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;
27 import static org.testng.AssertJUnit.fail;
29 import java.util.Arrays;
30 import java.util.BitSet;
31 import java.util.Collections;
32 import java.util.ConcurrentModificationException;
33 import java.util.List;
35 import org.testng.annotations.Test;
37 public class ColumnSelectionTest
40 @Test(groups = { "Functional" })
41 public void testAddElement()
43 ColumnSelection cs = new ColumnSelection();
47 cs.addElement(5); // ignored
48 List<Integer> sel = cs.getSelected();
49 assertEquals("[2, 5, 3]", sel.toString());
53 * Test the remove method - in particular to verify that remove(int i) removes
54 * the element whose value is i, _NOT_ the i'th element.
56 @Test(groups = { "Functional" })
57 public void testRemoveElement()
59 ColumnSelection cs = new ColumnSelection();
63 // removing elements not in the list has no effect
66 List<Integer> sel = cs.getSelected();
67 assertEquals(2, sel.size());
68 assertEquals(new Integer(2), sel.get(0));
69 assertEquals(new Integer(5), sel.get(1));
71 // removing an element in the list removes it
73 // ...and also from the read-only view
74 assertEquals(1, sel.size());
75 sel = cs.getSelected();
76 assertEquals(1, sel.size());
77 assertEquals(new Integer(5), sel.get(0));
81 * Test the method that finds the visible column position of an alignment
82 * column, allowing for hidden columns.
84 @Test(groups = { "Functional" })
85 public void testFindColumnPosition()
87 ColumnSelection cs = new ColumnSelection();
88 assertEquals(5, cs.findColumnPosition(5));
90 // hiding column 6 makes no difference
92 assertEquals(5, cs.findColumnPosition(5));
94 // hiding column 4 moves column 5 to column 4
96 assertEquals(4, cs.findColumnPosition(5));
98 // hiding columns 1 and 2 moves column 5 to column 2
100 assertEquals(2, cs.findColumnPosition(5));
104 * Test the code used to locate the reference sequence ruler origin
106 @Test(groups = { "Functional" })
107 public void testLocateVisibleBoundsofSequence()
109 ColumnSelection cs = new ColumnSelection();
110 SequenceI seq = new Sequence("RefSeq", "-A-SD-ASD--E---");
111 assertEquals(2, seq.findIndex(seq.getStart()));
115 Arrays.toString(new int[] { seq.findIndex(seq.getStart()) - 1,
116 seq.findIndex(seq.getEnd()) - 1, seq.getStart(),
117 seq.getEnd(), seq.findIndex(seq.getStart()) - 1,
118 seq.findIndex(seq.getEnd()) - 1 }),
119 Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
121 // hidden column on gap after end of sequence - should not affect bounds
124 Arrays.toString(new int[] { seq.findIndex(seq.getStart()) - 1,
125 seq.findIndex(seq.getEnd()) - 1, seq.getStart(),
126 seq.getEnd(), seq.findIndex(seq.getStart()) - 1,
127 seq.findIndex(seq.getEnd()) - 1 }),
128 Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
130 cs.revealAllHiddenColumns();
131 // hidden column on gap before beginning of sequence - should vis bounds by
135 Arrays.toString(new int[] { seq.findIndex(seq.getStart()) - 2,
136 seq.findIndex(seq.getEnd()) - 2, seq.getStart(),
137 seq.getEnd(), seq.findIndex(seq.getStart()) - 1,
138 seq.findIndex(seq.getEnd()) - 1 }),
139 Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
141 cs.revealAllHiddenColumns();
142 // hide columns around most of sequence - leave one residue remaining
143 cs.hideColumns(1, 3);
144 cs.hideColumns(6, 11);
146 cs.getVisibleSequenceStrings(0, 5, new SequenceI[] { seq })[0]);
148 Arrays.toString(new int[] { 1, 1, 3, 3,
