Registry.pm 45.9 KB
Newer Older
Ian Longden's avatar
Ian Longden committed
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
#
# Ensembl module for Registry
#
# Copyright EMBL/EBI
##
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code

=head1 NAME

Bio::EnsEMBL::Registry

=head1 SYNOPSIS

16
17
Bio::EnsEMBL::Registry->load_all("configuration_file");

18
19
$gene_adaptor =
  Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "gene" );
Ian Longden's avatar
Ian Longden committed
20
21
22
23


=head1 DESCRIPTION

24
25
All Adaptors are stored/registered using this module. This module should
then be used to get the adaptors needed.
Ian Longden's avatar
Ian Longden committed
26

27
28
The registry can be loaded from a configuration file using the load_all
method.
Ian Longden's avatar
Ian Longden committed
29

30
31
32
33
If a filename is passed to load_all then this is used.  Else if the
enviroment variable ENSEMBL_REGISTRY is set to the name on an existing
configuration file, then this is used.  Else if the file .ensembl_init
in your home directory exist, it is used.
Ian Longden's avatar
Ian Longden committed
34

35
36
For the Web server ENSEMBL_REGISTRY should be set in SiteDefs.pm.  This
will then be passed on to load_all.
37
38


39
40
41
42
43
The registry can also be loaded via the method load_registry_from_db
which given a database host will load the latest versions of the Ensembl
databases from it.

The four types of registries are for db adaptors, dba adaptors, dna adaptors
Ian Longden's avatar
Ian Longden committed
44
45
46
47
and the standard type.

=head2 db

48
These are registries for backwards compatibility and enable the subroutines
49
to add other adaptors to connections. 
Ian Longden's avatar
Ian Longden committed
50
51
52
53
54

e.g. get_all_db_adaptors, get_db_adaptor, add_db_adaptor, remove_db_adaptor
are the old DBAdaptor subroutines which are now redirected to the Registry.

So if before we had
55
56

    my $sfa = $self->adaptor()->db()->get_db_adaptor('blast');
Ian Longden's avatar
Ian Longden committed
57
58

We now want to change this to
59
60
61

    my $sfa =
      Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "blast" );
Ian Longden's avatar
Ian Longden committed
62
63
64
65
66
67
68
69
70


=head2 DBA

These are the stores for the DBAdaptors

The Registry will create all the DBConnections needed now if you set up the
configuration correctly. So instead of the old commands like

71
72
    my $db           = Bio::EnsEMBL::DBSQL::DBAdaptor->new(...);
    my $exon_adaptor = $db->get_ExonAdaptor;
Ian Longden's avatar
Ian Longden committed
73
74
75

we should now have just

76
77
    my $exon_adaptor =
      Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "exon" );
Ian Longden's avatar
Ian Longden committed
78
79
80
81
82


=head2 DNA

This is an internal Registry and allows the configuration of a dnadb. 
Steve Trevanion's avatar
Steve Trevanion committed
83
An example here is to set the est database to get its dna data from the core database.
Ian Longden's avatar
Ian Longden committed
84

85
86
87
    ## set the est db to use the core for getting dna data.
    # Bio::EnsEMBL::Utils::ConfigRegistry->dnadb_add(
    #         "Homo Sapiens", "core", "Homo Sapiens", "est" );
Ian Longden's avatar
Ian Longden committed
88
89
90
91
92
93
94
95
96


=head2 adaptors

This is the registry for all the general types of adaptors like GeneAdaptor, ExonAdaptor, 
Slice Adaptor etc.

These are accessed by the get_adaptor subroutine i.e.

97
98
    my $exon_adaptor =
      Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "exon" );
Ian Longden's avatar
Ian Longden committed
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113

=head1 CONTACT

Post questions to the Ensembl developer list: <ensembl-dev@ebi.ac.uk>


=head1 METHODS

=cut


package Bio::EnsEMBL::Registry;

use strict;

114
use Bio::EnsEMBL::DBSQL::DBAdaptor;
Ian Longden's avatar
Ian Longden committed
115
116
use Bio::EnsEMBL::Utils::Exception qw( deprecate throw warning );
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
117
use Bio::EnsEMBL::Utils::ConfigRegistry;
118
use DBI;
Ian Longden's avatar
Ian Longden committed
119

120
121
use Config::IniFiles;

Ian Longden's avatar
Ian Longden committed
122
123
use vars qw(%registry_register);

Glenn Proctor's avatar
Glenn Proctor committed
124
my $API_VERSION = 46;
125

Ian Longden's avatar
Ian Longden committed
126
127

=head2 load_all
128

129
130
131
132
133
134
135
136
 Will load the registry with the configuration file which is obtained
 from the first in the following and in that order.

  1) If an argument is passed to this method, this is used as the name
     of the configuration file to read.

  2) If the enviroment variable ENSEMBL_REGISTRY is set, this is used as
     the name of the configuration file to read.
Ian Longden's avatar
Ian Longden committed
137

138
139
  3) If the file .ensembl_init exist in the home directory, it is used
     as the configuration file.
Ian Longden's avatar
Ian Longden committed
140

141
142
143
144
145
146
147
148
  Arg [1]    : (optional) string
               Name of file to load the registry from.
  Arg [2]    : (optional) integer
               If not 0, will print out all information.
  Arg [3]    : (optional) integer
               If not 0, the db connection will not be cleared, if 0 or
               if not set the db connections will be cleared (this is
               the default).
Ian Longden's avatar
Ian Longden committed
149
150
151
  Example    : Bio::EnsEMBL::Registry->load_all();
  Returntype : none
  Exceptions : none
152
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
153
154

=cut
155

156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
sub load_all {
    my $class = shift;
    my ( $config_file, $verbose, $no_clear ) = @_;

    $config_file ||= $ENV{ENSEMBL_REGISTRY}
      || $ENV{HOME} . "/.ensembl_init";

    $verbose  ||= 0;
    $no_clear ||= 0;

    if ( !defined($config_file) ) {
        if ($verbose) {
            print( STDERR
                   "No default registry configuration to load.\n" );
        }
    } elsif ( !-e $config_file ) {
        if ($verbose) {
            printf( STDERR "Configuration file '%s' does not exist. "
                      . "Registry configuration not loaded.\n",
                    $config_file );
        }
    } else {
        if ( defined( $registry_register{'seen'} ) ) {
            if ( !$no_clear ) {
                if ($verbose) {
                    print( STDERR "Clearing previously loaded "
                           . "registry configuration\n" );
                }
                $class->clear();
            }
        }
        $registry_register{'seen'} = 1;

        if ($verbose) {
            printf( STDERR
                      "Loading registry configuration from '%s'.\n",
                    $config_file );
        }

