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 java.util.ArrayList;
31 import java.util.Arrays;
32 import java.util.List;
34 import org.testng.annotations.BeforeClass;
35 import org.testng.annotations.Test;
37 import jalview.bin.Cache;
38 import jalview.gui.JvOptionPane;
40 public class MapListTest
42 @BeforeClass(alwaysRun = true)
48 @BeforeClass(alwaysRun = true)
49 public void setUpJvOptionPane()
51 JvOptionPane.setInteractiveMode(false);
52 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
55 @Test(groups = { "Functional" })
56 public void testSomething()
58 MapList ml = new MapList(new int[] { 1, 5, 10, 15, 25, 20 },
61 MapList ml1 = new MapList(new int[] { 1, 3, 17, 4 },
64 MapList ml2 = new MapList(new int[] { 1, 60 }, new int[] { 1, 20 }, 3,
66 // test internal consistency
67 int to[] = new int[51];
69 MapList mldna = new MapList(new int[] { 2, 2, 6, 8, 12, 16 },
72 int[] frm = mldna.locateInFrom(1, 1);
73 testLocateFrom(mldna, 1, 1, new int[] { 2, 2, 6, 7 });
76 * for (int from=1; from<=51; from++) { int[] too=ml.shiftTo(from); int[]
77 * toofrom=ml.shiftFrom(too[0]);
78 * System.out.println("ShiftFrom("+from+")=="+too[0]+" %
79 * "+too[1]+"\t+-+\tShiftTo("+too[0]+")=="+toofrom[0]+" % "+toofrom[1]); }
83 private static void testLocateFrom(MapList mldna, int i, int j, int[] ks)
85 int[] frm = mldna.locateInFrom(i, j);
86 assertEquals("Failed test locate from " + i + " to " + j,
87 Arrays.toString(frm), Arrays.toString(ks));
91 * test routine. not incremental.
97 private void testMap(MapList ml, int fromS, int fromE)
99 // todo convert to JUnit style tests
100 for (int from = 1; from <= 25; from++)
102 int[] too = ml.shiftFrom(from);
103 System.out.print("ShiftFrom(" + from + ")==");
106 System.out.print("NaN\n");
110 System.out.print(too[0] + " % " + too[1] + " (" + too[2] + ")");
111 System.out.print("\t+--+\t");
112 int[] toofrom = ml.shiftTo(too[0]);
115 if (toofrom[0] != from)
117 System.err.println("Mapping not reflexive:" + from + " "
118 + too[0] + "->" + toofrom[0]);
120 System.out.println("ShiftTo(" + too[0] + ")==" + toofrom[0]
121 + " % " + toofrom[1] + " (" + toofrom[2] + ")");
125 System.out.println("ShiftTo(" + too[0] + ")=="
126 + "NaN! - not Bijective Mapping!");
130 int mmap[][] = ml.makeFromMap();
131 System.out.println("FromMap : (" + mmap[0][0] + " " + mmap[0][1] + " "
132 + mmap[0][2] + " " + mmap[0][3] + " ");
133 for (int i = 1; i <= mmap[1].length; i++)
135 if (mmap[1][i - 1] == -1)
137 System.out.print(i + "=XXX");
142 System.out.print(i + "=" + (mmap[0][2] + mmap[1][i - 1]));
146 System.out.print("\n");
150 System.out.print(",");
153 // test range function
154 System.out.print("\nTest locateInFrom\n");
156 int f = mmap[0][2], t = mmap[0][3];
159 System.out.println("Range " + f + " to " + t);
160 int rng[] = ml.locateInFrom(f, t);
163 for (int i = 0; i < rng.length; i++)
165 System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
170 System.out.println("No range!");
172 System.out.print("\nReversed\n");
173 rng = ml.locateInFrom(t, f);
176 for (int i = 0; i < rng.length; i++)
178 System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
183 System.out.println("No range!");
185 System.out.print("\n");
190 System.out.print("\n");
191 mmap = ml.makeToMap();
192 System.out.println("ToMap : (" + mmap[0][0] + " " + mmap[0][1] + " "
193 + mmap[0][2] + " " + mmap[0][3] + " ");
194 for (int i = 1; i <= mmap[1].length; i++)
196 if (mmap[1][i - 1] == -1)
198 System.out.print(i + "=XXX");
203 System.out.print(i + "=" + (mmap[0][2] + mmap[1][i - 1]));
207 System.out.print("\n");
211 System.out.print(",");
214 System.out.print("\n");
215 // test range function
216 System.out.print("\nTest locateInTo\n");
218 int f = mmap[0][2], t = mmap[0][3];
