ChainedAssemblyMapper.pm 21 KB
Newer Older
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19

#
# Ensembl module for Bio::EnsEMBL::ChainedAssemblyMapper
#
# Written by Graham McVicker
#
# Copyright GRL and EBI
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code

=head1 NAME

Bio::EnsEMBL::ChainedAssemblyMapper - 
Handles mapping between two coordinate systems using the information stored in
the assembly table

=head1 SYNOPSIS
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
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
    $db = Bio::EnsEMBL::DBSQL::DBAdaptor->new(...);
    $asma = $db->get_AssemblyMapperAdaptor();
    $csa  = $db->get_CoordSystemAdaptor();

    my $chr_cs = $cs_adaptor->fetch_by_name('chromosome', 'NCBI33');
    my $cln_cs   = $cs_adaptor->fetch_by_name('clone');

    $asm_mapper = $map_adaptor->fetch_by_CoordSystems($cs1, $cs2);

    #map to contig coordinate system from chromosomal
    @cln_coords = $asm_mapper->map('X', 1_000_000, 2_000_000, 1, $chr_cs);

    #map to chromosome coordinate system from contig
    @chr_coords = $asm_mapper->map('AL30421.1',100,10000,-1,$cln_cs);

    #list contig names for a region of chromsome
    @cln_ids = $asm_mapper->list_ids('13', 1_000_000, 1, $chr_cs);

    #list chromosome names for a contig region
    @chr_ids = $asm_mapper->list_ids('AL30421.1',1,1000,-1,$cln_cs);

=head1 DESCRIPTION

The ChainedAssemblyMapper is an extension of the regular AssemblyMapper that
allows for mappings between coordinate systems that require multi-step mapping.
For example if explicit mappings are defined between the following 
coordinate systems,
  chromosome <-> contig
  contig     <-> clone
the ChainedAssemblyMapper would be able to perform implicit mapping between
the chromosome and clone coordinate systems.  This should be transparent to
the user of this module, and users should not even realise that they are using
a chained assembly mapper as opposed to a normal assembly mapper.

=head1 CONTACT

Post general queries to B<ensembl-dev@ebi.ac.uk>

=head1 METHODS

=cut


my $FIRST = 'first';
my $MIDDLE = 'middle';
my $LAST  = 'last';

package Bio::EnsEMBL::ChainedAssemblyMapper;

use strict;
use warnings;
use integer; #use proper arithmetic bitshifts

use Bio::EnsEMBL::Mapper;
use Bio::EnsEMBL::Mapper::RangeRegistry;
use Bio::EnsEMBL::Utils::Exception qw(throw deprecate);

78
79
80
81
#2^20 = approx 10^6
my $CHUNKFACTOR = 20; 

# max size of the pair cache in the mappers
82
my $DEFAULT_MAX_PAIR_COUNT = 6000;
83
84
85
86
87
88
89
90
91
92
93
94

=head2 new

  Arg [1]    : Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor
  Arg [2]    : Bio::EnsEMBL::CoordSystem $src_cs
  Arg [3]    : Bio::EnsEMBL::CoordSystem $int_cs
  Arg [4]    : Bio::EnsEMBL::CoordSystem $dst_cs
  Example    : Should use AssemblyMapperAdaptor->fetch_by_CoordSystems
  Description: Creates a new AssemblyMapper
  Returntype : Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor
  Exceptions : thrown if wrong number of coord_systems are provided
  Caller     : AssemblyMapperAdaptor
95
  Status     : Stable
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113

=cut

sub new {
  my ($caller,$adaptor,@coord_systems) = @_;

  my $class = ref($caller) || $caller;

  my $self = {};
  bless $self, $class;

  $self->adaptor($adaptor);

  if(@coord_systems != 3) {
    throw('ChainedMapper can only map between 3 coordinate systems. ' .
          scalar(@coord_systems) . ' were provided');
  }

114
  #$adaptor->cache_seq_ids_with_mult_assemblys();
115

116
117
118
119
120
121
122
123
124
125
126
127
128
  # Set the component, intermediate and assembled coordinate systems
  $self->{'first_cs'}   = $coord_systems[0];
  $self->{'mid_cs'}   = $coord_systems[1];
  $self->{'last_cs'}   = $coord_systems[2];

  #maps between first and intermediate coord systems
  $self->{'first_mid_mapper'} = Bio::EnsEMBL::Mapper->new($FIRST, $MIDDLE);

