X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Futil%2FMapListTest.java;h=3f1f7f3b68550a66895d64cdb0c99b03bd619b9e;hb=27aed96d1aeae689818bd0a0028553186e3c3839;hp=bfb08372e1d02173ec40caee7e22cb32bf3f1f4a;hpb=000a5f8da7129b4e379dbd6b5cd1f0411224f58c;p=jalview.git

diff --git a/test/jalview/util/MapListTest.java b/test/jalview/util/MapListTest.java
index bfb0837..3f1f7f3 100644
--- a/test/jalview/util/MapListTest.java
+++ b/test/jalview/util/MapListTest.java
@@ -1,41 +1,78 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.util;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
+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 static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
 
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.BitSet;
 import java.util.List;
 
-import org.junit.Assert;
-import org.junit.Test;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+import jalview.bin.Cache;
+import jalview.gui.JvOptionPane;
 
 public class MapListTest
 {
+  @BeforeClass(alwaysRun = true)
+  public void setUp()
+  {
+    Cache.initLogger();
+  }
+  
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
 
-  @Test
+  @Test(groups = { "Functional" }, enabled = false)
   public void testSomething()
   {
-    MapList ml = new MapList(new int[]
-    { 1, 5, 10, 15, 25, 20 }, new int[]
-    { 51, 1 }, 1, 3);
-    MapList ml1 = new MapList(new int[]
-    { 1, 3, 17, 4 }, new int[]
-    { 51, 1 }, 1, 3);
-    MapList ml2 = new MapList(new int[]
-    { 1, 60 }, new int[]
-    { 1, 20 }, 3, 1);
+    MapList ml = new MapList(new int[] { 1, 5, 10, 15, 25, 20 },
+            new int[]
+            { 51, 1 }, 1, 3);
+    MapList ml1 = new MapList(new int[] { 1, 3, 17, 4 },
+            new int[]
+            { 51, 1 }, 1, 3);
+    MapList ml2 = new MapList(new int[] { 1, 60 }, new int[] { 1, 20 }, 3,
+            1);
     // test internal consistency
     int to[] = new int[51];
     testMap(ml, 1, 60);
-    MapList mldna = new MapList(new int[]
-    { 2, 2, 6, 8, 12, 16 }, new int[]
-    { 1, 3 }, 3, 1);
+    MapList mldna = new MapList(new int[] { 2, 2, 6, 8, 12, 16 },
+            new int[]
+            { 1, 3 }, 3, 1);
     int[] frm = mldna.locateInFrom(1, 1);
-    testLocateFrom(mldna, 1, 1, new int[]
-    { 2, 2, 6, 7 });
+    testLocateFrom(mldna, 1, 1, new int[] { 2, 2, 6, 7 });
     testMap(mldna, 1, 3);
     /*
      * for (int from=1; from<=51; from++) { int[] too=ml.shiftTo(from); int[]
@@ -48,7 +85,7 @@ public class MapListTest
   private static void testLocateFrom(MapList mldna, int i, int j, int[] ks)
   {
     int[] frm = mldna.locateInFrom(i, j);
-    Assert.assertEquals("Failed test locate from " + i + " to " + j,
+    assertEquals("Failed test locate from " + i + " to " + j,
             Arrays.toString(frm), Arrays.toString(ks));
   }
 
@@ -100,7 +137,7 @@ public class MapListTest
       if (mmap[1][i - 1] == -1)
       {
         System.out.print(i + "=XXX");
-  
+
       }
       else
       {
@@ -161,7 +198,7 @@ public class MapListTest
       if (mmap[1][i - 1] == -1)
       {
         System.out.print(i + "=XXX");
-  
+
       }
       else
       {
@@ -220,16 +257,14 @@ public class MapListTest
    * Tests for method that locates ranges in the 'from' map for given range in
    * the 'to' map.
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testLocateInFrom_noIntrons()
   {
     /*
      * Simple mapping with no introns
      */
-    int[] codons = new int[]
-    { 1, 12 };
-    int[] protein = new int[]
-    { 1, 4 };
+    int[] codons = new int[] { 1, 12 };
+    int[] protein = new int[] { 1, 4 };
     MapList ml = new MapList(codons, protein, 3, 1);
     assertEquals("[1, 3]", Arrays.toString(ml.locateInFrom(1, 1)));
     assertEquals("[4, 6]", Arrays.toString(ml.locateInFrom(2, 2)));
@@ -237,54 +272,82 @@ public class MapListTest
     assertEquals("[10, 12]", Arrays.toString(ml.locateInFrom(4, 4)));
     assertEquals("[1, 6]", Arrays.toString(ml.locateInFrom(1, 2)));
     assertEquals("[1, 9]", Arrays.toString(ml.locateInFrom(1, 3)));
+    // reversed range treated as if forwards:
+    assertEquals("[1, 9]", Arrays.toString(ml.locateInFrom(3, 1)));
     assertEquals("[1, 12]", Arrays.toString(ml.locateInFrom(1, 4)));
     assertEquals("[4, 9]", Arrays.toString(ml.locateInFrom(2, 3)));
     assertEquals("[4, 12]", Arrays.toString(ml.locateInFrom(2, 4)));
     assertEquals("[7, 12]", Arrays.toString(ml.locateInFrom(3, 4)));
     assertEquals("[10, 12]", Arrays.toString(ml.locateInFrom(4, 4)));
 
+    /*
+     * partial overlap
+     */
+    assertEquals("[1, 12]", Arrays.toString(ml.locateInFrom(1, 5)));
+    assertEquals("[1, 3]", Arrays.toString(ml.locateInFrom(-1, 1)));
+
+    /*
+     * no overlap
+     */
     assertNull(ml.locateInFrom(0, 0));
-    assertNull(ml.locateInFrom(1, 5));
-    assertNull(ml.locateInFrom(-1, 1));
+    
   }
 
