X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Futil%2FMappingUtilsTest.java;h=8cb1208bc69a9710cd6f32593cad9124a82305f5;hb=7b5d11bce39b76612773aa4d606ffbe55bb86a02;hp=0997fecd77e4556bc882e596863d724c63170a84;hpb=c17981672620e0b780a2338bd0c74e55cf9ddec2;p=jalview.git

diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java
index 0997fec..8cb1208 100644
--- a/test/jalview/util/MappingUtilsTest.java
+++ b/test/jalview/util/MappingUtilsTest.java
@@ -25,8 +25,6 @@ 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;
@@ -40,7 +38,7 @@ import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 import jalview.api.AlignViewportI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
 import jalview.commands.EditCommand.Edit;
@@ -66,9 +64,9 @@ public class MappingUtilsTest
   @BeforeClass(alwaysRun = true)
   public void setUp()
   {
-    Cache.initLogger();
+    Console.initLogger();
   }
-  
+
   @BeforeClass(alwaysRun = true)
   public void setUpJvOptionPane()
   {
@@ -1331,41 +1329,32 @@ public class MappingUtilsTest
     assertEquals(1, ranges.size());
     assertEquals(9, ranges.get(0)[1]);
   }
-  
+
   @Test(groups = "Functional")
-  public void testListToArray()
+  public void testFindOverlap()
   {
     List<int[]> ranges = new ArrayList<>();
-    
-    int[] result = MappingUtils.listToArray(ranges);
-    assertEquals(result.length, 0);
-    ranges.add(new int[] {24, 12});
-    result = MappingUtils.listToArray(ranges);
-    assertEquals(result.length, 2);
-    assertEquals(result[0], 24);
-    assertEquals(result[1], 12);
-    ranges.add(new int[] {-7, 30});
-    result = MappingUtils.listToArray(ranges);
-    assertEquals(result.length, 4);
-    assertEquals(result[0], 24);
-    assertEquals(result[1], 12);
-    assertEquals(result[2], -7);
-    assertEquals(result[3], 30);
-    try
-    {
-      MappingUtils.listToArray(null);
-      fail("Expected exception");
-    } catch (NullPointerException e)
-    {
-      // expected
-    }
+    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
+   * This scenario doesn't arise after JAL-3763 changes, but test left as still
+   * valid
+   * 
    * @throws IOException
    */
   @Test(groups = { "Functional" })
@@ -1461,22 +1450,4 @@ 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);
-  }
 }