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.Arrays;
33 import java.util.BitSet;
34 import java.util.Iterator;
35 import java.util.Random;
37 import org.testng.annotations.BeforeClass;
38 import org.testng.annotations.Test;
40 public class HiddenColumnsTest
43 @BeforeClass(alwaysRun = true)
44 public void setUpJvOptionPane()
46 JvOptionPane.setInteractiveMode(false);
47 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
51 * Test the method which counts the number of hidden columns
53 @Test(groups = { "Functional" })
54 public void testGetSize()
56 HiddenColumns hidden = new HiddenColumns();
57 assertEquals(0, hidden.getSize());
59 hidden.hideColumns(3, 5);
60 assertEquals(3, hidden.getSize());
62 hidden.hideColumns(8, 8);
63 assertEquals(4, hidden.getSize());
65 hidden.hideColumns(9, 14);
66 assertEquals(10, hidden.getSize());
68 ColumnSelection cs = new ColumnSelection();
69 hidden.revealAllHiddenColumns(cs);
70 assertEquals(0, hidden.getSize());
74 * Test the method that finds the visible column position of an alignment
75 * column, allowing for hidden columns.
77 @Test(groups = { "Functional" })
78 public void testFindColumnPosition()
80 HiddenColumns cs = new HiddenColumns();
81 assertEquals(5, cs.findColumnPosition(5));
83 // hiding column 6 makes no difference
85 assertEquals(5, cs.findColumnPosition(5));
87 // hiding column 4 moves column 5 to column 4
89 assertEquals(4, cs.findColumnPosition(5));
91 // hiding column 4 moves column 4 to position 3
92 assertEquals(3, cs.findColumnPosition(4));
94 // hiding columns 1 and 2 moves column 5 to column 2
96 assertEquals(2, cs.findColumnPosition(5));
98 // check with > 1 hidden column regions
99 // where some columns are in the hidden regions
100 HiddenColumns cs2 = new HiddenColumns();
101 cs2.hideColumns(5, 10);
102 cs2.hideColumns(20, 27);
103 cs2.hideColumns(40, 44);
105 // hiding columns 5-10 and 20-27 moves column 8 to column 4
106 assertEquals(4, cs2.findColumnPosition(8));
108 // and moves column 24 to 13
109 assertEquals(13, cs2.findColumnPosition(24));
111 // and moves column 28 to 14
112 assertEquals(14, cs2.findColumnPosition(28));
114 // and moves column 40 to 25
115 assertEquals(25, cs2.findColumnPosition(40));
117 // check when hidden columns start at 0 that the visible column
119 HiddenColumns cs3 = new HiddenColumns();
120 cs3.hideColumns(0, 4);
121 assertEquals(0, cs3.findColumnPosition(2));
123 // check that column after the last hidden region doesn't crash
124 assertEquals(46, cs2.findColumnPosition(65));
127 @Test(groups = { "Functional" })
128 public void testVisibleContigsIterator()
130 HiddenColumns cs = new HiddenColumns();
132 Iterator<int[]> visible = cs.getVisContigsIterator(3, 10);
133 int[] region = visible.next();
134 assertEquals("[3, 9]", Arrays.toString(region));
135 assertFalse(visible.hasNext());
137 cs.hideColumns(3, 6);
138 cs.hideColumns(8, 9);
139 cs.hideColumns(12, 12);
141 // Test both ends visible region
143 // start position is inclusive, end position exclusive
144 visible = cs.getVisContigsIterator(1, 13);
145 region = visible.next();
146 assertEquals("[1, 2]", Arrays.toString(region));
147 region = visible.next();
148 assertEquals("[7, 7]", Arrays.toString(region));
149 region = visible.next();
150 assertEquals("[10, 11]", Arrays.toString(region));
151 assertFalse(visible.hasNext());
153 // Test start hidden, end visible
154 visible = cs.getVisContigsIterator(4, 14);
155 region = visible.next();
156 assertEquals("[7, 7]", Arrays.toString(region));
157 region = visible.next();
158 assertEquals("[10, 11]", Arrays.toString(region));
159 region = visible.next();
160 assertEquals("[13, 13]", Arrays.toString(region));
161 assertFalse(visible.hasNext());
163 // Test start hidden, end hidden
164 visible = cs.getVisContigsIterator(3, 10);
165 region = visible.next();
166 assertEquals("[7, 7]", Arrays.toString(region));
167 assertFalse(visible.hasNext());
169 // Test start visible, end hidden
170 visible = cs.getVisContigsIterator(0, 13);
171 region = visible.next();
172 assertEquals("[0, 2]", Arrays.toString(region));
173 region = visible.next();
174 assertEquals("[7, 7]", Arrays.toString(region));
175 region = visible.next();
176 assertEquals("[10, 11]", Arrays.toString(region));
177 assertFalse(visible.hasNext());
180 visible = cs.getVisContigsIterator(4, 6);
181 assertFalse(visible.hasNext());
184 @Test(groups = { "Functional" })
185 public void testEquals()
187 HiddenColumns cs = new HiddenColumns();
188 cs.hideColumns(5, 9);
190 // a different set of hidden columns
191 HiddenColumns cs2 = new HiddenColumns();
193 // with no hidden columns
194 assertFalse(cs.equals(cs2));
195 assertFalse(cs2.equals(cs));
197 // with hidden columns added in a different order
198 cs2.hideColumns(6, 9);
199 cs2.hideColumns(5, 8);
201 assertTrue(cs.equals(cs2));
202 assertTrue(cs.equals(cs));
203 assertTrue(cs2.equals(cs));
204 assertTrue(cs2.equals(cs2));
207 @Test(groups = "Functional")
208 public void testCopyConstructor()
210 HiddenColumns cs = new HiddenColumns();
211 cs.hideColumns(10, 11);
212 cs.hideColumns(5, 7);
213 Iterator<int[]> regions = cs.iterator();
214 assertEquals("[5, 7]",
215 Arrays.toString(regions.next()));
217 HiddenColumns cs2 = new HiddenColumns(cs);
218 regions = cs2.iterator();
219 assertTrue(cs2.hasHiddenColumns());
220 assertEquals(2, cs2.getNumberOfRegions());
