2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import static org.testng.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.assertFalse;
25 import static org.testng.AssertJUnit.assertNull;
26 import static org.testng.AssertJUnit.assertSame;
27 import static org.testng.AssertJUnit.assertTrue;
28 import static org.testng.AssertJUnit.fail;
29 import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
31 import java.util.ArrayList;
32 import java.util.Arrays;
33 import java.util.BitSet;
34 import java.util.List;
36 import org.testng.annotations.BeforeClass;
37 import org.testng.annotations.Test;
39 import jalview.bin.Cache;
40 import jalview.gui.JvOptionPane;
42 public class MapListTest
44 @BeforeClass(alwaysRun = true)
50 @BeforeClass(alwaysRun = true)
51 public void setUpJvOptionPane()
53 JvOptionPane.setInteractiveMode(false);
54 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
57 @Test(groups = { "Functional" }, enabled = false)
58 public void testSomething()
60 MapList ml = new MapList(new int[] { 1, 5, 10, 15, 25, 20 },
63 MapList ml1 = new MapList(new int[] { 1, 3, 17, 4 },
66 MapList ml2 = new MapList(new int[] { 1, 60 }, new int[] { 1, 20 }, 3,
68 // test internal consistency
69 int to[] = new int[51];
71 MapList mldna = new MapList(new int[] { 2, 2, 6, 8, 12, 16 },
74 int[] frm = mldna.locateInFrom(1, 1);
75 testLocateFrom(mldna, 1, 1, new int[] { 2, 2, 6, 7 });
78 * for (int from=1; from<=51; from++) { int[] too=ml.shiftTo(from); int[]
79 * toofrom=ml.shiftFrom(too[0]);
80 * System.out.println("ShiftFrom("+from+")=="+too[0]+" %
81 * "+too[1]+"\t+-+\tShiftTo("+too[0]+")=="+toofrom[0]+" % "+toofrom[1]); }
85 private static void testLocateFrom(MapList mldna, int i, int j, int[] ks)
87 int[] frm = mldna.locateInFrom(i, j);
88 assertEquals("Failed test locate from " + i + " to " + j,
89 Arrays.toString(frm), Arrays.toString(ks));
93 * test routine. not incremental.
99 private void testMap(MapList ml, int fromS, int fromE)
101 // todo convert to JUnit style tests
102 for (int from = 1; from <= 25; from++)
104 int[] too = ml.shiftFrom(from);
105 System.out.print("ShiftFrom(" + from + ")==");
108 System.out.print("NaN\n");
112 System.out.print(too[0] + " % " + too[1] + " (" + too[2] + ")");
113 System.out.print("\t+--+\t");
114 int[] toofrom = ml.shiftTo(too[0]);
117 if (toofrom[0] != from)
119 System.err.println("Mapping not reflexive:" + from + " "
120 + too[0] + "->" + toofrom[0]);
122 System.out.println("ShiftTo(" + too[0] + ")==" + toofrom[0]
123 + " % " + toofrom[1] + " (" + toofrom[2] + ")");
127 System.out.println("ShiftTo(" + too[0] + ")=="
128 + "NaN! - not Bijective Mapping!");
132 int mmap[][] = ml.makeFromMap();
133 System.out.println("FromMap : (" + mmap[0][0] + " " + mmap[0][1] + " "
134 + mmap[0][2] + " " + mmap[0][3] + " ");
135 for (int i = 1; i <= mmap[1].length; i++)
137 if (mmap[1][i - 1] == -1)
139 System.out.print(i + "=XXX");
144 System.out.print(i + "=" + (mmap[0][2] + mmap[1][i - 1]));
148 System.out.print("\n");
152 System.out.print(",");
155 // test range function
156 System.out.print("\nTest locateInFrom\n");
158 int f = mmap[0][2], t = mmap[0][3];
161 System.out.println("Range " + f + " to " + t);
162 int rng[] = ml.locateInFrom(f, t);
165 for (int i = 0; i < rng.length; i++)
167 System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
172 System.out.println("No range!");
174 System.out.print("\nReversed\n");
175 rng = ml.locateInFrom(t, f);
178 for (int i = 0; i < rng.length; i++)
180 System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
185 System.out.println("No range!");
187 System.out.print("\n");
192 System.out.print("\n");
193 mmap = ml.makeToMap();
194 System.out.println("ToMap : (" + mmap[0][0] + " " + mmap[0][1] + " "
195 + mmap[0][2] + " " + mmap[0][3] + " ");
196 for (int i = 1; i <= mmap[1].length; i++)
198 if (mmap[1][i - 1] == -1)
200 System.out.print(i + "=XXX");
205 System.out.print(i + "=" + (mmap[0][2] + mmap[1][i - 1]));
209 System.out.print("\n");
213 System.out.print(",");
216 System.out.print("\n");
217 // test range function
218 System.out.print("\nTest locateInTo\n");
220 int f = mmap[0][2], t = mmap[0][3];
223 System.out.println("Range " + f + " to " + t);
224 int rng[] = ml.locateInTo(f, t);
227 for (int i = 0; i < rng.length; i++)
229 System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
234 System.out.println("No range!");
236 System.out.print("\nReversed\n");
237 rng = ml.locateInTo(t, f);
240 for (int i = 0; i < rng.length; i++)
242 System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
247 System.out.println("No range!");
251 System.out.print("\n");
257 * Tests for method that locates ranges in the 'from' map for given range in
260 @Test(groups = { "Functional" })
261 public void testLocateInFrom_noIntrons()
264 * Simple mapping with no introns
266 int[] codons = new int[] { 1, 12 };
267 int[] protein = new int[] { 1, 4 };
268 MapList ml = new MapList(codons, protein, 3, 1);
269 assertEquals("[1, 3]", Arrays.toString(ml.locateInFrom(1, 1)));
270 assertEquals("[4, 6]", Arrays.toString(ml.locateInFrom(2, 2)));
271 assertEquals("[7, 9]", Arrays.toString(ml.locateInFrom(3, 3)));
272 assertEquals("[10, 12]", Arrays.toString(ml.locateInFrom(4, 4)));
273 assertEquals("[1, 6]", Arrays.toString(ml.locateInFrom(1, 2)));
274 assertEquals("[1, 9]", Arrays.toString(ml.locateInFrom(1, 3)));
275 // reversed range treated as if forwards:
276 assertEquals("[1, 9]", Arrays.toString(ml.locateInFrom(3, 1)));
277 assertEquals("[1, 12]", Arrays.toString(ml.locateInFrom(1, 4)));
278 assertEquals("[4, 9]", Arrays.toString(ml.locateInFrom(2, 3)));
279 assertEquals("[4, 12]", Arrays.toString(ml.locateInFrom(2, 4)));
280 assertEquals("[7, 12]", Arrays.toString(ml.locateInFrom(3, 4)));
281 assertEquals("[10, 12]", Arrays.toString(ml.locateInFrom(4, 4)));
286 assertEquals("[1, 12]", Arrays.toString(ml.locateInFrom(1, 5)));
287 assertEquals("[1, 3]", Arrays.toString(ml.locateInFrom(-1, 1)));
292 assertNull(ml.locateInFrom(0, 0));
297 * Tests for method that locates ranges in the 'from' map for given range in
300 @Test(groups = { "Functional" })
301 public void testLocateInFrom_withIntrons()
304 * Exons at positions [2, 3, 5] [6, 7, 9] [10, 12, 14] [16, 17, 18] i.e.
