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.internal.junit.ArrayAsserts.assertArrayEquals;
30 import jalview.gui.JvOptionPane;
32 import java.util.ArrayList;
33 import java.util.Arrays;
34 import java.util.List;
36 import org.testng.annotations.BeforeClass;
37 import org.testng.annotations.Test;
39 public class MapListTest
42 @BeforeClass(alwaysRun = true)
43 public void setUpJvOptionPane()
45 JvOptionPane.setInteractiveMode(false);
46 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
49 @Test(groups = { "Functional" })
50 public void testSomething()
52 MapList ml = new MapList(new int[] { 1, 5, 10, 15, 25, 20 }, new int[] {
54 MapList ml1 = new MapList(new int[] { 1, 3, 17, 4 },
55 new int[] { 51, 1 }, 1, 3);
56 MapList ml2 = new MapList(new int[] { 1, 60 }, new int[] { 1, 20 }, 3,
58 // test internal consistency
59 int to[] = new int[51];
61 MapList mldna = new MapList(new int[] { 2, 2, 6, 8, 12, 16 }, new int[]
63 int[] frm = mldna.locateInFrom(1, 1);
64 testLocateFrom(mldna, 1, 1, new int[] { 2, 2, 6, 7 });
67 * for (int from=1; from<=51; from++) { int[] too=ml.shiftTo(from); int[]
68 * toofrom=ml.shiftFrom(too[0]);
69 * System.out.println("ShiftFrom("+from+")=="+too[0]+" %
70 * "+too[1]+"\t+-+\tShiftTo("+too[0]+")=="+toofrom[0]+" % "+toofrom[1]); }
74 private static void testLocateFrom(MapList mldna, int i, int j, int[] ks)
76 int[] frm = mldna.locateInFrom(i, j);
77 assertEquals("Failed test locate from " + i + " to " + j,
78 Arrays.toString(frm), Arrays.toString(ks));
82 * test routine. not incremental.
88 private void testMap(MapList ml, int fromS, int fromE)
90 // todo convert to JUnit style tests
91 for (int from = 1; from <= 25; from++)
93 int[] too = ml.shiftFrom(from);
94 System.out.print("ShiftFrom(" + from + ")==");
97 System.out.print("NaN\n");
101 System.out.print(too[0] + " % " + too[1] + " (" + too[2] + ")");
102 System.out.print("\t+--+\t");
103 int[] toofrom = ml.shiftTo(too[0]);
106 if (toofrom[0] != from)
108 System.err.println("Mapping not reflexive:" + from + " "
109 + too[0] + "->" + toofrom[0]);
111 System.out.println("ShiftTo(" + too[0] + ")==" + toofrom[0]
112 + " % " + toofrom[1] + " (" + toofrom[2] + ")");
116 System.out.println("ShiftTo(" + too[0] + ")=="
117 + "NaN! - not Bijective Mapping!");
121 int mmap[][] = ml.makeFromMap();
122 System.out.println("FromMap : (" + mmap[0][0] + " " + mmap[0][1] + " "
123 + mmap[0][2] + " " + mmap[0][3] + " ");
124 for (int i = 1; i <= mmap[1].length; i++)
126 if (mmap[1][i - 1] == -1)
128 System.out.print(i + "=XXX");
133 System.out.print(i + "=" + (mmap[0][2] + mmap[1][i - 1]));
137 System.out.print("\n");
141 System.out.print(",");
144 // test range function
145 System.out.print("\nTest locateInFrom\n");
147 int f = mmap[0][2], t = mmap[0][3];
150 System.out.println("Range " + f + " to " + t);
151 int rng[] = ml.locateInFrom(f, t);
154 for (int i = 0; i < rng.length; i++)
156 System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
161 System.out.println("No range!");
163 System.out.print("\nReversed\n");
164 rng = ml.locateInFrom(t, f);
167 for (int i = 0; i < rng.length; i++)
169 System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
174 System.out.println("No range!");
176 System.out.print("\n");
181 System.out.print("\n");
182 mmap = ml.makeToMap();
183 System.out.println("ToMap : (" + mmap[0][0] + " " + mmap[0][1] + " "
184 + mmap[0][2] + " " + mmap[0][3] + " ");
185 for (int i = 1; i <= mmap[1].length; i++)
187 if (mmap[1][i - 1] == -1)
189 System.out.print(i + "=XXX");
194 System.out.print(i + "=" + (mmap[0][2] + mmap[1][i - 1]));
