JAL-3700 additions and corrections to unit tests

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

diff --git a/test/jalview/datamodel/AlignedCodonFrameTest.java b/test/jalview/datamodel/AlignedCodonFrameTest.java
index fb4073a..e3fa027 100644 (file)
--- a/test/jalview/datamodel/AlignedCodonFrameTest.java
+++ b/test/jalview/datamodel/AlignedCodonFrameTest.java
@@ -22,20 +22,22 @@ package jalview.datamodel;
 
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
 
-import jalview.gui.JvOptionPane;
-import jalview.util.MapList;
-
 import java.util.Arrays;
 import java.util.List;
 
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
+import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
+import jalview.gui.JvOptionPane;
+import jalview.util.MapList;
+
 public class AlignedCodonFrameTest
 {
 
@@ -486,4 +488,61 @@ public class AlignedCodonFrameTest
     assertEquals(1, acf.getMappingsFromSequence(seq1).size());
     assertSame(before, acf.getMappingsFromSequence(seq1).get(0));
   }
+  
+  @Test(groups = { "Functional" })
+  public void testGetCoveringMapping()
+  {
+    SequenceI dna = new Sequence("dna", "acttcaATGGCGGACtaattt");
+    SequenceI cds = new Sequence("cds/7-15", "ATGGCGGAC");
+    cds.setDatasetSequence(dna);
+    SequenceI pep = new Sequence("pep", "MAD");
+    
+    /*
+     * with null argument or no mappings
+     */
+    AlignedCodonFrame acf = new AlignedCodonFrame();
+    assertNull(acf.getCoveringMapping(null,  null));
+    assertNull(acf.getCoveringMapping(dna,  null));
+    assertNull(acf.getCoveringMapping(null,  pep));
+    assertNull(acf.getCoveringMapping(dna,  pep));
+
+    /*
+     * with a non-covering mapping e.g. overlapping exon
+     */
+    MapList map = new MapList(new int[] { 7, 9 }, new int[] {
+        1, 1 }, 3, 1);
+    acf.addMap(dna, pep, map);
+    assertNull(acf.getCoveringMapping(dna,  pep));
+    
+    acf = new AlignedCodonFrame();
+    MapList map2 = new MapList(new int[] { 13, 18 }, new int[] {
+        2, 2 }, 3, 1);
+    acf.addMap(dna, pep, map2);
+    assertNull(acf.getCoveringMapping(dna,  pep));
+    
+    /*
+     * with a covering mapping from CDS (dataset) to protein
+     */
+    acf = new AlignedCodonFrame();
+    MapList map3 = new MapList(new int[] { 7, 15 }, new int[] {
+        1, 3 }, 3, 1);
+    acf.addMap(dna, pep, map3);
+    assertNull(acf.getCoveringMapping(dna,  pep));
+    SequenceToSequenceMapping mapping = acf.getCoveringMapping(cds,  pep);
+    assertNotNull(mapping);
+    
+    /*
+     * with a mapping that extends to stop codon
+     */
+    acf = new AlignedCodonFrame();
+    MapList map4 = new MapList(new int[] { 7, 18 }, new int[] {
+        1, 3 }, 3, 1);
+    acf.addMap(dna, pep, map4);
+    assertNull(acf.getCoveringMapping(dna,  pep));
+    assertNull(acf.getCoveringMapping(cds,  pep));
+    SequenceI cds2 = new Sequence("cds/7-18", "ATGGCGGACtaa");
+    cds2.setDatasetSequence(dna);
+    mapping = acf.getCoveringMapping(cds2,  pep);
+    assertNotNull(mapping);
+  }
 }