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.
21 package jalview.datamodel;
23 import static org.testng.Assert.assertNull;
24 import static org.testng.AssertJUnit.assertEquals;
25 import static org.testng.AssertJUnit.assertFalse;
26 import static org.testng.AssertJUnit.assertTrue;
28 import jalview.analysis.AlignmentGenerator;
29 import jalview.gui.JvOptionPane;
30 import jalview.util.Comparison;
32 import java.util.ArrayList;
33 import java.util.Arrays;
34 import java.util.BitSet;
35 import java.util.List;
36 import java.util.Random;
38 import org.testng.annotations.BeforeClass;
39 import org.testng.annotations.Test;
41 public class HiddenColumnsTest
44 @BeforeClass(alwaysRun = true)
45 public void setUpJvOptionPane()
47 JvOptionPane.setInteractiveMode(false);
48 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
52 * Test the method which counts the number of hidden columns
54 @Test(groups = { "Functional" })
55 public void testGetSize()
57 HiddenColumns hidden = new HiddenColumns();
58 assertEquals(0, hidden.getSize());
60 hidden.hideColumns(3, 5);
61 assertEquals(3, hidden.getSize());
63 hidden.hideColumns(8, 8);
64 assertEquals(4, hidden.getSize());
66 hidden.hideColumns(9, 14);
67 assertEquals(10, hidden.getSize());
69 ColumnSelection cs = new ColumnSelection();
70 hidden.revealAllHiddenColumns(cs);
71 assertEquals(0, hidden.getSize());
75 * Test the method that finds the visible column position of an alignment
76 * column, allowing for hidden columns.
78 @Test(groups = { "Functional" })
79 public void testFindColumnPosition()
81 HiddenColumns cs = new HiddenColumns();
82 assertEquals(5, cs.findColumnPosition(5));
84 // hiding column 6 makes no difference
86 assertEquals(5, cs.findColumnPosition(5));
88 // hiding column 4 moves column 5 to column 4
90 assertEquals(4, cs.findColumnPosition(5));
92 // hiding column 4 moves column 4 to position 3
93 assertEquals(3, cs.findColumnPosition(4));
95 // hiding columns 1 and 2 moves column 5 to column 2
97 assertEquals(2, cs.findColumnPosition(5));
99 // check with > 1 hidden column regions
100 // where some columns are in the hidden regions
101 HiddenColumns cs2 = new HiddenColumns();
102 cs2.hideColumns(5, 10);
103 cs2.hideColumns(20, 27);
104 cs2.hideColumns(40, 44);
106 // hiding columns 5-10 and 20-27 moves column 8 to column 4
107 assertEquals(4, cs2.findColumnPosition(8));
109 // and moves column 24 to 13
110 assertEquals(13, cs2.findColumnPosition(24));
112 // and moves column 28 to 14
113 assertEquals(14, cs2.findColumnPosition(28));
115 // and moves column 40 to 25
116 assertEquals(25, cs2.findColumnPosition(40));
118 // check when hidden columns start at 0 that the visible column
120 HiddenColumns cs3 = new HiddenColumns();
121 cs3.hideColumns(0, 4);
122 assertEquals(0, cs3.findColumnPosition(2));
127 * Test the method that finds the visible column position a given distance
128 * before another column
130 @Test(groups = { "Functional" })
131 public void testFindColumnNToLeft()
133 HiddenColumns cs = new HiddenColumns();
135 // test that without hidden columns, findColumnNToLeft returns
136 // position n to left of provided position
137 long pos = cs.subtractVisibleColumns(3, 10);
138 assertEquals(7, pos);
140 // 0 returns same position
141 pos = cs.subtractVisibleColumns(0, 10);
142 assertEquals(10, pos);
144 // overflow to left returns negative number
145 pos = cs.subtractVisibleColumns(3, 0);
146 assertEquals(-3, pos);
148 // test that with hidden columns to left of result column
149 // behaviour is the same as above
150 cs.hideColumns(1, 3);
152 // position n to left of provided position
153 pos = cs.subtractVisibleColumns(3, 10);
154 assertEquals(7, pos);
156 // 0 returns same position
157 pos = cs.subtractVisibleColumns(0, 10);
158 assertEquals(10, pos);
160 // test with one set of hidden columns between start and required position
161 cs.hideColumns(12, 15);
162 pos = cs.subtractVisibleColumns(8, 17);
163 assertEquals(5, pos);
165 // test with two sets of hidden columns between start and required position
166 cs.hideColumns(20, 21);
167 pos = cs.subtractVisibleColumns(8, 23);
168 assertEquals(9, pos);
170 // repeat last 2 tests with no hidden columns to left of required position
171 ColumnSelection colsel = new ColumnSelection();
172 cs.revealAllHiddenColumns(colsel);
174 // test with one set of hidden columns between start and required position
175 cs.hideColumns(12, 15);
