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  1. Project Clover database Thu Nov 7 2024 10:11:34 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
0.987373798.7%
 

Contributing tests

This file is covered by 21 tests. .

Source view

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  1 toggle @BeforeClass(alwaysRun = true)
48    public void setUpJvOptionPane()
49    {
50  1 JvOptionPane.setInteractiveMode(false);
51  1 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
52    }
53   
 
54  1 toggle @Test(groups = { "Functional" })
55    public void testAddElement()
56    {
57  1 ColumnSelection cs = new ColumnSelection();
58  1 cs.addElement(2);
59  1 cs.addElement(5);
60  1 cs.addElement(3);
61  1 cs.addElement(5); // ignored
62  1 List<Integer> sel = cs.getSelected();
63  1 assertEquals("[2, 5, 3]", sel.toString());
64    }
65   
 
66  1 toggle @Test(groups = { "Functional" })
67    public void testSetElementsFrom()
68    {
69  1 ColumnSelection fromcs = new ColumnSelection();
70  1 ColumnSelection tocs = new ColumnSelection();
71  1 HiddenColumns hidden = new HiddenColumns();
72   
73  1 fromcs.addElement(2);
74  1 fromcs.addElement(3);
75  1 fromcs.addElement(5);
76   
77  1 tocs.setElementsFrom(fromcs, hidden);
78  1 assertTrue(tocs.equals(fromcs));
79   
80  1 hidden.hideColumns(4, 6);
81  1 tocs.setElementsFrom(fromcs, hidden);
82   
83    // expect cols 2 and 3 to be selected but not 5
84  1 ColumnSelection expectcs = new ColumnSelection();
85  1 expectcs.addElement(2);
86  1 expectcs.addElement(3);
87  1 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  1 toggle @Test(groups = { "Functional" })
95    public void testRemoveElement()
96    {
97  1 ColumnSelection cs = new ColumnSelection();
98  1 cs.addElement(2);
99  1 cs.addElement(5);
100   
101    // removing elements not in the list has no effect
102  1 cs.removeElement(0);
103  1 cs.removeElement(1);
104  1 List<Integer> sel = cs.getSelected();
105  1 assertEquals(2, sel.size());
106  1 assertEquals(Integer.valueOf(2), sel.get(0));
107  1 assertEquals(Integer.valueOf(5), sel.get(1));
108   
109    // removing an element in the list removes it
110  1 cs.removeElement(2);
111    // ...and also from the read-only view
112  1 assertEquals(1, sel.size());
113  1 sel = cs.getSelected();
114  1 assertEquals(1, sel.size());
115  1 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  1 toggle @Test(groups = { "Functional" })
125    public void testHideColumns_withSelection()
126    {
127    // create random alignment
128  1 AlignmentGenerator gen = new AlignmentGenerator(false);
129  1 AlignmentI al = gen.generate(50, 20, 123, 5, 5);
130   
131  1 ColumnSelection cs = new ColumnSelection();
132    // select columns 4-6
133  1 cs.addElement(4);
134  1 cs.addElement(5);
135  1 cs.addElement(6);
136    // hide column 5 (and adjacent):
137  1 cs.hideSelectedColumns(5, al.getHiddenColumns());
138    // 4,5,6 now hidden:
139  1 Iterator<int[]> regions = al.getHiddenColumns().iterator();
140  1 assertEquals(1, al.getHiddenColumns().getNumberOfRegions());
141  1 assertEquals("[4, 6]", Arrays.toString(regions.next()));
142    // none now selected:
143  1 assertTrue(cs.getSelected().isEmpty());
144   
145    // repeat, hiding column 4 (5 and 6)
146  1 al = gen.generate(50, 20, 123, 5, 5);
147  1 cs = new ColumnSelection();
148  1 cs.addElement(4);
149  1 cs.addElement(5);
150  1 cs.addElement(6);
151  1 cs.hideSelectedColumns(4, al.getHiddenColumns());
152  1 regions = al.getHiddenColumns().iterator();
153  1 assertEquals(1, al.getHiddenColumns().getNumberOfRegions());
154  1 assertEquals("[4, 6]", Arrays.toString(regions.next()));
155  1 assertTrue(cs.getSelected().isEmpty());
156   
157    // repeat, hiding column (4, 5 and) 6
158  1 al = gen.generate(50, 20, 123, 5, 5);
159  1 cs = new ColumnSelection();
160  1 cs.addElement(4);
161  1 cs.addElement(5);
162  1 cs.addElement(6);
163  1 cs.hideSelectedColumns(6, al.getHiddenColumns());
164  1 regions = al.getHiddenColumns().iterator();
165  1 assertEquals(1, al.getHiddenColumns().getNumberOfRegions());
166  1 assertEquals("[4, 6]", Arrays.toString(regions.next()));
167  1 assertTrue(cs.getSelected().isEmpty());
168   
169    // repeat, with _only_ adjacent columns selected
170  1 al = gen.generate(50, 20, 123, 5, 5);
171  1 cs = new ColumnSelection();
172  1 cs.addElement(4);
173  1 cs.addElement(6);
174  1 cs.hideSelectedColumns(5, al.getHiddenColumns());
175  1 regions = al.getHiddenColumns().iterator();
176  1 assertEquals(1, al.getHiddenColumns().getNumberOfRegions());
177  1 assertEquals("[4, 6]", Arrays.toString(regions.next()));
178  1 assertTrue(cs.getSelected().isEmpty());
179    }
180   
181    /**
182    * Test the method that hides all (possibly disjoint) selected column ranges
183    */
 
