Registry.pm 19.8 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 16 17 18 19 20 21 22 23 24 25 26
#
# 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

$gene_adaptor = Bio::EnsEMBL::Registry->get_adaptor("Homo Sapiens","core","Gene"))


=head1 DESCRIPTION

All Adaptors are stored/registered using this module. This module should then
be used to get the adaptors needed.

The registry can be loaded from a configuration file. If the enviroment
variable ENSEMBL_REGISTRY is set then the file pointed to by it is executed.
If not set then if the file ~/.ensembl_init exists then this will be executed.
27 28
An example of such configuration file can be found in 
ensembl/modules/Bio/EnsEMBL/Utils/ensembl_init.example
Ian Longden's avatar
Ian Longden committed
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 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134
For the Web server ENSEMBL_REGISTRY should be set in SiteDefs.pm.

The four types of registrys are for db adaptors, dba adaptors, dna adaptors
and the standard type.

=head2 db

These are registrys for backwards compatibillity and enable the subroutines
to add other adaptors to connections.

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
   my $sfa = $self->adaptor()->db()->get_db_adaptor('blast');

We now want to change this to
   my $sfa =  Bio::EnsEMBL::Registry->get_db($self->adaptor->db,'blast');

OR preferably if the blast adaptor was set up in configure
   my $sfa = Bio::EnsEMBL::Registry->get_adaptor("Human","core","blast");


=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

my $db = Bio::EnsEMBL::DBSQL::DBAdaptor->new(....)
my $exon_adaptor = $db->get_ExonAdaptor;

we should now have just

my  $exon_adaptor = Bio::EnsEMBL::Registry->get_adaptor("Human","core","Exon");


=head2 DNA

This is an internal Registry and allows the configuration of a dnadb. 
An example here is to set the est database to get it's dna data from the core database.

## set the est db to use the core for getting dna data.
#Bio::EnsEMBL::Utils::ConfigRegistry->
#                         dnadb_add("Homo Sapiens","core","Homo Sapiens","est");


=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.

my  $exon_adaptor = Bio::EnsEMBL::Registry->get_adaptor("Human","core","Exon");

=head1 CONTACT

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


=head1 METHODS

=cut


package Bio::EnsEMBL::Registry;

use strict;

use Bio::EnsEMBL::DBSQL::MergedAdaptor;
use Bio::EnsEMBL::Utils::Exception qw( deprecate throw warning );
use Bio::EnsEMBL::Utils::Argument qw(rearrange);

use vars qw(%registry_register);

$registry_register{'_WARN'} = 0;



=head2 load_all
 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 conf file.
  2) If the enviroment variable ENSEMBL_REGISTRY is set this is used.
  3) If the file .ensembl_init exist in the home directory it is used

  Arg [1]    : (optional) string $arg file to load the registry from
  Example    : Bio::EnsEMBL::Registry->load_all();
  Returntype : none
  Exceptions : none


=cut
 
sub load_all{
  my $class = shift;
  my $web_reg = shift;

  #$registry_register{'_WARN'} = 0; # default report overwriting
  if(!defined($registry_register{'seen'})){
    $registry_register{'seen'}=1;
    if(defined($web_reg)){
#      print STDERR  "Loading conf from site defs file ".$web_reg."\n";
135 136 137 138 139 140
      if(-e $web_reg){
	unless (my $return = do $web_reg ){
	  throw "Error in Configuration\n $!\n";
	}
	# other wise it gets done again by the web initialisation stuff
	delete $INC{$web_reg}; 
Ian Longden's avatar
Ian Longden committed
141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179
      }
    }
    elsif(defined($ENV{ENSEMBL_REGISTRY}) and -e $ENV{ENSEMBL_REGISTRY}){
#      print STDERR  "Loading conf from ".$ENV{ENSEMBL_REGISTRY}."\n";
      unless (my $return = do $ENV{ENSEMBL_REGISTRY}){
	throw "Error in Configuration\n $!\n";
      }
    }
    elsif(-e $ENV{HOME}."/.ensembl_init"){
      do($ENV{HOME}."/.ensembl_init");
    }
#    else{
#      print STDERR "NO default configuration to load\n";
#    }
  }
#  else{
#    print STDERR "Already configured???\n";
#  }
}