  #maps between last and intermediate
  $self->{'last_mid_mapper'} = Bio::EnsEMBL::Mapper->new($LAST, $MIDDLE);

  #mapper that is actually used and is loaded by the mappings generated
  #by the other two mappers
129
130
131
  $self->{'first_last_mapper'} = Bio::EnsEMBL::Mapper->new($FIRST, $LAST,
                                                           $coord_systems[0],
                                                           $coord_systems[2]);
132
133
134
135
136
137

  #need registries to keep track of what regions are registered in source
  #and destination coordinate systems
  $self->{'first_registry'} = Bio::EnsEMBL::Mapper::RangeRegistry->new();
  $self->{'last_registry'} = Bio::EnsEMBL::Mapper::RangeRegistry->new();

138
139
  $self->{'max_pair_count'} = $DEFAULT_MAX_PAIR_COUNT;

140
141
142
143
  return $self;
}


144
145
146
147
148
149
150
151
152
153
154
=head2 max_pair_count

  Arg [1]    : (optional) int $max_pair_count
  Example    : $mapper->max_pair_count(100000)
  Description: Getter/Setter for the number of mapping pairs allowed in the
               internal cache. This can be used to override the default value
               (6000) to tune the performance and memory usage for certain
               scenarios. Higher value = bigger cache, more memory used
  Returntype : int
  Exceptions : none
  Caller     : general
155
  Status     : Stable
156
157
158
159
160
161
162
163
164
165
166

=cut

sub max_pair_count {
  my $self = shift;
  $self->{'max_pair_count'} = shift if(@_);
  return $self->{'max_pair_count'};
}



Graham McVicker's avatar
Graham McVicker committed
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182

=head2 register_all

  Arg [1]    : none
  Example    : $mapper->max_pair_count(10e6);
               $mapper->register_all();
  Description: Pre-registers all assembly information in this mapper.  The
               cache size should be set to a sufficiently large value
               so that all of the information can be stored.  This method
               is useful when *a lot* of mapping will be done in regions
               which are distributed around the genome.   After registration
               the mapper will consume a lot of memory but will not have to 
               perform any SQL and will be faster.
  Returntype : none
  Exceptions : none
  Caller     : specialised programs doing a lot of mapping
183
  Status     : Stable
Graham McVicker's avatar
Graham McVicker committed
184
185
186
187
188
189
190
191
192
193
194
195

=cut

sub register_all {
  my $self = shift;
  $self->adaptor->register_all_chained($self);
  return;
}




196
197
198
199
200
201
202
203
204
205
sub flush {
  my $self = shift;
  $self->{'first_registry'}->flush();
  $self->{'last_registry'}->flush();

  $self->{'first_mid_mapper'}->flush();
  $self->{'last_mid_mapper'}->flush();
  $self->{'first_last_mapper'}->flush();
}

206
207
208
209
210
211
212
213
214
215
216
217
=head2 size

  Args       : none
  Example    : $num_of_pairs = $mapper->size();
  Description: return the number of pairs currently stored.
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut 

218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
sub size {
  my $self = shift;
  return ( $self->{'first_last_mapper'}->{'pair_count'} +
           $self->{'last_mid_mapper'}->{'pair_count'} +
           $self->{'first_mid_mapper'}->{'pair_count'} );
}



=head2 map

  Arg [1]    : string $frm_seq_region
               The name of the sequence region to transform FROM
  Arg [2]    : int $frm_start
               The start of the region to transform FROM
  Arg [3]    : int $frm_end
               The end of the region to transform FROM
  Arg [4]    : int $strand
               The strand of the region to transform FROM
  Arg [5]    : Bio::EnsEMBL::CoordSystem
               The coordinate system to transform FROM
  Example    : @coords = $asm_mapper->map('X', 1_000_000, 2_000_000,
                                            1, $chr_cs);
  Description: Transforms coordinates from one coordinate system
               to another.
  Returntype : List of Bio::EnsEMBL::Mapper::Coordinate and/or
               Bio::EnsEMBL::Mapper:Gap objects
  Exceptions : thrown if the specified TO coordinat system is not one
               of the coordinate systems associated with this assembly mapper
  Caller     : general
248
  Status     : Stable
249
250
251
252
253
254

=cut

sub map {
  throw('Incorrect number of arguments.') if(@_ < 6);

