JAL-3751 only merge strictly contiguous ranges of mappings

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

diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java
index 5226819..2d0a4e5 100644 (file)
--- a/test/jalview/util/MappingUtilsTest.java
+++ b/test/jalview/util/MappingUtilsTest.java
@@ -25,7 +25,18 @@ import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
+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 jalview.api.AlignViewportI;
+import jalview.bin.Cache;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
 import jalview.commands.EditCommand.Edit;
@@ -46,17 +57,14 @@ import jalview.io.FileFormat;
 import jalview.io.FileFormatI;
 import jalview.io.FormatAdapter;
 
-import java.awt.Color;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
 public class MappingUtilsTest
 {
+  @BeforeClass(alwaysRun = true)
+  public void setUp()
+  {
+    Cache.initLogger();
+  }
+  
 
   @BeforeClass(alwaysRun = true)
   public void setUpJvOptionPane()
@@ -913,9 +921,9 @@ public class MappingUtilsTest
     MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
             proteinView, dnaView, dnaSelection, dnaHidden);
     assertEquals("[]", dnaSelection.getSelected().toString());
-    List<int[]> hidden = dnaHidden.getHiddenColumnsCopy();
-    assertEquals(1, hidden.size());
-    assertEquals("[0, 4]", Arrays.toString(hidden.get(0)));
+    Iterator<int[]> regions = dnaHidden.iterator();
+    assertEquals(1, dnaHidden.getNumberOfRegions());
+    assertEquals("[0, 4]", Arrays.toString(regions.next()));
 
     /*
      * Column 1 in protein picks up Seq1/K which maps to cols 0-3 in dna
@@ -930,9 +938,9 @@ public class MappingUtilsTest
     proteinSelection.hideSelectedColumns(1, hiddenCols);
     MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
             proteinView, dnaView, dnaSelection, dnaHidden);
-    hidden = dnaHidden.getHiddenColumnsCopy();
-    assertEquals(1, hidden.size());
-    assertEquals("[0, 3]", Arrays.toString(hidden.get(0)));
+    regions = dnaHidden.iterator();
+    assertEquals(1, dnaHidden.getNumberOfRegions());
+    assertEquals("[0, 3]", Arrays.toString(regions.next()));
 
     /*
      * Column 2 in protein picks up gaps only - no mapping
@@ -944,7 +952,7 @@ public class MappingUtilsTest
     proteinSelection.hideSelectedColumns(2, hiddenCols);
     MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
             proteinView, dnaView, dnaSelection, dnaHidden);
-    assertTrue(dnaHidden.getHiddenColumnsCopy().isEmpty());
+    assertEquals(0, dnaHidden.getNumberOfRegions());
 
     /*
      * Column 3 in protein picks up Seq1/P, Seq2/Q, Seq3/S which map to columns
@@ -959,9 +967,9 @@ public class MappingUtilsTest
     MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
             proteinView, dnaView, dnaSelection, dnaHidden);
     assertEquals("[0, 1, 2, 3]", dnaSelection.getSelected().toString());
-    hidden = dnaHidden.getHiddenColumnsCopy();
-    assertEquals(1, hidden.size());
-    assertEquals("[5, 10]", Arrays.toString(hidden.get(0)));
+    regions = dnaHidden.iterator();
+    assertEquals(1, dnaHidden.getNumberOfRegions());
+    assertEquals("[5, 10]", Arrays.toString(regions.next()));
 
     /*
      * Combine hiding columns 1 and 3 to get discontiguous hidden columns
@@ -974,10 +982,10 @@ public class MappingUtilsTest
     proteinSelection.hideSelectedColumns(3, hiddenCols);
     MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
             proteinView, dnaView, dnaSelection, dnaHidden);
-    hidden = dnaHidden.getHiddenColumnsCopy();
-    assertEquals(2, hidden.size());
-    assertEquals("[0, 3]", Arrays.toString(hidden.get(0)));
-    assertEquals("[5, 10]", Arrays.toString(hidden.get(1)));
+    regions = dnaHidden.iterator();
+    assertEquals(2, dnaHidden.getNumberOfRegions());
+    assertEquals("[0, 3]", Arrays.toString(regions.next()));
+    assertEquals("[5, 10]", Arrays.toString(regions.next()));
   }
 
   @Test(groups = { "Functional" })
@@ -1149,6 +1157,95 @@ public class MappingUtilsTest
     assertEquals("[12, 11, 8, 4]", Arrays.toString(ranges));
   }
 
+  @Test(groups = { "Functional" })
+  public void testRangeContains()
+  {
+    /*
+     * both forward ranges
+     */
+    assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        1, 10 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        2, 10 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        1, 9 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        4, 5 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        0, 9 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        -10, -9 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        1, 11 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        11, 12 }));
+
+    /*
+     * forward range, reverse query
+     */
+    assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        10, 1 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        9, 1 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        10, 2 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        5, 5 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        11, 1 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        10, 0 }));
+
+    /*
+     * reverse range, forward query
+     */
+    assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        1, 10 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        1, 9 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        2, 10 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        6, 6 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        6, 11 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        11, 20 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        -3, -2 }));
+
+    /*
+     * both reverse
+     */
+    assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        10, 1 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        9, 1 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        10, 2 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        3, 3 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        11, 1 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        10, 0 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        12, 11 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        -5, -8 }));
+
+    /*
+     * bad arguments
+     */
+    assertFalse(MappingUtils.rangeContains(new int[] { 1, 10, 12 },
+            new int[] {
+        1, 10 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 },
+            new int[] { 1 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, null));
+    assertFalse(MappingUtils.rangeContains(null, new int[] { 1, 10 }));
+  }
+
   @Test(groups = "Functional")
   public void testRemoveEndPositions()
   {