/*
* 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.AssertJUnit.fail;
import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.BitSet;
import java.util.List;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
import jalview.bin.Console;
import jalview.gui.JvOptionPane;
public class MapListTest
{
@BeforeClass(alwaysRun = true)
public void setUp()
{
Console.initLogger();
}
@BeforeClass(alwaysRun = true)
public void setUpJvOptionPane()
{
JvOptionPane.setInteractiveMode(false);
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
@Test(groups = { "Functional" }, enabled = false)
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)));
// reversed range treated as if forwards:
assertEquals("[1, 9]", Arrays.toString(ml.locateInFrom(3, 1)));
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)));
/*
* partial overlap
*/
assertEquals("[1, 12]", Arrays.toString(ml.locateInFrom(1, 5)));
assertEquals("[1, 3]", Arrays.toString(ml.locateInFrom(-1, 1)));
/*
* no overlap
*/
assertNull(ml.locateInFrom(0, 0));
}
/**
* 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)));
/*
* codons at 11-16, 21-26, 31-36 mapped to peptide positions 1, 3-4, 6-8
*/
ml = new MapList(new int[] { 11, 16, 21, 26, 31, 36 },
new int[]
{ 1, 1, 3, 4, 6, 8 }, 3, 1);
assertArrayEquals(new int[] { 11, 13 }, ml.locateInFrom(1, 1));
assertArrayEquals(new int[] { 11, 16 }, ml.locateInFrom(1, 3));
assertArrayEquals(new int[] { 11, 16, 21, 23 }, ml.locateInFrom(1, 4));
assertArrayEquals(new int[] { 14, 16, 21, 23 }, ml.locateInFrom(3, 4));
}
@Test(groups = { "Functional" })
public void testLocateInFrom_reverseStrand()
{
int[] codons = new int[] { 12, 1 };
int[] protein = new int[] { 1, 4 };
MapList ml = new MapList(codons, protein, 3, 1);
assertEquals("[12, 10]", Arrays.toString(ml.locateInFrom(1, 1)));
assertEquals("[9, 4]", Arrays.toString(ml.locateInFrom(2, 3)));
}
/**
* 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.
*/
@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)));
// reverse range treated as if forwards:
assertEquals("[2, 4]", Arrays.toString(ml.locateInTo(12, 4)));
/*
* 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)));
/*
* partial overlap
*/
assertEquals("[1, 4]", Arrays.toString(ml.locateInTo(1, 13)));
assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(-1, 2)));
/*
* no overlap
*/
assertNull(ml.locateInTo(0, 0));
}
/**
* 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);
/*
* 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)));
/*
* partial overlap
*/
assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(1, 2)));
assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(1, 4)));
assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(2, 4)));
/*
* no overlap
*/
assertNull(ml.locateInTo(4, 4));
}
/**
* 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));
assertEquals(ml.hashCode(), ml.hashCode());
assertTrue(ml.equals(ml1));
assertEquals(ml.hashCode(), ml1.hashCode());
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 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, 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, 3], [3, 7], [9, 10], [12, 12], [13, 14], [16, 17]}",
prettyPrint(ml.getFromRanges()));
assertEquals("{[1, 1], [2, 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 contiguous ranges
*/
@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 }); // contiguous
ranges.add(new int[] { 5, 5 }); // overlap!
