From 13e35e323f5498b1ae914d9ee7c368bcb97727d2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Thu, 8 May 2008 16:29:03 +0000
Subject: [PATCH] Reorganize order of attributes so that the ones which comes
straight out of the feature table are first and in the order thay are defined
in the SQL schema.
---
modules/Bio/EnsEMBL/Collection/Exon.pm | 26 +++++++++----------
.../Bio/EnsEMBL/Collection/RepeatFeature.pm | 15 ++++++-----
2 files changed, 21 insertions(+), 20 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Collection/Exon.pm b/modules/Bio/EnsEMBL/Collection/Exon.pm
index 5d5a89ab98..feb80c039b 100644
--- a/modules/Bio/EnsEMBL/Collection/Exon.pm
+++ b/modules/Bio/EnsEMBL/Collection/Exon.pm
@@ -27,23 +27,23 @@ End phase
=item 3.
-Stable ID
+Is-current
=item 4.
-Version
+Stable ID
=item 5.
-Created date
+Version
=item 6.
-Modified date
+Created date
=item 7.
-Is-current
+Modified date
=back
@@ -64,18 +64,18 @@ sub _create_feature {
my $feature = $this->SUPER::_create_feature( $feature_type, $args );
if ( !$this->lightweight() ) {
- my ( $phase, $end_phase, $stable_id, $version, $created_date,
- $modified_date, $is_current )
- = rearrange( [ 'PHASE', 'END_PHASE',
- 'STABLE_ID', 'VERSION',
- 'CREATED_DATE', 'MODIFIED_DATE',
- 'IS_CURRENT'
+ my ( $phase, $end_phase, $is_current, $stable_id, $version,
+ $created_date, $modified_date )
+ = rearrange( [ 'PHASE', 'END_PHASE',
+ 'IS_CURRENT', 'STABLE_ID',
+ 'VERSION', 'CREATED_DATE',
+ 'MODIFIED_DATE'
],
%{$args} );
push( @{$feature},
- $phase, $end_phase, $stable_id, $version, $created_date,
- $modified_date, $is_current );
+ $phase, $end_phase, $is_current, $stable_id, $version,
+ $created_date, $modified_date );
}
return $feature;
diff --git a/modules/Bio/EnsEMBL/Collection/RepeatFeature.pm b/modules/Bio/EnsEMBL/Collection/RepeatFeature.pm
index a53656d67b..22907c18fa 100644
--- a/modules/Bio/EnsEMBL/Collection/RepeatFeature.pm
+++ b/modules/Bio/EnsEMBL/Collection/RepeatFeature.pm
@@ -19,23 +19,23 @@ feature representation:
=item 1.
-Hit start
+Repeat start
=item 2.
-Hit end
+Repeat end
=item 3.
-Score
+Repeat consensus internal ID
=item 4.
-Repeat consensus internal ID
+Analysis internal ID
=item 5.
-Analysis internal ID
+Score
=back
@@ -66,9 +66,10 @@ sub _create_feature_fast {
if ( !$this->lightweight() ) {
push( @{$feature},
- $args->{'hstart'}, $args->{'hend'}, $args->{'score'},
+ $args->{'hstart'}, $args->{'hend'},
$args->{'repeat_consensus'}->dbID(),
- $args->{'analysis'}->dbID() );
+ $args->{'analysis'}->dbID(),
+ $args->{'score'} );
}
return $feature;
--
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