198 System.out.print("\n");
202 System.out.print(",");
205 System.out.print("\n");
206 // test range function
207 System.out.print("\nTest locateInTo\n");
209 int f = mmap[0][2], t = mmap[0][3];
212 System.out.println("Range " + f + " to " + t);
213 int rng[] = ml.locateInTo(f, t);
216 for (int i = 0; i < rng.length; i++)
218 System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
223 System.out.println("No range!");
225 System.out.print("\nReversed\n");
226 rng = ml.locateInTo(t, f);
229 for (int i = 0; i < rng.length; i++)
231 System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
236 System.out.println("No range!");
240 System.out.print("\n");
246 * Tests for method that locates ranges in the 'from' map for given range in
249 @Test(groups = { "Functional" })
250 public void testLocateInFrom_noIntrons()
253 * Simple mapping with no introns
255 int[] codons = new int[] { 1, 12 };
256 int[] protein = new int[] { 1, 4 };
257 MapList ml = new MapList(codons, protein, 3, 1);
258 assertEquals("[1, 3]", Arrays.toString(ml.locateInFrom(1, 1)));
259 assertEquals("[4, 6]", Arrays.toString(ml.locateInFrom(2, 2)));
260 assertEquals("[7, 9]", Arrays.toString(ml.locateInFrom(3, 3)));
261 assertEquals("[10, 12]", Arrays.toString(ml.locateInFrom(4, 4)));
262 assertEquals("[1, 6]", Arrays.toString(ml.locateInFrom(1, 2)));
263 assertEquals("[1, 9]", Arrays.toString(ml.locateInFrom(1, 3)));
264 assertEquals("[1, 12]", Arrays.toString(ml.locateInFrom(1, 4)));
265 assertEquals("[4, 9]", Arrays.toString(ml.locateInFrom(2, 3)));
266 assertEquals("[4, 12]", Arrays.toString(ml.locateInFrom(2, 4)));
267 assertEquals("[7, 12]", Arrays.toString(ml.locateInFrom(3, 4)));
268 assertEquals("[10, 12]", Arrays.toString(ml.locateInFrom(4, 4)));
270 assertNull(ml.locateInFrom(0, 0));
271 assertNull(ml.locateInFrom(1, 5));
272 assertNull(ml.locateInFrom(-1, 1));
276 * Tests for method that locates ranges in the 'from' map for given range in
279 @Test(groups = { "Functional" })
280 public void testLocateInFrom_withIntrons()
283 * Exons at positions [2, 3, 5] [6, 7, 9] [10, 12, 14] [16, 17, 18] i.e.
284 * 2-3, 5-7, 9-10, 12-12, 14-14, 16-18
286 int[] codons = { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
287 int[] protein = { 1, 4 };
288 MapList ml = new MapList(codons, protein, 3, 1);
289 assertEquals("[2, 3, 5, 5]", Arrays.toString(ml.locateInFrom(1, 1)));
290 assertEquals("[6, 7, 9, 9]", Arrays.toString(ml.locateInFrom(2, 2)));
291 assertEquals("[10, 10, 12, 12, 14, 14]",
292 Arrays.toString(ml.locateInFrom(3, 3)));
293 assertEquals("[16, 18]", Arrays.toString(ml.locateInFrom(4, 4)));
297 * Tests for method that locates ranges in the 'to' map for given range in the
300 @Test(groups = { "Functional" })
301 public void testLocateInTo_noIntrons()
304 * Simple mapping with no introns
306 int[] codons = new int[] { 1, 12 };
307 int[] protein = new int[] { 1, 4 };
308 MapList ml = new MapList(codons, protein, 3, 1);
309 assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(1, 3)));
310 assertEquals("[2, 2]", Arrays.toString(ml.locateInTo(4, 6)));
311 assertEquals("[3, 3]", Arrays.toString(ml.locateInTo(7, 9)));
312 assertEquals("[4, 4]", Arrays.toString(ml.locateInTo(10, 12)));
313 assertEquals("[1, 2]", Arrays.toString(ml.locateInTo(1, 6)));
314 assertEquals("[1, 3]", Arrays.toString(ml.locateInTo(1, 9)));
315 assertEquals("[1, 4]", Arrays.toString(ml.locateInTo(1, 12)));
316 assertEquals("[2, 2]", Arrays.toString(ml.locateInTo(4, 6)));
317 assertEquals("[2, 4]", Arrays.toString(ml.locateInTo(4, 12)));
320 * A part codon is treated as if a whole one.
