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.util.Comparison;
31 import java.util.Arrays;
32 import java.util.BitSet;
33 import java.util.Iterator;
34 import java.util.Random;
36 import org.testng.annotations.Test;
38 public class HiddenColumnsTest
41 * Test the method which counts the number of hidden columns
43 @Test(groups = { "Functional" })
44 public void testGetSize()
46 HiddenColumns hidden = new HiddenColumns();
47 assertEquals(0, hidden.getSize());
49 hidden.hideColumns(3, 5);
50 assertEquals(3, hidden.getSize());
52 hidden.hideColumns(8, 8);
53 assertEquals(4, hidden.getSize());
55 hidden.hideColumns(9, 14);
56 assertEquals(10, hidden.getSize());
58 ColumnSelection cs = new ColumnSelection();
59 hidden.revealAllHiddenColumns(cs);
60 assertEquals(0, hidden.getSize());
64 * Test the method that finds the visible column position of an alignment
65 * column, allowing for hidden columns.
67 @Test(groups = { "Functional" })
68 public void testFindColumnPosition()
70 HiddenColumns cs = new HiddenColumns();
71 assertEquals(5, cs.findColumnPosition(5));
73 // hiding column 6 makes no difference
75 assertEquals(5, cs.findColumnPosition(5));
77 // hiding column 4 moves column 5 to column 4
79 assertEquals(4, cs.findColumnPosition(5));
81 // hiding column 4 moves column 4 to position 3
82 assertEquals(3, cs.findColumnPosition(4));
84 // hiding columns 1 and 2 moves column 5 to column 2
86 assertEquals(2, cs.findColumnPosition(5));
88 // check with > 1 hidden column regions
89 // where some columns are in the hidden regions
90 HiddenColumns cs2 = new HiddenColumns();
91 cs2.hideColumns(5, 10);
92 cs2.hideColumns(20, 27);
93 cs2.hideColumns(40, 44);
95 // hiding columns 5-10 and 20-27 moves column 8 to column 4
96 assertEquals(4, cs2.findColumnPosition(8));
98 // and moves column 24 to 13
99 assertEquals(13, cs2.findColumnPosition(24));
101 // and moves column 28 to 14
102 assertEquals(14, cs2.findColumnPosition(28));
104 // and moves column 40 to 25
105 assertEquals(25, cs2.findColumnPosition(40));
107 // check when hidden columns start at 0 that the visible column
109 HiddenColumns cs3 = new HiddenColumns();
110 cs3.hideColumns(0, 4);
111 assertEquals(0, cs3.findColumnPosition(2));
113 // check that column after the last hidden region doesn't crash
114 assertEquals(46, cs2.findColumnPosition(65));
117 @Test(groups = { "Functional" })
118 public void testVisibleContigsIterator()
120 HiddenColumns cs = new HiddenColumns();
122 Iterator<int[]> visible = cs.getVisContigsIterator(3, 10);
123 int[] region = visible.next();
124 assertEquals("[3, 9]", Arrays.toString(region));
125 assertFalse(visible.hasNext());
127 cs.hideColumns(3, 6);
128 cs.hideColumns(8, 9);
129 cs.hideColumns(12, 12);
131 // Test both ends visible region
133 // start position is inclusive, end position exclusive
134 visible = cs.getVisContigsIterator(1, 13);
135 region = visible.next();
136 assertEquals("[1, 2]", Arrays.toString(region));
137 region = visible.next();
138 assertEquals("[7, 7]", Arrays.toString(region));
139 region = visible.next();
140 assertEquals("[10, 11]", Arrays.toString(region));
141 assertFalse(visible.hasNext());
143 // Test start hidden, end visible
144 visible = cs.getVisContigsIterator(4, 14);
145 region = visible.next();
146 assertEquals("[7, 7]", Arrays.toString(region));
147 region = visible.next();
148 assertEquals("[10, 11]", Arrays.toString(region));
149 region = visible.next();
150 assertEquals("[13, 13]", Arrays.toString(region));
151 assertFalse(visible.hasNext());
153 // Test start hidden, end hidden
154 visible = cs.getVisContigsIterator(3, 10);
155 region = visible.next();
156 assertEquals("[7, 7]", Arrays.toString(region));
157 assertFalse(visible.hasNext());
159 // Test start visible, end hidden
160 visible = cs.getVisContigsIterator(0, 13);
161 region = visible.next();
162 assertEquals("[0, 2]", Arrays.toString(region));
163 region = visible.next();
164 assertEquals("[7, 7]", Arrays.toString(region));
165 region = visible.next();
166 assertEquals("[10, 11]", Arrays.toString(region));
167 assertFalse(visible.hasNext());
170 visible = cs.getVisContigsIterator(4, 6);
171 assertFalse(visible.hasNext());
174 @Test(groups = { "Functional" })
175 public void testEquals()
177 HiddenColumns cs = new HiddenColumns();
178 cs.hideColumns(5, 9);
180 // a different set of hidden columns
181 HiddenColumns cs2 = new HiddenColumns();
183 // with no hidden columns
184 assertFalse(cs.equals(cs2));
185 assertFalse(cs2.equals(cs));
187 // with hidden columns added in a different order
188 cs2.hideColumns(6, 9);
189 cs2.hideColumns(5, 8);
191 assertTrue(cs.equals(cs2));
192 assertTrue(cs.equals(cs));
193 assertTrue(cs2.equals(cs));
194 assertTrue(cs2.equals(cs2));
197 @Test(groups = "Functional")
198 public void testCopyConstructor()
200 HiddenColumns cs = new HiddenColumns();
201 cs.hideColumns(10, 11);
202 cs.hideColumns(5, 7);
203 Iterator<int[]> regions = cs.iterator();
204 assertEquals("[5, 7]",
205 Arrays.toString(regions.next()));
207 HiddenColumns cs2 = new HiddenColumns(cs);
208 regions = cs2.iterator();
209 assertTrue(cs2.hasHiddenColumns());
210 assertEquals(2, cs2.getNumberOfRegions());
211 // hidden columns are held in column order
212 assertEquals("[5, 7]",
213 Arrays.toString(regions.next()));
214 assertEquals("[10, 11]",
