BaseFeatureAdaptor.pm 23.2 KB
Newer Older
1
#
Simon Potter's avatar
Simon Potter committed
2
# EnsEMBL module for Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor
3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50
#
# Cared for by Ewan Birney <birney@ebi.ac.uk>
#
# Copyright Ewan Birney
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code

=head1 NAME

Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor - Abstract Base class for 
                                          FeatureAdaptors

=head1 SYNOPSIS

Abstract class should not be instantiated.  Implementation of
abstract methods must be performed by subclasses.

=head1 DESCRIPTION

This is a base adaptor for feature adaptors. This base class is simply a way
of eliminating code duplication through the implementation of methods 
common to all feature adaptors.

=head1 AUTHOR - Ewan Birney

Email birney@ebi.ac.uk

Describe contact details 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::EnsEMBL::DBSQL::BaseFeatureAdaptor;
use vars qw(@ISA);
use strict;

# Object preamble - inherits from Bio::EnsEMBL::Root

use Bio::EnsEMBL::DBSQL::BaseAdaptor;
51
use Bio::EnsEMBL::Utils::Cache;
52 53 54

@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);

55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81
my $SLICE_FEATURE_CACHE_SIZE = 12;


=head2 new

  Arg [1]    : list of args @args
               Superclass constructor arguments
  Example    : none
  Description: Constructor which just initializes internal cache structures
  Returntype : Bio::EnsEMBL::BaseFeatureAdaptor
  Exceptions : none
  Caller     : implementing subclass constructors

=cut

sub new {
  my ($class, @args) = @_;

  my $self = $class->SUPER::new(@args);

  #initialize caching data structures
  tie(%{$self->{'_slice_feature_cache'}}, 
      'Bio::EnsEMBL::Utils::Cache',
      $SLICE_FEATURE_CACHE_SIZE);

  return $self;
}
82 83 84 85 86 87 88

=head2 generic_fetch

  Arg [1]    : (optional) string $constraint
               An SQL query constraint (i.e. part of the WHERE clause)
  Arg [2]    : (optional) string $logic_name
               the logic_name of the analysis of the features to obtain
89
  Example    : $fts = $a->generic_fetch('contig_id in (1234, 1235)', 'Swall');
90 91
  Description: Performs a database fetch and returns feature objects in
               contig coordinates.
92
  Returntype : listref of Bio::EnsEMBL::SeqFeature in contig coordinates
93 94 95 96
  Exceptions : none
  Caller     : BaseFeatureAdaptor, ProxyDnaAlignFeatureAdaptor::generic_fetch

=cut
97 98
  
sub generic_fetch {
99
  my ($self, $constraint, $logic_name, $mapper, $slice) = @_;
100 101 102 103 104 105
  
  my $tablename = $self->_tablename();
  my $columns = join(', ', $self->_columns());
  
  if($logic_name) {
    #determine the analysis id via the logic_name
106 107
    my $analysis = 
      $self->db->get_AnalysisAdaptor()->fetch_by_logic_name($logic_name);
108 109
    unless(defined $analysis && $analysis->dbID() ) {
      $self->warn("No analysis for logic name $logic_name exists\n");
Web Admin's avatar
Web Admin committed
110
      return [];
111 112 113 114 115 116 117 118 119 120
    }
    
    my $analysis_id = $analysis->dbID();
    
    if($constraint) {
      $constraint .= " AND analysis_id = $analysis_id";
    } else {
      $constraint = " analysis_id = $analysis_id";
    }
  } 
121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139
  
  my $sql = "SELECT $columns FROM $tablename ";

  my $default_where = $self->_default_where_clause;
  my $final_clause = $self->_final_clause;

  #append a where clause if it was defined
  if($constraint) { 
    $sql .= " where $constraint ";
    if($default_where) {
      $sql .= " and $default_where ";
    }
  } elsif($default_where) {
    $sql .= " where $default_where ";
  }

