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  1. Project Clover database Tue Mar 10 2026 14:58:44 GMT
  2. Package jalview.datamodel

File ColumnSelectionTest.java

 

Code metrics

6
368
22
1
724
511
29
0.08
16.73
22
1.32

Classes

Class Line # Actions
ColumnSelectionTest 44 368 29
0.00%
 

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1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
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.
11    *
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.
16    *
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.
20    */
21    package jalview.datamodel;
22   
23    import static org.testng.AssertJUnit.assertEquals;
24    import static org.testng.AssertJUnit.assertFalse;
25    import static org.testng.AssertJUnit.assertTrue;
26    import static org.testng.AssertJUnit.fail;
27   
28    import java.util.Arrays;
29    import java.util.BitSet;
30    import java.util.Collections;
31    import java.util.ConcurrentModificationException;
32    import java.util.Iterator;
33    import java.util.List;
34   
35    import org.testng.annotations.BeforeClass;
36    import org.testng.annotations.Test;
37   
38    import jalview.analysis.AlignmentGenerator;
39    import jalview.gui.JvOptionPane;
40    import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
41    import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField;
42    import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.ThresholdType;
43   
 
44    public class ColumnSelectionTest
45    {
46   
 
47  0 toggle @BeforeClass(alwaysRun = true)
48    public void setUpJvOptionPane()
49    {
50  0 JvOptionPane.setInteractiveMode(false);
51  0 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
52    }
53   
 
54  0 toggle @Test(groups = { "Functional" })
55    public void testAddElement()
56    {
57  0 ColumnSelection cs = new ColumnSelection();
58  0 cs.addElement(2);
59  0 cs.addElement(5);
60  0 cs.addElement(3);
61  0 cs.addElement(5); // ignored
62  0 List<Integer> sel = cs.getSelected();
63  0 assertEquals("[2, 5, 3]", sel.toString());
64    }
65   
 
66  0 toggle @Test(groups = { "Functional" })
67    public void testSetElementsFrom()
68    {
69  0 ColumnSelection fromcs = new ColumnSelection();
70  0 ColumnSelection tocs = new ColumnSelection();
71  0 HiddenColumns hidden = new HiddenColumns();
72   
73  0 fromcs.addElement(2);
74  0 fromcs.addElement(3);
75  0 fromcs.addElement(5);
76   
77  0 tocs.setElementsFrom(fromcs, hidden);
78  0 assertTrue(tocs.equals(fromcs));
79   
80  0 hidden.hideColumns(4, 6);
81  0 tocs.setElementsFrom(fromcs, hidden);
82   
83    // expect cols 2 and 3 to be selected but not 5
84  0 ColumnSelection expectcs = new ColumnSelection();
85  0 expectcs.addElement(2);
86  0 expectcs.addElement(3);
87  0 assertTrue(tocs.equals(expectcs));
88    }
89   
90    /**
91    * Test the remove method - in particular to verify that remove(int i) removes
92    * the element whose value is i, _NOT_ the i'th element.
93    */
 
94  0 toggle @Test(groups = { "Functional" })
95    public void testRemoveElement()
96    {
97  0 ColumnSelection cs = new ColumnSelection();
98  0 cs.addElement(2);
99  0 cs.addElement(5);
100   
101    // removing elements not in the list has no effect
102  0 cs.removeElement(0);
103  0 cs.removeElement(1);
104  0 List<Integer> sel = cs.getSelected();
105  0 assertEquals(2, sel.size());
106  0 assertEquals(Integer.valueOf(2), sel.get(0));
107  0 assertEquals(Integer.valueOf(5), sel.get(1));
108   
109    // removing an element in the list removes it
110  0 cs.removeElement(2);
111    // ...and also from the read-only view
112  0 assertEquals(1, sel.size());
113  0 sel = cs.getSelected();
114  0 assertEquals(1, sel.size());
115  0 assertEquals(Integer.valueOf(5), sel.get(0));
116    }
117   
118    /**
119    * Test the method that hides a specified column including any adjacent
120    * selected columns. This is a convenience method for the case where multiple
121    * column regions are selected and then hidden using menu option View | Hide |
122    * Selected Columns.
123    */
 
