $result = 0; # final return value of this method. # Watch the double negative! # result = 0 means "yes hits were found" # result = 1 means "no hits were found" (for the indicated iteration or all iterations) # If a iteration was not specified and there were multiple iterations, # this method should return true only if all iterations had no hits found. if( not defined $round ) { if( $self->{'_iterations'} > 1) { $result = 1; foreach my $i( 1..$self->{'_iterations'} ) { if( not defined $self->{"_iteration_$i"}->{'_no_hits_found'} ) { $result = 0; last; } } } else { $result = $self->{"_iteration_1"}->{'_no_hits_found'}; } } else { $result = $self->{"_iteration_$round"}->{'_no_hits_found'}; } return $result; } =head2 set_no_hits_found See documentation in L<Bio::Search::Result::ResultI::set_no_hits_found()|Bio::Search::Result::ResultI> =cut #----------- sub set_no_hits_found { #----------- my ($self, $round) = @_; $round ||= 1; $self->{"_iteration_$round"}->{'_no_hits_found'} = 1; } =head2 iterations See documentation in L<Bio::Search::Result::ResultI::iterations()|Bio::Search::Result::ResultI> =cut #---------------- sub iterations { #---------------- my ($self, $num ) = @_; if( defined $num ) { $self->{'_iterations'} = $num; } return $self->{'_iterations'}; } =head2 psiblast See documentation in L<Bio::Search::Result::ResultI::psiblast()|Bio::Search::Result::ResultI> =cut #---------------- sub psiblast { #---------------- my ($self, $val ) = @_; if( $val ) { $self->{'_psiblast'} = 1; } return $self->{'_psiblast'}; } =head2 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] <analysis_method> query=<name> <description> db=<database e.g.: [GenericResult] BLASTP query=YEL060C vacuolar protease B, db=PDBUNIQ Args : None =cut #--------------- sub to_string { #--------------- my $self = shift; my $str = "[GenericResult] " . $self->algorithm . " query=" . $self->query_name . " " . $self->query_description .", db=" . $self->database_name; return $str; } 1;