JAL-2738 assertion for derived protein variant added

diff --git a/test/jalview/io/vcf/VCFLoaderTest.java b/test/jalview/io/vcf/VCFLoaderTest.java
index 13c6f95..4a254d2 100644 (file)
--- a/test/jalview/io/vcf/VCFLoaderTest.java
+++ b/test/jalview/io/vcf/VCFLoaderTest.java
@@ -505,6 +505,31 @@ public class VCFLoaderTest
     assertTrue(sf.getValue("CSQ").toString().contains("transcript3"));
 
     /*
+     * verify variants computed on protein product for transcript3
+     * peptide is SWRECD
+     * codon variants are AGC/AGT position 1 which is synonymous
+     * and GAG/GGG which is E/G in position 4
+     * the insertion variant is not transferred to the peptide
+     */
+    DBRefEntry[] dbRefs = al.findName("transcript3").getDBRefs();
+    SequenceI peptide = null;
+    for (DBRefEntry dbref : dbRefs)
+    {
+      if (dbref.getMap().getMap().getFromRatio() == 3)
+      {
+        peptide = dbref.getMap().getTo();
+      }
+    }
+    List<SequenceFeature> proteinFeatures = peptide.getSequenceFeatures();
+    assertEquals(proteinFeatures.size(), 1);
+    sf = proteinFeatures.get(0);
+    assertEquals(sf.getFeatureGroup(), "VCF");
+    assertEquals(sf.getBegin(), 4);
+    assertEquals(sf.getEnd(), 4);
+    assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
+    assertEquals(sf.getDescription(), "p.Glu4Gly");
+
+    /*
      * verify variant feature(s) added to transcript4
      * at columns 13 (2) and 17 (2), positions 7 and 11
      */