X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Futil%2FMapListTest.java;h=03b3c99d2c4c121c13ccf09c6daeb53ab91574b6;hb=fc77dfd068b74f1ba81927c098b97667eb01e255;hp=71fbdfdbed6533bfbe72e2a244226c7b8a4c3af6;hpb=7c1fb6e8bb8c267d38b15f0b80c9a2b5e53cde4b;p=jalview.git

diff --git a/test/jalview/util/MapListTest.java b/test/jalview/util/MapListTest.java
index 71fbdfd..03b3c99 100644
--- a/test/jalview/util/MapListTest.java
+++ b/test/jalview/util/MapListTest.java
@@ -25,16 +25,18 @@ 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.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.gui.JvOptionPane;
 
 public class MapListTest
@@ -42,9 +44,9 @@ public class MapListTest
   @BeforeClass(alwaysRun = true)
   public void setUp()
   {
-    Cache.initLogger();
+    Console.initLogger();
   }
-  
+
   @BeforeClass(alwaysRun = true)
   public void setUpJvOptionPane()
   {
@@ -52,7 +54,7 @@ public class MapListTest
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
 
-  @Test(groups = { "Functional" })
+  @Test(groups = { "Functional" }, enabled = false)
   public void testSomething()
   {
     MapList ml = new MapList(new int[] { 1, 5, 10, 15, 25, 20 },
@@ -270,15 +272,25 @@ 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));
+
   }
 
   /**
@@ -300,6 +312,108 @@ public class MapListTest
     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 the overlap of the ranges in the 'from' map
+   * for given range in the 'to' map
+   */
+  @Test(groups = { "Functional" })
+  public void testGetOverlapsInFrom_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 = { 11, 14 };
+    MapList ml = new MapList(codons, protein, 3, 1);
+
+    assertEquals("[2, 3, 5, 5]",
+            Arrays.toString(ml.getOverlapsInFrom(11, 11)));
+    assertEquals("[2, 3, 5, 7, 9, 9]",
+            Arrays.toString(ml.getOverlapsInFrom(11, 12)));
+    // out of range 5' :
+    assertEquals("[2, 3, 5, 7, 9, 9]",
+            Arrays.toString(ml.getOverlapsInFrom(8, 12)));
+    // out of range 3' :
+    assertEquals("[10, 10, 12, 12, 14, 14, 16, 18]",
+            Arrays.toString(ml.getOverlapsInFrom(13, 16)));
+    // out of range both :
+    assertEquals("[2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18]",
+            Arrays.toString(ml.getOverlapsInFrom(1, 16)));
+    // no overlap:
+    assertNull(ml.getOverlapsInFrom(20, 25));
+  }
+
+  /**
+   * Tests for method that locates the overlap of the ranges in the 'to' map for
+   * given range in the 'from' map
+   */
+  @Test(groups = { "Functional" })
+  public void testGetOverlapsInTo_withIntrons()
+  {
+    /*
+     * Exons at positions [2, 3, 5] [6, 7, 9] [10, 12, 14] [17, 18, 19] i.e.
+     * 2-3, 5-7, 9-10, 12-12, 14-14, 17-19
+     */
+    int[] codons = { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 17, 19 };
+    /*
+     * Mapped proteins at positions 1, 3, 4, 6 in the sequence
+     */
+    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.getOverlapsInTo(1, 1));
+    assertNull(ml.getOverlapsInTo(4, 4));
+    assertNull(ml.getOverlapsInTo(15, 16));
+
+    /*
+     * nor from a range that includes no mapped position (exon)
+     */
+    assertNull(ml.getOverlapsInTo(15, 16));
+
+    // end of codon 1 maps to first peptide
+    assertEquals("[1, 1]", Arrays.toString(ml.getOverlapsInTo(2, 2)));
+    // end of codon 1 and start of codon 2 maps to first 2 peptides
+    assertEquals("[1, 1, 3, 3]", Arrays.toString(ml.getOverlapsInTo(3, 7)));
+
+    // range overlaps 5' end of dna:
+    assertEquals("[1, 1, 3, 3]", Arrays.toString(ml.getOverlapsInTo(1, 6)));
+    assertEquals("[1, 1, 3, 3]", Arrays.toString(ml.getOverlapsInTo(1, 8)));
+
+    // range overlaps 3' end of dna:
+    assertEquals("[6, 6]", Arrays.toString(ml.getOverlapsInTo(17, 24)));
+    assertEquals("[6, 6]", Arrays.toString(ml.getOverlapsInTo(16, 24)));
+
+    // dna positions 8, 11 are intron but include end of exon 2 and start of
+    // exon 3
+    assertEquals("[3, 4]", Arrays.toString(ml.getOverlapsInTo(8, 11)));
   }
 
   /**
@@ -324,6 +438,8 @@ 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.
@@ -335,9 +451,16 @@ 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));
   }
 
   /**
@@ -359,14 +482,7 @@ public class MapListTest
     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)));
@@ -380,6 +496,17 @@ 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));
   }
 
   /**
@@ -596,7 +723,8 @@ public class MapListTest
   public void testAddMapList_sameMap()
   {
     MapList ml = new MapList(new int[] { 11, 15, 20, 25, 35, 30 },
-            new int[] { 72, 22 }, 1, 3);
+            new int[]
+            { 72, 22 }, 1, 3);
     String before = ml.toString();
     ml.addMapList(ml);
     assertEquals(before, ml.toString());
@@ -779,11 +907,12 @@ public class MapListTest
     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 }); 
+    ranges.add(new int[] { 15, 25 });
+
     merged = MapList.coalesceRanges(ranges);
     assertEquals(2, merged.size());
     assertArrayEquals(new int[] { 10, 30 }, merged.get(0));
@@ -925,10 +1054,10 @@ public class MapListTest
     assertArrayEquals(new int[] { 71, 126 }, toRanges.get(1));
 
     /*
-     * method returns null if not all regions are mapped through
+     * 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, 3);
+    ml2 = new MapList(new int[] { 131, 180 }, new int[] { 201, 250 }, 1, 1);
     compound = ml1.traverse(ml2);
     assertNull(compound);
   }
@@ -957,4 +1086,433 @@ public class MapListTest
             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));
+  }
 }