215 Arrays.toString(regions.next()));
218 @Test(groups = "Functional")
219 public void testCopyConstructor2()
221 HiddenColumns cs = new HiddenColumns();
222 cs.hideColumns(10, 11);
223 cs.hideColumns(5, 7);
225 HiddenColumns cs2 = new HiddenColumns(cs, 3, 9, 1);
226 assertTrue(cs2.hasHiddenColumns());
227 Iterator<int[]> regions = cs2.iterator();
229 // only [5,7] returned, offset by 1
230 assertEquals("[4, 6]",
231 Arrays.toString(regions.next()));
232 assertEquals(3, cs2.getSize());
234 cs2 = new HiddenColumns(cs, 8, 15, 4);
235 regions = cs2.iterator();
236 assertTrue(cs2.hasHiddenColumns());
238 // only [10,11] returned, offset by 4
239 assertEquals("[6, 7]",
240 Arrays.toString(regions.next()));
241 assertEquals(2, cs2.getSize());
243 cs2 = new HiddenColumns(cs, 6, 10, 4);
244 assertFalse(cs2.hasHiddenColumns());
248 * Test the code used to locate the reference sequence ruler origin
250 @Test(groups = { "Functional" })
251 public void testLocateVisibleBoundsofSequence()
253 // create random alignment
254 AlignmentGenerator gen = new AlignmentGenerator(false);
255 AlignmentI al = gen.generate(50, 20, 123, 5, 5);
257 HiddenColumns cs = al.getHiddenColumns();
258 ColumnSelection colsel = new ColumnSelection();
260 SequenceI seq = new Sequence("RefSeq", "-A-SD-ASD--E---");
261 assertEquals(2, seq.findIndex(seq.getStart()));
264 assertEquals(seq.findIndex(seq.getStart()) - 1, cs.locateVisibleStartOfSequence(seq));
266 // hidden column on gap after end of sequence - should not affect bounds
267 colsel.hideSelectedColumns(13, al.getHiddenColumns());
268 assertEquals(seq.findIndex(seq.getStart()) - 1,cs.locateVisibleStartOfSequence(seq));
270 cs.revealAllHiddenColumns(colsel);
271 // hidden column on gap before beginning of sequence - should vis bounds by
273 colsel.hideSelectedColumns(0, al.getHiddenColumns());
274 assertEquals(seq.findIndex(seq.getStart()) - 2,cs.locateVisibleStartOfSequence(seq));
276 cs.revealAllHiddenColumns(colsel);
277 // hide columns around most of sequence - leave one residue remaining
278 cs.hideColumns(1, 3);
279 cs.hideColumns(6, 11);
281 cs.getVisibleSequenceStrings(0, 5, new SequenceI[]
284 assertEquals(1, cs.locateVisibleStartOfSequence(seq));
285 cs.revealAllHiddenColumns(colsel);
287 // hide whole sequence - should just get location of hidden region
288 // containing sequence
289 cs.hideColumns(1, 11);
290 assertEquals(0,cs.locateVisibleStartOfSequence(seq));
292 cs.revealAllHiddenColumns(colsel);
293 cs.hideColumns(0, 15);
294 assertEquals(0,cs.locateVisibleStartOfSequence(seq));
296 SequenceI seq2 = new Sequence("RefSeq2", "-------A-SD-ASD--E---");
298 cs.revealAllHiddenColumns(colsel);
299 cs.hideColumns(7, 17);
300 assertEquals(0,cs.locateVisibleStartOfSequence(seq2));
302 cs.revealAllHiddenColumns(colsel);
303 cs.hideColumns(3, 17);
304 assertEquals(0,cs.locateVisibleStartOfSequence(seq2));
306 cs.revealAllHiddenColumns(colsel);
307 cs.hideColumns(3, 19);
308 assertEquals(0,cs.locateVisibleStartOfSequence(seq2));
310 cs.revealAllHiddenColumns(colsel);
311 cs.hideColumns(0, 0);
312 assertEquals(0,cs.locateVisibleStartOfSequence(seq));
314 cs.revealAllHiddenColumns(colsel);
315 cs.hideColumns(0, 1);
316 assertEquals(1,cs.locateVisibleStartOfSequence(seq));
318 cs.revealAllHiddenColumns(colsel);
319 cs.hideColumns(0, 2);
320 assertEquals(0,cs.locateVisibleStartOfSequence(seq));
322 cs.revealAllHiddenColumns(colsel);
323 cs.hideColumns(1, 1);
324 assertEquals(2,cs.locateVisibleStartOfSequence(seq));
326 cs.revealAllHiddenColumns(colsel);
327 cs.hideColumns(1, 2);
328 assertEquals(1,cs.locateVisibleStartOfSequence(seq));
330 cs.revealAllHiddenColumns(colsel);
331 cs.hideColumns(1, 3);
332 assertEquals(1,cs.locateVisibleStartOfSequence(seq));
334 cs.revealAllHiddenColumns(colsel);
335 cs.hideColumns(0, 2);
336 cs.hideColumns(5, 6);
337 assertEquals(0,cs.locateVisibleStartOfSequence(seq));
339 cs.revealAllHiddenColumns(colsel);
340 cs.hideColumns(0, 2);
341 cs.hideColumns(5, 6);
342 cs.hideColumns(9, 10);
343 assertEquals(0,cs.locateVisibleStartOfSequence(seq));
345 cs.revealAllHiddenColumns(colsel);
346 cs.hideColumns(0, 2);
347 cs.hideColumns(7, 11);
348 assertEquals(0,cs.locateVisibleStartOfSequence(seq));
350 cs.revealAllHiddenColumns(colsel);
351 cs.hideColumns(2, 4);
352 cs.hideColumns(7, 11);
353 assertEquals(1,cs.locateVisibleStartOfSequence(seq));
355 cs.revealAllHiddenColumns(colsel);
356 cs.hideColumns(2, 4);
357 cs.hideColumns(7, 12);
358 assertEquals(1,cs.locateVisibleStartOfSequence(seq));
360 cs.revealAllHiddenColumns(colsel);
361 cs.hideColumns(1, 11);
362 assertEquals(0,cs.locateVisibleStartOfSequence(seq));
364 cs.revealAllHiddenColumns(colsel);
365 cs.hideColumns(0, 12);
366 assertEquals(0,cs.locateVisibleStartOfSequence(seq));
368 cs.revealAllHiddenColumns(colsel);
369 cs.hideColumns(0, 4);
370 cs.hideColumns(6, 12);
371 assertEquals(0,cs.locateVisibleStartOfSequence(seq));
373 cs.revealAllHiddenColumns(colsel);
374 cs.hideColumns(0, 1);
375 cs.hideColumns(3, 12);
376 assertEquals(0,cs.locateVisibleStartOfSequence(seq));
378 cs.revealAllHiddenColumns(colsel);
379 cs.hideColumns(3, 14);
380 cs.hideColumns(17, 19);
381 assertEquals(3,cs.locateVisibleStartOfSequence(seq2));
383 cs.revealAllHiddenColumns(colsel);
384 cs.hideColumns(3, 7);
385 cs.hideColumns(9, 14);
386 cs.hideColumns(17, 19);