305 * 2-3, 5-7, 9-10, 12-12, 14-14, 16-18
307 int[] codons = { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
308 int[] protein = { 1, 4 };
309 MapList ml = new MapList(codons, protein, 3, 1);
310 assertEquals("[2, 3, 5, 5]", Arrays.toString(ml.locateInFrom(1, 1)));
311 assertEquals("[6, 7, 9, 9]", Arrays.toString(ml.locateInFrom(2, 2)));
312 assertEquals("[10, 10, 12, 12, 14, 14]",
313 Arrays.toString(ml.locateInFrom(3, 3)));
314 assertEquals("[16, 18]", Arrays.toString(ml.locateInFrom(4, 4)));
317 * codons at 11-16, 21-26, 31-36 mapped to peptide positions 1, 3-4, 6-8
319 ml = new MapList(new int[] { 11, 16, 21, 26, 31, 36 },
321 { 1, 1, 3, 4, 6, 8 }, 3, 1);
322 assertArrayEquals(new int[] { 11, 13 }, ml.locateInFrom(1, 1));
323 assertArrayEquals(new int[] { 11, 16 }, ml.locateInFrom(1, 3));
324 assertArrayEquals(new int[] { 11, 16, 21, 23 }, ml.locateInFrom(1, 4));
325 assertArrayEquals(new int[] { 14, 16, 21, 23 }, ml.locateInFrom(3, 4));
329 @Test(groups = { "Functional" })
330 public void testLocateInFrom_reverseStrand()
332 int[] codons = new int[] { 12, 1 };
333 int[] protein = new int[] { 1, 4 };
334 MapList ml = new MapList(codons, protein, 3, 1);
335 assertEquals("[12, 10]", Arrays.toString(ml.locateInFrom(1, 1)));
336 assertEquals("[9, 4]", Arrays.toString(ml.locateInFrom(2, 3)));
340 * Tests for method that locates ranges in the 'to' map for given range in the
343 @Test(groups = { "Functional" })
344 public void testLocateInTo_noIntrons()
347 * Simple mapping with no introns
349 int[] codons = new int[] { 1, 12 };
350 int[] protein = new int[] { 1, 4 };
351 MapList ml = new MapList(codons, protein, 3, 1);
352 assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(1, 3)));
353 assertEquals("[2, 2]", Arrays.toString(ml.locateInTo(4, 6)));
354 assertEquals("[3, 3]", Arrays.toString(ml.locateInTo(7, 9)));
355 assertEquals("[4, 4]", Arrays.toString(ml.locateInTo(10, 12)));
356 assertEquals("[1, 2]", Arrays.toString(ml.locateInTo(1, 6)));
357 assertEquals("[1, 3]", Arrays.toString(ml.locateInTo(1, 9)));
358 assertEquals("[1, 4]", Arrays.toString(ml.locateInTo(1, 12)));
359 assertEquals("[2, 2]", Arrays.toString(ml.locateInTo(4, 6)));
360 assertEquals("[2, 4]", Arrays.toString(ml.locateInTo(4, 12)));
361 // reverse range treated as if forwards:
362 assertEquals("[2, 4]", Arrays.toString(ml.locateInTo(12, 4)));
365 * A part codon is treated as if a whole one.
367 assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(1, 1)));
368 assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(1, 2)));
369 assertEquals("[1, 2]", Arrays.toString(ml.locateInTo(1, 4)));
370 assertEquals("[1, 3]", Arrays.toString(ml.locateInTo(2, 8)));
371 assertEquals("[1, 4]", Arrays.toString(ml.locateInTo(3, 11)));
372 assertEquals("[2, 4]", Arrays.toString(ml.locateInTo(5, 11)));
377 assertEquals("[1, 4]", Arrays.toString(ml.locateInTo(1, 13)));
378 assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(-1, 2)));
383 assertNull(ml.locateInTo(0, 0));
387 * Tests for method that locates ranges in the 'to' map for given range in the
390 @Test(groups = { "Functional" })
391 public void testLocateInTo_withIntrons()
394 * Exons at positions [2, 3, 5] [6, 7, 9] [10, 12, 14] [16, 17, 18] i.e.
395 * 2-3, 5-7, 9-10, 12-12, 14-14, 16-18
397 int[] codons = { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
399 * Mapped proteins at positions 1, 3, 4, 6 in the sequence
401 int[] protein = { 1, 1, 3, 4, 6, 6 };
402 MapList ml = new MapList(codons, protein, 3, 1);
405 * Valid range or subrange of codon1 maps to protein1
407 assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(2, 2)));
408 assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(3, 3)));
409 assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(3, 5)));
410 assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(2, 3)));
411 assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(2, 5)));
413 // codon position 6 starts the next protein:
414 assertEquals("[1, 1, 3, 3]", Arrays.toString(ml.locateInTo(3, 6)));
416 // codon positions 7 to 17 (part) cover proteins 2/3/4 at positions 3/4/6
417 assertEquals("[3, 4, 6, 6]", Arrays.toString(ml.locateInTo(7, 17)));
422 assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(1, 2)));
423 assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(1, 4)));
424 assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(2, 4)));
429 assertNull(ml.locateInTo(4, 4));
433 * Test equals method.
