X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Futil%2FMapListTest.java;h=03b3c99d2c4c121c13ccf09c6daeb53ab91574b6;hb=fc7dac25fd7a4eac42083e9aa94d1e752cabbe8b;hp=07da78fe591a520d5846be1076327b489b4e65a5;hpb=a9e1fa623b6f66f2e32436ea43a31180784f5044;p=jalview.git diff --git a/test/jalview/util/MapListTest.java b/test/jalview/util/MapListTest.java index 07da78f..03b3c99 100644 --- a/test/jalview/util/MapListTest.java +++ b/test/jalview/util/MapListTest.java @@ -30,12 +30,13 @@ 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 @@ -43,7 +44,7 @@ public class MapListTest @BeforeClass(alwaysRun = true) public void setUp() { - Cache.initLogger(); + Console.initLogger(); } @BeforeClass(alwaysRun = true) @@ -53,7 +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 }, @@ -271,17 +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))); - // reversing the range reverses the result: - assertEquals("[12, 7]", Arrays.toString(ml.locateInFrom(4, 3))); // fails with [10, 9] ! + /* + * 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)); + } /** @@ -303,6 +312,18 @@ 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" }) @@ -314,8 +335,88 @@ public class MapListTest 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))); + } + + /** * Tests for method that locates ranges in the 'to' map for given range in the * 'from' map. */ @@ -337,8 +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))); - // reversing the 'from' range reverses the result - assertEquals("[4, 2]", Arrays.toString(ml.locateInTo(12, 4))); + // 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. @@ -350,9 +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)); } /** @@ -374,14 +482,6 @@ 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(1, 4)); - assertNull(ml.locateInTo(2, 4)); - assertNull(ml.locateInTo(4, 4)); - - /* * Valid range or subrange of codon1 maps to protein1 */ assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(2, 2))); @@ -395,6 +495,18 @@ 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)); } /** @@ -800,6 +912,7 @@ public class MapListTest 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)); @@ -941,10 +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); } @@ -1000,19 +1113,29 @@ public class MapListTest 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)); - assertNull(ml.locateInFrom(1, 7)); - assertNull(ml.locateInFrom(-1, 1)); /* * gene to CDS...from EMBL:MN908947 */ - int [] gene = new int[] { 266, 13468, 13468, 21555 }; - int [] cds = new int[] { 1, 21291 }; + 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]", Arrays.toString(ml.locateInFrom(13203, 13204))); + 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))); } /** @@ -1038,17 +1161,36 @@ public class MapListTest 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)); - assertNull(ml.locateInTo(1, 18)); - assertNull(ml.locateInTo(-1, 1)); + + /* + * 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 }; + 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))); + 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" }) @@ -1074,121 +1216,303 @@ public class MapListTest } List intervals = new ArrayList<>(); - assertNull(MapList.countPositions(intervals, 1)); - + 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)); - + 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)); - + 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)); - + 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)); - + 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)); - + 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)); + 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 testFindOverlapPositions() + public void testAddOffsetPositions() { - List ranges = new ArrayList<>(); - List overlaps = MapList.findOverlapPositions(ranges, 20, 30); - assertTrue(overlaps.isEmpty()); - ranges.add(new int[] {15, 25}); - overlaps = MapList.findOverlapPositions(ranges, 20, 30); - assertEquals(1, overlaps.size()); - assertArrayEquals(new int[] {6, 11}, overlaps.get(0)); + List 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 testMapWords() + public void testGetPositionsForOffsets() { List ranges = new ArrayList<>(); - + BitSet offsets = new BitSet(); + List 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)); + /* - * 1:1 (trivial) case + * boundary case - right end of first range overlaps */ - ranges.add(new int[] {2, 4}); - ranges.add(new int[] {6, 9}); - MapList.mapWords(ranges, 1, 1); - assertEquals(ranges.size(), 2); - assertArrayEquals(new int[] {2, 4}, ranges.get(0)); - assertArrayEquals(new int[] {6, 9}, ranges.get(1)); - + 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 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)); + /* - * 1:3 case (peptide to codon ranges) + * reverse range 1:1 (e.g. reverse strand gene to transcript) */ - MapList.mapWords(ranges, 1, 3); - assertEquals(ranges.size(), 2); - assertArrayEquals(new int[] {6, 14}, ranges.get(0)); - assertArrayEquals(new int[] {18, 29}, ranges.get(1)); - + 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)); + /* - * 3:1 case (codon or part codon to peptide) + * reverse range 3:1 (e.g. reverse strand gene to peptide) + * from EMBL:J03321 to P0CE20 */ ranges.clear(); - ranges.add(new int[] {0, 5}); // 2 whole codons - ranges.add(new int[] {7, 11}); // part + whole codon - ranges.add(new int[] {15, 19}); // whole + part codon - ranges.add(new int[] {23, 27}); // part + part codon - ranges.add(new int[] {30, 30}); // first base of codon - ranges.add(new int[] {31, 31}); // second base of codon - ranges.add(new int[] {32, 32}); // third base of codon - MapList.mapWords(ranges, 3, 1); - assertEquals(ranges.size(), 7); - assertArrayEquals(new int[] {0, 1}, ranges.get(0)); - assertArrayEquals(new int[] {2, 3}, ranges.get(1)); - assertArrayEquals(new int[] {5, 6}, ranges.get(2)); - assertArrayEquals(new int[] {7, 9}, ranges.get(3)); - assertArrayEquals(new int[] {10, 10}, ranges.get(4)); - assertArrayEquals(new int[] {10, 10}, ranges.get(5)); - assertArrayEquals(new int[] {10, 10}, ranges.get(6)); + 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)); } }