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ensembl-gh-mirror
ensembl
Commits
1a7d316d
Commit
1a7d316d
authored
Sep 06, 2004
by
Ian Longden
Browse files
dnadb now holds name core and not the adaptor so that forking and order are not important
parent
aa3c78a2
Changes
2
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2 changed files
with
67 additions
and
51 deletions
+67
-51
modules/Bio/EnsEMBL/Registry.pm
modules/Bio/EnsEMBL/Registry.pm
+39
-17
modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm
modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm
+28
-34
No files found.
modules/Bio/EnsEMBL/Registry.pm
View file @
1a7d316d
...
...
@@ -382,12 +382,17 @@ sub get_all_DBAdaptors{
=cut
sub
add_DNAAdaptor
{
my
(
$class
,
$species
,
$group
,
$
ada
p
)
=
@_
;
my
(
$class
,
$species
,
$group
,
$
dnadb_grou
p
)
=
@_
;
$species
=
$class
->
get_alias
(
$species
);
$registry_register
{
$species
}{
$group
}{'
_DNA
'}
=
$adap
;
if
(
$dnadb_group
->
isa
('
Bio::EnsEMBL::DBSQL::DBAdaptor
')){
# print STDERR "AHHH ".caller()."\n";
$registry_register
{
$species
}{
$group
}{'
_DNA
'}
=
$dnadb_group
->
group
();
}
else
{
# print STDERR "AHHH MEN ".caller()."\n";
$registry_register
{
$species
}{
$group
}{'
_DNA
'}
=
$dnadb_group
;
}
}
=head2 get_DNAAdaptor
...
...
@@ -404,7 +409,12 @@ sub get_DNAAdaptor{
my
(
$class
,
$species
,
$group
)
=
@_
;
$species
=
$class
->
get_alias
(
$species
);
return
$registry_register
{
$species
}{
$group
}{'
_DNA
'};
my
$new_group
=
$registry_register
{
$species
}{
$group
}{'
_DNA
'};
if
(
defined
$new_group
)
{
return
$class
->
get_DBAdaptor
(
$species
,
$new_group
);
}
else
{
return
undef
;
}
}
#
...
...
@@ -489,11 +499,11 @@ sub add_adaptor{
=cut
sub
set_get_via_dnadb_if_set
{
my
(
$class
,
$species
,
$type
)
=
@_
;
$registry_register
{
$class
->
get_alias
(
$species
)}{
$type
}{'
DNADB
'}
=
1
;
}
#
sub set_get_via_dnadb_if_set{
#
my ($class,$species,$type) = @_;
#
#
$registry_register{$class->get_alias($species)}{$type}{'DNADB'} = 1;
#
}
=head2 get_adaptor
...
...
@@ -508,15 +518,27 @@ sub set_get_via_dnadb_if_set{
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
();
$species
=
$class
->
get_alias
(
$species
);
my
%dnadb_adaptors
=
qw(Sequence 1 AssemblyMapper 1 KaryotypeBand 1 RepeatFeature 1 CoordSystem 1 AssemblyExceptionFeature 1 )
;
my
$dnadb_group
=
$registry_register
{
$species
}{
$group
}{
_DNA
};
if
(
defined
(
$dnadb_group
)
&&
defined
(
$dnadb_adaptors
{
$type
})
)
{
# print STDERR "new### $group $dnadb_group \n";
$group
=
$dnadb_group
;
}
# else{
# if (defined($dnadb_adaptors{$type}) ) {
# print STDERR "old### $species $group $type no dnadb \n";
# }
# }
#throw in a check to see if we should get the dnadb one and not the normal
# if(defined($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
)){
...
...
modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm
View file @
1a7d316d
...
...
@@ -110,16 +110,19 @@ sub gen_load{
}
elsif
(
$dba
->
isa
('
Bio::EnsEMBL::DBSQL::DBAdaptor
')){
#vega uses the core DBAdaptor so test if vega is in the dbname
if
(
$dba
->
dbc
->
dbname
()
=~
/vega/
){
if
(
!
defined
(
$dba
->
group
())){
$dba
->
group
('
vega
');
}
if
(
!
defined
(
$dba
->
group
())){
$dba
->
group
('
core
');
}
if
(
$dba
->
group
eq
"
estgene
"){
$config_sub
=
\
&
Bio::EnsEMBL::Utils::ConfigRegistry::
load_estgene
;
}
elsif
(
$dba
->
group
eq
"
est
"){
$config_sub
=
\
&
Bio::EnsEMBL::Utils::ConfigRegistry::
load_est
;
}
elsif
(
$dba
->
group
eq
"
vega
"){
$config_sub
=
\
&
Bio::EnsEMBL::Utils::ConfigRegistry::
load_vega
;
}
else
{
if
(
!
defined
(
$dba
->
group
())){
$dba
->
group
('
core
');
}
$config_sub
=
\
&
Bio::EnsEMBL::Utils::ConfigRegistry::
load_core
;
}
}
...
...
