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.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.assertFalse;
25 import static org.testng.AssertJUnit.assertSame;
26 import static org.testng.AssertJUnit.assertTrue;
28 import jalview.analysis.AlignmentGenerator;
29 import jalview.gui.JvOptionPane;
31 import java.util.Arrays;
32 import java.util.BitSet;
33 import java.util.List;
35 import org.testng.annotations.BeforeClass;
36 import org.testng.annotations.Test;
38 public class HiddenColumnsTest
41 @BeforeClass(alwaysRun = true)
42 public void setUpJvOptionPane()
44 JvOptionPane.setInteractiveMode(false);
45 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
49 * Test the method which counts the number of hidden columns
51 @Test(groups = { "Functional" })
52 public void testGetSize()
54 HiddenColumns hidden = new HiddenColumns();
55 assertEquals(0, hidden.getSize());
57 hidden.hideColumns(3, 5);
58 assertEquals(3, hidden.getSize());
60 hidden.hideColumns(8, 8);
61 assertEquals(4, hidden.getSize());
63 hidden.hideColumns(9, 14);
64 assertEquals(10, hidden.getSize());
66 ColumnSelection cs = new ColumnSelection();
67 hidden.revealAllHiddenColumns(cs);
68 assertEquals(0, hidden.getSize());
72 * Test the method that finds the visible column position of an alignment
73 * column, allowing for hidden columns.
75 @Test(groups = { "Functional" })
76 public void testFindColumnPosition()
78 HiddenColumns cs = new HiddenColumns();
79 assertEquals(5, cs.findColumnPosition(5));
81 // hiding column 6 makes no difference
83 assertEquals(5, cs.findColumnPosition(5));
85 // hiding column 4 moves column 5 to column 4
87 assertEquals(4, cs.findColumnPosition(5));
89 // hiding column 4 moves column 4 to position 3
90 assertEquals(3, cs.findColumnPosition(4));
92 // hiding columns 1 and 2 moves column 5 to column 2
94 assertEquals(2, cs.findColumnPosition(5));
96 // check with > 1 hidden column regions
97 // where some columns are in the hidden regions
98 HiddenColumns cs2 = new HiddenColumns();
99 cs2.hideColumns(5, 10);
100 cs2.hideColumns(20, 27);
101 cs2.hideColumns(40, 44);
103 // hiding columns 5-10 and 20-27 moves column 8 to column 4
104 assertEquals(4, cs2.findColumnPosition(8));
106 // and moves column 24 to 13
107 assertEquals(13, cs2.findColumnPosition(24));
109 // and moves column 28 to 14
110 assertEquals(14, cs2.findColumnPosition(28));
112 // and moves column 40 to 25
113 assertEquals(25, cs2.findColumnPosition(40));
115 // check when hidden columns start at 0 that the visible column
117 HiddenColumns cs3 = new HiddenColumns();
118 cs3.hideColumns(0, 4);
119 assertEquals(0, cs3.findColumnPosition(2));
124 * Test the method that finds the visible column position a given distance
125 * before another column
127 @Test(groups = { "Functional" })
128 public void testFindColumnNToLeft()
130 HiddenColumns cs = new HiddenColumns();
132 // test that without hidden columns, findColumnNToLeft returns
133 // position n to left of provided position
134 int pos = cs.subtractVisibleColumns(3, 10);
135 assertEquals(7, pos);
137 // 0 returns same position
138 pos = cs.subtractVisibleColumns(0, 10);
139 assertEquals(10, pos);
141 // overflow to left returns negative number
142 pos = cs.subtractVisibleColumns(3, 0);
143 assertEquals(-3, pos);