   /**
    * Tests for method that locates ranges in the 'from' map for given range in
    * the 'to' map.
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testLocateInFrom_withIntrons()
   {
     /*
      * Exons at positions [2, 3, 5] [6, 7, 9] [10, 12, 14] [16, 17, 18] i.e.
      * 2-3, 5-7, 9-10, 12-12, 14-14, 16-18
      */
-    int[] codons =
-    { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
-    int[] protein =
-    { 1, 4 };
+    int[] codons = { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
+    int[] protein = { 1, 4 };
     MapList ml = new MapList(codons, protein, 3, 1);
     assertEquals("[2, 3, 5, 5]", Arrays.toString(ml.locateInFrom(1, 1)));
     assertEquals("[6, 7, 9, 9]", Arrays.toString(ml.locateInFrom(2, 2)));
     assertEquals("[10, 10, 12, 12, 14, 14]",
             Arrays.toString(ml.locateInFrom(3, 3)));
     assertEquals("[16, 18]", Arrays.toString(ml.locateInFrom(4, 4)));
+    
+    /*
+     * codons at 11-16, 21-26, 31-36 mapped to peptide positions 1, 3-4, 6-8
+     */
+    ml = new MapList(new int[] { 11, 16, 21, 26, 31, 36 },
+            new int[]
+            { 1, 1, 3, 4, 6, 8 }, 3, 1);
+    assertArrayEquals(new int[] { 11, 13 }, ml.locateInFrom(1, 1));
+    assertArrayEquals(new int[] { 11, 16 }, ml.locateInFrom(1, 3));
+    assertArrayEquals(new int[] { 11, 16, 21, 23 }, ml.locateInFrom(1, 4));
+    assertArrayEquals(new int[] { 14, 16, 21, 23 }, ml.locateInFrom(3, 4));
+
+  }
+
+  @Test(groups = { "Functional" })
+  public void testLocateInFrom_reverseStrand()
+  {
+    int[] codons = new int[] { 12, 1 };
+    int[] protein = new int[] { 1, 4 };
+    MapList ml = new MapList(codons, protein, 3, 1);
+    assertEquals("[12, 10]", Arrays.toString(ml.locateInFrom(1, 1)));
+    assertEquals("[9, 4]", Arrays.toString(ml.locateInFrom(2, 3)));
   }
 
   /**
    * Tests for method that locates ranges in the 'to' map for given range in the
    * 'from' map.
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testLocateInTo_noIntrons()
   {
     /*
      * Simple mapping with no introns
      */
-    int[] codons = new int[]
-    { 1, 12 };
-    int[] protein = new int[]
-    { 1, 4 };
+    int[] codons = new int[] { 1, 12 };
+    int[] protein = new int[] { 1, 4 };
     MapList ml = new MapList(codons, protein, 3, 1);
     assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(1, 3)));
     assertEquals("[2, 2]", Arrays.toString(ml.locateInTo(4, 6)));
@@ -295,6 +358,8 @@ public class MapListTest
     assertEquals("[1, 4]", Arrays.toString(ml.locateInTo(1, 12)));
     assertEquals("[2, 2]", Arrays.toString(ml.locateInTo(4, 6)));
     assertEquals("[2, 4]", Arrays.toString(ml.locateInTo(4, 12)));
+    // reverse range treated as if forwards:
+    assertEquals("[2, 4]", Arrays.toString(ml.locateInTo(12, 4)));
 
     /*
      * A part codon is treated as if a whole one.
@@ -306,40 +371,38 @@ public class MapListTest
     assertEquals("[1, 4]", Arrays.toString(ml.locateInTo(3, 11)));
     assertEquals("[2, 4]", Arrays.toString(ml.locateInTo(5, 11)));
 
+    /*
+     * partial overlap
+     */
+    assertEquals("[1, 4]", Arrays.toString(ml.locateInTo(1, 13)));
+    assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(-1, 2)));
+    
+    /*
+     * no overlap
+     */
     assertNull(ml.locateInTo(0, 0));
-    assertNull(ml.locateInTo(1, 13));
-    assertNull(ml.locateInTo(-1, 1));
   }
 
   /**
    * Tests for method that locates ranges in the 'to' map for given range in the
    * 'from' map.
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testLocateInTo_withIntrons()
   {
     /*
      * Exons at positions [2, 3, 5] [6, 7, 9] [10, 12, 14] [16, 17, 18] i.e.
      * 2-3, 5-7, 9-10, 12-12, 14-14, 16-18
      */
-    int[] codons =
-    { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
+    int[] codons = { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
     /*
      * Mapped proteins at positions 1, 3, 4, 6 in the sequence
      */
-    int[] protein =
-    { 1, 1, 3, 4, 6, 6 };
+    int[] protein = { 1, 1, 3, 4, 6, 6 };
     MapList ml = new MapList(codons, protein, 3, 1);
 
     /*
-     * Can't map from an unmapped position
-     */
-    assertNull(ml.locateInTo(1, 2));
-    assertNull(ml.locateInTo(2, 4));
-    assertNull(ml.locateInTo(4, 4));
-
-    /*
-     * Valid range or subrange of codon1 maps to protein1.
+     * Valid range or subrange of codon1 maps to protein1
      */
     assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(2, 2)));
     assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(3, 3)));
@@ -353,18 +416,27 @@ public class MapListTest
     // codon positions 7 to 17 (part) cover proteins 2/3/4 at positions 3/4/6
     assertEquals("[3, 4, 6, 6]", Arrays.toString(ml.locateInTo(7, 17)));
 
+    /*
+     * partial overlap
+     */
+    assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(1, 2)));
+    assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(1, 4)));
+    assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(2, 4)));
+    
+    /*
+     * no overlap
+     */
+    assertNull(ml.locateInTo(4, 4));
   }
 
   /**
    * Test equals method.
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testEquals()
   {
-    int[] codons = new int[]
-    { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
-    int[] protein = new int[]
-    { 1, 4 };
+    int[] codons = new int[] { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
+    int[] protein = new int[] { 1, 4 };
     MapList ml = new MapList(codons, protein, 3, 1);
     MapList ml1 = new MapList(codons, protein, 3, 1); // same values
     MapList ml2 = new MapList(codons, protein, 2, 1); // fromRatio differs
@@ -375,7 +447,9 @@ public class MapListTest
     MapList ml7 = new MapList(codons, protein, 3, 1); // toShifts differ
 
     assertTrue(ml.equals(ml));
+    assertEquals(ml.hashCode(), ml.hashCode());
     assertTrue(ml.equals(ml1));
+    assertEquals(ml.hashCode(), ml1.hashCode());
     assertTrue(ml1.equals(ml));
 
     assertFalse(ml.equals(null));
@@ -407,27 +481,24 @@ public class MapListTest
   /**
    * Test for the method that flattens a list of ranges into a single array.
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testGetRanges()
   {
-    List<int[]> ranges = new ArrayList<int[]>();
-    ranges.add(new int[]
-    { 2, 3 });
-    ranges.add(new int[]
-    { 5, 6 });
-    assertEquals("[2, 3, 5, 6]", Arrays.toString(MapList.getRanges(ranges)));
+    List<int[]> ranges = new ArrayList<>();
+    ranges.add(new int[] { 2, 3 });
+    ranges.add(new int[] { 5, 6 });
+    assertEquals("[2, 3, 5, 6]",
+            Arrays.toString(MapList.getRanges(ranges)));
   }
 
