JAL-3725 helper methods for computing mapped feature range overlap

[jalview.git] / test / jalview / util / MappingUtilsTest.java

diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java
index 813edf8..0997fec 100644 (file)
--- a/test/jalview/util/MappingUtilsTest.java
+++ b/test/jalview/util/MappingUtilsTest.java
@@ -22,10 +22,13 @@ package jalview.util;
 
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 import static org.testng.AssertJUnit.fail;
 
+import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
+
 import java.awt.Color;
 import java.io.IOException;
 import java.util.ArrayList;
@@ -37,6 +40,7 @@ import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 import jalview.api.AlignViewportI;
+import jalview.bin.Cache;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
 import jalview.commands.EditCommand.Edit;
@@ -59,7 +63,12 @@ import jalview.io.FormatAdapter;
 
 public class MappingUtilsTest
 {
-
+  @BeforeClass(alwaysRun = true)
+  public void setUp()
+  {
+    Cache.initLogger();
+  }
+  
   @BeforeClass(alwaysRun = true)
   public void setUpJvOptionPane()
   {
@@ -1355,7 +1364,8 @@ public class MappingUtilsTest
   /**
    * Test mapping a sequence group where sequences in and outside the group
    * share a dataset sequence (e.g. alternative CDS for the same gene)
-   * 
+   * <p>
+   * This scenario doesn't arise after JAL-3763 changes, but test left as still valid
    * @throws IOException
    */
   @Test(groups = { "Functional" })
@@ -1377,6 +1387,9 @@ public class MappingUtilsTest
     SequenceI pep1 = new Sequence("pep1", "KF");
     SequenceI pep2 = new Sequence("pep2", "FG");
     SequenceI pep3 = new Sequence("pep3", "GP");
+    pep1.createDatasetSequence();
+    pep2.createDatasetSequence();
+    pep3.createDatasetSequence();
 
     /*
      * add mappings from coding positions of dna to respective peptides
@@ -1401,7 +1414,7 @@ public class MappingUtilsTest
             new SequenceI[]
             { pep1, pep2, pep3 });
     AlignViewportI cdnaView = new AlignViewport(cdna);
-    AlignViewportI proteinView = new AlignViewport(protein);
+    AlignViewportI peptideView = new AlignViewport(protein);
     protein.setCodonFrames(acfList);
 
     /*
@@ -1419,7 +1432,7 @@ public class MappingUtilsTest
      * Verify the mapped sequence group in dna is cds1 and cds3
      */
     SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg,
-            proteinView, cdnaView);
+            peptideView, cdnaView);
     assertTrue(mappedGroup.getColourText());
     assertSame(sg.getIdColour(), mappedGroup.getIdColour());
     assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour());
@@ -1438,7 +1451,7 @@ public class MappingUtilsTest
     sg.addSequence(cds1, false);
     sg.setStartRes(0);
     sg.setEndRes(cdna.getWidth() - 1);
-    mappedGroup = MappingUtils.mapSequenceGroup(sg, cdnaView, proteinView);
+    mappedGroup = MappingUtils.mapSequenceGroup(sg, cdnaView, peptideView);
     assertTrue(mappedGroup.getColourText());
     assertSame(sg.getIdColour(), mappedGroup.getIdColour());
     assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour());
@@ -1448,4 +1461,22 @@ public class MappingUtilsTest
     assertEquals(0, mappedGroup.getStartRes());
     assertEquals(1, mappedGroup.getEndRes()); // two columns
   }
+
+  @Test(groups = "Functional")
+  public void testFindOverlap()
+  {
+    List<int[]> ranges = new ArrayList<>();
+    ranges.add(new int[] {4, 8});
+    ranges.add(new int[] {10, 12});
+    ranges.add(new int[] {16, 19});
+    
+    int[] overlap = MappingUtils.findOverlap(ranges, 5,  13);
+    assertArrayEquals(overlap, new int[] {5, 12});
+    overlap = MappingUtils.findOverlap(ranges, -100, 100);
+    assertArrayEquals(overlap, new int[] {4, 19});
+    overlap = MappingUtils.findOverlap(ranges, 7, 17);
+    assertArrayEquals(overlap, new int[] {7, 17});
+    overlap = MappingUtils.findOverlap(ranges, 13, 15);
+    assertNull(overlap);
+  }
 }