Merge branch 'releases/Release_2_10_4_Branch' into develop

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

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 3e8390f..37b93fd 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());
@@ -2203,18 +2188,33 @@ 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("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(
+            "Aaa/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());
     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());
 
@@ -2223,13 +2223,13 @@ 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());