   /**
    * Check state after construction
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testConstructor()
   {
-    int[] codons =
-    { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
-    int[] protein =
-    { 1, 1, 3, 4, 6, 6 };
+    int[] codons = { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
+    int[] protein = { 1, 1, 3, 4, 6, 6 };
     MapList ml = new MapList(codons, protein, 3, 1);
     assertEquals(3, ml.getFromRatio());
     assertEquals(2, ml.getFromLowest());
@@ -449,7 +520,39 @@ public class MapListTest
     assertEquals(6, ml2.getToHighest());
     assertEquals("{[2, 3], [5, 7], [9, 10], [12, 12], [14, 14], [16, 18]}",
             prettyPrint(ml2.getFromRanges()));
-    assertEquals("{[1, 1], [3, 4], [6, 6]}", prettyPrint(ml2.getToRanges()));
+    assertEquals("{[1, 1], [3, 4], [6, 6]}",
+            prettyPrint(ml2.getToRanges()));
+
+    /*
+     * reverse direction
+     */
+    codons = new int[] { 9, 6 };
+    protein = new int[] { 100, 91, 80, 79 };
+    ml = new MapList(codons, protein, 3, 1);
+    assertEquals(6, ml.getFromLowest());
+    assertEquals(9, ml.getFromHighest());
+    assertEquals(79, ml.getToLowest());
+    assertEquals(100, ml.getToHighest());
+  }
+
+  /**
+   * Test constructor used to merge consecutive ranges but now just leaves them
+   * as supplied (JAL-3751)
+   */
+  @Test(groups = { "Functional" })
+  public void testConstructor_mergeRanges()
+  {
+    int[] codons = { 2, 3, 3, 7, 9, 10, 12, 12, 13, 14, 16, 17 };
+    int[] protein = { 1, 1, 2, 3, 6, 6 };
+    MapList ml = new MapList(codons, protein, 3, 1);
+    assertEquals(3, ml.getFromRatio());
+    assertEquals(2, ml.getFromLowest());
+    assertEquals(17, ml.getFromHighest());
+    assertEquals(1, ml.getToLowest());
+    assertEquals(6, ml.getToHighest());
+    assertEquals("{[2, 3], [3, 7], [9, 10], [12, 12], [13, 14], [16, 17]}",
+            prettyPrint(ml.getFromRanges()));
+    assertEquals("{[1, 1], [2, 3], [6, 6]}", prettyPrint(ml.getToRanges()));
   }
 
   /**
@@ -479,13 +582,11 @@ public class MapListTest
   /**
    * Test the method that creates an inverse mapping
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testGetInverse()
   {
-    int[] codons =
-    { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
-    int[] protein =
-    { 1, 1, 3, 4, 6, 6 };
+    int[] codons = { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
+    int[] protein = { 1, 1, 3, 4, 6, 6 };
 