145 // test that with hidden columns to left of result column
146 // behaviour is the same as above
147 cs.hideColumns(1, 3);
149 // position n to left of provided position
150 pos = cs.subtractVisibleColumns(3, 10);
151 assertEquals(7, pos);
153 // 0 returns same position
154 pos = cs.subtractVisibleColumns(0, 10);
155 assertEquals(10, pos);
157 // test with one set of hidden columns between start and required position
158 cs.hideColumns(12, 15);
159 pos = cs.subtractVisibleColumns(8, 17);
160 assertEquals(5, pos);
162 // test with two sets of hidden columns between start and required position
163 cs.hideColumns(20, 21);
164 pos = cs.subtractVisibleColumns(8, 23);
165 assertEquals(9, pos);
167 // repeat last 2 tests with no hidden columns to left of required position
168 ColumnSelection colsel = new ColumnSelection();
169 cs.revealAllHiddenColumns(colsel);
171 // test with one set of hidden columns between start and required position
172 cs.hideColumns(12, 15);
173 pos = cs.subtractVisibleColumns(8, 17);
174 assertEquals(5, pos);
176 // test with two sets of hidden columns between start and required position
177 cs.hideColumns(20, 21);
178 pos = cs.subtractVisibleColumns(8, 23);
179 assertEquals(9, pos);
183 @Test(groups = { "Functional" })
184 public void testGetVisibleContigs()
186 HiddenColumns cs = new HiddenColumns();
187 cs.hideColumns(3, 6);
188 cs.hideColumns(8, 9);
189 cs.hideColumns(12, 12);
191 // start position is inclusive, end position exclusive:
192 int[] visible = cs.getVisibleContigs(1, 13);
193 assertEquals("[1, 2, 7, 7, 10, 11]", Arrays.toString(visible));
195 visible = cs.getVisibleContigs(4, 14);
196 assertEquals("[7, 7, 10, 11, 13, 13]", Arrays.toString(visible));
198 visible = cs.getVisibleContigs(3, 10);
199 assertEquals("[7, 7]", Arrays.toString(visible));
201 visible = cs.getVisibleContigs(4, 6);
202 assertEquals("[]", Arrays.toString(visible));
205 @Test(groups = { "Functional" })
206 public void testEquals()
208 HiddenColumns cs = new HiddenColumns();
209 cs.hideColumns(5, 9);
211 // a different set of hidden columns
212 HiddenColumns cs2 = new HiddenColumns();
214 // with no hidden columns
215 assertFalse(cs.equals(cs2));
216 assertFalse(cs2.equals(cs));
218 // with hidden columns added in a different order
219 cs2.hideColumns(6, 9);
220 cs2.hideColumns(5, 8);
222 assertTrue(cs.equals(cs2));
223 assertTrue(cs.equals(cs));
224 assertTrue(cs2.equals(cs));
225 assertTrue(cs2.equals(cs2));
228 @Test(groups = "Functional")
229 public void testCopyConstructor()
231 HiddenColumns cs = new HiddenColumns();
232 cs.hideColumns(10, 11);
233 cs.hideColumns(5, 7);
234 assertEquals("[5, 7]", Arrays.toString(cs.getHiddenRegions().get(0)));
236 HiddenColumns cs2 = new HiddenColumns(cs);
237 assertTrue(cs2.hasHiddenColumns());
238 assertEquals(2, cs2.getHiddenRegions().size());
239 // hidden columns are held in column order
240 assertEquals("[5, 7]", Arrays.toString(cs2.getHiddenRegions().get(0)));
241 assertEquals("[10, 11]", Arrays.toString(cs2.getHiddenRegions().get(1)));
245 * Test the code used to locate the reference sequence ruler origin
247 @Test(groups = { "Functional" })
248 public void testLocateVisibleBoundsofSequence()
250 // create random alignment
251 AlignmentGenerator gen = new AlignmentGenerator(false);