387 assertEquals(9,cs.locateVisibleStartOfSequence(seq2));
389 cs.revealAllHiddenColumns(colsel);
390 cs.hideColumns(0, 1);
391 cs.hideColumns(3, 4);
392 cs.hideColumns(6, 8);
393 cs.hideColumns(10, 12);
394 assertEquals(6, cs.locateVisibleStartOfSequence(seq));
398 @Test(groups = { "Functional" })
399 public void testLocateVisibleBoundsPathologicals()
401 // test some pathological cases we missed
402 AlignmentI al = new Alignment(
404 { new Sequence("refseqGaptest", "KTDVTI----------NFI-----G----L") });
405 HiddenColumns cs = new HiddenColumns();
406 cs.hideInsertionsFor(al.getSequenceAt(0));
408 + al.getSequenceAt(0).getCharAt(cs.adjustForHiddenColumns(9)));
411 @Test(groups = { "Functional" })
412 public void testHideColumns()
414 // create random alignment
415 AlignmentGenerator gen = new AlignmentGenerator(false);
416 AlignmentI al = gen.generate(50, 20, 123, 5, 5);
418 ColumnSelection colsel = new ColumnSelection();
419 HiddenColumns cs = al.getHiddenColumns();
420 colsel.hideSelectedColumns(5, al.getHiddenColumns());
421 Iterator<int[]> regions = cs.iterator();
422 assertEquals(1, cs.getNumberOfRegions());
423 assertEquals("[5, 5]", Arrays.toString(regions.next()));
425 colsel.hideSelectedColumns(3, al.getHiddenColumns());
426 regions = cs.iterator();
427 assertEquals(2, cs.getNumberOfRegions());
428 // two hidden ranges, in order:
429 assertEquals("[3, 3]", Arrays.toString(regions.next()));
430 assertEquals("[5, 5]", Arrays.toString(regions.next()));
432 // hiding column 4 expands [3, 3] to [3, 4]
433 // and merges to [5, 5] to make [3, 5]
434 colsel.hideSelectedColumns(4, al.getHiddenColumns());
435 regions = cs.iterator();
436 assertEquals(1, cs.getNumberOfRegions());
437 assertEquals("[3, 5]", Arrays.toString(regions.next()));
439 // clear hidden columns (note they are added to selected)
440 cs.revealAllHiddenColumns(colsel);
441 // it is now actually null but getter returns an empty list
442 assertEquals(0, cs.getNumberOfRegions());
444 cs.hideColumns(3, 6);
445 regions = cs.iterator();
446 int[] firstHiddenRange = regions.next();
447 assertEquals("[3, 6]", Arrays.toString(firstHiddenRange));
449 // adding a subrange of already hidden should do nothing
450 cs.hideColumns(4, 5);
451 regions = cs.iterator();
452 assertEquals(1, cs.getNumberOfRegions());
453 assertEquals("[3, 6]",
454 Arrays.toString(regions.next()));
455 cs.hideColumns(3, 5);
456 regions = cs.iterator();
457 assertEquals(1, cs.getNumberOfRegions());
458 assertEquals("[3, 6]",
459 Arrays.toString(regions.next()));
460 cs.hideColumns(4, 6);
461 regions = cs.iterator();
462 assertEquals(1, cs.getNumberOfRegions());
463 assertEquals("[3, 6]",
464 Arrays.toString(regions.next()));
465 cs.hideColumns(3, 6);
466 regions = cs.iterator();
467 assertEquals(1, cs.getNumberOfRegions());
468 assertEquals("[3, 6]",
469 Arrays.toString(regions.next()));
471 cs.revealAllHiddenColumns(colsel);
472 cs.hideColumns(2, 4);
473 regions = cs.iterator();
474 assertEquals(1, cs.getNumberOfRegions());
475 assertEquals("[2, 4]", Arrays.toString(regions.next()));
477 // extend contiguous with 2 positions overlap
478 cs.hideColumns(3, 5);
479 regions = cs.iterator();
480 assertEquals(1, cs.getNumberOfRegions());
481 assertEquals("[2, 5]", Arrays.toString(regions.next()));
483 // extend contiguous with 1 position overlap
484 cs.hideColumns(5, 6);
485 regions = cs.iterator();
486 assertEquals(1, cs.getNumberOfRegions());
487 assertEquals("[2, 6]", Arrays.toString(regions.next()));
489 // extend contiguous with overlap both ends:
490 cs.hideColumns(1, 7);
491 regions = cs.iterator();
492 assertEquals(1, cs.getNumberOfRegions());
493 assertEquals("[1, 7]", Arrays.toString(regions.next()));
497 * Test the method that reveals a range of hidden columns given the start
498 * column of the range
500 @Test(groups = { "Functional" })
501 public void testRevealHiddenColumns()
503 ColumnSelection colsel = new ColumnSelection();
504 HiddenColumns cs = new HiddenColumns();
505 cs.hideColumns(5, 8);
506 colsel.addElement(10);
507 cs.revealHiddenColumns(5, colsel);
509 // hiddenColumns now empty
510 assertEquals(0, cs.getSize());
512 // revealed columns are marked as selected (added to selection):
513 assertEquals("[10, 5, 6, 7, 8]", colsel.getSelected().toString());
515 // calling with a column other than the range start does nothing:
516 colsel = new ColumnSelection();
517 cs = new HiddenColumns();
518 cs.hideColumns(5, 8);
520 int prevSize = cs.getSize();
521 cs.revealHiddenColumns(6, colsel);
522 assertEquals(prevSize, cs.getSize());
523 assertTrue(colsel.getSelected().isEmpty());
526 @Test(groups = { "Functional" })
527 public void testRevealAllHiddenColumns()
529 HiddenColumns hidden = new HiddenColumns();
530 ColumnSelection colsel = new ColumnSelection();
531 hidden.hideColumns(5, 8);
532 hidden.hideColumns(2, 3);
533 colsel.addElement(11);
534 colsel.addElement(1);
535 hidden.revealAllHiddenColumns(colsel);
538 * revealing hidden columns adds them (in order) to the (unordered)
542 // hiddenColumns now empty
543 assertEquals(0, hidden.getSize());
545 assertEquals("[11, 1, 2, 3, 5, 6, 7, 8]",
546 colsel.getSelected().toString());
549 @Test(groups = { "Functional" })
550 public void testIsVisible()
552 HiddenColumns cs = new HiddenColumns();
553 cs.hideColumns(2, 4);
554 cs.hideColumns(6, 7);
