Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

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

diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java
index 0997fec..9239ba5 100644 (file)
--- 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;
@@ -61,14 +59,15 @@ import jalview.io.FileFormat;
 import jalview.io.FileFormatI;
 import jalview.io.FormatAdapter;
 
+
 public class MappingUtilsTest
 {
   @BeforeClass(alwaysRun = true)
   public void setUp()
   {
-    Cache.initLogger();
+    Console.initLogger();
   }
-  
+
   @BeforeClass(alwaysRun = true)
   public void setUpJvOptionPane()
   {
@@ -1331,41 +1330,32 @@ 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" })
@@ -1462,21 +1452,58 @@ public class MappingUtilsTest
     assertEquals(1, mappedGroup.getEndRes()); // two columns
   }
 
+  // new for 2.12
   @Test(groups = "Functional")
-  public void testFindOverlap()
+  public void testAddRange()
   {
+    int[] range = { 1, 5 };
     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);
+  
+    // add to empty list:
+    MappingUtils.addRange(range, ranges);
+    assertEquals(1, ranges.size());
+    assertSame(range, ranges.get(0));
+  
+    // extend contiguous (same position):
+    MappingUtils.addRange(new int[] { 5, 10 }, ranges);
+    assertEquals(1, ranges.size());
+    assertEquals(1, ranges.get(0)[0]);
+    assertEquals(10, ranges.get(0)[1]);
+  
+    // extend contiguous (next position):
+    MappingUtils.addRange(new int[] { 11, 15 }, ranges);
+    assertEquals(1, ranges.size());
+    assertEquals(1, ranges.get(0)[0]);
+    assertEquals(15, ranges.get(0)[1]);
+  
+    // change direction: range is not merged:
+    MappingUtils.addRange(new int[] { 16, 10 }, ranges);
+    assertEquals(2, ranges.size());
+    assertEquals(16, ranges.get(1)[0]);
+    assertEquals(10, ranges.get(1)[1]);
+  
+    // extend reverse contiguous (same position):
+    MappingUtils.addRange(new int[] { 10, 8 }, ranges);
+    assertEquals(2, ranges.size());
+    assertEquals(16, ranges.get(1)[0]);
+    assertEquals(8, ranges.get(1)[1]);
+  
+    // extend reverse contiguous (next position):
+    MappingUtils.addRange(new int[] { 7, 6 }, ranges);
+    assertEquals(2, ranges.size());
+    assertEquals(16, ranges.get(1)[0]);
+    assertEquals(6, ranges.get(1)[1]);
+  
+    // change direction: range is not merged:
+    MappingUtils.addRange(new int[] { 6, 9 }, ranges);
+    assertEquals(3, ranges.size());
+    assertEquals(6, ranges.get(2)[0]);
+    assertEquals(9, ranges.get(2)[1]);
+  
+    // not contiguous: not merged
+    MappingUtils.addRange(new int[] { 11, 12 }, ranges);
+    assertEquals(4, ranges.size());
+    assertEquals(11, ranges.get(3)[0]);
+    assertEquals(12, ranges.get(3)[1]);
   }
 }