221 // hidden columns are held in column order
222 assertEquals("[5, 7]",
223 Arrays.toString(regions.next()));
224 assertEquals("[10, 11]",
225 Arrays.toString(regions.next()));
228 @Test(groups = "Functional")
229 public void testCopyConstructor2()
231 HiddenColumns cs = new HiddenColumns();
232 cs.hideColumns(10, 11);
233 cs.hideColumns(5, 7);
235 HiddenColumns cs2 = new HiddenColumns(cs, 3, 9, 1);
236 assertTrue(cs2.hasHiddenColumns());
237 Iterator<int[]> regions = cs2.iterator();
239 // only [5,7] returned, offset by 1
240 assertEquals("[4, 6]",
241 Arrays.toString(regions.next()));
242 assertEquals(3, cs2.getSize());
244 cs2 = new HiddenColumns(cs, 8, 15, 4);
245 regions = cs2.iterator();
246 assertTrue(cs2.hasHiddenColumns());
248 // only [10,11] returned, offset by 4
249 assertEquals("[6, 7]",
250 Arrays.toString(regions.next()));
251 assertEquals(2, cs2.getSize());
253 cs2 = new HiddenColumns(cs, 6, 10, 4);
254 assertFalse(cs2.hasHiddenColumns());
258 * Test the code used to locate the reference sequence ruler origin
260 @Test(groups = { "Functional" })
261 public void testLocateVisibleBoundsofSequence()
263 // create random alignment
264 AlignmentGenerator gen = new AlignmentGenerator(false);
265 AlignmentI al = gen.generate(50, 20, 123, 5, 5);
267 HiddenColumns cs = al.getHiddenColumns();
268 ColumnSelection colsel = new ColumnSelection();
270 SequenceI seq = new Sequence("RefSeq", "-A-SD-ASD--E---");
271 assertEquals(2, seq.findIndex(seq.getStart()));
274 assertEquals(seq.findIndex(seq.getStart()) - 1, cs.locateVisibleStartOfSequence(seq));
276 // hidden column on gap after end of sequence - should not affect bounds
277 colsel.hideSelectedColumns(13, al.getHiddenColumns());
278 assertEquals(seq.findIndex(seq.getStart()) - 1,cs.locateVisibleStartOfSequence(seq));
280 cs.revealAllHiddenColumns(colsel);
281 // hidden column on gap before beginning of sequence - should vis bounds by
283 colsel.hideSelectedColumns(0, al.getHiddenColumns());
284 assertEquals(seq.findIndex(seq.getStart()) - 2,cs.locateVisibleStartOfSequence(seq));
286 cs.revealAllHiddenColumns(colsel);
287 // hide columns around most of sequence - leave one residue remaining
288 cs.hideColumns(1, 3);
289 cs.hideColumns(6, 11);
291 cs.getVisibleSequenceStrings(0, 5, new SequenceI[]
294 assertEquals(1, cs.locateVisibleStartOfSequence(seq));
295 cs.revealAllHiddenColumns(colsel);
297 // hide whole sequence - should just get location of hidden region
298 // containing sequence
299 cs.hideColumns(1, 11);
300 assertEquals(0,cs.locateVisibleStartOfSequence(seq));
302 cs.revealAllHiddenColumns(colsel);
303 cs.hideColumns(0, 15);
304 assertEquals(0,cs.locateVisibleStartOfSequence(seq));
306 SequenceI seq2 = new Sequence("RefSeq2", "-------A-SD-ASD--E---");
308 cs.revealAllHiddenColumns(colsel);
309 cs.hideColumns(7, 17);
310 assertEquals(0,cs.locateVisibleStartOfSequence(seq2));
312 cs.revealAllHiddenColumns(colsel);
313 cs.hideColumns(3, 17);
314 assertEquals(0,cs.locateVisibleStartOfSequence(seq2));
316 cs.revealAllHiddenColumns(colsel);
317 cs.hideColumns(3, 19);
318 assertEquals(0,cs.locateVisibleStartOfSequence(seq2));
320 cs.revealAllHiddenColumns(colsel);
321 cs.hideColumns(0, 0);
322 assertEquals(0,cs.locateVisibleStartOfSequence(seq));
324 cs.revealAllHiddenColumns(colsel);
325 cs.hideColumns(0, 1);
326 assertEquals(1,cs.locateVisibleStartOfSequence(seq));
328 cs.revealAllHiddenColumns(colsel);
329 cs.hideColumns(0, 2);
330 assertEquals(0,cs.locateVisibleStartOfSequence(seq));
332 cs.revealAllHiddenColumns(colsel);
333 cs.hideColumns(1, 1);
334 assertEquals(2,cs.locateVisibleStartOfSequence(seq));
336 cs.revealAllHiddenColumns(colsel);
337 cs.hideColumns(1, 2);
338 assertEquals(1,cs.locateVisibleStartOfSequence(seq));
340 cs.revealAllHiddenColumns(colsel);
341 cs.hideColumns(1, 3);
342 assertEquals(1,cs.locateVisibleStartOfSequence(seq));
344 cs.revealAllHiddenColumns(colsel);
345 cs.hideColumns(0, 2);
346 cs.hideColumns(5, 6);
347 assertEquals(0,cs.locateVisibleStartOfSequence(seq));
349 cs.revealAllHiddenColumns(colsel);
350 cs.hideColumns(0, 2);
351 cs.hideColumns(5, 6);
352 cs.hideColumns(9, 10);
353 assertEquals(0,cs.locateVisibleStartOfSequence(seq));
355 cs.revealAllHiddenColumns(colsel);
356 cs.hideColumns(0, 2);
357 cs.hideColumns(7, 11);
358 assertEquals(0,cs.locateVisibleStartOfSequence(seq));
360 cs.revealAllHiddenColumns(colsel);
361 cs.hideColumns(2, 4);
362 cs.hideColumns(7, 11);
363 assertEquals(1,cs.locateVisibleStartOfSequence(seq));
365 cs.revealAllHiddenColumns(colsel);
366 cs.hideColumns(2, 4);
367 cs.hideColumns(7, 12);
368 assertEquals(1,cs.locateVisibleStartOfSequence(seq));
370 cs.revealAllHiddenColumns(colsel);
371 cs.hideColumns(1, 11);
372 assertEquals(0,cs.locateVisibleStartOfSequence(seq));
374 cs.revealAllHiddenColumns(colsel);
375 cs.hideColumns(0, 12);
376 assertEquals(0,cs.locateVisibleStartOfSequence(seq));
378 cs.revealAllHiddenColumns(colsel);
379 cs.hideColumns(0, 4);
380 cs.hideColumns(6, 12);
381 assertEquals(0,cs.locateVisibleStartOfSequence(seq));
383 cs.revealAllHiddenColumns(colsel);
384 cs.hideColumns(0, 1);
385 cs.hideColumns(3, 12);
386 assertEquals(0,cs.locateVisibleStartOfSequence(seq));
388 cs.revealAllHiddenColumns(colsel);
389 cs.hideColumns(3, 14);
390 cs.hideColumns(17, 19);
391 assertEquals(3,cs.locateVisibleStartOfSequence(seq2));
