Commit dfcd4545 authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
Browse files

POD and comment changes only. Some code in the POD was being formatted

as filled paragraphs.  Long lines shortened.  Spelling.
parent d26121e2
......@@ -15,42 +15,50 @@ Bio::EnsEMBL::Registry
Bio::EnsEMBL::Registry->load_all("configuration_file");
$gene_adaptor = Bio::EnsEMBL::Registry->get_adaptor("homo_sapiens","core","gene"))
$gene_adaptor =
Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "gene" );
=head1 DESCRIPTION
All Adaptors are stored/registered using this module. This module should then
be used to get the adaptors needed.
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 using the method load_all.
If a file is passed to load_all then this is used.
Else if the enviroment variable ENSEMBL_REGISTRY is set then this is used
Else if the file .ensembl_init in your home directory exist it is used.
The registry can be loaded from a configuration file using the load_all
method.
For the Web server ENSEMBL_REGISTRY should be set in SiteDefs.pm, which will
pass this on to load_all.
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.
For the Web server ENSEMBL_REGISTRY should be set in SiteDefs.pm. This
will then be passed on to load_all.
The registry can also be loaded via the method load_registry_from_db which
given a host will load the latest versions of the Ensembl databases from it.
The four types of registrys are for db adaptors, dba adaptors, dna adaptors
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
and the standard type.
=head2 db
These are registrys for backwards compatibillity and enable the subroutines
These are registries for backwards compatibility 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');
my $sfa = $self->adaptor()->db()->get_db_adaptor('blast');
We now want to change this to
my $sfa = Bio::EnsEMBL::Registry->get_adaptor("Human","core","blast");
my $sfa =
Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "blast" );
=head2 DBA
......@@ -60,12 +68,13 @@ 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;
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");
my $exon_adaptor =
Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "exon" );
=head2 DNA
......@@ -73,9 +82,9 @@ my $exon_adaptor = Bio::EnsEMBL::Registry->get_adaptor("Human","core","Exon");
This is an internal Registry and allows the configuration of a dnadb.
An example here is to set the est database to get its 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");
## 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
......@@ -85,7 +94,8 @@ Slice Adaptor etc.
These are accessed by the get_adaptor subroutine i.e.
my $exon_adaptor = Bio::EnsEMBL::Registry->get_adaptor("Human","core","Exon");
my $exon_adaptor =
Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "exon" );
=head1 CONTACT
......@@ -114,18 +124,26 @@ my $API_VERSION = 45;
=head2 load_all
Will load the registry with the configuration file which is obtained from
the first in the following and in that order.
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.
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
3) If the file .ensembl_init exist in the home directory, it is used
as the configuration file.
Arg [1] : (optional) string $arg file to load the registry from
Arg [2] : (optional) string if set prints out messages about conf file used.
Arg [3] : (optional) string if not 0 will print out all information
Arg [4] : (optional) string if 1 the db connection will not be cleared, if not set
the db connections will be cleared ( default )
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).
Example : Bio::EnsEMBL::Registry->load_all();
Returntype : none
Exceptions : none
......@@ -199,7 +217,7 @@ sub clear{
}
#
# db adaptors. (for backwards compatibillity)
# db adaptors. (for backwards compatibility)
#
=head2 add_db
......@@ -211,7 +229,7 @@ sub clear{
Returntype : none
Exceptions : none
Status : At Risk.
: This is here for backwards compatibillity only and may be removed
: This is here for backwards compatibility only and may be removed
: eventually. Solution is to make sure the db and the adaptor have
: the same species and the call is then no longer needed.
......@@ -234,7 +252,7 @@ sub add_db{
Returntype : adaptor
Exceptions : none
Status : At Risk.
: This is here for backwards compatibillity only and may be removed
: This is here for backwards compatibility only and may be removed
: eventually. Solution is to make sure the db and the adaptor have
: the same species and the call is then no longer needed.
......@@ -257,7 +275,7 @@ sub remove_db{
Returntype : adaptor
Exceptions : none
Status : At Risk.
: This is here for backwards compatibillity only and may be removed
: This is here for backwards compatibility only and may be removed
: eventually. Solution is to make sure the db and the adaptor have
: the same species then call get_DBAdaptor instead.
......@@ -281,7 +299,7 @@ sub get_db{
Returntype : adaptor
Exceptions : none
Status : At Risk.
: This is here for backwards compatibillity only and may be removed
: This is here for backwards compatibility only and may be removed
: eventually. Solution is to make sure the dbs all have
: the same species then call get_all_DBAdaptors(-species => "human");
......
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