124  0 toggle @Test(groups = { "Functional" })
125    public void testHideColumns_withSelection()
126    {
127    // create random alignment
128  0 AlignmentGenerator gen = new AlignmentGenerator(false);
129  0 AlignmentI al = gen.generate(50, 20, 123, 5, 5);
130   
131  0 ColumnSelection cs = new ColumnSelection();
132    // select columns 4-6
133  0 cs.addElement(4);
134  0 cs.addElement(5);
135  0 cs.addElement(6);
136    // hide column 5 (and adjacent):
137  0 cs.hideSelectedColumns(5, al.getHiddenColumns());
138    // 4,5,6 now hidden:
139  0 Iterator<int[]> regions = al.getHiddenColumns().iterator();
140  0 assertEquals(1, al.getHiddenColumns().getNumberOfRegions());
141  0 assertEquals("[4, 6]", Arrays.toString(regions.next()));
142    // none now selected:
143  0 assertTrue(cs.getSelected().isEmpty());
144   
145    // repeat, hiding column 4 (5 and 6)
146  0 al = gen.generate(50, 20, 123, 5, 5);
147  0 cs = new ColumnSelection();
148  0 cs.addElement(4);
149  0 cs.addElement(5);
150  0 cs.addElement(6);
151  0 cs.hideSelectedColumns(4, al.getHiddenColumns());
152  0 regions = al.getHiddenColumns().iterator();
153  0 assertEquals(1, al.getHiddenColumns().getNumberOfRegions());
154  0 assertEquals("[4, 6]", Arrays.toString(regions.next()));
155  0 assertTrue(cs.getSelected().isEmpty());
156   
157    // repeat, hiding column (4, 5 and) 6
158  0 al = gen.generate(50, 20, 123, 5, 5);
159  0 cs = new ColumnSelection();
160  0 cs.addElement(4);
161  0 cs.addElement(5);
162  0 cs.addElement(6);
163  0 cs.hideSelectedColumns(6, al.getHiddenColumns());
164  0 regions = al.getHiddenColumns().iterator();
165  0 assertEquals(1, al.getHiddenColumns().getNumberOfRegions());
166  0 assertEquals("[4, 6]", Arrays.toString(regions.next()));
167  0 assertTrue(cs.getSelected().isEmpty());
168   
169    // repeat, with _only_ adjacent columns selected
170  0 al = gen.generate(50, 20, 123, 5, 5);
171  0 cs = new ColumnSelection();
172  0 cs.addElement(4);
173  0 cs.addElement(6);
174  0 cs.hideSelectedColumns(5, al.getHiddenColumns());
175  0 regions = al.getHiddenColumns().iterator();
176  0 assertEquals(1, al.getHiddenColumns().getNumberOfRegions());
177  0 assertEquals("[4, 6]", Arrays.toString(regions.next()));
178  0 assertTrue(cs.getSelected().isEmpty());
179    }
180   
181    /**
182    * Test the method that hides all (possibly disjoint) selected column ranges
183    */
 
184  0 toggle @Test(groups = { "Functional" })
185    public void testHideSelectedColumns()
186    {
187    // create random alignment
188  0 AlignmentGenerator gen = new AlignmentGenerator(false);
189  0 AlignmentI al = gen.generate(50, 20, 123, 5, 5);
190   
191  0 ColumnSelection cs = new ColumnSelection();
192  0 int[] sel = { 2, 3, 4, 7, 8, 9, 20, 21, 22 };
193  0 for (int col : sel)
194    {
195  0 cs.addElement(col);
196    }
197   
198  0 HiddenColumns cols = al.getHiddenColumns();
199  0 cols.hideColumns(15, 18);
200   
201  0 cs.hideSelectedColumns(al);
202  0 assertTrue(cs.getSelected().isEmpty());
203  0 Iterator<int[]> regions = cols.iterator();
204  0 assertEquals(4, cols.getNumberOfRegions());
205  0 assertEquals("[2, 4]", Arrays.toString(regions.next()));
206  0 assertEquals("[7, 9]", Arrays.toString(regions.next()));
207  0 assertEquals("[15, 18]", Arrays.toString(regions.next()));
208  0 assertEquals("[20, 22]", Arrays.toString(regions.next()));
209    }
210   
211    /**
212    * Test the method that gets runs of selected columns ordered by column. If
213    * this fails, HideSelectedColumns may also fail
214    */
 