195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
        my $cfg = Config::IniFiles->new( -file => $config_file );
        if ( defined $cfg ) {

            # This is a map from group names to Ensembl DB adaptors.
            my %group2adaptor = (
                 'blast'   => 'Bio::EnsEMBL::External::BlastAdaptor',
                 'compara' => 'Bio::EnsEMBL::Compara::DBSQL::DBAdaptor',
                 'core'    => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
                 'estgene' => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
                 'funcgen' => 'Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor',
                 'haplotype' =>
                   'Bio::EnsEMBL::ExternalData::Haplotype::DBAdaptor',
                 'hive' => 'Bio::EnsEMBL::Hive::DBSQL::DBAdaptor',
                 'lite' => 'Bio::EnsEMBL::Lite::DBAdaptor',
                 'otherfeatures' => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
                 'pipeline' =>
                   'Bio::EnsEMBL::Pipeline::DBSQL::DBAdaptor',
                 'snp' =>
                   'Bio::EnsEMBL::ExternalData::SNPSQL::DBAdaptor',
                 'variation' =>
                   'Bio::EnsEMBL::Variation::DBSQL::DBAdaptor',
                 'vega' => 'Bio::EnsEMBL::DBSQL::DBAdaptor' );

            my %default_adaptor_args = ();

            if ( $cfg->SectionExists('default') ) {
                # The 'default' section is special.  It contain default
                # values that should be implicit to all other section in
223
224
225
226
227
228
229
230
231
232
233
234
235
                # this configuration file.  Aliases are added if there
                # is also a 'species' setting.

                my $alias = $cfg->val( 'default', 'alias' );
                $cfg->delval( 'default', 'alias' );

                my $species = $cfg->val( 'default', 'species' );

                if ( defined($alias) && defined($species) ) {
                    Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
                                     -species => $species,
                                     -alias => [ split( /\n/, $alias ) ]
                    );
236
                }
237

238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
                %default_adaptor_args =
                  map { '-' . $_ => $cfg->val( 'default', $_ ) }
                  $cfg->Parameters('default');
            }

            foreach my $section ( $cfg->Sections() ) {
                if ( $section eq 'default' )
                {    # We have already done the 'default' section.
                    next;
                }

                my $group = $cfg->val( $section, 'group' )
                  || $cfg->val( 'default', 'group' );

                if ( !defined($group) ) {
                    printf( STDERR "Key 'group' is undefined "
                              . "for configuration section '%s', "
                              . "skipping this section.\n",
                            $section );
                    next;
                }

                my $adaptor = $group2adaptor{ lc($group) };
                if ( !defined($adaptor) ) {
                    printf( STDERR "Unknown group '%s' "
                              . "for configuration section '%s', "
                              . "skipping this section.\n",
                            $group, $section );
                    next;
                }

269
270
271
272
273
                # Handle aliases.  A section must have both an 'alias'
                # setting and a 'species' setting for aliases to be
                # added.  The 'species' setting might be inherited from
                # the 'default' section.

274
275
276
                my $alias = $cfg->val( $section, 'alias' );
                $cfg->delval( $section, 'alias' );

277
278
279
280
281
282
283
284
285
286
287
                my $species = $cfg->val( $section, 'species' )
                  || $cfg->val( 'default', 'species' );

                if ( defined($alias) && defined($species) ) {
                    Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
                                     -species => $species,
                                     -alias => [ split( /\n/, $alias ) ]
                    );
                }

                # Fill in the adaptor initialization arguments.
288
289
290
291
292
293
294
295
296
297
298
299
300
                # We trust the user to provide sensible key-value pairs.
                my %adaptor_args = %default_adaptor_args;
                foreach my $parameter ( $cfg->Parameters($section) ) {
                    $adaptor_args{ '-' . $parameter } =
                      $cfg->val( $section, $parameter );
                }

                if ($verbose) {
                    printf( "Configuring adaptor '%s' "
                              . "for configuration section '%s'...\n",
                            $adaptor, $section );
                }

301
302
303
                eval "require $adaptor";
                if ($@) { die($@) }

304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
                $adaptor->new(%adaptor_args);

            } ## end foreach my $section ( $cfg->Sections...
        } else {
            # This is probably no ini-file but an old style piece
            # of configuration written in Perl.  We need to try to
            # require() it.

            eval { require($config_file) };
            if ($@) { die($@) }

            # To make the web code avoid doing this again:
            delete $INC{$config_file};
        }
    } ## end else [ if ( !defined($config_file...
319
} ## end sub load_all
320
321

=head2 clear
322

323
324
325
326
327
 Will clear the registry and disconnect from all databases.

  Example    : Bio::EnsEMBL::Registry->clear();
  Returntype : none
  Exceptions : none
328
  Status     : Stable
329
330
331
332
333
334
335
336
337
338
339

=cut

sub clear{
  my ($self);
  
  foreach my $dba (@{$registry_register{'_DBA'}}){
    if($dba->dbc->connected){
      $dba->dbc->db_handle->disconnect();
    }
  }
Ian Longden's avatar
Ian Longden committed
340
  %registry_register = ();
Ian Longden's avatar
Ian Longden committed
341
342
343
}

#
344
# db adaptors. (for backwards compatibility)
Ian Longden's avatar
Ian Longden committed
345
346
347
348
#

=head2 add_db

349
  Arg [1]    : db (DBAdaptor) to add adaptor to.
Ian Longden's avatar
Ian Longden committed
350
351
352
353
354
  Arg [2]    : name of the name to add the adaptor to in the registry.
  Arg [3]    : The adaptor to be added to the registry.
  Example    : Bio::EnsEMBL::Registry->add_db($db, "lite", $dba);
  Returntype : none
  Exceptions : none
355
  Status     : At Risk.
356
             : This is here for backwards compatibility only and may be removed 
357
358
359
             : eventually. Solution is to make sure the db and the adaptor have
             : the same species and the call is then no longer needed.
             
