X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Futil%2FMapListTest.java;h=6bbda783d705605d66e4afbae83348eba88679d5;hb=c17981672620e0b780a2338bd0c74e55cf9ddec2;hp=f3395caebacb2d1b012b6f86c648a947f8e80bd6;hpb=a738a37240b13fa22aa7a3333c0a58c71759ab22;p=jalview.git diff --git a/test/jalview/util/MapListTest.java b/test/jalview/util/MapListTest.java index f3395ca..6bbda78 100644 --- a/test/jalview/util/MapListTest.java +++ b/test/jalview/util/MapListTest.java @@ -27,8 +27,6 @@ import static org.testng.AssertJUnit.assertSame; import static org.testng.AssertJUnit.assertTrue; import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals; -import jalview.gui.JvOptionPane; - import java.util.ArrayList; import java.util.Arrays; import java.util.List; @@ -36,8 +34,16 @@ 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() @@ -49,17 +55,20 @@ public class MapListTest @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); @@ -294,6 +303,85 @@ public class MapListTest } /** + * 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. */ @@ -391,7 +479,9 @@ 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)); @@ -426,10 +516,11 @@ 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))); } /** @@ -461,7 +552,8 @@ 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 @@ -476,22 +568,23 @@ 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())); } /** @@ -542,8 +635,9 @@ 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] ] 1:3 to [ [51, 1] ]", s); } @@ -552,14 +646,16 @@ public class MapListTest 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()); @@ -579,7 +675,8 @@ 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()); @@ -593,8 +690,8 @@ public class MapListTest 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] ] 1:3 to [ [72, 53] ]", ml.toString()); } @@ -603,7 +700,7 @@ public class MapListTest public void testAddRange() { int[] range = { 1, 5 }; - List ranges = new ArrayList(); + List ranges = new ArrayList<>(); // add to empty list: MapList.addRange(range, ranges); @@ -680,13 +777,15 @@ public class MapListTest 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); + 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); + new int[] + { 20, 11 }, 1, 1); assertFalse(ml.isFromForwardStrand()); // all single position ranges - defaults to forward strand @@ -696,13 +795,13 @@ public class MapListTest } /** - * 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)); @@ -718,183 +817,154 @@ 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(2, merged.size()); - assertArrayEquals(new int[] { 1, 6 }, merged.get(0)); - assertArrayEquals(new int[] { 12, 7 }, merged.get(1)); - } - - /** - * Test the method that merges a list of ranges where possible - */ - @Test(groups = { "Functional" }) - public void testCoalesceRanges_withOverlap() - { - List ranges = new ArrayList(); - ranges.add(new int[] { 1, 3 }); - ranges.add(new int[] { 2, 5 }); - - /* - * [2, 5] should extend [1, 3] - */ - List merged = MapList.coalesceRanges(ranges); - assertEquals(1, merged.size()); + assertEquals(4, merged.size()); assertArrayEquals(new int[] { 1, 5 }, merged.get(0)); - - /* - * a subsumed interval should be dropped - */ - 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)); - - 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)); - - /* - * merge duplicate ranges - */ - 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)); - - /* - * reverse direction - */ + 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[] { 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 }); + ranges.add(new int[] { 10, 30 }); + ranges.add(new int[] { 15, 25 }); merged = MapList.coalesceRanges(ranges); - assertEquals(1, merged.size()); - assertArrayEquals(new int[] { 9, 0 }, merged.get(0)); + 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 + @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); - MapList ml2 = new MapList(new int[] { 1, 50 }, new int[] { 40, 