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Merge branch 'task/JAL-3608_property_set_laf_and_tests' into develop
[jalview.git] / test / jalview / datamodel / SequenceFeatureTest.java
diff --git a/test/jalview/datamodel/SequenceFeatureTest.java b/test/jalview/datamodel/SequenceFeatureTest.java
index c955979..f8479a3 100644 (file)
--- a/test/jalview/datamodel/SequenceFeatureTest.java
+++ b/test/jalview/datamodel/SequenceFeatureTest.java
@@ -26,11 +26,15 @@ import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
-import jalview.gui.JvOptionPane;
+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
 {
 
@@ -48,7 +52,7 @@ public class SequenceFeatureTest
             12.5f, "group");
     sf1.setValue("STRAND", "+");
     sf1.setValue("Note", "Testing");
-    Integer count = new Integer(7);
+    Integer count = Integer.valueOf(7);
     sf1.setValue("Count", count);
 
     SequenceFeature sf2 = new SequenceFeature(sf1);
@@ -106,7 +110,7 @@ public class SequenceFeatureTest
     assertEquals("+", sf1.getValue("STRAND"));
     assertNull(sf1.getValue("strand")); // case-sensitive
     assertEquals(".", sf1.getValue("unknown", "."));
-    Integer i = new Integer(27);
+    Integer i = Integer.valueOf(27);
     assertSame(i, sf1.getValue("Unknown", i));
   }
 
@@ -277,43 +281,79 @@ public class SequenceFeatureTest
   @Test(groups = { "Functional" })
   public void testGetDetailsReport()
   {
+    SequenceI seq = new Sequence("TestSeq", "PLRFQMD");
+    String seqName = seq.getName();
+
     // single locus, no group, no score
     SequenceFeature sf = new SequenceFeature("variant", "G,C", 22, 22, null);
-    String expected = "<br><table><tr><td>Type</td><td>variant</td><td></td></tr>"
-            + "<tr><td>Start/end</td><td>22</td><td></td></tr>"
+    String expected = "<br><table><tr><td>Location</td><td>TestSeq</td><td>22</td></tr>"
+            + "<tr><td>Type</td><td>variant</td><td></td></tr>"
             + "<tr><td>Description</td><td>G,C</td><td></td></tr></table>";
-    assertEquals(expected, sf.getDetailsReport());
+    assertEquals(expected, sf.getDetailsReport(seqName, null));
 
     // contact feature
     sf = new SequenceFeature("Disulphide Bond", "a description", 28, 31,
             null);
-    expected = "<br><table><tr><td>Type</td><td>Disulphide Bond</td><td></td></tr>"
-            + "<tr><td>Start/end</td><td>28:31</td><td></td></tr>"
+    expected = "<br><table><tr><td>Location</td><td>TestSeq</td><td>28:31</td></tr>"
+            + "<tr><td>Type</td><td>Disulphide Bond</td><td></td></tr>"
             + "<tr><td>Description</td><td>a description</td><td></td></tr></table>";
-    assertEquals(expected, sf.getDetailsReport());
+    assertEquals(expected, sf.getDetailsReport(seqName, null));
 
     sf = new SequenceFeature("variant", "G,C", 22, 33,
             12.5f, "group");
     sf.setValue("Parent", "ENSG001");
     sf.setValue("Child", "ENSP002");
-    expected = "<br><table><tr><td>Type</td><td>variant</td><td></td></tr>"
-            + "<tr><td>Start/end</td><td>22-33</td><td></td></tr>"
+    expected = "<br><table><tr><td>Location</td><td>TestSeq</td><td>22-33</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>Score</td><td>12.5</td><td></td></tr>"
             + "<tr><td>Group</td><td>group</td><td></td></tr>"
             + "<tr><td>Child</td><td></td><td>ENSP002</td></tr>"
             + "<tr><td>Parent</td><td></td><td>ENSG001</td></tr></table>";
-    assertEquals(expected, sf.getDetailsReport());
+    assertEquals(expected, sf.getDetailsReport(seqName, null));
 
     /*
      * feature with embedded html link in description
      */
     String desc = "<html>Fer2 Status: True Positive <a href=\"http://pfam.xfam.org/family/PF00111\">Pfam 8_8</a></html>";
     sf = new SequenceFeature("Pfam", desc, 8, 83, "Uniprot");
-    expected = "<br><table><tr><td>Type</td><td>Pfam</td><td></td></tr>"
-            + "<tr><td>Start/end</td><td>8-83</td><td></td></tr>"
+    expected = "<br><table><tr><td>Location</td><td>TestSeq</td><td>8-83</td></tr>"
+            + "<tr><td>Type</td><td>Pfam</td><td></td></tr>"
             + "<tr><td>Description</td><td>Fer2 Status: True Positive <a href=\"http://pfam.xfam.org/family/PF00111\">Pfam 8_8</a></td><td></td></tr>"
             + "<tr><td>Group</td><td>Uniprot</td><td></td></tr></table>";
-    assertEquals(expected, sf.getDetailsReport());
+    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, 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>Translated 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));
   }
 }