JAL-2920 don’t output variant/original sequence as three-letter codes for more than...

[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 c7f216e..ab79f10 100644 (file)
--- a/test/jalview/ws/dbsources/UniprotTest.java
+++ b/test/jalview/ws/dbsources/UniprotTest.java
@@ -69,6 +69,7 @@ public class UniprotTest
           + "<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>"
           + "<feature type=\"sequence variant\" description=\"Foo\"><variation>LL</variation><variation>LMV</variation><original>ML</original><location><begin position=\"42\"/><end position=\"43\"/></location></feature>"
+          + "<feature type=\"sequence variant\" description=\"Foo Too\"><variation>LL</variation><variation>LMVK</variation><original>MLML</original><location><begin position=\"42\"/><end position=\"45\"/></location></feature>"
           + "<sequence length=\"10\" mass=\"27410\" checksum=\"8CB760AACF88FE6C\" modified=\"2008-01-15\" version=\"1\">MHAPL VSKDL</sequence></entry>"
           + "</uniprot>";
 
@@ -104,7 +105,7 @@ public class UniprotTest
      * Check sequence features
      */
     Vector<UniprotFeature> features = entry.getFeature();
-    assertEquals(8, features.size());
+    assertEquals(9, features.size());
     UniprotFeature sf = features.get(0);
     assertEquals("signal peptide", sf.getType());
     assertNull(sf.getDescription());
@@ -159,9 +160,17 @@ public class UniprotTest
     assertEquals(42, sf.getBegin());
     assertEquals(43, sf.getEnd());
     Assert.assertEquals(Uniprot.getDescription(sf),
-            "p.MetLeu42LeuLeu" + "\n" + "p.MetLeu42LeuMetVal Foo"); /*
-                                                                    * Check cross-references
-                                                                    */
+            "p.MetLeu42LeuLeu" + "\n" + "p.MetLeu42LeuMetVal Foo");
+
+    sf = features.get(8);
+    assertEquals(42, sf.getBegin());
+    assertEquals(45, sf.getEnd());
+    Assert.assertEquals(Uniprot.getDescription(sf),
+            "p.MLML42LeuLeu" + "\n" + "p.MLML42LMVK Foo Too");
+
+    /*
+     * Check cross-references
+     */
     Vector<PDBEntry> xrefs = entry.getDbReference();
     assertEquals(3, xrefs.size());