lib/Bio/Search/Result/GenericResult.pm

   1 #
   2 # BioPerl module for Bio::Search::Result::GenericResult
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Jason Stajich <jason@bioperl.org>
   7 #
   8 # Copyright Jason Stajich
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11
  12 # POD documentation - main docs before the code
  13
  14 =head1 NAME
  15
  16 Bio::Search::Result::GenericResult - Generic Implementation of
  17 Bio::Search::Result::ResultI interface applicable to most search
  18 results.
  19
  20 =head1 SYNOPSIS
  21
  22
  23     # typically one gets Results from a SearchIO stream
  24     use Bio::SearchIO;
  25     my $io = Bio::SearchIO->new(-format => 'blast',
  26                                 -file   => 't/data/HUMBETGLOA.tblastx');
  27     while( my $result = $io->next_result ) {
  28         # process all search results within the input stream
  29         while( my $hit = $result->next_hit ) {
  30             # insert code here for hit processing
  31         }
  32     }
  33
  34     use Bio::Search::Result::GenericResult;
  35     my @hits = (); # would be a list of Bio::Search::Hit::HitI objects
  36     # typically these are created from a Bio::SearchIO stream
  37     my $result = Bio::Search::Result::GenericResult->new
  38         ( -query_name        => 'HUMBETGLOA',
  39           -query_accession   => ''
  40           -query_description => 'Human haplotype C4 beta-globin gene, complete cds.'
  41           -query_length      => 3002
  42           -database_name     => 'ecoli.aa'
  43           -database_letters  => 4662239,
  44           -database_entries  => 400,
  45           -parameters        => { 'e' => '0.001' },
  46           -statistics        => { 'kappa' => 0.731 },
  47           -algorithm         => 'blastp',
  48           -algorithm_version => '2.1.2',
  49           );
  50
  51     my $id = $result->query_name();
  52
  53     my $desc = $result->query_description();
  54
  55     my $name = $result->database_name();
  56
  57     my $size = $result->database_letters();
  58
  59     my $num_entries = $result->database_entries();
  60
  61     my $gap_ext = $result->get_parameter('e');
  62
  63     my @params = $result->available_parameters;
  64
  65     my $kappa = $result->get_statistic('kappa');
  66
  67     my @statnames = $result->available_statistics;
  68
  69 # TODO: Show how to configure a SearchIO stream so that it generates
  70 #       GenericResult objects.
  71
  72
  73 =head1 DESCRIPTION
  74
  75 This object is an implementation of the Bio::Search::Result::ResultI
  76 interface and provides a generic place to store results from a
  77 sequence database search.
  78
  79 Unless you're writing a parser, you won't ever need to create a
  80 GenericResult or any other ResultI-implementing object. If you use
  81 the SearchIO system, ResultI objects are created automatically from
  82 a SearchIO stream which returns Bio::Search::Result::ResultI objects.
  83
  84 For documentation on what you can do with GenericResult (and other ResultI
  85 objects), please see the API documentation in
  86 L<Bio::Search::Result::ResultI|Bio::Search::Result::ResultI>.
  87
  88 =head1 FEEDBACK
  89
  90 =head2 Mailing Lists
  91
  92 User feedback is an integral part of the evolution of this and other
  93 Bioperl modules. Send your comments and suggestions preferably to
  94 the Bioperl mailing list.  Your participation is much appreciated.
  95
  96   bioperl-l@bioperl.org                  - General discussion
  97   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  98
  99 =head2 Support
 100
 101 Please direct usage questions or support issues to the mailing list:
 102
 103 I<bioperl-l@bioperl.org>
 104
 105 rather than to the module maintainer directly. Many experienced and
 106 reponsive experts will be able look at the problem and quickly
 107 address it. Please include a thorough description of the problem
 108 with code and data examples if at all possible.