149 seq.findIndex(seq.getStart()) - 1,
150 seq.findIndex(seq.getEnd()) - 1 }),
151 Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
152 cs.revealAllHiddenColumns();
154 // hide whole sequence - should just get location of hidden region
155 // containing sequence
156 cs.hideColumns(1, 11);
158 Arrays.toString(new int[] { 0, 1, 0, 0,
159 seq.findIndex(seq.getStart()) - 1,
160 seq.findIndex(seq.getEnd()) - 1 }),
161 Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
165 @Test(groups={"Functional"})
166 public void testLocateVisibleBoundsPathologicals()
168 // test some pathological cases we missed
169 AlignmentI al = new Alignment(new SequenceI[] { new Sequence("refseqGaptest","KTDVTI----------NFI-----G----L")});
170 ColumnSelection cs = new ColumnSelection();
171 cs.hideInsertionsFor(al.getSequenceAt(0));
175 + al.getSequenceAt(0).getCharAt(
176 cs.adjustForHiddenColumns(9)));
180 @Test(groups = { "Functional" })
181 public void testHideColumns()
183 ColumnSelection cs = new ColumnSelection();
185 List<int[]> hidden = cs.getHiddenColumns();
186 assertEquals(1, hidden.size());
187 assertEquals("[5, 5]", Arrays.toString(hidden.get(0)));
190 assertEquals(2, hidden.size());
191 // two hidden ranges, in order:
192 assertSame(hidden, cs.getHiddenColumns());
193 assertEquals("[3, 3]", Arrays.toString(hidden.get(0)));
194 assertEquals("[5, 5]", Arrays.toString(hidden.get(1)));
196 // hiding column 4 expands [3, 3] to [3, 4]
197 // not fancy enough to coalesce this into [3, 5] though
199 hidden = cs.getHiddenColumns();
200 assertEquals(2, hidden.size());
201 assertEquals("[3, 4]", Arrays.toString(hidden.get(0)));
202 assertEquals("[5, 5]", Arrays.toString(hidden.get(1)));
204 // clear hidden columns (note they are added to selected)
205 cs.revealAllHiddenColumns();
206 // it is now actually null but getter returns an empty list
207 assertTrue(cs.getHiddenColumns().isEmpty());
209 cs.hideColumns(3, 6);
210 hidden = cs.getHiddenColumns();
211 int[] firstHiddenRange = hidden.get(0);
212 assertEquals("[3, 6]", Arrays.toString(firstHiddenRange));
214 // adding a subrange of already hidden should do nothing
215 cs.hideColumns(4, 5);
216 assertEquals(1, hidden.size());
217 assertSame(firstHiddenRange, cs.getHiddenColumns().get(0));
218 cs.hideColumns(3, 5);
219 assertEquals(1, hidden.size());
220 assertSame(firstHiddenRange, cs.getHiddenColumns().get(0));
221 cs.hideColumns(4, 6);
222 assertEquals(1, hidden.size());
223 assertSame(firstHiddenRange, cs.getHiddenColumns().get(0));
224 cs.hideColumns(3, 6);
225 assertEquals(1, hidden.size());
226 assertSame(firstHiddenRange, cs.getHiddenColumns().get(0));
228 cs.revealAllHiddenColumns();
229 cs.hideColumns(2, 4);
230 hidden = cs.getHiddenColumns();
231 assertEquals(1, hidden.size());
232 assertEquals("[2, 4]", Arrays.toString(hidden.get(0)));
234 // extend contiguous with 2 positions overlap
235 cs.hideColumns(3, 5);
236 assertEquals(1, hidden.size());
237 assertEquals("[2, 5]", Arrays.toString(hidden.get(0)));
239 // extend contiguous with 1 position overlap
240 cs.hideColumns(5, 6);
241 assertEquals(1, hidden.size());
242 assertEquals("[2, 6]", Arrays.toString(hidden.get(0)));
244 // extend contiguous with overlap both ends:
245 cs.hideColumns(1, 7);
246 assertEquals(1, hidden.size());
247 assertEquals("[1, 7]", Arrays.toString(hidden.get(0)));
251 * Test the method that hides a specified column including any adjacent
252 * selected columns. This is a convenience method for the case where multiple