     MapList ml = new MapList(codons, protein, 3, 1);
     MapList ml2 = ml.getInverse();
@@ -499,14 +600,833 @@ public class MapListTest
             prettyPrint(ml2.getFromRanges()));
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testToString()
   {
-    MapList ml = new MapList(new int[]
-    { 1, 5, 10, 15, 25, 20 }, new int[]
-    { 51, 1 }, 1, 3);
+    MapList ml = new MapList(new int[] { 1, 5, 10, 15, 25, 20 },
+            new int[]
+            { 51, 1 }, 1, 3);
     String s = ml.toString();
-    assertEquals("From (1:3) [ [1, 5] [10, 15] [25, 20] ] To [ [51, 1] ]",
+    assertEquals("[ [1, 5] [10, 15] [25, 20] ] 1:3 to [ [51, 1] ]", s);
+  }
+
+  @Test(groups = { "Functional" })
+  public void testAddMapList()
+  {
+    MapList ml = new MapList(new int[] { 11, 15, 20, 25, 35, 30 },
+            new int[]
+            { 72, 22 }, 1, 3);
+    assertEquals(11, ml.getFromLowest());
+    assertEquals(35, ml.getFromHighest());
+    assertEquals(22, ml.getToLowest());
+    assertEquals(72, ml.getToHighest());
+
+    MapList ml2 = new MapList(new int[] { 2, 4, 37, 40 },
+            new int[]
+            { 12, 17, 78, 83, 88, 96 }, 1, 3);
+    ml.addMapList(ml2);
+    assertEquals(2, ml.getFromLowest());
+    assertEquals(40, ml.getFromHighest());
+    assertEquals(12, ml.getToLowest());
+    assertEquals(96, ml.getToHighest());
+
+    String s = ml.toString();
+    assertEquals(
+            "[ [11, 15] [20, 25] [35, 30] [2, 4] [37, 40] ] 1:3 to [ [72, 22] [12, 17] [78, 83] [88, 96] ]",
             s);
   }
+
+  /**
+   * Test that confirms adding a map twice does nothing
+   */
+  @Test(groups = { "Functional" })
+  public void testAddMapList_sameMap()
+  {
+    MapList ml = new MapList(new int[] { 11, 15, 20, 25, 35, 30 },
+            new int[]
+            { 72, 22 }, 1, 3);
+    String before = ml.toString();
+    ml.addMapList(ml);
+    assertEquals(before, ml.toString());
+    ml.addMapList(new MapList(ml));
+    assertEquals(before, ml.toString());
+  }
+
+  @Test(groups = { "Functional" })
+  public void testAddMapList_contiguous()
+  {
+    MapList ml = new MapList(new int[] { 11, 15 }, new int[] { 72, 58 }, 1,
+            3);
+
+    MapList ml2 = new MapList(new int[] { 15, 16 }, new int[] { 58, 53 }, 1,
+            3);
+    ml.addMapList(ml2);
+    assertEquals("[ [11, 16] ] 1:3 to [ [72, 53] ]", ml.toString());
+  }
+
+  @Test(groups = "Functional")
+  public void testAddRange()
+  {
+    int[] range = { 1, 5 };
+    List<int[]> ranges = new ArrayList<>();
+
+    // add to empty list:
+    MapList.addRange(range, ranges);
+    assertEquals(1, ranges.size());
+    assertSame(range, ranges.get(0));
+
+    // extend contiguous (same position):
+    MapList.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):
+    MapList.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:
+    MapList.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):
+    MapList.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):
+    MapList.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:
+    MapList.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
+    MapList.addRange(new int[] { 11, 12 }, ranges);
+    assertEquals(4, ranges.size());
+    assertEquals(11, ranges.get(3)[0]);
+    assertEquals(12, ranges.get(3)[1]);
+  }
+
+  /**
+   * Check state after construction
+   */
+  @Test(groups = { "Functional" })
+  public void testConstructor_withLists()
+  {
+    /*
+     * reverse direction
+     */
+    int[][] codons = new int[][] { { 9, 6 } };
+    int[][] protein = new int[][] { { 100, 91 }, { 80, 79 } };
+    MapList ml = new MapList(Arrays.asList(codons), Arrays.asList(protein),
+            3, 1);
+    assertEquals(6, ml.getFromLowest());
+    assertEquals(9, ml.getFromHighest());
+    assertEquals(79, ml.getToLowest());
+    assertEquals(100, ml.getToHighest());
+  }
+
+  /**
+   * Test that method that inspects for the (first) forward or reverse from
+   * range. Single position ranges are ignored.
+   */
+  @Test(groups = { "Functional" })
+  public void testIsFromForwardStrand()
+  {
+    // [3-9] declares forward strand
+    MapList ml = new MapList(new int[] { 2, 2, 3, 9, 12, 11 },
+            new int[]
+            { 20, 11 }, 1, 1);
+    assertTrue(ml.isFromForwardStrand());
+
+    // [11-5] declares reverse strand ([13-14] is ignored)
+    ml = new MapList(new int[] { 2, 2, 11, 5, 13, 14 },
+            new int[]
+            { 20, 11 }, 1, 1);
+    assertFalse(ml.isFromForwardStrand());
+
+    // all single position ranges - defaults to forward strand
+    ml = new MapList(new int[] { 2, 2, 4, 4, 6, 6 }, new int[] { 3, 1 }, 1,
+            1);
+    assertTrue(ml.isFromForwardStrand());
+  }
+
+  /**
+   * Test the method that merges contiguous ranges
+   */
+  @Test(groups = { "Functional" })
+  public void testCoalesceRanges()
+  {
+    assertNull(MapList.coalesceRanges(null));
+    List<int[]> ranges = new ArrayList<>();
+    assertSame(ranges, MapList.coalesceRanges(ranges));
+    ranges.add(new int[] { 1, 3 });
+    assertSame(ranges, MapList.coalesceRanges(ranges));
+
+    // add non-contiguous range:
+    ranges.add(new int[] { 5, 6 });
+    assertSame(ranges, MapList.coalesceRanges(ranges));
+
+    // 'contiguous' range in opposite direction is not merged:
+    ranges.add(new int[] { 7, 6 });
+    assertSame(ranges, MapList.coalesceRanges(ranges));
+
+    // merging in forward direction:
+    ranges.clear();
+    ranges.add(new int[] { 1, 3 });
+    ranges.add(new int[] { 4, 5 }); // contiguous
+    ranges.add(new int[] { 5, 5 }); // overlap!
+    ranges.add(new int[] { 6, 7 }); // contiguous
+    List<int[]> merged = MapList.coalesceRanges(ranges);
+    assertEquals(2, merged.size());
+    assertArrayEquals(new int[] { 1, 5 }, merged.get(0));
+    assertArrayEquals(new int[] { 5, 7 }, merged.get(1));