 109
 110 =head2 Reporting Bugs
 111
 112 Report bugs to the Bioperl bug tracking system to help us keep track
 113 of the bugs and their resolution. Bug reports can be submitted via the
 114 web:
 115
 116   https://github.com/bioperl/bioperl-live/issues
 117
 118 =head1 AUTHOR - Jason Stajich and Steve Chervitz
 119
 120 Email jason@bioperl.org
 121 Email sac@bioperl.org
 122
 123 =head1 CONTRIBUTORS
 124
 125 Sendu Bala, bix@sendu.me.uk
 126
 127 =head1 APPENDIX
 128
 129 The rest of the documentation details each of the object methods.
 130 Internal methods are usually preceded with a _
 131
 132 =cut
 133
 134
 135 # Let the code begin...
 136
 137
 138 package Bio::Search::Result::GenericResult;
 139 use strict;
 140
 141 use Bio::Search::GenericStatistics;
 142 use Bio::Tools::Run::GenericParameters;
 143
 144 # bug #1420
 145 #use overload
 146 #    '""' => \&to_string;
 147
 148 use base qw(Bio::Root::Root Bio::Search::Result::ResultI);
 149
 150 =head2 new
 151
 152  Title   : new
 153  Usage   : my $obj = Bio::Search::Result::GenericResult->new();
 154  Function: Builds a new Bio::Search::Result::GenericResult object
 155  Returns : Bio::Search::Result::GenericResult
 156  Args    : -query_name        => Name of query Sequence
 157            -query_accession   => Query accession number (if available)
 158            -query_description => Description of query sequence
 159            -query_length      => Length of query sequence
 160            -database_name     => Name of database
 161            -database_letters  => Number of residues in database
 162            -database_entries  => Number of entries in database
 163            -hits              => array ref of Bio::Search::Hit::HitI objects
 164            -parameters        => hash ref of search parameters (key => value)
 165            -statistics        => hash ref of search statistics (key => value)
 166            -algorithm         => program name (blastx)
 167            -algorithm_version   => version of the algorithm (2.1.2)
 168            -algorithm_reference => literature reference string for this algorithm
 169            -rid               => value of the BLAST Request ID (eg. RID: ZABJ4EA7014)
 170            -hit_factory       => Bio::Factory::ObjectFactoryI capable of making
 171                                  Bio::Search::Hit::HitI objects
 172
 173 =cut
 174
 175 sub new {
 176   my($class,@args) = @_;
 177
 178   my $self = $class->SUPER::new(@args);
 179
 180   $self->{'_hits'} = [];
 181   $self->{'_hitindex'} = 0;
 182   $self->{'_statistics'} = Bio::Search::GenericStatistics->new();
 183   $self->{'_parameters'} = Bio::Tools::Run::GenericParameters->new();
 184
 185   my ($qname,$qacc,$qdesc,$qlen, $qgi,
 186       $dbname,$dblet,$dbent,$params,
 187       $stats, $hits, $algo, $algo_v,
 188       $prog_ref, $algo_r, $rid, $hit_factory) = $self->_rearrange([qw(QUERY_NAME
 189                                                   QUERY_ACCESSION
 190                                                   QUERY_DESCRIPTION
 191                                                   QUERY_LENGTH
 192                                                   QUERY_GI
 193                                                   DATABASE_NAME
 194                                                   DATABASE_LETTERS
 195                                                   DATABASE_ENTRIES
 196                                                   PARAMETERS
 197                                                   STATISTICS
 198                                                   HITS
 199                                                   ALGORITHM
 200                                                   ALGORITHM_VERSION
 201                                                   PROGRAM_REFERENCE
