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;
35 import org.testng.annotations.Test;
37 public class HiddenColumnsTest
40 * Test the method which counts the number of hidden columns
42 @Test(groups = { "Functional" })
43 public void testGetSize()
45 HiddenColumns hidden = new HiddenColumns();
46 assertEquals(0, hidden.getSize());
48 hidden.hideColumns(3, 5);
49 assertEquals(3, hidden.getSize());
51 hidden.hideColumns(8, 8);
52 assertEquals(4, hidden.getSize());
54 hidden.hideColumns(9, 14);
55 assertEquals(10, hidden.getSize());
57 ColumnSelection cs = new ColumnSelection();
58 hidden.revealAllHiddenColumns(cs);
59 assertEquals(0, hidden.getSize());
63 * Test the method that finds the visible column position of an alignment
64 * column, allowing for hidden columns.
66 @Test(groups = { "Functional" })
67 public void testFindColumnPosition()
69 HiddenColumns cs = new HiddenColumns();
70 assertEquals(5, cs.absoluteToVisibleColumn(5));
72 // hiding column 6 makes no difference
74 assertEquals(5, cs.absoluteToVisibleColumn(5));
76 // hiding column 4 moves column 5 to column 4
78 assertEquals(4, cs.absoluteToVisibleColumn(5));
80 // hiding column 4 moves column 4 to position 3
81 assertEquals(3, cs.absoluteToVisibleColumn(4));
83 // hiding columns 1 and 2 moves column 5 to column 2
85 assertEquals(2, cs.absoluteToVisibleColumn(5));
87 // check with > 1 hidden column regions
88 // where some columns are in the hidden regions
89 HiddenColumns cs2 = new HiddenColumns();
90 cs2.hideColumns(5, 10);
91 cs2.hideColumns(20, 27);
92 cs2.hideColumns(40, 44);
94 // hiding columns 5-10 and 20-27 moves column 8 to column 4
95 assertEquals(4, cs2.absoluteToVisibleColumn(8));
97 // and moves column 24 to 13
98 assertEquals(13, cs2.absoluteToVisibleColumn(24));
100 // and moves column 28 to 14
101 assertEquals(14, cs2.absoluteToVisibleColumn(28));
103 // and moves column 40 to 25
104 assertEquals(25, cs2.absoluteToVisibleColumn(40));
106 // check when hidden columns start at 0 that the visible column
108 HiddenColumns cs3 = new HiddenColumns();
109 cs3.hideColumns(0, 4);
110 assertEquals(0, cs3.absoluteToVisibleColumn(2));
112 // check that column after the last hidden region doesn't crash
113 assertEquals(46, cs2.absoluteToVisibleColumn(65));
116 @Test(groups = { "Functional" })
117 public void testVisibleContigsIterator()
119 HiddenColumns cs = new HiddenColumns();
121 Iterator<int[]> visible = cs.getVisContigsIterator(3, 10, false);
122 int[] region = visible.next();
123 assertEquals("[3, 9]", Arrays.toString(region));
124 assertFalse(visible.hasNext());
126 cs.hideColumns(3, 6);
127 cs.hideColumns(8, 9);
128 cs.hideColumns(12, 12);
130 // Test both ends visible region
132 // start position is inclusive, end position exclusive
133 visible = cs.getVisContigsIterator(1, 13, false);
134 region = visible.next();
135 assertEquals("[1, 2]", Arrays.toString(region));
136 region = visible.next();
137 assertEquals("[7, 7]", Arrays.toString(region));
138 region = visible.next();
139 assertEquals("[10, 11]", Arrays.toString(region));
140 assertFalse(visible.hasNext());
142 // Test start hidden, end visible
143 visible = cs.getVisContigsIterator(4, 14, false);
144 region = visible.next();
145 assertEquals("[7, 7]", Arrays.toString(region));
146 region = visible.next();
147 assertEquals("[10, 11]", Arrays.toString(region));
148 region = visible.next();
149 assertEquals("[13, 13]", Arrays.toString(region));
150 assertFalse(visible.hasNext());
152 // Test start hidden, end hidden
153 visible = cs.getVisContigsIterator(3, 10, false);
154 region = visible.next();
155 assertEquals("[7, 7]", Arrays.toString(region));
156 assertFalse(visible.hasNext());
158 // Test start visible, end hidden
159 visible = cs.getVisContigsIterator(0, 13, false);
160 region = visible.next();
161 assertEquals("[0, 2]", Arrays.toString(region));
162 region = visible.next();
163 assertEquals("[7, 7]", Arrays.toString(region));
164 region = visible.next();
165 assertEquals("[10, 11]", Arrays.toString(region));
166 assertFalse(visible.hasNext());
169 visible = cs.getVisContigsIterator(4, 6, false);
170 assertFalse(visible.hasNext());
173 @Test(groups = { "Functional" })
174 public void testEquals()
176 HiddenColumns cs = new HiddenColumns();
177 cs.hideColumns(5, 9);
179 // a different set of hidden columns
180 HiddenColumns cs2 = new HiddenColumns();
182 // with no hidden columns
183 assertFalse(cs.equals(cs2));
184 assertFalse(cs2.equals(cs));
186 // with the wrong kind of object
187 assertFalse(cs.equals(new HiddenColumnsCursor()));
189 // with a different hiddenColumns object - by size
190 HiddenColumns cs3 = new HiddenColumns();
191 cs3.hideColumns(2, 3);
192 assertFalse(cs.equals(cs3));
194 // with hidden columns added in a different order
195 cs2.hideColumns(6, 9);
196 assertFalse(cs.equals(cs2));
197 assertFalse(cs2.equals(cs));
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));
206 // different ranges, same size
207 cs.hideColumns(10, 12);
208 cs2.hideColumns(10, 15);
209 assertFalse(cs.equals(cs2));
213 @Test(groups = "Functional")
214 public void testCopyConstructor()
216 HiddenColumns cs = new HiddenColumns();
217 cs.hideColumns(10, 11);
218 cs.hideColumns(5, 7);
219 Iterator<int[]> regions = cs.iterator();
220 assertEquals("[5, 7]",
221 Arrays.toString(regions.next()));
223 HiddenColumns cs2 = new HiddenColumns(cs);
224 regions = cs2.iterator();
225 assertTrue(cs2.hasHiddenColumns());
226 assertEquals(2, cs2.getNumberOfRegions());
227 // hidden columns are held in column order
228 assertEquals("[5, 7]",
229 Arrays.toString(regions.next()));
230 assertEquals("[10, 11]",
231 Arrays.toString(regions.next()));
234 @Test(groups = "Functional")