215  0 toggle @Test(groups = { "Functional" })
216    public void testGetSelectedRanges()
217    {
218    /*
219    * getSelectedRanges returns ordered columns regardless
220    * of the order in which they are added
221    */
222  0 ColumnSelection cs = new ColumnSelection();
223  0 int[] sel = { 4, 3, 7, 21, 9, 20, 8, 22, 2 };
224  0 for (int col : sel)
225    {
226  0 cs.addElement(col);
227    }
228  0 List<int[]> range;
229  0 range = cs.getSelectedRanges();
230  0 assertEquals(3, range.size());
231  0 assertEquals("[2, 4]", Arrays.toString(range.get(0)));
232  0 assertEquals("[7, 9]", Arrays.toString(range.get(1)));
233  0 assertEquals("[20, 22]", Arrays.toString(range.get(2)));
234  0 cs.addElement(0);
235  0 cs.addElement(1);
236  0 range = cs.getSelectedRanges();
237  0 assertEquals(3, range.size());
238  0 assertEquals("[0, 4]", Arrays.toString(range.get(0)));
239    }
240   
 
241  0 toggle @Test(groups = { "Functional" })
242    public void testInvertColumnSelection()
243    {
244    // create random alignment
245  0 AlignmentGenerator gen = new AlignmentGenerator(false);
246  0 AlignmentI al = gen.generate(50, 20, 123, 5, 5);
247   
248  0 ColumnSelection cs = new ColumnSelection();
249  0 cs.addElement(4);
250  0 cs.addElement(6);
251  0 cs.addElement(8);
252   
253  0 HiddenColumns cols = al.getHiddenColumns();
254  0 cols.hideColumns(3, 3);
255  0 cols.hideColumns(6, 6);
256   
257    // invert selection from start (inclusive) to end (exclusive)
258  0 cs.invertColumnSelection(2, 9, al);
259  0 assertEquals("[2, 5, 7]", cs.getSelected().toString());
260   
261  0 cs.invertColumnSelection(1, 9, al);
262  0 assertEquals("[1, 4, 8]", cs.getSelected().toString());
263    }
264   
 
265  0 toggle @Test(groups = { "Functional" })
266    public void testMaxColumnSelection()
267    {
268  0 ColumnSelection cs = new ColumnSelection();
269  0 cs.addElement(0);
270  0 cs.addElement(513);
271  0 cs.addElement(1);
272  0 assertEquals(513, cs.getMax());
273  0 cs.removeElement(513);
274  0 assertEquals(1, cs.getMax());
275  0 cs.removeElement(1);
276  0 assertEquals(0, cs.getMax());
277  0 cs.addElement(512);
278  0 cs.addElement(513);
279  0 assertEquals(513, cs.getMax());
280   
281    }
282   
 
283  0 toggle @Test(groups = { "Functional" })
284    public void testMinColumnSelection()
285    {
286  0 ColumnSelection cs = new ColumnSelection();
287  0 cs.addElement(0);
288  0 cs.addElement(513);
289  0 cs.addElement(1);
290  0 assertEquals(0, cs.getMin());
291  0 cs.removeElement(0);
292  0 assertEquals(1, cs.getMin());
293  0 cs.addElement(0);
294  0 assertEquals(0, cs.getMin());
295    }
296   
 