435 @Test(groups = { "Functional" })
436 public void testEquals()
438 int[] codons = new int[] { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
439 int[] protein = new int[] { 1, 4 };
440 MapList ml = new MapList(codons, protein, 3, 1);
441 MapList ml1 = new MapList(codons, protein, 3, 1); // same values
442 MapList ml2 = new MapList(codons, protein, 2, 1); // fromRatio differs
443 MapList ml3 = new MapList(codons, protein, 3, 2); // toRatio differs
445 MapList ml6 = new MapList(codons, protein, 3, 1); // fromShifts differ
447 MapList ml7 = new MapList(codons, protein, 3, 1); // toShifts differ
449 assertTrue(ml.equals(ml));
450 assertEquals(ml.hashCode(), ml.hashCode());
451 assertTrue(ml.equals(ml1));
452 assertEquals(ml.hashCode(), ml1.hashCode());
453 assertTrue(ml1.equals(ml));
455 assertFalse(ml.equals(null));
456 assertFalse(ml.equals("hello"));
457 assertFalse(ml.equals(ml2));
458 assertFalse(ml.equals(ml3));
459 assertFalse(ml.equals(ml6));
460 assertFalse(ml.equals(ml7));
461 assertFalse(ml6.equals(ml7));
465 MapList ml4 = new MapList(codons, null, 3, 1); // toShifts null
466 assertFalse(ml.equals(ml4));
467 } catch (NullPointerException e)
469 // actually thrown by constructor before equals can be called
473 MapList ml5 = new MapList(null, protein, 3, 1); // fromShifts null
474 assertFalse(ml.equals(ml5));
475 } catch (NullPointerException e)
477 // actually thrown by constructor before equals can be called
482 * Test for the method that flattens a list of ranges into a single array.
484 @Test(groups = { "Functional" })
485 public void testGetRanges()
487 List<int[]> ranges = new ArrayList<>();
488 ranges.add(new int[] { 2, 3 });
489 ranges.add(new int[] { 5, 6 });
490 assertEquals("[2, 3, 5, 6]",
491 Arrays.toString(MapList.getRanges(ranges)));
495 * Check state after construction
497 @Test(groups = { "Functional" })
498 public void testConstructor()
500 int[] codons = { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
501 int[] protein = { 1, 1, 3, 4, 6, 6 };
502 MapList ml = new MapList(codons, protein, 3, 1);
503 assertEquals(3, ml.getFromRatio());
504 assertEquals(2, ml.getFromLowest());
505 assertEquals(18, ml.getFromHighest());
506 assertEquals(1, ml.getToLowest());
507 assertEquals(6, ml.getToHighest());
508 assertEquals("{[2, 3], [5, 7], [9, 10], [12, 12], [14, 14], [16, 18]}",
509 prettyPrint(ml.getFromRanges()));
510 assertEquals("{[1, 1], [3, 4], [6, 6]}", prettyPrint(ml.getToRanges()));
513 * Also copy constructor
515 MapList ml2 = new MapList(ml);
516 assertEquals(3, ml2.getFromRatio());
517 assertEquals(2, ml2.getFromLowest());
518 assertEquals(18, ml2.getFromHighest());
519 assertEquals(1, ml2.getToLowest());
520 assertEquals(6, ml2.getToHighest());
521 assertEquals("{[2, 3], [5, 7], [9, 10], [12, 12], [14, 14], [16, 18]}",
522 prettyPrint(ml2.getFromRanges()));
523 assertEquals("{[1, 1], [3, 4], [6, 6]}",
524 prettyPrint(ml2.getToRanges()));
529 codons = new int[] { 9, 6 };
530 protein = new int[] { 100, 91, 80, 79 };
531 ml = new MapList(codons, protein, 3, 1);
532 assertEquals(6, ml.getFromLowest());
533 assertEquals(9, ml.getFromHighest());
534 assertEquals(79, ml.getToLowest());
535 assertEquals(100, ml.getToHighest());
539 * Test constructor used to merge consecutive ranges but now just leaves them
540 * as supplied (JAL-3751)
542 @Test(groups = { "Functional" })
543 public void testConstructor_mergeRanges()
545 int[] codons = { 2, 3, 3, 7, 9, 10, 12, 12, 13, 14, 16, 17 };
546 int[] protein = { 1, 1, 2, 3, 6, 6 };
547 MapList ml = new MapList(codons, protein, 3, 1);
548 assertEquals(3, ml.getFromRatio());
549 assertEquals(2, ml.getFromLowest());
550 assertEquals(17, ml.getFromHighest());
551 assertEquals(1, ml.getToLowest());
552 assertEquals(6, ml.getToHighest());
553 assertEquals("{[2, 3], [3, 7], [9, 10], [12, 12], [13, 14], [16, 17]}",
554 prettyPrint(ml.getFromRanges()));
555 assertEquals("{[1, 1], [2, 3], [6, 6]}", prettyPrint(ml.getToRanges()));
559 * Convert a List of {[i, j], [k, l], ...} to "[[i, j], [k, l], ...]"