+    // verify input list is unchanged
+    assertEquals(4, ranges.size());
+    assertArrayEquals(new int[] { 1, 3 }, ranges.get(0));
+    assertArrayEquals(new int[] { 4, 5 }, ranges.get(1));
+    assertArrayEquals(new int[] { 5, 5 }, ranges.get(2));
+    assertArrayEquals(new int[] { 6, 7 }, ranges.get(3));
+
+    // merging in reverse direction:
+    ranges.clear();
+    ranges.add(new int[] { 7, 5 });
+    ranges.add(new int[] { 5, 4 }); // overlap
+    ranges.add(new int[] { 4, 4 }); // overlap
+    ranges.add(new int[] { 3, 1 }); // contiguous
+    merged = MapList.coalesceRanges(ranges);
+    assertEquals(3, merged.size());
+    assertArrayEquals(new int[] { 7, 5 }, merged.get(0));
+    assertArrayEquals(new int[] { 5, 4 }, merged.get(1));
+    assertArrayEquals(new int[] { 4, 1 }, merged.get(2));
+
+    // merging with switches of direction:
+    ranges.clear();
+    ranges.add(new int[] { 1, 3 });
+    ranges.add(new int[] { 4, 5 }); // contiguous
+    ranges.add(new int[] { 5, 5 }); // overlap
+    ranges.add(new int[] { 6, 6 }); // contiguous
+    ranges.add(new int[] { 12, 10 });
+    ranges.add(new int[] { 9, 8 }); // contiguous
+    ranges.add(new int[] { 8, 8 }); // overlap
+    ranges.add(new int[] { 7, 7 }); // contiguous
+    merged = MapList.coalesceRanges(ranges);
+    assertEquals(4, merged.size());
+    assertArrayEquals(new int[] { 1, 5 }, merged.get(0));
+    assertArrayEquals(new int[] { 5, 6 }, merged.get(1));
+    assertArrayEquals(new int[] { 12, 8 }, merged.get(2));
+    assertArrayEquals(new int[] { 8, 7 }, merged.get(3));
+    
+    // 'subsumed' ranges are preserved
+    ranges.clear();
+    ranges.add(new int[] { 10, 30 });
+    ranges.add(new int[] { 15, 25 }); 
+
+    merged = MapList.coalesceRanges(ranges);
+    assertEquals(2, merged.size());
+    assertArrayEquals(new int[] { 10, 30 }, merged.get(0));
+    assertArrayEquals(new int[] { 15, 25 }, merged.get(1));
+  }
+
+  /**
+   * Test the method that compounds ('traverses') two mappings
+   */
+  @Test(groups = "Functional")
+  public void testTraverse()
+  {
+    /*
+     * simple 1:1 plus 1:1 forwards
+     */
+    MapList ml1 = new MapList(new int[] { 3, 4, 8, 12 },
+            new int[]
+            { 5, 8, 11, 13 }, 1, 1);
+    assertEquals("{[3, 4], [8, 12]}", prettyPrint(ml1.getFromRanges()));
+    assertEquals("{[5, 8], [11, 13]}", prettyPrint(ml1.getToRanges()));
+
+    MapList ml2 = new MapList(new int[] { 1, 50 },
+            new int[]
+            { 40, 45, 70, 75, 90, 127 }, 1, 1);
+    assertEquals("{[1, 50]}", prettyPrint(ml2.getFromRanges()));
+    assertEquals("{[40, 45], [70, 75], [90, 127]}",
+            prettyPrint(ml2.getToRanges()));
+
+    MapList compound = ml1.traverse(ml2);
+
+    assertEquals(1, compound.getFromRatio());
+    assertEquals(1, compound.getToRatio());
+    List<int[]> fromRanges = compound.getFromRanges();
+    assertEquals(2, fromRanges.size());
+    assertArrayEquals(new int[] { 3, 4 }, fromRanges.get(0));
+    assertArrayEquals(new int[] { 8, 12 }, fromRanges.get(1));
+    List<int[]> toRanges = compound.getToRanges();
+    assertEquals(4, toRanges.size());
+    // 5-8 maps to 44-45,70-71
+    // 11-13 maps to 74-75,90
+    assertArrayEquals(new int[] { 44, 45 }, toRanges.get(0));
+    assertArrayEquals(new int[] { 70, 71 }, toRanges.get(1));
+    assertArrayEquals(new int[] { 74, 75 }, toRanges.get(2));
+    assertArrayEquals(new int[] { 90, 90 }, toRanges.get(3));
+
+    /*
+     * 1:1 over 1:1 backwards ('reverse strand')
+     */
+    ml1 = new MapList(new int[] { 1, 50 }, new int[] { 70, 119 }, 1, 1);
+    ml2 = new MapList(new int[] { 1, 500 },
+            new int[]
+            { 1000, 901, 600, 201 }, 1, 1);
+    compound = ml1.traverse(ml2);
+
+    assertEquals(1, compound.getFromRatio());
+    assertEquals(1, compound.getToRatio());
+    fromRanges = compound.getFromRanges();
+    assertEquals(1, fromRanges.size());
+    assertArrayEquals(new int[] { 1, 50 }, fromRanges.get(0));
+    toRanges = compound.getToRanges();
+    assertEquals(2, toRanges.size());
+    assertArrayEquals(new int[] { 931, 901 }, toRanges.get(0));
+    assertArrayEquals(new int[] { 600, 582}, toRanges.get(1));
+
+    /*
+     * 1:1 plus 1:3 should result in 1:3
+     */
+    ml1 = new MapList(new int[] { 1, 30 }, new int[] { 11, 40 }, 1, 1);
+    ml2 = new MapList(new int[] { 1, 100 }, new int[] { 1, 50, 91, 340 }, 1,
+            3);
+    compound = ml1.traverse(ml2);
+
+    assertEquals(1, compound.getFromRatio());
+    assertEquals(3, compound.getToRatio());
+    fromRanges = compound.getFromRanges();
+    assertEquals(1, fromRanges.size());
+    assertArrayEquals(new int[] { 1, 30 }, fromRanges.get(0));
+    // 11-40 maps to 31-50,91-160
+    toRanges = compound.getToRanges();
+    assertEquals(2, toRanges.size());
+    assertArrayEquals(new int[] { 31, 50 }, toRanges.get(0));
+    assertArrayEquals(new int[] { 91, 160 }, toRanges.get(1));
+
+    /*
+     * 3:1 plus 1:1 should result in 3:1
+     */
+    ml1 = new MapList(new int[] { 1, 30 }, new int[] { 11, 20 }, 3, 1);
+    ml2 = new MapList(new int[] { 1, 100 }, new int[] { 1, 15, 91, 175 }, 1,
+            1);
+    compound = ml1.traverse(ml2);
+
+    assertEquals(3, compound.getFromRatio());
+    assertEquals(1, compound.getToRatio());
+    fromRanges = compound.getFromRanges();
+    assertEquals(1, fromRanges.size());
+    assertArrayEquals(new int[] { 1, 30 }, fromRanges.get(0));
+    // 11-20 maps to 11-15, 91-95
+    toRanges = compound.getToRanges();
+    assertEquals(2, toRanges.size());
+    assertArrayEquals(new int[] { 11, 15 }, toRanges.get(0));
+    assertArrayEquals(new int[] { 91, 95 }, toRanges.get(1));
+
+    /*
+     * 1:3 plus 3:1 should result in 1:1
+     */
+    ml1 = new MapList(new int[] { 21, 40 }, new int[] { 13, 72 }, 1, 3);
+    ml2 = new MapList(new int[] { 1, 300 }, new int[] { 51, 70, 121, 200 },