235 public void testCopyConstructor2()
237 HiddenColumns cs = new HiddenColumns();
238 cs.hideColumns(10, 11);
239 cs.hideColumns(5, 7);
241 HiddenColumns cs2 = new HiddenColumns(cs, 3, 9, 1);
242 assertTrue(cs2.hasHiddenColumns());
243 Iterator<int[]> regions = cs2.iterator();
245 // only [5,7] returned, offset by 1
246 assertEquals("[4, 6]",
247 Arrays.toString(regions.next()));
248 assertEquals(3, cs2.getSize());
250 cs2 = new HiddenColumns(cs, 8, 15, 4);
251 regions = cs2.iterator();
252 assertTrue(cs2.hasHiddenColumns());
254 // only [10,11] returned, offset by 4
255 assertEquals("[6, 7]",
256 Arrays.toString(regions.next()));
257 assertEquals(2, cs2.getSize());
259 cs2 = new HiddenColumns(cs, 6, 10, 4);
260 assertFalse(cs2.hasHiddenColumns());
264 * Test the code used to locate the reference sequence ruler origin
266 @Test(groups = { "Functional" })
267 public void testLocateVisibleStartofSequence()
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()));
280 assertEquals(seq.findIndex(seq.getStart()) - 1, cs.locateVisibleStartOfSequence(seq));
282 // hidden column on gap after end of sequence - should not affect bounds
283 colsel.hideSelectedColumns(13, al.getHiddenColumns());
284 assertEquals(seq.findIndex(seq.getStart()) - 1,cs.locateVisibleStartOfSequence(seq));
286 cs.revealAllHiddenColumns(colsel);
287 // hidden column on gap before beginning of sequence - should vis bounds by
289 colsel.hideSelectedColumns(0, al.getHiddenColumns());
290 assertEquals(seq.findIndex(seq.getStart()) - 2,cs.locateVisibleStartOfSequence(seq));
292 cs.revealAllHiddenColumns(colsel);
293 // hide columns around most of sequence - leave one residue remaining
294 cs.hideColumns(1, 3);
295 cs.hideColumns(6, 11);
297 cs.getVisibleSequenceStrings(0, 5, new SequenceI[]
300 assertEquals(1, cs.locateVisibleStartOfSequence(seq));
301 cs.revealAllHiddenColumns(colsel);
303 // hide whole sequence - should just get location of hidden region
304 // containing sequence
305 cs.hideColumns(1, 11);
306 assertEquals(0,cs.locateVisibleStartOfSequence(seq));
308 cs.revealAllHiddenColumns(colsel);
309 cs.hideColumns(0, 15);
310 assertEquals(0,cs.locateVisibleStartOfSequence(seq));
312 SequenceI seq2 = new Sequence("RefSeq2", "-------A-SD-ASD--E---");
314 cs.revealAllHiddenColumns(colsel);
315 cs.hideColumns(7, 17);
316 assertEquals(0,cs.locateVisibleStartOfSequence(seq2));
318 cs.revealAllHiddenColumns(colsel);
319 cs.hideColumns(3, 17);
320 assertEquals(0,cs.locateVisibleStartOfSequence(seq2));
322 cs.revealAllHiddenColumns(colsel);
323 cs.hideColumns(3, 19);
324 assertEquals(0,cs.locateVisibleStartOfSequence(seq2));
326 cs.revealAllHiddenColumns(colsel);
327 cs.hideColumns(0, 0);
328 assertEquals(0,cs.locateVisibleStartOfSequence(seq));
330 cs.revealAllHiddenColumns(colsel);
331 cs.hideColumns(0, 1);
332 assertEquals(1,cs.locateVisibleStartOfSequence(seq));
334 cs.revealAllHiddenColumns(colsel);
335 cs.hideColumns(0, 2);
336 assertEquals(0,cs.locateVisibleStartOfSequence(seq));
338 cs.revealAllHiddenColumns(colsel);
339 cs.hideColumns(1, 1);
340 assertEquals(2,cs.locateVisibleStartOfSequence(seq));
342 cs.revealAllHiddenColumns(colsel);
343 cs.hideColumns(1, 2);
344 assertEquals(1,cs.locateVisibleStartOfSequence(seq));
346 cs.revealAllHiddenColumns(colsel);
347 cs.hideColumns(1, 3);
348 assertEquals(1,cs.locateVisibleStartOfSequence(seq));
350 cs.revealAllHiddenColumns(colsel);
351 cs.hideColumns(0, 2);
352 cs.hideColumns(5, 6);
353 assertEquals(0,cs.locateVisibleStartOfSequence(seq));
355 cs.revealAllHiddenColumns(colsel);
356 cs.hideColumns(0, 2);
357 cs.hideColumns(5, 6);
358 cs.hideColumns(9, 10);
359 assertEquals(0,cs.locateVisibleStartOfSequence(seq));
361 cs.revealAllHiddenColumns(colsel);
362 cs.hideColumns(0, 2);
363 cs.hideColumns(7, 11);
364 assertEquals(0,cs.locateVisibleStartOfSequence(seq));
366 cs.revealAllHiddenColumns(colsel);
367 cs.hideColumns(2, 4);
368 cs.hideColumns(7, 11);
369 assertEquals(1,cs.locateVisibleStartOfSequence(seq));
371 cs.revealAllHiddenColumns(colsel);
372 cs.hideColumns(2, 4);
373 cs.hideColumns(7, 12);
374 assertEquals(1,cs.locateVisibleStartOfSequence(seq));
376 cs.revealAllHiddenColumns(colsel);
377 cs.hideColumns(1, 11);
378 assertEquals(0,cs.locateVisibleStartOfSequence(seq));
380 cs.revealAllHiddenColumns(colsel);
381 cs.hideColumns(0, 12);
382 assertEquals(0,cs.locateVisibleStartOfSequence(seq));
384 cs.revealAllHiddenColumns(colsel);
385 cs.hideColumns(0, 4);
386 cs.hideColumns(6, 12);
387 assertEquals(0,cs.locateVisibleStartOfSequence(seq));
389 cs.revealAllHiddenColumns(colsel);
390 cs.hideColumns(0, 1);
391 cs.hideColumns(3, 12);
392 assertEquals(0,cs.locateVisibleStartOfSequence(seq));
394 cs.revealAllHiddenColumns(colsel);
395 cs.hideColumns(3, 14);
396 cs.hideColumns(17, 19);
397 assertEquals(3,cs.locateVisibleStartOfSequence(seq2));
399 cs.revealAllHiddenColumns(colsel);
400 cs.hideColumns(3, 7);
401 cs.hideColumns(9, 14);
402 cs.hideColumns(17, 19);
403 assertEquals(9,cs.locateVisibleStartOfSequence(seq2));
405 cs.revealAllHiddenColumns(colsel);
406 cs.hideColumns(0, 1);
407 cs.hideColumns(3, 4);
408 cs.hideColumns(6, 8);
409 cs.hideColumns(10, 12);
410 assertEquals(6, cs.locateVisibleStartOfSequence(seq));
414 @Test(groups = { "Functional" })
415 public void testLocateVisibleStartPathologicals()
417 // test some pathological cases we missed
418 AlignmentI al = new Alignment(
420 { new Sequence("refseqGaptest", "KTDVTI----------NFI-----G----L") });
421 HiddenColumns cs = new HiddenColumns();
422 cs.hideList(al.getSequenceAt(0).getInsertions());
424 + al.getSequenceAt(0).getCharAt(cs.visibleToAbsoluteColumn(9)));
