/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
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()
{
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);
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);
int[] frm = mldna.locateInFrom(1, 1);
testLocateFrom(mldna, 1, 1, new int[] { 2, 2, 6, 7 });
testMap(mldna, 1, 3);
/*
* for (int from=1; from<=51; from++) { int[] too=ml.shiftTo(from); int[]
* toofrom=ml.shiftFrom(too[0]);
* System.out.println("ShiftFrom("+from+")=="+too[0]+" %
* "+too[1]+"\t+-+\tShiftTo("+too[0]+")=="+toofrom[0]+" % "+toofrom[1]); }
*/
}
private static void testLocateFrom(MapList mldna, int i, int j, int[] ks)
{
int[] frm = mldna.locateInFrom(i, j);
assertEquals("Failed test locate from " + i + " to " + j,
Arrays.toString(frm), Arrays.toString(ks));
}
/**
* test routine. not incremental.
*
* @param ml
* @param fromS
* @param fromE
*/
private void testMap(MapList ml, int fromS, int fromE)
{
// todo convert to JUnit style tests
for (int from = 1; from <= 25; from++)
{
int[] too = ml.shiftFrom(from);
System.out.print("ShiftFrom(" + from + ")==");
if (too == null)
{
System.out.print("NaN\n");
}
else
{
System.out.print(too[0] + " % " + too[1] + " (" + too[2] + ")");
System.out.print("\t+--+\t");
int[] toofrom = ml.shiftTo(too[0]);
if (toofrom != null)
{
if (toofrom[0] != from)
{
System.err.println("Mapping not reflexive:" + from + " "
+ too[0] + "->" + toofrom[0]);
}
System.out.println("ShiftTo(" + too[0] + ")==" + toofrom[0]
+ " % " + toofrom[1] + " (" + toofrom[2] + ")");
}
else
{
System.out.println("ShiftTo(" + too[0] + ")=="
+ "NaN! - not Bijective Mapping!");
}
}
}
int mmap[][] = ml.makeFromMap();
System.out.println("FromMap : (" + mmap[0][0] + " " + mmap[0][1] + " "
+ mmap[0][2] + " " + mmap[0][3] + " ");
for (int i = 1; i <= mmap[1].length; i++)
{
if (mmap[1][i - 1] == -1)
{
System.out.print(i + "=XXX");
}
else
{
System.out.print(i + "=" + (mmap[0][2] + mmap[1][i - 1]));
}
if (i % 20 == 0)
{
System.out.print("\n");
}
else
{
System.out.print(",");
}
}
// test range function
System.out.print("\nTest locateInFrom\n");
{
int f = mmap[0][2], t = mmap[0][3];
while (f <= t)
{
System.out.println("Range " + f + " to " + t);
int rng[] = ml.locateInFrom(f, t);
if (rng != null)
{
for (int i = 0; i < rng.length; i++)
{
System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
}
}
else
{
System.out.println("No range!");
}
System.out.print("\nReversed\n");
rng = ml.locateInFrom(t, f);
if (rng != null)
{
for (int i = 0; i < rng.length; i++)
{
System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
}
}
else
{
System.out.println("No range!");
}
System.out.print("\n");
f++;
t--;
}
}
System.out.print("\n");
mmap = ml.makeToMap();
System.out.println("ToMap : (" + mmap[0][0] + " " + mmap[0][1] + " "
+ mmap[0][2] + " " + mmap[0][3] + " ");
for (int i = 1; i <= mmap[1].length; i++)
{
if (mmap[1][i - 1] == -1)
{
System.out.print(i + "=XXX");
}
else
{
System.out.print(i + "=" + (mmap[0][2] + mmap[1][i - 1]));
}
if (i % 20 == 0)
{
System.out.print("\n");
}
else
{
System.out.print(",");
}
}
System.out.print("\n");
// test range function
System.out.print("\nTest locateInTo\n");
{
int f = mmap[0][2], t = mmap[0][3];
while (f <= t)
{
System.out.println("Range " + f + " to " + t);
int rng[] = ml.locateInTo(f, t);
if (rng != null)
{
for (int i = 0; i < rng.length; i++)
{
System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
}
}
else
{
System.out.println("No range!");
}
System.out.print("\nReversed\n");
rng = ml.locateInTo(t, f);
if (rng != null)
{
for (int i = 0; i < rng.length; i++)
{
System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
}
}
else
{
System.out.println("No range!");
}
f++;
t--;
System.out.print("\n");
}
}
}
/**
* Tests for method that locates ranges in the 'from' map for given range in
* the 'to' map.