564 private String prettyPrint(List<int[]> ranges)
566 StringBuilder sb = new StringBuilder(ranges.size() * 5);
567 boolean first = true;
569 for (int[] range : ranges)
575 sb.append(Arrays.toString(range));
579 return sb.toString();
583 * Test the method that creates an inverse mapping
585 @Test(groups = { "Functional" })
586 public void testGetInverse()
588 int[] codons = { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
589 int[] protein = { 1, 1, 3, 4, 6, 6 };
591 MapList ml = new MapList(codons, protein, 3, 1);
592 MapList ml2 = ml.getInverse();
593 assertEquals(ml.getFromRatio(), ml2.getToRatio());
594 assertEquals(ml.getFromRatio(), ml2.getToRatio());
595 assertEquals(ml.getToHighest(), ml2.getFromHighest());
596 assertEquals(ml.getFromHighest(), ml2.getToHighest());
597 assertEquals(prettyPrint(ml.getFromRanges()),
598 prettyPrint(ml2.getToRanges()));
599 assertEquals(prettyPrint(ml.getToRanges()),
600 prettyPrint(ml2.getFromRanges()));
603 @Test(groups = { "Functional" })
604 public void testToString()
606 MapList ml = new MapList(new int[] { 1, 5, 10, 15, 25, 20 },
609 String s = ml.toString();
610 assertEquals("[ [1, 5] [10, 15] [25, 20] ] 1:3 to [ [51, 1] ]", s);
613 @Test(groups = { "Functional" })
614 public void testAddMapList()
616 MapList ml = new MapList(new int[] { 11, 15, 20, 25, 35, 30 },
619 assertEquals(11, ml.getFromLowest());
620 assertEquals(35, ml.getFromHighest());
621 assertEquals(22, ml.getToLowest());
622 assertEquals(72, ml.getToHighest());
624 MapList ml2 = new MapList(new int[] { 2, 4, 37, 40 },
626 { 12, 17, 78, 83, 88, 96 }, 1, 3);
628 assertEquals(2, ml.getFromLowest());
629 assertEquals(40, ml.getFromHighest());
630 assertEquals(12, ml.getToLowest());
631 assertEquals(96, ml.getToHighest());
633 String s = ml.toString();
635 "[ [11, 15] [20, 25] [35, 30] [2, 4] [37, 40] ] 1:3 to [ [72, 22] [12, 17] [78, 83] [88, 96] ]",
640 * Test that confirms adding a map twice does nothing
642 @Test(groups = { "Functional" })
643 public void testAddMapList_sameMap()
645 MapList ml = new MapList(new int[] { 11, 15, 20, 25, 35, 30 },
648 String before = ml.toString();
650 assertEquals(before, ml.toString());
651 ml.addMapList(new MapList(ml));
652 assertEquals(before, ml.toString());
655 @Test(groups = { "Functional" })
656 public void testAddMapList_contiguous()
658 MapList ml = new MapList(new int[] { 11, 15 }, new int[] { 72, 58 }, 1,
661 MapList ml2 = new MapList(new int[] { 15, 16 }, new int[] { 58, 53 }, 1,
664 assertEquals("[ [11, 16] ] 1:3 to [ [72, 53] ]", ml.toString());
668 * Check state after construction
670 @Test(groups = { "Functional" })
671 public void testConstructor_withLists()
676 int[][] codons = new int[][] { { 9, 6 } };
677 int[][] protein = new int[][] { { 100, 91 }, { 80, 79 } };
678 MapList ml = new MapList(Arrays.asList(codons), Arrays.asList(protein),
680 assertEquals(6, ml.getFromLowest());
681 assertEquals(9, ml.getFromHighest());
682 assertEquals(79, ml.getToLowest());
683 assertEquals(100, ml.getToHighest());
687 * Test that method that inspects for the (first) forward or reverse from
688 * range. Single position ranges are ignored.
690 @Test(groups = { "Functional" })
691 public void testIsFromForwardStrand()
693 // [3-9] declares forward strand
694 MapList ml = new MapList(new int[] { 2, 2, 3, 9, 12, 11 },
697 assertTrue(ml.isFromForwardStrand());
699 // [11-5] declares reverse strand ([13-14] is ignored)
700 ml = new MapList(new int[] { 2, 2, 11, 5, 13, 14 },
703 assertFalse(ml.isFromForwardStrand());
705 // all single position ranges - defaults to forward strand
706 ml = new MapList(new int[] { 2, 2, 4, 4, 6, 6 }, new int[] { 3, 1 }, 1,
708 assertTrue(ml.isFromForwardStrand());
712 * Test the method that merges contiguous ranges
714 @Test(groups = { "Functional" })
715 public void testCoalesceRanges()
717 assertNull(MapList.coalesceRanges(null));
718 List<int[]> ranges = new ArrayList<>();
719 assertSame(ranges, MapList.coalesceRanges(ranges));
720 ranges.add(new int[] { 1, 3 });
721 assertSame(ranges, MapList.coalesceRanges(ranges));
723 // add non-contiguous range:
724 ranges.add(new int[] { 5, 6 });
725 assertSame(ranges, MapList.coalesceRanges(ranges));
727 // 'contiguous' range in opposite direction is not merged:
728 ranges.add(new int[] { 7, 6 });
729 assertSame(ranges, MapList.coalesceRanges(ranges));
731 // merging in forward direction:
733 ranges.add(new int[] { 1, 3 });
734 ranges.add(new int[] { 4, 5 }); // contiguous
735 ranges.add(new int[] { 5, 5 }); // overlap!
736 ranges.add(new int[] { 6, 7 }); // contiguous
737 List<int[]> merged = MapList.coalesceRanges(ranges);
738 assertEquals(2, merged.size());
739 assertArrayEquals(new int[] { 1, 5 }, merged.get(0));
740 assertArrayEquals(new int[] { 5, 7 }, merged.get(1));
741 // verify input list is unchanged
742 assertEquals(4, ranges.size());
743 assertArrayEquals(new int[] { 1, 3 }, ranges.get(0));
744 assertArrayEquals(new int[] { 4, 5 }, ranges.get(1));
745 assertArrayEquals(new int[] { 5, 5 }, ranges.get(2));
746 assertArrayEquals(new int[] { 6, 7 }, ranges.get(3));
748 // merging in reverse direction:
750 ranges.add(new int[] { 7, 5 });
751 ranges.add(new int[] { 5, 4 }); // overlap
752 ranges.add(new int[] { 4, 4 }); // overlap
753 ranges.add(new int[] { 3, 1 }); // contiguous
754 merged = MapList.coalesceRanges(ranges);
755 assertEquals(3, merged.size());
756 assertArrayEquals(new int[] { 7, 5 }, merged.get(0));
757 assertArrayEquals(new int[] { 5, 4 }, merged.get(1));
758 assertArrayEquals(new int[] { 4, 1 }, merged.get(2));
760 // merging with switches of direction:
762 ranges.add(new int[] { 1, 3 });
763 ranges.add(new int[] { 4, 5 }); // contiguous
764 ranges.add(new int[] { 5, 5 }); // overlap
765 ranges.add(new int[] { 6, 6 }); // contiguous
766 ranges.add(new int[] { 12, 10 });
767 ranges.add(new int[] { 9, 8 }); // contiguous
768 ranges.add(new int[] { 8, 8 }); // overlap
