From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 7 Jun 2018 08:06:16 +0000 (+0100)
Subject: Merge branch 'releases/Release_2_10_4_Branch' of https://source.jalview.org/git/jalvi... 
X-Git-Tag: Release_2_10_5~56
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=78d33c82e8371198bee7751731095d65aa1fc07c;hp=a464d457723dd96a6319632a7b717542d9de3843;p=jalview.git

Merge branch 'releases/Release_2_10_4_Branch' of https://source.jalview.org/git/jalview.git into releases/Release_2_10_4_Branch
---

diff --git a/test/jalview/ws/dbsources/UniprotTest.java b/test/jalview/ws/dbsources/UniprotTest.java
index ab79f10..67d5d62 100644
--- a/test/jalview/ws/dbsources/UniprotTest.java
+++ b/test/jalview/ws/dbsources/UniprotTest.java
@@ -248,14 +248,39 @@ 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));
 
+    vars.add("W");
+    assertEquals("p.Lys23Tyr\np.Lys23Trp Hello",
+            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 a condensed representation
+    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