297  0 toggle @Test(groups = { "Functional" })
298    public void testEquals()
299    {
300  0 ColumnSelection cs = new ColumnSelection();
301  0 cs.addElement(0);
302  0 cs.addElement(513);
303  0 cs.addElement(1);
304   
305    // same selections added in a different order
306  0 ColumnSelection cs2 = new ColumnSelection();
307  0 cs2.addElement(1);
308  0 cs2.addElement(513);
309  0 cs2.addElement(0);
310   
311  0 assertTrue(cs.equals(cs2));
312  0 assertTrue(cs.equals(cs));
313  0 assertTrue(cs2.equals(cs));
314  0 assertTrue(cs2.equals(cs2));
315   
316  0 cs2.addElement(12);
317  0 assertFalse(cs.equals(cs2));
318  0 assertFalse(cs2.equals(cs));
319   
320  0 cs2.removeElement(12);
321  0 assertTrue(cs.equals(cs2));
322    }
323   
324    /*
325    cs2.hideSelectedColumns(88);
326    assertFalse(cs.equals(cs2));
327    /*
328    * unhiding a column adds it to selection!
329    */
330    /* cs2.revealHiddenColumns(88);
331    assertFalse(cs.equals(cs2));
332    cs.addElement(88);
333    assertTrue(cs.equals(cs2));
334    */
335   
336    /**
337    * Test the method that returns selected columns, in the order in which they
338    * were added
339    */
 
340  0 toggle @Test(groups = { "Functional" })
341    public void testGetSelected()
342    {
343  0 ColumnSelection cs = new ColumnSelection();
344  0 int[] sel = { 4, 3, 7, 21 };
345  0 for (int col : sel)
346    {
347  0 cs.addElement(col);
348    }
349   
350  0 List<Integer> selected = cs.getSelected();
351  0 assertEquals(4, selected.size());
352  0 assertEquals("[4, 3, 7, 21]", selected.toString());
353   
354    /*
355    * getSelected returns a read-only view of the list
356    * verify the view follows any changes in it
357    */
358  0 cs.removeElement(7);
359  0 cs.addElement(1);
360  0 cs.removeElement(4);
361  0 assertEquals("[3, 21, 1]", selected.toString());
362    }
363   
364    /**
365    * Test to verify that the list returned by getSelection cannot be modified
366    */
 
367  0 toggle @Test(groups = { "Functional" })
368    public void testGetSelected_isReadOnly()
369    {
370  0 ColumnSelection cs = new ColumnSelection();
371  0 cs.addElement(3);
372   
373  0 List<Integer> selected = cs.getSelected();
374  0 try
375    {
376  0 selected.clear();
377  0 fail("expected exception");
378    } catch (UnsupportedOperationException e)
379    {
380    // expected
381    }
382  0 try
383    {
384  0 selected.add(1);
385  0 fail("expected exception");
386    } catch (UnsupportedOperationException e)
387    {
388    // expected
389    }
390  0 try
391    {
392  0 selected.remove(3);
393  0 fail("expected exception");
394    } catch (UnsupportedOperationException e)
395    {
396    // expected
397    }
398  0 try
399    {
400  0 Collections.sort(selected);
401  0 fail("expected exception");
402    } catch (UnsupportedOperationException e)
403    {
404    // expected
405    }
406    }
407   
408    /**
409    * Test that demonstrates a ConcurrentModificationException is thrown if you
410    * change the selection while iterating over it
411    */
 
412  0 toggle @Test(
413    groups = "Functional",
414    expectedExceptions =
415    { ConcurrentModificationException.class })
416    public void testGetSelected_concurrentModification()
417    {
418  0 ColumnSelection cs = new ColumnSelection();
419  0 cs.addElement(0);
420  0 cs.addElement(1);
421  0 cs.addElement(2);
422   
423    /*
424    * simulate changing the list under us (e.g. in a separate
425    * thread) while iterating over it -> ConcurrentModificationException
426    */
427  0 List<Integer> selected = cs.getSelected();
428  0 for (Integer col : selected)
429    {
430  0 if (col.intValue() == 0)
431    {
432  0 cs.removeElement(1);
433    }
434    }
435    }
436   
 