322 assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(1, 1)));
323 assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(1, 2)));
324 assertEquals("[1, 2]", Arrays.toString(ml.locateInTo(1, 4)));
325 assertEquals("[1, 3]", Arrays.toString(ml.locateInTo(2, 8)));
326 assertEquals("[1, 4]", Arrays.toString(ml.locateInTo(3, 11)));
327 assertEquals("[2, 4]", Arrays.toString(ml.locateInTo(5, 11)));
329 assertNull(ml.locateInTo(0, 0));
330 assertNull(ml.locateInTo(1, 13));
331 assertNull(ml.locateInTo(-1, 1));
335 * Tests for method that locates ranges in the 'to' map for given range in the
338 @Test(groups = { "Functional" })
339 public void testLocateInTo_withIntrons()
342 * Exons at positions [2, 3, 5] [6, 7, 9] [10, 12, 14] [16, 17, 18] i.e.
343 * 2-3, 5-7, 9-10, 12-12, 14-14, 16-18
345 int[] codons = { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
347 * Mapped proteins at positions 1, 3, 4, 6 in the sequence
349 int[] protein = { 1, 1, 3, 4, 6, 6 };
350 MapList ml = new MapList(codons, protein, 3, 1);
353 * Can't map from an unmapped position
355 assertNull(ml.locateInTo(1, 2));
356 assertNull(ml.locateInTo(2, 4));
357 assertNull(ml.locateInTo(4, 4));
360 * Valid range or subrange of codon1 maps to protein1.
362 assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(2, 2)));
363 assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(3, 3)));
364 assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(3, 5)));
365 assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(2, 3)));
366 assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(2, 5)));
368 // codon position 6 starts the next protein:
369 assertEquals("[1, 1, 3, 3]", Arrays.toString(ml.locateInTo(3, 6)));
371 // codon positions 7 to 17 (part) cover proteins 2/3/4 at positions 3/4/6
372 assertEquals("[3, 4, 6, 6]", Arrays.toString(ml.locateInTo(7, 17)));
377 * Test equals method.
379 @Test(groups = { "Functional" })
380 public void testEquals()
382 int[] codons = new int[] { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
383 int[] protein = new int[] { 1, 4 };
384 MapList ml = new MapList(codons, protein, 3, 1);
385 MapList ml1 = new MapList(codons, protein, 3, 1); // same values
386 MapList ml2 = new MapList(codons, protein, 2, 1); // fromRatio differs
387 MapList ml3 = new MapList(codons, protein, 3, 2); // toRatio differs
389 MapList ml6 = new MapList(codons, protein, 3, 1); // fromShifts differ
391 MapList ml7 = new MapList(codons, protein, 3, 1); // toShifts differ
393 assertTrue(ml.equals(ml));
394 assertEquals(ml.hashCode(), ml.hashCode());
395 assertTrue(ml.equals(ml1));
396 assertEquals(ml.hashCode(), ml1.hashCode());
397 assertTrue(ml1.equals(ml));
399 assertFalse(ml.equals(null));
400 assertFalse(ml.equals("hello"));
401 assertFalse(ml.equals(ml2));
402 assertFalse(ml.equals(ml3));
403 assertFalse(ml.equals(ml6));
404 assertFalse(ml.equals(ml7));
405 assertFalse(ml6.equals(ml7));
409 MapList ml4 = new MapList(codons, null, 3, 1); // toShifts null
410 assertFalse(ml.equals(ml4));
411 } catch (NullPointerException e)
413 // actually thrown by constructor before equals can be called
417 MapList ml5 = new MapList(null, protein, 3, 1); // fromShifts null
418 assertFalse(ml.equals(ml5));
419 } catch (NullPointerException e)
421 // actually thrown by constructor before equals can be called
426 * Test for the method that flattens a list of ranges into a single array.
