Updates to reflect changes in SequenceOntologyMapper interface.

Removed dependencies on non-core APIs.

modules/t/sequenceOntologyMapper.t

@@ -25,10 +25,6 @@ use Bio::EnsEMBL::Slice;
 use Bio::EnsEMBL::SimpleFeature; 
 use Bio::EnsEMBL::MiscFeature; 
 use Bio::EnsEMBL::RepeatFeature;
-use Bio::EnsEMBL::Variation::VariationFeature;
-use Bio::EnsEMBL::Variation::StructuralVariationFeature;
-use Bio::EnsEMBL::Compara::ConstrainedElement; 
-use Bio::EnsEMBL::Funcgen::RegulatoryFeature;
 
 # Module compiles
 ok(1, 'Bio::EnsEMBL::Utils::SequenceOntologyMapper compiles');
@@ -37,22 +33,9 @@ ok(1, 'Bio::EnsEMBL::Utils::SequenceOntologyMapper compiles');
 # Test constructor
 #
 throws_ok { new Bio::EnsEMBL::Utils::SequenceOntologyMapper() } 
-  qr /No ontology term adaptor/, "constructor with no argument raises exception";
+  qr /No ontology term adaptor/, "constructor with no arg raises exception";
 throws_ok { new Bio::EnsEMBL::Utils::SequenceOntologyMapper(bless({}, 'Someclass')) } 
-  qr /Argument is not/, "constructor with object not of class OntologyTermAdaptor raises exception";
-
-# my $registry = 'Bio::EnsEMBL::Registry';
-# Bio::EnsEMBL::Registry->no_version_check(1);
-# Bio::EnsEMBL::Registry->no_cache_warnings(1);
-
-# $registry->load_registry_from_db(-host => '127.0.0.1',
-# 				 -port => 33061,
-# 				 -db_version => 73,
-# 				 -user => 'ensro',
-# 				 -no_cache => 1);
-				 
-# my $oa = $registry->get_adaptor( 'Multi', 'Ontology', 'OntologyTerm' );
-# assert_ref($oa, 'Bio::EnsEMBL::DBSQL::OntologyTermAdaptor');
+  qr /Argument is not/, "constructor with arg not of class OntologyTermAdaptor raises exception";
 
 my $omulti = Bio::EnsEMBL::Test::MultiTestDB->new('ontology');
 my $odb = $omulti->get_DBAdaptor('ontology');
@@ -62,33 +45,41 @@ my $mapper = Bio::EnsEMBL::Utils::SequenceOntologyMapper->new($oa);
 isa_ok($mapper, 'Bio::EnsEMBL::Utils::SequenceOntologyMapper');
 
 #
-# Test translate method
+# Test to_accession/to_name methods
 #
 my $multi = Bio::EnsEMBL::Test::MultiTestDB->new;
 my $db = $multi->get_DBAdaptor('core');
 
 my $mappings =
   [
-   { obj => Bio::EnsEMBL::Feature->new, term => 'region' },
-   { obj => Bio::EnsEMBL::Gene->new, term => 'gene' },
-   { obj => Bio::EnsEMBL::Transcript->new, term => 'transcript' },
-   { obj => Bio::EnsEMBL::Exon->new, term => 'exon' },
-   { obj => $db->get_SliceAdaptor->fetch_by_region('chromosome', '20', 30_270_000, 31_200_000), term => 'region' },
-   { obj => Bio::EnsEMBL::SimpleFeature->new(), term => 'biological_region' },
-   { obj => Bio::EnsEMBL::MiscFeature->new(), term => 'biological_region' },
-   { obj => Bio::EnsEMBL::RepeatFeature->new(), term => 'repeat_region' },
-   { obj => Bio::EnsEMBL::Variation::VariationFeature->new(), term => 'sequence_variant' },
-   { obj => Bio::EnsEMBL::Variation::StructuralVariationFeature->new(), term => 'structural_variant' },
-   { obj => Bio::EnsEMBL::Compara::ConstrainedElement->new(), term => 'DNA_constraint_sequence' }
-
-   # 'Bio::EnsEMBL::Funcgen::RegulatoryFeature' => 'regulatory_region'
+   # test generic feature
+   { obj => Bio::EnsEMBL::Feature->new(), accession => 'SO:0000001', name => 'region' },
+   # test various genes with/without biotypes
+   { obj => Bio::EnsEMBL::Gene->new(), accession => 'SO:0000704', name => 'gene' },
+   { obj => Bio::EnsEMBL::Gene->new(-biotype => 'protein_coding'), accession => 'SO:0001217', name => 'protein_coding_gene' },
+   { obj => Bio::EnsEMBL::Gene->new(-biotype => 'tRNA'), accession => 'SO:0001272', name => 'tRNA_gene' },
+   # test various transcripts with/without biotypes
+   { obj => Bio::EnsEMBL::Transcript->new(), accession => 'SO:0000673', name => 'transcript' },
+   { obj => Bio::EnsEMBL::Transcript->new(-biotype => 'processed_transcript'), accession => 'SO:0001503', name => 'processed_transcript' },
+   { obj => Bio::EnsEMBL::Transcript->new(-biotype => 'retrotransposed'), accession => 'SO:0000569', name => 'retrotransposed' },
+   # exons
+   { obj => Bio::EnsEMBL::Exon->new, accession => 'SO:0000147', name => 'exon' },
+   # slices
+   { obj => $db->get_SliceAdaptor->fetch_by_region('chromosome', '20', 30_270_000, 31_200_000), accession => 'SO:0000001', name => 'region' },
+   # simple features
+   { obj => Bio::EnsEMBL::SimpleFeature->new(), accession => 'SO:0001411', name => 'biological_region' },
+   # misc features
+   { obj => Bio::EnsEMBL::MiscFeature->new(), accession => 'SO:0001411', name => 'biological_region' },
+   # repeat feature
+   { obj => Bio::EnsEMBL::RepeatFeature->new(), accession => 'SO:0000657', name => 'repeat_region' },
   ];
 
 throws_ok { $mapper->translate( bless({}, 'Someclass')) } 
   qr /not found/, "translate method raises exception";
 
 map { 
-  print ref($_->{obj}) and is($mapper->translate($_->{obj}), $_->{term}, sprintf "%s translates as assumed", ref($_->{obj})) }
+  is($mapper->to_accession($_->{obj}), $_->{accession}, sprintf "%s maps to correct accession", ref($_->{obj})) and
+    is($mapper->to_name($_->{obj}), $_->{name}, sprintf "%s maps to correct", ref($_->{obj})) }
   @{$mappings};
 
 done_testing();