253 * column regions are selected and then hidden using menu option View | Hide |
256 @Test(groups = { "Functional" })
257 public void testHideColumns_withSelection()
259 ColumnSelection cs = new ColumnSelection();
260 // select columns 4-6
264 // hide column 5 (and adjacent):
267 List<int[]> hidden = cs.getHiddenColumns();
268 assertEquals(1, hidden.size());
269 assertEquals("[4, 6]", Arrays.toString(hidden.get(0)));
270 // none now selected:
271 assertTrue(cs.getSelected().isEmpty());
273 // repeat, hiding column 4 (5 and 6)
274 cs = new ColumnSelection();
279 hidden = cs.getHiddenColumns();
280 assertEquals(1, hidden.size());
281 assertEquals("[4, 6]", Arrays.toString(hidden.get(0)));
282 assertTrue(cs.getSelected().isEmpty());
284 // repeat, hiding column (4, 5 and) 6
285 cs = new ColumnSelection();
290 hidden = cs.getHiddenColumns();
291 assertEquals(1, hidden.size());
292 assertEquals("[4, 6]", Arrays.toString(hidden.get(0)));
293 assertTrue(cs.getSelected().isEmpty());
295 // repeat, with _only_ adjacent columns selected
296 cs = new ColumnSelection();
300 hidden = cs.getHiddenColumns();
301 assertEquals(1, hidden.size());
302 assertEquals("[4, 6]", Arrays.toString(hidden.get(0)));
303 assertTrue(cs.getSelected().isEmpty());
307 * Test the method that hides all (possibly disjoint) selected column ranges
309 @Test(groups = { "Functional" })
310 public void testHideSelectedColumns()
312 ColumnSelection cs = new ColumnSelection();
313 int[] sel = { 2, 3, 4, 7, 8, 9, 20, 21, 22 };
318 cs.hideColumns(15, 18);
320 cs.hideSelectedColumns();
321 assertTrue(cs.getSelected().isEmpty());
322 List<int[]> hidden = cs.getHiddenColumns();
323 assertEquals(4, hidden.size());
324 assertEquals("[2, 4]", Arrays.toString(hidden.get(0)));
325 assertEquals("[7, 9]", Arrays.toString(hidden.get(1)));
326 assertEquals("[15, 18]", Arrays.toString(hidden.get(2)));
327 assertEquals("[20, 22]", Arrays.toString(hidden.get(3)));
331 * Test the method that gets runs of selected columns ordered by column. If
332 * this fails, HideSelectedColumns may also fail
334 @Test(groups = { "Functional" })
335 public void testGetSelectedRanges()
338 * getSelectedRanges returns ordered columns regardless
339 * of the order in which they are added
341 ColumnSelection cs = new ColumnSelection();
342 int[] sel = { 4, 3, 7, 21, 9, 20, 8, 22, 2 };
348 range = cs.getSelectedRanges();
349 assertEquals(3, range.size());
350 assertEquals("[2, 4]", Arrays.toString(range.get(0)));
351 assertEquals("[7, 9]", Arrays.toString(range.get(1)));
352 assertEquals("[20, 22]", Arrays.toString(range.get(2)));
355 range = cs.getSelectedRanges();
356 assertEquals(3, range.size());
357 assertEquals("[0, 4]", Arrays.toString(range.get(0)));
361 * Test the method that reveals a range of hidden columns given the start
362 * column of the range
364 @Test(groups = { "Functional" })
365 public void testRevealHiddenColumns()
367 ColumnSelection cs = new ColumnSelection();
368 cs.hideColumns(5, 8);
370 cs.revealHiddenColumns(5);
371 // hidden columns list now null but getter returns empty list:
372 assertTrue(cs.getHiddenColumns().isEmpty());
373 // revealed columns are marked as selected (added to selection):
374 assertEquals("[10, 5, 6, 7, 8]", cs.getSelected().toString());
376 // calling with a column other than the range start does nothing:
377 cs = new ColumnSelection();
378 cs.hideColumns(5, 8);
379 List<int[]> hidden = cs.getHiddenColumns();