+            3, 1);
+    compound = ml1.traverse(ml2);
+
+    assertEquals(1, compound.getFromRatio());
+    assertEquals(1, compound.getToRatio());
+    fromRanges = compound.getFromRanges();
+    assertEquals(1, fromRanges.size());
+    assertArrayEquals(new int[] { 21, 40 }, fromRanges.get(0));
+    // 13-72 maps 3:1 to 55-70, 121-124
+    toRanges = compound.getToRanges();
+    assertEquals(2, toRanges.size());
+    assertArrayEquals(new int[] { 55, 70 }, toRanges.get(0));
+    assertArrayEquals(new int[] { 121, 124 }, toRanges.get(1));
+
+    /*
+     * 3:1 plus 1:3 should result in 1:1
+     */
+    ml1 = new MapList(new int[] { 31, 90 }, new int[] { 13, 32 }, 3, 1);
+    ml2 = new MapList(new int[] { 11, 40 }, new int[] { 41, 50, 71, 150 },
+            1, 3);
+    compound = ml1.traverse(ml2);
+
+    assertEquals(1, compound.getFromRatio());
+    assertEquals(1, compound.getToRatio());
+    fromRanges = compound.getFromRanges();
+    assertEquals(1, fromRanges.size());
+    assertArrayEquals(new int[] { 31, 90 }, fromRanges.get(0));
+    // 13-32 maps to 47-50,71-126
+    toRanges = compound.getToRanges();
+    assertEquals(2, toRanges.size());
+    assertArrayEquals(new int[] { 47, 50 }, toRanges.get(0));
+    assertArrayEquals(new int[] { 71, 126 }, toRanges.get(1));
+
+    /*
+     * if not all regions are mapped through, returns what is
+     */
+    ml1 = new MapList(new int[] { 1, 50 }, new int[] { 101, 150 }, 1, 1);
+    ml2 = new MapList(new int[] { 131, 180 }, new int[] { 201, 250 }, 1, 1);
+    compound = ml1.traverse(ml2);
+    assertNull(compound);
+  }
+
+  /**
+   * Test that method that inspects for the (first) forward or reverse 'to'
+   * range. Single position ranges are ignored.
+   */
+  @Test(groups = { "Functional" })
+  public void testIsToForwardsStrand()
+  {
+    // [3-9] declares forward strand
+    MapList ml = new MapList(new int[] { 20, 11 },
+            new int[]
+            { 2, 2, 3, 9, 12, 11 }, 1, 1);
+    assertTrue(ml.isToForwardStrand());
+
+    // [11-5] declares reverse strand ([13-14] is ignored)
+    ml = new MapList(new int[] { 20, 11 },
+            new int[]
+            { 2, 2, 11, 5, 13, 14 }, 1, 1);
+    assertFalse(ml.isToForwardStrand());
+
+    // all single position ranges - defaults to forward strand
+    ml = new MapList(new int[] { 3, 1 }, new int[] { 2, 2, 4, 4, 6, 6 }, 1,
+            1);
+    assertTrue(ml.isToForwardStrand());
+  }
+
+  /**
+   * Test for mapping with overlapping ranges
+   */
+  @Test(groups = { "Functional" })
+  public void testLocateInFrom_withOverlap()
+  {
+    /*
+     * gene to protein...
+     */
+    int[] codons = new int[] { 1, 12, 12, 17 };
+    int[] protein = new int[] { 1, 6 };
+    MapList ml = new MapList(codons, protein, 3, 1);
+    assertEquals("[1, 3]", Arrays.toString(ml.locateInFrom(1, 1)));
+    assertEquals("[4, 6]", Arrays.toString(ml.locateInFrom(2, 2)));
+    assertEquals("[7, 9]", Arrays.toString(ml.locateInFrom(3, 3)));
+    assertEquals("[10, 12]", Arrays.toString(ml.locateInFrom(4, 4)));
+    assertEquals("[12, 14]", Arrays.toString(ml.locateInFrom(5, 5)));
+    assertEquals("[15, 17]", Arrays.toString(ml.locateInFrom(6, 6)));
+    assertEquals("[1, 6]", Arrays.toString(ml.locateInFrom(1, 2)));
+    assertEquals("[1, 9]", Arrays.toString(ml.locateInFrom(1, 3)));
+    assertEquals("[1, 12]", Arrays.toString(ml.locateInFrom(1, 4)));
+    assertEquals("[1, 12, 12, 14]", Arrays.toString(ml.locateInFrom(1, 5)));
+    assertEquals("[1, 12, 12, 17]", Arrays.toString(ml.locateInFrom(1, 6)));
+    assertEquals("[4, 9]", Arrays.toString(ml.locateInFrom(2, 3)));
+    assertEquals("[7, 12, 12, 17]", Arrays.toString(ml.locateInFrom(3, 6)));
+
+    /*
+     * partial overlap of range
+     */
+    assertEquals("[4, 12, 12, 17]", Arrays.toString(ml.locateInFrom(2, 7)));
+    assertEquals("[1, 3]", Arrays.toString(ml.locateInFrom(-1, 1)));
+
+    /*
+     * no overlap in range
+     */
+    assertNull(ml.locateInFrom(0, 0));
+
+    /*
+     * gene to CDS...from EMBL:MN908947
+     */
+    int[] gene = new int[] { 266, 13468, 13468, 21555 };
+    int[] cds = new int[] { 1, 21291 };
+    ml = new MapList(gene, cds, 1, 1);
+    assertEquals("[13468, 13468]",
+            Arrays.toString(ml.locateInFrom(13203, 13203)));
+    assertEquals("[13468, 13468]",
+            Arrays.toString(ml.locateInFrom(13204, 13204)));
+    assertEquals("[13468, 13468, 13468, 13468]",
+            Arrays.toString(ml.locateInFrom(13203, 13204)));
+  }
+
+  /**
+   * Test for mapping with overlapping ranges
+   */
+  @Test(groups = { "Functional" })
+  public void testLocateInTo_withOverlap()
+  {
+    /*
+     * gene to protein...
+     */
+    int[] codons = new int[] { 1, 12, 12, 17 };
+    int[] protein = new int[] { 1, 6 };
+    MapList ml = new MapList(codons, protein, 3, 1);
+    assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(1, 1)));
+    assertEquals("[1, 3]", Arrays.toString(ml.locateInTo(3, 8)));
+    assertEquals("[1, 4]", Arrays.toString(ml.locateInTo(2, 11)));
+    assertEquals("[1, 4]", Arrays.toString(ml.locateInTo(3, 11)));
+
+    // we want base 12 to map to both of the amino acids it codes for
+    assertEquals("[4, 5]", Arrays.toString(ml.locateInTo(12, 12)));
+    assertEquals("[4, 5]", Arrays.toString(ml.locateInTo(11, 12)));
+    assertEquals("[4, 6]", Arrays.toString(ml.locateInTo(11, 15)));
+    assertEquals("[6, 6]", Arrays.toString(ml.locateInTo(15, 17)));
+
+    /*
+     * no overlap
+     */
+    assertNull(ml.locateInTo(0, 0));
+    
+    /*
+     * partial overlap
+     */
+    assertEquals("[1, 6]", Arrays.toString(ml.locateInTo(1, 18)));
+    assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(-1, 1)));
+
+    /*
+     * gene to CDS...from EMBL:MN908947
+     * the base at 13468 is used twice in transcription
+     */