176 pos = cs.subtractVisibleColumns(8, 17);
177 assertEquals(5, pos);
179 // test with two sets of hidden columns between start and required position
180 cs.hideColumns(20, 21);
181 pos = cs.subtractVisibleColumns(8, 23);
182 assertEquals(9, pos);
186 @Test(groups = { "Functional" })
187 public void testGetVisibleContigs()
189 HiddenColumns cs = new HiddenColumns();
191 int[] visible = cs.getVisibleContigs(3, 10);
192 assertEquals("[3, 9]", Arrays.toString(visible));
194 cs.hideColumns(3, 6);
195 cs.hideColumns(8, 9);
196 cs.hideColumns(12, 12);
198 // Test both ends visible region
200 // start position is inclusive, end position exclusive
201 visible = cs.getVisibleContigs(1, 13);
202 assertEquals("[1, 2, 7, 7, 10, 11]", Arrays.toString(visible));
204 // Test start hidden, end visible
205 visible = cs.getVisibleContigs(4, 14);
206 assertEquals("[7, 7, 10, 11, 13, 13]", Arrays.toString(visible));
208 // Test start hidden, end hidden
209 visible = cs.getVisibleContigs(3, 10);
210 assertEquals("[7, 7]", Arrays.toString(visible));
212 // Test start visible, end hidden
213 visible = cs.getVisibleContigs(0, 13);
214 assertEquals("[0, 2, 7, 7, 10, 11]", Arrays.toString(visible));
217 visible = cs.getVisibleContigs(4, 6);
218 assertEquals("[]", Arrays.toString(visible));
221 @Test(groups = { "Functional" })
222 public void testEquals()
224 HiddenColumns cs = new HiddenColumns();
225 cs.hideColumns(5, 9);
227 // a different set of hidden columns
228 HiddenColumns cs2 = new HiddenColumns();
230 // with no hidden columns
231 assertFalse(cs.equals(cs2));
232 assertFalse(cs2.equals(cs));
234 // with hidden columns added in a different order
235 cs2.hideColumns(6, 9);
236 cs2.hideColumns(5, 8);
238 assertTrue(cs.equals(cs2));
239 assertTrue(cs.equals(cs));
240 assertTrue(cs2.equals(cs));
241 assertTrue(cs2.equals(cs2));
244 @Test(groups = "Functional")
245 public void testCopyConstructor()
247 HiddenColumns cs = new HiddenColumns();
248 cs.hideColumns(10, 11);
249 cs.hideColumns(5, 7);
250 assertEquals("[5, 7]",
251 Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
253 HiddenColumns cs2 = new HiddenColumns(cs);
254 assertTrue(cs2.hasHiddenColumns());
255 assertEquals(2, cs2.getHiddenColumnsCopy().size());
256 // hidden columns are held in column order
257 assertEquals("[5, 7]",
258 Arrays.toString(cs2.getHiddenColumnsCopy().get(0)));
259 assertEquals("[10, 11]",
260 Arrays.toString(cs2.getHiddenColumnsCopy().get(1)));
264 * Test the code used to locate the reference sequence ruler origin
266 @Test(groups = { "Functional" })
267 public void testLocateVisibleBoundsofSequence()
269 // create random alignment
270 AlignmentGenerator gen = new AlignmentGenerator(false);
271 AlignmentI al = gen.generate(50, 20, 123, 5, 5);
273 HiddenColumns cs = al.getHiddenColumns();
274 ColumnSelection colsel = new ColumnSelection();
276 SequenceI seq = new Sequence("RefSeq", "-A-SD-ASD--E---");
277 assertEquals(2, seq.findIndex(seq.getStart()));
281 Arrays.toString(new int[]
282 { seq.findIndex(seq.getStart()) - 1, seq.findIndex(seq.getStart()) - 1,
283 seq.findIndex(seq.getEnd()) - 1 }),
284 Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
286 // hidden column on gap after end of sequence - should not affect bounds
287 colsel.hideSelectedColumns(13, al.getHiddenColumns());
289 Arrays.toString(new int[]
290 { seq.findIndex(seq.getStart()) - 1, seq.findIndex(seq.getStart()) - 1,
291 seq.findIndex(seq.getEnd()) - 1 }),
292 Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
294 cs.revealAllHiddenColumns(colsel);
295 // hidden column on gap before beginning of sequence - should vis bounds by
297 colsel.hideSelectedColumns(0, al.getHiddenColumns());
299 Arrays.toString(new int[]
300 { seq.findIndex(seq.getStart()) - 2, seq.findIndex(seq.getStart()) - 1,
301 seq.findIndex(seq.getEnd()) - 1 }),
302 Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
304 cs.revealAllHiddenColumns(colsel);
305 // hide columns around most of sequence - leave one residue remaining
306 cs.hideColumns(1, 3);
307 cs.hideColumns(6, 11);
309 cs.getVisibleSequenceStrings(0, 5, new SequenceI[]
315 { 1, seq.findIndex(seq.getStart()) - 1,
316 seq.findIndex(seq.getEnd()) - 1 }),
317 Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
318 cs.revealAllHiddenColumns(colsel);
320 // hide whole sequence - should just get location of hidden region
321 // containing sequence
322 cs.hideColumns(1, 11);
326 { 0, seq.findIndex(seq.getStart()) - 1,