437  0 toggle @Test(groups = "Functional")
438    public void testMarkColumns()
439    {
440  0 ColumnSelection cs = new ColumnSelection();
441  0 cs.addElement(5); // this will be cleared
442  0 BitSet toMark = new BitSet();
443  0 toMark.set(1);
444  0 toMark.set(3);
445  0 toMark.set(6);
446  0 toMark.set(9);
447   
448  0 assertTrue(cs.markColumns(toMark, 3, 8, false, false, false));
449  0 List<Integer> selected = cs.getSelected();
450  0 assertEquals(2, selected.size());
451  0 assertTrue(selected.contains(3));
452  0 assertTrue(selected.contains(6));
453    }
454   
 
455  0 toggle @Test(groups = "Functional")
456    public void testMarkColumns_extend()
457    {
458  0 ColumnSelection cs = new ColumnSelection();
459  0 cs.addElement(1);
460  0 cs.addElement(5);
461  0 BitSet toMark = new BitSet();
462  0 toMark.set(1);
463  0 toMark.set(3);
464  0 toMark.set(6);
465  0 toMark.set(9);
466   
467    /*
468    * extending selection of {3, 6} should leave {1, 3, 5, 6} selected
469    */
470  0 assertTrue(cs.markColumns(toMark, 3, 8, false, true, false));
471  0 List<Integer> selected = cs.getSelected();
472  0 assertEquals(4, selected.size());
473  0 assertTrue(selected.contains(1));
474  0 assertTrue(selected.contains(3));
475  0 assertTrue(selected.contains(5));
476  0 assertTrue(selected.contains(6));
477    }
478   
 
479  0 toggle @Test(groups = "Functional")
480    public void testMarkColumns_invert()
481    {
482  0 ColumnSelection cs = new ColumnSelection();
483  0 cs.addElement(5); // this will be cleared
484  0 BitSet toMark = new BitSet();
485  0 toMark.set(1);
486  0 toMark.set(3);
487  0 toMark.set(6);
488  0 toMark.set(9);
489   
490    /*
491    * inverted selection of {3, 6} should select {4, 5, 7, 8}
492    */
493  0 assertTrue(cs.markColumns(toMark, 3, 8, true, false, false));
494  0 List<Integer> selected = cs.getSelected();
495  0 assertEquals(4, selected.size());
496  0 assertTrue(selected.contains(4));
497  0 assertTrue(selected.contains(5));
498  0 assertTrue(selected.contains(7));
499  0 assertTrue(selected.contains(8));
500    }
501   
 
502  0 toggle @Test(groups = "Functional")
503    public void testMarkColumns_toggle()
504    {
505  0 ColumnSelection cs = new ColumnSelection();
506  0 cs.addElement(1); // outside change range
507  0 cs.addElement(3);
508  0 cs.addElement(4);
509  0 cs.addElement(10); // outside change range
510  0 BitSet toMark = new BitSet();
511  0 toMark.set(1);
512  0 toMark.set(3);
513  0 toMark.set(6);
514  0 toMark.set(9);
515   
516    /*
517    * toggling state of {3, 6} should leave {1, 4, 6, 10} selected
518    */
519  0 assertTrue(cs.markColumns(toMark, 3, 8, false, false, true));
520  0 List<Integer> selected = cs.getSelected();
521  0 assertEquals(4, selected.size());
522  0 assertTrue(selected.contains(1));
523  0 assertTrue(selected.contains(4));
524  0 assertTrue(selected.contains(6));
525  0 assertTrue(selected.contains(10));
526    }
527   
 
528  0 toggle @Test(groups = "Functional")
529    public void testCopyConstructor()
530    {
531  0 ColumnSelection cs = new ColumnSelection();
532  0 cs.addElement(3);
533  0 cs.addElement(1);
534   
535  0 ColumnSelection cs2 = new ColumnSelection(cs);
536  0 assertTrue(cs2.hasSelectedColumns());
537   
538    // order of column selection is preserved
539  0 assertEquals("[3, 1]", cs2.getSelected().toString());
540    }
541   
 