  #append additional clauses which may have been defined
  $sql .= " $final_clause";

140
  my $sth = $self->prepare($sql);
141 142 143
  
  $sth->execute;  

144
  return $self->_objs_from_sth($sth, $mapper, $slice);
145 146 147 148
}


=head2 fetch_by_dbID
149 150 151 152 153 154

  Arg [1]    : int $id
               the unique database identifier for the feature to be obtained 
  Example    : $feat = $adaptor->fetch_by_dbID(1234);
  Description: Returns the feature created from the database defined by the
               the id $id. 
155
  Returntype : Bio::EnsEMBL::SeqFeature
156 157
  Exceptions : thrown if $id is not defined
  Caller     : general
158 159 160 161 162 163 164 165 166 167 168 169 170

=cut

sub fetch_by_dbID{
  my ($self,$id) = @_;
  
  unless(defined $id) {
    $self->throw("fetch_by_dbID must have an id");
  }

  my $tablename = $self->_tablename();
  my $constraint = "${tablename}_id = $id";

171
  #return first element of _generic_fetch list
172
  my ($feat) = @{$self->generic_fetch($constraint)}; 
173
  return $feat;
174 175 176
}


177
=head2 fetch_all_by_RawContig_constraint
178

179 180
  Arg [1]    : Bio::EnsEMBL::RawContig $contig
               The contig object from which features are to be obtained
181 182 183 184
  Arg [2]    : (optional) string $constraint
               An SQL query constraint (i.e. part of the WHERE clause)
  Arg [3]    : (optional) string $logic_name
               the logic name of the type of features to obtain
185 186
  Example    : $fs = $a->fetch_all_by_Contig_constraint($ctg,'perc_ident>5.0');
  Description: Returns a listref of features created from the database which 
187 188 189
               are on the contig defined by $cid and fulfill the SQL constraint
               defined by $constraint. If logic name is defined, only features
               with an analysis of type $logic_name will be returned. 
190
  Returntype : listref of Bio::EnsEMBL::SeqFeature in contig coordinates
191 192
  Exceptions : thrown if $cid is not defined
  Caller     : general
193 194 195

=cut

196
sub fetch_all_by_RawContig_constraint {
197
  my ($self, $contig, $constraint, $logic_name) = @_;
198
  
199 200
  unless( defined $contig ) {
    $self->throw("fetch_by_Contig_constraint must have an contig");
201 202
  }

203 204 205 206 207 208
  unless( ref $contig && $contig->isa('Bio::EnsEMBL::RawContig')) {
    $self->throw("contig argument is not a Bio::EnsEMBL::RawContig object\n");
  }

  my $cid = $contig->dbID();

209 210 211 212 213 214
  if($constraint) {
    $constraint .= " AND contig_id = $cid";
  } else {
    $constraint = "contig_id = $cid";
  }

215
  return @$self->generic_fetch($constraint, $logic_name);
216 217
}

218

Arne Stabenau's avatar
Arne Stabenau committed
219
=head2 fetch_all_by_RawContig
220

221 222
  Arg [1]    : Bio::EnsEMBL::RawContig $contig 
               the contig from which features should be obtained
223 224
  Arg [2]    : (optional) string $logic_name
               the logic name of the type of features to obtain
225
  Example    : @fts = $a->fetch_all_by_RawContig($contig, 'wall');
226 227 228 229
  Description: Returns a list of features created from the database which are 
               are on the contig defined by $cid If logic name is defined, 
               only features with an analysis of type $logic_name will be 
               returned. 
230
  Returntype : listref of Bio::EnsEMBL::*Feature in contig coordinates
231 232 233 234
  Exceptions : none
  Caller     : general

=cut
235
   
Arne Stabenau's avatar
Arne Stabenau committed
236 237 238
sub fetch_all_by_RawContig {
  my ( $self, $contig, $logic_name ) = @_;

239
  return $self->fetch_all_by_RawContig_constraint($contig, '',$logic_name);
240 241 242
}


