/*
* 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.assertTrue;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import org.testng.annotations.Test;
public class MapListTest
{
@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()));
}
/**
* 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("From (1:3) [ [1, 5] [10, 15] [25, 20] ] To [ [51, 1] ]",
s);
}
}