393 cs.revealAllHiddenColumns(colsel);
394 cs.hideColumns(3, 7);
395 cs.hideColumns(9, 14);
396 cs.hideColumns(17, 19);
397 assertEquals(9,cs.locateVisibleStartOfSequence(seq2));
399 cs.revealAllHiddenColumns(colsel);
400 cs.hideColumns(0, 1);
401 cs.hideColumns(3, 4);
402 cs.hideColumns(6, 8);
403 cs.hideColumns(10, 12);
404 assertEquals(6, cs.locateVisibleStartOfSequence(seq));
408 @Test(groups = { "Functional" })
409 public void testLocateVisibleBoundsPathologicals()
411 // test some pathological cases we missed
412 AlignmentI al = new Alignment(
414 { new Sequence("refseqGaptest", "KTDVTI----------NFI-----G----L") });
415 HiddenColumns cs = new HiddenColumns();
416 cs.hideInsertionsFor(al.getSequenceAt(0));
418 + al.getSequenceAt(0).getCharAt(cs.adjustForHiddenColumns(9)));
421 @Test(groups = { "Functional" })
422 public void testHideColumns()
424 // create random alignment
425 AlignmentGenerator gen = new AlignmentGenerator(false);
426 AlignmentI al = gen.generate(50, 20, 123, 5, 5);
428 ColumnSelection colsel = new ColumnSelection();
429 HiddenColumns cs = al.getHiddenColumns();
430 colsel.hideSelectedColumns(5, al.getHiddenColumns());
431 Iterator<int[]> regions = cs.iterator();
432 assertEquals(1, cs.getNumberOfRegions());
433 assertEquals("[5, 5]", Arrays.toString(regions.next()));
435 colsel.hideSelectedColumns(3, al.getHiddenColumns());
436 regions = cs.iterator();
437 assertEquals(2, cs.getNumberOfRegions());
438 // two hidden ranges, in order:
439 assertEquals("[3, 3]", Arrays.toString(regions.next()));
440 assertEquals("[5, 5]", Arrays.toString(regions.next()));
442 // hiding column 4 expands [3, 3] to [3, 4]
443 // and merges to [5, 5] to make [3, 5]
444 colsel.hideSelectedColumns(4, al.getHiddenColumns());
445 regions = cs.iterator();
446 assertEquals(1, cs.getNumberOfRegions());
447 assertEquals("[3, 5]", Arrays.toString(regions.next()));
449 // clear hidden columns (note they are added to selected)
450 cs.revealAllHiddenColumns(colsel);
451 // it is now actually null but getter returns an empty list
452 assertEquals(0, cs.getNumberOfRegions());
454 cs.hideColumns(3, 6);
455 regions = cs.iterator();
456 int[] firstHiddenRange = regions.next();
457 assertEquals("[3, 6]", Arrays.toString(firstHiddenRange));
459 // adding a subrange of already hidden should do nothing
460 cs.hideColumns(4, 5);
461 regions = cs.iterator();
462 assertEquals(1, cs.getNumberOfRegions());
463 assertEquals("[3, 6]",
464 Arrays.toString(regions.next()));
465 cs.hideColumns(3, 5);
466 regions = cs.iterator();
467 assertEquals(1, cs.getNumberOfRegions());
468 assertEquals("[3, 6]",
469 Arrays.toString(regions.next()));
470 cs.hideColumns(4, 6);
471 regions = cs.iterator();
472 assertEquals(1, cs.getNumberOfRegions());
473 assertEquals("[3, 6]",
474 Arrays.toString(regions.next()));
475 cs.hideColumns(3, 6);
476 regions = cs.iterator();
477 assertEquals(1, cs.getNumberOfRegions());
478 assertEquals("[3, 6]",
479 Arrays.toString(regions.next()));
481 cs.revealAllHiddenColumns(colsel);
482 cs.hideColumns(2, 4);
483 regions = cs.iterator();
484 assertEquals(1, cs.getNumberOfRegions());
485 assertEquals("[2, 4]", Arrays.toString(regions.next()));
487 // extend contiguous with 2 positions overlap
488 cs.hideColumns(3, 5);
489 regions = cs.iterator();
490 assertEquals(1, cs.getNumberOfRegions());
491 assertEquals("[2, 5]", Arrays.toString(regions.next()));
493 // extend contiguous with 1 position overlap
494 cs.hideColumns(5, 6);
495 regions = cs.iterator();
496 assertEquals(1, cs.getNumberOfRegions());
497 assertEquals("[2, 6]", Arrays.toString(regions.next()));
499 // extend contiguous with overlap both ends:
500 cs.hideColumns(1, 7);
501 regions = cs.iterator();
502 assertEquals(1, cs.getNumberOfRegions());
503 assertEquals("[1, 7]", Arrays.toString(regions.next()));
507 * Test the method that reveals a range of hidden columns given the start
508 * column of the range
510 @Test(groups = { "Functional" })
511 public void testRevealHiddenColumns()
513 ColumnSelection colsel = new ColumnSelection();
514 HiddenColumns cs = new HiddenColumns();
515 cs.hideColumns(5, 8);
516 colsel.addElement(10);
517 cs.revealHiddenColumns(5, colsel);
519 // hiddenColumns now empty
520 assertEquals(0, cs.getSize());
522 // revealed columns are marked as selected (added to selection):
523 assertEquals("[10, 5, 6, 7, 8]", colsel.getSelected().toString());
525 // calling with a column other than the range start does nothing:
526 colsel = new ColumnSelection();
527 cs = new HiddenColumns();
528 cs.hideColumns(5, 8);
530 int prevSize = cs.getSize();
531 cs.revealHiddenColumns(6, colsel);
532 assertEquals(prevSize, cs.getSize());
533 assertTrue(colsel.getSelected().isEmpty());
536 @Test(groups = { "Functional" })
537 public void testRevealAllHiddenColumns()
539 HiddenColumns hidden = new HiddenColumns();
540 ColumnSelection colsel = new ColumnSelection();
541 hidden.hideColumns(5, 8);
542 hidden.hideColumns(2, 3);
543 colsel.addElement(11);
544 colsel.addElement(1);
545 hidden.revealAllHiddenColumns(colsel);
548 * revealing hidden columns adds them (in order) to the (unordered)
552 // hiddenColumns now empty
553 assertEquals(0, hidden.getSize());
555 assertEquals("[11, 1, 2, 3, 5, 6, 7, 8]",
556 colsel.getSelected().toString());
559 @Test(groups = { "Functional" })