555 assertTrue(cs.isVisible(0));
556 assertTrue(cs.isVisible(-99));
557 assertTrue(cs.isVisible(1));
558 assertFalse(cs.isVisible(2));
559 assertFalse(cs.isVisible(3));
560 assertFalse(cs.isVisible(4));
561 assertTrue(cs.isVisible(5));
562 assertFalse(cs.isVisible(6));
563 assertFalse(cs.isVisible(7));
567 * Test for the case when a hidden range encloses more one already hidden
570 @Test(groups = { "Functional" })
571 public void testHideColumns_subsumingHidden()
574 * JAL-2370 bug scenario:
575 * two hidden ranges subsumed by a third
577 HiddenColumns cs = new HiddenColumns();
578 cs.hideColumns(49, 59);
579 cs.hideColumns(69, 79);
580 Iterator<int[]> regions = cs.iterator();
581 assertEquals(2, cs.getNumberOfRegions());
582 assertEquals("[49, 59]", Arrays.toString(regions.next()));
583 assertEquals("[69, 79]", Arrays.toString(regions.next()));
585 cs.hideColumns(48, 80);
586 regions = cs.iterator();
587 assertEquals(1, cs.getNumberOfRegions());
588 assertEquals("[48, 80]", Arrays.toString(regions.next()));
591 * another...joining hidden ranges
593 cs = new HiddenColumns();
594 cs.hideColumns(10, 20);
595 cs.hideColumns(30, 40);
596 cs.hideColumns(50, 60);
597 // hiding 21-49 should merge to one range
598 cs.hideColumns(21, 49);
599 regions = cs.iterator();
600 assertEquals(1, cs.getNumberOfRegions());
601 assertEquals("[10, 60]", Arrays.toString(regions.next()));
604 * another...left overlap, subsumption, right overlap,
605 * no overlap of existing hidden ranges
607 cs = new HiddenColumns();
608 cs.hideColumns(10, 20);
609 cs.hideColumns(10, 20);
610 cs.hideColumns(30, 35);
611 cs.hideColumns(40, 50);
612 cs.hideColumns(60, 70);
614 cs.hideColumns(15, 45);
615 regions = cs.iterator();
616 assertEquals(2, cs.getNumberOfRegions());
617 assertEquals("[10, 50]", Arrays.toString(regions.next()));
618 assertEquals("[60, 70]", Arrays.toString(regions.next()));
621 @Test(groups = { "Functional" })
622 public void testHideBitset()
626 BitSet one = new BitSet();
630 cs = new HiddenColumns();
631 cs.hideMarkedBits(one);
632 assertEquals(1, cs.getNumberOfRegions());
635 cs = new HiddenColumns();
636 cs.hideMarkedBits(one);
637 assertEquals(1, cs.getNumberOfRegions());
640 cs = new HiddenColumns();
641 cs.hideMarkedBits(one);
642 assertEquals(1, cs.getNumberOfRegions());
646 cs = new HiddenColumns();
647 cs.hideMarkedBits(one);
648 assertEquals(2, cs.getNumberOfRegions());
650 assertEquals(0, cs.adjustForHiddenColumns(0));
651 assertEquals(2, cs.adjustForHiddenColumns(1));
652 assertEquals(4, cs.adjustForHiddenColumns(2));
656 cs = new HiddenColumns();
657 cs.hideMarkedBits(one);
659 assertEquals(1, cs.getNumberOfRegions());
661 assertEquals(0, cs.adjustForHiddenColumns(0));
662 assertEquals(1, cs.adjustForHiddenColumns(1));
663 assertEquals(2, cs.adjustForHiddenColumns(2));
664 assertEquals(4, cs.adjustForHiddenColumns(3));
667 @Test(groups = { "Functional" })
668 public void testMarkHiddenRegions()
670 BitSet toMark, fromMark;
671 long seed = -3241532;
672 Random number = new Random(seed);
673 for (int n = 0; n < 1000; n++)
675 // create a random bitfield
678 { number.nextLong(), number.nextLong(), number.nextLong() });
679 toMark.set(n * number.nextInt(10), n * (25 + number.nextInt(25)));
680 HiddenColumns hc = new HiddenColumns();
681 hc.hideMarkedBits(toMark);
683 // see if we can recover bitfield
684 hc.markHiddenRegions(fromMark = new BitSet());
685 assertEquals(toMark, fromMark);
689 @Test(groups = { "Functional" })
690 public void testRegionsToString()
692 HiddenColumns hc = new HiddenColumns();
694 String result = hc.regionsToString(",", "--");
695 assertEquals("", result);
697 hc.hideColumns(3, 7);
698 hc.hideColumns(10, 10);
699 hc.hideColumns(14, 15);
701 result = hc.regionsToString(",", "--");
702 assertEquals("3--7,10--10,14--15", result);
705 @Test(groups = "Functional")
706 public void testGetVisibleStartAndEndIndexTest()
708 Sequence seq = new Sequence("testSeq", "ABCDEFGHIJKLMNOPQRSTUVWXYZ");
709 AlignmentI align = new Alignment(new SequenceI[] { seq });
710 HiddenColumns hc = new HiddenColumns();
712 int[] startEnd = hc.getVisibleStartAndEndIndex(align.getWidth());
713 assertEquals(0, startEnd[0]);
714 assertEquals(25, startEnd[1]);
716 hc.hideColumns(0, 0);
717 startEnd = hc.getVisibleStartAndEndIndex(align.getWidth());
718 assertEquals(1, startEnd[0]);
719 assertEquals(25, startEnd[1]);
721 hc.hideColumns(6, 9);
722 hc.hideColumns(11, 12);
723 startEnd = hc.getVisibleStartAndEndIndex(align.getWidth());
724 assertEquals(1, startEnd[0]);
725 assertEquals(25, startEnd[1]);
727 hc.hideColumns(24, 25);
728 startEnd = hc.getVisibleStartAndEndIndex(align.getWidth());
729 System.out.println(startEnd[0] + " : " + startEnd[1]);
730 assertEquals(1, startEnd[0]);
731 assertEquals(23, startEnd[1]);
734 @Test(groups = "Functional")
735 public void testGetRegionWithEdgeAtRes()
737 HiddenColumns hc = new HiddenColumns();
739 int[] result = hc.getRegionWithEdgeAtRes(5);
742 hc.hideColumns(3, 7);
743 hc.hideColumns(10, 10);
744 hc.hideColumns(14, 15);
746 result = hc.getRegionWithEdgeAtRes(2);
747 assertEquals(3, result[0]);
748 assertEquals(7, result[1]);
750 result = hc.getRegionWithEdgeAtRes(5);
751 assertEquals(10, result[0]);
752 assertEquals(10, result[1]);
754 result = hc.getRegionWithEdgeAtRes(6);
757 result = hc.getRegionWithEdgeAtRes(0);