@@ -195,10 +198,6 @@ sub load_core{
}
foreach
my
$type
(
qw(Sequence AssemblyMapper KaryotypeBand RepeatFeature CoordSystem AssemblyExceptionFeature)
){
Bio::EnsEMBL::
Registry
->
set_get_via_dnadb_if_set
(
$dba
->
species
,
$type
);
}
}
...
...
@@ -221,7 +220,6 @@ sub load_SNP{
sub
attach_database
{
my
(
$class
,
$species
,
$core
,
$name1
)
=
@_
;
print
STDERR
"
attach_databse called
"
.
caller
()
.
"
\n
";
my
$first
=
Bio::EnsEMBL::
Registry
->
get_DBAdaptor
(
$species
,
$name1
);
my
$coredb
=
Bio::EnsEMBL::
Registry
->
get_DBAdaptor
(
$species
,
$core
);
...
...
@@ -232,7 +230,6 @@ sub attach_database{
sub
attach_dna
{
my
(
$class
,
$species
,
$main
,
$attach
)
=
@_
;
print
STDERR
"
attach_dna called
"
.
caller
()
.
"
\n
";
my
$no_seq
=
Bio::EnsEMBL::
Registry
->
get_DBAdaptor
(
$species
,
$main
);
my
$seq
=
Bio::EnsEMBL::
Registry
->
get_DBAdaptor
(
$species
,
$attach
);
...
...
@@ -282,16 +279,14 @@ sub load_estgene{
Bio::EnsEMBL::
Registry
->
add_adaptor
(
$dba
->
species
,
$dba
->
group
,
$key
,
$pairs
{
$key
});
}
#if dnadb has been set then for the follwing use it.
foreach
my
$type
(
qw(Sequence AssemblyMapper KaryotypeBand RepeatFeature CoordSystem AssemblyExceptionFeature)
){
Bio::EnsEMBL::
Registry
->
set_get_via_dnadb_if_set
(
$dba
->
species
,
$type
);
}
## if the core exists then set this for the dna getting
my
$core
=
$reg
->
get_DBAdaptor
(
$dba
->
species
,"
core
");
if
(
defined
(
$core
)){
$reg
->
add_DNAAdaptor
(
$dba
->
species
,
$dba
->
group
,
$core
);
}
# #if dnadb has been set then for the follwing use it.
# foreach my $type (qw(Sequence AssemblyMapper KaryotypeBand RepeatFeature CoordSystem AssemblyExceptionFeature)){
# Bio::EnsEMBL::Registry->set_get_via_dnadb_if_set($dba->species,$type);
# }
$reg
->
add_DNAAdaptor
(
$dba
->
species
,
$dba
->
group
,"
core
");
}
...
...
@@ -305,13 +300,13 @@ sub load_est{
}
#if dnadb has been set then for the follwing use it.
foreach
my
$type
(
qw(Sequence AssemblyMapper KaryotypeBand RepeatFeature CoordSystem AssemblyExceptionFeature)
){
Bio::EnsEMBL::
Registry
->
set_get_via_dnadb_if_set
(
$dba
->
species
,
$type
);
}
my
$core
=
$reg
->
get_DBAdaptor
(
$dba
->
species
,"
core
");
if
(
defined
(
$core
)){
$reg
->
add_DNAAdaptor
(
$dba
->
species
,
$dba
->
group
,
$
core
);
}
#
foreach my $type (qw(Sequence AssemblyMapper KaryotypeBand RepeatFeature CoordSystem AssemblyExceptionFeature)){
#
Bio::EnsEMBL::Registry->set_get_via_dnadb_if_set($dba->species,$type);
#
}
#
my $core = $reg->get_DBAdaptor($dba->species,"core");
#
if(defined($core)){
$reg
->
add_DNAAdaptor
(
$dba
->
species
,
$dba
->
group
,
"
core
"
);
#
}
}
...
...
@@ -323,10 +318,10 @@ sub load_vega{
foreach
my
$key
(
keys
%pairs
){
Bio::EnsEMBL::
Registry
->
add_adaptor
(
$dba
->
species
,
$dba
->
group
,
$key
,
$pairs
{
$key
});
}
my
$core
=
$reg
->
get_DBAdaptor
(
$dba
->
species
,"
core
");
if
(
defined
(
$core
)){
$reg
->
add_DNAAdaptor
(
$dba
->
species
,
$dba
->
group
,
$
core
);
}
#
my $core = $reg->get_DBAdaptor($dba->species,"core");
#
if(defined($core)){
$reg
->
add_DNAAdaptor
(
$dba
->
species
,
$dba
->
group
,
"
core
"
);
#
}
}
...
...
@@ -397,7 +392,6 @@ sub load_pipeline{
sub
dnadb_add
{
my
$class
=
shift
;
my
(
$dnaspecies
,
$dnagroup
,
$species
,
$group
)
=
@_
;
print
STDERR
"
dnadb_add called
"
.
caller
()
.
"
\n
";
my
$dnadb
=
Bio::EnsEMBL::
Registry
->
get_DBAdaptor
(
$dnaspecies
,
$dnagroup
);
my
$featdb
=
Bio::EnsEMBL::
Registry
->
get_DBAdaptor
(
$species
,
$group
);
...
...
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