769 ranges.add(new int[] { 7, 7 }); // contiguous
770 merged = MapList.coalesceRanges(ranges);
771 assertEquals(4, merged.size());
772 assertArrayEquals(new int[] { 1, 5 }, merged.get(0));
773 assertArrayEquals(new int[] { 5, 6 }, merged.get(1));
774 assertArrayEquals(new int[] { 12, 8 }, merged.get(2));
775 assertArrayEquals(new int[] { 8, 7 }, merged.get(3));
777 // 'subsumed' ranges are preserved
779 ranges.add(new int[] { 10, 30 });
780 ranges.add(new int[] { 15, 25 });
781 merged = MapList.coalesceRanges(ranges);
782 assertEquals(2, merged.size());
783 assertArrayEquals(new int[] { 10, 30 }, merged.get(0));
784 assertArrayEquals(new int[] { 15, 25 }, merged.get(1));
788 * Test the method that compounds ('traverses') two mappings
790 @Test(groups = "Functional")
791 public void testTraverse()
794 * simple 1:1 plus 1:1 forwards
796 MapList ml1 = new MapList(new int[] { 3, 4, 8, 12 },
798 { 5, 8, 11, 13 }, 1, 1);
799 assertEquals("{[3, 4], [8, 12]}", prettyPrint(ml1.getFromRanges()));
800 assertEquals("{[5, 8], [11, 13]}", prettyPrint(ml1.getToRanges()));
802 MapList ml2 = new MapList(new int[] { 1, 50 },
804 { 40, 45, 70, 75, 90, 127 }, 1, 1);
805 assertEquals("{[1, 50]}", prettyPrint(ml2.getFromRanges()));
806 assertEquals("{[40, 45], [70, 75], [90, 127]}",
807 prettyPrint(ml2.getToRanges()));
809 MapList compound = ml1.traverse(ml2);
811 assertEquals(1, compound.getFromRatio());
812 assertEquals(1, compound.getToRatio());
813 List<int[]> fromRanges = compound.getFromRanges();
814 assertEquals(2, fromRanges.size());
815 assertArrayEquals(new int[] { 3, 4 }, fromRanges.get(0));
816 assertArrayEquals(new int[] { 8, 12 }, fromRanges.get(1));
817 List<int[]> toRanges = compound.getToRanges();
818 assertEquals(4, toRanges.size());
819 // 5-8 maps to 44-45,70-71
820 // 11-13 maps to 74-75,90
821 assertArrayEquals(new int[] { 44, 45 }, toRanges.get(0));
822 assertArrayEquals(new int[] { 70, 71 }, toRanges.get(1));
823 assertArrayEquals(new int[] { 74, 75 }, toRanges.get(2));
824 assertArrayEquals(new int[] { 90, 90 }, toRanges.get(3));
827 * 1:1 over 1:1 backwards ('reverse strand')
829 ml1 = new MapList(new int[] { 1, 50 }, new int[] { 70, 119 }, 1, 1);
830 ml2 = new MapList(new int[] { 1, 500 },
832 { 1000, 901, 600, 201 }, 1, 1);
833 compound = ml1.traverse(ml2);
835 assertEquals(1, compound.getFromRatio());
836 assertEquals(1, compound.getToRatio());
837 fromRanges = compound.getFromRanges();
838 assertEquals(1, fromRanges.size());
839 assertArrayEquals(new int[] { 1, 50 }, fromRanges.get(0));
840 toRanges = compound.getToRanges();
841 assertEquals(2, toRanges.size());
842 assertArrayEquals(new int[] { 931, 901 }, toRanges.get(0));
843 assertArrayEquals(new int[] { 600, 582}, toRanges.get(1));
846 * 1:1 plus 1:3 should result in 1:3
848 ml1 = new MapList(new int[] { 1, 30 }, new int[] { 11, 40 }, 1, 1);
849 ml2 = new MapList(new int[] { 1, 100 }, new int[] { 1, 50, 91, 340 }, 1,
851 compound = ml1.traverse(ml2);
853 assertEquals(1, compound.getFromRatio());
854 assertEquals(3, compound.getToRatio());
855 fromRanges = compound.getFromRanges();
856 assertEquals(1, fromRanges.size());
857 assertArrayEquals(new int[] { 1, 30 }, fromRanges.get(0));
858 // 11-40 maps to 31-50,91-160
859 toRanges = compound.getToRanges();
860 assertEquals(2, toRanges.size());
861 assertArrayEquals(new int[] { 31, 50 }, toRanges.get(0));
862 assertArrayEquals(new int[] { 91, 160 }, toRanges.get(1));
865 * 3:1 plus 1:1 should result in 3:1
867 ml1 = new MapList(new int[] { 1, 30 }, new int[] { 11, 20 }, 3, 1);
868 ml2 = new MapList(new int[] { 1, 100 }, new int[] { 1, 15, 91, 175 }, 1,
870 compound = ml1.traverse(ml2);
872 assertEquals(3, compound.getFromRatio());
873 assertEquals(1, compound.getToRatio());
874 fromRanges = compound.getFromRanges();
875 assertEquals(1, fromRanges.size());
876 assertArrayEquals(new int[] { 1, 30 }, fromRanges.get(0));
877 // 11-20 maps to 11-15, 91-95
878 toRanges = compound.getToRanges();
879 assertEquals(2, toRanges.size());
880 assertArrayEquals(new int[] { 11, 15 }, toRanges.get(0));
881 assertArrayEquals(new int[] { 91, 95 }, toRanges.get(1));
884 * 1:3 plus 3:1 should result in 1:1
886 ml1 = new MapList(new int[] { 21, 40 }, new int[] { 13, 72 }, 1, 3);
887 ml2 = new MapList(new int[] { 1, 300 }, new int[] { 51, 70, 121, 200 },
889 compound = ml1.traverse(ml2);
891 assertEquals(1, compound.getFromRatio());
892 assertEquals(1, compound.getToRatio());
893 fromRanges = compound.getFromRanges();
894 assertEquals(1, fromRanges.size());
895 assertArrayEquals(new int[] { 21, 40 }, fromRanges.get(0));
896 // 13-72 maps 3:1 to 55-70, 121-124
897 toRanges = compound.getToRanges();
898 assertEquals(2, toRanges.size());
899 assertArrayEquals(new int[] { 55, 70 }, toRanges.get(0));
900 assertArrayEquals(new int[] { 121, 124 }, toRanges.get(1));
903 * 3:1 plus 1:3 should result in 1:1
905 ml1 = new MapList(new int[] { 31, 90 }, new int[] { 13, 32 }, 3, 1);
906 ml2 = new MapList(new int[] { 11, 40 }, new int[] { 41, 50, 71, 150 },
908 compound = ml1.traverse(ml2);
910 assertEquals(1, compound.getFromRatio());
911 assertEquals(1, compound.getToRatio());
912 fromRanges = compound.getFromRanges();
913 assertEquals(1, fromRanges.size());
914 assertArrayEquals(new int[] { 31, 90 }, fromRanges.get(0));
915 // 13-32 maps to 47-50,71-126
916 toRanges = compound.getToRanges();
917 assertEquals(2, toRanges.size());
918 assertArrayEquals(new int[] { 47, 50 }, toRanges.get(0));
919 assertArrayEquals(new int[] { 71, 126 }, toRanges.get(1));
922 * if not all regions are mapped through, returns what is
924 ml1 = new MapList(new int[] { 1, 50 }, new int[] { 101, 150 }, 1, 1);
925 ml2 = new MapList(new int[] { 131, 180 }, new int[] { 201, 250 }, 1, 1);
926 compound = ml1.traverse(ml2);
927 assertNull(compound);
931 * Test that method that inspects for the (first) forward or reverse 'to'
932 * range. Single position ranges are ignored.
