Updated POD for fetch_all_by_Transcript, updated test and test data

modules/Bio/EnsEMBL/DBSQL/TranscriptSupportingFeatureAdaptor.pm

@@ -63,12 +63,15 @@ use vars qw(@ISA);
 
   Arg [1]    : Bio::EnsEMBL::Transcript $transcript 
                The transcript to fetch supporting features for
+  Arg [2]	 : String (optional)
+  			   Feature type to filter upon (either 'dna_align_feature' or 'protein_align_feature')
   Example    : @sfs = @{$supporting_feat_adaptor->fetch_all_by_Transcript($transcript)};
+  			   @sfs = @{$supporting_feat_adaptor->fetch_all_by_Transcript($transcript, $feature_type)};	
   Description: Retrieves supporting features (evidence) for a given transcript. 
   Returntype : list of Bio::EnsEMBL::BaseAlignFeatures in the same coordinate
                system as the $transcript argument
   Exceptions : warning if $transcript is not in the database (i.e. dbID not defined)
-               throw if a retrieved supporting feature is of unknown type 
+               throw if a retrieved or requested supporting feature is of unknown type 
   Caller     : Bio::EnsEMBL::Transcript
   Status     : Stable
 
@@ -117,19 +120,18 @@ sub fetch_all_by_Transcript {
  
       push @{$out_feature_type->{$type}}, $new_feature if ($new_feature);
     }
-  }
-	  $sth->finish();
-
-   
-   if(defined $feature_type){
-   	return $out_feature_type->{$feature_type};
-   }else{
+    }
+	
+	$sth->finish();
    
-  	while(my ($feature_type, $new_features) = each(%$out_feature_type)){
-  		push @$out, @{$new_features};
+    if(defined $feature_type){
+      return $out_feature_type->{$feature_type};
+    }else{
+      while(my ($feature_type, $new_features) = each(%$out_feature_type)){
+      	push @$out, @{$new_features};
   	}
   	
-  }
+    }
   
    return $out;
 }

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

@@ -23,4 +23,5 @@
 21738	18273	1282	469283	31166507	31196939	1	97759	ensembl	protein_coding	KNOWN	\N	1	21738	ENST00000217347	1	2004-12-06 12:00:00	2004-12-06 12:00:00
 21739	18274	1282	469283	31210077	31225346	1	0	ensembl	protein_coding	NOVEL	\N	1	21739	ENST00000300425	1	2004-12-06 12:00:00	2004-12-06 12:00:00
 21740	18275	1282	965899	10060	10405	1	0	ensembl	protein_coding	NOVEL	\N	1	21740	ENST00000355555	1	2004-12-06 12:00:00	2004-12-06 12:00:00
-21741	18276	1282	317101	20000	21000	1	\N	ensembl	protein_coding	NOVEL	weird	1	21741	ENST00000111111	1	2014-12-11 14:00:00	2014-12-11 14:00:00
\ No newline at end of file
+21741	18276	1282	469290	1	150	1	\N	ensembl	protein_coding	NOVEL	weird	1	21741	ENST00000111111	1	2014-12-11 14:00:00	2014-12-11 14:00:00
+21742	18276	1282	317101	20000	21000	1	\N	ensembl	protein_coding	NOVEL	weird	1	21742	ENST00000222222	1	2016-08-15 14:00:00	2016-08-15 17:00:00
\ No newline at end of file

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

-21741	dna_align_feature	1449321
-21741	dna_align_feature	11290104
-21741	protein_align_feature	813252
-21741	protein_align_feature	813424
-21741	protein_align_feature	813184
\ No newline at end of file
+21742	dna_align_feature	1449321
+21742	dna_align_feature	11290104
+21742	protein_align_feature	813252
+21742	protein_align_feature	813424
+21742	protein_align_feature	813184
\ No newline at end of file

modules/t/transcriptSupportingFeatureAdaptor.t

@@ -15,13 +15,10 @@
 
 use strict;
 use Test::More;
+use Test::Exception;
 use Test::Warnings;
 use Bio::EnsEMBL::Test::MultiTestDB;
 
-use Bio::EnsEMBL::DnaDnaAlignFeature;
-use Bio::EnsEMBL::Test::TestUtils;
-use Data::Dumper;
-
 our $verbose = 0;
 
 my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
@@ -31,7 +28,7 @@ ok(1);
 #Fetch Transcript by stable_id and ensure it has a slice
 my $db = $multi->get_DBAdaptor('core');
 my $ta = $db->get_TranscriptAdaptor();
-my $tr = $ta->fetch_by_stable_id( "ENST00000111111" );
+my $tr = $ta->fetch_by_stable_id( "ENST00000222222" );
 ok($tr, "Fetched the Transcript by stable_id");
 ok($tr->slice(), "Transcript has slice");
 
@@ -66,5 +63,10 @@ foreach my $supporting_feature(@$supporting_features_dnas){
 	ok('Bio::EnsEMBL::DnaDnaAlignFeature' eq ref $supporting_feature, "Got back the right ref type: Bio::EnsEMBL::DnaDnaAlignFeature");
 }
 
+#Test exceptions with unknown feature_types
+dies_ok { $tsf_adaptor->fetch_all_by_Transcript($tr, "unknown_feature_type") } 'fetch_all_by_Transcript dies with unknown feature_type';
+throws_ok {$tsf_adaptor->fetch_all_by_Transcript($tr, "unknown_feature_type") } qr/feature type must be dna_align_feature or protein_align_feature/, 
+           'feature type must be dna_align_feature or protein_align_feature';
+
 
 done_testing();