 202                                                   ALGORITHM_REFERENCE
 203                                                   RID
 204                                                   HIT_FACTORY
 205                                                  )],@args);
 206
 207   $algo_r ||= $prog_ref;
 208   defined $algo   && $self->algorithm($algo);
 209   defined $algo_v && $self->algorithm_version($algo_v);
 210   defined $algo_r && $self->algorithm_reference($algo_r);
 211
 212   defined $rid && $self->rid($rid);
 213
 214   defined $qname && $self->query_name($qname);
 215   defined $qacc  && $self->query_accession($qacc);
 216   defined $qdesc && $self->query_description($qdesc);
 217   defined $qlen  && $self->query_length($qlen);
 218   defined $qgi   && $self->query_gi($qgi);
 219   defined $dbname && $self->database_name($dbname);
 220   defined $dblet  && $self->database_letters($dblet);
 221   defined $dbent  && $self->database_entries($dbent);
 222
 223   defined $hit_factory && $self->hit_factory($hit_factory);
 224
 225   if( defined $params ) {
 226       if( ref($params) !~ /hash/i ) {
 227           $self->throw("Must specify a hash reference with the parameter '-parameters");
 228       }
 229       while( my ($key,$value) = each %{$params} ) {
 230           $self->{'_parameters'}->set_parameter($key   =>   $value);
 231                # $self->add_parameter($key,$value);
 232       }
 233   }
 234   if( defined $stats ) {
 235       if( ref($stats) !~ /hash/i ) {
 236           $self->throw("Must specify a hash reference with the parameter '-statistics");
 237       }
 238       while( my ($key,$value) = each %{$stats} ) {
 239           $self->{'_statistics'}->set_statistic($key   =>   $value);
 240           # $self->add_statistic($key,$value);
 241       }
 242   }
 243
 244   if( defined $hits  ) {
 245       $self->throw("Must define arrayref of Hits when initializing a $class\n") unless ref($hits) =~ /array/i;
 246
 247       foreach my $s ( @$hits ) {
 248           $self->add_hit($s);
 249       }
 250   }
 251   return $self;
 252 }
 253
 254 =head2 algorithm
 255
 256  Title   : algorithm
 257  Usage   : my $r_type = $hsp->algorithm
 258  Function: Obtain the name of the algorithm used to obtain the Result
 259  Returns : string (e.g., BLASTP)
 260  Args    : [optional] scalar string to set value
 261
 262 =cut
 263
 264 sub algorithm{
 265     my ($self,$value) = @_;
 266     my $previous = $self->{'_algorithm'};
 267     if( defined $value || ! defined $previous ) {
 268         $value = $previous = '' unless defined $value;
 269         $self->{'_algorithm'} = $value;
 270     }
 271     return $previous;
 272 }
 273
 274 =head2 algorithm_version
 275
 276  Title   : algorithm_version
 277  Usage   : my $r_version = $hsp->algorithm_version
 278  Function: Obtain the version of the algorithm used to obtain the Result
 279  Returns : string (e.g., 2.1.2)
 280  Args    : [optional] scalar string to set algorithm version value
 281
 282 =cut
 283
 284 sub algorithm_version{
 285     my ($self,$value) = @_;
 286     my $previous = $self->{'_algorithm_version'};
 287     if( defined $value || ! defined $previous ) {
 288         $value = $previous = '' unless defined $value;
 289         $self->{'_algorithm_version'} = $value;
 290     }
 291
 292     return $previous;
 293 }
 294
 295 =head2 Bio::Search::Result::ResultI interface methods
 296
 297 Bio::Search::Result::ResultI implementation
 298
 299 =head2 next_hit
 300
 301  Title   : next_hit
 302  Usage   : while( $hit = $result->next_hit()) { ... }
 303  Function: Returns the next available Hit object, representing potential
 304            matches between the query and various entities from the database.
