JAL-3017 parse multiple variant elements for uniprot 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 0ee4388..b187b67 100644 (file)
--- a/test/jalview/ws/dbsources/UniprotTest.java
+++ b/test/jalview/ws/dbsources/UniprotTest.java
@@ -35,6 +35,7 @@ import java.io.Reader;
 import java.io.StringReader;
 import java.util.Vector;
 
+import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
@@ -66,6 +67,7 @@ public class UniprotTest
           + "<feature type=\"sequence variant\"><original>M</original><variation>L</variation><location><position position=\"41\"/></location></feature>"
           + "<feature type=\"sequence variant\" description=\"Pathogenic\"><original>M</original><variation>L</variation><location><position position=\"41\"/></location></feature>"
           + "<feature type=\"sequence variant\" description=\"Pathogenic\"><original>M</original><location><position position=\"41\"/></location></feature>"
+          + "<feature type=\"sequence variant\" description=\"Foo\"><variation>L</variation><variation>LMV</variation><original>M</original><location><position position=\"42\"/></location></feature>"
           + "<sequence length=\"10\" mass=\"27410\" checksum=\"8CB760AACF88FE6C\" modified=\"2008-01-15\" version=\"1\">MHAPL VSKDL</sequence></entry>"
           + "</uniprot>";
 
@@ -101,7 +103,7 @@ public class UniprotTest
      * Check sequence features
      */
     Vector<UniprotFeature> features = entry.getFeature();
-    assertEquals(6, features.size());
+    assertEquals(7, features.size());
     UniprotFeature sf = features.get(0);
     assertEquals("signal peptide", sf.getType());
     assertNull(sf.getDescription());
@@ -141,6 +143,16 @@ public class UniprotTest
     assertEquals(41, sf.getPosition());
     assertEquals(41, sf.getBegin());
     assertEquals(41, sf.getEnd());
+
+    sf = features.get(6);
+    assertEquals("sequence variant", sf.getType());
+    assertEquals("Foo",
+            sf.getDescription());
+    assertEquals(42, sf.getPosition());
+    assertEquals(42, sf.getBegin());
+    assertEquals(42, sf.getEnd());
+    Assert.assertEquals(Uniprot.getDescription(sf),
+            "p.Met42Leu<br/>p.Met42LeuMetVal Foo");
     /*
      * Check cross-references
      */
@@ -221,10 +233,14 @@ public class UniprotTest
 
     uf.setPosition(23);
     uf.setOriginal("K");
-    uf.setVariation("y");
+    Vector<String> vars = new Vector();
+    vars.add("y");
+    uf.setVariation(vars);
     assertEquals("p.Lys23Tyr Hello", Uniprot.getDescription(uf));
 
-    uf.setVariation("z"); // unknown variant - fails gracefully
+    vars.clear();
+    vars.add("z"); // unknown variant - fails gracefully
+    uf.setVariation(vars);
     assertEquals("p.Lys23z Hello", Uniprot.getDescription(uf));
 
     uf.setVariation(null); // variant missing - is ignored