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 bd81d30..9239ba5 100644 (file)
--- a/test/jalview/util/MappingUtilsTest.java
+++ b/test/jalview/util/MappingUtilsTest.java
@@ -22,19 +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.AssertJUnit.fail;
-
-import java.awt.Color;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Iterator;
-import java.util.List;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
+import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
 
 import java.awt.Color;
 import java.io.IOException;
@@ -47,7 +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;
@@ -68,12 +59,13 @@ 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)
@@ -1340,39 +1332,30 @@ public class MappingUtilsTest
   }
 
   @Test(groups = "Functional")
-  public void testListToArray()
+  public void testFindOverlap()
   {
     List<int[]> ranges = new ArrayList<>();
-
-    int[] result = MappingUtils.rangeListToArray(ranges);
-    assertEquals(result.length, 0);
-    ranges.add(new int[] { 24, 12 });
-    result = MappingUtils.rangeListToArray(ranges);
-    assertEquals(result.length, 2);
-    assertEquals(result[0], 24);
-    assertEquals(result[1], 12);
-    ranges.add(new int[] { -7, 30 });
-    result = MappingUtils.rangeListToArray(ranges);
-    assertEquals(result.length, 4);
-    assertEquals(result[0], 24);
-    assertEquals(result[1], 12);
-    assertEquals(result[2], -7);
-    assertEquals(result[3], 30);
-    try
-    {
-      MappingUtils.rangeListToArray(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" })
@@ -1468,4 +1451,59 @@ public class MappingUtilsTest
     assertEquals(0, mappedGroup.getStartRes());
     assertEquals(1, mappedGroup.getEndRes()); // two columns
   }
+
+  // new for 2.12
+  @Test(groups = "Functional")
+  public void testAddRange()
+  {
+    int[] range = { 1, 5 };
+    List<int[]> ranges = new ArrayList<>();
+  
+    // 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]);
+  }
 }