JAL-3567 adjust layout of linked feature report, unit test

[jalview.git] / test / jalview / datamodel / SequenceFeatureTest.java

diff --git a/test/jalview/datamodel/SequenceFeatureTest.java b/test/jalview/datamodel/SequenceFeatureTest.java
index 673ea29..e105659 100644 (file)
--- a/test/jalview/datamodel/SequenceFeatureTest.java
+++ b/test/jalview/datamodel/SequenceFeatureTest.java
@@ -26,10 +26,14 @@ import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
+import java.util.ArrayList;
+import java.util.List;
+
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 import jalview.gui.JvOptionPane;
+import jalview.util.MapList;
 
 public class SequenceFeatureTest
 {
@@ -319,4 +323,37 @@ public class SequenceFeatureTest
             + "<tr><td>Group</td><td>Uniprot</td><td></td></tr></table>";
     assertEquals(expected, sf.getDetailsReport(seqName, null));
   }
+
+  /**
+   * Feature details report for a virtual feature should include original and
+   * mapped locations, and also derived peptide consequence if it can be
+   * determined
+   */
+  @Test(groups = { "Functional" })
+  public void testGetDetailsReport_virtualFeature()
+  {
+    SequenceI cds = new Sequence("Cds/101-121", "CCTttgAGAtttCAAatgGAT");
+    SequenceI seq = new Sequence("TestSeq/8-14", "PLRFQMD");
+    MapList map = new MapList(new int[] { 101, 118 }, new int[] { 8, 13 },
+            3, 1);
+    Mapping mapping = new Mapping(seq.getDatasetSequence(), map);
+    List<SequenceFeature> features = new ArrayList<>();
+    // vary ttg (Leu) to ttc (Phe)
+    SequenceFeature sf = new SequenceFeature("variant", "G,C", 106, 106,
+            null);
+    sf.setValue("alleles", "G,C"); // needed to compute peptide consequence!
+    features.add(sf);
+
+    MappedFeatures mf = new MappedFeatures(mapping, cds, 9, 'L', features);
+
+    String expected = "<br><table><tr><td>Location</td><td>Cds</td><td>106</td></tr>"
+            + "<tr><td>Peptide Location</td><td>TestSeq</td><td>9</td></tr>"
+            + "<tr><td>Type</td><td>variant</td><td></td></tr>"
+            + "<tr><td>Description</td><td>G,C</td><td></td></tr>"
+            + "<tr><td>Consequence</td><td><i>Imputed by Jalview</i></td><td>p.Leu9Phe</td></tr>"
+            + "<tr><td>alleles</td><td></td><td>G,C</td></tr>"
+            + "</table>";
+
+    assertEquals(expected, sf.getDetailsReport(seq.getName(), mf));
+  }
 }