/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
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()
{
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()));
}
/**
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<int[]> ranges = new ArrayList<int[]>();
+
+ // 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<int[]> ranges = new ArrayList<int[]>();
+ 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<int[]> 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<int[]> ranges = new ArrayList<int[]>();
+ ranges.add(new int[] { 1, 3 });
+ ranges.add(new int[] { 2, 5 });
+
+ /*
+ * [2, 5] should extend [1, 3]
+ */
+ List<int[]> 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
+ 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<int[]> fromRanges = compound.getFromRanges();
+ assertEquals(fromRanges.size(), 2);
+ assertArrayEquals(new int[] { 3, 4 }, fromRanges.get(0));
+ assertArrayEquals(new int[] { 8, 12 }, fromRanges.get(1));
+ List<int[]> 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);
+ }
}
git://source.jalview.org / jalview.git / blobdiff