+    int[] gene = new int[] { 266, 13468, 13468, 21555 };
+    int[] cds = new int[] { 1, 21291 };
+    ml = new MapList(gene, cds, 1, 1);
+    assertEquals("[13203, 13204]",
+            Arrays.toString(ml.locateInTo(13468, 13468)));
+    
+    /*
+     * gene to protein
+     * the base at 13468 is in the codon for 4401N and also 4402R
+     */
+    gene = new int[] { 266, 13468, 13468, 21552 }; // stop codon excluded
+    protein = new int[] { 1, 7096 };
+    ml = new MapList(gene, protein, 3, 1);
+    assertEquals("[4401, 4402]",
+            Arrays.toString(ml.locateInTo(13468, 13468)));
+  }
+
+  @Test(groups = { "Functional" })
+  public void testTraverseToPosition()
+  {
+    List<int[]> ranges = new ArrayList<>();
+    assertNull(MapList.traverseToPosition(ranges, 0));
+
+    ranges.add(new int[] { 3, 6 });
+    assertNull(MapList.traverseToPosition(ranges, 0));
+  }
+
+  @Test(groups = { "Functional" })
+  public void testCountPositions()
+  {
+    try
+    {
+      MapList.countPositions(null, 1);
+      fail("expected exception");
+    } catch (NullPointerException e)
+    {
+      // expected
+    }
+
+    List<int[]> intervals = new ArrayList<>();
+    assertNull(MapList.countPositions(intervals, 1));
+
+    /*
+     * forward strand
+     */
+    intervals.add(new int[] { 10, 20 });
+    assertNull(MapList.countPositions(intervals, 9));
+    assertNull(MapList.countPositions(intervals, 21));
+    assertArrayEquals(new int[] { 1, 1 },
+            MapList.countPositions(intervals, 10));
+    assertArrayEquals(new int[] { 6, 1 },
+            MapList.countPositions(intervals, 15));
+    assertArrayEquals(new int[] { 11, 1 },
+            MapList.countPositions(intervals, 20));
+
+    intervals.add(new int[] { 25, 25 });
+    assertArrayEquals(new int[] { 12, 1 },
+            MapList.countPositions(intervals, 25));
+
+    // next interval repeats position 25 - which should be counted twice if
+    // traversed
+    intervals.add(new int[] { 25, 26 });
+    assertArrayEquals(new int[] { 12, 1 },
+            MapList.countPositions(intervals, 25));
+    assertArrayEquals(new int[] { 14, 1 },
+            MapList.countPositions(intervals, 26));
+
+    /*
+     * reverse strand
+     */
+    intervals.clear();
+    intervals.add(new int[] { 5, -5 });
+    assertNull(MapList.countPositions(intervals, 6));
+    assertNull(MapList.countPositions(intervals, -6));
+    assertArrayEquals(new int[] { 1, -1 },
+            MapList.countPositions(intervals, 5));
+    assertArrayEquals(new int[] { 7, -1 },
+            MapList.countPositions(intervals, -1));
+    assertArrayEquals(new int[] { 11, -1 },
+            MapList.countPositions(intervals, -5));
+
+    /*
+     * reverse then forward
+     */
+    intervals.add(new int[] { 5, 10 });
+    assertArrayEquals(new int[] { 13, 1 },
+            MapList.countPositions(intervals, 6));
+
+    /*
+     * reverse then forward then reverse
+     */
+    intervals.add(new int[] { -10, -20 });
+    assertArrayEquals(new int[] { 20, -1 },
+            MapList.countPositions(intervals, -12));
+
+    /*
+     * an interval [x, x] is treated as forward
+     */
+    intervals.add(new int[] { 30, 30 });
+    assertArrayEquals(new int[] { 29, 1 },
+            MapList.countPositions(intervals, 30));
+
+    /*
+     * it is the first matched occurrence that is returned
+     */
+    intervals.clear();
+    intervals.add(new int[] { 1, 2 });
+    intervals.add(new int[] { 2, 3 });
+    assertArrayEquals(new int[] { 2, 1 },
+            MapList.countPositions(intervals, 2));
+    intervals.add(new int[] { -1, -2 });
+    intervals.add(new int[] { -2, -3 });
+    assertArrayEquals(new int[] { 6, -1 },
+            MapList.countPositions(intervals, -2));
+  }
+
+  /**
+   * Tests for helper method that adds any overlap (plus offset) to a set of
+   * overlaps
+   */
+  @Test(groups = { "Functional" })
+  public void testAddOffsetPositions()
+  {
+    List<int[]> mapped = new ArrayList<>();
+    int[] range = new int[] {10, 20};
+    BitSet offsets = new BitSet();
+
+    MapList.addOffsetPositions(mapped, 0, range, offsets);
+    assertTrue(mapped.isEmpty()); // nothing marked for overlap
+
+    offsets.set(11);
+    MapList.addOffsetPositions(mapped, 0, range, offsets);
+    assertTrue(mapped.isEmpty()); // no offset 11 in range
+
+    offsets.set(4, 6); // this sets bits 4 and 5
+    MapList.addOffsetPositions(mapped, 0, range, offsets);
+    assertEquals(1, mapped.size());
+    assertArrayEquals(new int[] { 14, 15 }, mapped.get(0));
+
+    mapped.clear();
+    offsets.set(10);
+    MapList.addOffsetPositions(mapped, 0, range, offsets);
+    assertEquals(2, mapped.size());
+    assertArrayEquals(new int[] { 14, 15 }, mapped.get(0));
+    assertArrayEquals(new int[] { 20, 20 }, mapped.get(1));
+
+    /*
+     * reverse range
+     */
+    range = new int[] { 20, 10 };
+    mapped.clear();
+    offsets.clear();
+    MapList.addOffsetPositions(mapped, 0, range, offsets);
+    assertTrue(mapped.isEmpty()); // nothing marked for overlap
+    offsets.set(11);
+    MapList.addOffsetPositions(mapped, 0, range, offsets);
+    assertTrue(mapped.isEmpty()); // no offset 11 in range
+    offsets.set(0);
+    offsets.set(10);
+    offsets.set(6, 8); // sets bits 6 and 7
+    MapList.addOffsetPositions(mapped, 0, range, offsets);
+    assertEquals(3, mapped.size());
+    assertArrayEquals(new int[] { 20, 20 }, mapped.get(0));
+    assertArrayEquals(new int[] { 14, 13 }, mapped.get(1));
+    assertArrayEquals(new int[] { 10, 10 }, mapped.get(2));
+  }
+  
+  @Test(groups = { "Functional" })
+  public void testGetPositionsForOffsets()
+  {
+    List<int[]> ranges = new ArrayList<>();
+    BitSet offsets = new BitSet();
+    List<int[]> mapped = MapList.getPositionsForOffsets(ranges, offsets);
+    assertTrue(mapped.isEmpty()); // no ranges and no offsets!