760 result = hc.getRegionWithEdgeAtRes(7);
761 assertEquals(14, result[0]);
762 assertEquals(15, result[1]);
764 result = hc.getRegionWithEdgeAtRes(8);
765 assertEquals(14, result[0]);
766 assertEquals(15, result[1]);
768 result = hc.getRegionWithEdgeAtRes(16);
772 @Test(groups = "Functional")
773 public void testPropagateInsertions()
775 // create an alignment with no gaps - this will be the profile seq and other
777 AlignmentGenerator gen = new AlignmentGenerator(false);
778 AlignmentI al = gen.generate(25, 10, 1234, 0, 0);
780 // get the profileseq
781 SequenceI profileseq = al.getSequenceAt(0);
782 SequenceI gappedseq = new Sequence(profileseq);
783 gappedseq.insertCharAt(5, al.getGapCharacter());
784 gappedseq.insertCharAt(6, al.getGapCharacter());
785 gappedseq.insertCharAt(7, al.getGapCharacter());
786 gappedseq.insertCharAt(8, al.getGapCharacter());
788 // create an alignment view with the gapped sequence
789 SequenceI[] seqs = new SequenceI[1];
791 AlignmentI newal = new Alignment(seqs);
792 HiddenColumns hidden = new HiddenColumns();
793 hidden.hideColumns(15, 17);
795 AlignmentView view = new AlignmentView(newal, hidden, null, true, false,
798 // confirm that original contigs are as expected
799 Iterator<int[]> visible = hidden.getVisContigsIterator(0, 25);
800 int[] region = visible.next();
801 assertEquals("[0, 14]", Arrays.toString(region));
802 region = visible.next();
803 assertEquals("[18, 24]", Arrays.toString(region));
805 // propagate insertions
806 HiddenColumns result = HiddenColumns.propagateInsertions(profileseq, al,
809 // confirm that the contigs have changed to account for the gaps
810 visible = result.getVisContigsIterator(0, 25);
811 region = visible.next();
812 assertEquals("[0, 10]", Arrays.toString(region));
813 region = visible.next();
814 assertEquals("[14, 24]", Arrays.toString(region));
816 // confirm the alignment has been changed so that the other sequences have
817 // gaps inserted where the columns are hidden
818 assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[10]));
819 assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[11]));
820 assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[12]));
821 assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[13]));
822 assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[14]));
826 @Test(groups = "Functional")
827 public void testPropagateInsertionsOverlap()
829 // test propagateInsertions where gaps and hiddenColumns overlap
831 // create an alignment with no gaps - this will be the profile seq and other
833 AlignmentGenerator gen = new AlignmentGenerator(false);
834 AlignmentI al = gen.generate(20, 10, 1234, 0, 0);
836 // get the profileseq
837 SequenceI profileseq = al.getSequenceAt(0);
838 SequenceI gappedseq = new Sequence(profileseq);
839 gappedseq.insertCharAt(5, al.getGapCharacter());
840 gappedseq.insertCharAt(6, al.getGapCharacter());
841 gappedseq.insertCharAt(7, al.getGapCharacter());
842 gappedseq.insertCharAt(8, al.getGapCharacter());
844 // create an alignment view with the gapped sequence
845 SequenceI[] seqs = new SequenceI[1];
847 AlignmentI newal = new Alignment(seqs);
849 // hide columns so that some overlap with the gaps
850 HiddenColumns hidden = new HiddenColumns();
851 hidden.hideColumns(7, 10);
853 AlignmentView view = new AlignmentView(newal, hidden, null, true, false,
856 // confirm that original contigs are as expected
857 Iterator<int[]> visible = hidden.getVisContigsIterator(0, 20);
858 int[] region = visible.next();
859 assertEquals("[0, 6]", Arrays.toString(region));
860 region = visible.next();
861 assertEquals("[11, 19]", Arrays.toString(region));
862 assertFalse(visible.hasNext());
864 // propagate insertions
865 HiddenColumns result = HiddenColumns.propagateInsertions(profileseq, al,
868 // confirm that the contigs have changed to account for the gaps
869 visible = result.getVisContigsIterator(0, 20);
870 region = visible.next();
871 assertEquals("[0, 4]", Arrays.toString(region));
872 region = visible.next();
873 assertEquals("[7, 19]", Arrays.toString(region));
874 assertFalse(visible.hasNext());
876 // confirm the alignment has been changed so that the other sequences have
877 // gaps inserted where the columns are hidden
878 assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[4]));
879 assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[5]));
880 assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[6]));
881 assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[7]));
884 @Test(groups = "Functional")
885 public void testHasHiddenColumns()
887 HiddenColumns h = new HiddenColumns();
889 // new HiddenColumns2 has no hidden cols
890 assertFalse(h.hasHiddenColumns());
892 // some columns hidden, returns true
893 h.hideColumns(5, 10);
894 assertTrue(h.hasHiddenColumns());
896 // reveal columns, no hidden cols again
897 ColumnSelection sel = new ColumnSelection();
898 h.revealAllHiddenColumns(sel);
899 assertFalse(h.hasHiddenColumns());
902 @Test(groups = "Functional")
903 public void testHasManyHiddenColumns()
905 HiddenColumns h = new HiddenColumns();
907 // new HiddenColumns2 has no hidden cols
908 assertFalse(h.hasManyHiddenColumns());
910 // one set of columns hidden, returns false
911 h.hideColumns(5, 10);
912 assertFalse(h.hasManyHiddenColumns());
914 // two sets hidden, returns true
