X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Futil%2FMappingUtilsTest.java;h=8cb1208bc69a9710cd6f32593cad9124a82305f5;hb=fc7dac25fd7a4eac42083e9aa94d1e752cabbe8b;hp=3c1dbbbb8a69aab64ad1947453621ec5feaf7954;hpb=708cc06af06aa2912319ad736bcfecb62081de39;p=jalview.git

diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java
index 3c1dbbb..8cb1208 100644
--- a/test/jalview/util/MappingUtilsTest.java
+++ b/test/jalview/util/MappingUtilsTest.java
@@ -22,8 +22,10 @@ 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.internal.junit.ArrayAsserts.assertArrayEquals;
 
 import java.awt.Color;
 import java.io.IOException;
@@ -36,6 +38,7 @@ import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 import jalview.api.AlignViewportI;
+import jalview.bin.Console;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
 import jalview.commands.EditCommand.Edit;
@@ -58,6 +61,11 @@ import jalview.io.FormatAdapter;
 
 public class MappingUtilsTest
 {
+  @BeforeClass(alwaysRun = true)
+  public void setUp()
+  {
+    Console.initLogger();
+  }
 
   @BeforeClass(alwaysRun = true)
   public void setUpJvOptionPane()
@@ -1322,9 +1330,30 @@ public class MappingUtilsTest
     assertEquals(9, ranges.get(0)[1]);
   }
 
+  @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);
+  }
+
   /**
    * 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
    */
@@ -1347,6 +1376,9 @@ 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
@@ -1371,7 +1403,7 @@ 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);
 
     /*
@@ -1389,7 +1421,7 @@ 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());
@@ -1408,7 +1440,7 @@ 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());