255
  my ($self, $frm_seq_region_name, $frm_start,
256
257
258
259
260
261
      $frm_end, $frm_strand, $frm_cs, $fastmap) = @_;

  my $mapper  = $self->{'first_last_mapper'};
  my $first_cs  = $self->{'first_cs'};
  my $last_cs  = $self->{'last_cs'};

262
263
  my $is_insert = ($frm_end + 1 == $frm_start);

264
265
266
  my $frm;
  my $registry;

267
268
269
270
  my @tmp;
  push @tmp, $frm_seq_region_name;
  my $seq_region_id = @{$self->adaptor()->seq_regions_to_ids($frm_cs, \@tmp)}[0];

271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
  #speed critical section:
  #try to do simple pointer equality comparisons of the coord system objects
  #first since this is likely to work most of the time and is much faster
  #than a function call

  if($frm_cs == $first_cs ||
     ($frm_cs != $last_cs && $frm_cs->equals($first_cs))) {
    $frm = $FIRST;
    $registry = $self->{'first_registry'};
  } elsif($frm_cs == $last_cs || $frm_cs->equals($last_cs)) {
    $frm = $LAST;
    $registry = $self->{'last_registry'};
  } else {
    throw("Coordinate system " . $frm_cs->name . " " . $frm_cs->version .
          " is neither the first nor the last coordinate system " .
          " of this ChainedAssemblyMapper");
  }

  #the minimum area we want to register if registration is necessary is
  #about 1MB. Break requested ranges into chunks of 1MB and then register
  #this larger region if we have a registry miss.

  #use bitwise shift for fast and easy integer multiplication and division
  my ($min_start, $min_end);

296
297
298
299
300
301
302
  if($is_insert) {
    $min_start = (($frm_end >> $CHUNKFACTOR) << $CHUNKFACTOR);
    $min_end   = ((($frm_start >> $CHUNKFACTOR) + 1) << $CHUNKFACTOR) - 1 ;
  } else {
    $min_start = (($frm_start >> $CHUNKFACTOR) << $CHUNKFACTOR);
    $min_end   = ((($frm_end >> $CHUNKFACTOR) + 1) << $CHUNKFACTOR) - 1 ;
  }
303
304
305
306

  #get a list of ranges in the requested region that have not been registered,
  #and register them at the same

307
308
309
  my $ranges;

  if($is_insert) {
310
    $ranges = $registry->check_and_register($seq_region_id, $frm_end,
311
312
                                            $frm_start, $min_start, $min_end);
  } else {
313
    $ranges = $registry->check_and_register($seq_region_id, $frm_start,
314
315
                                            $frm_end, $min_start, $min_end);
  }
316
317

  if(defined($ranges)) {
318
    if( $self->size() > $self->{'max_pair_count'} ) {
319
      $self->flush();
320
321
322

      if($is_insert) {
        $ranges = $registry->check_and_register
323
          ($seq_region_id, $frm_end, $frm_start, $min_start, $min_end);
324
325
      } else {
        $ranges = $registry->check_and_register
326
          ($seq_region_id, $frm_start, $frm_end, $min_start, $min_end);
327
      }
328
    }
329
    $self->adaptor->register_chained($self,$frm,$seq_region_id,$ranges);
330
331
332
  }

  if($fastmap) {
333
    return $mapper->fastmap($seq_region_id, $frm_start, $frm_end,
334
                            $frm_strand, $frm);
335
336
  }

337
  return $mapper->map_coordinates($seq_region_id, $frm_start, $frm_end,
338
339
340
341
342
343
                                  $frm_strand, $frm);
}


sub fastmap {
  my $self = shift;
344
  return $self->map(@_,1);
345
346
347
}


348
=head2 list_ids
349
350
351
352
353
354
355
356
357

  Arg [1]    : string $frm_seq_region
               The name of the sequence region of interest
  Arg [2]    : int $frm_start
               The start of the region of interest
  Arg [3]    : int $frm_end
               The end of the region to transform of interest
  Arg [5]    : Bio::EnsEMBL::CoordSystem $frm_cs
               The coordinate system to obtain overlapping ids of
358
  Example    : foreach $id ($asm_mapper->list_ids('X',1,1000,$chr_cs)) {...}
359
  Description: Retrieves a list of overlapping seq_region internal identifiers
360
361
362
363
               of another coordinate system.  This is the same as the
               list_seq_regions method but uses internal identfiers rather 
               than seq_region strings
  Returntype : List of ints
364
365
  Exceptions : none
  Caller     : general
366
  Status     : Stable
367
368
369
370