=head2 check_if_already_there

  Arg [DBNAME] : string
                 The name of the database to check for.
  Arg [HOST] : (optional) string
               The domain name of the database host to check for
  Arg [PORT] : int
               The port to check for when connecting to the database
  Arg [DRIVER] : (optional) string
                 The type of database driver to check for

  Description: Check to see if the database is already stored.
  Returntype : 0 if not found else the species and group.
  Exceptions : none
  

=cut

  
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199
#sub check_if_already_there{
#  my ($class) = shift;
#
#  my ($dbname,$host,$driver,$port,$species, $group ) =
#    rearrange([qw(DBNAME HOST DRIVER PORT SPECIES GROUP)], @_);
#
#  if(defined($registry_register{'_DBA'})){
#    foreach my $db (@{$registry_register{'_DBA'}}){
#      my $dbc= $db->db();
#      if($dbc->host() eq $host and $dbc->dbname() eq $dbname
#	 and $dbc->driver() eq $driver and $dbc->port() eq $port){
#	if(defined($species) and defined($group) and 
#	   $db->species eq $species and $db->group eq $group){
#	  return ($db->species(),$db->group());
#	}
#      }
#    }
#  }
#  return 0;
#}
Ian Longden's avatar
Ian Longden committed
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220


#
# add ons.
#

=head2 add_db

  Arg [1]    : db to add adaptor to.
  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

=cut

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


221 222 223
  if($db->species() ne $adap->species){
    $registry_register{$db->species()}{$db->group()}{'_special'}{$name} = $adap;
  }
Ian Longden's avatar
Ian Longden committed
224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257
}

=head2 remove_db

  Arg [1]    : db to remove adaptor from.
  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

=cut

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

  my $ret = $registry_register{$db->species()}{$db->group()}{'_special'}{$name};
  $registry_register{$db->species()}{$db->group()}{'_special'}{$name} = undef;

  return $ret;
}

=head2 get_db

  Arg [1]    : db to get adaptor from.
  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

=cut

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

258 259 260 261 262
  my $ret = Bio::EnsEMBL::Registry->get_DBAdaptor($db->species,$name);

  if(defined($ret)){
    return $ret;
  }
Ian Longden's avatar
Ian Longden committed
263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278
  return $registry_register{$db->species()}{$db->group()}{'_special'}{$name};
}

=head2 get_all_db_adaptors

  Arg [1]    : db to get all the adaptor from.
  Example    : my $db = Bio::EnsEMBL::Registry->get_all_db_adaptors($db);
  Returntype : adaptor
  Exceptions : none

=cut

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

279 280
 foreach my $key (keys %{$registry_register{$class->get_alias($db->species())}{$db->group()}{'_special'}}){
   $ret{$key} = $registry_register{$class->get_alias($db->species())}{$db->group()}{'_special'}{$key};
Ian Longden's avatar
Ian Longden committed
281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484
 }

  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

=cut

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

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

  $registry_register{$species}{$group}{'_DB'} = $adap;

  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

=cut

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

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

  if(defined($group)){ # group defined so return standard DB Adaptor
    return  $registry_register{$species}{$group}{'_DB'};
  }
  else{ #return a merged db adaptor
    return  new_merged Bio::EnsEMBL::DBSQL::DBAdaptor($species);
  }
}

=head2 get_all_DBAdaptors

  Example    : @dba = @{Bio::EnsEMBL::Registry->get_all_DBAdaptors();
  Returntype : list of DBAdaptors
  Exceptions : none

=cut

sub get_all_DBAdaptors{
  my ($class)=@_;

  return @{$registry_register{'_DBA'}};
}

#
# 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.
  Arg [3]    : The adaptor to be added to the registry as a DNA adaptor.
  Example    : Bio::EnsEMBL::Registry->add_DNAAdaptor("Human", "core", $dnaAdap);
  Returntype : none
  Exceptions : none

=cut

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

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

  $registry_register{$species}{$group}{'_DNA'} = $adap;

}

=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

=cut

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

  $species = $class->get_alias($species);
  return  $registry_register{$species}{$group}{'_DNA'};
}

#
# 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


=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
#

  if(defined($reset)){ # JUST REST THE HASH VLAUE NO MORE PROCESSING NEEDED
    $registry_register{$species}{$group}{$type} = $adap;
    return;
  }
  if(defined($registry_register{$species}{$group}{$type})){ 
    print STDERR ("Overwriting Adaptor in Registry for $species $group $type\n");
    $registry_register{$species}{$group}{$type} = $adap;
   return;
  }
  $registry_register{$species}{$group}{$type} = $adap;

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

#  print STDERR "REGADD  $species \t $group \t $type\t to the registry\n";

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

}


=head2 set_get_via_dnadb_if_set

  set the flag so that for this type of adaptor the data is obtained
  from the dna source and not centrally i.e. estgenes where the sequence
  data is held in the core.

