X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2Fvcf%2FVCFLoaderTest.java;h=70992829b5c5c91fc16e1d0e1f01fdb30b9ef868;hb=321caefc5a40cd735c93e0bfa450e0e04abc485d;hp=a02cc5a82c587253b55355bf28b1472d695b89a8;hpb=14b1b2a878190d5fffda298c4b9a901c72c74ad3;p=jalview.git

diff --git a/test/jalview/io/vcf/VCFLoaderTest.java b/test/jalview/io/vcf/VCFLoaderTest.java
index a02cc5a..7099282 100644
--- a/test/jalview/io/vcf/VCFLoaderTest.java
+++ b/test/jalview/io/vcf/VCFLoaderTest.java
@@ -170,7 +170,7 @@ public class VCFLoaderTest
     assertEquals(sf.getFeatureGroup(), "VCF");
     assertEquals(sf.getBegin(), 1);
     assertEquals(sf.getEnd(), 1);
-    assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
+    assertEquals(sf.getType(), SequenceOntologyI.NONSYNONYMOUS_VARIANT);
     assertEquals(sf.getDescription(), "p.Ser1Thr");
   }
 
@@ -425,7 +425,7 @@ public class VCFLoaderTest
     assertEquals(sf.getFeatureGroup(), "VCF");
     assertEquals(sf.getBegin(), 6);
     assertEquals(sf.getEnd(), 6);
-    assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
+    assertEquals(sf.getType(), SequenceOntologyI.NONSYNONYMOUS_VARIANT);
     assertEquals(sf.getDescription(), "p.Ala6Gly");
   }
 
@@ -570,12 +570,19 @@ public class VCFLoaderTest
       }
     }
     List<SequenceFeature> proteinFeatures = peptide.getSequenceFeatures();
-    assertEquals(proteinFeatures.size(), 1);
+    SequenceFeatures.sortFeatures(proteinFeatures, true);
+    assertEquals(proteinFeatures.size(), 2);
     sf = proteinFeatures.get(0);
     assertEquals(sf.getFeatureGroup(), "VCF");
+    assertEquals(sf.getBegin(), 1);
+    assertEquals(sf.getEnd(), 1);
+    assertEquals(sf.getType(), SequenceOntologyI.SYNONYMOUS_VARIANT);
+    assertEquals(sf.getDescription(), "AGT");
+    sf = proteinFeatures.get(1);
+    assertEquals(sf.getFeatureGroup(), "VCF");
     assertEquals(sf.getBegin(), 4);
     assertEquals(sf.getEnd(), 4);
-    assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
+    assertEquals(sf.getType(), SequenceOntologyI.NONSYNONYMOUS_VARIANT);
     assertEquals(sf.getDescription(), "p.Glu4Gly");
 
     /*