JAL-1793 update spike build to latest incl stop and synonymous variants on peptides

[jalview.git] / test / jalview / io / vcf / VCFLoaderTest.java

diff --git a/test/jalview/io/vcf/VCFLoaderTest.java b/test/jalview/io/vcf/VCFLoaderTest.java
index a02cc5a..7099282 100644 (file)
--- 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");
 
     /*