221 System.out.println("Range " + f + " to " + t);
222 int rng[] = ml.locateInTo(f, t);
225 for (int i = 0; i < rng.length; i++)
227 System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
232 System.out.println("No range!");
234 System.out.print("\nReversed\n");
235 rng = ml.locateInTo(t, f);
238 for (int i = 0; i < rng.length; i++)
240 System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
245 System.out.println("No range!");
249 System.out.print("\n");
255 * Tests for method that locates ranges in the 'from' map for given range in
258 @Test(groups = { "Functional" })
259 public void testLocateInFrom_noIntrons()
262 * Simple mapping with no introns
264 int[] codons = new int[] { 1, 12 };
265 int[] protein = new int[] { 1, 4 };
266 MapList ml = new MapList(codons, protein, 3, 1);
267 assertEquals("[1, 3]", Arrays.toString(ml.locateInFrom(1, 1)));
268 assertEquals("[4, 6]", Arrays.toString(ml.locateInFrom(2, 2)));
269 assertEquals("[7, 9]", Arrays.toString(ml.locateInFrom(3, 3)));
270 assertEquals("[10, 12]", Arrays.toString(ml.locateInFrom(4, 4)));
271 assertEquals("[1, 6]", Arrays.toString(ml.locateInFrom(1, 2)));
272 assertEquals("[1, 9]", Arrays.toString(ml.locateInFrom(1, 3)));
273 assertEquals("[1, 12]", Arrays.toString(ml.locateInFrom(1, 4)));
274 assertEquals("[4, 9]", Arrays.toString(ml.locateInFrom(2, 3)));
275 assertEquals("[4, 12]", Arrays.toString(ml.locateInFrom(2, 4)));
276 assertEquals("[7, 12]", Arrays.toString(ml.locateInFrom(3, 4)));
277 assertEquals("[10, 12]", Arrays.toString(ml.locateInFrom(4, 4)));
279 assertNull(ml.locateInFrom(0, 0));
280 assertNull(ml.locateInFrom(1, 5));
281 assertNull(ml.locateInFrom(-1, 1));
285 * Tests for method that locates ranges in the 'from' map for given range in
288 @Test(groups = { "Functional" })
289 public void testLocateInFrom_withIntrons()
292 * Exons at positions [2, 3, 5] [6, 7, 9] [10, 12, 14] [16, 17, 18] i.e.
293 * 2-3, 5-7, 9-10, 12-12, 14-14, 16-18
295 int[] codons = { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
296 int[] protein = { 1, 4 };
297 MapList ml = new MapList(codons, protein, 3, 1);
298 assertEquals("[2, 3, 5, 5]", Arrays.toString(ml.locateInFrom(1, 1)));
299 assertEquals("[6, 7, 9, 9]", Arrays.toString(ml.locateInFrom(2, 2)));
300 assertEquals("[10, 10, 12, 12, 14, 14]",
301 Arrays.toString(ml.locateInFrom(3, 3)));
302 assertEquals("[16, 18]", Arrays.toString(ml.locateInFrom(4, 4)));
306 * Tests for method that locates the overlap of the ranges in the 'from' map
307 * for given range in the 'to' map
309 @Test(groups = { "Functional" })
310 public void testGetOverlapsInFrom_withIntrons()
313 * Exons at positions [2, 3, 5] [6, 7, 9] [10, 12, 14] [16, 17, 18] i.e.
314 * 2-3, 5-7, 9-10, 12-12, 14-14, 16-18
316 int[] codons = { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
317 int[] protein = { 11, 14 };
318 MapList ml = new MapList(codons, protein, 3, 1);
320 assertEquals("[2, 3, 5, 5]",
321 Arrays.toString(ml.getOverlapsInFrom(11, 11)));
322 assertEquals("[2, 3, 5, 7, 9, 9]",
323 Arrays.toString(ml.getOverlapsInFrom(11, 12)));
325 assertEquals("[2, 3, 5, 7, 9, 9]",
326 Arrays.toString(ml.getOverlapsInFrom(8, 12)));
328 assertEquals("[10, 10, 12, 12, 14, 14, 16, 18]",
329 Arrays.toString(ml.getOverlapsInFrom(13, 16)));
330 // out of range both :
331 assertEquals("[2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18]",
332 Arrays.toString(ml.getOverlapsInFrom(1, 16)));
334 assertNull(ml.getOverlapsInFrom(20, 25));
338 * Tests for method that locates the overlap of the ranges in the 'to' map
339 * for given range in the 'from' map
341 @Test(groups = { "Functional" })
342 public void testGetOverlapsInTo_withIntrons()
345 * Exons at positions [2, 3, 5] [6, 7, 9] [10, 12, 14] [17, 18, 19] i.e.
