--- /dev/null
+package jalview.util;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import org.junit.Assert;
+import org.junit.Test;
+
+public class MapListTest
+{
+
+ @Test
+ 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);
+ Assert.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
+ 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
+ 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
+ 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
+ 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
+ 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
+ public void testGetRanges()
+ {
+ List<int[]> ranges = new ArrayList<int[]>();
+ 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
+ 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()));
+ }
+
+ /**
+ * Convert a List of {[i, j], [k, l], ...} to "[[i, j], [k, l], ...]"
+ *
+ * @param ranges
+ * @return
+ */
+ private String prettyPrint(List<int[]> 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
+ 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()));
+ }
+}
git://source.jalview.org / jalview.git / blobdiff