Ian Longden's avatar
Ian Longden committed
360
361
362
363
364
365
=cut

sub add_db{
  my ($class, $db, $name, $adap) = @_;


366
367
  if(lc($db->species()) ne lc($adap->species)){
    $registry_register{lc($db->species())}{lc($db->group())}{'_special'}{lc($name)} = $adap;
368
  }
Ian Longden's avatar
Ian Longden committed
369
370
371
372
}

=head2 remove_db

373
  Arg [1]    : db (DBAdaptor) to remove adaptor from.
Ian Longden's avatar
Ian Longden committed
374
375
376
377
  Arg [2]    : name to remove the adaptor from in the registry.
  Example    : my $db = Bio::EnsEMBL::Registry->remove_db($db, "lite");
  Returntype : adaptor
  Exceptions : none
378
  Status     : At Risk.
379
             : This is here for backwards compatibility only and may be removed 
380
381
             : eventually. Solution is to make sure the db and the adaptor have
             : the same species and the call is then no longer needed.
Ian Longden's avatar
Ian Longden committed
382
383
384
385
386
387

=cut

sub remove_db{
  my ($class, $db, $name) = @_;

388
389
  my $ret = $registry_register{lc($db->species())}{lc($db->group())}{'_special'}{lc($name)};
  $registry_register{lc($db->species())}{lc($db->group())}{'_special'}{lc($name)} = undef;
Ian Longden's avatar
Ian Longden committed
390
391
392
393
394
395

  return $ret;
}

=head2 get_db

396
  Arg [1]    : db (DBAdaptor) to get adaptor from.
Ian Longden's avatar
Ian Longden committed
397
398
399
400
  Arg [2]    : name to get the adaptor for in the registry.
  Example    : my $db = Bio::EnsEMBL::Registry->get_db("Human", "core", "lite");
  Returntype : adaptor
  Exceptions : none
401
  Status     : At Risk.
402
             : This is here for backwards compatibility only and may be removed 
403
404
             : eventually. Solution is to make sure the db and the adaptor have
             : the same species then call get_DBAdaptor instead.
Ian Longden's avatar
Ian Longden committed
405
406
407
408
409
410

=cut

sub get_db{
  my ($class, $db, $name) = @_;

411
  my $ret = Bio::EnsEMBL::Registry->get_DBAdaptor(lc($db->species),lc($name));
412
413
414
415

  if(defined($ret)){
    return $ret;
  }
416
  return $registry_register{lc($db->species())}{lc($db->group())}{'_special'}{lc($name)};
Ian Longden's avatar
Ian Longden committed
417
418
419
420
}

=head2 get_all_db_adaptors

421
  Arg [1]    : db (DBAdaptor) to get all the adaptors from.
Ian Longden's avatar
Ian Longden committed
422
423
424
  Example    : my $db = Bio::EnsEMBL::Registry->get_all_db_adaptors($db);
  Returntype : adaptor
  Exceptions : none
425
  Status     : At Risk.
426
             : This is here for backwards compatibility only and may be removed 
427
428
429
             : eventually. Solution is to make sure the dbs all have
             : the same species then call get_all_DBAdaptors(-species => "human");

Ian Longden's avatar
Ian Longden committed
430
431
432
433
434
435
436

=cut

sub get_all_db_adaptors{
  my ($class,$db) = @_;
  my %ret=();

Ian Longden's avatar
Ian Longden committed
437
438
439
440
# we now also want to add all the DBAdaptors for the same species.
# as add_db_adaptor does not add if it is from the same species.

  foreach my $dba (@{$registry_register{'_DBA'}}){
441
    if(lc($dba->species()) eq lc($db->species())){
Ian Longden's avatar
Ian Longden committed
442
443
444
445
      $ret{$dba->group()} = $dba;
    } 
  }

446
 foreach my $key (keys %{$registry_register{$class->get_alias($db->species())}{lc($db->group())}{'_special'}}){
447
   $ret{$key} = $registry_register{$class->get_alias($db->species())}{lc($db->group())}{'_special'}{$key};
Ian Longden's avatar
Ian Longden committed
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
 }

  return \%ret;
}


#
# DBAdaptors
#

=head2 add_DBAdaptor

  Arg [1]    : name of the species to add the adaptor to in the registry.
  Arg [2]    : name of the group to add the adaptor to in the registry.
  Arg [3]    : The DBAaptor to be added to the registry.
  Example    : Bio::EnsEMBL::Registry->add_DBAdaptor("Human", "core", $dba);
  Returntype : none
  Exceptions : none
466
467
  caller     : internal
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
468
469
470
471
472
473

=cut

sub add_DBAdaptor{
  my ($class, $species, $group, $adap) = @_;

474
475
476
477
478
  if(!($class->alias_exists($species))){
    $class->add_alias($species,$species);
  }
  

Ian Longden's avatar
Ian Longden committed
479
480
  $species = $class->get_alias($species);

481
  $registry_register{$species}{lc($group)}{'_DB'} = $adap;
Ian Longden's avatar
Ian Longden committed
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502

  if(!defined($registry_register{'_DBA'})){
    my @list =();
    push(@list,$adap);
    $registry_register{'_DBA'}= \@list;
  }
  else{
    push(@{$registry_register{'_DBA'}},$adap);
  }

}



=head2 get_DBAdaptor

  Arg [1]    : name of the species to get the adaptor for in the registry.
  Arg [2]    : name of the group to get the adaptor for in the registry.
  Example    : $dba = Bio::EnsEMBL::Registry->get_DBAdaptor("Human", "core");
  Returntype : DBAdaptor
  Exceptions : none
503
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
504
505
506
507
508
509
510
511

=cut

sub get_DBAdaptor{
  my ($class, $species, $group) = @_;

  $species = $class->get_alias($species);

512
513
  return  $registry_register{$species}{lc($group)}{'_DB'};

Ian Longden's avatar
Ian Longden committed
514
515
516
517
}

=head2 get_all_DBAdaptors

518
519
520
521
522
523
524
525
  Arg [SPECIES]: (optional) string 
                  species name to get adaptors for
  Arg [GROUP]  : (optional) string 
                  group name to get adaptors for
  Example      : @dba = @{Bio::EnsEMBL::Registry->get_all_DBAdaptors()};
               : @human_dbas = @{Bio::EnsEMBL::Registry->get_all_DBAdaptors(-species => 'human')};
  Returntype   : list of DBAdaptors
  Exceptions   : none
526
  Status       : Stable
Ian Longden's avatar
Ian Longden committed
527
528
529
530

=cut

sub get_all_DBAdaptors{
531
532
  my ($class,@args)=@_;
  my @ret;
Ian Longden's avatar
Ian Longden committed
533

534
535
536
537
538
539
  my ($species, $group) = 
    rearrange([qw(SPECIES GROUP)], @args);
  if(defined($species)){
    $species = $class->get_alias($species);
  }
  foreach my $dba (@{$registry_register{'_DBA'}}){
540
    if(!defined($species) || lc($species) eq lc($dba->species)){
541
542
543
544
545
546
547
548
      if(!defined($group) || lc($group) eq lc($dba->group)){
	push @ret, $dba;
      }
    }
  }


  return \@ret;
Ian Longden's avatar
Ian Longden committed
549
550
}

551
552
553
554
555
556
=head2 get_all_DBAdaptors_by_connection

  Arg [1]    :dbconnection to use to find DBAdaptors
  Returntype : reference to list of DBAdaptors
  Exceptions : none.
  Example    : @dba = @{Bio::EnsEMBL::Registry->get_all_DBAdaptors_by_connection($dbc);
557
  Status     : Stable
558
559
560
561
562
563
564
565
566