346 * 2-3, 5-7, 9-10, 12-12, 14-14, 17-19
348 int[] codons = { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 17, 19 };
350 * Mapped proteins at positions 1, 3, 4, 6 in the sequence
352 int[] protein = { 1, 1, 3, 4, 6, 6 };
353 MapList ml = new MapList(codons, protein, 3, 1);
356 * Can't map from an unmapped position
358 assertNull(ml.getOverlapsInTo(1, 1));
359 assertNull(ml.getOverlapsInTo(4, 4));
360 assertNull(ml.getOverlapsInTo(15, 16));
363 * nor from a range that includes no mapped position (exon)
365 assertNull(ml.getOverlapsInTo(15, 16));
367 // end of codon 1 maps to first peptide
368 assertEquals("[1, 1]", Arrays.toString(ml.getOverlapsInTo(2, 2)));
369 // end of codon 1 and start of codon 2 maps to first 2 peptides
370 assertEquals("[1, 1, 3, 3]", Arrays.toString(ml.getOverlapsInTo(3, 7)));
372 // range overlaps 5' end of dna:
373 assertEquals("[1, 1, 3, 3]", Arrays.toString(ml.getOverlapsInTo(1, 6)));
374 assertEquals("[1, 1, 3, 3]", Arrays.toString(ml.getOverlapsInTo(1, 8)));
376 // range overlaps 3' end of dna:
377 assertEquals("[6, 6]", Arrays.toString(ml.getOverlapsInTo(17, 24)));
378 assertEquals("[6, 6]", Arrays.toString(ml.getOverlapsInTo(16, 24)));
380 // dna positions 8, 11 are intron but include end of exon 2 and start of exon 3
381 assertEquals("[3, 4]", Arrays.toString(ml.getOverlapsInTo(8, 11)));
385 * Tests for method that locates ranges in the 'to' map for given range in the
388 @Test(groups = { "Functional" })
389 public void testLocateInTo_noIntrons()
392 * Simple mapping with no introns
394 int[] codons = new int[] { 1, 12 };
395 int[] protein = new int[] { 1, 4 };
396 MapList ml = new MapList(codons, protein, 3, 1);
397 assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(1, 3)));
398 assertEquals("[2, 2]", Arrays.toString(ml.locateInTo(4, 6)));
399 assertEquals("[3, 3]", Arrays.toString(ml.locateInTo(7, 9)));
400 assertEquals("[4, 4]", Arrays.toString(ml.locateInTo(10, 12)));
401 assertEquals("[1, 2]", Arrays.toString(ml.locateInTo(1, 6)));
402 assertEquals("[1, 3]", Arrays.toString(ml.locateInTo(1, 9)));
403 assertEquals("[1, 4]", Arrays.toString(ml.locateInTo(1, 12)));
404 assertEquals("[2, 2]", Arrays.toString(ml.locateInTo(4, 6)));
405 assertEquals("[2, 4]", Arrays.toString(ml.locateInTo(4, 12)));
408 * A part codon is treated as if a whole one.
410 assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(1, 1)));
411 assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(1, 2)));
412 assertEquals("[1, 2]", Arrays.toString(ml.locateInTo(1, 4)));
413 assertEquals("[1, 3]", Arrays.toString(ml.locateInTo(2, 8)));
414 assertEquals("[1, 4]", Arrays.toString(ml.locateInTo(3, 11)));
415 assertEquals("[2, 4]", Arrays.toString(ml.locateInTo(5, 11)));
417 assertNull(ml.locateInTo(0, 0));
418 assertNull(ml.locateInTo(1, 13));
419 assertNull(ml.locateInTo(-1, 1));
423 * Tests for method that locates ranges in the 'to' map for given range in the
426 @Test(groups = { "Functional" })
427 public void testLocateInTo_withIntrons()
430 * Exons at positions [2, 3, 5] [6, 7, 9] [10, 12, 14] [16, 17, 18] i.e.
431 * 2-3, 5-7, 9-10, 12-12, 14-14, 16-18
433 int[] codons = { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
435 * Mapped proteins at positions 1, 3, 4, 6 in the sequence
437 int[] protein = { 1, 1, 3, 4, 6, 6 };
438 MapList ml = new MapList(codons, protein, 3, 1);
441 * Can't map from an unmapped position
443 assertNull(ml.locateInTo(1, 2));
444 assertNull(ml.locateInTo(2, 4));
445 assertNull(ml.locateInTo(4, 4));
448 * Valid range or subrange of codon1 maps to protein1.
