From 06366e07c7f28dc24cdcfd856d608770e05adf36 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Mon, 16 Feb 2009 13:56:54 +0000
Subject: [PATCH] Clean up new(), esp. POD.
---
modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm | 71 ++++++++++++++------------
1 file changed, 39 insertions(+), 32 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
index 6f2465bfe0..82cd968421 100755
--- a/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
@@ -56,38 +56,45 @@ my $reg = "Bio::EnsEMBL::Registry";
=head2 new
Arg [-DNADB]: (optional) Bio::EnsEMBL::DBSQL::DBAdaptor DNADB
- All sequence, assembly, contig information etc, will be
- retrieved from this database instead.
+ All sequence, assembly, contig information etc, will
+ be retrieved from this database instead.
+
Arg [-NO_CACHE]: (optional) int 1
- This option will turn off caching for slice features, so,
- every time a set of features is retrieved, they will come from
- the database instead of the cache. This option is only recommended
- for advanced users, specially if you need to store and retrieve
- features. It might reduce performance when querying the database if
- not used properly. If in doubt, do not use it or ask in ensembl-dev
+ This option will turn off caching for slice features,
+ so, every time a set of features is retrieved,
+ they will come from the database instead of the
+ cache. This option is only recommended for advanced
+ users, specially if you need to store and retrieve
+ features. It might reduce performance when querying
+ the database if not used properly. If in doubt, do
+ not use it or ask in ensembl-dev.
+
Arg [..] : Other args are passed to superclass
Bio::EnsEMBL::DBSQL::DBConnection
+
Example : $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(
- -user => 'root',
- -dbname => 'pog',
- -host => 'caldy',
- -driver => 'mysql' );
+ -user => 'root',
+ -dbname => 'pog',
+ -host => 'caldy',
+ -driver => 'mysql'
+ );
+
Exmaple2 : $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(
- -species => 'Homo_sapiens',
- -group => 'core'
- -user => 'root',
- -dbname => 'pog',
- -host => 'caldy',
- -driver => 'mysql');
+ -species => 'Homo_sapiens',
+ -group => 'core' -user => 'root',
+ -dbname => 'pog',
+ -host => 'caldy',
+ -driver => 'mysql'
+ );
Exmaple3 : $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(
- -species => 'staphylococcus_aureus',
- -group => 'core'
- -user => 'root',
- -dbname => 'staphylococcus_collection_1_52_1a',
- -multispecies_db => 1,
- -host => 'caldy',
- -driver => 'mysql');
+ -species => 'staphylococcus_aureus',
+ -group => 'core' -user => 'root',
+ -dbname => 'staphylococcus_collection_1_52_1a',
+ -multispecies_db => 1,
+ -host => 'caldy',
+ -driver => 'mysql'
+ );
Description: Constructor for DBAdaptor.
Returntype : Bio::EnsEMBL::DBSQL::DBAdaptor
@@ -103,13 +110,13 @@ sub new {
my $self = bless {}, $class;
my ( $is_multispecies, $species, $species_id, $group, $con, $dnadb,
- $no_cache )
- = rearrange( [ 'MULTISPECIES_DB', 'SPECIES',
- 'SPECIES_ID', 'GROUP',
- 'DBCONN', 'DNADB',
- 'NO_CACHE'
- ],
- @args );
+ $no_cache )
+ = rearrange( [
+ 'MULTISPECIES_DB', 'SPECIES', 'SPECIES_ID', 'GROUP',
+ 'DBCONN', 'DNADB', 'NO_CACHE'
+ ],
+ @args
+ );
if ( defined($con) ) { $self->dbc($con) }
else {
--
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