934 @Test(groups = { "Functional" })
935 public void testIsToForwardsStrand()
937 // [3-9] declares forward strand
938 MapList ml = new MapList(new int[] { 20, 11 },
940 { 2, 2, 3, 9, 12, 11 }, 1, 1);
941 assertTrue(ml.isToForwardStrand());
943 // [11-5] declares reverse strand ([13-14] is ignored)
944 ml = new MapList(new int[] { 20, 11 },
946 { 2, 2, 11, 5, 13, 14 }, 1, 1);
947 assertFalse(ml.isToForwardStrand());
949 // all single position ranges - defaults to forward strand
950 ml = new MapList(new int[] { 3, 1 }, new int[] { 2, 2, 4, 4, 6, 6 }, 1,
952 assertTrue(ml.isToForwardStrand());
956 * Test for mapping with overlapping ranges
958 @Test(groups = { "Functional" })
959 public void testLocateInFrom_withOverlap()
964 int[] codons = new int[] { 1, 12, 12, 17 };
965 int[] protein = new int[] { 1, 6 };
966 MapList ml = new MapList(codons, protein, 3, 1);
967 assertEquals("[1, 3]", Arrays.toString(ml.locateInFrom(1, 1)));
968 assertEquals("[4, 6]", Arrays.toString(ml.locateInFrom(2, 2)));
969 assertEquals("[7, 9]", Arrays.toString(ml.locateInFrom(3, 3)));
970 assertEquals("[10, 12]", Arrays.toString(ml.locateInFrom(4, 4)));
971 assertEquals("[12, 14]", Arrays.toString(ml.locateInFrom(5, 5)));
972 assertEquals("[15, 17]", Arrays.toString(ml.locateInFrom(6, 6)));
973 assertEquals("[1, 6]", Arrays.toString(ml.locateInFrom(1, 2)));
974 assertEquals("[1, 9]", Arrays.toString(ml.locateInFrom(1, 3)));
975 assertEquals("[1, 12]", Arrays.toString(ml.locateInFrom(1, 4)));
976 assertEquals("[1, 12, 12, 14]", Arrays.toString(ml.locateInFrom(1, 5)));
977 assertEquals("[1, 12, 12, 17]", Arrays.toString(ml.locateInFrom(1, 6)));
978 assertEquals("[4, 9]", Arrays.toString(ml.locateInFrom(2, 3)));
979 assertEquals("[7, 12, 12, 17]", Arrays.toString(ml.locateInFrom(3, 6)));
982 * partial overlap of range
984 assertEquals("[4, 12, 12, 17]", Arrays.toString(ml.locateInFrom(2, 7)));
985 assertEquals("[1, 3]", Arrays.toString(ml.locateInFrom(-1, 1)));
988 * no overlap in range
990 assertNull(ml.locateInFrom(0, 0));
993 * gene to CDS...from EMBL:MN908947
995 int[] gene = new int[] { 266, 13468, 13468, 21555 };
996 int[] cds = new int[] { 1, 21291 };
997 ml = new MapList(gene, cds, 1, 1);
998 assertEquals("[13468, 13468]",
999 Arrays.toString(ml.locateInFrom(13203, 13203)));
1000 assertEquals("[13468, 13468]",
1001 Arrays.toString(ml.locateInFrom(13204, 13204)));
1002 assertEquals("[13468, 13468, 13468, 13468]",
1003 Arrays.toString(ml.locateInFrom(13203, 13204)));
1007 * Test for mapping with overlapping ranges
1009 @Test(groups = { "Functional" })
1010 public void testLocateInTo_withOverlap()
1013 * gene to protein...