560 public void testIsVisible()
562 HiddenColumns cs = new HiddenColumns();
563 cs.hideColumns(2, 4);
564 cs.hideColumns(6, 7);
565 assertTrue(cs.isVisible(0));
566 assertTrue(cs.isVisible(-99));
567 assertTrue(cs.isVisible(1));
568 assertFalse(cs.isVisible(2));
569 assertFalse(cs.isVisible(3));
570 assertFalse(cs.isVisible(4));
571 assertTrue(cs.isVisible(5));
572 assertFalse(cs.isVisible(6));
573 assertFalse(cs.isVisible(7));
577 * Test for the case when a hidden range encloses more one already hidden
580 @Test(groups = { "Functional" })
581 public void testHideColumns_subsumingHidden()
584 * JAL-2370 bug scenario:
585 * two hidden ranges subsumed by a third
587 HiddenColumns cs = new HiddenColumns();
588 cs.hideColumns(49, 59);
589 cs.hideColumns(69, 79);
590 Iterator<int[]> regions = cs.iterator();
591 assertEquals(2, cs.getNumberOfRegions());
592 assertEquals("[49, 59]", Arrays.toString(regions.next()));
593 assertEquals("[69, 79]", Arrays.toString(regions.next()));
595 cs.hideColumns(48, 80);
596 regions = cs.iterator();
597 assertEquals(1, cs.getNumberOfRegions());
598 assertEquals("[48, 80]", Arrays.toString(regions.next()));
601 * another...joining hidden ranges
603 cs = new HiddenColumns();
604 cs.hideColumns(10, 20);
605 cs.hideColumns(30, 40);
606 cs.hideColumns(50, 60);
607 // hiding 21-49 should merge to one range
608 cs.hideColumns(21, 49);
609 regions = cs.iterator();
610 assertEquals(1, cs.getNumberOfRegions());
611 assertEquals("[10, 60]", Arrays.toString(regions.next()));
614 * another...left overlap, subsumption, right overlap,
615 * no overlap of existing hidden ranges
617 cs = new HiddenColumns();
618 cs.hideColumns(10, 20);
619 cs.hideColumns(10, 20);
620 cs.hideColumns(30, 35);
621 cs.hideColumns(40, 50);
622 cs.hideColumns(60, 70);
624 cs.hideColumns(15, 45);
625 regions = cs.iterator();
626 assertEquals(2, cs.getNumberOfRegions());
627 assertEquals("[10, 50]", Arrays.toString(regions.next()));
628 assertEquals("[60, 70]", Arrays.toString(regions.next()));
631 @Test(groups = { "Functional" })
632 public void testHideBitset()
636 BitSet one = new BitSet();
640 cs = new HiddenColumns();
641 cs.hideMarkedBits(one);
642 assertEquals(1, cs.getNumberOfRegions());
645 cs = new HiddenColumns();
646 cs.hideMarkedBits(one);
647 assertEquals(1, cs.getNumberOfRegions());
650 cs = new HiddenColumns();
651 cs.hideMarkedBits(one);
652 assertEquals(1, cs.getNumberOfRegions());
656 cs = new HiddenColumns();
657 cs.hideMarkedBits(one);
658 assertEquals(2, cs.getNumberOfRegions());
660 assertEquals(0, cs.adjustForHiddenColumns(0));
661 assertEquals(2, cs.adjustForHiddenColumns(1));
662 assertEquals(4, cs.adjustForHiddenColumns(2));
666 cs = new HiddenColumns();
667 cs.hideMarkedBits(one);
669 assertEquals(1, cs.getNumberOfRegions());
671 assertEquals(0, cs.adjustForHiddenColumns(0));
672 assertEquals(1, cs.adjustForHiddenColumns(1));
673 assertEquals(2, cs.adjustForHiddenColumns(2));
674 assertEquals(4, cs.adjustForHiddenColumns(3));
677 @Test(groups = { "Functional" })
678 public void testMarkHiddenRegions()
680 BitSet toMark, fromMark;
681 long seed = -3241532;
682 Random number = new Random(seed);
683 for (int n = 0; n < 1000; n++)
685 // create a random bitfield
688 { number.nextLong(), number.nextLong(), number.nextLong() });
689 toMark.set(n * number.nextInt(10), n * (25 + number.nextInt(25)));
690 HiddenColumns hc = new HiddenColumns();
691 hc.hideMarkedBits(toMark);
693 // see if we can recover bitfield
694 hc.markHiddenRegions(fromMark = new BitSet());
695 assertEquals(toMark, fromMark);
699 @Test(groups = { "Functional" })
700 public void testRegionsToString()
702 HiddenColumns hc = new HiddenColumns();
704 String result = hc.regionsToString(",", "--");
705 assertEquals("", result);
707 hc.hideColumns(3, 7);
708 hc.hideColumns(10, 10);
709 hc.hideColumns(14, 15);
711 result = hc.regionsToString(",", "--");
712 assertEquals("3--7,10--10,14--15", result);
715 @Test(groups = "Functional")
716 public void testGetVisibleStartAndEndIndexTest()
718 Sequence seq = new Sequence("testSeq", "ABCDEFGHIJKLMNOPQRSTUVWXYZ");
719 AlignmentI align = new Alignment(new SequenceI[] { seq });
720 HiddenColumns hc = new HiddenColumns();
722 int[] startEnd = hc.getVisibleStartAndEndIndex(align.getWidth());
723 assertEquals(0, startEnd[0]);
724 assertEquals(25, startEnd[1]);
726 hc.hideColumns(0, 0);
727 startEnd = hc.getVisibleStartAndEndIndex(align.getWidth());
728 assertEquals(1, startEnd[0]);
729 assertEquals(25, startEnd[1]);
731 hc.hideColumns(6, 9);
732 hc.hideColumns(11, 12);
733 startEnd = hc.getVisibleStartAndEndIndex(align.getWidth());
734 assertEquals(1, startEnd[0]);
735 assertEquals(25, startEnd[1]);
737 hc.hideColumns(24, 25);
738 startEnd = hc.getVisibleStartAndEndIndex(align.getWidth());
739 System.out.println(startEnd[0] + " : " + startEnd[1]);
740 assertEquals(1, startEnd[0]);
741 assertEquals(23, startEnd[1]);
744 @Test(groups = "Functional")
745 public void testGetRegionWithEdgeAtRes()
747 HiddenColumns hc = new HiddenColumns();
749 int[] result = hc.getRegionWithEdgeAtRes(5);
752 hc.hideColumns(3, 7);
753 hc.hideColumns(10, 10);
754 hc.hideColumns(14, 15);
756 result = hc.getRegionWithEdgeAtRes(2);
757 assertEquals(3, result[0]);
758 assertEquals(7, result[1]);
760 result = hc.getRegionWithEdgeAtRes(5);
761 assertEquals(10, result[0]);
762 assertEquals(10, result[1]);
