Merge branch 'spikes/mungo' into trialMerge

[jalview.git] / test / jalview / analysis / AlignmentUtilsTests.java

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index be6ba60..2b45eee 100644 (file)
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -2218,6 +2218,21 @@ public class AlignmentUtilsTests
             sf.links.get(0));
     assertEquals(cosmic, sf.getFeatureGroup());
 
+    // AAA -> AAG synonymous
+    sf = sfs.get(4);
+    assertEquals(1, sf.getBegin());
+    assertEquals(1, sf.getEnd());
+    assertEquals("synonymous_variant", sf.getType());
+    assertEquals("AAG", sf.getDescription());
+    assertEquals("var4", sf.getValue("ID"));
+    assertEquals("None", sf.getValue("clinical_significance"));
+    assertEquals("ID=var4;clinical_significance=None", sf.getAttributes());
+    assertEquals(1, sf.links.size());
+    assertEquals(
+            "AAG var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4",
+            sf.links.get(0));
+    assertEquals(cosmic, sf.getFeatureGroup());
+
     // TTT -> TTC synonymous
     sf = sfs.get(5);
     assertEquals(2, sf.getBegin());