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ensembl-gh-mirror
ensembl
Commits
19ab0154
Commit
19ab0154
authored
Sep 10, 2004
by
Ian Longden
Browse files
backwards compatibillity fix
parent
e1538de3
Changes
3
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3 changed files
with
19 additions
and
152 deletions
+19
-152
modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
+1
-1
modules/Bio/EnsEMBL/Registry.pm
modules/Bio/EnsEMBL/Registry.pm
+5
-59
modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm
modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm
+13
-92
No files found.
modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
View file @
19ab0154
...
...
@@ -681,7 +681,7 @@ sub dnadb {
if
(
@
_
)
{
my
$arg
=
shift
;
$reg
->
add_DNAAdaptor
(
$self
->
species
(),
$self
->
group
(),
$arg
->
group
());
$reg
->
add_DNAAdaptor
(
$self
->
species
(),
$self
->
group
(),
$arg
->
species
(),
$arg
->
group
());
}
# return $self->{'dnadb'} || $self;
...
...
modules/Bio/EnsEMBL/Registry.pm
View file @
19ab0154
...
...
@@ -159,47 +159,6 @@ sub load_all{
}
}
#=head2 check_if_already_there
#
# Arg [DBNAME] : string
# The name of the database to check for.
# Arg [HOST] : (optional) string
# The domain name of the database host to check for
# Arg [PORT] : int
# The port to check for when connecting to the database
# Arg [DRIVER] : (optional) string
# The type of database driver to check for
#
# Description: Check to see if the database is already stored.
# Returntype : 0 if not found else the species and group.
# Exceptions : none
#
#
#=cut
#sub check_if_already_there{
# my ($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;
#}
#
# add ons.
#
...
...
@@ -382,16 +341,15 @@ sub get_all_DBAdaptors{
=cut
sub
add_DNAAdaptor
{
my
(
$class
,
$species
,
$group
,
$dnadb_group
)
=
@_
;
my
(
$class
,
$species
,
$group
,
$dnadb_species
,
$dnadb_group
)
=
@_
;
$species
=
$class
->
get_alias
(
$species
);
if
(
$dnadb_group
->
isa
('
Bio::EnsEMBL::DBSQL::DBAdaptor
')){
# print STDERR "AHHH ".caller()."\n";
$registry_register
{
$species
}{
$group
}{'
_DNA
'}
=
$dnadb_group
->
group
();
deprecated
("");
}
else
{
# print STDERR "AHHH MEN ".caller()."\n";
$registry_register
{
$species
}{
$group
}{'
_DNA
'}
=
$dnadb_group
;
$registry_register
{
$species
}{
$group
}{'
_DNA2
'}
=
$dnadb_species
;
}
}
...
...
@@ -410,8 +368,9 @@ sub get_DNAAdaptor{
$species
=
$class
->
get_alias
(
$species
);
my
$new_group
=
$registry_register
{
$species
}{
$group
}{'
_DNA
'};
my
$new_species
=
$registry_register
{
$species
}{
$group
}{'
_DNA2
'};
if
(
defined
$new_group
)
{
return
$class
->
get_DBAdaptor
(
$species
,
$new_group
);
return
$class
->
get_DBAdaptor
(
$
new_
species
,
$new_group
);
}
else
{
return
undef
;
}
...
...
@@ -525,25 +484,12 @@ sub get_adaptor{
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
(
$ret
)){
return
undef
;
# throw("COULD NOT FIND ADAPTOR species=$species\tgroup=$group\ttype=$type\n");
}
if
(
!
ref
(
$ret
)){
# not instantiated yet
my
$dba
=
$registry_register
{
$species
}{
$group
}{'
_DB
'};
...
...
modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm
View file @
19ab0154
...
...
@@ -52,6 +52,15 @@ use Bio::EnsEMBL::Utils::Exception qw(warning throw deprecate stack_trace_dump)
=cut
#
# 1) core. no need to add dnadb
# 2) not core add dnadb
# 3)
#
sub
gen_load
{
my
(
$dba
)
=
@_
;
my
$config_sub
;
...
...