450 assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(2, 2)));
451 assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(3, 3)));
452 assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(3, 5)));
453 assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(2, 3)));
454 assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(2, 5)));
456 // codon position 6 starts the next protein:
457 assertEquals("[1, 1, 3, 3]", Arrays.toString(ml.locateInTo(3, 6)));
459 // codon positions 7 to 17 (part) cover proteins 2/3/4 at positions 3/4/6
460 assertEquals("[3, 4, 6, 6]", Arrays.toString(ml.locateInTo(7, 17)));
465 * Test equals method.
467 @Test(groups = { "Functional" })
468 public void testEquals()
470 int[] codons = new int[] { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
471 int[] protein = new int[] { 1, 4 };
472 MapList ml = new MapList(codons, protein, 3, 1);
473 MapList ml1 = new MapList(codons, protein, 3, 1); // same values
474 MapList ml2 = new MapList(codons, protein, 2, 1); // fromRatio differs
475 MapList ml3 = new MapList(codons, protein, 3, 2); // toRatio differs
477 MapList ml6 = new MapList(codons, protein, 3, 1); // fromShifts differ
479 MapList ml7 = new MapList(codons, protein, 3, 1); // toShifts differ
481 assertTrue(ml.equals(ml));
482 assertEquals(ml.hashCode(), ml.hashCode());
483 assertTrue(ml.equals(ml1));
484 assertEquals(ml.hashCode(), ml1.hashCode());
485 assertTrue(ml1.equals(ml));
487 assertFalse(ml.equals(null));
488 assertFalse(ml.equals("hello"));
489 assertFalse(ml.equals(ml2));
490 assertFalse(ml.equals(ml3));
491 assertFalse(ml.equals(ml6));
492 assertFalse(ml.equals(ml7));
493 assertFalse(ml6.equals(ml7));
497 MapList ml4 = new MapList(codons, null, 3, 1); // toShifts null
498 assertFalse(ml.equals(ml4));
499 } catch (NullPointerException e)
501 // actually thrown by constructor before equals can be called
505 MapList ml5 = new MapList(null, protein, 3, 1); // fromShifts null
506 assertFalse(ml.equals(ml5));
507 } catch (NullPointerException e)
509 // actually thrown by constructor before equals can be called
514 * Test for the method that flattens a list of ranges into a single array.
516 @Test(groups = { "Functional" })
517 public void testGetRanges()
519 List<int[]> ranges = new ArrayList<>();
520 ranges.add(new int[] { 2, 3 });
521 ranges.add(new int[] { 5, 6 });
522 assertEquals("[2, 3, 5, 6]",
523 Arrays.toString(MapList.getRanges(ranges)));
527 * Check state after construction
529 @Test(groups = { "Functional" })
530 public void testConstructor()
532 int[] codons = { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
533 int[] protein = { 1, 1, 3, 4, 6, 6 };
534 MapList ml = new MapList(codons, protein, 3, 1);
535 assertEquals(3, ml.getFromRatio());
536 assertEquals(2, ml.getFromLowest());
537 assertEquals(18, ml.getFromHighest());
538 assertEquals(1, ml.getToLowest());
539 assertEquals(6, ml.getToHighest());
540 assertEquals("{[2, 3], [5, 7], [9, 10], [12, 12], [14, 14], [16, 18]}",
541 prettyPrint(ml.getFromRanges()));
542 assertEquals("{[1, 1], [3, 4], [6, 6]}", prettyPrint(ml.getToRanges()));
545 * Also copy constructor
547 MapList ml2 = new MapList(ml);
548 assertEquals(3, ml2.getFromRatio());
549 assertEquals(2, ml2.getFromLowest());
550 assertEquals(18, ml2.getFromHighest());
551 assertEquals(1, ml2.getToLowest());
552 assertEquals(6, ml2.getToHighest());
553 assertEquals("{[2, 3], [5, 7], [9, 10], [12, 12], [14, 14], [16, 18]}",
554 prettyPrint(ml2.getFromRanges()));
555 assertEquals("{[1, 1], [3, 4], [6, 6]}",
556 prettyPrint(ml2.getToRanges()));
561 codons = new int[] { 9, 6 };
562 protein = new int[] { 100, 91, 80, 79 };
563 ml = new MapList(codons, protein, 3, 1);
564 assertEquals(6, ml.getFromLowest());
565 assertEquals(9, ml.getFromHighest());
566 assertEquals(79, ml.getToLowest());
567 assertEquals(100, ml.getToHighest());
571 * Test constructor used to merge consecutive ranges but now just leaves them
572 * as supplied (JAL-3751)
574 @Test(groups = { "Functional" })
575 public void testConstructor_mergeRanges()
577 int[] codons = { 2, 3, 3, 7, 9, 10, 12, 12, 13, 14, 16, 17 };
578 int[] protein = { 1, 1, 2, 3, 6, 6 };
579 MapList ml = new MapList(codons, protein, 3, 1);
580 assertEquals(3, ml.getFromRatio());
581 assertEquals(2, ml.getFromLowest());
582 assertEquals(17, ml.getFromHighest());
583 assertEquals(1, ml.getToLowest());
584 assertEquals(6, ml.getToHighest());
585 assertEquals("{[2, 3], [3, 7], [9, 10], [12, 12], [13, 14], [16, 17]}",
586 prettyPrint(ml.getFromRanges()));
587 assertEquals("{[1, 1], [2, 3], [6, 6]}", prettyPrint(ml.getToRanges()));
591 * Convert a List of {[i, j], [k, l], ...} to "[[i, j], [k, l], ...]"