=cut

sub get_all_DBAdaptors_by_connection{
  my ($self, $dbc_orig) = @_;
  my @return;

  foreach my $dba ( @{$registry_register{'_DBA'}}){
    my $dbc = $dba->dbc;
Web Admin's avatar
Web Admin committed
567
    if($dbc && $dbc->can('equals') && $dbc->equals($dbc_orig)){
568
569
570
571
572
573
574
      push @return, $dba;
    }
  }
  return \@return;
}


Ian Longden's avatar
Ian Longden committed
575
576
577
578
579
580
581
582
#
# DNA Adaptors
#

=head2 add_DNAAdaptor

  Arg [1]    : name of the species to add the adaptor to in the registry.
  Arg [2]    : name of the group to add the adaptor to in the registry.
583
584
585
  Arg [3]    : name of the species to get the dna from
  Arg [4]    : name of the group to get the dna from
  Example    : Bio::EnsEMBL::Registry->add_DNAAdaptor("Human", "estgene", "Human", "core");
Ian Longden's avatar
Ian Longden committed
586
587
  Returntype : none
  Exceptions : none
588
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
589
590
591
592

=cut

sub add_DNAAdaptor{
Ian Longden's avatar
Ian Longden committed
593
  my ($class, $species, $group, $dnadb_species, $dnadb_group) = @_;
Ian Longden's avatar
Ian Longden committed
594
595

  $species = $class->get_alias($species);
596
  $dnadb_species = $class->get_alias($dnadb_species);
597
  if($dnadb_group->isa('Bio::EnsEMBL::DBSQL::DBAdaptor')){
Ian Longden's avatar
Ian Longden committed
598
    deprecated("");
599
600
  }
  else{
601
602
    $registry_register{$species}{lc($group)}{'_DNA'} = $dnadb_group;
    $registry_register{$species}{lc($group)}{'_DNA2'} = $dnadb_species;
603
  }
Ian Longden's avatar
Ian Longden committed
604
605
606
607
608
609
610
611
612
}

=head2 get_DNAAdaptor

  Arg [1]    : name of the species to get the adaptor for in the registry.
  Arg [2]    : name of the group to get the adaptor for in the registry.
  Example    : $dnaAdap = Bio::EnsEMBL::Registry->get_DNAAdaptor("Human", "core");
  Returntype : adaptor
  Exceptions : none
613
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
614
615
616
617
618
619
620

=cut

sub get_DNAAdaptor{
  my ($class, $species, $group) = @_;

  $species = $class->get_alias($species);
621
622
  my $new_group = $registry_register{$species}{lc($group)}{'_DNA'};
  my $new_species = $registry_register{$species}{lc($group)}{'_DNA2'};
623
  if( defined $new_group ) {
Ian Longden's avatar
Ian Longden committed
624
    return  $class->get_DBAdaptor($new_species,$new_group);
625
626
627
  } else {
    return undef;
  }
Ian Longden's avatar
Ian Longden committed
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
}

#
# General Adaptors
#

=head2 add_adaptor

  Arg [1]    : name of the species to add the adaptor to in the registry.
  Arg [2]    : name of the group to add the adaptor to in the registry.
  Arg [3]    : name of the type to add the adaptor to in the registry.
  Arg [4]    : The DBAaptor to be added to the registry.
  Arg [5]    : (optional) if set okay to overwrite.
  Example    : Bio::EnsEMBL::Registry->add_adaptor("Human", "core", "Gene", $adap);
  Returntype : none
  Exceptions : none
644
645
  Caller     : internal
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662


=cut

sub add_adaptor{
  my ($class,$species,$group,$type,$adap, $reset)= @_;

  $species = $class->get_alias($species);

#
# Becouse the adaptors are not stored initially only there class paths when
# the adaptors are obtained we need to store these instead.
# It is not necessarily an error if the registry is overwritten without
# the reset set but it is an indication that we are overwriting a database
# which should be a warning for now
#

663
  if(defined($reset)){ # JUST REST THE HASH VALUE NO MORE PROCESSING NEEDED
664
    $registry_register{$species}{lc($group)}{lc($type)} = $adap;
Ian Longden's avatar
Ian Longden committed
665
666
    return;
  }
667
  if(defined($registry_register{$species}{lc($group)}{lc($type)})){ 
Glenn Proctor's avatar
Glenn Proctor committed
668
    #print STDERR ("Overwriting Adaptor in Registry for $species $group $type\n");
669
    $registry_register{$species}{lc($group)}{lc($type)} = $adap;
Ian Longden's avatar
Ian Longden committed
670
671
   return;
  }
672
  $registry_register{$species}{lc($group)}{lc($type)} = $adap;
Ian Longden's avatar
Ian Longden committed
673
674
675

  if(!defined ($registry_register{$species}{'list'})){
    my @list =();
676
    push(@list,$type);
Ian Longden's avatar
Ian Longden committed
677
678
679
    $registry_register{$species}{'list'}= \@list;
  }
  else{
680
    push(@{$registry_register{$species}{'list'}},$type);
Ian Longden's avatar
Ian Longden committed
681
682
  }

683

Ian Longden's avatar
Ian Longden committed
684

685
  if(!defined ($registry_register{lc($type)}{$species})){
Ian Longden's avatar
Ian Longden committed
686
687
    my @list =();
    push(@list,$adap);
688
    $registry_register{lc($type)}{$species}= \@list;
Ian Longden's avatar
Ian Longden committed
689
690
  }
  else{
691
    push(@{$registry_register{lc($type)}{$species}},$adap);
Ian Longden's avatar
Ian Longden committed
692
693
694
695
696
697
698
699
700
701
702
703
704
  }

}


=head2 get_adaptor

  Arg [1]    : name of the species to add the adaptor to in the registry.
  Arg [2]    : name of the group to add the adaptor to in the registry.
  Arg [3]    : name of the type to add the adaptor to in the registry.
  Example    : $adap = Bio::EnsEMBL::Registry->get_adaptor("Human", "core", "Gene");
  Returntype : adaptor
  Exceptions : none
705
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
706
707
708
709
710
711

=cut

sub get_adaptor{
  my ($class,$species,$group,$type)= @_;
 