426 // KM: no idea what this is meant to be testing... seems to be an unfinished
430 @Test(groups = { "Functional" })
431 public void testHideColumns()
433 // create random alignment
434 AlignmentGenerator gen = new AlignmentGenerator(false);
435 AlignmentI al = gen.generate(50, 20, 123, 5, 5);
437 ColumnSelection colsel = new ColumnSelection();
438 HiddenColumns cs = al.getHiddenColumns();
439 colsel.hideSelectedColumns(5, al.getHiddenColumns());
440 Iterator<int[]> regions = cs.iterator();
441 assertEquals(1, cs.getNumberOfRegions());
442 assertEquals("[5, 5]", Arrays.toString(regions.next()));
444 colsel.hideSelectedColumns(3, al.getHiddenColumns());
445 regions = cs.iterator();
446 assertEquals(2, cs.getNumberOfRegions());
447 // two hidden ranges, in order:
448 assertEquals("[3, 3]", Arrays.toString(regions.next()));
449 assertEquals("[5, 5]", Arrays.toString(regions.next()));
451 // hiding column 4 expands [3, 3] to [3, 4]
452 // and merges to [5, 5] to make [3, 5]
453 colsel.hideSelectedColumns(4, al.getHiddenColumns());
454 regions = cs.iterator();
455 assertEquals(1, cs.getNumberOfRegions());
456 assertEquals("[3, 5]", Arrays.toString(regions.next()));
458 // clear hidden columns (note they are added to selected)
459 cs.revealAllHiddenColumns(colsel);
460 // it is now actually null but getter returns an empty list
461 assertEquals(0, cs.getNumberOfRegions());
463 cs.hideColumns(3, 6);
464 regions = cs.iterator();
465 int[] firstHiddenRange = regions.next();
466 assertEquals("[3, 6]", Arrays.toString(firstHiddenRange));
468 // adding a subrange of already hidden should do nothing
469 cs.hideColumns(4, 5);
470 regions = cs.iterator();
471 assertEquals(1, cs.getNumberOfRegions());
472 assertEquals("[3, 6]",
473 Arrays.toString(regions.next()));
474 cs.hideColumns(3, 5);
475 regions = cs.iterator();
476 assertEquals(1, cs.getNumberOfRegions());
477 assertEquals("[3, 6]",
478 Arrays.toString(regions.next()));
479 cs.hideColumns(4, 6);
480 regions = cs.iterator();
481 assertEquals(1, cs.getNumberOfRegions());
482 assertEquals("[3, 6]",
483 Arrays.toString(regions.next()));
484 cs.hideColumns(3, 6);
485 regions = cs.iterator();
486 assertEquals(1, cs.getNumberOfRegions());
487 assertEquals("[3, 6]",
488 Arrays.toString(regions.next()));
490 cs.revealAllHiddenColumns(colsel);
491 cs.hideColumns(2, 4);
492 regions = cs.iterator();
493 assertEquals(1, cs.getNumberOfRegions());
494 assertEquals("[2, 4]", Arrays.toString(regions.next()));
496 // extend contiguous with 2 positions overlap
497 cs.hideColumns(3, 5);
498 regions = cs.iterator();
499 assertEquals(1, cs.getNumberOfRegions());
500 assertEquals("[2, 5]", Arrays.toString(regions.next()));
502 // extend contiguous with 1 position overlap
503 cs.hideColumns(5, 6);
504 regions = cs.iterator();
505 assertEquals(1, cs.getNumberOfRegions());
506 assertEquals("[2, 6]", Arrays.toString(regions.next()));
508 // extend contiguous with overlap both ends:
509 cs.hideColumns(1, 7);
510 regions = cs.iterator();
511 assertEquals(1, cs.getNumberOfRegions());
512 assertEquals("[1, 7]", Arrays.toString(regions.next()));
514 cs.revealAllHiddenColumns(colsel);
515 cs.hideColumns(15, 18);
516 cs.hideColumns(2, 4);
517 cs.hideColumns(7, 9);
518 regions = cs.iterator();
519 assertEquals(3, cs.getNumberOfRegions());
520 assertEquals("[2, 4]", Arrays.toString(regions.next()));
521 assertEquals("[7, 9]", Arrays.toString(regions.next()));
522 assertEquals("[15, 18]", Arrays.toString(regions.next()));
526 * Test the method that reveals a range of hidden columns given the start
527 * column of the range
529 @Test(groups = { "Functional" })
530 public void testRevealHiddenColumns()
532 ColumnSelection colsel = new ColumnSelection();
533 HiddenColumns cs = new HiddenColumns();
535 // test with null hidden columns
536 cs.revealHiddenColumns(5, colsel);
537 assertTrue(colsel.getSelected().isEmpty());
539 cs.hideColumns(5, 8);
540 colsel.addElement(10);
541 cs.revealHiddenColumns(5, colsel);
543 // hiddenColumns now empty
544 assertEquals(0, cs.getSize());
546 // revealed columns are marked as selected (added to selection):
547 assertEquals("[10, 5, 6, 7, 8]", colsel.getSelected().toString());
549 // calling with a column other than the range start does nothing:
550 colsel = new ColumnSelection();
551 cs = new HiddenColumns();
552 cs.hideColumns(5, 8);
554 int prevSize = cs.getSize();
555 cs.revealHiddenColumns(6, colsel);
556 assertEquals(prevSize, cs.getSize());
557 assertTrue(colsel.getSelected().isEmpty());
559 // reveal hidden columns when there is more than one region
560 cs.hideColumns(20, 23);
561 // now there are 2 hidden regions
562 assertEquals(2, cs.getNumberOfRegions());
564 cs.revealHiddenColumns(20, colsel);
566 // hiddenColumns now has one region
567 assertEquals(1, cs.getNumberOfRegions());
569 // revealed columns are marked as selected (added to selection):
570 assertEquals("[20, 21, 22, 23]", colsel.getSelected().toString());
572 // call with a column past the end of the hidden column ranges
574 cs.revealHiddenColumns(20, colsel);
575 // hiddenColumns still has 1 region
576 assertEquals(1, cs.getNumberOfRegions());
577 assertTrue(colsel.getSelected().isEmpty());
580 @Test(groups = { "Functional" })
581 public void testRevealAllHiddenColumns()
583 HiddenColumns hidden = new HiddenColumns();
584 ColumnSelection colsel = new ColumnSelection();
586 // test with null hidden columns
587 hidden.revealAllHiddenColumns(colsel);
588 assertTrue(colsel.getSelected().isEmpty());
590 hidden.hideColumns(5, 8);
591 hidden.hideColumns(2, 3);
592 colsel.addElement(11);
593 colsel.addElement(1);
594 hidden.revealAllHiddenColumns(colsel);
597 * revealing hidden columns adds them (in order) to the (unordered)