252 AlignmentI al = gen.generate(50, 20, 123, 5, 5);
254 HiddenColumns cs = al.getHiddenColumns();
255 ColumnSelection colsel = new ColumnSelection();
257 SequenceI seq = new Sequence("RefSeq", "-A-SD-ASD--E---");
258 assertEquals(2, seq.findIndex(seq.getStart()));
262 Arrays.toString(new int[] { seq.findIndex(seq.getStart()) - 1,
263 seq.findIndex(seq.getEnd()) - 1, seq.getStart(),
264 seq.getEnd(), seq.findIndex(seq.getStart()) - 1,
265 seq.findIndex(seq.getEnd()) - 1 }),
266 Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
268 // hidden column on gap after end of sequence - should not affect bounds
269 colsel.hideSelectedColumns(13, al.getHiddenColumns());
271 Arrays.toString(new int[] { seq.findIndex(seq.getStart()) - 1,
272 seq.findIndex(seq.getEnd()) - 1, seq.getStart(),
273 seq.getEnd(), seq.findIndex(seq.getStart()) - 1,
274 seq.findIndex(seq.getEnd()) - 1 }),
275 Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
277 cs.revealAllHiddenColumns(colsel);
278 // hidden column on gap before beginning of sequence - should vis bounds by
280 colsel.hideSelectedColumns(0, al.getHiddenColumns());
282 Arrays.toString(new int[] { seq.findIndex(seq.getStart()) - 2,
283 seq.findIndex(seq.getEnd()) - 2, seq.getStart(),
284 seq.getEnd(), seq.findIndex(seq.getStart()) - 1,
285 seq.findIndex(seq.getEnd()) - 1 }),
286 Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
288 cs.revealAllHiddenColumns(colsel);
289 // hide columns around most of sequence - leave one residue remaining
290 cs.hideColumns(1, 3);
291 cs.hideColumns(6, 11);
293 cs.getVisibleSequenceStrings(0, 5, new SequenceI[] { seq })[0]);
295 Arrays.toString(new int[] { 1, 1, 3, 3,
296 seq.findIndex(seq.getStart()) - 1,
297 seq.findIndex(seq.getEnd()) - 1 }),
298 Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
299 cs.revealAllHiddenColumns(colsel);
301 // hide whole sequence - should just get location of hidden region
302 // containing sequence
303 cs.hideColumns(1, 11);
305 Arrays.toString(new int[] { 0, 1, 0, 0,
306 seq.findIndex(seq.getStart()) - 1,
307 seq.findIndex(seq.getEnd()) - 1 }),
308 Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
312 @Test(groups = { "Functional" })
313 public void testLocateVisibleBoundsPathologicals()
315 // test some pathological cases we missed
316 AlignmentI al = new Alignment(new SequenceI[] { new Sequence(
317 "refseqGaptest", "KTDVTI----------NFI-----G----L") });
318 HiddenColumns cs = new HiddenColumns();
319 cs.hideInsertionsFor(al.getSequenceAt(0));
323 + al.getSequenceAt(0).getCharAt(
324 cs.adjustForHiddenColumns(9)));
328 @Test(groups = { "Functional" })
329 public void testHideColumns()
331 // create random alignment
332 AlignmentGenerator gen = new AlignmentGenerator(false);
333 AlignmentI al = gen.generate(50, 20, 123, 5, 5);
335 ColumnSelection colsel = new ColumnSelection();
336 HiddenColumns cs = al.getHiddenColumns();
337 colsel.hideSelectedColumns(5, al.getHiddenColumns());
338 List<int[]> hidden = cs.getHiddenRegions();
339 assertEquals(1, hidden.size());
340 assertEquals("[5, 5]", Arrays.toString(hidden.get(0)));
342 colsel.hideSelectedColumns(3, al.getHiddenColumns());
343 assertEquals(2, hidden.size());
344 // two hidden ranges, in order:
345 assertSame(hidden, cs.getHiddenRegions());