428 @Test(groups = { "Functional" })
429 public void testGetRanges()
431 List<int[]> ranges = new ArrayList<>();
432 ranges.add(new int[] { 2, 3 });
433 ranges.add(new int[] { 5, 6 });
434 assertEquals("[2, 3, 5, 6]", Arrays.toString(MapList.getRanges(ranges)));
438 * Check state after construction
440 @Test(groups = { "Functional" })
441 public void testConstructor()
443 int[] codons = { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
444 int[] protein = { 1, 1, 3, 4, 6, 6 };
445 MapList ml = new MapList(codons, protein, 3, 1);
446 assertEquals(3, ml.getFromRatio());
447 assertEquals(2, ml.getFromLowest());
448 assertEquals(18, ml.getFromHighest());
449 assertEquals(1, ml.getToLowest());
450 assertEquals(6, ml.getToHighest());
451 assertEquals("{[2, 3], [5, 7], [9, 10], [12, 12], [14, 14], [16, 18]}",
452 prettyPrint(ml.getFromRanges()));
453 assertEquals("{[1, 1], [3, 4], [6, 6]}", prettyPrint(ml.getToRanges()));
456 * Also copy constructor
458 MapList ml2 = new MapList(ml);
459 assertEquals(3, ml2.getFromRatio());
460 assertEquals(2, ml2.getFromLowest());
461 assertEquals(18, ml2.getFromHighest());
462 assertEquals(1, ml2.getToLowest());
463 assertEquals(6, ml2.getToHighest());
464 assertEquals("{[2, 3], [5, 7], [9, 10], [12, 12], [14, 14], [16, 18]}",
465 prettyPrint(ml2.getFromRanges()));
466 assertEquals("{[1, 1], [3, 4], [6, 6]}", prettyPrint(ml2.getToRanges()));
471 codons = new int[] { 9, 6 };
472 protein = new int[] { 100, 91, 80, 79 };
473 ml = new MapList(codons, protein, 3, 1);
474 assertEquals(6, ml.getFromLowest());
475 assertEquals(9, ml.getFromHighest());
476 assertEquals(79, ml.getToLowest());
477 assertEquals(100, ml.getToHighest());
481 * Test constructor can merge consecutive ranges
483 @Test(groups = { "Functional" })
484 public void testConstructor_mergeRanges()
486 int[] codons = { 2, 3, 3, 7, 9, 10, 12, 12, 14, 14, 16, 17 };
487 int[] protein = { 1, 1, 1, 3, 6, 6 };
488 MapList ml = new MapList(codons, protein, 3, 1);
489 assertEquals(3, ml.getFromRatio());
490 assertEquals(2, ml.getFromLowest());
491 assertEquals(17, ml.getFromHighest());
492 assertEquals(1, ml.getToLowest());
493 assertEquals(6, ml.getToHighest());
494 assertEquals("{[2, 7], [9, 10], [12, 12], [14, 14], [16, 17]}",
495 prettyPrint(ml.getFromRanges()));
496 assertEquals("{[1, 3], [6, 6]}", prettyPrint(ml.getToRanges()));
500 * Convert a List of {[i, j], [k, l], ...} to "[[i, j], [k, l], ...]"
505 private String prettyPrint(List<int[]> ranges)
507 StringBuilder sb = new StringBuilder(ranges.size() * 5);
508 boolean first = true;
510 for (int[] range : ranges)
516 sb.append(Arrays.toString(range));
520 return sb.toString();
524 * Test the method that creates an inverse mapping
526 @Test(groups = { "Functional" })
527 public void testGetInverse()
529 int[] codons = { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
530 int[] protein = { 1, 1, 3, 4, 6, 6 };
532 MapList ml = new MapList(codons, protein, 3, 1);
533 MapList ml2 = ml.getInverse();
534 assertEquals(ml.getFromRatio(), ml2.getToRatio());
535 assertEquals(ml.getFromRatio(), ml2.getToRatio());
536 assertEquals(ml.getToHighest(), ml2.getFromHighest());
537 assertEquals(ml.getFromHighest(), ml2.getToHighest());
538 assertEquals(prettyPrint(ml.getFromRanges()),
539 prettyPrint(ml2.getToRanges()));
540 assertEquals(prettyPrint(ml.getToRanges()),
541 prettyPrint(ml2.getFromRanges()));
544 @Test(groups = { "Functional" })
545 public void testToString()
547 MapList ml = new MapList(new int[] { 1, 5, 10, 15, 25, 20 }, new int[] {
549 String s = ml.toString();
550 assertEquals("[ [1, 5] [10, 15] [25, 20] ] 1:3 to [ [51, 1] ]", s);
553 @Test(groups = { "Functional" })
554 public void testAddMapList()