601 // hiddenColumns now empty
602 assertEquals(0, hidden.getSize());
604 assertEquals("[11, 1, 2, 3, 5, 6, 7, 8]",
605 colsel.getSelected().toString());
608 @Test(groups = { "Functional" })
609 public void testIsVisible()
611 HiddenColumns cs = new HiddenColumns();
612 cs.hideColumns(2, 4);
613 cs.hideColumns(6, 7);
614 assertTrue(cs.isVisible(0));
615 assertTrue(cs.isVisible(-99));
616 assertTrue(cs.isVisible(1));
617 assertFalse(cs.isVisible(2));
618 assertFalse(cs.isVisible(3));
619 assertFalse(cs.isVisible(4));
620 assertTrue(cs.isVisible(5));
621 assertFalse(cs.isVisible(6));
622 assertFalse(cs.isVisible(7));
623 assertTrue(cs.isVisible(8));
627 * Test for the case when a hidden range encloses more one already hidden
630 @Test(groups = { "Functional" })
631 public void testHideColumns_subsumingHidden()
634 * JAL-2370 bug scenario:
635 * two hidden ranges subsumed by a third
637 HiddenColumns cs = new HiddenColumns();
638 cs.hideColumns(49, 59);
639 cs.hideColumns(69, 79);
640 Iterator<int[]> regions = cs.iterator();
641 assertEquals(2, cs.getNumberOfRegions());
642 assertEquals("[49, 59]", Arrays.toString(regions.next()));
643 assertEquals("[69, 79]", Arrays.toString(regions.next()));
645 cs.hideColumns(48, 80);
646 regions = cs.iterator();
647 assertEquals(1, cs.getNumberOfRegions());
648 assertEquals("[48, 80]", Arrays.toString(regions.next()));
651 * another...joining hidden ranges
653 cs = new HiddenColumns();
654 cs.hideColumns(10, 20);
655 cs.hideColumns(30, 40);
656 cs.hideColumns(50, 60);
657 // hiding 21-49 should merge to one range
658 cs.hideColumns(21, 49);
659 regions = cs.iterator();
660 assertEquals(1, cs.getNumberOfRegions());
661 assertEquals("[10, 60]", Arrays.toString(regions.next()));
664 * another...left overlap, subsumption, right overlap,
665 * no overlap of existing hidden ranges
667 cs = new HiddenColumns();
668 cs.hideColumns(10, 20);
669 cs.hideColumns(10, 20);
670 cs.hideColumns(30, 35);
671 cs.hideColumns(40, 50);
672 cs.hideColumns(60, 70);
674 cs.hideColumns(15, 45);
675 regions = cs.iterator();
676 assertEquals(2, cs.getNumberOfRegions());
677 assertEquals("[10, 50]", Arrays.toString(regions.next()));
678 assertEquals("[60, 70]", Arrays.toString(regions.next()));
681 @Test(groups = { "Functional" })
682 public void testHideColumns_BitSet()
686 BitSet one = new BitSet();
690 cs = new HiddenColumns();
692 assertEquals(1, cs.getNumberOfRegions());
695 cs = new HiddenColumns();
697 assertEquals(1, cs.getNumberOfRegions());
700 cs = new HiddenColumns();
702 assertEquals(1, cs.getNumberOfRegions());
706 cs = new HiddenColumns();
708 assertEquals(2, cs.getNumberOfRegions());
710 assertEquals(0, cs.visibleToAbsoluteColumn(0));
711 assertEquals(2, cs.visibleToAbsoluteColumn(1));
712 assertEquals(4, cs.visibleToAbsoluteColumn(2));
716 cs = new HiddenColumns();
719 assertEquals(1, cs.getNumberOfRegions());
721 assertEquals(0, cs.visibleToAbsoluteColumn(0));
722 assertEquals(1, cs.visibleToAbsoluteColumn(1));
723 assertEquals(2, cs.visibleToAbsoluteColumn(2));
724 assertEquals(4, cs.visibleToAbsoluteColumn(3));
727 @Test(groups = { "Functional" })
728 public void hideColumns_BitSetAndRange()
730 HiddenColumns hc = new HiddenColumns();
731 hc.hideColumns(3, 5);
732 hc.hideColumns(15, 20);
733 hc.hideColumns(45, 60);
735 BitSet tohide = new BitSet();
737 // all unhidden if tohide is empty and range covers hidden
738 hc.hideColumns(tohide, 1, 70);
739 assertTrue(!hc.hasHiddenColumns());
741 hc.hideColumns(3, 5);
742 hc.hideColumns(15, 20);
743 hc.hideColumns(45, 60);
745 // but not if range does not cover hidden
746 hc.hideColumns(tohide, 23, 40);
747 assertTrue(hc.hasHiddenColumns());
749 // and partial unhide if range partially covers
750 hc.hideColumns(tohide, 1, 17);
751 Iterator<int[]> it = hc.iterator();
752 assertTrue(it.hasNext());
753 int[] region = it.next();
755 assertEquals(18, region[0]);
756 assertEquals(20, region[1]);
758 assertTrue(it.hasNext());
761 assertEquals(45, region[0]);
762 assertEquals(60, region[1]);
764 assertFalse(it.hasNext());
767 @Test(groups = { "Functional" })
768 public void testRegionsToString()
770 HiddenColumns hc = new HiddenColumns();
772 String result = hc.regionsToString(",", "--");
773 assertEquals("", result);
775 hc.hideColumns(3, 7);
776 hc.hideColumns(10, 10);
777 hc.hideColumns(14, 15);
779 result = hc.regionsToString(",", "--");
780 assertEquals("3--7,10--10,14--15", result);
783 @Test(groups = "Functional")
784 public void testGetVisibleStartAndEndIndex()
786 Sequence seq = new Sequence("testSeq", "ABCDEFGHIJKLMNOPQRSTUVWXYZ");
787 AlignmentI align = new Alignment(new SequenceI[] { seq });
788 HiddenColumns hc = new HiddenColumns();
790 int[] startEnd = hc.getVisibleStartAndEndIndex(align.getWidth());
791 assertEquals(0, startEnd[0]);
792 assertEquals(25, startEnd[1]);
794 hc.hideColumns(0, 0);
795 startEnd = hc.getVisibleStartAndEndIndex(align.getWidth());
796 assertEquals(1, startEnd[0]);
797 assertEquals(25, startEnd[1]);
799 hc.hideColumns(6, 9);
800 hc.hideColumns(11, 12);
801 startEnd = hc.getVisibleStartAndEndIndex(align.getWidth());
802 assertEquals(1, startEnd[0]);
803 assertEquals(25, startEnd[1]);
805 hc.hideColumns(24, 25);
806 startEnd = hc.getVisibleStartAndEndIndex(align.getWidth());
807 System.out.println(startEnd[0] + " : " + startEnd[1]);
808 assertEquals(1, startEnd[0]);
809 assertEquals(23, startEnd[1]);
811 // force lowest range to start of alignment
812 hc = new HiddenColumns();
813 hc.hideColumns(3, 4);
814 startEnd = hc.getVisibleStartAndEndIndex(align.getWidth());
815 assertEquals(0, startEnd[0]);
816 assertEquals(25, startEnd[1]);
819 @Test(groups = "Functional")
820 public void testGetRegionWithEdgeAtRes()
