ENSCORESW-2758: default align type is NULL

modules/Bio/EnsEMBL/ProteinFeature.pm

@@ -108,7 +108,7 @@ sub new {
   $self->{'external_data'} = $external_data || '';
   $self->{'hit_description'} = $hit_description || '';
   $self->{'cigar_string'} = $cigar_string || '';
-  $self->{'align_type'} = $align_type || '';
+  $self->{'align_type'} = $align_type;
 
   return $self;
 }

sql/patch_93_94_c.sql

+-- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+-- Copyright [2016-2018] EMBL-European Bioinformatics Institute
+--
+-- Licensed under the Apache License, Version 2.0 (the "License");
+-- you may not use this file except in compliance with the License.
+-- You may obtain a copy of the License at
+--
+--      http://www.apache.org/licenses/LICENSE-2.0
+--
+-- Unless required by applicable law or agreed to in writing, software
+-- distributed under the License is distributed on an "AS IS" BASIS,
+-- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+-- See the License for the specific language governing permissions and
+-- limitations under the License.
+
+# patch_93_94_c.sql
+#
+# Title: Default align_type is 'ensembl'
+#
+# Description:
+#   Ensure default align_type in align_feature tables is 'ensembl'
+
+ALTER TABLE protein_feature MODIFY COLUMN align_type ENUM('ensembl', 'cigar', 'cigarplus', 'vulgar', 'mdtag') DEFAULT NULL;
+UPDATE protein_feature SET align_type = NULL WHERE align_type = '';
+
+# patch identifier
+INSERT INTO meta (species_id, meta_key, meta_value)
+  VALUES (NULL, 'patch', 'patch_93_94_c.sql|default_aln_type');

sql/table.sql

@@ -317,6 +317,8 @@ INSERT INTO meta (species_id, meta_key, meta_value)
   VALUES (NULL, 'patch', 'patch_93_94_a.sql|schema_version');
 INSERT INTO meta (species_id, meta_key, meta_value)
   VALUES (NULL, 'patch', 'patch_93_94_b.sql|nullable_ox_analysis');
+INSERT INTO meta (species_id, meta_key, meta_value)
+  VALUES (NULL, 'patch', 'patch_93_94_c.sql|default_aln_type');
 
 
 /**
@@ -962,7 +964,7 @@ CREATE TABLE protein_feature (
   external_data               TEXT,
   hit_description             TEXT,
   cigar_line                  TEXT,
-  align_type                  ENUM('ensembl', 'cigar', 'cigarplus', 'vulgar', 'mdtag'),
+  align_type                  ENUM('ensembl', 'cigar', 'cigarplus', 'vulgar', 'mdtag') DEFAULT NULL,
 
   UNIQUE KEY aln_idx (translation_id,hit_name,seq_start,seq_end,hit_start,hit_end,analysis_id),
   PRIMARY KEY (protein_feature_id),