556 MapList ml = new MapList(new int[] { 11, 15, 20, 25, 35, 30 },
557 new int[] { 72, 22 }, 1, 3);
558 assertEquals(11, ml.getFromLowest());
559 assertEquals(35, ml.getFromHighest());
560 assertEquals(22, ml.getToLowest());
561 assertEquals(72, ml.getToHighest());
563 MapList ml2 = new MapList(new int[] { 2, 4, 37, 40 }, new int[] { 12,
564 17, 78, 83, 88, 96 }, 1, 3);
566 assertEquals(2, ml.getFromLowest());
567 assertEquals(40, ml.getFromHighest());
568 assertEquals(12, ml.getToLowest());
569 assertEquals(96, ml.getToHighest());
571 String s = ml.toString();
573 "[ [11, 15] [20, 25] [35, 30] [2, 4] [37, 40] ] 1:3 to [ [72, 22] [12, 17] [78, 83] [88, 96] ]",
578 * Test that confirms adding a map twice does nothing
580 @Test(groups = { "Functional" })
581 public void testAddMapList_sameMap()
583 MapList ml = new MapList(new int[] { 11, 15, 20, 25, 35, 30 },
584 new int[] { 72, 22 }, 1, 3);
585 String before = ml.toString();
587 assertEquals(before, ml.toString());
588 ml.addMapList(new MapList(ml));
589 assertEquals(before, ml.toString());
592 @Test(groups = { "Functional" })
593 public void testAddMapList_contiguous()
595 MapList ml = new MapList(new int[] { 11, 15 }, new int[] { 72, 58 }, 1,
598 MapList ml2 = new MapList(new int[] { 15, 16 }, new int[] { 58, 53 },
601 assertEquals("[ [11, 16] ] 1:3 to [ [72, 53] ]", ml.toString());
604 @Test(groups = "Functional")
605 public void testAddRange()
607 int[] range = { 1, 5 };
608 List<int[]> ranges = new ArrayList<>();
610 // add to empty list:
611 MapList.addRange(range, ranges);
612 assertEquals(1, ranges.size());
613 assertSame(range, ranges.get(0));
615 // extend contiguous (same position):
616 MapList.addRange(new int[] { 5, 10 }, ranges);
617 assertEquals(1, ranges.size());
618 assertEquals(1, ranges.get(0)[0]);
619 assertEquals(10, ranges.get(0)[1]);
621 // extend contiguous (next position):
622 MapList.addRange(new int[] { 11, 15 }, ranges);
623 assertEquals(1, ranges.size());
624 assertEquals(1, ranges.get(0)[0]);
625 assertEquals(15, ranges.get(0)[1]);
627 // change direction: range is not merged:
628 MapList.addRange(new int[] { 16, 10 }, ranges);
629 assertEquals(2, ranges.size());
630 assertEquals(16, ranges.get(1)[0]);
631 assertEquals(10, ranges.get(1)[1]);
633 // extend reverse contiguous (same position):
634 MapList.addRange(new int[] { 10, 8 }, ranges);
635 assertEquals(2, ranges.size());
636 assertEquals(16, ranges.get(1)[0]);
637 assertEquals(8, ranges.get(1)[1]);
639 // extend reverse contiguous (next position):
640 MapList.addRange(new int[] { 7, 6 }, ranges);
641 assertEquals(2, ranges.size());
642 assertEquals(16, ranges.get(1)[0]);
643 assertEquals(6, ranges.get(1)[1]);
645 // change direction: range is not merged:
646 MapList.addRange(new int[] { 6, 9 }, ranges);
647 assertEquals(3, ranges.size());
648 assertEquals(6, ranges.get(2)[0]);
649 assertEquals(9, ranges.get(2)[1]);
651 // not contiguous: not merged
652 MapList.addRange(new int[] { 11, 12 }, ranges);
653 assertEquals(4, ranges.size());
654 assertEquals(11, ranges.get(3)[0]);
655 assertEquals(12, ranges.get(3)[1]);
659 * Check state after construction
661 @Test(groups = { "Functional" })
662 public void testConstructor_withLists()
667 int[][] codons = new int[][] { { 9, 6 } };
668 int[][] protein = new int[][] { { 100, 91 }, { 80, 79 } };
669 MapList ml = new MapList(Arrays.asList(codons), Arrays.asList(protein),
671 assertEquals(6, ml.getFromLowest());
672 assertEquals(9, ml.getFromHighest());
673 assertEquals(79, ml.getToLowest());
674 assertEquals(100, ml.getToHighest());
678 * Test that method that inspects for the (first) forward or reverse from
679 * range. Single position ranges are ignored.