712
  $species = $class->get_alias($species);
713
  my %dnadb_adaptors = qw(sequence  1 assemblymapper 1  karyotypeband 1 repeatfeature 1 coordsystem 1  assemblyexceptionfeature 1 );
714

715
  my $dnadb_group =  $registry_register{$species}{lc($group)}{_DNA};
716

717
718
  if( defined($dnadb_group) && defined($dnadb_adaptors{lc($type)}) ) {
      $species = $registry_register{$species}{lc($group)}{'_DNA2'};
719
      $group = $dnadb_group;
Ian Longden's avatar
Ian Longden committed
720
721
  }

722
  my $ret = $registry_register{$species}{lc($group)}{lc($type)};
Ian Longden's avatar
Ian Longden committed
723
  if(!defined($ret)){
724
    return undef;
Ian Longden's avatar
Ian Longden committed
725
726
  }
  if(!ref($ret)){ # not instantiated yet
727
    my $dba = $registry_register{$species}{lc($group)}{'_DB'};
Ian Longden's avatar
Ian Longden committed
728
729
730
731
732
733
734
    my $module = $ret;
    eval "require $module";

    if($@) {
      warning("$module cannot be found.\nException $@\n");
      return undef;
    }
735
736
737
738
    if(!defined($registry_register{$species}{lc($group)}{'CHECKED'})){
      $registry_register{$species}{lc($group)}{'CHECKED'} = 1;
      $class->version_check($dba);
    }
Ian Longden's avatar
Ian Longden committed
739
740
741
742
743
744
745
746
747
748
    my $adap = "$module"->new($dba);
    Bio::EnsEMBL::Registry->add_adaptor($species, $group, $type, $adap, "reset");
    $ret = $adap;
  }

  return $ret;
}

=head2 get_all_adaptors

749
750
751
752
753
754
  Arg [SPECIES] : (optional) string 
                  species name to get adaptors for
  Arg [GROUP] : (optional) string 
                  group name to get adaptors for
  Arg [TYPE] : (optional) string 
                  type to get adaptors for
Ian Longden's avatar
Ian Longden committed
755
  Example    : @adaps = @{Bio::EnsEMBL::Registry->get_all_adaptors()};
756
  Returntype : ref to list of adaptors
Ian Longden's avatar
Ian Longden committed
757
  Exceptions : none
758
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
759
760
761
762

=cut

sub get_all_adaptors{
763
764
765
766
  my ($class,@args)= @_;
  my ($species, $group, $type);
  my @ret=();
  my (%species_hash, %group_hash, %type_hash);
Ian Longden's avatar
Ian Longden committed
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

  if(@args == 1){ #old species only one parameter
    warn("-SPECIES argument should now be used to get species adaptors");
    $species = $args[0];
  }
  else{
    # new style -SPECIES, -GROUP, -TYPE
    ($species, $group, $type) =
      rearrange([qw(SPECIES GROUP TYPE)], @args);
  }

  if(defined($species)){
    $species_hash{$species} = 1;
  }
  else{
    # get list of species
    foreach my $dba (@{$registry_register{'_DBA'}}){
      $species_hash{lc($dba->species())} = 1;
    }
  }
  if(defined($group)){
    $group_hash{$group} = 1;
  }
  else{
    foreach my $dba (@{$registry_register{'_DBA'}}){
      $group_hash{lc($dba->group())} = 1;
    }
  }
  if(defined($type)){
    $type_hash{$type} =1;
  }
  else{
    foreach my $dba (@{$registry_register{'_DBA'}}){ 
801
	foreach my $ty (@{$registry_register{lc($dba->species)}{'list'}}){
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
	  $type_hash{lc($ty)} = 1;
	}
      }
  }
  
  ### NOW NEED TO INSTANTIATE BY CALLING get_adaptor
  foreach my $sp (keys %species_hash){
    foreach my $gr (keys %group_hash){
      foreach my $ty (keys %type_hash){
	my $temp = $class->get_adaptor($sp,$gr,$ty);
	if(defined($temp)){
	  push @ret, $temp;
	}
      }
    }
  }
  return (\@ret);
Ian Longden's avatar
Ian Longden committed
819
820
821
822
823
824
825
826
827
828
829
}


=head2 add_alias

  Arg [1]    : name of the species to add alias for
  Arg [2]    : name of the alias
  Example    : Bio::EnsEMBL::Registry->add_alias("Homo Sapiens","Human");
  Description: add alternative name for the species.
  Returntype : none
  Exceptions : none
830
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
831
832
833
834
835
836

=cut

sub add_alias{
  my ($class, $species,$key) = @_;

837
  $registry_register{'_ALIAS'}{lc($key)} = lc($species);
Ian Longden's avatar
Ian Longden committed
838
839
840
841
842
843
844
845
}

=head2 get_alias

  Arg [1]    : name of the possible alias to get species for
  Example    : Bio::EnsEMBL::Registry->get_alias("Human");
  Description: get proper species name.
  Returntype : species name
846
  Exceptions : none
847
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
848
849
850
851

=cut

sub get_alias{
852
  my ($class, $key) = @_;
Ian Longden's avatar
Ian Longden committed
853

854
  if(!defined($registry_register{'_ALIAS'}{lc($key)})){
855
    return $key;
Ian Longden's avatar
Ian Longden committed
856
  }
857
  return $registry_register{'_ALIAS'}{lc($key)};
Ian Longden's avatar
Ian Longden committed
858
}
859
860
861
862

=head2 alias_exists

  Arg [1]    : name of the possible alias to get species for
Ian Longden's avatar
Ian Longden committed
863
  Example    : Bio::EnsEMBL::Registry->alias_exists("Human");
864
865
866
  Description: does the species name exist.
  Returntype : 1 if exists else 0
  Exceptions : none
867
  Status     : Stable
868
869
870
871
872
873

=cut

sub alias_exists{
  my ($class, $key) = @_;

874
  if(defined($registry_register{'_ALIAS'}{lc($key)})){
875
876
877
878
    return 1;
  }
  return 0;
}
879

880
881
882
883
884
885
886
=head2 set_disconnect_when_inactive

  Example    : Bio::EnsEMBL::Registry->set_disconnect_when_inactive();
  Description: Set the flag to make sure that the database connection is dropped if
               not being used on each database.
  Returntype : none
  Exceptions : none
887
  Status     : Stable
888
889
890

=cut

891
sub set_disconnect_when_inactive{
892
  foreach my $dba ( @{get_all_DBAdaptors()}){
893
894
    my $dbc = $dba->dbc;
    #disconnect if connected
895
    $dbc->disconnect_if_idle() if $dbc->connected();
896
897
898
    $dbc->disconnect_when_inactive(1);
  }
}
Ian Longden's avatar
Ian Longden committed
899