346 assertEquals("[3, 3]", Arrays.toString(hidden.get(0)));
347 assertEquals("[5, 5]", Arrays.toString(hidden.get(1)));
349 // hiding column 4 expands [3, 3] to [3, 4]
350 // and merges to [5, 5] to make [3, 5]
351 colsel.hideSelectedColumns(4, al.getHiddenColumns());
352 hidden = cs.getHiddenRegions();
353 assertEquals(1, hidden.size());
354 assertEquals("[3, 5]", Arrays.toString(hidden.get(0)));
356 // clear hidden columns (note they are added to selected)
357 cs.revealAllHiddenColumns(colsel);
358 // it is now actually null but getter returns an empty list
359 assertTrue(cs.getHiddenRegions().isEmpty());
361 cs.hideColumns(3, 6);
362 hidden = cs.getHiddenRegions();
363 int[] firstHiddenRange = hidden.get(0);
364 assertEquals("[3, 6]", Arrays.toString(firstHiddenRange));
366 // adding a subrange of already hidden should do nothing
367 cs.hideColumns(4, 5);
368 assertEquals(1, hidden.size());
369 assertSame(firstHiddenRange, cs.getHiddenRegions().get(0));
370 cs.hideColumns(3, 5);
371 assertEquals(1, hidden.size());
372 assertSame(firstHiddenRange, cs.getHiddenRegions().get(0));
373 cs.hideColumns(4, 6);
374 assertEquals(1, hidden.size());
375 assertSame(firstHiddenRange, cs.getHiddenRegions().get(0));
376 cs.hideColumns(3, 6);
377 assertEquals(1, hidden.size());
378 assertSame(firstHiddenRange, cs.getHiddenRegions().get(0));
380 cs.revealAllHiddenColumns(colsel);
381 cs.hideColumns(2, 4);
382 hidden = cs.getHiddenRegions();
383 assertEquals(1, hidden.size());
384 assertEquals("[2, 4]", Arrays.toString(hidden.get(0)));
386 // extend contiguous with 2 positions overlap
387 cs.hideColumns(3, 5);
388 assertEquals(1, hidden.size());
389 assertEquals("[2, 5]", Arrays.toString(hidden.get(0)));
391 // extend contiguous with 1 position overlap
392 cs.hideColumns(5, 6);
393 assertEquals(1, hidden.size());
394 assertEquals("[2, 6]", Arrays.toString(hidden.get(0)));
396 // extend contiguous with overlap both ends:
397 cs.hideColumns(1, 7);
398 assertEquals(1, hidden.size());
399 assertEquals("[1, 7]", Arrays.toString(hidden.get(0)));
403 * Test the method that reveals a range of hidden columns given the start
404 * column of the range
406 @Test(groups = { "Functional" })
407 public void testRevealHiddenColumns()
409 ColumnSelection colsel = new ColumnSelection();
410 HiddenColumns cs = new HiddenColumns();
411 cs.hideColumns(5, 8);
412 colsel.addElement(10);
413 cs.revealHiddenColumns(5, colsel);
414 // hidden columns list now null but getter returns empty list:
415 assertTrue(cs.getHiddenRegions().isEmpty());
416 // revealed columns are marked as selected (added to selection):
417 assertEquals("[10, 5, 6, 7, 8]", colsel.getSelected().toString());
419 // calling with a column other than the range start does nothing:
420 colsel = new ColumnSelection();
421 cs = new HiddenColumns();
422 cs.hideColumns(5, 8);
423 List<int[]> hidden = cs.getHiddenRegions();
424 cs.revealHiddenColumns(6, colsel);
425 assertSame(hidden, cs.getHiddenRegions());
426 assertTrue(colsel.getSelected().isEmpty());
429 @Test(groups = { "Functional" })
430 public void testRevealAllHiddenColumns()
432 HiddenColumns cs = new HiddenColumns();
433 ColumnSelection colsel = new ColumnSelection();
434 cs.hideColumns(5, 8);
435 cs.hideColumns(2, 3);
436 colsel.addElement(11);