 305  Returns : a Bio::Search::Hit::HitI object or undef if there are no more.
 306  Args    : none
 307
 308
 309 =cut
 310
 311 sub next_hit {
 312     my ($self,@args) = @_;
 313     my $index = $self->_nexthitindex;
 314     return if $index > scalar @{$self->{'_hits'}};
 315
 316     my $hit = $self->{'_hits'}->[$index];
 317     if (ref($hit) eq 'HASH') {
 318         my $factory = $self->hit_factory || $self->throw("Tried to get a Hit, but it was a hash ref and we have no hit factory");
 319         $hit = $factory->create_object(%{$hit});
 320         $self->{'_hits'}->[$index] = $hit;
 321         delete $self->{_hashes}->{$index};
 322     }
 323     return $hit;
 324 }
 325
 326 =head2 query_name
 327
 328  Title   : query_name
 329  Usage   : $id = $result->query_name();
 330  Function: Get the string identifier of the query used by the
 331            algorithm that performed the search.
 332  Returns : a string.
 333  Args    : [optional] new string value for query name
 334
 335 =cut
 336
 337 sub query_name {
 338     my ($self,$value) = @_;
 339     my $previous = $self->{'_queryname'};
 340     if( defined $value || ! defined $previous ) {
 341         $value = $previous = '' unless defined $value;
 342         $self->{'_queryname'} = $value;
 343     }
 344     return $previous;
 345 }
 346
 347 =head2 query_accession
 348
 349  Title   : query_accession
 350  Usage   : $id = $result->query_accession();
 351  Function: Get the accession (if available) for the query sequence
 352  Returns : a string
 353  Args    : [optional] new string value for accession
 354
 355 =cut
 356
 357 sub query_accession {
 358     my ($self,$value) = @_;
 359     my $previous = $self->{'_queryacc'};
 360     if( defined $value || ! defined $previous ) {
 361         $value = $previous = '' unless defined $value;
 362         $self->{'_queryacc'} = $value;
 363     }
 364     return $previous;
 365 }
 366
 367 =head2 query_gi
 368
 369  Title   : query_gi
 370  Usage   : $acc = $hit->query_gi();
 371  Function: Retrieve the NCBI Unique ID (aka the GI #),
 372            if available, for the query
 373  Returns : a scalar string (empty string if not set)
 374  Args    : none
 375
 376 =cut
 377
 378 sub query_gi {
 379     my ($self,$value) = @_;
 380     if( defined $value ) {
 381         $self->{'_query_gi'} = $value;
 382     } else {
 383         $self->{'_query_gi'} = $self->query_name =~ m{^gi\|(\d+)} ? $1 : '';
 384     }
 385     return $self->{'_query_gi'};
 386 }
 387
 388 =head2 query_length
 389
 390  Title   : query_length
 391  Usage   : $id = $result->query_length();
 392  Function: Get the length of the query sequence
 393            used in the search.
 394  Returns : a number
 395  Args    :  [optional] new integer value for query length
 396
 397 =cut
 398
 399 sub query_length {
 400     my ($self,$value) = @_;
 401     my $previous = $self->{'_querylength'};
 402     if( defined $value || ! defined $previous ) {
 403         $value = $previous = 0 unless defined $value;
 404         $self->{'_querylength'} = $value;
 405     }
 406     return $previous;
 407 }
 408
 409 =head2 query_description
 410
 411  Title   : query_description
 412  Usage   : $id = $result->query_description();
 413  Function: Get the description of the query sequence
 414            used in the search.
 415  Returns : a string
 416  Args    : [optional] new string for the query description
 417
 418 =cut
 419
 420 sub query_description {
 421     my ($self,$value) = @_;
 422     my $previous = $self->{'_querydesc'};
 423     if( defined $value || ! defined $previous ) {
 424         $value = $previous = '' unless defined $value;
 425         $self->{'_querydesc'} = $value;
 426     }
 427     return $previous;
 428 }
 429
 430
 431 =head2 database_name
 432
 433  Title   : database_name
 434  Usage   : $name = $result->database_name()
 435  Function: Used to obtain the name of the database that the query was searched
 436            against by the algorithm.