900
901
902
903
904
905
906

=head2 disconnect_all

  Example    : Bio::EnsEMBL::Registry->disconnect_all();
  Description: disconnect from all the databases.
  Returntype : none
  Exceptions : none
907
  Status     : Stable
908
909
910

=cut

911
sub disconnect_all {
Web Admin's avatar
fixed  
Web Admin committed
912
  foreach my $dba ( @{get_all_DBAdaptors()||[]} ){
913
    my $dbc = $dba->dbc;
Web Admin's avatar
Web Admin committed
914
    next unless $dbc;
915
916
917
918
    #disconnect if connected
    $dbc->disconnect_if_idle() if $dbc->connected();
  }
}
919

920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
=head2 change_access

  Will change the username and password for a set of databases.
  if host,user or database names are missing then these are not checked.
  So for example if you do not specify a database then ALL databases on
  the specified  host and port will be changed.

  Arg [1]    : name of the host to change access on
  Arg [2]    : port number to change access on
  Arg [3]    : name of the user to change access on
  Arg [4]    : name of the database to change access on
  Arg [5]    : name of the new user
  Arg [6]    : new password

  Example    : Bio::EnsEMBL::Registry->get_alias("Human");
  Description: change username and password on one or more databases
  Returntype : none
  Exceptions : none
938
  Status     : Stable
939
940
941
942

=cut

sub change_access{
Steve Trevanion's avatar
Steve Trevanion committed
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
my $self = shift;
    my ($host,$port,$user,$dbname,$new_user,$new_pass) = @_;
    foreach my $dba ( @{$registry_register{'_DBA'}}){
	my $dbc = $dba->dbc;
	if((!defined($host) or $host eq $dbc->host) and
	   (!defined($port) or $port eq $dbc->port) and
	   (!defined($user) or $user eq $dbc->username) and
	   (!defined($dbname) or $dbname eq $dbc->dbname)){
	    if($dbc->connected()){
		$dbc->db_handle->disconnect();
		$dbc->connected(undef);
	    }
	    # over write the username and password
	    $dbc->username($new_user);
	    $dbc->password($new_pass);
	}
959
960
961
    }
}

962
963


964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
1001
1002
1003
1004
1005
1006
1007
=head2 load_registry_from_url

  Arg [1]    : string $url
  Example : load_registry_from_url("mysql://anonymous@ensembldb.ensembl.org:3306");
  Description: Will load the correct versions of the ensembl databases for the
               software release it can find on a database instance into the 
               registry. Also adds a set of standard aliases. The url format is:
               mysql://[[username][:password]@]hostname[:port].
               You can also request a specific version for the databases by adding
               a slash and the version number but your script may crash as the API
               version won't match the DB version.
  Exceptions : None.
  Status     : Stable
 
=cut

sub load_registry_from_url {
  my ($self, $url, $verbose) = @_;

  if ($url =~ /mysql\:\/\/([^\@]+\@)?([^\:\/]+)(\:\d+)?(\/\d+)?/) {
    my $user_pass = $1;
    my $host = $2;
    my $port = $3;
    my $version = $4;

    $user_pass =~ s/\@$//;
    my ($user, $pass) = $user_pass =~ m/([^\:]+)(\:.+)?/;
    $pass =~ s/^\:// if ($pass);
    $port =~ s/^\:// if ($port);
    $version =~ s/^\/// if ($version);

    $self->load_registry_from_db(
        -host=> $host,
        -user => $user,
        -pass => $pass,
        -port => $port,
        -db_version => $version,
        -verbose => $verbose);
  } else {
    throw("Only MySQL URLs are accepted at the moment");
  }
}


1008
=head2 load_registry_from_db
1009

1010
1011
1012
1013
1014
1015
1016
1017
1018
  Arg [HOST] : The domain name of the database host to connect to.
               
  Arg [USER] : string
               The name of the database user to connect with
  Arg [PASS] : (optional) string
               The password to be used to connect to the database
  Arg [PORT] : int
               The port to use when connecting to the database
  Arg [VERBOSE]: (optional) Wether to print database messages 
1019
1020
1021
1022
1023
1024
  Arg [DB_VERSION]: (optional) By default, only databases corresponding
               to this API version are loaded. This allows the script to
               use databases from another version although it might not
               work properly. This option should only be used for
               production or testing purposes and if you really know what
               you are doing.
1025
1026
1027
1028
1029

  Example : load_registry_from_db( -host => 'ensembldb.ensembl.org',
				   -user => 'anonymous',
				   -verbose => "1" );

1030
  Description: Will load the correct versions of the ensembl databases for the
1031
               software release it can find on a database instance into the 
1032
               registry. Also adds a set of standard aliases.
1033
1034

  Exceptions : None.
1035
  Status     : Stable
1036
1037
 
=cut
1038

1039
sub load_registry_from_db {
1040
  my($self, @args) = @_;
1041
1042
  my ($host, $port, $user, $pass, $verbose, $db_version) =
    rearrange([qw(HOST PORT USER PASS VERBOSE DB_VERSION)], @args);
1043
1044
1045
1046
1047
1048
1049



  my $go_version = 0;
  my $compara_version =0;

  $user ||= "ensro";
1050
  $port ||= 3306;
1051
1052
1053
1054
1055
1056
  my $db = DBI->connect( "DBI:mysql:host=$host;port=$port" , $user, $pass );

  my $res = $db->selectall_arrayref( "show databases" );
  my @dbnames = map {$_->[0] } @$res;
  
  my %temp;
1057
  my $software_version = $self->software_version();
1058
1059
1060
  if (defined($db_version)) {
    $software_version = $db_version;
  }
1061
  print "Will only load $software_version databases\n" if ($verbose);
1062
1063
  for my $db (@dbnames){
    if($db =~ /^([a-z]+_[a-z]+_[a-z]+)_(\d+)_(\d+[a-z]*)/){
1064
      if($2 eq $software_version){
1065
1066
1067
1068
	$temp{$1} = $2."_".$3;
      }
    }
    elsif($db =~ /^ensembl_compara_(\d+)/){
1069
      if($1 eq $software_version){
1070
1071
1072
1073
	$compara_version = $1;
      }
    }
    elsif($db =~ /^ensembl_go_(\d+)/){
1074
      if($1 eq $software_version){
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100
1101
1102
1103
	$go_version = $1;
      }
    }
  }
  