1015 int[] codons = new int[] { 1, 12, 12, 17 };
1016 int[] protein = new int[] { 1, 6 };
1017 MapList ml = new MapList(codons, protein, 3, 1);
1018 assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(1, 1)));
1019 assertEquals("[1, 3]", Arrays.toString(ml.locateInTo(3, 8)));
1020 assertEquals("[1, 4]", Arrays.toString(ml.locateInTo(2, 11)));
1021 assertEquals("[1, 4]", Arrays.toString(ml.locateInTo(3, 11)));
1023 // we want base 12 to map to both of the amino acids it codes for
1024 assertEquals("[4, 5]", Arrays.toString(ml.locateInTo(12, 12)));
1025 assertEquals("[4, 5]", Arrays.toString(ml.locateInTo(11, 12)));
1026 assertEquals("[4, 6]", Arrays.toString(ml.locateInTo(11, 15)));
1027 assertEquals("[6, 6]", Arrays.toString(ml.locateInTo(15, 17)));
1032 assertNull(ml.locateInTo(0, 0));
1037 assertEquals("[1, 6]", Arrays.toString(ml.locateInTo(1, 18)));
1038 assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(-1, 1)));
1041 * gene to CDS...from EMBL:MN908947
1042 * the base at 13468 is used twice in transcription
1044 int[] gene = new int[] { 266, 13468, 13468, 21555 };
1045 int[] cds = new int[] { 1, 21291 };
1046 ml = new MapList(gene, cds, 1, 1);
1047 assertEquals("[13203, 13204]",
1048 Arrays.toString(ml.locateInTo(13468, 13468)));
1052 * the base at 13468 is in the codon for 4401N and also 4402R
1054 gene = new int[] { 266, 13468, 13468, 21552 }; // stop codon excluded
1055 protein = new int[] { 1, 7096 };
1056 ml = new MapList(gene, protein, 3, 1);
1057 assertEquals("[4401, 4402]",
1058 Arrays.toString(ml.locateInTo(13468, 13468)));
1061 @Test(groups = { "Functional" })
1062 public void testTraverseToPosition()
1064 List<int[]> ranges = new ArrayList<>();
1065 assertNull(MapList.traverseToPosition(ranges, 0));
1067 ranges.add(new int[] { 3, 6 });
1068 assertNull(MapList.traverseToPosition(ranges, 0));
1071 @Test(groups = { "Functional" })
1072 public void testCountPositions()
1076 MapList.countPositions(null, 1);
1077 fail("expected exception");
1078 } catch (NullPointerException e)
1083 List<int[]> intervals = new ArrayList<>();
1084 assertNull(MapList.countPositions(intervals, 1));
1089 intervals.add(new int[] { 10, 20 });
1090 assertNull(MapList.countPositions(intervals, 9));
1091 assertNull(MapList.countPositions(intervals, 21));
1092 assertArrayEquals(new int[] { 1, 1 },
1093 MapList.countPositions(intervals, 10));
1094 assertArrayEquals(new int[] { 6, 1 },
1095 MapList.countPositions(intervals, 15));
1096 assertArrayEquals(new int[] { 11, 1 },
1097 MapList.countPositions(intervals, 20));
1099 intervals.add(new int[] { 25, 25 });
1100 assertArrayEquals(new int[] { 12, 1 },
1101 MapList.countPositions(intervals, 25));
1103 // next interval repeats position 25 - which should be counted twice if
1105 intervals.add(new int[] { 25, 26 });
1106 assertArrayEquals(new int[] { 12, 1 },
1107 MapList.countPositions(intervals, 25));
1108 assertArrayEquals(new int[] { 14, 1 },
1109 MapList.countPositions(intervals, 26));
1115 intervals.add(new int[] { 5, -5 });
1116 assertNull(MapList.countPositions(intervals, 6));
1117 assertNull(MapList.countPositions(intervals, -6));
1118 assertArrayEquals(new int[] { 1, -1 },
1119 MapList.countPositions(intervals, 5));
1120 assertArrayEquals(new int[] { 7, -1 },
1121 MapList.countPositions(intervals, -1));
1122 assertArrayEquals(new int[] { 11, -1 },
1123 MapList.countPositions(intervals, -5));
1126 * reverse then forward
1128 intervals.add(new int[] { 5, 10 });
1129 assertArrayEquals(new int[] { 13, 1 },
1130 MapList.countPositions(intervals, 6));
1133 * reverse then forward then reverse
1135 intervals.add(new int[] { -10, -20 });
1136 assertArrayEquals(new int[] { 20, -1 },
1137 MapList.countPositions(intervals, -12));
1140 * an interval [x, x] is treated as forward
1142 intervals.add(new int[] { 30, 30 });
1143 assertArrayEquals(new int[] { 29, 1 },
1144 MapList.countPositions(intervals, 30));
1147 * it is the first matched occurrence that is returned
1150 intervals.add(new int[] { 1, 2 });
1151 intervals.add(new int[] { 2, 3 });
1152 assertArrayEquals(new int[] { 2, 1 },
1153 MapList.countPositions(intervals, 2));
1154 intervals.add(new int[] { -1, -2 });
1155 intervals.add(new int[] { -2, -3 });
1156 assertArrayEquals(new int[] { 6, -1 },
1157 MapList.countPositions(intervals, -2));
1161 * Tests for helper method that adds any overlap (plus offset) to a set of
1164 @Test(groups = { "Functional" })
1165 public void testAddOffsetPositions()
1167 List<int[]> mapped = new ArrayList<>();
1168 int[] range = new int[] {10, 20};
1169 BitSet offsets = new BitSet();
1171 MapList.addOffsetPositions(mapped, 0, range, offsets);
1172 assertTrue(mapped.isEmpty()); // nothing marked for overlap
1175 MapList.addOffsetPositions(mapped, 0, range, offsets);
1176 assertTrue(mapped.isEmpty()); // no offset 11 in range
1178 offsets.set(4, 6); // this sets bits 4 and 5
1179 MapList.addOffsetPositions(mapped, 0, range, offsets);
1180 assertEquals(1, mapped.size());
1181 assertArrayEquals(new int[] { 14, 15 }, mapped.get(0));
1185 MapList.addOffsetPositions(mapped, 0, range, offsets);
1186 assertEquals(2, mapped.size());
1187 assertArrayEquals(new int[] { 14, 15 }, mapped.get(0));
1188 assertArrayEquals(new int[] { 20, 20 }, mapped.get(1));
1193 range = new int[] { 20, 10 };
1196 MapList.addOffsetPositions(mapped, 0, range, offsets);
1197 assertTrue(mapped.isEmpty()); // nothing marked for overlap
1199 MapList.addOffsetPositions(mapped, 0, range, offsets);
1200 assertTrue(mapped.isEmpty()); // no offset 11 in range
1203 offsets.set(6, 8); // sets bits 6 and 7
1204 MapList.addOffsetPositions(mapped, 0, range, offsets);
1205 assertEquals(3, mapped.size());
1206 assertArrayEquals(new int[] { 20, 20 }, mapped.get(0));
1207 assertArrayEquals(new int[] { 14, 13 }, mapped.get(1));
1208 assertArrayEquals(new int[] { 10, 10 }, mapped.get(2));
1211 @Test(groups = { "Functional" })
1212 public void testGetPositionsForOffsets()
1214 List<int[]> ranges = new ArrayList<>();
1215 BitSet offsets = new BitSet();
1216 List<int[]> mapped = MapList.getPositionsForOffsets(ranges, offsets);
1217 assertTrue(mapped.isEmpty()); // no ranges and no offsets!