327 seq.findIndex(seq.getEnd()) - 1 }),
328 Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
330 cs.revealAllHiddenColumns(colsel);
331 cs.hideColumns(0, 15);
334 { 0, seq.findIndex(seq.getStart()) - 1,
335 seq.findIndex(seq.getEnd()) - 1 }),
336 Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
338 SequenceI seq2 = new Sequence("RefSeq2", "-------A-SD-ASD--E---");
340 cs.revealAllHiddenColumns(colsel);
341 cs.hideColumns(7, 17);
345 { 0, seq2.findIndex(seq2.getStart()) - 1,
346 seq2.findIndex(seq2.getEnd()) - 1 }),
347 Arrays.toString(cs.locateVisibleBoundsOfSequence(seq2)));
349 cs.revealAllHiddenColumns(colsel);
350 cs.hideColumns(3, 17);
354 { 0, seq2.findIndex(seq2.getStart()) - 1,
355 seq2.findIndex(seq2.getEnd()) - 1 }),
356 Arrays.toString(cs.locateVisibleBoundsOfSequence(seq2)));
358 cs.revealAllHiddenColumns(colsel);
359 cs.hideColumns(3, 19);
363 { 0, seq2.findIndex(seq2.getStart()) - 1,
364 seq2.findIndex(seq2.getEnd()) - 1 }),
365 Arrays.toString(cs.locateVisibleBoundsOfSequence(seq2)));
367 cs.revealAllHiddenColumns(colsel);
368 cs.hideColumns(0, 0);
369 int[] test = cs.locateVisibleBoundsOfSequence(seq);
370 assertEquals(Arrays.toString(new int[] { 0, 1, 11 }),
371 Arrays.toString(test));
373 cs.revealAllHiddenColumns(colsel);
374 cs.hideColumns(0, 1);
375 test = cs.locateVisibleBoundsOfSequence(seq);
376 assertEquals(Arrays.toString(new int[] { 1, 1, 11 }),
377 Arrays.toString(test));
379 cs.revealAllHiddenColumns(colsel);
380 cs.hideColumns(0, 2);
381 test = cs.locateVisibleBoundsOfSequence(seq);
382 assertEquals(Arrays.toString(new int[] { 0, 1, 11 }),
383 Arrays.toString(test));
385 cs.revealAllHiddenColumns(colsel);
386 cs.hideColumns(1, 1);
387 test = cs.locateVisibleBoundsOfSequence(seq);
388 assertEquals(Arrays.toString(new int[] { 2, 1, 11 }),
389 Arrays.toString(test));
391 cs.revealAllHiddenColumns(colsel);
392 cs.hideColumns(1, 2);
393 test = cs.locateVisibleBoundsOfSequence(seq);
394 assertEquals(Arrays.toString(new int[] { 1, 1, 11 }),
395 Arrays.toString(test));
397 cs.revealAllHiddenColumns(colsel);
398 cs.hideColumns(1, 3);
399 test = cs.locateVisibleBoundsOfSequence(seq);
400 assertEquals(Arrays.toString(new int[] { 1, 1, 11 }),
401 Arrays.toString(test));
403 cs.revealAllHiddenColumns(colsel);
404 cs.hideColumns(0, 2);
405 cs.hideColumns(5, 6);
406 test = cs.locateVisibleBoundsOfSequence(seq);
407 assertEquals(Arrays.toString(new int[] { 0, 1, 11 }),
408 Arrays.toString(test));
410 cs.revealAllHiddenColumns(colsel);
411 cs.hideColumns(0, 2);
412 cs.hideColumns(5, 6);
413 cs.hideColumns(9, 10);
414 test = cs.locateVisibleBoundsOfSequence(seq);
415 assertEquals(Arrays.toString(new int[] { 0, 1, 11 }),
416 Arrays.toString(test));
418 cs.revealAllHiddenColumns(colsel);
419 cs.hideColumns(0, 2);
420 cs.hideColumns(7, 11);
421 test = cs.locateVisibleBoundsOfSequence(seq);
422 assertEquals(Arrays.toString(new int[] { 0, 1, 11 }),
423 Arrays.toString(test));
425 cs.revealAllHiddenColumns(colsel);
426 cs.hideColumns(2, 4);
427 cs.hideColumns(7, 11);
428 test = cs.locateVisibleBoundsOfSequence(seq);
429 assertEquals(Arrays.toString(new int[] { 1, 1, 11 }),
430 Arrays.toString(test));
432 cs.revealAllHiddenColumns(colsel);
433 cs.hideColumns(2, 4);
434 cs.hideColumns(7, 12);
435 test = cs.locateVisibleBoundsOfSequence(seq);
436 assertEquals(Arrays.toString(new int[] { 1, 1, 11 }),
437 Arrays.toString(test));
439 cs.revealAllHiddenColumns(colsel);
440 cs.hideColumns(1, 11);
441 test = cs.locateVisibleBoundsOfSequence(seq);
442 assertEquals(Arrays.toString(new int[] { 0, 1, 11 }),
443 Arrays.toString(test));
445 cs.revealAllHiddenColumns(colsel);
446 cs.hideColumns(0, 12);
447 test = cs.locateVisibleBoundsOfSequence(seq);
448 assertEquals(Arrays.toString(new int[] { 0, 1, 11 }),
449 Arrays.toString(test));
451 cs.revealAllHiddenColumns(colsel);
452 cs.hideColumns(0, 4);
453 cs.hideColumns(6, 12);
454 test = cs.locateVisibleBoundsOfSequence(seq);
455 assertEquals(Arrays.toString(new int[] { 0, 1, 11 }),
456 Arrays.toString(test));
458 cs.revealAllHiddenColumns(colsel);
459 cs.hideColumns(0, 1);
460 cs.hideColumns(3, 12);
461 test = cs.locateVisibleBoundsOfSequence(seq);
462 assertEquals(Arrays.toString(new int[] { 0, 1, 11 }),
463 Arrays.toString(test));
465 // These tests cover different behaviour to original
466 // locateVisibleBoundsOfSequence
467 // Previously first values of each were 3,9 and 6 respectively.