=cut


371
sub list_ids {
372
  throw('Incorrect number of arguments.') if(@_ != 5);
373
  my($self, $frm_seq_region_name, $frm_start, $frm_end, $frm_cs) = @_;
374

375
376
  my $is_insert = ($frm_start == $frm_end + 1);

377
378
379
380
381
  #the minimum area we want to register if registration is necessary is
  #about 1MB. Break requested ranges into chunks of 1MB and then register
  #this larger region if we have a registry miss.

  #use bitwise shift for fast and easy integer multiplication and division
382
  my ($min_start, $min_end);
383

384
385
386
387
388
389
390
  if($is_insert) {
    $min_start = (($frm_end >> $CHUNKFACTOR) << $CHUNKFACTOR);
    $min_end   = ((($frm_start >> $CHUNKFACTOR) + 1) << $CHUNKFACTOR) - 1;
  } else {
    $min_start = (($frm_start >> $CHUNKFACTOR) << $CHUNKFACTOR);
    $min_end   = ((($frm_end >> $CHUNKFACTOR) + 1) << $CHUNKFACTOR) - 1;
  }
391

392
393
394
395
  my @tmp;
  push @tmp, $frm_seq_region_name;
  my $seq_region_id = @{$self->adaptor()->seq_regions_to_ids($frm_cs, \@tmp)}[0];

396
397
  if($frm_cs->equals($self->{'first_cs'})) {
    my $registry = $self->{'first_registry'};
398
399
400

    my $ranges;

401

402
403
    if($is_insert) {
      $ranges = $registry->check_and_register
404
        ($seq_region_id, $frm_end, $frm_start, $min_start, $min_end);
405
406
    } else {
      $ranges = $registry->check_and_register
407
        ($seq_region_id, $frm_start, $frm_end, $min_start, $min_end);
408
    }
409
410

    if(defined($ranges)) {
411
      $self->adaptor->register_chained($self,$FIRST,$seq_region_id,$ranges);
412
413
414
    }

    return map {$_->to()->id()}
415
      $self->first_last_mapper()->list_pairs($seq_region_id, $frm_start,
416
417
418
419
				  $frm_end, $FIRST);

  } elsif($frm_cs->equals($self->{'last_cs'})) {
    my $registry = $self->{'last_registry'};
420
421
422
423

    my $ranges;
    if($is_insert) {
      $ranges = $registry->check_and_register
424
        ($seq_region_id, $frm_end, $frm_start, $min_start, $min_end);
425
426
    } else {
      $ranges = $registry->check_and_register
427
        ($seq_region_id, $frm_start, $frm_end, $min_start, $min_end);
428
    }
429
430

    if(defined($ranges)) {
431
      $self->adaptor->register_chained($self,$LAST,$seq_region_id,$ranges);
432
433
434
    }

    return map {$_->from()->id()}
435
      $self->first_last_mapper()->list_pairs($seq_region_id, $frm_start,
436
437
438
439
440
441
442
443
444
				  $frm_end, $LAST);
  } else {
    throw("Coordinate system " . $frm_cs->name . " " . $frm_cs->version .
          " is neither the first nor the last coordinate system " .
          " of this ChainedAssemblyMapper");
  }
}


445
=head2 list_seq_regions
446
447
448
449
450
451
452
453
454

  Arg [1]    : string $frm_seq_region
               The name of the sequence region of interest
  Arg [2]    : int $frm_start
               The start of the region of interest
  Arg [3]    : int $frm_end
               The end of the region to transform of interest
  Arg [5]    : Bio::EnsEMBL::CoordSystem $frm_cs
               The coordinate system to obtain overlapping ids of
455
  Example    : foreach $id ($asm_mapper->list_ids('X',1,1000,$ctg_cs)) {...}
456
  Description: Retrieves a list of overlapping seq_region internal identifiers
457
458
459
               of another coordinate system.  This is the same as the 
               list_ids method but uses seq_region names rather internal ids
  Returntype : List of strings
460
461
  Exceptions : none
  Caller     : general
462
  Status     : Stable
463
464
465