681 @Test(groups = { "Functional" })
682 public void testIsFromForwardStrand()
684 // [3-9] declares forward strand
685 MapList ml = new MapList(new int[] { 2, 2, 3, 9, 12, 11 }, new int[] {
687 assertTrue(ml.isFromForwardStrand());
689 // [11-5] declares reverse strand ([13-14] is ignored)
690 ml = new MapList(new int[] { 2, 2, 11, 5, 13, 14 },
691 new int[] { 20, 11 }, 1, 1);
692 assertFalse(ml.isFromForwardStrand());
694 // all single position ranges - defaults to forward strand
695 ml = new MapList(new int[] { 2, 2, 4, 4, 6, 6 }, new int[] { 3, 1 }, 1,
697 assertTrue(ml.isFromForwardStrand());
701 * Test the method that merges a list of ranges where possible
703 @Test(groups = { "Functional" })
704 public void testCoalesceRanges()
706 assertNull(MapList.coalesceRanges(null));
707 List<int[]> ranges = new ArrayList<>();
708 assertSame(ranges, MapList.coalesceRanges(ranges));
709 ranges.add(new int[] { 1, 3 });
710 assertSame(ranges, MapList.coalesceRanges(ranges));
712 // add non-contiguous range:
713 ranges.add(new int[] { 5, 6 });
714 assertSame(ranges, MapList.coalesceRanges(ranges));
716 // 'contiguous' range in opposite direction is not merged:
717 ranges.add(new int[] { 7, 6 });
718 assertSame(ranges, MapList.coalesceRanges(ranges));
720 // merging in forward direction:
722 ranges.add(new int[] { 1, 3 });
723 ranges.add(new int[] { 4, 5 });
724 ranges.add(new int[] { 5, 5 });
725 ranges.add(new int[] { 5, 7 });
726 List<int[]> merged = MapList.coalesceRanges(ranges);
727 assertEquals(1, merged.size());
728 assertArrayEquals(new int[] { 1, 7 }, merged.get(0));
729 // verify input list is unchanged
730 assertEquals(4, ranges.size());
731 assertArrayEquals(new int[] { 1, 3 }, ranges.get(0));
732 assertArrayEquals(new int[] { 4, 5 }, ranges.get(1));
733 assertArrayEquals(new int[] { 5, 5 }, ranges.get(2));
734 assertArrayEquals(new int[] { 5, 7 }, ranges.get(3));
736 // merging in reverse direction:
738 ranges.add(new int[] { 7, 5 });
739 ranges.add(new int[] { 5, 4 });
740 ranges.add(new int[] { 4, 4 });
741 ranges.add(new int[] { 3, 1 });
742 merged = MapList.coalesceRanges(ranges);
743 assertEquals(1, merged.size());
744 assertArrayEquals(new int[] { 7, 1 }, merged.get(0));
746 // merging with switches of direction:
748 ranges.add(new int[] { 1, 3 });
749 ranges.add(new int[] { 4, 5 });
750 ranges.add(new int[] { 5, 5 });
751 ranges.add(new int[] { 6, 6 });
752 ranges.add(new int[] { 12, 10 });
753 ranges.add(new int[] { 9, 8 });
754 ranges.add(new int[] { 8, 8 });
755 ranges.add(new int[] { 7, 7 });
756 merged = MapList.coalesceRanges(ranges);
757 assertEquals(2, merged.size());
758 assertArrayEquals(new int[] { 1, 6 }, merged.get(0));
759 assertArrayEquals(new int[] { 12, 7 }, merged.get(1));
763 * Test the method that merges a list of ranges where possible
765 @Test(groups = { "Functional" })
766 public void testCoalesceRanges_withOverlap()
768 List<int[]> ranges = new ArrayList<>();
769 ranges.add(new int[] { 1, 3 });
770 ranges.add(new int[] { 2, 5 });
773 * [2, 5] should extend [1, 3]
775 List<int[]> merged = MapList.coalesceRanges(ranges);
776 assertEquals(1, merged.size());
777 assertArrayEquals(new int[] { 1, 5 }, merged.get(0));
780 * a subsumed interval should be dropped
783 ranges.add(new int[] { 1, 6 });
784 ranges.add(new int[] { 2, 4 });
785 merged = MapList.coalesceRanges(ranges);