596 private String prettyPrint(List<int[]> ranges)
598 StringBuilder sb = new StringBuilder(ranges.size() * 5);
599 boolean first = true;
601 for (int[] range : ranges)
607 sb.append(Arrays.toString(range));
611 return sb.toString();
615 * Test the method that creates an inverse mapping
617 @Test(groups = { "Functional" })
618 public void testGetInverse()
620 int[] codons = { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
621 int[] protein = { 1, 1, 3, 4, 6, 6 };
623 MapList ml = new MapList(codons, protein, 3, 1);
624 MapList ml2 = ml.getInverse();
625 assertEquals(ml.getFromRatio(), ml2.getToRatio());
626 assertEquals(ml.getFromRatio(), ml2.getToRatio());
627 assertEquals(ml.getToHighest(), ml2.getFromHighest());
628 assertEquals(ml.getFromHighest(), ml2.getToHighest());
629 assertEquals(prettyPrint(ml.getFromRanges()),
630 prettyPrint(ml2.getToRanges()));
631 assertEquals(prettyPrint(ml.getToRanges()),
632 prettyPrint(ml2.getFromRanges()));
635 @Test(groups = { "Functional" })
636 public void testToString()
638 MapList ml = new MapList(new int[] { 1, 5, 10, 15, 25, 20 },
641 String s = ml.toString();
642 assertEquals("[ [1, 5] [10, 15] [25, 20] ] 1:3 to [ [51, 1] ]", s);
645 @Test(groups = { "Functional" })
646 public void testAddMapList()
648 MapList ml = new MapList(new int[] { 11, 15, 20, 25, 35, 30 },
651 assertEquals(11, ml.getFromLowest());
652 assertEquals(35, ml.getFromHighest());
653 assertEquals(22, ml.getToLowest());
654 assertEquals(72, ml.getToHighest());
656 MapList ml2 = new MapList(new int[] { 2, 4, 37, 40 },
658 { 12, 17, 78, 83, 88, 96 }, 1, 3);
660 assertEquals(2, ml.getFromLowest());
661 assertEquals(40, ml.getFromHighest());
662 assertEquals(12, ml.getToLowest());
663 assertEquals(96, ml.getToHighest());
665 String s = ml.toString();
667 "[ [11, 15] [20, 25] [35, 30] [2, 4] [37, 40] ] 1:3 to [ [72, 22] [12, 17] [78, 83] [88, 96] ]",
672 * Test that confirms adding a map twice does nothing
674 @Test(groups = { "Functional" })
675 public void testAddMapList_sameMap()
677 MapList ml = new MapList(new int[] { 11, 15, 20, 25, 35, 30 },
680 String before = ml.toString();
682 assertEquals(before, ml.toString());
683 ml.addMapList(new MapList(ml));
684 assertEquals(before, ml.toString());
687 @Test(groups = { "Functional" })
688 public void testAddMapList_contiguous()
690 MapList ml = new MapList(new int[] { 11, 15 }, new int[] { 72, 58 }, 1,
693 MapList ml2 = new MapList(new int[] { 15, 16 }, new int[] { 58, 53 }, 1,
696 assertEquals("[ [11, 16] ] 1:3 to [ [72, 53] ]", ml.toString());
699 @Test(groups = "Functional")
700 public void testAddRange()
702 int[] range = { 1, 5 };
703 List<int[]> ranges = new ArrayList<>();
705 // add to empty list:
706 MapList.addRange(range, ranges);
707 assertEquals(1, ranges.size());
708 assertSame(range, ranges.get(0));
710 // extend contiguous (same position):
711 MapList.addRange(new int[] { 5, 10 }, ranges);
712 assertEquals(1, ranges.size());
713 assertEquals(1, ranges.get(0)[0]);
714 assertEquals(10, ranges.get(0)[1]);
716 // extend contiguous (next position):
717 MapList.addRange(new int[] { 11, 15 }, ranges);