*/
@Test(groups = { "Functional" })
public void testLocateInFrom_noIntrons()
{
/*
* Simple mapping with no introns
*/
int[] codons = new int[] { 1, 12 };
int[] protein = new int[] { 1, 4 };
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("[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("[4, 9]", Arrays.toString(ml.locateInFrom(2, 3)));
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)));
assertNull(ml.locateInFrom(0, 0));
assertNull(ml.locateInFrom(1, 5));
assertNull(ml.locateInFrom(-1, 1));
}
/**
* Tests for method that locates ranges in the 'from' map for given range in
* the 'to' map.
*/
@Test(groups = { "Functional" })
public void testLocateInFrom_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 = { 1, 4 };
MapList ml = new MapList(codons, protein, 3, 1);
assertEquals("[2, 3, 5, 5]", Arrays.toString(ml.locateInFrom(1, 1)));
assertEquals("[6, 7, 9, 9]", Arrays.toString(ml.locateInFrom(2, 2)));
assertEquals("[10, 10, 12, 12, 14, 14]",
Arrays.toString(ml.locateInFrom(3, 3)));
assertEquals("[16, 18]", Arrays.toString(ml.locateInFrom(4, 4)));
}
/**
* Tests for method that locates ranges in the 'to' map for given range in the
* 'from' map.
*/
@Test(groups = { "Functional" })
public void testLocateInTo_noIntrons()
{
/*
* Simple mapping with no introns
*/
int[] codons = new int[] { 1, 12 };
int[] protein = new int[] { 1, 4 };
MapList ml = new MapList(codons, protein, 3, 1);
assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(1, 3)));
assertEquals("[2, 2]", Arrays.toString(ml.locateInTo(4, 6)));
assertEquals("[3, 3]", Arrays.toString(ml.locateInTo(7, 9)));
assertEquals("[4, 4]", Arrays.toString(ml.locateInTo(10, 12)));
assertEquals("[1, 2]", Arrays.toString(ml.locateInTo(1, 6)));
assertEquals("[1, 3]", Arrays.toString(ml.locateInTo(1, 9)));
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)));
/*
* A part codon is treated as if a whole one.
*/
assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(1, 1)));
assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(1, 2)));
assertEquals("[1, 2]", Arrays.toString(ml.locateInTo(1, 4)));
assertEquals("[1, 3]", Arrays.toString(ml.locateInTo(2, 8)));
assertEquals("[1, 4]", Arrays.toString(ml.locateInTo(3, 11)));
assertEquals("[2, 4]", Arrays.toString(ml.locateInTo(5, 11)));
assertNull(ml.locateInTo(0, 0));
assertNull(ml.locateInTo(1, 13));
assertNull(ml.locateInTo(-1, 1));
}
/**
* Tests for method that locates ranges in the 'to' map for given range in the
* 'from' map.
*/
@Test(groups = { "Functional" })
public void testLocateInTo_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 };
/*
* 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.locateInTo(1, 2));
assertNull(ml.locateInTo(2, 4));
assertNull(ml.locateInTo(4, 4));
/*
* 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)));
assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(3, 5)));
assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(2, 3)));
assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(2, 5)));
// codon position 6 starts the next protein:
assertEquals("[1, 1, 3, 3]", Arrays.toString(ml.locateInTo(3, 6)));
// 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)));
}
/**
* Test equals method.