764 result = hc.getRegionWithEdgeAtRes(6);
767 result = hc.getRegionWithEdgeAtRes(0);
770 result = hc.getRegionWithEdgeAtRes(7);
771 assertEquals(14, result[0]);
772 assertEquals(15, result[1]);
774 result = hc.getRegionWithEdgeAtRes(8);
775 assertEquals(14, result[0]);
776 assertEquals(15, result[1]);
779 @Test(groups = "Functional")
780 public void testPropagateInsertions()
782 // create an alignment with no gaps - this will be the profile seq and other
784 AlignmentGenerator gen = new AlignmentGenerator(false);
785 AlignmentI al = gen.generate(25, 10, 1234, 0, 0);
787 // get the profileseq
788 SequenceI profileseq = al.getSequenceAt(0);
789 SequenceI gappedseq = new Sequence(profileseq);
790 gappedseq.insertCharAt(5, al.getGapCharacter());
791 gappedseq.insertCharAt(6, al.getGapCharacter());
792 gappedseq.insertCharAt(7, al.getGapCharacter());
793 gappedseq.insertCharAt(8, al.getGapCharacter());
795 // create an alignment view with the gapped sequence
796 SequenceI[] seqs = new SequenceI[1];
798 AlignmentI newal = new Alignment(seqs);
799 HiddenColumns hidden = new HiddenColumns();
800 hidden.hideColumns(15, 17);
802 AlignmentView view = new AlignmentView(newal, hidden, null, true, false,
805 // confirm that original contigs are as expected
806 Iterator<int[]> visible = hidden.getVisContigsIterator(0, 25);
807 int[] region = visible.next();
808 assertEquals("[0, 14]", Arrays.toString(region));
809 region = visible.next();
810 assertEquals("[18, 24]", Arrays.toString(region));
812 // propagate insertions
813 HiddenColumns result = HiddenColumns.propagateInsertions(profileseq, al,
816 // confirm that the contigs have changed to account for the gaps
817 visible = result.getVisContigsIterator(0, 25);
818 region = visible.next();
819 assertEquals("[0, 10]", Arrays.toString(region));
820 region = visible.next();
821 assertEquals("[14, 24]", Arrays.toString(region));
823 // confirm the alignment has been changed so that the other sequences have
824 // gaps inserted where the columns are hidden
825 assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[10]));
826 assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[11]));
827 assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[12]));
828 assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[13]));
829 assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[14]));
833 @Test(groups = "Functional")
834 public void testPropagateInsertionsOverlap()
836 // test propagateInsertions where gaps and hiddenColumns overlap
838 // create an alignment with no gaps - this will be the profile seq and other
840 AlignmentGenerator gen = new AlignmentGenerator(false);
841 AlignmentI al = gen.generate(20, 10, 1234, 0, 0);
843 // get the profileseq
844 SequenceI profileseq = al.getSequenceAt(0);
845 SequenceI gappedseq = new Sequence(profileseq);
846 gappedseq.insertCharAt(5, al.getGapCharacter());
847 gappedseq.insertCharAt(6, al.getGapCharacter());
848 gappedseq.insertCharAt(7, al.getGapCharacter());
849 gappedseq.insertCharAt(8, al.getGapCharacter());
851 // create an alignment view with the gapped sequence
852 SequenceI[] seqs = new SequenceI[1];
854 AlignmentI newal = new Alignment(seqs);
856 // hide columns so that some overlap with the gaps
857 HiddenColumns hidden = new HiddenColumns();
858 hidden.hideColumns(7, 10);
860 AlignmentView view = new AlignmentView(newal, hidden, null, true, false,
863 // confirm that original contigs are as expected
864 Iterator<int[]> visible = hidden.getVisContigsIterator(0, 20);
865 int[] region = visible.next();
866 assertEquals("[0, 6]", Arrays.toString(region));
867 region = visible.next();
868 assertEquals("[11, 19]", Arrays.toString(region));
869 assertFalse(visible.hasNext());
871 // propagate insertions
872 HiddenColumns result = HiddenColumns.propagateInsertions(profileseq, al,
875 // confirm that the contigs have changed to account for the gaps
876 visible = result.getVisContigsIterator(0, 20);
877 region = visible.next();
878 assertEquals("[0, 4]", Arrays.toString(region));
879 region = visible.next();
880 assertEquals("[7, 19]", Arrays.toString(region));
881 assertFalse(visible.hasNext());
883 // confirm the alignment has been changed so that the other sequences have
884 // gaps inserted where the columns are hidden
885 assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[4]));
886 assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[5]));
887 assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[6]));
888 assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[7]));
891 @Test(groups = "Functional")
892 public void testHasHiddenColumns()
894 HiddenColumns h = new HiddenColumns();
896 // new HiddenColumns2 has no hidden cols
897 assertFalse(h.hasHiddenColumns());
899 // some columns hidden, returns true
900 h.hideColumns(5, 10);
901 assertTrue(h.hasHiddenColumns());
903 // reveal columns, no hidden cols again
904 ColumnSelection sel = new ColumnSelection();
905 h.revealAllHiddenColumns(sel);
906 assertFalse(h.hasHiddenColumns());
909 @Test(groups = "Functional")
910 public void testHasManyHiddenColumns()
912 HiddenColumns h = new HiddenColumns();
914 // new HiddenColumns2 has no hidden cols
915 assertFalse(h.hasManyHiddenColumns());
917 // one set of columns hidden, returns false
918 h.hideColumns(5, 10);
919 assertFalse(h.hasManyHiddenColumns());