718 assertEquals(1, ranges.size());
719 assertEquals(1, ranges.get(0)[0]);
720 assertEquals(15, ranges.get(0)[1]);
722 // change direction: range is not merged:
723 MapList.addRange(new int[] { 16, 10 }, ranges);
724 assertEquals(2, ranges.size());
725 assertEquals(16, ranges.get(1)[0]);
726 assertEquals(10, ranges.get(1)[1]);
728 // extend reverse contiguous (same position):
729 MapList.addRange(new int[] { 10, 8 }, ranges);
730 assertEquals(2, ranges.size());
731 assertEquals(16, ranges.get(1)[0]);
732 assertEquals(8, ranges.get(1)[1]);
734 // extend reverse contiguous (next position):
735 MapList.addRange(new int[] { 7, 6 }, ranges);
736 assertEquals(2, ranges.size());
737 assertEquals(16, ranges.get(1)[0]);
738 assertEquals(6, ranges.get(1)[1]);
740 // change direction: range is not merged:
741 MapList.addRange(new int[] { 6, 9 }, ranges);
742 assertEquals(3, ranges.size());
743 assertEquals(6, ranges.get(2)[0]);
744 assertEquals(9, ranges.get(2)[1]);
746 // not contiguous: not merged
747 MapList.addRange(new int[] { 11, 12 }, ranges);
748 assertEquals(4, ranges.size());
749 assertEquals(11, ranges.get(3)[0]);
750 assertEquals(12, ranges.get(3)[1]);
754 * Check state after construction
756 @Test(groups = { "Functional" })
757 public void testConstructor_withLists()
762 int[][] codons = new int[][] { { 9, 6 } };
763 int[][] protein = new int[][] { { 100, 91 }, { 80, 79 } };
764 MapList ml = new MapList(Arrays.asList(codons), Arrays.asList(protein),
766 assertEquals(6, ml.getFromLowest());
767 assertEquals(9, ml.getFromHighest());
768 assertEquals(79, ml.getToLowest());
769 assertEquals(100, ml.getToHighest());
773 * Test that method that inspects for the (first) forward or reverse from
774 * range. Single position ranges are ignored.
776 @Test(groups = { "Functional" })
777 public void testIsFromForwardStrand()
779 // [3-9] declares forward strand
780 MapList ml = new MapList(new int[] { 2, 2, 3, 9, 12, 11 },
783 assertTrue(ml.isFromForwardStrand());
785 // [11-5] declares reverse strand ([13-14] is ignored)
786 ml = new MapList(new int[] { 2, 2, 11, 5, 13, 14 },
789 assertFalse(ml.isFromForwardStrand());
791 // all single position ranges - defaults to forward strand
792 ml = new MapList(new int[] { 2, 2, 4, 4, 6, 6 }, new int[] { 3, 1 }, 1,
794 assertTrue(ml.isFromForwardStrand());
798 * Test the method that merges contiguous ranges
800 @Test(groups = { "Functional" })
801 public void testCoalesceRanges()
803 assertNull(MapList.coalesceRanges(null));
804 List<int[]> ranges = new ArrayList<>();
805 assertSame(ranges, MapList.coalesceRanges(ranges));
806 ranges.add(new int[] { 1, 3 });
807 assertSame(ranges, MapList.coalesceRanges(ranges));
809 // add non-contiguous range:
810 ranges.add(new int[] { 5, 6 });
811 assertSame(ranges, MapList.coalesceRanges(ranges));
813 // 'contiguous' range in opposite direction is not merged:
814 ranges.add(new int[] { 7, 6 });
815 assertSame(ranges, MapList.coalesceRanges(ranges));
817 // merging in forward direction:
819 ranges.add(new int[] { 1, 3 });
820 ranges.add(new int[] { 4, 5 }); // contiguous
821 ranges.add(new int[] { 5, 5 }); // overlap!
