JAL-3725 restrict mapped virtual feature location to mapped region

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

diff --git a/test/jalview/datamodel/SequenceFeatureTest.java b/test/jalview/datamodel/SequenceFeatureTest.java
index 673ea29..bd5e9ac 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
 {
@@ -44,8 +48,8 @@ public class SequenceFeatureTest
   @Test(groups = { "Functional" })
   public void testCopyConstructors()
   {
-    SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33,
-            12.5f, "group");
+    SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33, 12.5f,
+            "group");
     sf1.setValue("STRAND", "+");
     sf1.setValue("Note", "Testing");
     Integer count = Integer.valueOf(7);
@@ -79,8 +83,8 @@ public class SequenceFeatureTest
     /*
      * copy constructor modifying type/begin/end/group/score
      */
-    SequenceFeature sf4 = new SequenceFeature(sf1, "Disulfide bond", 12,
-            15, "group3", -9.1f);
+    SequenceFeature sf4 = new SequenceFeature(sf1, "Disulfide bond", 12, 15,
+            "group3", -9.1f);
     assertEquals("Disulfide bond", sf4.getType());
     assertTrue(sf4.isContactFeature());
     assertEquals("desc", sf4.getDescription());
@@ -100,8 +104,8 @@ public class SequenceFeatureTest
   @Test(groups = { "Functional" })
   public void testGetValue()
   {
-    SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33,
-            12.5f, "group");
+    SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33, 12.5f,
+            "group");
     sf1.setValue("STRAND", "+");
     assertEquals("+", sf1.getValue("STRAND"));
     assertNull(sf1.getValue("strand")); // case-sensitive
@@ -133,15 +137,15 @@ public class SequenceFeatureTest
   @Test(groups = { "Functional" })
   public void testEqualsAndHashCode()
   {
-    SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33,
-            12.5f, "group");
+    SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33, 12.5f,
+            "group");
     sf1.setValue("ID", "id");
     sf1.setValue("Name", "name");
     sf1.setValue("Parent", "parent");
     sf1.setStrand("+");
     sf1.setPhase("1");
-    SequenceFeature sf2 = new SequenceFeature("type", "desc", 22, 33,
-            12.5f, "group");
+    SequenceFeature sf2 = new SequenceFeature("type", "desc", 22, 33, 12.5f,
+            "group");
     sf2.setValue("ID", "id");
     sf2.setValue("Name", "name");
     sf2.setValue("Parent", "parent");
@@ -154,10 +158,10 @@ public class SequenceFeatureTest
     assertEquals(sf1.hashCode(), sf2.hashCode());
 
     // changing type breaks equals:
-    SequenceFeature sf3 = new SequenceFeature("type", "desc", 22, 33,
-            12.5f, "group");
-    SequenceFeature sf4 = new SequenceFeature("Type", "desc", 22, 33,
-            12.5f, "group");
+    SequenceFeature sf3 = new SequenceFeature("type", "desc", 22, 33, 12.5f,
+            "group");
+    SequenceFeature sf4 = new SequenceFeature("Type", "desc", 22, 33, 12.5f,
+            "group");
     assertFalse(sf3.equals(sf4));
 
     // changing description breaks equals:
@@ -191,7 +195,8 @@ public class SequenceFeatureTest
 
     // changing start position breaks equals:
     int restorei = sf2.getBegin();
-    sf2 = new SequenceFeature(sf2, 21, sf2.getEnd(), sf2.getFeatureGroup(), sf2.getScore());
+    sf2 = new SequenceFeature(sf2, 21, sf2.getEnd(), sf2.getFeatureGroup(),
+            sf2.getScore());
     assertFalse(sf1.equals(sf2));
     sf2 = new SequenceFeature(sf2, restorei, sf2.getEnd(),
             sf2.getFeatureGroup(), sf2.getScore());
@@ -206,9 +211,11 @@ public class SequenceFeatureTest
 
     // changing feature group breaks equals:
     restores = sf2.getFeatureGroup();
-    sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(), "Group", sf2.getScore());
+    sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(), "Group",
+            sf2.getScore());
     assertFalse(sf1.equals(sf2));
-    sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(), restores, sf2.getScore());
+    sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(), restores,
+            sf2.getScore());
 
     // changing ID breaks equals:
     restores = (String) sf2.getValue("ID");
@@ -281,7 +288,8 @@ public class SequenceFeatureTest
     String seqName = seq.getName();
 
     // single locus, no group, no score
-    SequenceFeature sf = new SequenceFeature("variant", "G,C", 22, 22, null);
+    SequenceFeature sf = new SequenceFeature("variant", "G,C", 22, 22,
+            null);
     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>";
@@ -295,8 +303,7 @@ public class SequenceFeatureTest
             + "<tr><td>Description</td><td>a description</td><td></td></tr></table>";
     assertEquals(expected, sf.getDetailsReport(seqName, null));
 
-    sf = new SequenceFeature("variant", "G,C", 22, 33,
-            12.5f, "group");
+    sf = new SequenceFeature("variant", "G,C", 22, 33, 12.5f, "group");
     sf.setValue("Parent", "ENSG001");
     sf.setValue("Child", "ENSP002");
     expected = "<br><table><tr><td>Location</td><td>TestSeq</td><td>22-33</td></tr>"
@@ -319,4 +326,51 @@ 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, 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));
+    
+
+    /*
+     * exon feature extending beyond mapped range; mapped location should be
+     * restricted to peptide mapped range limit i.e. 10-13
+     */
+    SequenceFeature sf2 = new SequenceFeature("exon", "exon 1", 109, 230, null);
+    features.add(sf2);
+    expected = "<br><table><tr><td>Location</td><td>Cds</td><td>109-230</td></tr>"
+            + "<tr><td>Peptide Location</td><td>TestSeq</td><td>10-13</td></tr>"
+            + "<tr><td>Type</td><td>exon</td><td></td></tr>"
+            + "<tr><td>Description</td><td>exon 1</td><td></td></tr>"
+            + "</table>";
+    assertEquals(expected, sf2.getDetailsReport(seq.getName(), mf));
+  }
 }