ranges.add(new int[] { 6, 7 }); // contiguous
List merged = MapList.coalesceRanges(ranges);
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[] { 6, 7 }, ranges.get(3));
// merging in reverse direction:
ranges.clear();
ranges.add(new int[] { 7, 5 });
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(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 }); // 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 }); // contiguous
ranges.add(new int[] { 8, 8 }); // overlap
ranges.add(new int[] { 7, 7 }); // contiguous
merged = MapList.coalesceRanges(ranges);
assertEquals(4, merged.size());
assertArrayEquals(new int[] { 1, 5 }, merged.get(0));
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[] { 10, 30 });
ranges.add(new int[] { 15, 25 });
merged = MapList.coalesceRanges(ranges);
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(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);
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(1, compound.getFromRatio());
assertEquals(1, compound.getToRatio());
List fromRanges = compound.getFromRanges();
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(4, toRanges.size());
// 5-8 maps to 44-45,70-71
// 11-13 maps to 74-75,90
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);
compound = ml1.traverse(ml2);
assertEquals(1, compound.getFromRatio());
assertEquals(1, compound.getToRatio());
fromRanges = compound.getFromRanges();
assertEquals(1, fromRanges.size());
assertArrayEquals(new int[] { 1, 50 }, fromRanges.get(0));
toRanges = compound.getToRanges();
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);
compound = ml1.traverse(ml2);
assertEquals(1, compound.getFromRatio());
assertEquals(3, compound.getToRatio());
fromRanges = compound.getFromRanges();
assertEquals(1, fromRanges.size());
assertArrayEquals(new int[] { 1, 30 }, fromRanges.get(0));
// 11-40 maps to 31-50,91-160
toRanges = compound.getToRanges();
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);
compound = ml1.traverse(ml2);
assertEquals(3, compound.getFromRatio());
assertEquals(1, compound.getToRatio());
fromRanges = compound.getFromRanges();
assertEquals(1, fromRanges.size());
assertArrayEquals(new int[] { 1, 30 }, fromRanges.get(0));
// 11-20 maps to 11-15, 91-95
toRanges = compound.getToRanges();
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
*/
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(1, compound.getFromRatio());
assertEquals(1, compound.getToRatio());
fromRanges = compound.getFromRanges();
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(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
*/
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(1, compound.getFromRatio());
assertEquals(1, compound.getToRatio());
fromRanges = compound.getFromRanges();
assertEquals(1, fromRanges.size());
assertArrayEquals(new int[] { 31, 90 }, fromRanges.get(0));
// 13-32 maps to 47-50,71-126
toRanges = compound.getToRanges();
assertEquals(2, toRanges.size());
assertArrayEquals(new int[] { 47, 50 }, toRanges.get(0));
assertArrayEquals(new int[] { 71, 126 }, toRanges.get(1));
/*
* if not all regions are mapped through, returns what is
*/
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, 1);
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());
}
/**
* Test for mapping with overlapping ranges
*/
@Test(groups = { "Functional" })
public void testLocateInFrom_withOverlap()
{
/*
* gene to protein...
*/
int[] codons = new int[] { 1, 12, 12, 17 };
int[] protein = new int[] { 1, 6 };
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("[12, 14]", Arrays.toString(ml.locateInFrom(5, 5)));
assertEquals("[15, 17]", Arrays.toString(ml.locateInFrom(6, 6)));
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("[1, 12, 12, 14]", Arrays.toString(ml.locateInFrom(1, 5)));
assertEquals("[1, 12, 12, 17]", Arrays.toString(ml.locateInFrom(1, 6)));
assertEquals("[4, 9]", Arrays.toString(ml.locateInFrom(2, 3)));
assertEquals("[7, 12, 12, 17]", Arrays.toString(ml.locateInFrom(3, 6)));
/*
* partial overlap of range
*/
assertEquals("[4, 12, 12, 17]", Arrays.toString(ml.locateInFrom(2, 7)));
assertEquals("[1, 3]", Arrays.toString(ml.locateInFrom(-1, 1)));
/*
* no overlap in range
*/
assertNull(ml.locateInFrom(0, 0));
/*
* gene to CDS...from EMBL:MN908947
*/
int[] gene = new int[] { 266, 13468, 13468, 21555 };
int[] cds = new int[] { 1, 21291 };
ml = new MapList(gene, cds, 1, 1);
assertEquals("[13468, 13468]",
Arrays.toString(ml.locateInFrom(13203, 13203)));
assertEquals("[13468, 13468]",
Arrays.toString(ml.locateInFrom(13204, 13204)));
assertEquals("[13468, 13468, 13468, 13468]",
Arrays.toString(ml.locateInFrom(13203, 13204)));
}
/**
* Test for mapping with overlapping ranges
*/
@Test(groups = { "Functional" })
public void testLocateInTo_withOverlap()
{
/*
* gene to protein...
