From 91b2f5aafaa14ed12a4090fc8b90ccbd1f2dd43f Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Wed, 13 Apr 2016 12:51:53 +0100
Subject: [PATCH] moved method to parent class
---
modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm | 47 ++++++++++++++++++
.../Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm | 48 -------------------
2 files changed, 47 insertions(+), 48 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm
index 2640874188..f206ddc523 100755
--- a/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm
@@ -1113,5 +1113,52 @@ sub get_dumped_data {
return eval ($data); ## no critic
}
+#
+# Given a logic name and an existing constraint this will
+# add an analysis table constraint to the feature. Note that if no
+# analysis_id exists in the columns of the primary table then no
+# constraint is added at all
+#
+sub _logic_name_to_constraint {
+ my $self = shift;
+ my $constraint = shift;
+ my $logic_name = shift;
+
+ return $constraint if(!$logic_name);
+
+ #make sure that an analysis_id exists in the primary table
+ my ($prim_tab) = $self->_tables();
+ my $prim_synonym = $prim_tab->[1];
+
+ my $found_analysis=0;
+ foreach my $col ($self->_columns) {
+ my ($syn,$col_name) = split(/\./,$col);
+ next if($syn ne $prim_synonym);
+ if($col_name eq 'analysis_id') {
+ $found_analysis = 1;
+ last;
+ }
+ }
+
+ if(!$found_analysis) {
+ warning("This feature is not associated with an analysis.\n" .
+ "Ignoring logic_name argument = [$logic_name].\n");
+ return $constraint;
+ }
+
+ my $aa = $self->db->get_AnalysisAdaptor();
+ my $an = $aa->fetch_by_logic_name($logic_name);
+
+ if ( !defined($an) ) {
+ return undef;
+ }
+
+ my $an_id = $an->dbID();
+
+ $constraint .= ' AND' if($constraint);
+ $constraint .= " ${prim_synonym}.analysis_id = $an_id";
+ return $constraint;
+}
+
1;
diff --git a/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
index 477715299e..06e320d1ad 100755
--- a/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
@@ -1166,54 +1166,6 @@ sub _remap {
}
-#
-# Given a logic name and an existing constraint this will
-# add an analysis table constraint to the feature. Note that if no
-# analysis_id exists in the columns of the primary table then no
-# constraint is added at all
-#
-sub _logic_name_to_constraint {
- my $self = shift;
- my $constraint = shift;
- my $logic_name = shift;
-
- return $constraint if(!$logic_name);
-
- #make sure that an analysis_id exists in the primary table
- my ($prim_tab) = $self->_tables();
- my $prim_synonym = $prim_tab->[1];
-
- my $found_analysis=0;
- foreach my $col ($self->_columns) {
- my ($syn,$col_name) = split(/\./,$col);
- next if($syn ne $prim_synonym);
- if($col_name eq 'analysis_id') {
- $found_analysis = 1;
- last;
- }
- }
-
- if(!$found_analysis) {
- warning("This feature is not associated with an analysis.\n" .
- "Ignoring logic_name argument = [$logic_name].\n");
- return $constraint;
- }
-
- my $aa = $self->db->get_AnalysisAdaptor();
- my $an = $aa->fetch_by_logic_name($logic_name);
-
- if ( !defined($an) ) {
- return undef;
- }
-
- my $an_id = $an->dbID();
-
- $constraint .= ' AND' if($constraint);
- $constraint .= " ${prim_synonym}.analysis_id = $an_id";
- return $constraint;
-}
-
-
=head2 store
Arg [1] : list of Bio::EnsEMBL::SeqFeature
--
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