542  0 toggle @Test(groups = { "Functional" })
543    public void testStretchGroup_expand()
544    {
545    /*
546    * test that emulates clicking column 4 (selected)
547    * and dragging right to column 5 (all base 0)
548    */
549  0 ColumnSelection cs = new ColumnSelection();
550  0 cs.addElement(4);
551  0 SequenceGroup sg = new SequenceGroup();
552  0 sg.setStartRes(4);
553  0 sg.setEndRes(4);
554  0 cs.stretchGroup(5, sg, 4, 4);
555  0 assertEquals(cs.getSelected().size(), 2);
556  0 assertTrue(cs.contains(4));
557  0 assertTrue(cs.contains(5));
558  0 assertEquals(sg.getStartRes(), 4);
559  0 assertEquals(sg.getEndRes(), 5);
560   
561    /*
562    * emulate drag right with columns 10-20 already selected
563    */
564  0 cs.clear();
565  0 for (int i = 10; i <= 20; i++)
566    {
567  0 cs.addElement(i);
568    }
569  0 assertEquals(cs.getSelected().size(), 11);
570  0 sg = new SequenceGroup();
571  0 sg.setStartRes(10);
572  0 sg.setEndRes(20);
573  0 cs.stretchGroup(21, sg, 10, 20);
574  0 assertEquals(cs.getSelected().size(), 12);
575  0 assertTrue(cs.contains(10));
576  0 assertTrue(cs.contains(21));
577  0 assertEquals(sg.getStartRes(), 10);
578  0 assertEquals(sg.getEndRes(), 21);
579    }
580   
 
581  0 toggle @Test(groups = { "Functional" })
582    public void testStretchGroup_shrink()
583    {
584    /*
585    * emulate drag left to 19 with columns 10-20 already selected
586    */
587  0 ColumnSelection cs = new ColumnSelection();
588  0 for (int i = 10; i <= 20; i++)
589    {
590  0 cs.addElement(i);
591    }
592  0 assertEquals(cs.getSelected().size(), 11);
593  0 SequenceGroup sg = new SequenceGroup();
594  0 sg.setStartRes(10);
595  0 sg.setEndRes(20);
596  0 cs.stretchGroup(19, sg, 10, 20);
597  0 assertEquals(cs.getSelected().size(), 10);
598  0 assertTrue(cs.contains(10));
599  0 assertTrue(cs.contains(19));
600  0 assertFalse(cs.contains(20));
601  0 assertEquals(sg.getStartRes(), 10);
602  0 assertEquals(sg.getEndRes(), 19);
603    }
604   
 