468 cs.revealAllHiddenColumns(colsel);
469 cs.hideColumns(3, 14);
470 cs.hideColumns(17, 19);
474 { 3, seq2.findIndex(seq2.getStart()) - 1,
475 seq2.findIndex(seq2.getEnd()) - 1 }),
476 Arrays.toString(cs.locateVisibleBoundsOfSequence(seq2)));
478 cs.revealAllHiddenColumns(colsel);
479 cs.hideColumns(3, 7);
480 cs.hideColumns(9, 14);
481 cs.hideColumns(17, 19);
485 { 9, seq2.findIndex(seq2.getStart()) - 1,
486 seq2.findIndex(seq2.getEnd()) - 1 }),
487 Arrays.toString(cs.locateVisibleBoundsOfSequence(seq2)));
489 cs.revealAllHiddenColumns(colsel);
490 cs.hideColumns(0, 1);
491 cs.hideColumns(3, 4);
492 cs.hideColumns(6, 8);
493 cs.hideColumns(10, 12);
494 test = cs.locateVisibleBoundsOfSequence(seq);
495 assertEquals(Arrays.toString(new int[] { 6, 1, 11 }),
496 Arrays.toString(test));
500 @Test(groups = { "Functional" })
501 public void testLocateVisibleBoundsPathologicals()
503 // test some pathological cases we missed
504 AlignmentI al = new Alignment(
506 { new Sequence("refseqGaptest", "KTDVTI----------NFI-----G----L") });
507 HiddenColumns cs = new HiddenColumns();
508 cs.hideInsertionsFor(al.getSequenceAt(0));
510 + al.getSequenceAt(0).getCharAt(cs.adjustForHiddenColumns(9)));
514 @Test(groups = { "Functional" })
515 public void testHideColumns()
517 // create random alignment
518 AlignmentGenerator gen = new AlignmentGenerator(false);
519 AlignmentI al = gen.generate(50, 20, 123, 5, 5);
521 ColumnSelection colsel = new ColumnSelection();
522 HiddenColumns cs = al.getHiddenColumns();
523 colsel.hideSelectedColumns(5, al.getHiddenColumns());
524 List<int[]> hidden = cs.getHiddenColumnsCopy();
525 assertEquals(1, hidden.size());
526 assertEquals("[5, 5]", Arrays.toString(hidden.get(0)));
528 colsel.hideSelectedColumns(3, al.getHiddenColumns());
529 hidden = cs.getHiddenColumnsCopy();
530 assertEquals(2, hidden.size());
531 // two hidden ranges, in order:
532 assertEquals(hidden.size(), cs.getHiddenColumnsCopy().size());
533 assertEquals("[3, 3]", Arrays.toString(hidden.get(0)));
534 assertEquals("[5, 5]", Arrays.toString(hidden.get(1)));
536 // hiding column 4 expands [3, 3] to [3, 4]
537 // and merges to [5, 5] to make [3, 5]
538 colsel.hideSelectedColumns(4, al.getHiddenColumns());
539 hidden = cs.getHiddenColumnsCopy();
540 assertEquals(1, hidden.size());
541 assertEquals("[3, 5]", Arrays.toString(hidden.get(0)));
543 // clear hidden columns (note they are added to selected)
544 cs.revealAllHiddenColumns(colsel);
545 // it is now actually null but getter returns an empty list
546 assertTrue(cs.getHiddenColumnsCopy().isEmpty());
548 cs.hideColumns(3, 6);
549 hidden = cs.getHiddenColumnsCopy();
550 int[] firstHiddenRange = hidden.get(0);
551 assertEquals("[3, 6]", Arrays.toString(firstHiddenRange));
553 // adding a subrange of already hidden should do nothing
554 cs.hideColumns(4, 5);
555 hidden = cs.getHiddenColumnsCopy();
556 assertEquals(1, hidden.size());
557 assertEquals("[3, 6]",
558 Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
559 cs.hideColumns(3, 5);
560 hidden = cs.getHiddenColumnsCopy();
561 assertEquals(1, hidden.size());
562 assertEquals("[3, 6]",
563 Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
564 cs.hideColumns(4, 6);
565 hidden = cs.getHiddenColumnsCopy();
566 assertEquals(1, hidden.size());
567 assertEquals("[3, 6]",
568 Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
569 cs.hideColumns(3, 6);
570 hidden = cs.getHiddenColumnsCopy();
571 assertEquals(1, hidden.size());
572 assertEquals("[3, 6]",
573 Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
575 cs.revealAllHiddenColumns(colsel);
576 cs.hideColumns(2, 4);
577 hidden = cs.getHiddenColumnsCopy();
578 assertEquals(1, hidden.size());
579 assertEquals("[2, 4]", Arrays.toString(hidden.get(0)));
581 // extend contiguous with 2 positions overlap
582 cs.hideColumns(3, 5);
583 hidden = cs.getHiddenColumnsCopy();
584 assertEquals(1, hidden.size());
585 assertEquals("[2, 5]", Arrays.toString(hidden.get(0)));
587 // extend contiguous with 1 position overlap
588 cs.hideColumns(5, 6);
589 hidden = cs.getHiddenColumnsCopy();
590 assertEquals(1, hidden.size());
591 assertEquals("[2, 6]", Arrays.toString(hidden.get(0)));
593 // extend contiguous with overlap both ends:
594 cs.hideColumns(1, 7);
595 hidden = cs.getHiddenColumnsCopy();
596 assertEquals(1, hidden.size());
597 assertEquals("[1, 7]", Arrays.toString(hidden.get(0)));
601 * Test the method that reveals a range of hidden columns given the start
602 * column of the range
604 @Test(groups = { "Functional" })
605 public void testRevealHiddenColumns()
607 ColumnSelection colsel = new ColumnSelection();
608 HiddenColumns cs = new HiddenColumns();
609 cs.hideColumns(5, 8);
610 colsel.addElement(10);
611 cs.revealHiddenColumns(5, colsel);
613 // hiddenColumns now empty
614 assertEquals(0, cs.getSize());
616 // revealed columns are marked as selected (added to selection):