45, 70, - 75, 90, 127 }, 1, 1); + 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(compound.getFromRatio(), 1); - assertEquals(compound.getToRatio(), 1); + assertEquals(1, compound.getFromRatio()); + assertEquals(1, compound.getToRatio()); List fromRanges = compound.getFromRanges(); - assertEquals(fromRanges.size(), 2); + 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(toRanges.size(), 2); + assertEquals(4, toRanges.size()); // 5-8 maps to 44-45,70-71 // 11-13 maps to 74-75,90 - assertArrayEquals(new int[] { 44, 45, 70, 71 }, toRanges.get(0)); - assertArrayEquals(new int[] { 74, 75, 90, 90 }, toRanges.get(1)); + 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); + new int[] + { 1000, 901, 600, 201 }, 1, 1); compound = ml1.traverse(ml2); - assertEquals(compound.getFromRatio(), 1); - assertEquals(compound.getToRatio(), 1); + assertEquals(1, compound.getFromRatio()); + assertEquals(1, compound.getToRatio()); fromRanges = compound.getFromRanges(); - assertEquals(fromRanges.size(), 1); + assertEquals(1, fromRanges.size()); assertArrayEquals(new int[] { 1, 50 }, fromRanges.get(0)); toRanges = compound.getToRanges(); - assertEquals(toRanges.size(), 1); - assertArrayEquals(new int[] { 931, 901, 600, 582 }, toRanges.get(0)); + 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); + ml2 = new MapList(new int[] { 1, 100 }, new int[] { 1, 50, 91, 340 }, 1, + 3); compound = ml1.traverse(ml2); - assertEquals(compound.getFromRatio(), 1); - assertEquals(compound.getToRatio(), 3); + assertEquals(1, compound.getFromRatio()); + assertEquals(3, compound.getToRatio()); fromRanges = compound.getFromRanges(); - assertEquals(fromRanges.size(), 1); + assertEquals(1, fromRanges.size()); assertArrayEquals(new int[] { 1, 30 }, fromRanges.get(0)); // 11-40 maps to 31-50,91-160 toRanges = compound.getToRanges(); - assertEquals(toRanges.size(), 1); - assertArrayEquals(new int[] { 31, 50, 91, 160 }, toRanges.get(0)); + 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); + ml2 = new MapList(new int[] { 1, 100 }, new int[] { 1, 15, 91, 175 }, 1, + 1); compound = ml1.traverse(ml2); - assertEquals(compound.getFromRatio(), 3); - assertEquals(compound.getToRatio(), 1); + assertEquals(3, compound.getFromRatio()); + assertEquals(1, compound.getToRatio()); fromRanges = compound.getFromRanges(); - assertEquals(fromRanges.size(), 1); + assertEquals(1, fromRanges.size()); assertArrayEquals(new int[] { 1, 30 }, fromRanges.get(0)); // 11-20 maps to 11-15, 91-95 toRanges = compound.getToRanges(); - assertEquals(toRanges.size(), 1); - assertArrayEquals(new int[] { 11, 15, 91, 95 }, toRanges.get(0)); + 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 @@ -904,15 +974,16 @@ public class MapListTest 3, 1); compound = ml1.traverse(ml2); - assertEquals(compound.getFromRatio(), 1); - assertEquals(compound.getToRatio(), 1); + assertEquals(1, compound.getFromRatio()); + assertEquals(1, compound.getToRatio()); fromRanges = compound.getFromRanges(); - assertEquals(fromRanges.size(), 1); + 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(toRanges.size(), 1); - assertArrayEquals(new int[] { 55, 70, 121, 124 }, toRanges.get(0)); + 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 @@ -922,14 +993,48 @@ public class MapListTest 1, 3); compound = ml1.traverse(ml2); - assertEquals(compound.getFromRatio(), 1); - assertEquals(compound.getToRatio(), 1); + assertEquals(1, compound.getFromRatio()); + assertEquals(1, compound.getToRatio()); fromRanges = compound.getFromRanges(); - assertEquals(fromRanges.size(), 1); + assertEquals(1, fromRanges.size()); assertArrayEquals(new int[] { 31, 90 }, fromRanges.get(0)); // 13-32 maps to 47-50,71-126 toRanges = compound.getToRanges(); - assertEquals(toRanges.size(), 1); - assertArrayEquals(new int[] { 47, 50, 71, 126 }, toRanges.get(0)); + 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 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()); } }