380 cs.revealHiddenColumns(6);
381 assertSame(hidden, cs.getHiddenColumns());
382 assertTrue(cs.getSelected().isEmpty());
385 @Test(groups = { "Functional" })
386 public void testRevealAllHiddenColumns()
388 ColumnSelection cs = new ColumnSelection();
389 cs.hideColumns(5, 8);
390 cs.hideColumns(2, 3);
393 cs.revealAllHiddenColumns();
396 * revealing hidden columns adds them (in order) to the (unordered)
399 assertTrue(cs.getHiddenColumns().isEmpty());
400 assertEquals("[11, 1, 2, 3, 5, 6, 7, 8]", cs.getSelected().toString());
403 @Test(groups = { "Functional" })
404 public void testIsVisible()
406 ColumnSelection cs = new ColumnSelection();
407 cs.hideColumns(2, 4);
408 cs.hideColumns(6, 7);
409 assertTrue(cs.isVisible(0));
410 assertTrue(cs.isVisible(-99));
411 assertTrue(cs.isVisible(1));
412 assertFalse(cs.isVisible(2));
413 assertFalse(cs.isVisible(3));
414 assertFalse(cs.isVisible(4));
415 assertTrue(cs.isVisible(5));
416 assertFalse(cs.isVisible(6));
417 assertFalse(cs.isVisible(7));
420 @Test(groups = { "Functional" })
421 public void testGetVisibleContigs()
423 ColumnSelection cs = new ColumnSelection();
424 cs.hideColumns(3, 6);
425 cs.hideColumns(8, 9);
426 cs.hideColumns(12, 12);
428 // start position is inclusive, end position exclusive:
429 int[] visible = cs.getVisibleContigs(1, 13);
430 assertEquals("[1, 2, 7, 7, 10, 11]", Arrays.toString(visible));
432 visible = cs.getVisibleContigs(4, 14);
433 assertEquals("[7, 7, 10, 11, 13, 13]", Arrays.toString(visible));
435 visible = cs.getVisibleContigs(3, 10);
436 assertEquals("[7, 7]", Arrays.toString(visible));
438 visible = cs.getVisibleContigs(4, 6);
439 assertEquals("[]", Arrays.toString(visible));
442 @Test(groups = { "Functional" })
443 public void testInvertColumnSelection()
445 ColumnSelection cs = new ColumnSelection();
449 cs.hideColumns(3, 3);
450 cs.hideColumns(6, 6);
452 // invert selection from start (inclusive) to end (exclusive)
453 // hidden columns are _not_ changed
454 cs.invertColumnSelection(2, 9);
455 assertEquals("[2, 5, 7]", cs.getSelected().toString());
457 cs.invertColumnSelection(1, 9);
458 assertEquals("[1, 4, 8]", cs.getSelected().toString());
461 @Test(groups = { "Functional" })
462 public void testMaxColumnSelection()
464 ColumnSelection cs = new ColumnSelection();
468 assertEquals(513, cs.getMax());
469 cs.removeElement(513);
470 assertEquals(1, cs.getMax());
472 assertEquals(0, cs.getMax());
475 assertEquals(513, cs.getMax());
479 @Test(groups = { "Functional" })
480 public void testMinColumnSelection()
482 ColumnSelection cs = new ColumnSelection();
486 assertEquals(0, cs.getMin());
488 assertEquals(1, cs.getMin());
490 assertEquals(0, cs.getMin());
493 @Test(groups = { "Functional" })
494 public void testEquals()
496 ColumnSelection cs = new ColumnSelection();
504 // same selections added in a different order
505 ColumnSelection cs2 = new ColumnSelection();
510 // with no hidden columns
511 assertFalse(cs.equals(cs2));
512 assertFalse(cs2.equals(cs));
514 // with hidden columns added in a different order
515 cs2.hideColumns(6, 9);
516 cs2.hideColumns(5, 8);
519 assertTrue(cs.equals(cs2));
520 assertTrue(cs.equals(cs));
521 assertTrue(cs2.equals(cs));
522 assertTrue(cs2.equals(cs2));
525 assertFalse(cs.equals(cs2));
526 assertFalse(cs2.equals(cs));
528 cs2.removeElement(12);
529 assertTrue(cs.equals(cs2));
532 assertFalse(cs.equals(cs2));
534 * unhiding a column adds it to selection!