  @dbnames =();
  
  foreach my $key ( keys %temp){
    push @dbnames, $key."_".$temp{$key};
  }	 
  # register core databases
  
  my @core_dbs = grep { /^[a-z]+_[a-z]+_core_\d+_/ } @dbnames;
  
  for my $coredb ( @core_dbs ) {
    my ($species, $num ) = ( $coredb =~ /(^[a-z]+_[a-z]+)_core_(\d+)/ );
    my $dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new
      ( -group => "core",
	-species => $species,
	-host => $host,
	-user => $user,
	-pass => $pass,
	-port => $port,
	-dbname => $coredb
      );
    (my $sp = $species ) =~ s/_/ /g;
    $self->add_alias( $species, $sp );
    print $coredb." loaded\n" if ($verbose);
  }
1104

1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
  # register cdna databases
  
  my @cdna_dbs = grep { /^[a-z]+_[a-z]+_cdna_\d+_/ } @dbnames;
  
  for my $cdnadb ( @cdna_dbs ) {
    my ($species, $num ) = ( $cdnadb =~ /(^[a-z]+_[a-z]+)_cdna_(\d+)/ );
    my $dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new
      ( -group => "cdna",
	-species => $species,
	-host => $host,
	-user => $user,
	-pass => $pass,
	-port => $port,
	-dbname => $cdnadb
      );
    (my $sp = $species ) =~ s/_/ /g;
    $self->add_alias( $species, $sp );
    print $cdnadb." loaded\n" if ($verbose);
  }

1125
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137
1138
1139
1140
1141
  my @vega_dbs = grep { /^[a-z]+_[a-z]+_vega_\d+_/ } @dbnames;
  
  for my $vegadb ( @vega_dbs ) {
    my ($species, $num ) = ( $vegadb =~ /(^[a-z]+_[a-z]+)_vega_(\d+)/ );
    my $dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new
      ( -group => "vega",
	-species => $species,
	-host => $host,
	-user => $user,
	-pass => $pass,
	-port => $port,
	-dbname => $vegadb
      );
    (my $sp = $species ) =~ s/_/ /g;
    $self->add_alias( $species, $sp );
    print $vegadb." loaded\n" if ($verbose);
  }
1142
  
Ian Longden's avatar
Ian Longden committed
1143
  my @other_dbs = grep { /^[a-z]+_[a-z]+_otherfeatures_\d+_/ } @dbnames;
1144
  
Ian Longden's avatar
Ian Longden committed
1145
1146
  for my $other_db ( @other_dbs ) {
    my ($species, $num) = ( $other_db =~ /(^[a-z]+_[a-z]+)_otherfeatures_(\d+)/ );
1147
    my $dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new
Ian Longden's avatar
Ian Longden committed
1148
      ( -group => "otherfeatures",
1149
1150
1151
1152
1153
	-species => $species,
	-host => $host,
	-user => $user,
	-pass => $pass,
	-port => $port,
Ian Longden's avatar
Ian Longden committed
1154
	-dbname => $other_db
1155
      );
1156
1157
      (my $sp = $species ) =~ s/_/ /g;
      $self->add_alias( $species, $sp );
1158
      print $other_db." loaded\n" if ($verbose);       
1159
1160
1161
1162
1163
1164
1165
1166
1167
1168
1169
1170
1171
1172
1173
1174
1175
1176
1177
1178
1179
1180
1181
1182
1183
  }
  
  
  eval "require Bio::EnsEMBL::Variation::DBSQL::DBAdaptor";
  if($@) {
    #ignore variations as code required not there for this
    print "Bio::EnsEMBL::Variation::DBSQL::DBAdaptor module not found so variation databases will be ignored if found\n" if ($verbose);
  }
  else{
    my @variation_dbs = grep { /^[a-z]+_[a-z]+_variation_\d+_/ } @dbnames;
    
    for my $variation_db ( @variation_dbs ) {
      my ($species, $num ) = ( $variation_db =~ /(^[a-z]+_[a-z]+)_variation_(\d+)/ );
      my $dba = Bio::EnsEMBL::Variation::DBSQL::DBAdaptor->new
	( -group => "variation",
	  -species => $species,
	  -host => $host,
	  -user => $user,
	  -pass => $pass,
	  -port => $port,
	  -dbname => $variation_db
	);
      print $variation_db." loaded\n" if ($verbose);
    }
  }
Nathan Johnson's avatar
Nathan Johnson committed
1184
1185
1186
1187
1188
1189
1190

  eval "require Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor";
  if($@) {
    #ignore funcgen DBs as code required not there for this
	  print "Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor module not found so functional genomics databases will be ignored if found\n" if ($verbose);
  }
  else{
Steve Trevanion's avatar
Steve Trevanion committed
1191
    my @funcgen_dbs = grep { /^[a-z]+_[a-z]+_funcgen_\d+_/ } @dbnames;
Nathan Johnson's avatar
Nathan Johnson committed
1192
1193
1194
1195
1196
1197
1198
1199
1200
1201
1202
1203
1204
1205
1206
1207
    
    for my $funcgen_db ( @funcgen_dbs ) {
		my ($species, $num ) = ( $funcgen_db =~ /(^[a-z]+_[a-z]+)_funcgen_(\d+)/ );
		my $dba = Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor->new
		  ( -group => "funcgen",
			-species => $species,
			-host => $host,
			-user => $user,
			-pass => $pass,
			-port => $port,
			-dbname => $funcgen_db
		  );
		print $funcgen_db." loaded\n" if ($verbose);
    }
  }

1208
1209
1210
1211
1212
1213
1214
1215
1216
1217
1218
1219
1220
1221
1222
1223
1224
1225
1226
1227
1228
1229
1230
1231
1232
1233
1234
1235
1236
1237
  
  #Compara
  if($compara_version){
    eval "require Bio::EnsEMBL::Compara::DBSQL::DBAdaptor";
    if($@) {
      #ignore compara as code required not there for this
      print "Bio::EnsEMBL::Compara::DBSQL::DBAdaptor not found so compara database ensembl_compara_$compara_version will be ignored\n" if ($verbose);
    }
    else{
      my $compara_db = "ensembl_compara_".$compara_version;

      my $dba = Bio::EnsEMBL::Compara::DBSQL::DBAdaptor->new
	( -group => "compara",
	  -species => "multi",
	  -host => $host,
	  -user => $user,
	  -pass => $pass,
	  -port => $port,
	  -dbname => $compara_db
	);
      print $compara_db." loaded\n" if ($verbose);       
    }
  }
  else{
    print "No Compara database found" if ($verbose);
  }