921 // two sets hidden, returns true
922 h.hideColumns(15, 17);
923 assertTrue(h.hasManyHiddenColumns());
925 // back to one block, asserts false
926 h.hideColumns(11, 14);
927 assertFalse(h.hasManyHiddenColumns());
930 @Test(groups = "Functional")
931 public void testAdjustForHiddenColumns()
933 HiddenColumns h = new HiddenColumns();
934 // returns input value when there are no hidden columns
935 assertEquals(10, h.adjustForHiddenColumns(10));
937 h.hideColumns(20, 30);
938 assertEquals(10, h.adjustForHiddenColumns(10));
939 assertEquals(20 + 11, h.adjustForHiddenColumns(20));
940 assertEquals(35 + 11, h.adjustForHiddenColumns(35));
943 assertEquals(10 + 3, h.adjustForHiddenColumns(10));
944 assertEquals(20 + 14, h.adjustForHiddenColumns(20));
945 assertEquals(35 + 14, h.adjustForHiddenColumns(35));
947 ColumnSelection sel = new ColumnSelection();
948 h.revealAllHiddenColumns(sel);
950 assertEquals(4, h.adjustForHiddenColumns(2));
953 @Test(groups = "Functional")
954 public void testGetHiddenBoundaryLeft()
956 HiddenColumns h = new HiddenColumns();
958 // returns same value if no hidden cols
959 assertEquals(3, h.getHiddenBoundaryLeft(3));
961 h.hideColumns(5, 10);
962 assertEquals(10, h.getHiddenBoundaryLeft(15));
963 assertEquals(3, h.getHiddenBoundaryLeft(3));
964 assertEquals(7, h.getHiddenBoundaryLeft(7));
966 h.hideColumns(15, 20);
967 assertEquals(10, h.getHiddenBoundaryLeft(15));
968 assertEquals(20, h.getHiddenBoundaryLeft(21));
971 @Test(groups = "Functional")
972 public void testGetHiddenBoundaryRight()
974 HiddenColumns h = new HiddenColumns();
976 // returns same value if no hidden cols
977 assertEquals(3, h.getHiddenBoundaryRight(3));
979 h.hideColumns(5, 10);
980 assertEquals(5, h.getHiddenBoundaryRight(3));
981 assertEquals(15, h.getHiddenBoundaryRight(15));
982 assertEquals(7, h.getHiddenBoundaryRight(7));
984 h.hideColumns(15, 20);
985 assertEquals(15, h.getHiddenBoundaryRight(7));
986 assertEquals(15, h.getHiddenBoundaryRight(14));
989 @Test(groups = "Functional")
990 public void testIterator()
992 HiddenColumns h = new HiddenColumns();
993 Iterator<int[]> result = h.iterator();
994 assertFalse(result.hasNext());
996 h.hideColumns(5, 10);
997 result = h.iterator();
998 int[] next = result.next();
999 assertEquals(5, next[0]);
1000 assertEquals(10, next[1]);
1001 assertFalse(result.hasNext());
1003 h.hideColumns(22, 23);
1004 result = h.iterator();
1005 next = result.next();
1006 assertEquals(5, next[0]);
1007 assertEquals(10, next[1]);
1008 next = result.next();
1009 assertEquals(22, next[0]);
1010 assertEquals(23, next[1]);
1011 assertFalse(result.hasNext());
1013 // test for only one hidden region at start of alignment
1014 ColumnSelection sel = new ColumnSelection();
1015 h.revealAllHiddenColumns(sel);
1016 h.hideColumns(0, 1);
1017 result = h.iterator();
1018 next = result.next();
1019 assertEquals(0, next[0]);
1020 assertEquals(1, next[1]);
1021 assertFalse(result.hasNext());
1024 @Test(groups = "Functional")
1025 public void testGetVisibleSequenceStrings()
1027 HiddenColumns h = new HiddenColumns();
1028 SequenceI seq1 = new Sequence("TEST1", "GALMFWKQESPVICYHRNDT");
1029 SequenceI seq2 = new Sequence("TEST2", "VICYHRNDTGA");
1030 SequenceI[] seqs = new SequenceI[2];
1033 String[] result = h.getVisibleSequenceStrings(5, 10, seqs);
1034 assertEquals(2, result.length);
1035 assertEquals("WKQES", result[0]);
1036 assertEquals("RNDTG", result[1]);
1038 h.hideColumns(6, 8);
1039 result = h.getVisibleSequenceStrings(5, 10, seqs);
1040 assertEquals(2, result.length);
1041 assertEquals("WS", result[0]);
1042 assertEquals("RG", result[1]);
1044 SequenceI seq = new Sequence("RefSeq", "-A-SD-ASD--E---");
1045 ColumnSelection sel = new ColumnSelection();
1046 h.revealAllHiddenColumns(sel);
1047 h.hideColumns(1, 3);
1048 h.hideColumns(6, 11);
1050 h.getVisibleSequenceStrings(0, 5, new SequenceI[]
1054 @Test(groups = "Functional")
1055 public void testHideInsertionsFor()
1057 HiddenColumns h = new HiddenColumns();
1058 HiddenColumns h2 = new HiddenColumns();
1059 SequenceI seq1 = new Sequence("TEST1", "GAL---MFW-KQESPVICY--HRNDT");
1060 SequenceI seq2 = new Sequence("TEST1", "GALMFWKQESPVICYHRNDT");
1062 h.hideInsertionsFor(seq2);
1063 assertTrue(h.equals(h2));
1065 h.hideInsertionsFor(seq1);
1066 h2.hideColumns(3, 5);
1067 h2.hideColumns(9, 9);
1068 h2.hideColumns(19, 20);
1069 assertTrue(h.equals(h2));
1072 @Test(groups = "Functional")
1073 public void testHideMarkedBits()
1075 HiddenColumns h = new HiddenColumns();
1076 HiddenColumns h2 = new HiddenColumns();
1078 BitSet tohide = new BitSet(21);
1079 h.hideMarkedBits(tohide);
1080 assertTrue(h.equals(h2));
1082 // NB in hideMarkedBits, the last bit is not set to hidden
1086 h.hideMarkedBits(tohide);
1088 h2.hideColumns(3, 5);
1089 h2.hideColumns(9, 9);
1090 h2.hideColumns(19, 20);
1091 assertTrue(h.equals(h2));
1094 @Test(groups = "Functional")
1095 public void testMakeVisibleAnnotation()
1097 HiddenColumns h = new HiddenColumns();
1098 Annotation[] anns = new Annotation[] { null, null, new Annotation(1),
1099 new Annotation(2), new Annotation(3), null, null, new Annotation(4),
1100 new Annotation(5), new Annotation(6), new Annotation(7),
1101 new Annotation(8) };
1102 AlignmentAnnotation ann = new AlignmentAnnotation("an", "some an",
1105 // without hidden cols, just truncates
