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

[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..67d5d62 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 +67,9 @@ 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>"
+          + "<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>";
 
@@ -101,7 +105,7 @@ public class UniprotTest
      * Check sequence features
      */
     Vector<UniprotFeature> features = entry.getFeature();
-    assertEquals(6, features.size());
+    assertEquals(9, features.size());
     UniprotFeature sf = features.get(0);
     assertEquals("signal peptide", sf.getType());
     assertNull(sf.getDescription());
@@ -141,6 +145,29 @@ 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" + "\n" + "p.Met42LeuMetVal Foo");
+
+    sf = features.get(7);
+    assertEquals(42, sf.getBegin());
+    assertEquals(43, sf.getEnd());
+    Assert.assertEquals(Uniprot.getDescription(sf),
+            "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
      */
@@ -221,10 +248,39 @@ 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.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.setOriginal("K");
     assertEquals("p.Lys23z Hello", Uniprot.getDescription(uf));
 
     uf.setVariation(null); // variant missing - is ignored