 437  Returns : a scalar string
 438  Args    : [optional] new string for the db name
 439
 440 =cut
 441
 442 sub database_name {
 443     my ($self,$value) = @_;
 444     my $previous = $self->{'_dbname'};
 445     if( defined $value || ! defined $previous ) {
 446         $value = $previous = '' unless defined $value;
 447         $self->{'_dbname'} = $value;
 448     }
 449     return $previous;
 450 }
 451
 452 =head2 database_letters
 453
 454  Title   : database_letters
 455  Usage   : $size = $result->database_letters()
 456  Function: Used to obtain the size of database that was searched against.
 457  Returns : a scalar integer (units specific to algorithm, but probably the
 458            total number of residues in the database, if available) or undef if
 459            the information was not available to the Processor object.
 460  Args    : [optional] new scalar integer for number of letters in db
 461
 462
 463 =cut
 464
 465 sub database_letters {
 466     my ($self,$value) = @_;
 467     my $previous = $self->{'_dbletters'};
 468     if( defined $value || ! defined $previous ) {
 469         $value = $previous = '' unless defined $value;
 470         $self->{'_dbletters'} = $value;
 471     }
 472     return $previous;
 473 }
 474
 475 =head2 database_entries
 476
 477  Title   : database_entries
 478  Usage   : $num_entries = $result->database_entries()
 479  Function: Used to obtain the number of entries contained in the database.
 480  Returns : a scalar integer representing the number of entities in the database
 481            or undef if the information was not available.
 482  Args    : [optional] new integer for the number of sequence entries in the db
 483
 484
 485 =cut
 486
 487 sub database_entries {
 488     my ($self,$value) = @_;
 489     my $previous = $self->{'_dbentries'};
 490     if( defined $value || ! defined $previous ) {
 491         $value = $previous = '' unless defined $value;
 492         $self->{'_dbentries'} = $value;
 493     }
 494     return $previous;
 495 }
 496
 497 =head2 get_parameter
 498
 499  Title   : get_parameter
 500  Usage   : my $gap_ext = $report->get_parameter('gapext')
 501  Function: Returns the value for a specific parameter used
 502            when running this report
 503  Returns : string
 504  Args    : name of parameter (string)
 505
 506 =cut
 507
 508 sub get_parameter {
 509    my ($self,$name) = @_;
 510    return $self->{'_parameters'}->get_parameter($name);
 511 }
 512
 513 =head2 available_parameters
 514
 515  Title   : available_parameters
 516  Usage   : my @params = $report->available_paramters
 517  Function: Returns the names of the available parameters
 518  Returns : Return list of available parameters used for this report
 519  Args    : none
 520
 521 =cut
 522
 523 sub available_parameters{
 524    my ($self) = @_;
 525    return $self->{'_parameters'}->available_parameters;
 526 }
 527
 528
 529 =head2 get_statistic
 530
 531  Title   : get_statistic
 532  Usage   : my $gap_ext = $report->get_statistic('kappa')
 533  Function: Returns the value for a specific statistic available
 534            from this report
 535  Returns : string
 536  Args    : name of statistic (string)
 537
 538 =cut
 539
 540 sub get_statistic{
 541    my ($self,$key) = @_;
 542    return $self->{'_statistics'}->get_statistic($key);
 543 }
 544
 545 =head2 available_statistics
 546
 547  Title   : available_statistics
 548  Usage   : my @statnames = $report->available_statistics
 549  Function: Returns the names of the available statistics
 550  Returns : Return list of available statistics used for this report
 551  Args    : none
 552
 553 =cut
 554
 555 sub available_statistics{
 556    my ($self) = @_;
 557    return $self->{'_statistics'}->available_statistics;
 558 }
 559
 560 =head2 Bio::Search::Report
 561
 562 Bio::Search::Result::GenericResult specific methods
 563
 564 =head2 add_hit
 565
 566  Title   : add_hit
 567  Usage   : $report->add_hit($hit)
 568  Function: Adds a HitI to the stored list of hits
 569  Returns : Number of HitI currently stored
 570  Args    : Bio::Search::Hit::HitI
 571
 572 =cut
 573
 574 sub add_hit {
 575     my ($self,$s) = @_;
 576     if (ref($s) eq 'HASH' || $s->isa('Bio::Search::Hit::HitI') ) {
 577         push @{$self->{'_hits'}}, $s;
 578     }
 579     else {
 580         $self->throw("Passed in " .ref($s)." as a Hit which is not a Bio::Search::HitI.");
 581     }
 582
 583     if (ref($s) eq 'HASH') {
 584         $self->{_hashes}->{$#{$self->{'_hits'}}} = 1;
 585     }
 586     return scalar @{$self->{'_hits'}};
