X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Futil%2FMapListTest.java;h=1acc9e1f30515a6f91a5e59dea335254cc3343c1;hb=86b84a537a05d03a21ba115bffe3575cedf98be0;hp=9a0bdd723230f6e31b59aec14e32c1b649a691a8;hpb=37de9310bec3501cbc6381e0c3dcb282fcaad812;p=jalview.git diff --git a/test/jalview/util/MapListTest.java b/test/jalview/util/MapListTest.java index 9a0bdd7..1acc9e1 100644 --- a/test/jalview/util/MapListTest.java +++ b/test/jalview/util/MapListTest.java @@ -27,15 +27,25 @@ 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() { @@ -381,7 +391,9 @@ 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)); @@ -416,7 +428,7 @@ 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))); @@ -593,7 +605,7 @@ 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); @@ -692,7 +704,7 @@ public class MapListTest 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)); @@ -753,7 +765,7 @@ public class MapListTest @Test(groups = { "Functional" }) public void testCoalesceRanges_withOverlap() { - List ranges = new ArrayList(); + List ranges = new ArrayList<>(); ranges.add(new int[] { 1, 3 }); ranges.add(new int[] { 2, 5 }); @@ -804,4 +816,155 @@ public class MapListTest 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()); + } }