243
=head2 fetch_all_by_RawContig_and_score
244 245
  Arg [1]    : Bio::EnsEMBL::RawContig $contig 
               the contig from which features should be obtained
246
  Arg [2]    : (optional) float $score
247 248 249
               the lower bound of the score of the features to obtain
  Arg [3]    : (optional) string $logic_name
               the logic name of the type of features to obtain
250
  Example    : @fts = $a->fetch_by_RawContig_and_score(1, 50.0, 'Swall');
251
  Description: Returns a list of features created from the database which are 
252
               are on the contig defined by $cid and which have score greater  
253 254
               than score.  If logic name is defined, only features with an 
               analysis of type $logic_name will be returned. 
255
  Returntype : listref of Bio::EnsEMBL::*Feature in contig coordinates
256 257 258 259 260
  Exceptions : thrown if $score is not defined
  Caller     : general

=cut

261
sub fetch_all_by_RawContig_and_score{
262
  my($self, $contig, $score, $logic_name) = @_;
263 264 265

  my $constraint;

266
  if(defined $score){
267 268 269
    $constraint = "score > $score";
  }
    
270
  return $self->fetch_all_by_RawContig_constraint($contig, $constraint, 
271
					       $logic_name);
272 273 274
}


275
=head2 fetch_all_by_Slice
276 277 278 279 280

  Arg [1]    : Bio::EnsEMBL::Slice $slice
               the slice from which to obtain features
  Arg [2]    : (optional) string $logic_name
               the logic name of the type of features to obtain
281 282 283 284 285 286
  Example    : $fts = $a->fetch_all_by_Slice($slice, 'Swall');
  Description: Returns a listref of features created from the database 
               which are on the Slice defined by $slice. If $logic_name is 
               defined only features with an analysis of type $logic_name 
               will be returned. 
  Returntype : listref of Bio::EnsEMBL::SeqFeatures in Slice coordinates
287 288 289 290 291
  Exceptions : none
  Caller     : Bio::EnsEMBL::Slice

=cut

292
sub fetch_all_by_Slice {
293 294 295
  my ($self, $slice, $logic_name) = @_;
  
  #fetch by constraint with empty constraint
296
  return $self->fetch_all_by_Slice_constraint($slice, '', $logic_name);
297 298 299
}


300
=head2 fetch_all_by_Slice_and_score
301 302 303

  Arg [1]    : Bio::EnsEMBL::Slice $slice
               the slice from which to obtain features
304
  Arg [2]    : (optional) float $score
305 306 307
               lower bound of the the score of the features retrieved
  Arg [3]    : (optional) string $logic_name
               the logic name of the type of features to obtain
308
  Example    : $fts = $a->fetch_all_by_Slice($slice, 'Swall');
309 310 311 312 313
  Description: Returns a list of features created from the database which are 
               are on the Slice defined by $slice and which have a score 
               greated than $score. If $logic_name is defined, 
               only features with an analysis of type $logic_name will be 
               returned. 
314
  Returntype : listref of Bio::EnsEMBL::SeqFeatures in Slice coordinates
315 316 317 318 319
  Exceptions : none
  Caller     : Bio::EnsEMBL::Slice

=cut

320
sub fetch_all_by_Slice_and_score {
321 322 323
  my ($self, $slice, $score, $logic_name) = @_;
  my $constraint;

324
  if(defined $score) {
325 326 327
    $constraint = "score > $score";
  }

328 329
  return $self->fetch_all_by_Slice_constraint($slice, $constraint, 
					      $logic_name);
330 331 332
}  