*/
@Test(groups = { "Functional" })
public void testEquals()
{
int[] codons = new int[] { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
int[] protein = new int[] { 1, 4 };
MapList ml = new MapList(codons, protein, 3, 1);
MapList ml1 = new MapList(codons, protein, 3, 1); // same values
MapList ml2 = new MapList(codons, protein, 2, 1); // fromRatio differs
MapList ml3 = new MapList(codons, protein, 3, 2); // toRatio differs
codons[2] = 4;
MapList ml6 = new MapList(codons, protein, 3, 1); // fromShifts differ
protein[1] = 3;
MapList ml7 = new MapList(codons, protein, 3, 1); // toShifts differ
assertTrue(ml.equals(ml));
assertTrue(ml.equals(ml1));
assertTrue(ml1.equals(ml));
assertFalse(ml.equals(null));
assertFalse(ml.equals("hello"));
assertFalse(ml.equals(ml2));
assertFalse(ml.equals(ml3));
assertFalse(ml.equals(ml6));
assertFalse(ml.equals(ml7));
assertFalse(ml6.equals(ml7));
try
{
MapList ml4 = new MapList(codons, null, 3, 1); // toShifts null
assertFalse(ml.equals(ml4));
} catch (NullPointerException e)
{
// actually thrown by constructor before equals can be called
}
try
{
MapList ml5 = new MapList(null, protein, 3, 1); // fromShifts null
assertFalse(ml.equals(ml5));
} catch (NullPointerException e)
{
// actually thrown by constructor before equals can be called
}
}
/**
* Test for the method that flattens a list of ranges into a single array.
*/
@Test(groups = { "Functional" })
public void testGetRanges()
{
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)));
}
/**
* Check state after construction
*/
@Test(groups = { "Functional" })
public void testConstructor()
{
int[] codons = { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
int[] protein = { 1, 1, 3, 4, 6, 6 };
MapList ml = new MapList(codons, protein, 3, 1);
assertEquals(3, ml.getFromRatio());
assertEquals(2, ml.getFromLowest());
assertEquals(18, ml.getFromHighest());
assertEquals(1, ml.getToLowest());
assertEquals(6, ml.getToHighest());
assertEquals("{[2, 3], [5, 7], [9, 10], [12, 12], [14, 14], [16, 18]}",
prettyPrint(ml.getFromRanges()));
assertEquals("{[1, 1], [3, 4], [6, 6]}", prettyPrint(ml.getToRanges()));
/*
* Also copy constructor
*/
MapList ml2 = new MapList(ml);
assertEquals(3, ml2.getFromRatio());
assertEquals(2, ml2.getFromLowest());
assertEquals(18, ml2.getFromHighest());
assertEquals(1, ml2.getToLowest());
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()));
/*
* 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()));
}
/**
* Convert a List of {[i, j], [k, l], ...} to "[[i, j], [k, l], ...]"
*
* @param ranges
* @return
*/
private String prettyPrint(List ranges)
{
StringBuilder sb = new StringBuilder(ranges.size() * 5);
boolean first = true;
sb.append("{");
for (int[] range : ranges)
{
if (!first)
{
sb.append(", ");
}
sb.append(Arrays.toString(range));
first = false;
}
sb.append("}");
return sb.toString();
}
/**
* Test the method that creates an inverse mapping
*/
@Test(groups = { "Functional" })
public void testGetInverse()
{
int[] codons = { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
int[] protein = { 1, 1, 3, 4, 6, 6 };
MapList ml = new MapList(codons, protein, 3, 1);
MapList ml2 = ml.getInverse();
assertEquals(ml.getFromRatio(), ml2.getToRatio());
assertEquals(ml.getFromRatio(), ml2.getToRatio());
assertEquals(ml.getToHighest(), ml2.getFromHighest());
assertEquals(ml.getFromHighest(), ml2.getToHighest());
assertEquals(prettyPrint(ml.getFromRanges()),
prettyPrint(ml2.getToRanges()));
assertEquals(prettyPrint(ml.getToRanges()),
prettyPrint(ml2.getFromRanges()));
}
@Test(groups = { "Functional" })
public void testToString()
{
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);
}
@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));
}
}