536 cs2.revealHiddenColumns(88);
537 assertFalse(cs.equals(cs2));
539 assertTrue(cs.equals(cs2));
543 * Test the method that returns selected columns, in the order in which they
546 @Test(groups = { "Functional" })
547 public void testGetSelected()
549 ColumnSelection cs = new ColumnSelection();
550 int[] sel = { 4, 3, 7, 21 };
556 List<Integer> selected = cs.getSelected();
557 assertEquals(4, selected.size());
558 assertEquals("[4, 3, 7, 21]", selected.toString());
561 * getSelected returns a read-only view of the list
562 * verify the view follows any changes in it
567 assertEquals("[3, 21, 1]", selected.toString());
571 * Test to verify that the list returned by getSelection cannot be modified
573 @Test(groups = { "Functional" })
574 public void testGetSelected_isReadOnly()
576 ColumnSelection cs = new ColumnSelection();
579 List<Integer> selected = cs.getSelected();
583 fail("expected exception");
584 } catch (UnsupportedOperationException e)
591 fail("expected exception");
592 } catch (UnsupportedOperationException e)
599 fail("expected exception");
600 } catch (UnsupportedOperationException e)
606 Collections.sort(selected);
607 fail("expected exception");
608 } catch (UnsupportedOperationException e)
615 * Test that demonstrates a ConcurrentModificationException is thrown if you
616 * change the selection while iterating over it
619 groups = "Functional",
620 expectedExceptions = { ConcurrentModificationException.class })
621 public void testGetSelected_concurrentModification()
623 ColumnSelection cs = new ColumnSelection();
629 * simulate changing the list under us (e.g. in a separate
630 * thread) while iterating over it -> ConcurrentModificationException
632 List<Integer> selected = cs.getSelected();
633 for (Integer col : selected)
635 if (col.intValue() == 0)
642 @Test(groups = "Functional")
643 public void testMarkColumns()
645 ColumnSelection cs = new ColumnSelection();
646 cs.addElement(5); // this will be cleared
647 BitSet toMark = new BitSet();
653 assertTrue(cs.markColumns(toMark, 3, 8, false, false, false));
654 List<Integer> selected = cs.getSelected();
655 assertEquals(2, selected.size());
656 assertTrue(selected.contains(3));
657 assertTrue(selected.contains(6));
660 @Test(groups = "Functional")
661 public void testMarkColumns_extend()
663 ColumnSelection cs = new ColumnSelection();
666 BitSet toMark = new BitSet();
673 * extending selection of {3, 6} should leave {1, 3, 5, 6} selected
675 assertTrue(cs.markColumns(toMark, 3, 8, false, true, false));
676 List<Integer> selected = cs.getSelected();
677 assertEquals(4, selected.size());
678 assertTrue(selected.contains(1));
679 assertTrue(selected.contains(3));
680 assertTrue(selected.contains(5));
681 assertTrue(selected.contains(6));
684 @Test(groups = "Functional")
685 public void testMarkColumns_invert()
687 ColumnSelection cs = new ColumnSelection();
688 cs.addElement(5); // this will be cleared
689 BitSet toMark = new BitSet();
696 * inverted selection of {3, 6} should select {4, 5, 7, 8}
698 assertTrue(cs.markColumns(toMark, 3, 8, true, false, false));
699 List<Integer> selected = cs.getSelected();
700 assertEquals(4, selected.size());
701 assertTrue(selected.contains(4));
702 assertTrue(selected.contains(5));
703 assertTrue(selected.contains(7));
704 assertTrue(selected.contains(8));
707 @Test(groups = "Functional")
708 public void testMarkColumns_toggle()
710 ColumnSelection cs = new ColumnSelection();
711 cs.addElement(1); // outside change range
714 cs.addElement(10); // outside change range
715 BitSet toMark = new BitSet();
722 * toggling state of {3, 6} should leave {1, 4, 6, 10} selected
724 assertTrue(cs.markColumns(toMark, 3, 8, false, false, true));
725 List<Integer> selected = cs.getSelected();
726 assertEquals(4, selected.size());
727 assertTrue(selected.contains(1));
728 assertTrue(selected.contains(4));
729 assertTrue(selected.contains(6));
730 assertTrue(selected.contains(10));
733 @Test(groups = "Functional")
734 public void testCopyConstructor()
736 ColumnSelection cs = new ColumnSelection();
739 cs.hideColumns(10, 11);
740 cs.hideColumns(5, 7);
741 assertEquals("[5, 7]", Arrays.toString(cs.getHiddenColumns().get(0)));
743 ColumnSelection cs2 = new ColumnSelection(cs);
744 assertTrue(cs2.hasSelectedColumns());
745 assertTrue(cs2.hasHiddenColumns());
746 // order of column selection is preserved
747 assertEquals("[3, 1]", cs2.getSelected().toString());
748 assertEquals(2, cs2.getHiddenColumns().size());
749 // hidden columns are held in column order
750 assertEquals("[5, 7]", Arrays.toString(cs2.getHiddenColumns().get(0)));
751 assertEquals("[10, 11]", Arrays.toString(cs2.getHiddenColumns().get(1)));