  Arg [1]    : name of the species to set flag for.
  Arg [2]    : name of the type to set flag for. (i.e. Sequence)
  Example    : Bio::EnsEMBL::Registry->set_get_via_dnadb_if_set("Human","Sequence");
  Returntype : none
  Exceptions : none
  
  

=cut

sub set_get_via_dnadb_if_set{
  my ($class,$species,$type) = @_;

485
  $registry_register{$class->get_alias($species)}{$type}{'DNADB'} = 1;
Ian Longden's avatar
Ian Longden committed
486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512
}

=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

=cut

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

  $species = $class->get_alias($species);
 
  #throw in a check to see if we should get the dnadb one and not the normal
  if(defined($registry_register{$species}{$type}{'DNADB'}) && $class->get_DNAAdaptor($species,$group)){
    my $dna = $class->get_DNAAdaptor($species,$group);
    $species = $dna->species();
    $group = $dna->group();
  }

  my $ret = $registry_register{$species}{$group}{$type};
  if(!defined($ret)){
513 514
    return undef;
#    throw("COULD NOT FIND ADAPTOR species=$species\tgroup=$group\ttype=$type\n");
Ian Longden's avatar
Ian Longden committed
515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601
  }
  if(!ref($ret)){ # not instantiated yet
    my $dba = $registry_register{$species}{$group}{'_DB'};
    my $module = $ret;
    eval "require $module";

    if($@) {
      warning("$module cannot be found.\nException $@\n");
      return undef;
    }
    my $adap = "$module"->new($dba);
    Bio::EnsEMBL::Registry->add_adaptor($species, $group, $type, $adap, "reset");
    $ret = $adap;
  }

  return $ret;
}

=head2 get_all_adaptors

  Arg [1]    : name of the species to get the adaptors for.
  Example    : @adaps = @{Bio::EnsEMBL::Registry->get_all_adaptors()};
  Returntype : list of adaptors
  Exceptions : none

=cut

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

  $species = get_alias($species);
  return $registry_register{$species}{'list'};
}


=head2 get_MergedAdaptor

  Arg [1]    : name of the species to get the adaptors for in the registry.
  Arg [2]    : name of the type to get the adaptors for in the registry.
  Example    : $merged = Bio::EnsEMBL::Registry->get_MergedAdaptor("Mouse","Gene");
  Returntype : Bio::EnsEMBL::DBSQL::MergedAdaptor
  Exceptions : none

=cut

sub get_MergedAdaptor{
  my ($class,$species,$type)=@_;

  $species = $class->get_alias($species);
  my $ret = new Bio::EnsEMBL::DBSQL::MergedAdaptor();
  $ret->add_list(@{$registry_register{$type}{$species}});

  return $ret;
}

=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

=cut

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

  $registry_register{'_ALIAS'}{$key} = $species;
}

=head2 get_alias

  Arg [1]    : name of the possible alias to get species for
  Arg [2]    : if set will not throw if not found.
  Example    : Bio::EnsEMBL::Registry->get_alias("Human");
  Description: get proper species name.
  Returntype : species name
  Exceptions : if not found and second argument

=cut

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

  if(!defined($registry_register{'_ALIAS'}{$key})){
602
    return $key;
Ian Longden's avatar
Ian Longden committed
603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770
  }
  return $registry_register{'_ALIAS'}{$key};
}

#
# Web specific routines
#


=head2 load_registry_with_web_adaptors
  Will load the registry with all the Adaptors used in the Web server.
  Providing Sitedefs and SpeciesDefs can be found on PERL5LIB path.

  Example    : Bio::EnsEMBL::Registry->load_registry_with_web_adaptors();
  Returntype : none
  Exceptions : Will die if Sitedefs or SpeciesDefs is not found on the
               PERL5LIB path.