333
=head2 fetch_all_by_Slice_constraint
334

335 336 337 338 339
  Arg [1]    : Bio::EnsEMBL::Slice $slice
               the slice from which to obtain features
  Arg [2]    : (optional) string $constraint
               An SQL query constraint (i.e. part of the WHERE clause)
  Arg [3]    : (optional) string $logic_name
340
               the logic name of the type of features to obtain
341 342
  Example    : $fs = $a->fetch_all_by_Slice_constraint($slc, 'perc_ident > 5');
  Description: Returns a listref of features created from the database which 
343 344 345 346
               are on the Slice defined by $slice and fulfill the SQL 
               constraint defined by $constraint. If logic name is defined, 
               only features with an analysis of type $logic_name will be 
               returned. 
347
  Returntype : listref of Bio::EnsEMBL::SeqFeatures in Slice coordinates
348 349
  Exceptions : thrown if $slice is not defined
  Caller     : Bio::EnsEMBL::Slice
350 351 352

=cut

353
sub fetch_all_by_Slice_constraint {
354
  my($self, $slice, $constraint, $logic_name) = @_;
355

356 357
  unless(defined $slice && ref $slice && $slice->isa("Bio::EnsEMBL::Slice")) {
    $self->throw("Slice arg must be a Bio::EnsEMBL::Slice not a [$slice]\n");
358 359
  }

360 361
  $logic_name = '' unless $logic_name;
  $constraint = '' unless $constraint;
362

363
  #check the cache and return if we have already done this query
Web Admin's avatar
Web Admin committed
364
  my $key = join($slice->name, $constraint, $logic_name);
365 366
  return $self->{'_slice_feature_cache'}{$key} 
    if $self->{'_slice_feature_cache'}{$key};
Web Admin's avatar
Web Admin committed
367
    
368 369 370 371
  my $slice_start  = $slice->chr_start();
  my $slice_end    = $slice->chr_end();
  my $slice_strand = $slice->strand();
		 
372 373
  my $mapper = 
    $self->db->get_AssemblyMapperAdaptor->fetch_by_type($slice->assembly_type);
374 375

  #get the list of contigs this slice is on
376
  my @cids = 
377
    $mapper->list_contig_ids( $slice->chr_name, $slice_start ,$slice_end );
378
  
Web Admin's avatar
Web Admin committed
379
  return [] unless scalar(@cids);
380 381 382

  my $cid_list = join(',',@cids);

383
  #construct the SQL constraint for the contig ids 
384 385 386 387 388
  if($constraint) {
    $constraint .= " AND contig_id IN ($cid_list)";
  } else {
    $constraint = "contig_id IN ($cid_list)";
  }
389

390
  #for speed the remapping to slice may be done at the time of object creation
391 392
  my $features = 
    $self->generic_fetch($constraint, $logic_name, $mapper, $slice); 
Graham McVicker's avatar
Graham McVicker committed
393
  
394 395
  if(@$features && (!$features->[0]->can('contig') || 
		    $features->[0]->contig == $slice)) {
Graham McVicker's avatar
Graham McVicker committed
396
    #features have been converted to slice coords already, cache and return
Web Admin's avatar
Web Admin committed
397
    return $self->{'_slice_feature_cache'}{$key} = $features;
398
  }
399

400 401
  #remapping has not been done, we have to do our own conversion from
  # raw contig coords to slice coords
402

403
  my @out = ();
404
  
405 406
  my ($feat_start, $feat_end, $feat_strand); 

407
  foreach my $f (@$features) {
408
    #since feats were obtained in contig coords, attached seq is a contig
409
    my $contig_id = $f->contig->dbID();
410

411
    my ($chr_name, $start, $end, $strand) = 
412 413
      $mapper->fast_to_assembly($contig_id, $f->start(), 
				$f->end(),$f->strand(),"rawcontig");
414

415
    # undefined start means gap
416
    next unless defined $start;     
417

418
    # maps to region outside desired area 
419
    next if ($start > $slice_end) || ($end < $slice_start);  
420 421
    
    #shift the feature start, end and strand in one call
422
    if($slice_strand == -1) {
423
      $f->move( $slice_end - $end + 1, $slice_end - $start + 1, $strand * -1 );
424 425 426 427
    } else {
      $f->move( $start - $slice_start + 1, $end - $slice_start + 1, $strand );
    }
    