617 assertEquals("[10, 5, 6, 7, 8]", colsel.getSelected().toString());
619 // calling with a column other than the range start does nothing:
620 colsel = new ColumnSelection();
621 cs = new HiddenColumns();
622 cs.hideColumns(5, 8);
624 int prevSize = cs.getSize();
625 cs.revealHiddenColumns(6, colsel);
626 assertEquals(prevSize, cs.getSize());
627 assertTrue(colsel.getSelected().isEmpty());
630 @Test(groups = { "Functional" })
631 public void testRevealAllHiddenColumns()
633 HiddenColumns hidden = new HiddenColumns();
634 ColumnSelection colsel = new ColumnSelection();
635 hidden.hideColumns(5, 8);
636 hidden.hideColumns(2, 3);
637 colsel.addElement(11);
638 colsel.addElement(1);
639 hidden.revealAllHiddenColumns(colsel);
642 * revealing hidden columns adds them (in order) to the (unordered)
646 // hiddenColumns now empty
647 assertEquals(0, hidden.getSize());
649 assertEquals("[11, 1, 2, 3, 5, 6, 7, 8]",
650 colsel.getSelected().toString());
653 @Test(groups = { "Functional" })
654 public void testIsVisible()
656 HiddenColumns cs = new HiddenColumns();
657 cs.hideColumns(2, 4);
658 cs.hideColumns(6, 7);
659 assertTrue(cs.isVisible(0));
660 assertTrue(cs.isVisible(-99));
661 assertTrue(cs.isVisible(1));
662 assertFalse(cs.isVisible(2));
663 assertFalse(cs.isVisible(3));
664 assertFalse(cs.isVisible(4));
665 assertTrue(cs.isVisible(5));
666 assertFalse(cs.isVisible(6));
667 assertFalse(cs.isVisible(7));
671 * Test for the case when a hidden range encloses more one already hidden
674 @Test(groups = { "Functional" })
675 public void testHideColumns_subsumingHidden()
678 * JAL-2370 bug scenario:
679 * two hidden ranges subsumed by a third
681 HiddenColumns cs = new HiddenColumns();
682 cs.hideColumns(49, 59);
683 cs.hideColumns(69, 79);
684 List<int[]> hidden = cs.getHiddenColumnsCopy();
685 assertEquals(2, hidden.size());
686 assertEquals("[49, 59]", Arrays.toString(hidden.get(0)));
687 assertEquals("[69, 79]", Arrays.toString(hidden.get(1)));
689 cs.hideColumns(48, 80);
690 hidden = cs.getHiddenColumnsCopy();
691 assertEquals(1, hidden.size());
692 assertEquals("[48, 80]", Arrays.toString(hidden.get(0)));
695 * another...joining hidden ranges
697 cs = new HiddenColumns();
698 cs.hideColumns(10, 20);
699 cs.hideColumns(30, 40);
700 cs.hideColumns(50, 60);
701 // hiding 21-49 should merge to one range
702 cs.hideColumns(21, 49);
703 hidden = cs.getHiddenColumnsCopy();
704 assertEquals(1, hidden.size());
705 assertEquals("[10, 60]", Arrays.toString(hidden.get(0)));
708 * another...left overlap, subsumption, right overlap,
709 * no overlap of existing hidden ranges
711 cs = new HiddenColumns();
712 cs.hideColumns(10, 20);
713 cs.hideColumns(10, 20);
714 cs.hideColumns(30, 35);
715 cs.hideColumns(40, 50);
716 cs.hideColumns(60, 70);
718 cs.hideColumns(15, 45);
719 hidden = cs.getHiddenColumnsCopy();
720 assertEquals(2, hidden.size());
721 assertEquals("[10, 50]", Arrays.toString(hidden.get(0)));
722 assertEquals("[60, 70]", Arrays.toString(hidden.get(1)));
725 @Test(groups = { "Functional" })
726 public void testHideBitset()
730 BitSet one = new BitSet();
734 cs = new HiddenColumns();
735 cs.hideMarkedBits(one);
736 assertEquals(1, cs.getHiddenColumnsCopy().size());
739 cs = new HiddenColumns();
740 cs.hideMarkedBits(one);
741 assertEquals(1, cs.getHiddenColumnsCopy().size());
744 cs = new HiddenColumns();
745 cs.hideMarkedBits(one);
746 assertEquals(1, cs.getHiddenColumnsCopy().size());
750 cs = new HiddenColumns();
751 cs.hideMarkedBits(one);
752 assertEquals(2, cs.getHiddenColumnsCopy().size());
754 assertEquals(0, cs.adjustForHiddenColumns(0));
755 assertEquals(2, cs.adjustForHiddenColumns(1));
756 assertEquals(4, cs.adjustForHiddenColumns(2));
760 cs = new HiddenColumns();
761 cs.hideMarkedBits(one);
763 assertEquals(1, cs.getHiddenColumnsCopy().size());
765 assertEquals(0, cs.adjustForHiddenColumns(0));
766 assertEquals(1, cs.adjustForHiddenColumns(1));
767 assertEquals(2, cs.adjustForHiddenColumns(2));
768 assertEquals(4, cs.adjustForHiddenColumns(3));
771 @Test(groups = { "Functional" })
772 public void testMarkHiddenRegions()
774 BitSet toMark, fromMark;
775 long seed = -3241532;
776 Random number = new Random(seed);
777 for (int n = 0; n < 1000; n++)
779 // create a random bitfield
782 { number.nextLong(), number.nextLong(), number.nextLong() });
783 toMark.set(n * number.nextInt(10), n * (25 + number.nextInt(25)));
784 HiddenColumns hc = new HiddenColumns();
785 hc.hideMarkedBits(toMark);
787 // see if we can recover bitfield
788 hc.markHiddenRegions(fromMark = new BitSet());
789 assertEquals(toMark, fromMark);
793 @Test(groups = { "Functional" })
794 public void testFindHiddenRegionPositions()
796 HiddenColumns hc = new HiddenColumns();
798 List<Integer> positions = hc.findHiddenRegionPositions();
799 assertTrue(positions.isEmpty());
801 hc.hideColumns(3, 7);
802 hc.hideColumns(10, 10);
803 hc.hideColumns(14, 15);