=cut

sub load_registy_with_web_adaptors{
  my $class = shift;


  eval{ require SiteDefs };
  if ($@){ die "Can't use SiteDefs.pm - $@\n"; }
    SiteDefs->import(qw(:ALL));

  eval{ require SpeciesDefs };
  if ($@){ die "Can't use SpeciesDefs.pm - $@\n"; }
  my $conf = new SpeciesDefs();

}

=head2 set_default_track
  Sets a flag to say that that this species/group are a default track and do not
  need to be added as another web track.

  Arg [1]    : name of the species to get the adaptors for in the registry.
  Arg [2]    : name of the type to get the adaptors for in the registry.
  Example    : $merged = Bio::EnsEMBL::Registry->set_default_track("Human","core");
  Returntype : none
  Exceptions : none

=cut

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

  $registry_register{'def_track'}{$species}{$group} = 1;
}

=head2 default_track
  Check flag to see if this is a default track

  Arg [1]    : name of the species to get the adaptors for in the registry.
  Arg [2]    : name of the type to get the adaptors for in the registry.
  Example    : $merged = Bio::EnsEMBL::Registry->set_default_track("Human","core");
  Returntype : int 
  Exceptions : none

=cut

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

  if(defined($registry_register{'def_track'}{$species}{$group})){
    return 1;
  }
  
  return 0;
}


=head2 add_new_tracks
  Will add new gene tracks to the configuration of the WEB server if they are
  not of the type default and the configuration already has genes in the display.

  Arg [1]    : hash of the default configuration of the web page
  Returntype : none
  Exceptions : none
  Called by  : UserConfig.pm
  
=cut

sub add_new_tracks{
  my($class, $conf) = @_;

  my $start = 0;
  my $reg = $class;
  my $species_reg = $reg->get_alias($conf->{'species'},"nothrow");
  my $view =  $conf->{'type'};
  if(defined($species_reg)){
    my $config = $conf->{'general'}->{$view};
    foreach my $dba ($reg->get_all_DBAdaptors()){
      #      if($dba->species eq $species_reg and !$reg->default_track($dba->species,$dba->group)){
      if(!$reg->default_track($dba->species,$dba->group)){
	if($start == 0){
	  if(exists($config->{'vega_transcript_lite'}) and defined($config->{'vega_transcript_lite'}->{'pos'})){
	    $start = $config->{'vega_transcript_lite'}->{'pos'};
	  }
	  elsif(exists($config->{'transcript_lite'}) and defined($config->{'transcript_lite'}->{'pos'})){
	    $start = $config->{'transcript_lite'}->{'pos'};
	  }
	  else{ # no transcripts on this view so do not add track here
	    #    print STDERR "no transcript options on this display \n";
	    next;
	  }
	  $start ++;
	}
	else{
	  if(exists($config->{'vega_transcript_lite'}) and defined($config->{'vega_transcript_lite'}->{'pos'})){
	    $start++;
	  }
	  elsif(exists($config->{'transcript_lite'}) and defined($config->{'transcript_lite'}->{'pos'})){
	    $start++;
	  }
	  else{ # no transcripts on this view so do not add track here
	    #    print STDERR "no transcript options on this display \n";
	    next;
	  }
	}
	$reg->_add_new_track( $conf->{'general'}->{$view}, $dba, $start);
      }
    }
  }
}


=head2 _add_new_track
 
  Arg [1]    : hash of the configuration  
  Arg [2]    : dbadaptor to use to get track info from
  Arg [3]    : start index to place track in the right place
  Returntype : none
  Exceptions : none
  Called by  : add_new_tracks

=cut

sub _add_new_track{
  my ($class, $config, $dba, $start ) = @_;


  my $KEY = $dba->group();

  $config->{$KEY} ={
		    'on'    => "on",
		    'compact' => 'yes',
		    'pos'     => $start,
		    'str'     => 'b',
		    'src'     => 'all', # 'ens' or 'all'
		    'available'=> 'species '.$dba->species(),
		    'dba'  => $dba,		   
#		    'colours' => {$config->{'_colourmap'}->colourSet( 'vega_gene' )},
		    'glyphset' => 'generic_transcript',
		    'dep'      => 6,
		   };

  push @{ $config->{'_artefacts'} }, $KEY;
  push @{ $config->{'_settings'}->{'features'}}, [$KEY => $KEY] ;
  
# [ 'transcript_lite'      => "Ensembl Trans."  ],  
  return;
}


1;