X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Futil%2FMapListTest.java;h=07da78fe591a520d5846be1076327b489b4e65a5;hb=d5289472f112190875559c98fc184d64fa7d5072;hp=c442b6f3fefac2a04830359b0912940a13e6d45b;hpb=1e8c7a9ab9f5da589d0aa2482fd2e3361c320d57;p=jalview.git diff --git a/test/jalview/util/MapListTest.java b/test/jalview/util/MapListTest.java index c442b6f..07da78f 100644 --- a/test/jalview/util/MapListTest.java +++ b/test/jalview/util/MapListTest.java @@ -25,31 +25,51 @@ 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.List; +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(groups = { "Functional" }) public void testSomething() { - 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); MapList ml1 = new MapList(new int[] { 1, 3, 17, 4 }, - new int[] { 51, 1 }, 1, 3); + 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 }); testMap(mldna, 1, 3); @@ -256,6 +276,8 @@ public class MapListTest 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] ! assertNull(ml.locateInFrom(0, 0)); assertNull(ml.locateInFrom(1, 5)); @@ -283,7 +305,17 @@ public class MapListTest assertEquals("[16, 18]", Arrays.toString(ml.locateInFrom(4, 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. */ @@ -305,6 +337,8 @@ 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))); /* * A part codon is treated as if a whole one. @@ -343,11 +377,12 @@ public class MapListTest * 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. + * 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))); @@ -360,7 +395,6 @@ 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))); - } /** @@ -381,7 +415,9 @@ 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)); @@ -416,10 +452,11 @@ public class MapListTest @Test(groups = { "Functional" }) public void testGetRanges() { - List ranges = new ArrayList(); + List 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))); + assertEquals("[2, 3, 5, 6]", + Arrays.toString(MapList.getRanges(ranges))); } /** @@ -451,7 +488,8 @@ 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 @@ -466,22 +504,23 @@ public class MapListTest } /** - * Test constructor can merge consecutive ranges + * 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, 14, 14, 16, 17 }; - int[] protein = { 1, 1, 1, 3, 6, 6 }; + 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, 7], [9, 10], [12, 12], [14, 14], [16, 17]}", + assertEquals("{[2, 3], [3, 7], [9, 10], [12, 12], [13, 14], [16, 17]}", prettyPrint(ml.getFromRanges())); - assertEquals("{[1, 3], [6, 6]}", prettyPrint(ml.getToRanges())); + assertEquals("{[1, 1], [2, 3], [6, 6]}", prettyPrint(ml.getToRanges())); } /** @@ -532,25 +571,27 @@ public class MapListTest @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("[ [1, 5] [10, 15] [25, 20] ] To [ [51, 1] ]", - s); + 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); + 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); + 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()); @@ -559,27 +600,43 @@ public class MapListTest String s = ml.toString(); assertEquals( - "[ [11, 15] [20, 25] [35, 30] [2, 4] [37, 40] ] To [ [72, 22] [12, 17] [78, 83] [88, 96] ]", + "[ [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); + MapList ml2 = new MapList(new int[] { 15, 16 }, new int[] { 58, 53 }, 1, + 3); ml.addMapList(ml2); - assertEquals("[ [11, 16] ] To [ [72, 53] ]", ml.toString()); + assertEquals("[ [11, 16] ] 1:3 to [ [72, 53] ]", ml.toString()); } @Test(groups = "Functional") public void testAddRange() { int[] range = { 1, 5 }; - List ranges = new ArrayList(); + List ranges = new ArrayList<>(); // add to empty list: MapList.addRange(range, ranges); @@ -655,27 +712,32 @@ public class MapListTest @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); + 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); + 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 a list of ranges where possible + * Test the method that merges contiguous ranges */ @Test(groups = { "Functional" }) public void testCoalesceRanges() { assertNull(MapList.coalesceRanges(null)); - List ranges = new ArrayList(); + List ranges = new ArrayList<>(); assertSame(ranges, MapList.coalesceRanges(ranges)); ranges.add(new int[] { 1, 3 }); assertSame(ranges, MapList.coalesceRanges(ranges)); @@ -691,100 +753,442 @@ public class MapListTest // merging in forward direction: ranges.clear(); ranges.add(new int[] { 1, 3 }); - ranges.add(new int[] { 4, 5 }); - ranges.add(new int[] { 5, 5 }); - ranges.add(new int[] { 5, 7 }); + ranges.add(new int[] { 4, 5 }); // contiguous + ranges.add(new int[] { 5, 5 }); // overlap! + ranges.add(new int[] { 6, 7 }); // contiguous List merged = MapList.coalesceRanges(ranges); - assertEquals(1, merged.size()); - assertArrayEquals(new int[] { 1, 7 }, merged.get(0)); + 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[] { 5, 7 }, ranges.get(3)); + 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 }); - ranges.add(new int[] { 4, 4 }); - ranges.add(new int[] { 3, 1 }); + 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(1, merged.size()); - assertArrayEquals(new int[] { 7, 1 }, merged.get(0)); + 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 }); - ranges.add(new int[] { 5, 5 }); - ranges.add(new int[] { 6, 6 }); + 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 }); - ranges.add(new int[] { 8, 8 }); - ranges.add(new int[] { 7, 7 }); + 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[] { 1, 6 }, merged.get(0)); - assertArrayEquals(new int[] { 12, 7 }, merged.get(1)); + assertArrayEquals(new int[] { 10, 30 }, merged.get(0)); + assertArrayEquals(new int[] { 15, 25 }, merged.get(1)); } /** - * Test the method that merges a list of ranges where possible + * 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 fromRanges = compound.getFromRanges(); + assertEquals(2, fromRanges.size()); + assertArrayEquals(new int[] { 3, 4 }, fromRanges.get(0)); + assertArrayEquals(new int[] { 8, 12 }, fromRanges.get(1)); + List 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)); + + /* + * method returns null if not all regions are mapped through + */ + 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); + 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 testCoalesceRanges_withOverlap() + public void testIsToForwardsStrand() { - List ranges = new ArrayList(); - ranges.add(new int[] { 1, 3 }); - ranges.add(new int[] { 2, 5 }); + // [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() + { /* - * [2, 5] should extend [1, 3] + * gene to protein... */ - List merged = MapList.coalesceRanges(ranges); - assertEquals(1, merged.size()); - assertArrayEquals(new int[] { 1, 5 }, merged.get(0)); + 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))); + + assertNull(ml.locateInFrom(0, 0)); + assertNull(ml.locateInFrom(1, 7)); + assertNull(ml.locateInFrom(-1, 1)); /* - * a subsumed interval should be dropped + * gene to CDS...from EMBL:MN908947 */ - ranges.clear(); - ranges.add(new int[] { 1, 6 }); - ranges.add(new int[] { 2, 4 }); - merged = MapList.coalesceRanges(ranges); - assertEquals(1, merged.size()); - assertArrayEquals(new int[] { 1, 6 }, merged.get(0)); + 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))); + } - ranges.clear(); - ranges.add(new int[] { 1, 5 }); - ranges.add(new int[] { 1, 6 }); - merged = MapList.coalesceRanges(ranges); - assertEquals(1, merged.size()); - assertArrayEquals(new int[] { 1, 6 }, merged.get(0)); + /** + * 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))); + + assertNull(ml.locateInTo(0, 0)); + assertNull(ml.locateInTo(1, 18)); + assertNull(ml.locateInTo(-1, 1)); /* - * merge duplicate ranges + * gene to CDS...from EMBL:MN908947 */ - ranges.clear(); - ranges.add(new int[] { 1, 3 }); - ranges.add(new int[] { 1, 3 }); - merged = MapList.coalesceRanges(ranges); - assertEquals(1, merged.size()); - assertArrayEquals(new int[] { 1, 3 }, merged.get(0)); + 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))); + } + + @Test(groups = { "Functional" }) + public void testTraverseToPosition() + { + List 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 intervals = new ArrayList<>(); + assertNull(MapList.countPositions(intervals, 1)); + /* - * reverse direction + * 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)); + } + + @Test(groups = { "Functional" }) + public void testFindOverlapPositions() + { + 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)); + } + + @Test(groups = { "Functional" }) + public void testMapWords() + { + List ranges = new ArrayList<>(); + + /* + * 1:1 (trivial) case + */ + 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)); + + /* + * 1:3 case (peptide to codon ranges) + */ + 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)); + + /* + * 3:1 case (codon or part codon to peptide) */ ranges.clear(); - ranges.add(new int[] { 9, 5 }); - ranges.add(new int[] { 9, 4 }); - ranges.add(new int[] { 8, 3 }); - ranges.add(new int[] { 3, 2 }); - ranges.add(new int[] { 1, 0 }); - merged = MapList.coalesceRanges(ranges); - assertEquals(1, merged.size()); - assertArrayEquals(new int[] { 9, 0 }, merged.get(0)); + 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)); } }