Merge branch 'feature/JAL-984splitAdjuster' into features/JAL-1793VCF

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

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 3e8390f..be6ba60 100644 (file)
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -2157,23 +2157,8 @@ public class AlignmentUtilsTests
             sf.links.get(0));
     assertEquals(ensembl, sf.getFeatureGroup());
 
-    // AAA -> TAA -> stop codon
-    sf = sfs.get(1);
-    assertEquals(1, sf.getBegin());
-    assertEquals(1, sf.getEnd());
-    assertEquals("nonsynonymous_variant", sf.getType());
-    assertEquals("p.Lys1null", sf.getDescription()); // stop codon badly handled
-    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(
-            "p.Lys1null var3|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var3",
-            sf.links.get(0));
-    assertEquals(dbSnp, sf.getFeatureGroup());
-
     // AAA -> CAA -> K/Q
-    sf = sfs.get(2);
+    sf = sfs.get(1);
     assertEquals(1, sf.getBegin());
     assertEquals(1, sf.getEnd());
     assertEquals("nonsynonymous_variant", sf.getType());
@@ -2188,7 +2173,7 @@ public class AlignmentUtilsTests
     assertEquals(dbSnp, sf.getFeatureGroup());
 
     // AAA -> GAA -> K/E
-    sf = sfs.get(3);
+    sf = sfs.get(2);
     assertEquals(1, sf.getBegin());
     assertEquals(1, sf.getEnd());
     assertEquals("nonsynonymous_variant", sf.getType());
@@ -2203,6 +2188,21 @@ public class AlignmentUtilsTests
             sf.links.get(0));
     assertEquals(ensembl, sf.getFeatureGroup());
 
+    // AAA -> TAA -> stop codon
+    sf = sfs.get(3);
+    assertEquals(1, sf.getBegin());
+    assertEquals(1, sf.getEnd());
+    assertEquals("stop_gained", sf.getType());
+    assertEquals("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",
+            sf.links.get(0));
+    assertEquals(dbSnp, sf.getFeatureGroup());
+
     // AAA -> AAG synonymous
     sf = sfs.get(4);
     assertEquals(1, sf.getBegin());