 587 }
 588
 589 =head2 hit_factory
 590
 591  Title   : hit_factory
 592  Usage   : $hit->hit_factory($hit_factory)
 593  Function: Get/set the factory used to build HitI objects if necessary.
 594  Returns : Bio::Factory::ObjectFactoryI
 595  Args    : Bio::Factory::ObjectFactoryI
 596
 597 =cut
 598
 599 sub hit_factory {
 600     my $self = shift;
 601     if (@_) { $self->{_hit_factory} = shift }
 602     return $self->{_hit_factory} || return;
 603 }
 604
 605 =head2 rewind
 606
 607  Title   : rewind
 608  Usage   : $result->rewind;
 609  Function: Allow one to reset the Hit iterator to the beginning
 610            Since this is an in-memory implementation
 611  Returns : none
 612  Args    : none
 613
 614 =cut
 615
 616 sub rewind{
 617    my ($self) = @_;
 618    $self->{'_hitindex'} = 0;
 619 }
 620
 621
 622 =head2 _nexthitindex
 623
 624  Title   : _nexthitindex
 625  Usage   : private
 626
 627 =cut
 628
 629 sub _nexthitindex{
 630    my ($self,@args) = @_;
 631    return $self->{'_hitindex'}++;
 632 }
 633
 634
 635 =head2 add_parameter
 636
 637  Title   : add_parameter
 638  Usage   : $report->add_parameter('gapext', 11);
 639  Function: Adds a parameter
 640  Returns : none
 641  Args    : key  - key value name for this parama
 642            value - value for this parameter
 643
 644 =cut
 645
 646 sub add_parameter {
 647    my ($self,$key,$value) = @_;
 648    $self->{'_parameters'}->set_parameter($key => $value);
 649 }
 650
 651
 652 =head2 add_statistic
 653
 654  Title   : add_statistic
 655  Usage   : $report->add_statistic('lambda', 2.3);
 656  Function: Adds a parameter
 657  Returns : none
 658  Args    : key  - key value name for this parama
 659            value - value for this parameter
 660
 661 =cut
 662
 663 sub add_statistic {
 664    my ($self,$key,$value) = @_;
 665    $self->{'_statistics'}->set_statistic($key => $value);
 666    return;
 667 }
 668
 669
 670 =head2 num_hits
 671
 672  Title   : num_hits
 673  Usage   : my $hitcount= $result->num_hits
 674  Function: returns the number of hits for this query result
 675  Returns : integer
 676  Args    : none
 677
 678 =cut
 679
 680 sub num_hits{
 681    my ($self) = shift;
 682    if (not defined $self->{'_hits'}) {
 683        $self->throw("Can't get Hits: data not collected.");
 684     }
 685     return scalar(@{$self->{'_hits'}});
 686 }
 687
 688
 689 =head2 hits
 690
 691  Title   : hits
 692  Usage   : my @hits = $result->hits
 693  Function: Returns the available hits for this Result
 694  Returns : Array of L<Bio::Search::Hit::HitI> objects
 695  Args    : none
 696
 697
 698 =cut
 699
 700 sub hits {
 701     my ($self) = shift;
 702
 703     foreach my $i (keys %{$self->{_hashes} || {}}) {
 704         my $factory = $self->hit_factory || $self->throw("Tried to get a Hit, but it was a hash ref and we have no hit factory");
 705         $self->{'_hits'}->[$i] = $factory->create_object(%{$self->{'_hits'}->[$i]});
 706         delete $self->{_hashes}->{$i};
 707     }
 708
 709     my @hits = ();
 710     if (ref $self->{'_hits'}) {
 711         @hits = @{$self->{'_hits'}};
 712     }
 713     return @hits;
 714 }
 715
 716 =head2 algorithm_reference
 717
 718  Title   : algorithm_reference
 719  Usage   : $obj->algorithm_reference($newval)
 720  Function:
 721  Returns : string containing literature reference for the algorithm
 722  Args    : newvalue string (optional)
 723  Comments: Formerly named program_reference(), which is still supported
 724            for backwards compatibility.