805 positions = hc.findHiddenRegionPositions();
806 assertEquals(3, positions.size());
807 assertEquals(3, positions.get(0).intValue());
808 assertEquals(5, positions.get(1).intValue());
809 assertEquals(8, positions.get(2).intValue());
812 @Test(groups = { "Functional" })
813 public void testRegionsToString()
815 HiddenColumns hc = new HiddenColumns();
817 String result = hc.regionsToString(",", "--");
818 assertEquals("", result);
820 hc.hideColumns(3, 7);
821 hc.hideColumns(10, 10);
822 hc.hideColumns(14, 15);
824 result = hc.regionsToString(",", "--");
825 assertEquals("3--7,10--10,14--15", result);
828 @Test(groups = "Functional")
829 public void testGetVisibleStartAndEndIndexTest()
831 Sequence seq = new Sequence("testSeq", "ABCDEFGHIJKLMNOPQRSTUVWXYZ");
832 AlignmentI align = new Alignment(new SequenceI[] { seq });
833 HiddenColumns hc = new HiddenColumns();
835 int[] startEnd = hc.getVisibleStartAndEndIndex(align.getWidth());
836 assertEquals(0, startEnd[0]);
837 assertEquals(25, startEnd[1]);
839 hc.hideColumns(0, 0);
840 startEnd = hc.getVisibleStartAndEndIndex(align.getWidth());
841 assertEquals(1, startEnd[0]);
842 assertEquals(25, startEnd[1]);
844 hc.hideColumns(6, 9);
845 hc.hideColumns(11, 12);
846 startEnd = hc.getVisibleStartAndEndIndex(align.getWidth());
847 assertEquals(1, startEnd[0]);
848 assertEquals(25, startEnd[1]);
850 hc.hideColumns(24, 25);
851 startEnd = hc.getVisibleStartAndEndIndex(align.getWidth());
852 System.out.println(startEnd[0] + " : " + startEnd[1]);
853 assertEquals(1, startEnd[0]);
854 assertEquals(23, startEnd[1]);
857 @Test(groups = "Functional")
858 public void testGetRegionWithEdgeAtRes()
860 HiddenColumns hc = new HiddenColumns();
862 int[] result = hc.getRegionWithEdgeAtRes(5);
865 hc.hideColumns(3, 7);
866 hc.hideColumns(10, 10);
867 hc.hideColumns(14, 15);
869 result = hc.getRegionWithEdgeAtRes(2);
870 assertEquals(3, result[0]);
871 assertEquals(7, result[1]);
873 result = hc.getRegionWithEdgeAtRes(5);
874 assertEquals(10, result[0]);
875 assertEquals(10, result[1]);
877 result = hc.getRegionWithEdgeAtRes(6);
880 result = hc.getRegionWithEdgeAtRes(0);
883 result = hc.getRegionWithEdgeAtRes(7);
884 assertEquals(14, result[0]);
885 assertEquals(15, result[1]);
887 result = hc.getRegionWithEdgeAtRes(8);
888 assertEquals(14, result[0]);
889 assertEquals(15, result[1]);
892 @Test(groups = "Functional")
893 public void testPropagateInsertions()
895 // create an alignment with no gaps - this will be the profile seq and other
897 AlignmentGenerator gen = new AlignmentGenerator(false);
898 AlignmentI al = gen.generate(25, 10, 1234, 0, 0);
900 // get the profileseq
901 SequenceI profileseq = al.getSequenceAt(0);
902 SequenceI gappedseq = new Sequence(profileseq);
903 gappedseq.insertCharAt(5, al.getGapCharacter());
904 gappedseq.insertCharAt(6, al.getGapCharacter());
905 gappedseq.insertCharAt(7, al.getGapCharacter());
906 gappedseq.insertCharAt(8, al.getGapCharacter());
908 // create an alignment view with the gapped sequence
909 SequenceI[] seqs = new SequenceI[1];
911 AlignmentI newal = new Alignment(seqs);
912 HiddenColumns hidden = new HiddenColumns();
913 hidden.hideColumns(15, 17);
915 AlignmentView view = new AlignmentView(newal, hidden, null, true, false,
918 // confirm that original contigs are as expected
919 int[] oldcontigs = hidden.getVisibleContigs(0, 25);
920 int[] testcontigs = { 0, 14, 18, 24 };
921 assertTrue(Arrays.equals(oldcontigs, testcontigs));
923 // propagate insertions
924 HiddenColumns result = HiddenColumns.propagateInsertions(profileseq, al,
927 // confirm that the contigs have changed to account for the gaps
928 int[] newcontigs = result.getVisibleContigs(0, 25);
931 assertTrue(Arrays.equals(newcontigs, testcontigs));
933 // confirm the alignment has been changed so that the other sequences have
934 // gaps inserted where the columns are hidden
935 assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[10]));
936 assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[11]));
937 assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[12]));
938 assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[13]));
939 assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[14]));
943 @Test(groups = "Functional")
944 public void testPropagateInsertionsOverlap()
946 // test propagateInsertions where gaps and hiddenColumns overlap
948 // create an alignment with no gaps - this will be the profile seq and other
950 AlignmentGenerator gen = new AlignmentGenerator(false);
951 AlignmentI al = gen.generate(20, 10, 1234, 0, 0);
953 // get the profileseq
954 SequenceI profileseq = al.getSequenceAt(0);
955 SequenceI gappedseq = new Sequence(profileseq);
956 gappedseq.insertCharAt(5, al.getGapCharacter());
957 gappedseq.insertCharAt(6, al.getGapCharacter());
958 gappedseq.insertCharAt(7, al.getGapCharacter());
959 gappedseq.insertCharAt(8, al.getGapCharacter());