605  0 toggle @Test(groups = { "Functional" })
606    public void testFilterAnnotations()
607    {
608  0 ColumnSelection cs = new ColumnSelection();
609  0 AlignmentAnnotation alann = new AlignmentAnnotation("dummy",
610    "dummyDesc", null);
611   
612    /*
613    * filter with no conditions clears the selection
614    */
615  0 Annotation[] anns = new Annotation[] { null };
616  0 AnnotationFilterParameter filter = new AnnotationFilterParameter();
617  0 cs.addElement(3);
618  0 alann.annotations = anns;
619  0 int added = cs.filterAnnotations(alann, filter);
620  0 assertEquals(0, added);
621  0 assertTrue(cs.isEmpty());
622   
623    /*
624    * select on description (regex)
625    */
626  0 filter.setRegexString("w.rld");
627  0 filter.addRegexSearchField(SearchableAnnotationField.DESCRIPTION);
628  0 Annotation helix = new Annotation("(", "hello", '<', 2f);
629  0 Annotation sheet = new Annotation("(", "world", '<', 2f);
630  0 alann.annotations = new Annotation[] { null, helix, sheet };
631  0 added = cs.filterAnnotations(alann, filter);
632  0 assertEquals(1, added);
633  0 assertTrue(cs.contains(2));
634   
635    /*
636    * select on label (invalid regex, exact match)
637    */
638  0 filter = new AnnotationFilterParameter();
639  0 filter.setRegexString("(");
640  0 filter.addRegexSearchField(SearchableAnnotationField.DISPLAY_STRING);
641  0 alann.annotations = new Annotation[] { null, helix, sheet };
642  0 added = cs.filterAnnotations(alann, filter);
643  0 assertEquals(2, added);
644  0 assertTrue(cs.contains(1));
645  0 assertTrue(cs.contains(2));
646   
647    /*
648    * select Helix (secondary structure symbol H)
649    */
650  0 filter = new AnnotationFilterParameter();
651  0 filter.setFilterAlphaHelix(true);
652  0 helix = new Annotation("x", "desc", 'H', 0f);
653  0 sheet = new Annotation("x", "desc", 'E', 1f);
654  0 Annotation turn = new Annotation("x", "desc", 'S', 2f);
655  0 Annotation ann4 = new Annotation("x", "desc", 'Y', 3f);
656  0 alann.annotations = new Annotation[] { null, helix, sheet, turn, ann4 };
657  0 added = cs.filterAnnotations(alann, filter);
658  0 assertEquals(1, added);
659  0 assertTrue(cs.contains(1));
660   
661    /*
662    * select Helix and Sheet (E)
663    */
664  0 filter.setFilterBetaSheet(true);
665  0 alann.annotations = new Annotation[] { null, helix, sheet, turn, ann4 };
666  0 added = cs.filterAnnotations(alann, filter);
667  0 assertEquals(2, added);
668  0 assertTrue(cs.contains(1));
669  0 assertTrue(cs.contains(2));
670   
671    /*
672    * select Sheet and Turn (S)
673    */
674  0 filter.setFilterAlphaHelix(false);
675  0 filter.setFilterTurn(true);
676  0 alann.annotations = new Annotation[] { null, helix, sheet, turn, ann4 };
677  0 added = cs.filterAnnotations(alann, filter);
678  0 assertEquals(2, added);
679  0 assertTrue(cs.contains(2));
680  0 assertTrue(cs.contains(3));
681   
682    /*
683    * select value < 2f (ann1, ann2)
684    */
685  0 filter = new AnnotationFilterParameter();
686  0 filter.setThresholdType(ThresholdType.BELOW_THRESHOLD);
687  0 filter.setThresholdValue(2f);
688  0 alann.annotations = new Annotation[] { null, helix, sheet, turn, ann4 };
689  0 added = cs.filterAnnotations(alann, filter);
690  0 assertEquals(2, added);
691  0 assertTrue(cs.contains(1));
692  0 assertTrue(cs.contains(2));
693   
694    /*
695    * select value > 2f (ann4 only)
696    */
697  0 filter.setThresholdType(ThresholdType.ABOVE_THRESHOLD);
698  0 alann.annotations = new Annotation[] { null, helix, sheet, turn, ann4 };
699  0 added = cs.filterAnnotations(alann, filter);
700  0 assertEquals(1, added);
701  0 assertTrue(cs.contains(4));
702   
703    /*
704    * select >2f or Helix
705    */
706  0 filter.setFilterAlphaHelix(true);
707  0 alann.annotations = new Annotation[] { null, helix, sheet, turn, ann4 };
708  0 added = cs.filterAnnotations(alann, filter);
709  0 assertEquals(2, added);
710  0 assertTrue(cs.contains(1));
711  0 assertTrue(cs.contains(4));
712   
713    /*
714    * select < 1f or Helix; one annotation matches both
715    * return value should only count it once
716    */
717  0 filter.setThresholdType(ThresholdType.BELOW_THRESHOLD);
718  0 filter.setThresholdValue(1f);
719  0 alann.annotations = new Annotation[] { null, helix, sheet, turn, ann4 };
720  0 added = cs.filterAnnotations(alann, filter);
721  0 assertEquals(1, added);
722  0 assertTrue(cs.contains(1));
723    }
724    }
  • Report generated by OpenClover v 4.4.1 on Tue Mar 10 2026 14:59:17 GMT using coverage data from Thu Jan 1 1970 01:00:00 GMT.
  • OpenClover is free and open-source software.