 725
 726 =cut
 727
 728 sub algorithm_reference{
 729    my ($self,$value) = @_;
 730    if( defined $value) {
 731       $self->{'algorithm_reference'} = $value;
 732     }
 733     return $self->{'algorithm_reference'};
 734 }
 735
 736 =head2 program_reference
 737
 738  Title   : program_reference
 739  Usage   : $obj->program_reference()
 740  Function:
 741  Returns : string containing literature reference for the algorithm
 742  Args    :
 743  Comments: Deprecated - use algorithm_reference() instead.
 744
 745 =cut
 746
 747 sub program_reference { shift->algorithm_reference(@_); }
 748
 749 =head2 rid
 750
 751  Title   : rid
 752  Usage   : $obj->rid($newval)
 753  Function:
 754  Returns : value of the BLAST Request ID (eg. RID: ZABJ4EA7014)
 755  Args    : newvalue (optional)
 756  Comments: The default implementation in ResultI returns an empty string
 757            rather than throwing a NotImplemented exception, since
 758            the RID may not always be available and is not critical.
 759            See: (1) https://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/BLAST/rid.html
 760                 (2) https://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node63.html
 761 =cut
 762
 763 sub rid{
 764     my ($self,$value) = @_;
 765     if( defined $value) {
 766            $self->{'rid'} = $value;
 767         }
 768         return $self->{'rid'};
 769 }
 770
 771 =head2 no_hits_found
 772
 773 See documentation in L<Bio::Search::Result::ResultI::no_hits_found()|Bio::Search::Result::ResultI>
 774
 775 =cut
 776
 777 sub no_hits_found {
 778     my $self = shift;
 779
 780     # Watch the double negative!
 781     # result = 0 means "yes hits were found"
 782     # result = 1 means "no hits were found"
 783
 784     return $self->{'_no_hits_found'};
 785 }
 786
 787
 788 =head2 set_no_hits_found
 789
 790 See documentation in L<Bio::Search::Result::ResultI::set_no_hits_found()|Bio::Search::Result::ResultI>
 791
 792 =cut
 793
 794 sub set_no_hits_found {
 795     my $self = shift;
 796     $self->{'_no_hits_found'} = 1;
 797 }
 798
 799
 800 =head2 to_string
 801
 802  Title   : to_string
 803  Usage   : print $blast->to_string;
 804  Function: Returns a string representation for the Blast result.
 805            Primarily intended for debugging purposes.
 806  Example : see usage
 807  Returns : A string of the form:
 808            [GenericResult] <analysis_method> query=<name> <description> db=<database
 809            e.g.:
 810            [GenericResult] BLASTP query=YEL060C vacuolar protease B, db=PDBUNIQ
 811  Args    : None
 812
 813 =cut
 814
 815 sub to_string {
 816     my $self = shift;
 817     my $str = ref($self) . ", algorithm= " . $self->algorithm . ", query=" . $self->query_name . " " . $self->query_description .", db=" . $self->database_name;
 818     return $str;
 819 }
 820
 821 1;