428
    $f->contig($slice);
429
    
Web Admin's avatar
Web Admin committed
430
    push @out,$f;
431 432
  }
  
433
  #update the cache
Web Admin's avatar
Web Admin committed
434
  return $self->{'_slice_feature_cache'}{$key} = \@out;
435 436 437
}


438
=head2 store
439

440
  Arg [1]    : list of Bio::EnsEMBL::SeqFeature
441 442 443 444 445 446 447
  Example    : $adaptor->store(@feats);
  Description: ABSTRACT  Subclasses are responsible for implementing this 
               method.  It should take a list of features and store them in 
               the database.
  Returntype : none
  Exceptions : thrown method is not implemented by subclass
  Caller     : general
448 449 450 451 452 453 454 455 456 457

=cut

sub store{
  my $self = @_;

  $self->throw("Abstract method store not defined by implementing subclass\n");
}


458 459 460 461 462 463 464 465 466
=head2 remove

  Arg [1]    : A feature $feature 
  Example    : $feature_adaptor->remove($feature);
  Description: This removes a feature from the database.  The table the
               feature is removed from is defined by the abstract method
               _tablename, and the primary key of the table is assumed
               to be _tablename() . '_id'.  The feature argument must 
               be an object implementing the dbID method, and for the
467
               feature to be removed from the database a dbID value must
468 469 470 471 472 473 474 475
               be returned.
  Returntype : none
  Exceptions : thrown if $feature arg does not implement dbID(), or if 
               $feature->dbID is not a true value               
  Caller     : general

=cut

476

477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500
sub remove {
  my ($self, $feature) = @_;

  unless($feature->can('dbID')) {
    $self->throw("Feature [$feature] does not implement method dbID");
  }

  unless($feature->dbID) {
    $self->warn("BaseFeatureAdaptor::remove - dbID not defined - " .
                "feature could not be removed");
  }

  my $table = $self->_tablename();

  my $sth = $self->prepare("DELETE FROM $table WHERE ${table}_id = ?");
  $sth->execute($feature->dbID());

  #unset the feature dbID
  $feature->dbID('');
  
  return;
}


501

502
=head2 remove_by_RawContig
503 504

  Arg [1]    : Bio::Ensembl::RawContig $contig 
505
  Example    : $feature_adaptor->remove_by_RawContig($contig);
506 507 508 509
  Description: This removes features from the database which lie on a removed
               contig.  The table the features are removed from is defined by 
               the abstract method_tablename, and the primary key of the table
               is assumed to be contig_id.
510
  Returntype : none
511
  Exceptions : thrown if no contig is supplied
512 513 514 515
  Caller     : general

=cut

516
sub remove_by_RawContig {
517
  my ($self, $contig) = @_;
518

519 520 521
  unless($contig) {
    $self->throw("BaseFeatureAdaptor::remove - no contig supplied: ".
		 "Deletion of features failed.");
522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539
  }

  my $table = $self->_tablename();

  # RepeatFeatureAdaptor returns 2 table names so need to so do some cleaning
  # up of the returned table name.  This has the form:
  #  table_name1 t1, table_name2 t2

  my @tables = split(/,/,$table);

  foreach my $table_name (@tables) {
    # Not pretty this but there is no need to delete anything from the 
    # repeat_consensus table
    next if ($table_name =~ /repeat_consensus/);

    my ($actual_table) = $table_name =~ /(^\w+)/;  # lose the table alias, if there is one

    my $sth = $self->prepare("DELETE FROM $actual_table WHERE contig_id = ?");
540
    $sth->execute($contig->dbID);
541 542 543 544 545 546 547
  }

  return;
}



548 549
=head2 _tablename

550 551 552 553 554 555 556 557
  Args       : none
  Example    : $tablename = $self->_table_name()
  Description: ABSTRACT PROTECTED Subclasses are responsible for implementing
               this method.  It should return the name of the table to be
               used to obtain features.  
  Returntype : string
  Exceptions : thrown if not implemented by subclass
  Caller     : BaseFeatureAdaptor::generic_fetch
558 559 560 561 562 563 564