822 HiddenColumns hc = new HiddenColumns();
824 int[] result = hc.getRegionWithEdgeAtRes(5);
827 hc.hideColumns(3, 7);
828 hc.hideColumns(10, 10);
829 hc.hideColumns(14, 15);
831 result = hc.getRegionWithEdgeAtRes(2);
832 assertEquals(3, result[0]);
833 assertEquals(7, result[1]);
835 result = hc.getRegionWithEdgeAtRes(4);
836 assertEquals(10, result[0]);
837 assertEquals(10, result[1]);
839 result = hc.getRegionWithEdgeAtRes(5);
840 assertEquals(10, result[0]);
841 assertEquals(10, result[1]);
843 result = hc.getRegionWithEdgeAtRes(6);
846 result = hc.getRegionWithEdgeAtRes(0);
849 result = hc.getRegionWithEdgeAtRes(7);
850 assertEquals(14, result[0]);
851 assertEquals(15, result[1]);
853 result = hc.getRegionWithEdgeAtRes(8);
854 assertEquals(14, result[0]);
855 assertEquals(15, result[1]);
857 result = hc.getRegionWithEdgeAtRes(16);
861 @Test(groups = "Functional")
862 public void testPropagateInsertions()
864 // create an alignment with no gaps - this will be the profile seq and other
866 AlignmentGenerator gen = new AlignmentGenerator(false);
867 AlignmentI al = gen.generate(25, 10, 1234, 0, 0);
869 // get the profileseq
870 SequenceI profileseq = al.getSequenceAt(0);
871 SequenceI gappedseq = new Sequence(profileseq);
872 gappedseq.insertCharAt(5, al.getGapCharacter());
873 gappedseq.insertCharAt(6, al.getGapCharacter());
874 gappedseq.insertCharAt(7, al.getGapCharacter());
875 gappedseq.insertCharAt(8, al.getGapCharacter());
877 // force different kinds of padding
878 al.getSequenceAt(3).deleteChars(2, 23);
879 al.getSequenceAt(4).deleteChars(2, 27);
880 al.getSequenceAt(5).deleteChars(10, 27);
882 // create an alignment view with the gapped sequence
883 SequenceI[] seqs = new SequenceI[1];
885 AlignmentI newal = new Alignment(seqs);
886 HiddenColumns hidden = new HiddenColumns();
887 hidden.hideColumns(15, 17);
889 AlignmentView view = new AlignmentView(newal, hidden, null, true, false,
892 // confirm that original contigs are as expected
893 Iterator<int[]> visible = hidden.getVisContigsIterator(0, 25, false);
894 int[] region = visible.next();
895 assertEquals("[0, 14]", Arrays.toString(region));
896 region = visible.next();
897 assertEquals("[18, 24]", Arrays.toString(region));
899 // propagate insertions
900 HiddenColumns result = HiddenColumns.propagateInsertions(profileseq, al,
903 // confirm that the contigs have changed to account for the gaps
904 visible = result.getVisContigsIterator(0, 25, false);
905 region = visible.next();
906 assertEquals("[0, 10]", Arrays.toString(region));
907 region = visible.next();
908 assertEquals("[14, 24]", Arrays.toString(region));
910 // confirm the alignment has been changed so that the other sequences have
911 // gaps inserted where the columns are hidden
912 assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[10]));
913 assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[11]));
914 assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[12]));
915 assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[13]));
916 assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[14]));
920 @Test(groups = "Functional")
921 public void testPropagateInsertionsOverlap()
923 // test propagateInsertions where gaps and hiddenColumns overlap
925 // create an alignment with no gaps - this will be the profile seq and other
927 AlignmentGenerator gen = new AlignmentGenerator(false);
928 AlignmentI al = gen.generate(20, 10, 1234, 0, 0);
930 // get the profileseq
931 SequenceI profileseq = al.getSequenceAt(0);
932 SequenceI gappedseq = new Sequence(profileseq);
933 gappedseq.insertCharAt(5, al.getGapCharacter());
934 gappedseq.insertCharAt(6, al.getGapCharacter());
935 gappedseq.insertCharAt(7, al.getGapCharacter());
936 gappedseq.insertCharAt(8, al.getGapCharacter());
938 // create an alignment view with the gapped sequence
939 SequenceI[] seqs = new SequenceI[1];
941 AlignmentI newal = new Alignment(seqs);
943 // hide columns so that some overlap with the gaps
944 HiddenColumns hidden = new HiddenColumns();
945 hidden.hideColumns(7, 10);
947 AlignmentView view = new AlignmentView(newal, hidden, null, true, false,
950 // confirm that original contigs are as expected
951 Iterator<int[]> visible = hidden.getVisContigsIterator(0, 20, false);
952 int[] region = visible.next();
953 assertEquals("[0, 6]", Arrays.toString(region));
954 region = visible.next();
955 assertEquals("[11, 19]", Arrays.toString(region));
956 assertFalse(visible.hasNext());
958 // propagate insertions
959 HiddenColumns result = HiddenColumns.propagateInsertions(profileseq, al,
962 // confirm that the contigs have changed to account for the gaps
963 visible = result.getVisContigsIterator(0, 20, false);
964 region = visible.next();
965 assertEquals("[0, 4]", Arrays.toString(region));
966 region = visible.next();
967 assertEquals("[7, 19]", Arrays.toString(region));
968 assertFalse(visible.hasNext());
970 // confirm the alignment has been changed so that the other sequences have
971 // gaps inserted where the columns are hidden
972 assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[4]));
973 assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[5]));
974 assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[6]));
975 assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[7]));
978 @Test(groups = "Functional")
979 public void testHasHiddenColumns()
981 HiddenColumns h = new HiddenColumns();
983 // new HiddenColumns2 has no hidden cols
984 assertFalse(h.hasHiddenColumns());
986 // some columns hidden, returns true
987 h.hideColumns(5, 10);
988 assertTrue(h.hasHiddenColumns());
990 // reveal columns, no hidden cols again
991 ColumnSelection sel = new ColumnSelection();