786 assertEquals(1, merged.size());
787 assertArrayEquals(new int[] { 1, 6 }, merged.get(0));
790 ranges.add(new int[] { 1, 5 });
791 ranges.add(new int[] { 1, 6 });
792 merged = MapList.coalesceRanges(ranges);
793 assertEquals(1, merged.size());
794 assertArrayEquals(new int[] { 1, 6 }, merged.get(0));
797 * merge duplicate ranges
800 ranges.add(new int[] { 1, 3 });
801 ranges.add(new int[] { 1, 3 });
802 merged = MapList.coalesceRanges(ranges);
803 assertEquals(1, merged.size());
804 assertArrayEquals(new int[] { 1, 3 }, merged.get(0));
810 ranges.add(new int[] { 9, 5 });
811 ranges.add(new int[] { 9, 4 });
812 ranges.add(new int[] { 8, 3 });
813 ranges.add(new int[] { 3, 2 });
814 ranges.add(new int[] { 1, 0 });
815 merged = MapList.coalesceRanges(ranges);
816 assertEquals(1, merged.size());
817 assertArrayEquals(new int[] { 9, 0 }, merged.get(0));
821 * Test the method that compounds ('traverses') two mappings
823 @Test(groups = "Functional")
824 public void testTraverse()
827 * simple 1:1 plus 1:1 forwards
829 MapList ml1 = new MapList(new int[] { 3, 4, 8, 12 }, new int[] { 5, 8,
831 assertEquals("{[3, 4], [8, 12]}", prettyPrint(ml1.getFromRanges()));
832 assertEquals("{[5, 8], [11, 13]}", prettyPrint(ml1.getToRanges()));
834 MapList ml2 = new MapList(new int[] { 1, 50 }, new int[] { 40, 45, 70,
835 75, 90, 127 }, 1, 1);
836 assertEquals("{[1, 50]}", prettyPrint(ml2.getFromRanges()));
837 assertEquals("{[40, 45], [70, 75], [90, 127]}",
838 prettyPrint(ml2.getToRanges()));
840 MapList compound = ml1.traverse(ml2);
842 assertEquals(1, compound.getFromRatio());
843 assertEquals(1, compound.getToRatio());
844 List<int[]> fromRanges = compound.getFromRanges();
845 assertEquals(2, fromRanges.size());
846 assertArrayEquals(new int[] { 3, 4 }, fromRanges.get(0));
847 assertArrayEquals(new int[] { 8, 12 }, fromRanges.get(1));
848 List<int[]> toRanges = compound.getToRanges();
849 assertEquals(4, toRanges.size());
850 // 5-8 maps to 44-45,70-71
851 // 11-13 maps to 74-75,90
852 assertArrayEquals(new int[] { 44, 45 }, toRanges.get(0));
853 assertArrayEquals(new int[] { 70, 71 }, toRanges.get(1));
854 assertArrayEquals(new int[] { 74, 75 }, toRanges.get(2));
855 assertArrayEquals(new int[] { 90, 90 }, toRanges.get(3));
858 * 1:1 over 1:1 backwards ('reverse strand')
860 ml1 = new MapList(new int[] { 1, 50 }, new int[] { 70, 119 }, 1, 1);
861 ml2 = new MapList(new int[] { 1, 500 },
862 new int[] { 1000, 901, 600, 201 }, 1, 1);
863 compound = ml1.traverse(ml2);
865 assertEquals(1, compound.getFromRatio());
866 assertEquals(1, compound.getToRatio());
867 fromRanges = compound.getFromRanges();
868 assertEquals(1, fromRanges.size());
869 assertArrayEquals(new int[] { 1, 50 }, fromRanges.get(0));
870 toRanges = compound.getToRanges();
871 assertEquals(2, toRanges.size());
872 assertArrayEquals(new int[] { 931, 901 }, toRanges.get(0));
873 assertArrayEquals(new int[] { 600, 582 }, toRanges.get(1));
876 * 1:1 plus 1:3 should result in 1:3
878 ml1 = new MapList(new int[] { 1, 30 }, new int[] { 11, 40 }, 1, 1);
879 ml2 = new MapList(new int[] { 1, 100 }, new int[] { 1, 50, 91, 340 },
881 compound = ml1.traverse(ml2);
883 assertEquals(1, compound.getFromRatio());
884 assertEquals(3, compound.getToRatio());
885 fromRanges = compound.getFromRanges();
886 assertEquals(1, fromRanges.size());