=cut

sub _tablename {
  my $self = shift;

  $self->throw("abstract method _tablename not defined by implementing" .
Simon Potter's avatar
Simon Potter committed
565
               " subclass of BaseFeatureAdaptor");
566 567 568
  return undef;
}

569

570 571
=head2 _columns

572 573 574 575 576 577 578 579
  Args       : none
  Example    : $tablename = $self->_columns()
  Description: ABSTRACT PROTECTED Subclasses are responsible for implementing
               this method.  It should return a list of columns to be used
               for feature creation
  Returntype : list of strings
  Exceptions : thrown if not implemented by subclass
  Caller     : BaseFeatureAdaptor::generic_fetch
580 581 582 583 584 585 586

=cut

sub _columns {
  my $self = shift;

  $self->throw("abstract method _columns not defined by implementing" .
Simon Potter's avatar
Simon Potter committed
587
               " subclass of BaseFeatureAdaptor");
588 589 590
}


591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631
=head2 _default_where_clause

  Arg [1]    : none
  Example    : none
  Description: May be overridden to provide an additional where constraint to 
               the SQL query which is generated to fetch feature records.
               This constraint is always appended to the end of the generated
               where clause and thus may be used to add a join between tables
  Returntype : string
  Exceptions : none
  Caller     : generic_fetch

=cut

sub _default_where_clause {
  my $self = shift;

  return '';
}


=head2 _final_clause

  Arg [1]    : none
  Example    : none
  Description: May be overriden to provide an additional clause to the end
               of the SQL query used to fetch feature records.  
               This is useful to add a required ORDER BY clause to the 
               query for example.
  Returntype : string
  Exceptions : none
  Caller     : generic_fetch

=cut

sub _final_clause {
  my $self = shift;

  return '';
}

632
=head2 _objs_from_sth
633 634 635 636 637 638 639 640 641 642 643 644 645

  Arg [1]    : DBI::row_hashref $hashref containing key-value pairs 
               for each of the columns specified by the _columns method
  Example    : my @feats = $self->_obj_from_hashref
  Description: ABSTRACT PROTECTED The subclass is responsible for implementing
               this method.  It should take in a DBI row hash reference and
               return a list of created features in contig coordinates.
  Returntype : list of Bio::EnsEMBL::*Features in contig coordinates
  Exceptions : thrown if not implemented by subclass
  Caller     : BaseFeatureAdaptor::generic_fetch

=cut

646
sub _objs_from_sth {
647 648 649
  my $self = shift;

  $self->throw("abstract method _obj_from_hashref not defined by implementing"
Simon Potter's avatar
Simon Potter committed
650
             . " subclass of BaseFeatureAdaptor");
651 652
} 

653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672

=head2 deleteObj

  Arg [1]    : none
  Example    : none
  Description: Cleans up internal caches and references to other objects so
               that correct garbage collection may occur.
  Returntype : none
  Exceptions : none
  Caller     : Bio::EnsEMBL::DBConnection::deleteObj

=cut

sub deleteObj {
  my $self = shift;

  #flush feature cache
  %{$self->{'_slice_feature_cache'}} = ();
}

673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736



=head2 fetch_by_Contig_constraint

  Arg [1]    : none
  Example    : none
  Description: DEPRECATED use fetch_all_by_RawContig_constraint instead
  Returntype : none
  Exceptions : none
  Caller     : none

=cut

sub fetch_by_Contig_constraint {
  my ($self, @args) = @_;

  $self->warn("fetch_by_Contig_constraint has been renamed fetch_all_by_RawContig_constraint\n" . caller);

  return $self->fetch_all_by_RawContig_constraint(@args);
}



=head2 fetch_by_Contig

  Arg [1]    : none
  Example    : none
  Description: DEPRECATED use fetch_all_by_RawContig instead
  Returntype : none
  Exceptions : none
  Caller     : none