1106 h.makeVisibleAnnotation(3, 5, ann);
1107 assertEquals(3, ann.annotations.length);
1108 assertEquals(2.0f, ann.annotations[0].value);
1109 assertEquals(3.0f, ann.annotations[1].value);
1110 assertNull(ann.annotations[2]);
1112 anns = new Annotation[] { null, null, new Annotation(1),
1113 new Annotation(2), new Annotation(3), null, null, new Annotation(4),
1114 new Annotation(5), new Annotation(6), new Annotation(7),
1115 new Annotation(8) };
1116 ann = new AlignmentAnnotation("an", "some an", anns);
1117 h.hideColumns(4, 7);
1118 h.makeVisibleAnnotation(1, 9, ann);
1119 assertEquals(5, ann.annotations.length);
1120 assertNull(ann.annotations[0]);
1121 assertEquals(1.0f, ann.annotations[1].value);
1122 assertEquals(2.0f, ann.annotations[2].value);
1123 assertEquals(5.0f, ann.annotations[3].value);
1124 assertEquals(6.0f, ann.annotations[4].value);
1126 anns = new Annotation[] { null, null, new Annotation(1),
1127 new Annotation(2), new Annotation(3), null, null, new Annotation(4),
1128 new Annotation(5), new Annotation(6), new Annotation(7),
1129 new Annotation(8) };
1130 ann = new AlignmentAnnotation("an", "some an", anns);
1131 h.hideColumns(1, 2);
1132 h.makeVisibleAnnotation(1, 9, ann);
1133 assertEquals(3, ann.annotations.length);
1134 assertEquals(2.0f, ann.annotations[0].value);
1135 assertEquals(5.0f, ann.annotations[1].value);
1136 assertEquals(6.0f, ann.annotations[2].value);
1139 @Test(groups = "Functional")
1140 public void testSubtractVisibleColumns()
1142 HiddenColumns h = new HiddenColumns();
1143 int result = h.subtractVisibleColumns(1, 10);
1144 assertEquals(9, result);
1146 h.hideColumns(7, 9);
1147 result = h.subtractVisibleColumns(4, 10);
1148 assertEquals(3, result);
1150 h.hideColumns(14, 15);
1151 result = h.subtractVisibleColumns(4, 10);
1152 assertEquals(3, result);
1154 result = h.subtractVisibleColumns(10, 17);
1155 assertEquals(2, result);
1157 result = h.subtractVisibleColumns(1, 7);
1158 assertEquals(5, result);
1160 result = h.subtractVisibleColumns(1, 8);
1161 assertEquals(5, result);
1163 result = h.subtractVisibleColumns(3, 15);
1164 assertEquals(10, result);
1166 ColumnSelection sel = new ColumnSelection();
1167 h.revealAllHiddenColumns(sel);
1168 h.hideColumns(0, 30);
1169 result = h.subtractVisibleColumns(31, 0);
1170 assertEquals(-31, result);
1172 HiddenColumns cs = new HiddenColumns();
1174 // test that without hidden columns, findColumnNToLeft returns
1175 // position n to left of provided position
1176 long pos = cs.subtractVisibleColumns(3, 10);
1177 assertEquals(7, pos);
1179 // 0 returns same position
1180 pos = cs.subtractVisibleColumns(0, 10);
1181 assertEquals(10, pos);
1183 // overflow to left returns negative number
1184 pos = cs.subtractVisibleColumns(3, 0);
1185 assertEquals(-3, pos);
1187 // test that with hidden columns to left of result column
1188 // behaviour is the same as above
1189 cs.hideColumns(1, 3);
1191 // position n to left of provided position
1192 pos = cs.subtractVisibleColumns(3, 10);
1193 assertEquals(7, pos);
1195 // 0 returns same position
1196 pos = cs.subtractVisibleColumns(0, 10);
1197 assertEquals(10, pos);
1199 // test with one set of hidden columns between start and required position
1200 cs.hideColumns(12, 15);
1201 pos = cs.subtractVisibleColumns(8, 17);
1202 assertEquals(5, pos);
1204 // test with two sets of hidden columns between start and required position
1205 cs.hideColumns(20, 21);
1206 pos = cs.subtractVisibleColumns(8, 23);
1207 assertEquals(9, pos);
1209 // repeat last 2 tests with no hidden columns to left of required position
1210 ColumnSelection colsel = new ColumnSelection();
1211 cs.revealAllHiddenColumns(colsel);
1213 // test with one set of hidden columns between start and required position
1214 cs.hideColumns(12, 15);
1215 pos = cs.subtractVisibleColumns(8, 17);
1216 assertEquals(5, pos);
1218 // test with two sets of hidden columns between start and required position
1219 cs.hideColumns(20, 21);
1220 pos = cs.subtractVisibleColumns(8, 23);
1221 assertEquals(9, pos);
1226 @Test(groups = "Functional")
1227 public void testBoundedIterator()
1229 HiddenColumns h = new HiddenColumns();
1230 Iterator<int[]> it = h.getBoundedIterator(0, 10);
1232 // no hidden columns = nothing to iterate over
1233 assertFalse(it.hasNext());
1235 // [start,end] contains all hidden columns
1236 // all regions are returned
1237 h.hideColumns(3, 10);
1238 h.hideColumns(14, 16);
1239 it = h.getBoundedIterator(0, 20);
1240 assertTrue(it.hasNext());
1241 int[] next = it.next();
1242 assertEquals(3, next[0]);
1243 assertEquals(10, next[1]);
1245 assertEquals(14, next[0]);
1246 assertEquals(16, next[1]);
1247 assertFalse(it.hasNext());
1249 // [start,end] overlaps a region
1250 // 1 region returned
1251 it = h.getBoundedIterator(5, 7);
1252 assertTrue(it.hasNext());
1254 assertEquals(3, next[0]);
1255 assertEquals(10, next[1]);
1256 assertFalse(it.hasNext());
1258 // [start,end] fully contains 1 region and start of last
1259 // - 2 regions returned
1260 it = h.getBoundedIterator(3, 15);
1261 assertTrue(it.hasNext());
1263 assertEquals(3, next[0]);
1264 assertEquals(10, next[1]);
1266 assertEquals(14, next[0]);
1267 assertEquals(16, next[1]);
1268 assertFalse(it.hasNext());
1270 // [start,end] contains end of first region and whole of last region
1271 // - 2 regions returned
1272 it = h.getBoundedIterator(4, 20);