=cut

466
sub list_seq_regions {
467
468
469
470
471
  throw('Incorrect number of arguments.') if(@_ != 5);
  my($self, $frm_seq_region, $frm_start, $frm_end, $frm_cs) = @_;

  #retrieve the seq_region names
  my @seq_regs =
472
    $self->list_ids($frm_seq_region,$frm_start,$frm_end,$frm_cs);
473
474
475
476
477
478
479
480
481
482

  #The seq_regions are from the 'to' coordinate system not the
  #from coordinate system we used to obtain them
  my $to_cs;
  if($frm_cs->equals($self->first_CoordSystem())) {
    $to_cs = $self->last_CoordSystem();
  } else {
    $to_cs = $self->first_CoordSystem();
  }

483
484
  #convert them to names
  return @{$self->adaptor()->seq_ids_to_regions(\@seq_regs)};
485
486
487
488
489
490
491
}






492
493
494
495
496
497
498
499
500
501
502
503
=head2 first_last_mapper

  Args       : none
  Example    : $mapper = $cam->first_last_mapper();
  Description: return the mapper.
  Returntype : Bio::EnsEMBL::Mapper
  Exceptions : none
  Caller     : internal
  Status     : Stable

=cut 

504
505
506
507
508
sub first_last_mapper {
  my $self = shift;
  return $self->{'first_last_mapper'};
}

509
510
511
512
513
514
515
516
517
518
519
520
521
=head2 first_middle_mapper

  Args       : none
  Example    : $mapper = $cam->first_middle_mapper();
  Description: return the mapper.
  Returntype : Bio::EnsEMBL::Mapper
  Exceptions : none
  Caller     : internal
  Status     : Stable

=cut 

 
522
523
524
525
526
sub first_middle_mapper {
  my $self = shift;
  return $self->{'first_mid_mapper'};
}

527
528
529
530
531
532
533
534
535
536
537
538
=head2 last_middle_mapper

  Args       : none
  Example    : $mapper = $cam->last_middle_mapper();
  Description: return the mapper.
  Returntype : Bio::EnsEMBL::Mapper
  Exceptions : none
  Caller     : internal
  Status     : Stable

=cut 

539
540
541
542
543
544
sub last_middle_mapper {
  my $self = shift;
  return $self->{'last_mid_mapper'};
}


545
546
547
548
549
550
551
552
553
554
555
556
=head2 first_CoordSystem

  Args       : none
  Example    : $coordsys = $cam->first_CoordSystem();
  Description: return the CoordSystem.
  Returntype : Bio::EnsEMBL::CoordSystem
  Exceptions : none
  Caller     : internal
  Status     : Stable

=cut 

557
558
559
560
561
562
sub first_CoordSystem {
  my $self = shift;
  return $self->{'first_cs'};
}


563
564
565
566
567
568
569
570
571
572
573
574
=head2 middle_CoordSystem

  Args       : none
  Example    : $coordsys = $cam->middle_CoordSystem();
  Description: return the CoordSystem.
  Returntype : Bio::EnsEMBL::CoordSystem
  Exceptions : none
  Caller     : internal
  Status     : Stable

=cut 

575
576
577
578
579
sub middle_CoordSystem {
  my $self = shift;
  return $self->{'mid_cs'};
}

580
581
582
583
584
585
586
587
588
589
590
591
=head2 last_CoordSystem

  Args       : none
  Example    : $coordsys = $cam->last_CoordSystem();
  Description: return the CoordSystem.
  Returntype : Bio::EnsEMBL::CoordSystem
  Exceptions : none
  Caller     : internal
  Status     : Stable

=cut 

592
593
594
595
596
sub last_CoordSystem {
  my $self = shift;
  return $self->{'last_cs'};
}

597
598
599
600
601
602
603
604
605
606
607
608
=head2 first_registry

  Args       : none
  Example    : $coordsys = $cam->first_registry();
  Description: return the Registry.
  Returntype : Bio::EnsEMBL::Mapper::RangeRegistry
  Exceptions : none
  Caller     : internal
  Status     : Stable

=cut 
 
609
610
611
612
613
sub first_registry {
  my $self = shift;
  return $self->{'first_registry'};
}

614
615
616
617
618
619
620
621
622
623
624
625
=head2 lsst_registry

  Args       : none
  Example    : $coordsys = $cam->lsst_registry();
  Description: return the Registry.
  Returntype : Bio::EnsEMBL::Mapper::RangeRegistry
  Exceptions : none
  Caller     : internal
  Status     : Stable