437 colsel.addElement(1);
438 cs.revealAllHiddenColumns(colsel);
441 * revealing hidden columns adds them (in order) to the (unordered)
444 assertTrue(cs.getHiddenRegions().isEmpty());
445 assertEquals("[11, 1, 2, 3, 5, 6, 7, 8]", colsel.getSelected()
449 @Test(groups = { "Functional" })
450 public void testIsVisible()
452 HiddenColumns cs = new HiddenColumns();
453 cs.hideColumns(2, 4);
454 cs.hideColumns(6, 7);
455 assertTrue(cs.isVisible(0));
456 assertTrue(cs.isVisible(-99));
457 assertTrue(cs.isVisible(1));
458 assertFalse(cs.isVisible(2));
459 assertFalse(cs.isVisible(3));
460 assertFalse(cs.isVisible(4));
461 assertTrue(cs.isVisible(5));
462 assertFalse(cs.isVisible(6));
463 assertFalse(cs.isVisible(7));
467 * Test for the case when a hidden range encloses more one already hidden
470 @Test(groups = { "Functional" })
471 public void testHideColumns_subsumingHidden()
474 * JAL-2370 bug scenario:
475 * two hidden ranges subsumed by a third
477 HiddenColumns cs = new HiddenColumns();
478 cs.hideColumns(49, 59);
479 cs.hideColumns(69, 79);
480 List<int[]> hidden = cs.getHiddenRegions();
481 assertEquals(2, hidden.size());
482 assertEquals("[49, 59]", Arrays.toString(hidden.get(0)));
483 assertEquals("[69, 79]", Arrays.toString(hidden.get(1)));
485 cs.hideColumns(48, 80);
486 hidden = cs.getHiddenRegions();
487 assertEquals(1, hidden.size());
488 assertEquals("[48, 80]", Arrays.toString(hidden.get(0)));
491 * another...joining hidden ranges
493 cs = new HiddenColumns();
494 cs.hideColumns(10, 20);
495 cs.hideColumns(30, 40);
496 cs.hideColumns(50, 60);
497 // hiding 21-49 should merge to one range
498 cs.hideColumns(21, 49);
499 hidden = cs.getHiddenRegions();
500 assertEquals(1, hidden.size());
501 assertEquals("[10, 60]", Arrays.toString(hidden.get(0)));
504 * another...left overlap, subsumption, right overlap,
505 * no overlap of existing hidden ranges
507 cs = new HiddenColumns();
508 cs.hideColumns(10, 20);
509 cs.hideColumns(10, 20);
510 cs.hideColumns(30, 35);
511 cs.hideColumns(40, 50);
512 cs.hideColumns(60, 70);
514 cs.hideColumns(15, 45);
515 hidden = cs.getHiddenRegions();
516 assertEquals(2, hidden.size());
517 assertEquals("[10, 50]", Arrays.toString(hidden.get(0)));
518 assertEquals("[60, 70]", Arrays.toString(hidden.get(1)));
521 @Test(groups = { "Functional" })
522 public void testHideBitset()
526 BitSet one = new BitSet();
530 cs = new HiddenColumns();
531 cs.hideMarkedBits(one);
532 assertEquals(1, cs.getHiddenRegions().size());
535 cs = new HiddenColumns();
536 cs.hideMarkedBits(one);
537 assertEquals(1, cs.getHiddenRegions().size());
540 cs = new HiddenColumns();
541 cs.hideMarkedBits(one);
542 assertEquals(1, cs.getHiddenRegions().size());
546 cs = new HiddenColumns();
547 cs.hideMarkedBits(one);
548 assertEquals(2, cs.getHiddenRegions().size());
550 assertEquals(0, cs.adjustForHiddenColumns(0));
551 assertEquals(2, cs.adjustForHiddenColumns(1));
552 assertEquals(4, cs.adjustForHiddenColumns(2));
556 cs = new HiddenColumns();
557 cs.hideMarkedBits(one);
559 assertEquals(1, cs.getHiddenRegions().size());
561 assertEquals(0, cs.adjustForHiddenColumns(0));
562 assertEquals(1, cs.adjustForHiddenColumns(1));
563 assertEquals(2, cs.adjustForHiddenColumns(2));
564 assertEquals(4, cs.adjustForHiddenColumns(3));