992 h.revealAllHiddenColumns(sel);
993 assertFalse(h.hasHiddenColumns());
996 @Test(groups = "Functional")
997 public void testHasManyHiddenColumns()
999 HiddenColumns h = new HiddenColumns();
1001 // h has no hidden cols
1002 assertFalse(h.hasMultiHiddenColumnRegions());
1004 // one set of columns hidden, returns false
1005 h.hideColumns(5, 10);
1006 assertFalse(h.hasMultiHiddenColumnRegions());
1008 // two sets hidden, returns true
1009 h.hideColumns(15, 17);
1010 assertTrue(h.hasMultiHiddenColumnRegions());
1012 // back to one block, asserts false
1013 h.hideColumns(11, 14);
1014 assertFalse(h.hasMultiHiddenColumnRegions());
1017 @Test(groups = "Functional")
1018 public void testAdjustForHiddenColumns()
1020 HiddenColumns h = new HiddenColumns();
1021 // returns input value when there are no hidden columns
1022 assertEquals(10, h.visibleToAbsoluteColumn(10));
1024 h.hideColumns(20, 30);
1025 assertEquals(10, h.visibleToAbsoluteColumn(10));
1026 assertEquals(20 + 11, h.visibleToAbsoluteColumn(20));
1027 assertEquals(35 + 11, h.visibleToAbsoluteColumn(35));
1029 h.hideColumns(5, 7);
1030 assertEquals(10 + 3, h.visibleToAbsoluteColumn(10));
1031 assertEquals(20 + 14, h.visibleToAbsoluteColumn(20));
1032 assertEquals(35 + 14, h.visibleToAbsoluteColumn(35));
1034 ColumnSelection sel = new ColumnSelection();
1035 h.revealAllHiddenColumns(sel);
1036 h.hideColumns(0, 1);
1037 assertEquals(4, h.visibleToAbsoluteColumn(2));
1040 @Test(groups = "Functional")
1041 public void testGetHiddenBoundaryLeft()
1043 HiddenColumns h = new HiddenColumns();
1045 // returns same value if no hidden cols
1046 assertEquals(3, h.getHiddenBoundaryLeft(3));
1048 h.hideColumns(5, 10);
1049 assertEquals(10, h.getHiddenBoundaryLeft(15));
1050 assertEquals(3, h.getHiddenBoundaryLeft(3));
1051 assertEquals(7, h.getHiddenBoundaryLeft(7));
1053 h.hideColumns(15, 20);
1054 assertEquals(10, h.getHiddenBoundaryLeft(15));
1055 assertEquals(20, h.getHiddenBoundaryLeft(21));
1058 @Test(groups = "Functional")
1059 public void testGetHiddenBoundaryRight()
1061 HiddenColumns h = new HiddenColumns();
1063 // returns same value if no hidden cols
1064 assertEquals(3, h.getHiddenBoundaryRight(3));
1066 h.hideColumns(5, 10);
1067 assertEquals(5, h.getHiddenBoundaryRight(3));
1068 assertEquals(15, h.getHiddenBoundaryRight(15));
1069 assertEquals(7, h.getHiddenBoundaryRight(7));
1071 h.hideColumns(15, 20);
1072 assertEquals(15, h.getHiddenBoundaryRight(7));
1073 assertEquals(15, h.getHiddenBoundaryRight(14));
1075 // returns same value if there is no next hidden column
1076 assertEquals(22, h.getHiddenBoundaryRight(22));
1079 @Test(groups = "Functional")
1080 public void testIterator()
1082 HiddenColumns h = new HiddenColumns();
1083 Iterator<int[]> result = h.iterator();
1084 assertFalse(result.hasNext());
1086 h.hideColumns(5, 10);
1087 result = h.iterator();
1088 int[] next = result.next();
1089 assertEquals(5, next[0]);
1090 assertEquals(10, next[1]);
1091 assertFalse(result.hasNext());
1093 h.hideColumns(22, 23);
1094 result = h.iterator();
1095 next = result.next();
1096 assertEquals(5, next[0]);
1097 assertEquals(10, next[1]);
1098 next = result.next();
1099 assertEquals(22, next[0]);
1100 assertEquals(23, next[1]);
1101 assertFalse(result.hasNext());
1103 // test for only one hidden region at start of alignment
1104 ColumnSelection sel = new ColumnSelection();
1105 h.revealAllHiddenColumns(sel);
1106 h.hideColumns(0, 1);
1107 result = h.iterator();
1108 next = result.next();
1109 assertEquals(0, next[0]);
1110 assertEquals(1, next[1]);
1111 assertFalse(result.hasNext());
1114 @Test(groups = "Functional")
1115 public void testGetVisibleSequenceStrings()
1117 HiddenColumns h = new HiddenColumns();
1118 SequenceI seq1 = new Sequence("TEST1", "GALMFWKQESPVICYHRNDT");
1119 SequenceI seq2 = new Sequence("TEST2", "VICYHRNDTGA");
1120 SequenceI[] seqs = new SequenceI[2];
1123 String[] result = h.getVisibleSequenceStrings(5, 10, seqs);
1124 assertEquals(2, result.length);
1125 assertEquals("WKQES", result[0]);
1126 assertEquals("RNDTG", result[1]);
1128 h.hideColumns(6, 8);
1129 result = h.getVisibleSequenceStrings(5, 10, seqs);
1130 assertEquals(2, result.length);
1131 assertEquals("WS", result[0]);
1132 assertEquals("RG", result[1]);
1134 SequenceI seq = new Sequence("RefSeq", "-A-SD-ASD--E---");
1135 ColumnSelection sel = new ColumnSelection();
1136 h.revealAllHiddenColumns(sel);
1137 h.hideColumns(1, 3);
1138 h.hideColumns(6, 11);
1140 h.getVisibleSequenceStrings(0, 5, new SequenceI[]
1144 @Test(groups = "Functional")
1145 public void testHideInsertionsFor()
1147 HiddenColumns h = new HiddenColumns();
1148 HiddenColumns h2 = new HiddenColumns();
1149 SequenceI seq1 = new Sequence("TEST1", "GAL---MFW-KQESPVICY--HRNDT");
1150 SequenceI seq2 = new Sequence("TEST1", "GALMFWKQESPVICYHRNDT");
1152 h.hideList(seq2.getInsertions());
1153 assertTrue(h.equals(h2));
1155 h.hideList(seq1.getInsertions());
1156 h2.hideColumns(3, 5);
1157 h2.hideColumns(9, 9);
1158 h2.hideColumns(19, 20);
1159 assertTrue(h.equals(h2));
1162 @Test(groups = "Functional")
1163 public void testHideColumns_BitSet_range()
1165 HiddenColumns h = new HiddenColumns();
1166 HiddenColumns h2 = new HiddenColumns();
1168 BitSet tohide = new BitSet(21);
1169 h.hideColumns(tohide);
1170 assertTrue(h.equals(h2));
1172 // when setting bitset, first param is invlusive, second exclusive
1176 h.hideColumns(tohide, 5, 23);
1178 h2.hideColumns(5, 5);
1179 h2.hideColumns(9, 9);
1180 h2.hideColumns(15, 20);
1181 assertTrue(h.equals(h2));
1185 h.hideColumns(tohide, 23, 30);
1186 assertTrue(h.equals(h2));
1189 h.hideColumns(tohide, 30, 45);
1190 h2.hideColumns(41, 41);
