test changes for addition of external_db_id and hcoverage to XXXalignfeatures.

modules/t/dnaAlignFeatureAdaptor.t

@@ -2,7 +2,7 @@ use strict;
 
 BEGIN { $| = 1;
 	use Test;
-	plan tests => 23;
+	plan tests => 25;
 }
 
 
@@ -97,6 +97,8 @@ my $score      = 80;
 my $percent_id = 90;
 my $evalue     = 23.2;
 my $cigar_string = '100M';
+my $hcoverage  = 99.5;
+my $external_db_id = 2200;
 
 $feat = Bio::EnsEMBL::DnaDnaAlignFeature->new
   (-START  => $start,
@@ -111,7 +113,9 @@ $feat = Bio::EnsEMBL::DnaDnaAlignFeature->new
    -PERCENT_ID => $percent_id,
    -SCORE    => $score,
    -P_VALUE => $evalue,
-   -ANALYSIS => $analysis);
+   -ANALYSIS => $analysis,
+   -HCOVERAGE => $hcoverage,
+   -EXTERNAL_DB_ID => $external_db_id );
 
 ok(!$feat->is_stored($db));
 
@@ -137,6 +141,8 @@ ok($feat->percent_id == $percent_id);
 ok($feat->score == $score);
 ok($feat->p_value == $evalue);
 ok($feat->analysis->logic_name eq $analysis->logic_name);
+ok($feat->external_db_id == $external_db_id);
+ok($feat->hcoverage == $hcoverage);
 
 $multi->restore('core', 'dna_align_feature');
 

modules/t/proteinAlignFeatureAdaptor.t

 
 BEGIN { $| = 1;
 	use Test;
-	plan tests => 22;
+	plan tests => 24;
 }
 
 
@@ -98,6 +98,8 @@ my $score      = 80;
 my $percent_id = 90;
 my $evalue     = 23.2;
 my $cigar_string = '100M';
+my $hcoverage  = 99.5;
+my $external_db_id = 2200;
 
 $feat = Bio::EnsEMBL::DnaPepAlignFeature->new
   (-START  => $start,
@@ -112,7 +114,9 @@ $feat = Bio::EnsEMBL::DnaPepAlignFeature->new
    -PERCENT_ID => $percent_id,
    -SCORE    => $score,
    -P_VALUE => $evalue,
-   -ANALYSIS => $analysis);
+   -ANALYSIS => $analysis,
+   -HCOVERAGE => $hcoverage,
+   -EXTERNAL_DB_ID => $external_db_id );
 
 ok(!$feat->is_stored($db));
 
@@ -137,6 +141,8 @@ ok($feat->percent_id == $percent_id);
 ok($feat->score == $score);
 ok($feat->p_value == $evalue);
 ok($feat->analysis->logic_name eq $analysis->logic_name);
+ok($feat->external_db_id == $external_db_id);
+ok($feat->hcoverage == $hcoverage);
 
 $multi->restore('core', 'protein_align_feature');
 

modules/t/test-genome-DBs/homo_sapiens/core/dna_align_feature.sql

@@ -13,10 +13,13 @@ CREATE TABLE `dna_align_feature` (
   `evalue` double default NULL,
   `perc_ident` float default NULL,
   `cigar_line` text collate latin1_bin,
-  PRIMARY KEY  (`dna_align_feature_id`),
+  `external_db_id` smallint(5) unsigned default NULL,
+  `hcoverage` double default NULL,
+   PRIMARY KEY  (`dna_align_feature_id`),
   KEY `seq_region_idx` (`seq_region_id`,`analysis_id`,`seq_region_start`,`score`),
   KEY `seq_region_idx_2` (`seq_region_id`,`seq_region_start`),
   KEY `hit_idx` (`hit_name`),
-  KEY `analysis_idx` (`analysis_id`)
+  KEY `analysis_idx` (`analysis_id`),
+  KEY `external_db_idx` (`external_db_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
 

modules/t/test-genome-DBs/homo_sapiens/core/meta.txt

-1	schema_version	46
+1	schema_version	47
 2	assembly.default	NCBI34
 33	species.classification	Chordata
 32	species.classification	Vertebrata

modules/t/test-genome-DBs/homo_sapiens/core/protein_align_feature.sql

@@ -11,11 +11,14 @@ CREATE TABLE `protein_align_feature` (
   `score` double default NULL,
   `evalue` double default NULL,
   `perc_ident` float default NULL,
-  `cigar_line` text collate latin1_bin,
-  PRIMARY KEY  (`protein_align_feature_id`),
+  `cigar_line` text collate latin1_bin,  
+  `external_db_id` smallint(5) unsigned default NULL,
+  `hcoverage` double default NULL,
+   PRIMARY KEY  (`protein_align_feature_id`),
   KEY `seq_region_idx` (`seq_region_id`,`analysis_id`,`seq_region_start`,`score`),
   KEY `seq_region_idx_2` (`seq_region_id`,`seq_region_start`),
   KEY `hit_idx` (`hit_name`),
-  KEY `analysis_idx` (`analysis_id`)
+  KEY `analysis_idx` (`analysis_id`),
+  KEY `external_db_idx` (`external_db_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;