From dfcd4545d008166c3b79494a137477ec90a1b749 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Tue, 29 May 2007 11:16:05 +0000
Subject: [PATCH] POD and comment changes only. Some code in the POD was being
formatted as filled paragraphs. Long lines shortened. Spelling.
---
modules/Bio/EnsEMBL/Registry.pm | 92 ++++++++++++++++++++-------------
1 file changed, 55 insertions(+), 37 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Registry.pm b/modules/Bio/EnsEMBL/Registry.pm
index 8cc1f628c2..adb505144b 100644
--- a/modules/Bio/EnsEMBL/Registry.pm
+++ b/modules/Bio/EnsEMBL/Registry.pm
@@ -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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