JAL-2897 more informative description on synonymous variants

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

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 2b45eee..0559e6b 100644 (file)
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -2193,13 +2193,13 @@ public class AlignmentUtilsTests
     assertEquals(1, sf.getBegin());
     assertEquals(1, sf.getEnd());
     assertEquals("stop_gained", sf.getType());
-    assertEquals("TAA", sf.getDescription());
+    assertEquals("Aaa/Taa", sf.getDescription());
     assertEquals("var3", sf.getValue("ID"));
     assertEquals("Bad", sf.getValue("clinical_significance"));
     assertEquals("ID=var3;clinical_significance=Bad", sf.getAttributes());
     assertEquals(1, sf.links.size());
     assertEquals(
-            "TAA var3|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var3",
+            "Aaa/Taa var3|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var3",
             sf.links.get(0));
     assertEquals(dbSnp, sf.getFeatureGroup());
 
@@ -2208,13 +2208,13 @@ public class AlignmentUtilsTests
     assertEquals(1, sf.getBegin());
     assertEquals(1, sf.getEnd());
     assertEquals("synonymous_variant", sf.getType());
-    assertEquals("AAG", sf.getDescription());
+    assertEquals("aaA/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",
+            "aaA/aaG var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4",
             sf.links.get(0));
     assertEquals(cosmic, sf.getFeatureGroup());
 
@@ -2238,13 +2238,13 @@ public class AlignmentUtilsTests
     assertEquals(2, sf.getBegin());
     assertEquals(2, sf.getEnd());
     assertEquals("synonymous_variant", sf.getType());
-    assertEquals("TTC", sf.getDescription());
+    assertEquals("ttT/ttC", sf.getDescription());
     assertEquals("var6", sf.getValue("ID"));
     assertNull(sf.getValue("clinical_significance"));
     assertEquals("ID=var6", sf.getAttributes());
     assertEquals(1, sf.links.size());
     assertEquals(
-            "TTC var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
+            "ttT/ttC var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
             sf.links.get(0));
     assertEquals(dbSnp, sf.getFeatureGroup());