961 // create an alignment view with the gapped sequence
962 SequenceI[] seqs = new SequenceI[1];
964 AlignmentI newal = new Alignment(seqs);
966 // hide columns so that some overlap with the gaps
967 HiddenColumns hidden = new HiddenColumns();
968 hidden.hideColumns(7, 10);
970 AlignmentView view = new AlignmentView(newal, hidden, null, true, false,
973 // confirm that original contigs are as expected
974 int[] oldcontigs = hidden.getVisibleContigs(0, 20);
975 int[] testcontigs = { 0, 6, 11, 19 };
976 assertTrue(Arrays.equals(oldcontigs, testcontigs));
978 // propagate insertions
979 HiddenColumns result = HiddenColumns.propagateInsertions(profileseq, al,
982 // confirm that the contigs have changed to account for the gaps
983 int[] newcontigs = result.getVisibleContigs(0, 20);
986 assertTrue(Arrays.equals(newcontigs, testcontigs));
988 // confirm the alignment has been changed so that the other sequences have
989 // gaps inserted where the columns are hidden
990 assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[4]));
991 assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[5]));
992 assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[6]));
993 assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[7]));
996 @Test(groups = "Functional")
997 public void testHasHiddenColumns()
999 HiddenColumns h = new HiddenColumns();
1001 // new HiddenColumns2 has no hidden cols
1002 assertFalse(h.hasHiddenColumns());
1004 // some columns hidden, returns true
1005 h.hideColumns(5, 10);
1006 assertTrue(h.hasHiddenColumns());
1008 // reveal columns, no hidden cols again
1009 ColumnSelection sel = new ColumnSelection();
1010 h.revealAllHiddenColumns(sel);
1011 assertFalse(h.hasHiddenColumns());
1014 @Test(groups = "Functional")
1015 public void testHasManyHiddenColumns()
1017 HiddenColumns h = new HiddenColumns();
1019 // new HiddenColumns2 has no hidden cols
1020 assertFalse(h.hasManyHiddenColumns());
1022 // one set of columns hidden, returns false
1023 h.hideColumns(5, 10);
1024 assertFalse(h.hasManyHiddenColumns());
1026 // two sets hidden, returns true
1027 h.hideColumns(15, 17);
1028 assertTrue(h.hasManyHiddenColumns());
1030 // back to one block, asserts false
1031 h.hideColumns(11, 14);
1032 assertFalse(h.hasManyHiddenColumns());
1035 @Test(groups = "Functional")
1036 public void testAdjustForHiddenColumns()
1038 HiddenColumns h = new HiddenColumns();
1039 // returns input value when there are no hidden columns
1040 assertEquals(10, h.adjustForHiddenColumns(10));
1042 h.hideColumns(20, 30);
1043 assertEquals(10, h.adjustForHiddenColumns(10));
1044 assertEquals(20 + 11, h.adjustForHiddenColumns(20));
1045 assertEquals(35 + 11, h.adjustForHiddenColumns(35));
1047 h.hideColumns(5, 7);
1048 assertEquals(10 + 3, h.adjustForHiddenColumns(10));
1049 assertEquals(20 + 14, h.adjustForHiddenColumns(20));
1050 assertEquals(35 + 14, h.adjustForHiddenColumns(35));
1052 ColumnSelection sel = new ColumnSelection();
1053 h.revealAllHiddenColumns(sel);
1054 h.hideColumns(0, 1);
1055 assertEquals(4, h.adjustForHiddenColumns(2));
1058 @Test(groups = "Functional")
1059 public void testGetHiddenBoundaryLeft()
1061 HiddenColumns h = new HiddenColumns();
1063 // returns same value if no hidden cols
1064 assertEquals(3, h.getHiddenBoundaryLeft(3));
1066 h.hideColumns(5, 10);
1067 assertEquals(10, h.getHiddenBoundaryLeft(15));
1068 assertEquals(3, h.getHiddenBoundaryLeft(3));
1069 assertEquals(7, h.getHiddenBoundaryLeft(7));
1071 h.hideColumns(15, 20);
1072 assertEquals(10, h.getHiddenBoundaryLeft(15));
1073 assertEquals(20, h.getHiddenBoundaryLeft(21));
1076 @Test(groups = "Functional")
1077 public void testGetHiddenBoundaryRight()
1079 HiddenColumns h = new HiddenColumns();
1081 // returns same value if no hidden cols
1082 assertEquals(3, h.getHiddenBoundaryRight(3));
1084 h.hideColumns(5, 10);
1085 assertEquals(5, h.getHiddenBoundaryRight(3));
1086 assertEquals(15, h.getHiddenBoundaryRight(15));
1087 assertEquals(7, h.getHiddenBoundaryRight(7));
1089 h.hideColumns(15, 20);
1090 assertEquals(15, h.getHiddenBoundaryRight(7));
1091 assertEquals(15, h.getHiddenBoundaryRight(14));
1094 @Test(groups = "Functional")
1095 public void testGetHiddenColumnsCopy()
1097 HiddenColumns h = new HiddenColumns();
1098 ArrayList<int[]> result = h.getHiddenColumnsCopy();
1099 assertTrue(result.isEmpty());
1101 h.hideColumns(5, 10);
1102 result = h.getHiddenColumnsCopy();
1103 assertEquals(1, result.size());
1104 assertEquals(5, result.get(0)[0]);
1105 assertEquals(10, result.get(0)[1]);
1107 h.hideColumns(22, 23);
1108 result = h.getHiddenColumnsCopy();
1109 assertEquals(2, result.size());
1110 assertEquals(5, result.get(0)[0]);
1111 assertEquals(10, result.get(0)[1]);
1112 assertEquals(22, result.get(1)[0]);
1113 assertEquals(23, result.get(1)[1]);
1115 // test for only one hidden region at start of alignment
1116 ColumnSelection sel = new ColumnSelection();
