JAL-2049 unit test updated for HGVS syntax, feature group = "Jalview"

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 860d979..2fc5325 100644 (file)
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -1968,60 +1968,65 @@ public class AlignmentUtilsTests
     SequenceFeature sf = sfs[0];
     assertEquals(1, sf.getBegin());
     assertEquals(1, sf.getEnd());
-    assertEquals("K->E", sf.getDescription());
+    assertEquals("p.Lys1Glu", sf.getDescription());
     assertEquals("var1.125A>G", sf.getValue("ID"));
     assertNull(sf.getValue("clinical_significance"));
     assertEquals("ID=var1.125A>G", sf.getAttributes());
     assertEquals(1, sf.links.size());
     // link to variation is urlencoded
     assertEquals(
-            "K->E var1.125A>G|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var1.125A%3EG",
+            "p.Lys1Glu var1.125A>G|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var1.125A%3EG",
             sf.links.get(0));
+    assertEquals("Jalview", sf.getFeatureGroup());
     sf = sfs[1];
     assertEquals(1, sf.getBegin());
     assertEquals(1, sf.getEnd());
-    assertEquals("K->Q", sf.getDescription());
+    assertEquals("p.Lys1Gln", sf.getDescription());
     assertEquals("var2", sf.getValue("ID"));
     assertEquals("Dodgy", sf.getValue("clinical_significance"));
     assertEquals("ID=var2;clinical_significance=Dodgy", sf.getAttributes());
     assertEquals(1, sf.links.size());
     assertEquals(
-            "K->Q var2|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var2",
+            "p.Lys1Gln var2|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var2",
             sf.links.get(0));
+    assertEquals("Jalview", sf.getFeatureGroup());
     sf = sfs[2];
     assertEquals(1, sf.getBegin());
     assertEquals(1, sf.getEnd());
-    assertEquals("K->N", sf.getDescription());
+    assertEquals("p.Lys1Asn", sf.getDescription());
     assertEquals("var4", sf.getValue("ID"));
     assertEquals("Benign", sf.getValue("clinical_significance"));
     assertEquals("ID=var4;clinical_significance=Benign", sf.getAttributes());
     assertEquals(1, sf.links.size());
     assertEquals(
-            "K->N var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4",
+            "p.Lys1Asn var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4",
             sf.links.get(0));
+    assertEquals("Jalview", sf.getFeatureGroup());
     sf = sfs[3];
     assertEquals(3, sf.getBegin());
     assertEquals(3, sf.getEnd());
-    assertEquals("P->H", sf.getDescription());
+    assertEquals("p.Pro3His", sf.getDescription());
     assertEquals("var6", sf.getValue("ID"));
     assertEquals("Good", sf.getValue("clinical_significance"));
     assertEquals("ID=var6;clinical_significance=Good", sf.getAttributes());
     assertEquals(1, sf.links.size());
     assertEquals(
-            "P->H var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
+            "p.Pro3His var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
             sf.links.get(0));
     // var5 generates two distinct protein variant features
+    assertEquals("Jalview", sf.getFeatureGroup());
     sf = sfs[4];
     assertEquals(3, sf.getBegin());
     assertEquals(3, sf.getEnd());
-    assertEquals("P->R", sf.getDescription());
+    assertEquals("p.Pro3Arg", sf.getDescription());
     assertEquals("var6", sf.getValue("ID"));
     assertEquals("Good", sf.getValue("clinical_significance"));
     assertEquals("ID=var6;clinical_significance=Good", sf.getAttributes());
     assertEquals(1, sf.links.size());
     assertEquals(
-            "P->R var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
+            "p.Pro3Arg var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
             sf.links.get(0));
+    assertEquals("Jalview", sf.getFeatureGroup());
   }
 
   /**