+    
+    offsets.set(5, 1000);
+    mapped = MapList.getPositionsForOffsets(ranges, offsets);
+    assertTrue(mapped.isEmpty()); // no ranges
+    
+    /*
+     * one range with overlap of offsets
+     */
+    ranges.add(new int[] {15, 25});
+    mapped = MapList.getPositionsForOffsets(ranges, offsets);
+    assertEquals(1, mapped.size());
+    assertArrayEquals(new int[] {20,  25}, mapped.get(0));
+    
+    /*
+     * two ranges
+     */
+    ranges.add(new int[] {300, 320});
+    mapped = MapList.getPositionsForOffsets(ranges, offsets);
+    assertEquals(2, mapped.size());
+    assertArrayEquals(new int[] {20,  25}, mapped.get(0));
+    assertArrayEquals(new int[] {300, 320}, mapped.get(1));
+    
+    /*
+     * boundary case - right end of first range overlaps
+     */
+    offsets.clear();
+    offsets.set(10);
+    mapped = MapList.getPositionsForOffsets(ranges, offsets);
+    assertEquals(1, mapped.size());
+    assertArrayEquals(new int[] {25,  25}, mapped.get(0));
+    
+    /*
+     * boundary case - left end of second range overlaps
+     */
+    offsets.set(11);
+    mapped = MapList.getPositionsForOffsets(ranges, offsets);
+    assertEquals(2, mapped.size());
+    assertArrayEquals(new int[] {25,  25}, mapped.get(0));
+    assertArrayEquals(new int[] {300, 300}, mapped.get(1));
+    
+    /*
+     * offsets into a circular range are reported in
+     * the order in which they are traversed
+     */
+    ranges.clear();
+    ranges.add(new int[] {100, 150});
+    ranges.add(new int[] {60, 80});
+    offsets.clear();
+    offsets.set(45, 55); // sets bits 45 to 54
+    mapped = MapList.getPositionsForOffsets(ranges, offsets);
+    assertEquals(2, mapped.size());
+    assertArrayEquals(new int[] {145, 150}, mapped.get(0)); // offsets 45-50
+    assertArrayEquals(new int[] {60, 63}, mapped.get(1)); // offsets 51-54
+
+    /*
+     * reverse range overlap is reported with start < end
+     */
+    ranges.clear();
+    ranges.add(new int[] {4321, 4000});
+    offsets.clear();
+    offsets.set(20, 22); // sets bits 20 and 21
+    offsets.set(30);
+    mapped = MapList.getPositionsForOffsets(ranges, offsets);
+    assertEquals(2, mapped.size());
+    assertArrayEquals(new int[] {4301, 4300}, mapped.get(0));
+    assertArrayEquals(new int[] {4291, 4291}, mapped.get(1));
+  }
+  
+  @Test(groups = { "Functional" })
+  public void testGetMappedOffsetsForPositions()
+  {
+    /*
+     * start by verifying the examples in the method's Javadoc!
+     */
+    List<int[]> ranges = new ArrayList<>();
+    ranges.add(new int[] {10, 20});
+    ranges.add(new int[] {31, 40});
+    BitSet overlaps = MapList.getMappedOffsetsForPositions(1, 9, ranges, 1, 1);
+    assertTrue(overlaps.isEmpty());
+    overlaps = MapList.getMappedOffsetsForPositions(1, 11, ranges, 1, 1);
+    assertEquals(2, overlaps.cardinality());
+    assertTrue(overlaps.get(0));
+    assertTrue(overlaps.get(1));
+    overlaps = MapList.getMappedOffsetsForPositions(15, 35, ranges, 1, 1);
+    assertEquals(11, overlaps.cardinality());
+    for (int i = 5 ; i <= 11 ; i++)
+    {
+      assertTrue(overlaps.get(i));
+    }
+    
+    ranges.clear();
+    ranges.add(new int[] {1, 200});
+    overlaps = MapList.getMappedOffsetsForPositions(9, 9, ranges, 1, 3);
+    assertEquals(3, overlaps.cardinality());
+    assertTrue(overlaps.get(24));
+    assertTrue(overlaps.get(25));
+    assertTrue(overlaps.get(26));
+    
+    ranges.clear();
+    ranges.add(new int[] {101, 150});
+    ranges.add(new int[] {171, 180});
+    overlaps = MapList.getMappedOffsetsForPositions(101, 102, ranges, 3, 1);
+    assertEquals(1, overlaps.cardinality());
+    assertTrue(overlaps.get(0));
+    overlaps = MapList.getMappedOffsetsForPositions(150, 171, ranges, 3, 1);
+    assertEquals(1, overlaps.cardinality());
+    assertTrue(overlaps.get(16));
+    
+    ranges.clear();
+    ranges.add(new int[] {101, 150});
+    ranges.add(new int[] {21, 30});
+    overlaps = MapList.getMappedOffsetsForPositions(24, 40, ranges, 3, 1);
+    assertEquals(3, overlaps.cardinality());
+    assertTrue(overlaps.get(17));
+    assertTrue(overlaps.get(18));
+    assertTrue(overlaps.get(19));
+    
+    /*
+     * reverse range 1:1 (e.g. reverse strand gene to transcript)
+     */
+    ranges.clear();
+    ranges.add(new int[] {20, 10});
+    overlaps = MapList.getMappedOffsetsForPositions(12, 13, ranges, 1, 1);
+    assertEquals(2, overlaps.cardinality());
+    assertTrue(overlaps.get(7));
+    assertTrue(overlaps.get(8));
+    
+    /*
+     * reverse range 3:1 (e.g. reverse strand gene to peptide)
+     * from EMBL:J03321 to P0CE20
+     */
+    ranges.clear();
+    ranges.add(new int[] {1480, 488});
+    overlaps = MapList.getMappedOffsetsForPositions(1460, 1460, ranges, 3, 1);
+    // 1460 is the end of the 7th codon
+    assertEquals(1, overlaps.cardinality());
+    assertTrue(overlaps.get(6));
+    // add one base (part codon)
+    overlaps = MapList.getMappedOffsetsForPositions(1459, 1460, ranges, 3, 1);
+    assertEquals(2, overlaps.cardinality());
+    assertTrue(overlaps.get(6));
+    assertTrue(overlaps.get(7));
+    // add second base (part codon)
+    overlaps = MapList.getMappedOffsetsForPositions(1458, 1460, ranges, 3, 1);
+    assertEquals(2, overlaps.cardinality());
+    assertTrue(overlaps.get(6));
+    assertTrue(overlaps.get(7));
+    // add third base (whole codon)
+    overlaps = MapList.getMappedOffsetsForPositions(1457, 1460, ranges, 3, 1);
+    assertEquals(2, overlaps.cardinality());
+    assertTrue(overlaps.get(6));
+    assertTrue(overlaps.get(7));
+    // add one more base (part codon)
+    overlaps = MapList.getMappedOffsetsForPositions(1456, 1460, ranges, 3, 1);
+    assertEquals(3, overlaps.cardinality());
+    assertTrue(overlaps.get(6));
+    assertTrue(overlaps.get(7));
+    assertTrue(overlaps.get(8));
+  }
 }