1117 h.revealAllHiddenColumns(sel);
1118 h.hideColumns(0, 1);
1119 result = h.getHiddenColumnsCopy();
1120 assertEquals(1, result.size());
1121 assertEquals(0, result.get(0)[0]);
1122 assertEquals(1, result.get(0)[1]);
1125 @Test(groups = "Functional")
1126 public void testGetVisibleSequenceStrings()
1128 HiddenColumns h = new HiddenColumns();
1129 SequenceI seq1 = new Sequence("TEST1", "GALMFWKQESPVICYHRNDT");
1130 SequenceI seq2 = new Sequence("TEST2", "VICYHRNDTGA");
1131 SequenceI[] seqs = new SequenceI[2];
1134 String[] result = h.getVisibleSequenceStrings(5, 10, seqs);
1135 assertEquals(2, result.length);
1136 assertEquals("WKQES", result[0]);
1137 assertEquals("RNDTG", result[1]);
1139 h.hideColumns(6, 8);
1140 result = h.getVisibleSequenceStrings(5, 10, seqs);
1141 assertEquals(2, result.length);
1142 assertEquals("WS", result[0]);
1143 assertEquals("RG", result[1]);
1145 SequenceI seq = new Sequence("RefSeq", "-A-SD-ASD--E---");
1146 ColumnSelection sel = new ColumnSelection();
1147 h.revealAllHiddenColumns(sel);
1148 h.hideColumns(1, 3);
1149 h.hideColumns(6, 11);
1151 h.getVisibleSequenceStrings(0, 5, new SequenceI[]
1155 @Test(groups = "Functional")
1156 public void testHideInsertionsFor()
1158 HiddenColumns h = new HiddenColumns();
1159 HiddenColumns h2 = new HiddenColumns();
1160 SequenceI seq1 = new Sequence("TEST1", "GAL---MFW-KQESPVICY--HRNDT");
1161 SequenceI seq2 = new Sequence("TEST1", "GALMFWKQESPVICYHRNDT");
1163 h.hideInsertionsFor(seq2);
1164 assertTrue(h.equals(h2));
1166 h.hideInsertionsFor(seq1);
1167 h2.hideColumns(3, 5);
1168 h2.hideColumns(9, 9);
1169 h2.hideColumns(19, 20);
1170 assertTrue(h.equals(h2));
1173 @Test(groups = "Functional")
1174 public void testHideMarkedBits()
1176 HiddenColumns h = new HiddenColumns();
1177 HiddenColumns h2 = new HiddenColumns();
1179 BitSet tohide = new BitSet(21);
1180 h.hideMarkedBits(tohide);
1181 assertTrue(h.equals(h2));
1183 // NB in hideMarkedBits, the last bit is not set to hidden
1187 h.hideMarkedBits(tohide);
1189 h2.hideColumns(3, 5);
1190 h2.hideColumns(9, 9);
1191 h2.hideColumns(19, 20);
1192 assertTrue(h.equals(h2));
1195 @Test(groups = "Functional")
1196 public void testMakeVisibleAnnotation()
1198 HiddenColumns h = new HiddenColumns();
1199 Annotation[] anns = new Annotation[] { null, null, new Annotation(1),
1200 new Annotation(2), new Annotation(3), null, null, new Annotation(4),
1201 new Annotation(5), new Annotation(6), new Annotation(7),
1202 new Annotation(8) };
1203 AlignmentAnnotation ann = new AlignmentAnnotation("an", "some an",
1206 // without hidden cols, just truncates
1207 h.makeVisibleAnnotation(3, 5, ann);
1208 assertEquals(3, ann.annotations.length);
1209 assertEquals(2.0f, ann.annotations[0].value);
1210 assertEquals(3.0f, ann.annotations[1].value);
1211 assertNull(ann.annotations[2]);
1213 anns = new Annotation[] { null, null, new Annotation(1),
1214 new Annotation(2), new Annotation(3), null, null, new Annotation(4),
1215 new Annotation(5), new Annotation(6), new Annotation(7),
1216 new Annotation(8) };
1217 ann = new AlignmentAnnotation("an", "some an", anns);
1218 h.hideColumns(4, 7);
1219 h.makeVisibleAnnotation(1, 9, ann);
1220 assertEquals(5, ann.annotations.length);
1221 assertNull(ann.annotations[0]);
1222 assertEquals(1.0f, ann.annotations[1].value);
1223 assertEquals(2.0f, ann.annotations[2].value);
1224 assertEquals(5.0f, ann.annotations[3].value);
1225 assertEquals(6.0f, ann.annotations[4].value);
1227 anns = new Annotation[] { null, null, new Annotation(1),
1228 new Annotation(2), new Annotation(3), null, null, new Annotation(4),
1229 new Annotation(5), new Annotation(6), new Annotation(7),
1230 new Annotation(8) };
1231 ann = new AlignmentAnnotation("an", "some an", anns);
1232 h.hideColumns(1, 2);
1233 h.makeVisibleAnnotation(1, 9, ann);
1234 assertEquals(3, ann.annotations.length);
1235 assertEquals(2.0f, ann.annotations[0].value);
1236 assertEquals(5.0f, ann.annotations[1].value);
1237 assertEquals(6.0f, ann.annotations[2].value);
1240 @Test(groups = "Functional")
1241 public void testSubtractVisibleColumns()
1243 HiddenColumns h = new HiddenColumns();
1244 int result = h.subtractVisibleColumns(1, 10);
1245 assertEquals(9, result);
1247 h.hideColumns(7, 9);
1248 result = h.subtractVisibleColumns(4, 10);
1249 assertEquals(3, result);
1251 h.hideColumns(14, 15);
1252 result = h.subtractVisibleColumns(4, 10);
1253 assertEquals(3, result);
1255 result = h.subtractVisibleColumns(10, 17);
1256 assertEquals(2, result);
1258 result = h.subtractVisibleColumns(1, 7);
1259 assertEquals(5, result);
1261 result = h.subtractVisibleColumns(1, 8);
1262 assertEquals(5, result);
1264 result = h.subtractVisibleColumns(3, 15);
1265 assertEquals(10, result);
1267 ColumnSelection sel = new ColumnSelection();
1268 h.revealAllHiddenColumns(sel);
1269 h.hideColumns(0, 30);
1270 result = h.subtractVisibleColumns(31, 0);
1271 assertEquals(-31, result);