  #GO
  if($go_version){
1238
    eval "require Bio::EnsEMBL::ExternalData::GO::GOAdaptor";
1239
1240
    if($@) {
      #ignore go as code required not there for this
1241
1242
#      print $@;
      print "GO software not installed so go database ensemb_go_$go_version will be ignored\n" if ($verbose);
1243
1244
1245
1246
1247
1248
1249
1250
1251
1252
1253
1254
1255
1256
1257
1258
1259
1260
    }
    else{
      my $go_db = "ensembl_go_".$go_version;
      my $dba = Bio::EnsEMBL::ExternalData::GO::GOAdaptor->new
	( -group => "go",
	  -species => "multi",
	  -host => $host,
	  -user => $user,
	  -pass => $pass,
	  -port => $port,
	  -dbname => $go_db
	);
      print $go_db." loaded\n" if ($verbose);              
    }
  }
  else{
    print "No go database found" if ($verbose);
  }
1261
1262
1263
1264
1265
1266
1267

  #hard coded aliases for the different species

  my @aliases = ('chimp','PanTro1', 'Pan', 'P_troglodytes');
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Pan_troglodytes",
						 -alias => \@aliases);
  
Ian Longden's avatar
Ian Longden committed
1268
  @aliases = ('elegans','worm');
1269
1270
1271
1272
1273
1274
1275
1276
1277
1278
1279
1280
1281
1282
1283
1284
1285
1286
1287
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Caenorhabditis_elegans", 
						 -alias => \@aliases);
  
  @aliases = ('tetraodon');
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Tetraodon_nigroviridis",
						 -alias => \@aliases);
  
  @aliases = ('H_Sapiens', 'homo sapiens', 'Homo_Sapiens', 'Homo', 'human', 'Hg17','ensHS', '9606');
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Homo_sapiens",
						 -alias => \@aliases);
  
  @aliases = ('M_Musculus', 'mus musculus', 'Mus_Musculus', 'Mus', 'mouse','Mm5','ensMM','10090');
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Mus_musculus",
						 -alias => \@aliases);
  
  @aliases = ('R_Norvegicus', 'rattus norvegicus', 'Rattus_Norvegicus', 'Rattus', 'rat', 'Rn3', '10116');
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Rattus_norvegicus",
                                               -alias => \@aliases);
  
Ian Longden's avatar
Ian Longden committed
1288
1289
  @aliases = ('T_Rubripes', 'Fugu', 'takifugu');
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Takifugu_rubripes",
1290
1291
						 -alias => \@aliases);
  
Ian Longden's avatar
Ian Longden committed
1292
  @aliases = ('G_Gallus', 'gallus gallus', 'Chicken', 'GalGal2');
1293
1294
1295
1296
1297
1298
1299
1300
1301
1302
1303
1304
1305
1306
1307
1308
1309
1310
1311
1312
1313
1314
1315
1316
1317
1318
1319
1320
1321
1322
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Gallus_Gallus",
						 -alias => \@aliases);
  
  @aliases = ('D_Rerio', 'danio rerio', 'Danio_Rerio', 'Danio', 'zebrafish', 'zfish');
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Danio_rerio",
						 -alias => \@aliases);
  
  @aliases = ('X_Tropicalis', 'xenopus tropicalis','Xenopus_tropicalis', 'Xenopus');
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Xenopus_tropicalis",
						 -alias => \@aliases);
  
  @aliases = ('A_Gambiae', 'Anopheles Gambiae','Anopheles_gambiae', 'Anopheles','mosquito');
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Anopheles_gambiae",
						 -alias => \@aliases);
  
  
  @aliases = ('D_Melanogaster', 'drosophila melanogaster', 'Drosophila_melanogaster', 'drosophila', 'fly');
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Drosophila_melanogaster",
						 -alias => \@aliases);
  
  @aliases = ('S_Cerevisiae', 'Saccharomyces Cerevisiae', 
	      'Saccharomyces_cerevisiae', 'Saccharomyces', 'yeast');
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Saccharomyces_cerevisiae",
						 -alias => \@aliases);

  @aliases = ('C_Familiaris', 'Canis Familiaris', 
	      'Canis_familiaris', 'Canis', 'dog');
  
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Canis_familiaris",
						 -alias => \@aliases);
Ian Longden's avatar
Ian Longden committed
1323

1324
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Ciona_intestinalis",
Ian Longden's avatar
Ian Longden committed
1325
1326
						 -alias => ['ciona','Ciona intestinalis']);

1327
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Bos_taurus",
Ian Longden's avatar
Ian Longden committed
1328
1329
1330
1331
1332
1333
1334
1335
1336
1337
1338
1339
1340
1341
1342
1343
1344
1345
1346
1347
1348
1349
1350
1351
1352
1353
1354
1355
1356
1357
1358
1359
1360
1361
1362
1363
1364
1365
1366
1367
1368
1369
1370
1371
1372
1373
1374
1375
1376
						 -alias => ['cow','bos_taurus']);

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Macaca_mulatta",
						 -alias => ['rhesus','rhesus_monkey','macaca mulatta']);

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Otolemur_garnettii",
						 -alias => ['bushbaby','Otolemur garnettii']);

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Oryctolagus_cuniculus",
						 -alias => ['rabbit','Oryctolagus cuniculus']);

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Felis_catus",
						 -alias => ['cat','felis catus']);

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Sus_scrofa",
						 -alias => ['pig','sus scrofa']);

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Sorex_araneus",
						 -alias => ['shrew','european_shrew','Sorex araneus']);

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Erinaceus_europaeus",
						 -alias => ['western_european_hegdehog','Erinaceus europaeus']);

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Myotis_lucifugus",
						 -alias => ['microbat','little_brown_bat']);

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Dasypus_novemcinctus",
						 -alias => ['armadillo','arma','Dasypus novemcinctu']);

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Loxodonta_africana",
						 -alias => ['african_elephant','elephant','Loxodonta africana']);

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Echinops_telfairi",
						 -alias => ['tenrec','madagascar_hedgehog','lesser_hedgehog','Echinops telfairi']);

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Monodelphis_domestica",
						 -alias => ['opossum','Monodelphis domestica']);

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Ornithorhynchus_anatinus",
						 -alias => ['platypus','Ornithorhynchus anatinus']);

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Gasterosteus_aculeatus",
						 -alias => ['stickleback','Gasterosteus aculeatus']);

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Oryzias_latipes",
						 -alias => ['medaka','Oryzias latipes']);



1377
1378
1379
1380
1381
  @aliases = ('compara');
  
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "multi",
						 -alias => \@aliases);

1382
1383
  
}
1384
1385


Ian Longden's avatar
Ian Longden committed
1386
1387