From 68ded492cc54aa0c1ad11b9999d70c27586167e8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Tue, 11 Aug 2009 10:15:49 +0000
Subject: [PATCH] Remove on-the-fly addition of computed aliases. Now only
uses aliases from the meta table (the meta_key 'species.alias').
---
modules/Bio/EnsEMBL/Registry.pm | 47 +--------------------------------
1 file changed, 1 insertion(+), 46 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Registry.pm b/modules/Bio/EnsEMBL/Registry.pm
index fc5bd7325c..453b689b1a 100644
--- a/modules/Bio/EnsEMBL/Registry.pm
+++ b/modules/Bio/EnsEMBL/Registry.pm
@@ -1849,57 +1849,12 @@ sub find_and_add_aliases {
my @aliases;
my $species = $dba->species();
- # Some aliases are added programatically.
- # 1) The "species_name"
- # 2) The "species name"
- # 3) The "sname" (1+last part)
- # 4) The "snam" (1+3 letters)
- # 5) The "spenam" (3+3 letters)
-
- # Others are read from the meta table.
- # 6) Any species.alias
- # 7) The species.taxonomy_id
- # 8) The assembly.name
- # 9) The species.common_name (if it exists)
-
- # Add the unaltered species name as an alias.
- my $alias = $species;
- push( @aliases, $alias );
-
- # Remove the underscore from the species name and add the result as
- # an alias.
- $alias =~ tr [_] [ ];
- push( @aliases, $alias );
-
- # Add the first letter from the furst part of the species name,
- # together with the whole second part as an alias.
- $species =~ /^(.)[^_]*_(.*)$/;
- $alias = $1 . $2;
- push( @aliases, $alias );
-
- # As above, but only use the three first letter from the second
- # part.
- $species =~ /^(.)[^_]*_(...).*$/;
- $alias = $1 . $2;
- push( @aliases, $alias );
-
- # As above, but use three letters from first and second part.
- $species =~ /^(...)[^_]*_(...).*$/;
- $alias = $1 . $2;
- push( @aliases, $alias );
-
- # Get data from meta table:
-
if ( defined($dbh) ) {
my $dbname = $dba->dbc()->dbname();
my $sth = $dbh->prepare(
sprintf(
"SELECT meta_value FROM %s.meta "
- . "WHERE meta_key IN ("
- . "'species.alias', "
- . "'species.taxonomy_id', "
- . "'assembly.name', "
- . "'species.common_name') "
+ . "WHERE meta_key = 'species.alias' "
. "AND species_id = ?",
$dbh->quote_identifier($dbname) ) );
--
GitLab