915 h.hideColumns(15, 17);
916 assertTrue(h.hasManyHiddenColumns());
918 // back to one block, asserts false
919 h.hideColumns(11, 14);
920 assertFalse(h.hasManyHiddenColumns());
923 @Test(groups = "Functional")
924 public void testAdjustForHiddenColumns()
926 HiddenColumns h = new HiddenColumns();
927 // returns input value when there are no hidden columns
928 assertEquals(10, h.adjustForHiddenColumns(10));
930 h.hideColumns(20, 30);
931 assertEquals(10, h.adjustForHiddenColumns(10));
932 assertEquals(20 + 11, h.adjustForHiddenColumns(20));
933 assertEquals(35 + 11, h.adjustForHiddenColumns(35));
936 assertEquals(10 + 3, h.adjustForHiddenColumns(10));
937 assertEquals(20 + 14, h.adjustForHiddenColumns(20));
938 assertEquals(35 + 14, h.adjustForHiddenColumns(35));
940 ColumnSelection sel = new ColumnSelection();
941 h.revealAllHiddenColumns(sel);
943 assertEquals(4, h.adjustForHiddenColumns(2));
946 @Test(groups = "Functional")
947 public void testGetHiddenBoundaryLeft()
949 HiddenColumns h = new HiddenColumns();
951 // returns same value if no hidden cols
952 assertEquals(3, h.getHiddenBoundaryLeft(3));
954 h.hideColumns(5, 10);
955 assertEquals(10, h.getHiddenBoundaryLeft(15));
956 assertEquals(3, h.getHiddenBoundaryLeft(3));
957 assertEquals(7, h.getHiddenBoundaryLeft(7));
959 h.hideColumns(15, 20);
960 assertEquals(10, h.getHiddenBoundaryLeft(15));
961 assertEquals(20, h.getHiddenBoundaryLeft(21));
964 @Test(groups = "Functional")
965 public void testGetHiddenBoundaryRight()
967 HiddenColumns h = new HiddenColumns();
969 // returns same value if no hidden cols
970 assertEquals(3, h.getHiddenBoundaryRight(3));
972 h.hideColumns(5, 10);
973 assertEquals(5, h.getHiddenBoundaryRight(3));
974 assertEquals(15, h.getHiddenBoundaryRight(15));
975 assertEquals(7, h.getHiddenBoundaryRight(7));
977 h.hideColumns(15, 20);
978 assertEquals(15, h.getHiddenBoundaryRight(7));
979 assertEquals(15, h.getHiddenBoundaryRight(14));
982 @Test(groups = "Functional")
983 public void testIterator()
985 HiddenColumns h = new HiddenColumns();
986 Iterator<int[]> result = h.iterator();
987 assertFalse(result.hasNext());
989 h.hideColumns(5, 10);
990 result = h.iterator();
991 int[] next = result.next();
992 assertEquals(5, next[0]);
993 assertEquals(10, next[1]);
994 assertFalse(result.hasNext());
996 h.hideColumns(22, 23);
997 result = h.iterator();
998 next = result.next();
999 assertEquals(5, next[0]);
1000 assertEquals(10, next[1]);
1001 next = result.next();
1002 assertEquals(22, next[0]);
1003 assertEquals(23, next[1]);
1004 assertFalse(result.hasNext());
1006 // test for only one hidden region at start of alignment
1007 ColumnSelection sel = new ColumnSelection();
1008 h.revealAllHiddenColumns(sel);
1009 h.hideColumns(0, 1);
1010 result = h.iterator();
1011 next = result.next();
1012 assertEquals(0, next[0]);
1013 assertEquals(1, next[1]);
1014 assertFalse(result.hasNext());
1017 @Test(groups = "Functional")
1018 public void testGetVisibleSequenceStrings()
1020 HiddenColumns h = new HiddenColumns();
1021 SequenceI seq1 = new Sequence("TEST1", "GALMFWKQESPVICYHRNDT");
1022 SequenceI seq2 = new Sequence("TEST2", "VICYHRNDTGA");
1023 SequenceI[] seqs = new SequenceI[2];
1026 String[] result = h.getVisibleSequenceStrings(5, 10, seqs);
1027 assertEquals(2, result.length);
1028 assertEquals("WKQES", result[0]);
1029 assertEquals("RNDTG", result[1]);
1031 h.hideColumns(6, 8);
1032 result = h.getVisibleSequenceStrings(5, 10, seqs);
1033 assertEquals(2, result.length);
1034 assertEquals("WS", result[0]);
1035 assertEquals("RG", result[1]);
1037 SequenceI seq = new Sequence("RefSeq", "-A-SD-ASD--E---");
1038 ColumnSelection sel = new ColumnSelection();
1039 h.revealAllHiddenColumns(sel);
1040 h.hideColumns(1, 3);
1041 h.hideColumns(6, 11);
1043 h.getVisibleSequenceStrings(0, 5, new SequenceI[]
1047 @Test(groups = "Functional")
1048 public void testHideInsertionsFor()
1050 HiddenColumns h = new HiddenColumns();
1051 HiddenColumns h2 = new HiddenColumns();
1052 SequenceI seq1 = new Sequence("TEST1", "GAL---MFW-KQESPVICY--HRNDT");
1053 SequenceI seq2 = new Sequence("TEST1", "GALMFWKQESPVICYHRNDT");
1055 h.hideInsertionsFor(seq2);
1056 assertTrue(h.equals(h2));
1058 h.hideInsertionsFor(seq1);
1059 h2.hideColumns(3, 5);
1060 h2.hideColumns(9, 9);
1061 h2.hideColumns(19, 20);
1062 assertTrue(h.equals(h2));
1065 @Test(groups = "Functional")
1066 public void testHideMarkedBits()
1068 HiddenColumns h = new HiddenColumns();
1069 HiddenColumns h2 = new HiddenColumns();
1071 BitSet tohide = new BitSet(21);
1072 h.hideMarkedBits(tohide);
1073 assertTrue(h.equals(h2));
1075 // NB in hideMarkedBits, the last bit is not set to hidden
1079 h.hideMarkedBits(tohide);
1081 h2.hideColumns(3, 5);
1082 h2.hideColumns(9, 9);
1083 h2.hideColumns(19, 20);
1084 assertTrue(h.equals(h2));
1087 @Test(groups = "Functional")
1088 public void testMakeVisibleAnnotation()
1090 HiddenColumns h = new HiddenColumns();
1091 Annotation[] anns = new Annotation[] { null, null, new Annotation(1),
1092 new Annotation(2), new Annotation(3), null, null, new Annotation(4),
1093 new Annotation(5), new Annotation(6), new Annotation(7),
1094 new Annotation(8) };
1095 AlignmentAnnotation ann = new AlignmentAnnotation("an", "some an",
1098 // without hidden cols, just truncates
1099 h.makeVisibleAnnotation(3, 5, ann);
