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Merge branch 'bug/JAL-2846' into develop
[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 ab79f10..060c303 100644 (file)
--- a/test/jalview/ws/dbsources/UniprotTest.java
+++ b/test/jalview/ws/dbsources/UniprotTest.java
@@ -154,19 +154,22 @@ public class UniprotTest
     assertEquals(42, sf.getBegin());
     assertEquals(42, sf.getEnd());
     Assert.assertEquals(Uniprot.getDescription(sf),
-            "p.Met42Leu" + "\n" + "p.Met42LeuMetVal Foo");
+            "<html>p.Met42Leu" + "<br/>&nbsp;&nbsp;"
+                    + "p.Met42LeuMetVal Foo</html>");
 
     sf = features.get(7);
     assertEquals(42, sf.getBegin());
     assertEquals(43, sf.getEnd());
     Assert.assertEquals(Uniprot.getDescription(sf),
-            "p.MetLeu42LeuLeu" + "\n" + "p.MetLeu42LeuMetVal Foo");
+            "<html>p.MetLeu42LeuLeu" + "<br/>&nbsp;&nbsp;"
+                    + "p.MetLeu42LeuMetVal Foo</html>");
 
     sf = features.get(8);
     assertEquals(42, sf.getBegin());
     assertEquals(45, sf.getEnd());
     Assert.assertEquals(Uniprot.getDescription(sf),
-            "p.MLML42LeuLeu" + "\n" + "p.MLML42LMVK Foo Too");
+            "<html>p.MLML42LeuLeu" + "<br/>&nbsp;&nbsp;"
+                    + "p.MLML42LMVK Foo Too</html>");
 
     /*
      * Check cross-references
@@ -248,14 +251,38 @@ public class UniprotTest
 
     uf.setPosition(23);
     uf.setOriginal("K");
-    Vector<String> vars = new Vector();
+    Vector<String> vars = new Vector<>();
     vars.add("y");
     uf.setVariation(vars);
     assertEquals("p.Lys23Tyr Hello", Uniprot.getDescription(uf));
 
+    // multiple variants generate an html description over more than one line
+    vars.add("W");
+    assertEquals("<html>p.Lys23Tyr<br/>&nbsp;&nbsp;p.Lys23Trp Hello</html>",
+            Uniprot.getDescription(uf));
+
+    /*
+     * indel cases
+     * up to 3 bases (original or variant) are shown using 3 letter code
+     */
+    vars.clear();
+    vars.add("KWE");
+    uf.setOriginal("KLS");
+    assertEquals("p.LysLeuSer23LysTrpGlu Hello",
+            Uniprot.getDescription(uf));
+
+    // adding a fourth original base switches to single letter code
+    uf.setOriginal("KLST");
+    assertEquals("p.KLST23LysTrpGlu Hello", Uniprot.getDescription(uf));
+
+    // adding a fourth variant switches to single letter code
+    vars.clear();
+    vars.add("KWES");
+    assertEquals("p.KLST23KWES Hello", Uniprot.getDescription(uf));
+
     vars.clear();
     vars.add("z"); // unknown variant - fails gracefully
-    uf.setVariation(vars);
+    uf.setOriginal("K");
     assertEquals("p.Lys23z Hello", Uniprot.getDescription(uf));
 
     uf.setVariation(null); // variant missing - is ignored