822 ranges.add(new int[] { 6, 7 }); // contiguous
823 List<int[]> merged = MapList.coalesceRanges(ranges);
824 assertEquals(2, merged.size());
825 assertArrayEquals(new int[] { 1, 5 }, merged.get(0));
826 assertArrayEquals(new int[] { 5, 7 }, merged.get(1));
827 // verify input list is unchanged
828 assertEquals(4, ranges.size());
829 assertArrayEquals(new int[] { 1, 3 }, ranges.get(0));
830 assertArrayEquals(new int[] { 4, 5 }, ranges.get(1));
831 assertArrayEquals(new int[] { 5, 5 }, ranges.get(2));
832 assertArrayEquals(new int[] { 6, 7 }, ranges.get(3));
834 // merging in reverse direction:
836 ranges.add(new int[] { 7, 5 });
837 ranges.add(new int[] { 5, 4 }); // overlap
838 ranges.add(new int[] { 4, 4 }); // overlap
839 ranges.add(new int[] { 3, 1 }); // contiguous
840 merged = MapList.coalesceRanges(ranges);
841 assertEquals(3, merged.size());
842 assertArrayEquals(new int[] { 7, 5 }, merged.get(0));
843 assertArrayEquals(new int[] { 5, 4 }, merged.get(1));
844 assertArrayEquals(new int[] { 4, 1 }, merged.get(2));
846 // merging with switches of direction:
848 ranges.add(new int[] { 1, 3 });
849 ranges.add(new int[] { 4, 5 }); // contiguous
850 ranges.add(new int[] { 5, 5 }); // overlap
851 ranges.add(new int[] { 6, 6 }); // contiguous
852 ranges.add(new int[] { 12, 10 });
853 ranges.add(new int[] { 9, 8 }); // contiguous
854 ranges.add(new int[] { 8, 8 }); // overlap
855 ranges.add(new int[] { 7, 7 }); // contiguous
856 merged = MapList.coalesceRanges(ranges);
857 assertEquals(4, merged.size());
858 assertArrayEquals(new int[] { 1, 5 }, merged.get(0));
859 assertArrayEquals(new int[] { 5, 6 }, merged.get(1));
860 assertArrayEquals(new int[] { 12, 8 }, merged.get(2));
861 assertArrayEquals(new int[] { 8, 7 }, merged.get(3));
863 // 'subsumed' ranges are preserved
865 ranges.add(new int[] { 10, 30 });
866 ranges.add(new int[] { 15, 25 });
867 merged = MapList.coalesceRanges(ranges);
868 assertEquals(2, merged.size());
869 assertArrayEquals(new int[] { 10, 30 }, merged.get(0));
870 assertArrayEquals(new int[] { 15, 25 }, merged.get(1));
874 * Test the method that compounds ('traverses') two mappings
876 @Test(groups = "Functional")
877 public void testTraverse()
880 * simple 1:1 plus 1:1 forwards
882 MapList ml1 = new MapList(new int[] { 3, 4, 8, 12 },
884 { 5, 8, 11, 13 }, 1, 1);
885 assertEquals("{[3, 4], [8, 12]}", prettyPrint(ml1.getFromRanges()));
886 assertEquals("{[5, 8], [11, 13]}", prettyPrint(ml1.getToRanges()));
888 MapList ml2 = new MapList(new int[] { 1, 50 },
890 { 40, 45, 70, 75, 90, 127 }, 1, 1);
891 assertEquals("{[1, 50]}", prettyPrint(ml2.getFromRanges()));
892 assertEquals("{[40, 45], [70, 75], [90, 127]}",
893 prettyPrint(ml2.getToRanges()));
895 MapList compound = ml1.traverse(ml2);
897 assertEquals(1, compound.getFromRatio());
898 assertEquals(1, compound.getToRatio());
899 List<int[]> fromRanges = compound.getFromRanges();
900 assertEquals(2, fromRanges.size());
901 assertArrayEquals(new int[] { 3, 4 }, fromRanges.get(0));
902 assertArrayEquals(new int[] { 8, 12 }, fromRanges.get(1));
903 List<int[]> toRanges = compound.getToRanges();
904 assertEquals(4, toRanges.size());
905 // 5-8 maps to 44-45,70-71
906 // 11-13 maps to 74-75,90
907 assertArrayEquals(new int[] { 44, 45 }, toRanges.get(0));
908 assertArrayEquals(new int[] { 70, 71 }, toRanges.get(1));
909 assertArrayEquals(new int[] { 74, 75 }, toRanges.get(2));
910 assertArrayEquals(new int[] { 90, 90 }, toRanges.get(3));
913 * 1:1 over 1:1 backwards ('reverse strand')
915 ml1 = new MapList(new int[] { 1, 50 }, new int[] { 70, 119 }, 1, 1);
916 ml2 = new MapList(new int[] { 1, 500 },
918 { 1000, 901, 600, 201 }, 1, 1);
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[] { 1, 50 }, fromRanges.get(0));
926 toRanges = compound.getToRanges();
927 assertEquals(2, toRanges.size());
928 assertArrayEquals(new int[] { 931, 901 }, toRanges.get(0));