1100 assertEquals(3, ann.annotations.length);
1101 assertEquals(2.0f, ann.annotations[0].value);
1102 assertEquals(3.0f, ann.annotations[1].value);
1103 assertNull(ann.annotations[2]);
1105 anns = new Annotation[] { null, null, new Annotation(1),
1106 new Annotation(2), new Annotation(3), null, null, new Annotation(4),
1107 new Annotation(5), new Annotation(6), new Annotation(7),
1108 new Annotation(8) };
1109 ann = new AlignmentAnnotation("an", "some an", anns);
1110 h.hideColumns(4, 7);
1111 h.makeVisibleAnnotation(1, 9, ann);
1112 assertEquals(5, ann.annotations.length);
1113 assertNull(ann.annotations[0]);
1114 assertEquals(1.0f, ann.annotations[1].value);
1115 assertEquals(2.0f, ann.annotations[2].value);
1116 assertEquals(5.0f, ann.annotations[3].value);
1117 assertEquals(6.0f, ann.annotations[4].value);
1119 anns = new Annotation[] { null, null, new Annotation(1),
1120 new Annotation(2), new Annotation(3), null, null, new Annotation(4),
1121 new Annotation(5), new Annotation(6), new Annotation(7),
1122 new Annotation(8) };
1123 ann = new AlignmentAnnotation("an", "some an", anns);
1124 h.hideColumns(1, 2);
1125 h.makeVisibleAnnotation(1, 9, ann);
1126 assertEquals(3, ann.annotations.length);
1127 assertEquals(2.0f, ann.annotations[0].value);
1128 assertEquals(5.0f, ann.annotations[1].value);
1129 assertEquals(6.0f, ann.annotations[2].value);
1132 @Test(groups = "Functional")
1133 public void testSubtractVisibleColumns()
1135 HiddenColumns h = new HiddenColumns();
1136 int result = h.subtractVisibleColumns(1, 10);
1137 assertEquals(9, result);
1139 h.hideColumns(7, 9);
1140 result = h.subtractVisibleColumns(4, 10);
1141 assertEquals(3, result);
1143 h.hideColumns(14, 15);
1144 result = h.subtractVisibleColumns(4, 10);
1145 assertEquals(3, result);
1147 result = h.subtractVisibleColumns(10, 17);
1148 assertEquals(2, result);
1150 result = h.subtractVisibleColumns(1, 7);
1151 assertEquals(5, result);
1153 result = h.subtractVisibleColumns(1, 8);
1154 assertEquals(5, result);
1156 result = h.subtractVisibleColumns(3, 15);
1157 assertEquals(10, result);
1159 ColumnSelection sel = new ColumnSelection();
1160 h.revealAllHiddenColumns(sel);
1161 h.hideColumns(0, 30);
1162 result = h.subtractVisibleColumns(31, 0);
1163 assertEquals(-31, result);
1165 HiddenColumns cs = new HiddenColumns();
1167 // test that without hidden columns, findColumnNToLeft returns
1168 // position n to left of provided position
1169 long pos = cs.subtractVisibleColumns(3, 10);
1170 assertEquals(7, pos);
1172 // 0 returns same position
1173 pos = cs.subtractVisibleColumns(0, 10);
1174 assertEquals(10, pos);
1176 // overflow to left returns negative number
1177 pos = cs.subtractVisibleColumns(3, 0);
1178 assertEquals(-3, pos);
1180 // test that with hidden columns to left of result column
1181 // behaviour is the same as above
1182 cs.hideColumns(1, 3);
1184 // position n to left of provided position
1185 pos = cs.subtractVisibleColumns(3, 10);
1186 assertEquals(7, pos);
1188 // 0 returns same position
1189 pos = cs.subtractVisibleColumns(0, 10);
1190 assertEquals(10, pos);
1192 // test with one set of hidden columns between start and required position
1193 cs.hideColumns(12, 15);
1194 pos = cs.subtractVisibleColumns(8, 17);
1195 assertEquals(5, pos);
1197 // test with two sets of hidden columns between start and required position
1198 cs.hideColumns(20, 21);
1199 pos = cs.subtractVisibleColumns(8, 23);
1200 assertEquals(9, pos);
1202 // repeat last 2 tests with no hidden columns to left of required position
1203 ColumnSelection colsel = new ColumnSelection();
1204 cs.revealAllHiddenColumns(colsel);
1206 // test with one set of hidden columns between start and required position
1207 cs.hideColumns(12, 15);
1208 pos = cs.subtractVisibleColumns(8, 17);
1209 assertEquals(5, pos);
1211 // test with two sets of hidden columns between start and required position
1212 cs.hideColumns(20, 21);
1213 pos = cs.subtractVisibleColumns(8, 23);
1214 assertEquals(9, pos);
1219 @Test(groups = "Functional")
1220 public void testBoundedIterator()
1222 HiddenColumns h = new HiddenColumns();
1223 Iterator<int[]> it = h.getBoundedIterator(0, 10);
1225 // no hidden columns = nothing to iterate over
1226 assertFalse(it.hasNext());
1228 // [start,end] contains all hidden columns
1229 // all regions are returned
1230 h.hideColumns(3, 10);
1231 h.hideColumns(14, 16);
1232 it = h.getBoundedIterator(0, 20);
1233 assertTrue(it.hasNext());
1234 int[] next = it.next();
1235 assertEquals(3, next[0]);
1236 assertEquals(10, next[1]);
1238 assertEquals(14, next[0]);
1239 assertEquals(16, next[1]);
1240 assertFalse(it.hasNext());
1242 // [start,end] overlaps a region
1243 // 1 region returned
1244 it = h.getBoundedIterator(5, 7);
1245 assertTrue(it.hasNext());
1247 assertEquals(3, next[0]);
1248 assertEquals(10, next[1]);
1249 assertFalse(it.hasNext());
1251 // [start,end] fully contains 1 region and start of last
1252 // - 2 regions returned
1253 it = h.getBoundedIterator(3, 15);
1254 assertTrue(it.hasNext());
1256 assertEquals(3, next[0]);
1257 assertEquals(10, next[1]);
1259 assertEquals(14, next[0]);
1260 assertEquals(16, next[1]);
1261 assertFalse(it.hasNext());
1263 // [start,end] contains end of first region and whole of last region
1264 // - 2 regions returned
1265 it = h.getBoundedIterator(4, 20);
