X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Futil%2FMapListTest.java;h=029b6811df6f26a92c53ddcc091e69e7c0b1b7c8;hb=c5060a3a565a47414ff8d137642df8dd3e0648b0;hp=de3994eda433ded55a4c866d742902bd9eaae50b;hpb=8f118c154e74caaef6bec19acd0466904ac424d4;p=jalview.git diff --git a/test/jalview/util/MapListTest.java b/test/jalview/util/MapListTest.java index de3994e..029b681 100644 --- a/test/jalview/util/MapListTest.java +++ b/test/jalview/util/MapListTest.java @@ -23,17 +23,29 @@ package jalview.util; import static org.testng.AssertJUnit.assertEquals; import static org.testng.AssertJUnit.assertFalse; import static org.testng.AssertJUnit.assertNull; +import static org.testng.AssertJUnit.assertSame; import static org.testng.AssertJUnit.assertTrue; +import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals; + +import jalview.gui.JvOptionPane; import java.util.ArrayList; import java.util.Arrays; import java.util.List; +import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; public class MapListTest { + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() + { + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + } + @Test(groups = { "Functional" }) public void testSomething() { @@ -414,7 +426,7 @@ 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))); @@ -450,6 +462,36 @@ public class MapListTest 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())); + + /* + * reverse direction + */ + codons = new int[] { 9, 6 }; + protein = new int[] { 100, 91, 80, 79 }; + ml = new MapList(codons, protein, 3, 1); + assertEquals(6, ml.getFromLowest()); + assertEquals(9, ml.getFromHighest()); + assertEquals(79, ml.getToLowest()); + assertEquals(100, ml.getToHighest()); + } + + /** + * Test constructor can merge consecutive ranges + */ + @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 }; + 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]}", + prettyPrint(ml.getFromRanges())); + assertEquals("{[1, 3], [6, 6]}", prettyPrint(ml.getToRanges())); } /** @@ -503,7 +545,424 @@ public class MapListTest MapList ml = new MapList(new int[] { 1, 5, 10, 15, 25, 20 }, new int[] { 51, 1 }, 1, 3); String s = ml.toString(); - assertEquals("From (1:3) [ [1, 5] [10, 15] [25, 20] ] To [ [51, 1] ]", + assertEquals("[ [1, 5] [10, 15] [25, 20] ] 1:3 to [ [51, 1] ]", s); + } + + @Test(groups = { "Functional" }) + public void testAddMapList() + { + MapList ml = new MapList(new int[] { 11, 15, 20, 25, 35, 30 }, + new int[] { 72, 22 }, 1, 3); + assertEquals(11, ml.getFromLowest()); + assertEquals(35, ml.getFromHighest()); + assertEquals(22, ml.getToLowest()); + assertEquals(72, ml.getToHighest()); + + MapList ml2 = new MapList(new int[] { 2, 4, 37, 40 }, new int[] { 12, + 17, 78, 83, 88, 96 }, 1, 3); + ml.addMapList(ml2); + assertEquals(2, ml.getFromLowest()); + assertEquals(40, ml.getFromHighest()); + assertEquals(12, ml.getToLowest()); + assertEquals(96, ml.getToHighest()); + + String s = ml.toString(); + assertEquals( + "[ [11, 15] [20, 25] [35, 30] [2, 4] [37, 40] ] 1:3 to [ [72, 22] [12, 17] [78, 83] [88, 96] ]", s); } + + /** + * Test that confirms adding a map twice does nothing + */ + @Test(groups = { "Functional" }) + public void testAddMapList_sameMap() + { + MapList ml = new MapList(new int[] { 11, 15, 20, 25, 35, 30 }, + new int[] { 72, 22 }, 1, 3); + String before = ml.toString(); + ml.addMapList(ml); + assertEquals(before, ml.toString()); + ml.addMapList(new MapList(ml)); + assertEquals(before, ml.toString()); + } + + @Test(groups = { "Functional" }) + public void testAddMapList_contiguous() + { + MapList ml = new MapList(new int[] { 11, 15 }, new int[] { 72, 58 }, 1, + 3); + + MapList ml2 = new MapList(new int[] { 15, 16 }, new int[] { 58, 53 }, + 1, 3); + ml.addMapList(ml2); + assertEquals("[ [11, 16] ] 1:3 to [ [72, 53] ]", ml.toString()); + } + + @Test(groups = "Functional") + public void testAddRange() + { + int[] range = { 1, 5 }; + List ranges = new ArrayList<>(); + + // add to empty list: + MapList.addRange(range, ranges); + assertEquals(1, ranges.size()); + assertSame(range, ranges.get(0)); + + // extend contiguous (same position): + MapList.addRange(new int[] { 5, 10 }, ranges); + assertEquals(1, ranges.size()); + assertEquals(1, ranges.get(0)[0]); + assertEquals(10, ranges.get(0)[1]); + + // extend contiguous (next position): + MapList.addRange(new int[] { 11, 15 }, ranges); + assertEquals(1, ranges.size()); + assertEquals(1, ranges.get(0)[0]); + assertEquals(15, ranges.get(0)[1]); + + // change direction: range is not merged: + MapList.addRange(new int[] { 16, 10 }, ranges); + assertEquals(2, ranges.size()); + assertEquals(16, ranges.get(1)[0]); + assertEquals(10, ranges.get(1)[1]); + + // extend reverse contiguous (same position): + MapList.addRange(new int[] { 10, 8 }, ranges); + assertEquals(2, ranges.size()); + assertEquals(16, ranges.get(1)[0]); + assertEquals(8, ranges.get(1)[1]); + + // extend reverse contiguous (next position): + MapList.addRange(new int[] { 7, 6 }, ranges); + assertEquals(2, ranges.size()); + assertEquals(16, ranges.get(1)[0]); + assertEquals(6, ranges.get(1)[1]); + + // change direction: range is not merged: + MapList.addRange(new int[] { 6, 9 }, ranges); + assertEquals(3, ranges.size()); + assertEquals(6, ranges.get(2)[0]); + assertEquals(9, ranges.get(2)[1]); + + // not contiguous: not merged + MapList.addRange(new int[] { 11, 12 }, ranges); + assertEquals(4, ranges.size()); + assertEquals(11, ranges.get(3)[0]); + assertEquals(12, ranges.get(3)[1]); + } + + /** + * Check state after construction + */ + @Test(groups = { "Functional" }) + public void testConstructor_withLists() + { + /* + * reverse direction + */ + int[][] codons = new int[][] { { 9, 6 } }; + int[][] protein = new int[][] { { 100, 91 }, { 80, 79 } }; + MapList ml = new MapList(Arrays.asList(codons), Arrays.asList(protein), + 3, 1); + assertEquals(6, ml.getFromLowest()); + assertEquals(9, ml.getFromHighest()); + assertEquals(79, ml.getToLowest()); + assertEquals(100, ml.getToHighest()); + } + + /** + * Test that method that inspects for the (first) forward or reverse from + * range. Single position ranges are ignored. + */ + @Test(groups = { "Functional" }) + public void testIsFromForwardStrand() + { + // [3-9] declares forward strand + MapList ml = new MapList(new int[] { 2, 2, 3, 9, 12, 11 }, new int[] { + 20, 11 }, 1, 1); + assertTrue(ml.isFromForwardStrand()); + + // [11-5] declares reverse strand ([13-14] is ignored) + ml = new MapList(new int[] { 2, 2, 11, 5, 13, 14 }, + new int[] { 20, 11 }, 1, 1); + assertFalse(ml.isFromForwardStrand()); + + // all single position ranges - defaults to forward strand + ml = new MapList(new int[] { 2, 2, 4, 4, 6, 6 }, new int[] { 3, 1 }, 1, + 1); + assertTrue(ml.isFromForwardStrand()); + } + + /** + * Test the method that merges a list of ranges where possible + */ + @Test(groups = { "Functional" }) + public void testCoalesceRanges() + { + assertNull(MapList.coalesceRanges(null)); + List ranges = new ArrayList<>(); + assertSame(ranges, MapList.coalesceRanges(ranges)); + ranges.add(new int[] { 1, 3 }); + assertSame(ranges, MapList.coalesceRanges(ranges)); + + // add non-contiguous range: + ranges.add(new int[] { 5, 6 }); + assertSame(ranges, MapList.coalesceRanges(ranges)); + + // 'contiguous' range in opposite direction is not merged: + ranges.add(new int[] { 7, 6 }); + assertSame(ranges, MapList.coalesceRanges(ranges)); + + // merging in forward direction: + ranges.clear(); + ranges.add(new int[] { 1, 3 }); + ranges.add(new int[] { 4, 5 }); + ranges.add(new int[] { 5, 5 }); + ranges.add(new int[] { 5, 7 }); + List merged = MapList.coalesceRanges(ranges); + assertEquals(1, merged.size()); + assertArrayEquals(new int[] { 1, 7 }, merged.get(0)); + // 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)); + + // 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 }); + merged = MapList.coalesceRanges(ranges); + assertEquals(1, merged.size()); + assertArrayEquals(new int[] { 7, 1 }, merged.get(0)); + + // 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[] { 12, 10 }); + ranges.add(new int[] { 9, 8 }); + ranges.add(new int[] { 8, 8 }); + ranges.add(new int[] { 7, 7 }); + 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()); + 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 + */ + 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)); + } + + /** + * 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); + MapList ml2 = new MapList(new int[] { 1, 50 }, new int[] { 40, 45, 70, + 75, 90, 127 }, 1, 1); + MapList compound = ml1.traverse(ml2); + + assertEquals(compound.getFromRatio(), 1); + assertEquals(compound.getToRatio(), 1); + List fromRanges = compound.getFromRanges(); + assertEquals(fromRanges.size(), 2); + assertArrayEquals(new int[] { 3, 4 }, fromRanges.get(0)); + assertArrayEquals(new int[] { 8, 12 }, fromRanges.get(1)); + List toRanges = compound.getToRanges(); + assertEquals(toRanges.size(), 2); + // 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)); + + /* + * 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(compound.getFromRatio(), 1); + assertEquals(compound.getToRatio(), 1); + fromRanges = compound.getFromRanges(); + assertEquals(fromRanges.size(), 1); + 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)); + + /* + * 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(compound.getFromRatio(), 1); + assertEquals(compound.getToRatio(), 3); + fromRanges = compound.getFromRanges(); + assertEquals(fromRanges.size(), 1); + 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)); + + /* + * 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(compound.getFromRatio(), 3); + assertEquals(compound.getToRatio(), 1); + fromRanges = compound.getFromRanges(); + assertEquals(fromRanges.size(), 1); + 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)); + + /* + * 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(compound.getFromRatio(), 1); + assertEquals(compound.getToRatio(), 1); + fromRanges = compound.getFromRanges(); + assertEquals(fromRanges.size(), 1); + 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)); + + /* + * 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(compound.getFromRatio(), 1); + assertEquals(compound.getToRatio(), 1); + fromRanges = compound.getFromRanges(); + assertEquals(fromRanges.size(), 1); + 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)); + + /* + * 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()); + } }