929 assertArrayEquals(new int[] { 600, 582 }, toRanges.get(1));
932 * 1:1 plus 1:3 should result in 1:3
934 ml1 = new MapList(new int[] { 1, 30 }, new int[] { 11, 40 }, 1, 1);
935 ml2 = new MapList(new int[] { 1, 100 }, new int[] { 1, 50, 91, 340 }, 1,
937 compound = ml1.traverse(ml2);
939 assertEquals(1, compound.getFromRatio());
940 assertEquals(3, compound.getToRatio());
941 fromRanges = compound.getFromRanges();
942 assertEquals(1, fromRanges.size());
943 assertArrayEquals(new int[] { 1, 30 }, fromRanges.get(0));
944 // 11-40 maps to 31-50,91-160
945 toRanges = compound.getToRanges();
946 assertEquals(2, toRanges.size());
947 assertArrayEquals(new int[] { 31, 50 }, toRanges.get(0));
948 assertArrayEquals(new int[] { 91, 160 }, toRanges.get(1));
951 * 3:1 plus 1:1 should result in 3:1
953 ml1 = new MapList(new int[] { 1, 30 }, new int[] { 11, 20 }, 3, 1);
954 ml2 = new MapList(new int[] { 1, 100 }, new int[] { 1, 15, 91, 175 }, 1,
956 compound = ml1.traverse(ml2);
958 assertEquals(3, compound.getFromRatio());
959 assertEquals(1, compound.getToRatio());
960 fromRanges = compound.getFromRanges();
961 assertEquals(1, fromRanges.size());
962 assertArrayEquals(new int[] { 1, 30 }, fromRanges.get(0));
963 // 11-20 maps to 11-15, 91-95
964 toRanges = compound.getToRanges();
965 assertEquals(2, toRanges.size());
966 assertArrayEquals(new int[] { 11, 15 }, toRanges.get(0));
967 assertArrayEquals(new int[] { 91, 95 }, toRanges.get(1));
970 * 1:3 plus 3:1 should result in 1:1
972 ml1 = new MapList(new int[] { 21, 40 }, new int[] { 13, 72 }, 1, 3);
973 ml2 = new MapList(new int[] { 1, 300 }, new int[] { 51, 70, 121, 200 },
975 compound = ml1.traverse(ml2);
977 assertEquals(1, compound.getFromRatio());
978 assertEquals(1, compound.getToRatio());
979 fromRanges = compound.getFromRanges();
980 assertEquals(1, fromRanges.size());
981 assertArrayEquals(new int[] { 21, 40 }, fromRanges.get(0));
982 // 13-72 maps 3:1 to 55-70, 121-124
983 toRanges = compound.getToRanges();
984 assertEquals(2, toRanges.size());
985 assertArrayEquals(new int[] { 55, 70 }, toRanges.get(0));
986 assertArrayEquals(new int[] { 121, 124 }, toRanges.get(1));
989 * 3:1 plus 1:3 should result in 1:1
991 ml1 = new MapList(new int[] { 31, 90 }, new int[] { 13, 32 }, 3, 1);
992 ml2 = new MapList(new int[] { 11, 40 }, new int[] { 41, 50, 71, 150 },
994 compound = ml1.traverse(ml2);
996 assertEquals(1, compound.getFromRatio());
997 assertEquals(1, compound.getToRatio());
998 fromRanges = compound.getFromRanges();
999 assertEquals(1, fromRanges.size());
1000 assertArrayEquals(new int[] { 31, 90 }, fromRanges.get(0));
1001 // 13-32 maps to 47-50,71-126
1002 toRanges = compound.getToRanges();
1003 assertEquals(2, toRanges.size());
1004 assertArrayEquals(new int[] { 47, 50 }, toRanges.get(0));
1005 assertArrayEquals(new int[] { 71, 126 }, toRanges.get(1));
1008 * method returns null if not all regions are mapped through
1010 ml1 = new MapList(new int[] { 1, 50 }, new int[] { 101, 150 }, 1, 1);
1011 ml2 = new MapList(new int[] { 131, 180 }, new int[] { 201, 250 }, 1, 3);
1012 compound = ml1.traverse(ml2);
1013 assertNull(compound);
1017 * Test that method that inspects for the (first) forward or reverse 'to'
1018 * range. Single position ranges are ignored.
1020 @Test(groups = { "Functional" })
1021 public void testIsToForwardsStrand()
1023 // [3-9] declares forward strand
1024 MapList ml = new MapList(new int[] { 20, 11 },
1026 { 2, 2, 3, 9, 12, 11 }, 1, 1);
1027 assertTrue(ml.isToForwardStrand());
1029 // [11-5] declares reverse strand ([13-14] is ignored)
1030 ml = new MapList(new int[] { 20, 11 },
1032 { 2, 2, 11, 5, 13, 14 }, 1, 1);
1033 assertFalse(ml.isToForwardStrand());
1035 // all single position ranges - defaults to forward strand
1036 ml = new MapList(new int[] { 3, 1 }, new int[] { 2, 2, 4, 4, 6, 6 }, 1,
1038 assertTrue(ml.isToForwardStrand());