*/
int[] codons = new int[] { 1, 12, 12, 17 };
int[] protein = new int[] { 1, 6 };
MapList ml = new MapList(codons, protein, 3, 1);
assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(1, 1)));
assertEquals("[1, 3]", Arrays.toString(ml.locateInTo(3, 8)));
assertEquals("[1, 4]", Arrays.toString(ml.locateInTo(2, 11)));
assertEquals("[1, 4]", Arrays.toString(ml.locateInTo(3, 11)));
// we want base 12 to map to both of the amino acids it codes for
assertEquals("[4, 5]", Arrays.toString(ml.locateInTo(12, 12)));
assertEquals("[4, 5]", Arrays.toString(ml.locateInTo(11, 12)));
assertEquals("[4, 6]", Arrays.toString(ml.locateInTo(11, 15)));
assertEquals("[6, 6]", Arrays.toString(ml.locateInTo(15, 17)));
/*
* no overlap
*/
assertNull(ml.locateInTo(0, 0));
/*
* partial overlap
*/
assertEquals("[1, 6]", Arrays.toString(ml.locateInTo(1, 18)));
assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(-1, 1)));
/*
* gene to CDS...from EMBL:MN908947
* the base at 13468 is used twice in transcription
*/
int[] gene = new int[] { 266, 13468, 13468, 21555 };
int[] cds = new int[] { 1, 21291 };
ml = new MapList(gene, cds, 1, 1);
assertEquals("[13203, 13204]",
Arrays.toString(ml.locateInTo(13468, 13468)));
/*
* gene to protein
* the base at 13468 is in the codon for 4401N and also 4402R
*/
gene = new int[] { 266, 13468, 13468, 21552 }; // stop codon excluded
protein = new int[] { 1, 7096 };
ml = new MapList(gene, protein, 3, 1);
assertEquals("[4401, 4402]",
Arrays.toString(ml.locateInTo(13468, 13468)));
}
@Test(groups = { "Functional" })
public void testTraverseToPosition()
{
List ranges = new ArrayList<>();
assertNull(MapList.traverseToPosition(ranges, 0));
ranges.add(new int[] { 3, 6 });
assertNull(MapList.traverseToPosition(ranges, 0));
}
@Test(groups = { "Functional" })
public void testCountPositions()
{
try
{
MapList.countPositions(null, 1);
fail("expected exception");
} catch (NullPointerException e)
{
// expected
}
List intervals = new ArrayList<>();
assertNull(MapList.countPositions(intervals, 1));
/*
* forward strand
*/
intervals.add(new int[] { 10, 20 });
assertNull(MapList.countPositions(intervals, 9));
assertNull(MapList.countPositions(intervals, 21));
assertArrayEquals(new int[] { 1, 1 },
MapList.countPositions(intervals, 10));
assertArrayEquals(new int[] { 6, 1 },
MapList.countPositions(intervals, 15));
assertArrayEquals(new int[] { 11, 1 },
MapList.countPositions(intervals, 20));
intervals.add(new int[] { 25, 25 });
assertArrayEquals(new int[] { 12, 1 },
MapList.countPositions(intervals, 25));
// next interval repeats position 25 - which should be counted twice if
// traversed
intervals.add(new int[] { 25, 26 });
assertArrayEquals(new int[] { 12, 1 },
MapList.countPositions(intervals, 25));
assertArrayEquals(new int[] { 14, 1 },
MapList.countPositions(intervals, 26));
/*
* reverse strand
*/
intervals.clear();
intervals.add(new int[] { 5, -5 });
assertNull(MapList.countPositions(intervals, 6));
assertNull(MapList.countPositions(intervals, -6));
assertArrayEquals(new int[] { 1, -1 },
MapList.countPositions(intervals, 5));
assertArrayEquals(new int[] { 7, -1 },
MapList.countPositions(intervals, -1));
assertArrayEquals(new int[] { 11, -1 },
MapList.countPositions(intervals, -5));
/*
* reverse then forward
*/
intervals.add(new int[] { 5, 10 });
assertArrayEquals(new int[] { 13, 1 },
MapList.countPositions(intervals, 6));
/*
* reverse then forward then reverse
*/
intervals.add(new int[] { -10, -20 });
assertArrayEquals(new int[] { 20, -1 },
MapList.countPositions(intervals, -12));
/*
* an interval [x, x] is treated as forward
*/
intervals.add(new int[] { 30, 30 });
assertArrayEquals(new int[] { 29, 1 },
MapList.countPositions(intervals, 30));
/*
* it is the first matched occurrence that is returned
*/
intervals.clear();
intervals.add(new int[] { 1, 2 });
intervals.add(new int[] { 2, 3 });
assertArrayEquals(new int[] { 2, 1 },
MapList.countPositions(intervals, 2));
intervals.add(new int[] { -1, -2 });
intervals.add(new int[] { -2, -3 });
assertArrayEquals(new int[] { 6, -1 },