887 assertArrayEquals(new int[] { 1, 30 }, fromRanges.get(0));
888 // 11-40 maps to 31-50,91-160
889 toRanges = compound.getToRanges();
890 assertEquals(2, toRanges.size());
891 assertArrayEquals(new int[] { 31, 50 }, toRanges.get(0));
892 assertArrayEquals(new int[] { 91, 160 }, toRanges.get(1));
895 * 3:1 plus 1:1 should result in 3:1
897 ml1 = new MapList(new int[] { 1, 30 }, new int[] { 11, 20 }, 3, 1);
898 ml2 = new MapList(new int[] { 1, 100 }, new int[] { 1, 15, 91, 175 },
900 compound = ml1.traverse(ml2);
902 assertEquals(3, compound.getFromRatio());
903 assertEquals(1, compound.getToRatio());
904 fromRanges = compound.getFromRanges();
905 assertEquals(1, fromRanges.size());
906 assertArrayEquals(new int[] { 1, 30 }, fromRanges.get(0));
907 // 11-20 maps to 11-15, 91-95
908 toRanges = compound.getToRanges();
909 assertEquals(2, toRanges.size());
910 assertArrayEquals(new int[] { 11, 15 }, toRanges.get(0));
911 assertArrayEquals(new int[] { 91, 95 }, toRanges.get(1));
914 * 1:3 plus 3:1 should result in 1:1
916 ml1 = new MapList(new int[] { 21, 40 }, new int[] { 13, 72 }, 1, 3);
917 ml2 = new MapList(new int[] { 1, 300 }, new int[] { 51, 70, 121, 200 },
919 compound = ml1.traverse(ml2);
921 assertEquals(1, compound.getFromRatio());
922 assertEquals(1, compound.getToRatio());
923 fromRanges = compound.getFromRanges();
924 assertEquals(1, fromRanges.size());
925 assertArrayEquals(new int[] { 21, 40 }, fromRanges.get(0));
926 // 13-72 maps 3:1 to 55-70, 121-124
927 toRanges = compound.getToRanges();
928 assertEquals(2, toRanges.size());
929 assertArrayEquals(new int[] { 55, 70 }, toRanges.get(0));
930 assertArrayEquals(new int[] { 121, 124 }, toRanges.get(1));
933 * 3:1 plus 1:3 should result in 1:1
935 ml1 = new MapList(new int[] { 31, 90 }, new int[] { 13, 32 }, 3, 1);
936 ml2 = new MapList(new int[] { 11, 40 }, new int[] { 41, 50, 71, 150 },
938 compound = ml1.traverse(ml2);
940 assertEquals(1, compound.getFromRatio());
941 assertEquals(1, compound.getToRatio());
942 fromRanges = compound.getFromRanges();
943 assertEquals(1, fromRanges.size());
944 assertArrayEquals(new int[] { 31, 90 }, fromRanges.get(0));
945 // 13-32 maps to 47-50,71-126
946 toRanges = compound.getToRanges();
947 assertEquals(2, toRanges.size());
948 assertArrayEquals(new int[] { 47, 50 }, toRanges.get(0));
949 assertArrayEquals(new int[] { 71, 126 }, toRanges.get(1));
952 * method returns null if not all regions are mapped through
954 ml1 = new MapList(new int[] { 1, 50 }, new int[] { 101, 150 }, 1, 1);
955 ml2 = new MapList(new int[] { 131, 180 }, new int[] { 201, 250 }, 1, 3);
956 compound = ml1.traverse(ml2);
957 assertNull(compound);
961 * Test that method that inspects for the (first) forward or reverse 'to' range.
962 * Single position ranges are ignored.
964 @Test(groups = { "Functional" })
965 public void testIsToForwardsStrand()
967 // [3-9] declares forward strand
968 MapList ml = new MapList(new int[] { 20, 11 },
970 { 2, 2, 3, 9, 12, 11 }, 1, 1);
971 assertTrue(ml.isToForwardStrand());
973 // [11-5] declares reverse strand ([13-14] is ignored)
974 ml = new MapList(new int[] { 20, 11 },
976 { 2, 2, 11, 5, 13, 14 }, 1, 1);
977 assertFalse(ml.isToForwardStrand());
979 // all single position ranges - defaults to forward strand
980 ml = new MapList(new int[] { 3, 1 }, new int[] { 2, 2, 4, 4, 6, 6 }, 1,
982 assertTrue(ml.isToForwardStrand());