diff --git a/modules/Bio/EnsEMBL/Registry.pm b/modules/Bio/EnsEMBL/Registry.pm index 50f260af31b3b7305ebdaf13144c45ddbbbd717d..aff59f281a173c2f769f4a8191ef2faa53e47715 100644 --- a/modules/Bio/EnsEMBL/Registry.pm +++ b/modules/Bio/EnsEMBL/Registry.pm @@ -150,9 +150,13 @@ sub load_all{ elsif(-e $ENV{HOME}."/.ensembl_init"){ do($ENV{HOME}."/.ensembl_init"); } - print STDERR "NO default configuration to load\n"; + else{ + print STDERR "NO default configuration to load\n"; + } + } + else{ + print STDERR "Already configured???\n"; } - print STDERR "Already configured???\n"; } #=head2 check_if_already_there @@ -692,46 +696,27 @@ sub default_track{ =cut sub add_new_tracks{ - my($class, $conf) = @_; + my($class, $conf, $pos) = @_; my $start = 0; my $reg = $class; my $species_reg = $reg->get_alias($conf->{'species'},"nothrow"); - my $view = $conf->{'type'}; + my %pars; + print STDERR "Species $species_reg check for default tracks\n"; if(defined($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); + $pars{'available'} = "species ".$reg->get_alias($dba->species()); + $pars{'db_alias'} = $dba->group(); +# print STDERR "Adding new track for ".$dba->species."\t".$dba->group."\n"; + $conf->add_new_track_generictranscript('',$dba->group()."_yo","black",$pos,%pars); + # my( $self, $code, $text_label, $colour, $pos, %pars ) = @_; + $pos++; } } } + return $pos; + } @@ -747,7 +732,7 @@ sub add_new_tracks{ =cut sub _add_new_track{ - my ($class, $config, $dba, $start ) = @_; + my ($class, $conf, $config, $dba, $start ) = @_; my $KEY = $dba->group();