MapList.countPositions(intervals, -2));
}
/**
* Tests for helper method that adds any overlap (plus offset) to a set of
* overlaps
*/
@Test(groups = { "Functional" })
public void testAddOffsetPositions()
{
List mapped = new ArrayList<>();
int[] range = new int[] { 10, 20 };
BitSet offsets = new BitSet();
MapList.addOffsetPositions(mapped, 0, range, offsets);
assertTrue(mapped.isEmpty()); // nothing marked for overlap
offsets.set(11);
MapList.addOffsetPositions(mapped, 0, range, offsets);
assertTrue(mapped.isEmpty()); // no offset 11 in range
offsets.set(4, 6); // this sets bits 4 and 5
MapList.addOffsetPositions(mapped, 0, range, offsets);
assertEquals(1, mapped.size());
assertArrayEquals(new int[] { 14, 15 }, mapped.get(0));
mapped.clear();
offsets.set(10);
MapList.addOffsetPositions(mapped, 0, range, offsets);
assertEquals(2, mapped.size());
assertArrayEquals(new int[] { 14, 15 }, mapped.get(0));
assertArrayEquals(new int[] { 20, 20 }, mapped.get(1));
/*
* reverse range
*/
range = new int[] { 20, 10 };
mapped.clear();
offsets.clear();
MapList.addOffsetPositions(mapped, 0, range, offsets);
assertTrue(mapped.isEmpty()); // nothing marked for overlap
offsets.set(11);
MapList.addOffsetPositions(mapped, 0, range, offsets);
assertTrue(mapped.isEmpty()); // no offset 11 in range
offsets.set(0);
offsets.set(10);
offsets.set(6, 8); // sets bits 6 and 7
MapList.addOffsetPositions(mapped, 0, range, offsets);
assertEquals(3, mapped.size());
assertArrayEquals(new int[] { 20, 20 }, mapped.get(0));
assertArrayEquals(new int[] { 14, 13 }, mapped.get(1));
assertArrayEquals(new int[] { 10, 10 }, mapped.get(2));
}
@Test(groups = { "Functional" })
public void testGetPositionsForOffsets()
{
List ranges = new ArrayList<>();
BitSet offsets = new BitSet();
List mapped = MapList.getPositionsForOffsets(ranges, offsets);
assertTrue(mapped.isEmpty()); // no ranges and no offsets!
offsets.set(5, 1000);
mapped = MapList.getPositionsForOffsets(ranges, offsets);
assertTrue(mapped.isEmpty()); // no ranges
/*
* one range with overlap of offsets
*/
ranges.add(new int[] { 15, 25 });
mapped = MapList.getPositionsForOffsets(ranges, offsets);
assertEquals(1, mapped.size());
assertArrayEquals(new int[] { 20, 25 }, mapped.get(0));
/*
* two ranges
*/
ranges.add(new int[] { 300, 320 });
mapped = MapList.getPositionsForOffsets(ranges, offsets);
assertEquals(2, mapped.size());
assertArrayEquals(new int[] { 20, 25 }, mapped.get(0));
assertArrayEquals(new int[] { 300, 320 }, mapped.get(1));
/*
* boundary case - right end of first range overlaps
*/
offsets.clear();
offsets.set(10);
mapped = MapList.getPositionsForOffsets(ranges, offsets);
assertEquals(1, mapped.size());
assertArrayEquals(new int[] { 25, 25 }, mapped.get(0));
/*
* boundary case - left end of second range overlaps
*/
offsets.set(11);
mapped = MapList.getPositionsForOffsets(ranges, offsets);
assertEquals(2, mapped.size());
assertArrayEquals(new int[] { 25, 25 }, mapped.get(0));
assertArrayEquals(new int[] { 300, 300 }, mapped.get(1));
/*
* offsets into a circular range are reported in
* the order in which they are traversed
*/
ranges.clear();
ranges.add(new int[] { 100, 150 });
ranges.add(new int[] { 60, 80 });
offsets.clear();
offsets.set(45, 55); // sets bits 45 to 54
mapped = MapList.getPositionsForOffsets(ranges, offsets);
assertEquals(2, mapped.size());
assertArrayEquals(new int[] { 145, 150 }, mapped.get(0)); // offsets 45-50
assertArrayEquals(new int[] { 60, 63 }, mapped.get(1)); // offsets 51-54
/*
* reverse range overlap is reported with start < end
*/
ranges.clear();
ranges.add(new int[] { 4321, 4000 });
offsets.clear();
offsets.set(20, 22); // sets bits 20 and 21
offsets.set(30);
mapped = MapList.getPositionsForOffsets(ranges, offsets);
assertEquals(2, mapped.size());
assertArrayEquals(new int[] { 4301, 4300 }, mapped.get(0));
assertArrayEquals(new int[] { 4291, 4291 }, mapped.get(1));
}
@Test(groups = { "Functional" })
public void testGetMappedOffsetsForPositions()
{
/*
* start by verifying the examples in the method's Javadoc!