1266 assertTrue(it.hasNext());
1268 assertEquals(3, next[0]);
1269 assertEquals(10, next[1]);
1271 assertEquals(14, next[0]);
1272 assertEquals(16, next[1]);
1273 assertFalse(it.hasNext());
1276 @Test(groups = "Functional")
1277 public void testBoundedStartIterator()
1279 HiddenColumns h = new HiddenColumns();
1280 Iterator<Integer> it = h.getBoundedStartIterator(0, 10);
1282 // no hidden columns = nothing to iterate over
1283 assertFalse(it.hasNext());
1285 // [start,end] contains all hidden columns
1286 // all regions are returned
1287 h.hideColumns(3, 10);
1288 h.hideColumns(14, 16);
1289 it = h.getBoundedStartIterator(0, 20);
1290 assertTrue(it.hasNext());
1291 int next = it.next();
1292 assertEquals(3, next);
1294 assertEquals(6, next);
1295 assertFalse(it.hasNext());
1297 // [start,end] does not contain a start of a region
1298 // no regions to iterate over
1299 it = h.getBoundedStartIterator(4, 5);
1300 assertFalse(it.hasNext());
1302 // [start,end] fully contains 1 region and start of last
1303 // - 2 regions returned
1304 it = h.getBoundedStartIterator(3, 7);
1305 assertTrue(it.hasNext());
1307 assertEquals(3, next);
1309 assertEquals(6, next);
1310 assertFalse(it.hasNext());
1312 // [start,end] contains whole of last region
1313 // - 1 region returned
1314 it = h.getBoundedStartIterator(4, 20);
1315 assertTrue(it.hasNext());
1317 assertEquals(6, next);
1318 assertFalse(it.hasNext());
1321 @Test(groups = "Functional")
1322 public void testVisibleBlocksVisBoundsIterator()
1324 HiddenColumns h = new HiddenColumns();
1325 Iterator<int[]> regions = h.getVisibleBlocksIterator(0, 30, true);
1327 // only 1 visible region spanning 0-30 if nothing is hidden
1328 assertTrue(regions.hasNext());
1329 int[] region = regions.next();
1330 assertEquals(0, region[0]);
1331 assertEquals(30, region[1]);
1332 assertFalse(regions.hasNext());
1334 // hide 1 region in middle
1335 // 2 regions one on either side
1336 // second region boundary accounts for hidden columns
1337 h.hideColumns(10, 15);
1338 regions = h.getVisibleBlocksIterator(0, 30, true);
1340 assertTrue(regions.hasNext());
1341 region = regions.next();
1342 assertEquals(0, region[0]);
1343 assertEquals(9, region[1]);
1344 region = regions.next();
1345 assertEquals(16, region[0]);
1346 assertEquals(36, region[1]);
1347 assertFalse(regions.hasNext());
1349 // single hidden region at left
1350 h = new HiddenColumns();
1351 h.hideColumns(0, 5);
1352 regions = h.getVisibleBlocksIterator(0, 30, true);
1354 assertTrue(regions.hasNext());
1355 region = regions.next();
1356 assertEquals(6, region[0]);
1357 assertEquals(36, region[1]);
1358 assertFalse(regions.hasNext());
1360 // single hidden region at right
1361 h = new HiddenColumns();
1362 h.hideColumns(27, 30);
1363 regions = h.getVisibleBlocksIterator(0, 30, true);
1365 assertTrue(regions.hasNext());
1366 region = regions.next();
1367 assertEquals(0, region[0]);
1368 assertEquals(26, region[1]);
1369 region = regions.next();
1370 assertEquals(31, region[0]);
1371 assertEquals(34, region[1]);
1372 assertFalse(regions.hasNext());
1374 // hidden region at left + hidden region in middle
1375 h = new HiddenColumns();
1376 h.hideColumns(0, 5);
1377 h.hideColumns(23, 25);
1378 regions = h.getVisibleBlocksIterator(0, 30, true);
1380 assertTrue(regions.hasNext());
1381 region = regions.next();
1382 assertEquals(6, region[0]);
1383 assertEquals(22, region[1]);
1384 region = regions.next();
1385 assertEquals(26, region[0]);
1386 assertEquals(39, region[1]);
1387 assertFalse(regions.hasNext());
1389 // hidden region at right + hidden region in middle
1390 h = new HiddenColumns();
1391 h.hideColumns(27, 30);
1392 h.hideColumns(11, 14);
1393 regions = h.getVisibleBlocksIterator(0, 30, true);
1395 assertTrue(regions.hasNext());
1396 region = regions.next();
1397 assertEquals(0, region[0]);
1398 assertEquals(10, region[1]);
1399 region = regions.next();
1400 assertEquals(15, region[0]);
1401 assertEquals(26, region[1]);
1402 region = regions.next();
1403 assertEquals(31, region[0]);
1404 assertEquals(38, region[1]);
1405 assertFalse(regions.hasNext());
1407 // hidden region at left and right
1408 h = new HiddenColumns();
1409 h.hideColumns(27, 35);
1410 h.hideColumns(0, 4);
1411 regions = h.getVisibleBlocksIterator(0, 30, true);
1413 assertTrue(regions.hasNext());
1414 region = regions.next();
1415 assertEquals(5, region[0]);
1416 assertEquals(26, region[1]);
1417 region = regions.next();
1418 assertEquals(36, region[0]);
1419 assertEquals(44, region[1]);
1420 assertFalse(regions.hasNext());
1422 // multiple hidden regions
1423 h = new HiddenColumns();
1424 h.hideColumns(1, 1);
1425 h.hideColumns(3, 5);
1426 h.hideColumns(9, 11);
1427 h.hideColumns(22, 26);
1429 regions = h.getVisibleBlocksIterator(0, 30, true);
1431 assertTrue(regions.hasNext());
1432 region = regions.next();
1433 assertEquals(0, region[0]);
1434 assertEquals(0, region[1]);
1435 region = regions.next();
1436 assertEquals(2, region[0]);
1437 assertEquals(2, region[1]);
1438 region = regions.next();
1439 assertEquals(6, region[0]);
1440 assertEquals(8, region[1]);
1441 region = regions.next();
1442 assertEquals(12, region[0]);
1443 assertEquals(21, region[1]);
1444 region = regions.next();
1445 assertEquals(27, region[0]);
1446 assertEquals(42, region[1]);
1447 assertFalse(regions.hasNext());