@@ -102,6 +111,9 @@ sub gen_load{
$config_sub
=
\
&
Bio::EnsEMBL::Utils::ConfigRegistry::
load_haplotype
;
}
elsif
(
$dba
->
isa
('
Bio::EnsEMBL::Variation::DBSQL::DBAdaptor
')){
if
(
!
defined
(
$dba
->
group
())){
$dba
->
group
('
variation
');
}
$config_sub
=
\
&
Bio::EnsEMBL::Utils::ConfigRegistry::
load_variation
;
}
elsif
(
$dba
->
isa
('
Bio::EnsEMBL::DBSQL::DBAdaptor
')){
...
...
@@ -203,7 +215,7 @@ sub load_and_attach_dnadb_to_core{
load_adaptors
(
$dba
);
$reg
->
add_DNAAdaptor
(
$dba
->
species
,
$dba
->
group
,"
core
");
$reg
->
add_DNAAdaptor
(
$dba
->
species
,
$dba
->
group
,
$dba
->
species
,
"
core
");
}
# those that do not need to attach to core:-#
...
...
@@ -258,62 +270,6 @@ sub load_vega{
#special cases;-
sub
load_blast
{
my
(
$dba
)
=
@_
;
}
sub
add_blast_link
{
my
(
$class
,
$species
,
$group
)
=
@_
;
my
$dba
=
undef
;
my
$blast
=
undef
;
print
STDERR
"
add_blast_link called
\n
";
if
(
$dba
=
Bio::EnsEMBL::
Registry
->
get_DBAdaptor
(
$species
,
$group
)){
}
else
{
throw
("
Cannot find
$species
$group
in the registry
\n
");
}
if
(
$blast
=
Bio::EnsEMBL::
Registry
->
get_adaptor
("
NONE
",
"
blast
",
"
Blast
")){
$dba
->
add_db_adaptor
("
Blast
",
$blast
);
}
else
{
throw
("
Sorry no Blast database has been set up to link to.
\n
");
}
}
sub
load_go
{
my
(
$class
,
$dba
)
=
@_
;
# shouldnt go into the registry ... sorry
}
#sub dnadb_add{
# my $class = shift;
# my ($dnaspecies, $dnagroup, $species, $group) = @_;
#
# print STDERR "dnadb_add CALLED\n";
#
# my $dnadb = Bio::EnsEMBL::Registry->get_DBAdaptor($dnaspecies, $dnagroup);
# my $featdb = Bio::EnsEMBL::Registry->get_DBAdaptor($species, $group);
#
# $featdb->dnadb($dnadb);
#}
#
#
sub
add_alias
{
my
(
$class
,
@args
)
=
@_
;
my
(
$species
,
$aliases
)
=
rearrange
([
qw(SPECIES ALIAS)
],
@args
);
...
...
@@ -328,40 +284,6 @@ sub add_alias{
}
}
#
#
#sub get_alias{
# my ($class, $key) = @_;
# return Bio::EnsEMBL::Registry->get_alias($key);
#}
#
#
#
#sub attach_database{
# my ($class, $species, $core, $name1) = @_;
#
#
# print STDERR " attach_databse called\n";
#
# my $first = Bio::EnsEMBL::Registry->get_DBAdaptor($species,$name1);
# my $coredb = Bio::EnsEMBL::Registry->get_DBAdaptor($species,$core);
#
# Bio::EnsEMBL::Registry->add_db($coredb,$name1, $first);
#
#}
#
#sub attach_dna{
# my ($class, $species, $main, $attach) = @_;
# print STDERR " attach_dna called\n";
#
# my $no_seq = Bio::EnsEMBL::Registry->get_DBAdaptor($species,$main);
# my $seq = Bio::EnsEMBL::Registry->get_DBAdaptor($species,$attach);
#
# Bio::EnsEMBL::Registry->add_DNAAdaptor($species,$no_seq->group,$attach);
#}
#
# overwrite/load new types. Done this way to enable no changes to CVS for
# external users. External users should add there own "GROUPS" in the file
...
...
@@ -369,6 +291,5 @@ sub add_alias{
#
eval
{
require
Bio::EnsEMBL::Utils::
User_defined_load
};
#if ($@){ print STDERR "No user defined loads\n"; }
1
;
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