JAL-2920 use HGVS notation for protein variant feature

[jalview.git] / test / jalview / ws / dbsources / UniprotTest.java

diff --git a/test/jalview/ws/dbsources/UniprotTest.java b/test/jalview/ws/dbsources/UniprotTest.java
index c603a11..0ee4388 100644 (file)
--- a/test/jalview/ws/dbsources/UniprotTest.java
+++ b/test/jalview/ws/dbsources/UniprotTest.java
@@ -123,22 +123,21 @@ public class UniprotTest
 
     sf = features.get(3);
     assertEquals("sequence variant", sf.getType());
-    assertEquals("Variation: 'L' Original: 'M'", sf.getDescription());
+    assertNull(sf.getDescription());
     assertEquals(41, sf.getPosition());
     assertEquals(41, sf.getBegin());
     assertEquals(41, sf.getEnd());
 
     sf = features.get(4);
     assertEquals("sequence variant", sf.getType());
-    assertEquals("Pathogenic Variation: 'L' Original: 'M'",
-            sf.getDescription());
+    assertEquals("Pathogenic", sf.getDescription());
     assertEquals(41, sf.getPosition());
     assertEquals(41, sf.getBegin());
     assertEquals(41, sf.getEnd());
 
     sf = features.get(5);
     assertEquals("sequence variant", sf.getType());
-    assertEquals("Pathogenic Original: 'M'", sf.getDescription());
+    assertEquals("Pathogenic", sf.getDescription());
     assertEquals(41, sf.getPosition());
     assertEquals(41, sf.getBegin());
     assertEquals(41, sf.getEnd());
@@ -210,4 +209,25 @@ public class UniprotTest
     assertEquals(expectedDescription,
             Uniprot.getUniprotEntryDescription(entry));
   }
+
+  @Test(groups = { "Functional" })
+  public void testGetDescription()
+  {
+    UniprotFeature uf = new UniprotFeature();
+    assertEquals("", Uniprot.getDescription(uf));
+
+    uf.setDescription("Hello");
+    assertEquals("Hello", Uniprot.getDescription(uf));
+
+    uf.setPosition(23);
+    uf.setOriginal("K");
+    uf.setVariation("y");
+    assertEquals("p.Lys23Tyr Hello", Uniprot.getDescription(uf));
+
+    uf.setVariation("z"); // unknown variant - fails gracefully
+    assertEquals("p.Lys23z Hello", Uniprot.getDescription(uf));
+
+    uf.setVariation(null); // variant missing - is ignored
+    assertEquals("Hello", Uniprot.getDescription(uf));
+  }
 }