*/
List ranges = new ArrayList<>();
ranges.add(new int[] { 10, 20 });
ranges.add(new int[] { 31, 40 });
BitSet overlaps = MapList.getMappedOffsetsForPositions(1, 9, ranges, 1,
1);
assertTrue(overlaps.isEmpty());
overlaps = MapList.getMappedOffsetsForPositions(1, 11, ranges, 1, 1);
assertEquals(2, overlaps.cardinality());
assertTrue(overlaps.get(0));
assertTrue(overlaps.get(1));
overlaps = MapList.getMappedOffsetsForPositions(15, 35, ranges, 1, 1);
assertEquals(11, overlaps.cardinality());
for (int i = 5; i <= 11; i++)
{
assertTrue(overlaps.get(i));
}
ranges.clear();
ranges.add(new int[] { 1, 200 });
overlaps = MapList.getMappedOffsetsForPositions(9, 9, ranges, 1, 3);
assertEquals(3, overlaps.cardinality());
assertTrue(overlaps.get(24));
assertTrue(overlaps.get(25));
assertTrue(overlaps.get(26));
ranges.clear();
ranges.add(new int[] { 101, 150 });
ranges.add(new int[] { 171, 180 });
overlaps = MapList.getMappedOffsetsForPositions(101, 102, ranges, 3, 1);
assertEquals(1, overlaps.cardinality());
assertTrue(overlaps.get(0));
overlaps = MapList.getMappedOffsetsForPositions(150, 171, ranges, 3, 1);
assertEquals(1, overlaps.cardinality());
assertTrue(overlaps.get(16));
ranges.clear();
ranges.add(new int[] { 101, 150 });
ranges.add(new int[] { 21, 30 });
overlaps = MapList.getMappedOffsetsForPositions(24, 40, ranges, 3, 1);
assertEquals(3, overlaps.cardinality());
assertTrue(overlaps.get(17));
assertTrue(overlaps.get(18));
assertTrue(overlaps.get(19));
/*
* reverse range 1:1 (e.g. reverse strand gene to transcript)
*/
ranges.clear();
ranges.add(new int[] { 20, 10 });
overlaps = MapList.getMappedOffsetsForPositions(12, 13, ranges, 1, 1);
assertEquals(2, overlaps.cardinality());
assertTrue(overlaps.get(7));
assertTrue(overlaps.get(8));
/*
* reverse range 3:1 (e.g. reverse strand gene to peptide)
* from EMBL:J03321 to P0CE20
*/
ranges.clear();
ranges.add(new int[] { 1480, 488 });
overlaps = MapList.getMappedOffsetsForPositions(1460, 1460, ranges, 3,
1);
// 1460 is the end of the 7th codon
assertEquals(1, overlaps.cardinality());
assertTrue(overlaps.get(6));
// add one base (part codon)
overlaps = MapList.getMappedOffsetsForPositions(1459, 1460, ranges, 3,
1);
assertEquals(2, overlaps.cardinality());
assertTrue(overlaps.get(6));
assertTrue(overlaps.get(7));
// add second base (part codon)
overlaps = MapList.getMappedOffsetsForPositions(1458, 1460, ranges, 3,
1);
assertEquals(2, overlaps.cardinality());
assertTrue(overlaps.get(6));
assertTrue(overlaps.get(7));
// add third base (whole codon)
overlaps = MapList.getMappedOffsetsForPositions(1457, 1460, ranges, 3,
1);
assertEquals(2, overlaps.cardinality());
assertTrue(overlaps.get(6));
assertTrue(overlaps.get(7));
// add one more base (part codon)
overlaps = MapList.getMappedOffsetsForPositions(1456, 1460, ranges, 3,
1);
assertEquals(3, overlaps.cardinality());
assertTrue(overlaps.get(6));
assertTrue(overlaps.get(7));
assertTrue(overlaps.get(8));
}
}