=cut 

626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
sub last_registry {
  my $self = shift;
  return $self->{'last_registry'};
}





#
# Methods supplied to maintain polymorphism with AssemblyMapper
# there is no real assembled or component in the chained mapper, since the
# ordering is arbitrary and both ends might actually be assembled, but these
# methods provide convenient synonyms
#
641
642
643
644
645
646
647
648
649
650
651
652
653

=head2 mapper

  Args       : none
  Example    : $mapper = $cam->mapper();
  Description: return the first_last_mapper.
  Returntype : Bio::EnsEMBL::Mapper
  Exceptions : none
  Caller     : internal
  Status     : Stable

=cut 

654
655
656
657
sub mapper {
  my $self = shift;
  return $self->first_last_mapper();
}
658
659
660
661
662
663
664
665
666
667
668
669
670
671

=head2 assembled_CoordSystem

  Args       : none
  Example    : $coordsys = $cam->assembled_CoordSystem();
  Description: return the first CoordSystem.
  Returntype : Bio::EnsEMBL::CoordSystem
  Exceptions : none
  Caller     : internal
  Status     : Stable

=cut 


672
673
674
675
sub assembled_CoordSystem {
  my $self = shift;
  return $self->{'first_cs'};
}
676
677
678
679
680
681
682
683
684
685
686
687
688

=head2 component_CoordSystem

  Args       : none
  Example    : $coordsys = $cam->component_CoordSystem();
  Description: return the last CoordSystem.
  Returntype : Bio::EnsEMBL::CoordSystem
  Exceptions : none
  Caller     : internal
  Status     : Stable

=cut 

689
690
691
692
693
694
695
696
697
698
699
700
701
702
sub component_CoordSystem {
  my $self = shift;
  return $self->{'last_cs'};
}


=head2 adaptor

  Arg [1]    : Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor $adaptor
  Example    : none
  Description: get/set for this objects database adaptor
  Returntype : Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor
  Exceptions : none
  Caller     : general
703
  Status     : Stable
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
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
800
801
802
803
804
805
806

=cut

sub adaptor {
  my $self = shift;
  $self->{'adaptor'} = shift if(@_);
  return $self->{'adaptor'};
}


=head2 in_assembly

  Description: Deprecated. Use map() or list_ids() instead

=cut

sub in_assembly {
  my ($self, $object) = @_;

  deprecate('Use map() or list_ids() instead.');

  my $csa = $self->db->get_CoordSystemAdaptor();

  my $top_level = $csa->fetch_top_level();

  my $asma = $self->adaptor->fetch_by_CoordSystems($object->coord_system(),
                                                   $top_level);

  my @list = $asma->list_ids($object->seq_region(), $object->start(),
                             $object->end(), $object->coord_system());

  return (@list > 0);
}


=head2 map_coordinates_to_assembly

  Description: DEPRECATED use map() instead

=cut

sub map_coordinates_to_assembly {
  my ($self, $contig_id, $start, $end, $strand) = @_;

  deprecate('Use map() instead.');

  #not sure if contig_id is seq_region_id or name...
  return $self->map($contig_id, $start, $end, $strand,
                   $self->contig_CoordSystem());

}


=head2 fast_to_assembly

  Description: DEPRECATED use map() instead

=cut

sub fast_to_assembly {
  my ($self, $contig_id, $start, $end, $strand) = @_;

  deprecate('Use map() instead.');

  #not sure if contig_id is seq_region_id or name...
  return $self->map($contig_id, $start, $end, $strand,
                    $self->contig_CoordSystem());
}


=head2 map_coordinates_to_rawcontig

  Description: DEPRECATED use map() instead

=cut

sub map_coordinates_to_rawcontig {
  my ($self, $chr_name, $start, $end, $strand) = @_;

  deprecate('Use map() instead.');

  return $self->map($chr_name, $start, $end, $strand,
                    $self->assembled_CoordSystem());

}

=head2 list_contig_ids
  Description: DEPRECATED Use list_ids instead

=cut

sub list_contig_ids {
  my ($self, $chr_name, $start, $end) = @_;

  deprecate('Use list_ids() instead.');

  return $self->list_ids($chr_name, $start, $end, 
                         $self->assembled_CoordSystem());
}



1;