1219 offsets.set(5, 1000);
1220 mapped = MapList.getPositionsForOffsets(ranges, offsets);
1221 assertTrue(mapped.isEmpty()); // no ranges
1224 * one range with overlap of offsets
1226 ranges.add(new int[] {15, 25});
1227 mapped = MapList.getPositionsForOffsets(ranges, offsets);
1228 assertEquals(1, mapped.size());
1229 assertArrayEquals(new int[] {20, 25}, mapped.get(0));
1234 ranges.add(new int[] {300, 320});
1235 mapped = MapList.getPositionsForOffsets(ranges, offsets);
1236 assertEquals(2, mapped.size());
1237 assertArrayEquals(new int[] {20, 25}, mapped.get(0));
1238 assertArrayEquals(new int[] {300, 320}, mapped.get(1));
1241 * boundary case - right end of first range overlaps
1245 mapped = MapList.getPositionsForOffsets(ranges, offsets);
1246 assertEquals(1, mapped.size());
1247 assertArrayEquals(new int[] {25, 25}, mapped.get(0));
1250 * boundary case - left end of second range overlaps
1253 mapped = MapList.getPositionsForOffsets(ranges, offsets);
1254 assertEquals(2, mapped.size());
1255 assertArrayEquals(new int[] {25, 25}, mapped.get(0));
1256 assertArrayEquals(new int[] {300, 300}, mapped.get(1));
1259 * offsets into a circular range are reported in
1260 * the order in which they are traversed
1263 ranges.add(new int[] {100, 150});
1264 ranges.add(new int[] {60, 80});
1266 offsets.set(45, 55); // sets bits 45 to 54
1267 mapped = MapList.getPositionsForOffsets(ranges, offsets);
1268 assertEquals(2, mapped.size());
1269 assertArrayEquals(new int[] {145, 150}, mapped.get(0)); // offsets 45-50
1270 assertArrayEquals(new int[] {60, 63}, mapped.get(1)); // offsets 51-54
1273 * reverse range overlap is reported with start < end
1276 ranges.add(new int[] {4321, 4000});
1278 offsets.set(20, 22); // sets bits 20 and 21
1280 mapped = MapList.getPositionsForOffsets(ranges, offsets);
1281 assertEquals(2, mapped.size());
1282 assertArrayEquals(new int[] {4301, 4300}, mapped.get(0));
1283 assertArrayEquals(new int[] {4291, 4291}, mapped.get(1));
1286 @Test(groups = { "Functional" })
1287 public void testGetMappedOffsetsForPositions()
1290 * start by verifying the examples in the method's Javadoc!
1292 List<int[]> ranges = new ArrayList<>();
1293 ranges.add(new int[] {10, 20});
1294 ranges.add(new int[] {31, 40});
1295 BitSet overlaps = MapList.getMappedOffsetsForPositions(1, 9, ranges, 1, 1);
1296 assertTrue(overlaps.isEmpty());
1297 overlaps = MapList.getMappedOffsetsForPositions(1, 11, ranges, 1, 1);
1298 assertEquals(2, overlaps.cardinality());
1299 assertTrue(overlaps.get(0));
1300 assertTrue(overlaps.get(1));
1301 overlaps = MapList.getMappedOffsetsForPositions(15, 35, ranges, 1, 1);
1302 assertEquals(11, overlaps.cardinality());
1303 for (int i = 5 ; i <= 11 ; i++)
1305 assertTrue(overlaps.get(i));
1309 ranges.add(new int[] {1, 200});
1310 overlaps = MapList.getMappedOffsetsForPositions(9, 9, ranges, 1, 3);
1311 assertEquals(3, overlaps.cardinality());
1312 assertTrue(overlaps.get(24));
1313 assertTrue(overlaps.get(25));
1314 assertTrue(overlaps.get(26));
1317 ranges.add(new int[] {101, 150});
1318 ranges.add(new int[] {171, 180});
1319 overlaps = MapList.getMappedOffsetsForPositions(101, 102, ranges, 3, 1);
1320 assertEquals(1, overlaps.cardinality());
1321 assertTrue(overlaps.get(0));
1322 overlaps = MapList.getMappedOffsetsForPositions(150, 171, ranges, 3, 1);
1323 assertEquals(1, overlaps.cardinality());
1324 assertTrue(overlaps.get(16));
1327 ranges.add(new int[] {101, 150});
1328 ranges.add(new int[] {21, 30});
1329 overlaps = MapList.getMappedOffsetsForPositions(24, 40, ranges, 3, 1);
1330 assertEquals(3, overlaps.cardinality());
1331 assertTrue(overlaps.get(17));
1332 assertTrue(overlaps.get(18));
1333 assertTrue(overlaps.get(19));
1336 * reverse range 1:1 (e.g. reverse strand gene to transcript)
1339 ranges.add(new int[] {20, 10});
1340 overlaps = MapList.getMappedOffsetsForPositions(12, 13, ranges, 1, 1);
1341 assertEquals(2, overlaps.cardinality());
1342 assertTrue(overlaps.get(7));
1343 assertTrue(overlaps.get(8));
1346 * reverse range 3:1 (e.g. reverse strand gene to peptide)
1347 * from EMBL:J03321 to P0CE20
1350 ranges.add(new int[] {1480, 488});
1351 overlaps = MapList.getMappedOffsetsForPositions(1460, 1460, ranges, 3, 1);
1352 // 1460 is the end of the 7th codon
1353 assertEquals(1, overlaps.cardinality());
1354 assertTrue(overlaps.get(6));
1355 // add one base (part codon)
1356 overlaps = MapList.getMappedOffsetsForPositions(1459, 1460, ranges, 3, 1);
1357 assertEquals(2, overlaps.cardinality());
1358 assertTrue(overlaps.get(6));
1359 assertTrue(overlaps.get(7));
1360 // add second base (part codon)
1361 overlaps = MapList.getMappedOffsetsForPositions(1458, 1460, ranges, 3, 1);
1362 assertEquals(2, overlaps.cardinality());
1363 assertTrue(overlaps.get(6));
1364 assertTrue(overlaps.get(7));
1365 // add third base (whole codon)
1366 overlaps = MapList.getMappedOffsetsForPositions(1457, 1460, ranges, 3, 1);
1367 assertEquals(2, overlaps.cardinality());
1368 assertTrue(overlaps.get(6));
1369 assertTrue(overlaps.get(7));
1370 // add one more base (part codon)
1371 overlaps = MapList.getMappedOffsetsForPositions(1456, 1460, ranges, 3, 1);
1372 assertEquals(3, overlaps.cardinality());
1373 assertTrue(overlaps.get(6));
1374 assertTrue(overlaps.get(7));
1375 assertTrue(overlaps.get(8));