=cut

sub fetch_by_Contig {
  my ($self, @args) = @_;

  $self->warn("fetch_by_Contig has been renamed fetch_all_by_RawContig\n" . caller);

  return $self->fetch_all_by_RawContig(@args);
}


=head2 fetch_by_Contig_and_score

  Arg [1]    : none
  Example    : none
  Description: DEPRECATED use fetch_all_by_RawContig_and_score instead
  Returntype : none
  Exceptions : none
  Caller     : none

=cut

sub fetch_by_Contig_and_score {
  my ($self, @args) = @_;

  $self->warn("fetch_by_Contig_and_score has been renamed fetch_all_by_RawContig_and_score\n" . caller);

  return $self->fetch_all_by_RawContig_and_score(@args);
}


737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799

=head2 fetch_all_by_Contig

  Arg [1]    : none
  Example    : none
  Description: DEPRECATED use fetch_all_by_RawContig instead
  Returntype : none
  Exceptions : none
  Caller     : none

=cut

sub fetch_all_by_Contig {
  my ($self, @args) = @_;

  $self->warn("fetch_all_by_Contig has been renamed fetch_all_by_RawContig\n" . caller);

  return $self->fetch_all_by_RawContig(@args);
}


=head2 fetch_all_by_Contig_and_score

  Arg [1]    : none
  Example    : none
  Description: DEPRECATED use fetch_all_by_RawContig_and_score instead
  Returntype : none
  Exceptions : none
  Caller     : none

=cut

sub fetch_all_by_Contig_and_score {
  my ($self, @args) = @_;

  $self->warn("fetch_all_by_Contig_and_score has been renamed fetch_all_by_RawContig_and_score\n" . caller);

  return $self->fetch_all_by_RawContig_and_score(@args);
}


=head2 fetch_all_by_Contig_constraint

  Arg [1]    : none
  Example    : none
  Description: DEPRECATED use fetch_all_by_RawContig_constraint instead
  Returntype : none
  Exceptions : none
  Caller     : none

=cut

sub fetch_all_by_Contig_constraint {
  my ($self, @args) = @_;

  $self->warn("fetch_all_by_Contig_constraint has been renamed fetch_all_by_RawContig_constraint\n" . caller);

  return $self->fetch_all_by_RawContig_constraint(@args);
}




800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862
=head2 fetch_by_Slice_and_score

  Arg [1]    : none
  Example    : none
  Description: DEPRECATED use fetch_all_by_Slice_and_score instead
  Returntype : none
  Exceptions : none
  Caller     : none

=cut

sub fetch_by_Slice_and_score {
  my ($self, @args) = @_;

  $self->warn("fetch_by_Slice_and_score has been renamed fetch_all_by_Slice_and_score\n" . caller);

  return $self->fetch_all_by_Slice_and_score(@args);
}


=head2 fetch_by_Slice_constraint

  Arg [1]    : none
  Example    : none
  Description: DEPRECATED use fetch_all_by_Slice_constraint instead
  Returntype : none
  Exceptions : none
  Caller     : none

=cut

sub fetch_by_Slice_constraint {
  my ($self, @args) = @_;

  $self->warn("fetch_by_Slice_constraint has been renamed fetch_all_by_Slice_constraint\n" . caller);

  return $self->fetch_all_by_Slice_constraint(@args);
}



=head2 fetch_by_Slice

  Arg [1]    : none
  Example    : none
  Description: DEPRECATED use fetch_all_by_Slice instead
  Returntype : none
  Exceptions : none
  Caller     : none

=cut

sub fetch_by_Slice {
  my ($self, @args) = @_;

  $self->warn("fetch_by_Slice has been renamed fetch_all_by_Slice\n" . caller);

  return $self->fetch_all_by_Slice(@args);
}




863 864 865
1;