1273 assertTrue(it.hasNext());
1275 assertEquals(3, next[0]);
1276 assertEquals(10, next[1]);
1278 assertEquals(14, next[0]);
1279 assertEquals(16, next[1]);
1280 assertFalse(it.hasNext());
1283 @Test(groups = "Functional")
1284 public void testBoundedStartIterator()
1286 HiddenColumns h = new HiddenColumns();
1287 Iterator<Integer> it = h.getBoundedStartIterator(0, 10);
1289 // no hidden columns = nothing to iterate over
1290 assertFalse(it.hasNext());
1292 // [start,end] contains all hidden columns
1293 // all regions are returned
1294 h.hideColumns(3, 10);
1295 h.hideColumns(14, 16);
1296 it = h.getBoundedStartIterator(0, 20);
1297 assertTrue(it.hasNext());
1298 int next = it.next();
1299 assertEquals(3, next);
1301 assertEquals(6, next);
1302 assertFalse(it.hasNext());
1304 // [start,end] does not contain a start of a region
1305 // no regions to iterate over
1306 it = h.getBoundedStartIterator(4, 5);
1307 assertFalse(it.hasNext());
1309 // [start,end] fully contains 1 region and start of last
1310 // - 2 regions returned
1311 it = h.getBoundedStartIterator(3, 7);
1312 assertTrue(it.hasNext());
1314 assertEquals(3, next);
1316 assertEquals(6, next);
1317 assertFalse(it.hasNext());
1319 // [start,end] contains whole of last region
1320 // - 1 region returned
1321 it = h.getBoundedStartIterator(4, 20);
1322 assertTrue(it.hasNext());
1324 assertEquals(6, next);
1325 assertFalse(it.hasNext());
1328 @Test(groups = "Functional")
1329 public void testVisibleBlocksVisBoundsIterator()
1331 HiddenColumns h = new HiddenColumns();
1332 Iterator<int[]> regions = h.getVisibleBlocksIterator(0, 30, true);
1334 // only 1 visible region spanning 0-30 if nothing is hidden
1335 assertTrue(regions.hasNext());
1336 int[] region = regions.next();
1337 assertEquals(0, region[0]);
1338 assertEquals(30, region[1]);
1339 assertFalse(regions.hasNext());
1341 // hide 1 region in middle
1342 // 2 regions one on either side
1343 // second region boundary accounts for hidden columns
1344 h.hideColumns(10, 15);
1345 regions = h.getVisibleBlocksIterator(0, 30, true);
1347 assertTrue(regions.hasNext());
1348 region = regions.next();
1349 assertEquals(0, region[0]);
1350 assertEquals(9, region[1]);
1351 region = regions.next();
1352 assertEquals(16, region[0]);
1353 assertEquals(36, region[1]);
1354 assertFalse(regions.hasNext());
1356 // single hidden region at left
1357 h = new HiddenColumns();
1358 h.hideColumns(0, 5);
1359 regions = h.getVisibleBlocksIterator(0, 30, true);
1361 assertTrue(regions.hasNext());
1362 region = regions.next();
1363 assertEquals(6, region[0]);
1364 assertEquals(36, region[1]);
1365 assertFalse(regions.hasNext());
1367 // single hidden region at right
1368 h = new HiddenColumns();
1369 h.hideColumns(27, 30);
1370 regions = h.getVisibleBlocksIterator(0, 30, true);
1372 assertTrue(regions.hasNext());
1373 region = regions.next();
1374 assertEquals(0, region[0]);
1375 assertEquals(26, region[1]);
1376 region = regions.next();
1377 assertEquals(31, region[0]);
1378 assertEquals(34, region[1]);
1379 assertFalse(regions.hasNext());
1381 // hidden region at left + hidden region in middle
1382 h = new HiddenColumns();
1383 h.hideColumns(0, 5);
1384 h.hideColumns(23, 25);
1385 regions = h.getVisibleBlocksIterator(0, 30, true);
1387 assertTrue(regions.hasNext());
1388 region = regions.next();
1389 assertEquals(6, region[0]);
1390 assertEquals(22, region[1]);
1391 region = regions.next();
1392 assertEquals(26, region[0]);
1393 assertEquals(39, region[1]);
1394 assertFalse(regions.hasNext());
1396 // hidden region at right + hidden region in middle
1397 h = new HiddenColumns();
1398 h.hideColumns(27, 30);
1399 h.hideColumns(11, 14);
1400 regions = h.getVisibleBlocksIterator(0, 30, true);
1402 assertTrue(regions.hasNext());
1403 region = regions.next();
1404 assertEquals(0, region[0]);
1405 assertEquals(10, region[1]);
1406 region = regions.next();
1407 assertEquals(15, region[0]);
1408 assertEquals(26, region[1]);
1409 region = regions.next();
1410 assertEquals(31, region[0]);
1411 assertEquals(38, region[1]);
1412 assertFalse(regions.hasNext());
1414 // hidden region at left and right
1415 h = new HiddenColumns();
1416 h.hideColumns(27, 35);
1417 h.hideColumns(0, 4);
1418 regions = h.getVisibleBlocksIterator(0, 30, true);
1420 assertTrue(regions.hasNext());
1421 region = regions.next();
1422 assertEquals(5, region[0]);
1423 assertEquals(26, region[1]);
1424 region = regions.next();
1425 assertEquals(36, region[0]);
1426 assertEquals(44, region[1]);
1427 assertFalse(regions.hasNext());
1429 // multiple hidden regions
1430 h = new HiddenColumns();
1431 h.hideColumns(1, 1);
1432 h.hideColumns(3, 5);
1433 h.hideColumns(9, 11);
1434 h.hideColumns(22, 26);
1436 regions = h.getVisibleBlocksIterator(0, 30, true);
1438 assertTrue(regions.hasNext());
1439 region = regions.next();
1440 assertEquals(0, region[0]);
1441 assertEquals(0, region[1]);
1442 region = regions.next();
1443 assertEquals(2, region[0]);
1444 assertEquals(2, region[1]);
1445 region = regions.next();
1446 assertEquals(6, region[0]);
1447 assertEquals(8, region[1]);
1448 region = regions.next();
1449 assertEquals(12, region[0]);
1450 assertEquals(21, region[1]);
1451 region = regions.next();
1452 assertEquals(27, region[0]);
1453 assertEquals(42, region[1]);
1454 assertFalse(regions.hasNext());