1191 assertTrue(h.equals(h2));
1195 h.hideColumns(tohide, 17, 50);
1196 h2 = new HiddenColumns();
1197 h2.hideColumns(17, 20);
1198 h2.hideColumns(25, 27);
1199 h2.hideColumns(41, 41);
1202 @Test(groups = "Functional")
1203 public void testOffsetByVisibleColumns()
1205 HiddenColumns h = new HiddenColumns();
1206 int result = h.offsetByVisibleColumns(-1, 10);
1207 assertEquals(9, result);
1209 h.hideColumns(7, 9);
1210 result = h.offsetByVisibleColumns(-4, 10);
1211 assertEquals(3, result);
1213 h.hideColumns(14, 15);
1214 result = h.offsetByVisibleColumns(-4, 10);
1215 assertEquals(3, result);
1217 result = h.offsetByVisibleColumns(-10, 17);
1218 assertEquals(2, result);
1220 result = h.offsetByVisibleColumns(-1, 7);
1221 assertEquals(5, result);
1223 result = h.offsetByVisibleColumns(-1, 8);
1224 assertEquals(5, result);
1226 result = h.offsetByVisibleColumns(-3, 15);
1227 assertEquals(10, result);
1229 ColumnSelection sel = new ColumnSelection();
1230 h.revealAllHiddenColumns(sel);
1231 h.hideColumns(0, 30);
1232 result = h.offsetByVisibleColumns(-31, 0);
1233 assertEquals(-31, result);
1235 HiddenColumns cs = new HiddenColumns();
1237 // test that without hidden columns, offsetByVisibleColumns returns
1238 // position n to left of provided position
1239 long pos = cs.offsetByVisibleColumns(-3, 10);
1240 assertEquals(7, pos);
1242 // 0 returns same position
1243 pos = cs.offsetByVisibleColumns(0, 10);
1244 assertEquals(10, pos);
1246 // overflow to left returns negative number
1247 pos = cs.offsetByVisibleColumns(-3, 0);
1248 assertEquals(-3, pos);
1250 // test that with hidden columns to left of result column
1251 // behaviour is the same as above
1252 cs.hideColumns(1, 3);
1254 // position n to left of provided position
1255 pos = cs.offsetByVisibleColumns(-3, 10);
1256 assertEquals(7, pos);
1258 // 0 returns same position
1259 pos = cs.offsetByVisibleColumns(0, 10);
1260 assertEquals(10, pos);
1262 // test with one set of hidden columns between start and required position
1263 cs.hideColumns(12, 15);
1264 pos = cs.offsetByVisibleColumns(-8, 17);
1265 assertEquals(5, pos);
1267 // test with two sets of hidden columns between start and required position
1268 cs.hideColumns(20, 21);
1269 pos = cs.offsetByVisibleColumns(-8, 23);
1270 assertEquals(9, pos);
1272 // repeat last 2 tests with no hidden columns to left of required position
1273 ColumnSelection colsel = new ColumnSelection();
1274 cs.revealAllHiddenColumns(colsel);
1276 // test with one set of hidden columns between start and required position
1277 cs.hideColumns(12, 15);
1278 pos = cs.offsetByVisibleColumns(-8, 17);
1279 assertEquals(5, pos);
1281 // test with two sets of hidden columns between start and required position
1282 cs.hideColumns(20, 21);
1283 pos = cs.offsetByVisibleColumns(-8, 23);
1284 assertEquals(9, pos);
1286 // test with right (positive) offsets
1288 // test that without hidden columns, offsetByVisibleColumns returns
1289 // position n to right of provided position
1290 pos = cs.offsetByVisibleColumns(3, 7);
1291 assertEquals(10, pos);
1293 // test that with hidden columns to left of result column
1294 // behaviour is the same as above
1295 cs.hideColumns(1, 3);
1297 // test with one set of hidden columns between start and required position
1298 cs.hideColumns(12, 15);
1299 pos = cs.offsetByVisibleColumns(8, 5);
1300 assertEquals(17, pos);
1302 // test with two sets of hidden columns between start and required position
1303 cs.hideColumns(20, 21);
1304 pos = cs.offsetByVisibleColumns(8, 9);
1305 assertEquals(23, pos);
1307 // repeat last 2 tests with no hidden columns to left of required position
1308 colsel = new ColumnSelection();
1309 cs.revealAllHiddenColumns(colsel);
1311 // test with one set of hidden columns between start and required position
1312 cs.hideColumns(12, 15);
1313 pos = cs.offsetByVisibleColumns(8, 5);
1314 assertEquals(17, pos);
1316 // test with two sets of hidden columns between start and required position
1317 cs.hideColumns(20, 21);
1318 pos = cs.offsetByVisibleColumns(8, 9);
1319 assertEquals(23, pos);
1322 @Test(groups = "Functional")
1323 public void testBoundedIterator()
1325 HiddenColumns h = new HiddenColumns();
1326 Iterator<int[]> it = h.getBoundedIterator(0, 10);
1328 // no hidden columns = nothing to iterate over
1329 assertFalse(it.hasNext());
1331 // [start,end] contains all hidden columns
1332 // all regions are returned
1333 h.hideColumns(3, 10);
1334 h.hideColumns(14, 16);
1335 it = h.getBoundedIterator(0, 20);
1336 assertTrue(it.hasNext());
1337 int[] next = it.next();
1338 assertEquals(3, next[0]);
1339 assertEquals(10, next[1]);
1341 assertEquals(14, next[0]);
1342 assertEquals(16, next[1]);
1343 assertFalse(it.hasNext());
1345 // [start,end] overlaps a region
1346 // 1 region returned
1347 it = h.getBoundedIterator(5, 7);
1348 assertTrue(it.hasNext());
1350 assertEquals(3, next[0]);
1351 assertEquals(10, next[1]);
1352 assertFalse(it.hasNext());
1354 // [start,end] fully contains 1 region and start of last
1355 // - 2 regions returned
1356 it = h.getBoundedIterator(3, 15);
1357 assertTrue(it.hasNext());
1359 assertEquals(3, next[0]);
1360 assertEquals(10, next[1]);
1362 assertEquals(14, next[0]);
1363 assertEquals(16, next[1]);
1364 assertFalse(it.hasNext());
1366 // [start,end] contains end of first region and whole of last region
1367 // - 2 regions returned
1368 it = h.getBoundedIterator(4, 20);
1369 assertTrue(it.hasNext());
1371 assertEquals(3, next[0]);
1372 assertEquals(10, next[1]);
1374 assertEquals(14, next[0]);
1375 assertEquals(16, next[1]);
1376 assertFalse(it.hasNext());
1379 @Test(groups = "Functional")
1380 public void testBoundedStartIterator()
1382 HiddenColumns h = new HiddenColumns();
1383 Iterator<Integer> it = h.getBoundedStartIterator(0, 10);
1385 // no hidden columns = nothing to iterate over
1386 assertFalse(it.hasNext());
1388 // [start,end] contains all hidden columns
1389 // all regions are returned
1390 h.hideColumns(3, 10);
1391 h.hideColumns(14, 16);
1392 it = h.getBoundedStartIterator(0, 20);
1393 assertTrue(it.hasNext());
1394 int next = it.next();
1395 assertEquals(3, next);
1397 assertEquals(6, next);
1398 assertFalse(it.hasNext());
1400 // [start,end] does not contain a start of a region
1401 // no regions to iterate over
1402 it = h.getBoundedStartIterator(4, 5);
1403 assertFalse(it.hasNext());
1405 // [start,end] fully contains 1 region and start of last
1406 // - 2 regions returned
1407 it = h.getBoundedStartIterator(3, 7);
1408 assertTrue(it.hasNext());
1410 assertEquals(3, next);
1412 assertEquals(6, next);
1413 assertFalse(it.hasNext());
1415 // [start,end] contains whole of last region
1416 // - 1 region returned
1417 it = h.getBoundedStartIterator(4, 20);
1418 assertTrue(it.hasNext());
1420 assertEquals(6, next);
1421 assertFalse(it.hasNext());
1424 @Test(groups = "Functional")
1425 public void testVisibleBlocksVisBoundsIterator()
1427 HiddenColumns h = new HiddenColumns();
1428 Iterator<int[]> regions = h.getVisContigsIterator(0, 31, true);
1430 // only 1 visible region spanning 0-30 if nothing is hidden
1431 assertTrue(regions.hasNext());
1432 int[] region = regions.next();
1433 assertEquals(0, region[0]);
1434 assertEquals(30, region[1]);
1435 assertFalse(regions.hasNext());
1437 // hide 1 region in middle
1438 // 2 regions one on either side
1439 // second region boundary accounts for hidden columns
1440 h.hideColumns(10, 15);
1441 regions = h.getVisContigsIterator(0, 31, true);
1443 assertTrue(regions.hasNext());
1444 region = regions.next();
1445 assertEquals(0, region[0]);
1446 assertEquals(9, region[1]);
1447 region = regions.next();
1448 assertEquals(16, region[0]);
1449 assertEquals(36, region[1]);
1450 assertFalse(regions.hasNext());
1452 // single hidden region at left
1453 h = new HiddenColumns();
1454 h.hideColumns(0, 5);
1455 regions = h.getVisContigsIterator(0, 31, true);
1457 assertTrue(regions.hasNext());
1458 region = regions.next();
1459 assertEquals(6, region[0]);
1460 assertEquals(36, region[1]);
1461 assertFalse(regions.hasNext());
1463 // single hidden region at right
1464 h = new HiddenColumns();
1465 h.hideColumns(27, 30);
1466 regions = h.getVisContigsIterator(0, 31, true);
1468 assertTrue(regions.hasNext());
1469 region = regions.next();
1470 assertEquals(0, region[0]);
1471 assertEquals(26, region[1]);
1472 region = regions.next();
1473 assertEquals(31, region[0]);
1474 assertEquals(34, region[1]);
1475 assertFalse(regions.hasNext());
1477 // hidden region at left + hidden region in middle
1478 h = new HiddenColumns();
1479 h.hideColumns(0, 5);
1480 h.hideColumns(23, 25);
1481 regions = h.getVisContigsIterator(0, 31, true);
1483 assertTrue(regions.hasNext());
1484 region = regions.next();
1485 assertEquals(6, region[0]);
1486 assertEquals(22, region[1]);
1487 region = regions.next();
1488 assertEquals(26, region[0]);
1489 assertEquals(39, region[1]);
1490 assertFalse(regions.hasNext());
1492 // hidden region at right + hidden region in middle
1493 h = new HiddenColumns();
1494 h.hideColumns(27, 30);
1495 h.hideColumns(11, 14);
1496 regions = h.getVisContigsIterator(0, 31, true);
1498 assertTrue(regions.hasNext());
1499 region = regions.next();
1500 assertEquals(0, region[0]);
1501 assertEquals(10, region[1]);
1502 region = regions.next();
1503 assertEquals(15, region[0]);
1504 assertEquals(26, region[1]);
1505 region = regions.next();
1506 assertEquals(31, region[0]);
1507 assertEquals(38, region[1]);
1508 assertFalse(regions.hasNext());
1510 // hidden region at left and right
1511 h = new HiddenColumns();
1512 h.hideColumns(27, 35);
1513 h.hideColumns(0, 4);
1514 regions = h.getVisContigsIterator(0, 31, true);
1516 assertTrue(regions.hasNext());
1517 region = regions.next();
1518 assertEquals(5, region[0]);
1519 assertEquals(26, region[1]);
1520 region = regions.next();
1521 assertEquals(36, region[0]);
1522 assertEquals(44, region[1]);
1523 assertFalse(regions.hasNext());
1525 // multiple hidden regions
1526 h = new HiddenColumns();
1527 h.hideColumns(1, 1);
1528 h.hideColumns(3, 5);
1529 h.hideColumns(9, 11);
1530 h.hideColumns(22, 26);
1532 regions = h.getVisContigsIterator(0, 31, true);
1534 assertTrue(regions.hasNext());
1535 region = regions.next();
1536 assertEquals(0, region[0]);
1537 assertEquals(0, region[1]);
1538 region = regions.next();
1539 assertEquals(2, region[0]);
1540 assertEquals(2, region[1]);
1541 region = regions.next();
1542 assertEquals(6, region[0]);
1543 assertEquals(8, region[1]);
1544 region = regions.next();
1545 assertEquals(12, region[0]);
1546 assertEquals(21, region[1]);
1547 region = regions.next();
1548 assertEquals(27, region[0]);
1549 assertEquals(42, region[1]);
1550 assertFalse(regions.hasNext());
1554 * the VisibleColsIterator is tested elsewhere, this just tests that
1555 * it can be retrieved from HiddenColumns
1557 @Test(groups = "Functional")
1558 public void testGetVisibleColsIterator()
1560 HiddenColumns h = new HiddenColumns();
1561 Iterator<Integer> it = h.getVisibleColsIterator(0, 10);
1563 assertTrue(it instanceof VisibleColsIterator);
1566 @Test(groups = "Functional")
1567 public void testHashCode()
1569 HiddenColumns h = new HiddenColumns();
1570 h.hideColumns(0, 25);
1572 int result = h.hashCode();
1573 assertTrue(result > 0);
1575 h.hideColumns(30, 50);
1576 assertTrue(h.hashCode() > 0);
1577 assertTrue(result != h.hashCode());