184  1 toggle @Test(groups = { "Functional" })
185    public void testHideSelectedColumns()
186    {
187    // create random alignment
188  1 AlignmentGenerator gen = new AlignmentGenerator(false);
189  1 AlignmentI al = gen.generate(50, 20, 123, 5, 5);
190   
191  1 ColumnSelection cs = new ColumnSelection();
192  1 int[] sel = { 2, 3, 4, 7, 8, 9, 20, 21, 22 };
193  1 for (int col : sel)
194    {
195  9 cs.addElement(col);
196    }
197   
198  1 HiddenColumns cols = al.getHiddenColumns();
199  1 cols.hideColumns(15, 18);
200   
201  1 cs.hideSelectedColumns(al);
202  1 assertTrue(cs.getSelected().isEmpty());
203  1 Iterator<int[]> regions = cols.iterator();
204  1 assertEquals(4, cols.getNumberOfRegions());
205  1 assertEquals("[2, 4]", Arrays.toString(regions.next()));
206  1 assertEquals("[7, 9]", Arrays.toString(regions.next()));
207  1 assertEquals("[15, 18]", Arrays.toString(regions.next()));
208  1 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  1 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  1 ColumnSelection cs = new ColumnSelection();
223  1 int[] sel = { 4, 3, 7, 21, 9, 20, 8, 22, 2 };
224  1 for (int col : sel)
225    {
226  9 cs.addElement(col);
227    }
228  1 List<int[]> range;
229  1 range = cs.getSelectedRanges();
230  1 assertEquals(3, range.size());
231  1 assertEquals("[2, 4]", Arrays.toString(range.get(0)));
232  1 assertEquals("[7, 9]", Arrays.toString(range.get(1)));
233  1 assertEquals("[20, 22]", Arrays.toString(range.get(2)));
234  1 cs.addElement(0);
235  1 cs.addElement(1);
236  1 range = cs.getSelectedRanges();
237  1 assertEquals(3, range.size());
238  1 assertEquals("[0, 4]", Arrays.toString(range.get(0)));
239    }
240   
 
241  1 toggle @Test(groups = { "Functional" })
242    public void testInvertColumnSelection()
243    {
244    // create random alignment
245  1 AlignmentGenerator gen = new AlignmentGenerator(false);
246  1 AlignmentI al = gen.generate(50, 20, 123, 5, 5);
247   
248  1 ColumnSelection cs = new ColumnSelection();
249  1 cs.addElement(4);
250  1 cs.addElement(6);
251  1 cs.addElement(8);
252   
253  1 HiddenColumns cols = al.getHiddenColumns();
254  1 cols.hideColumns(3, 3);
255  1 cols.hideColumns(6, 6);
256   
257    // invert selection from start (inclusive) to end (exclusive)
258  1 cs.invertColumnSelection(2, 9, al);
259  1 assertEquals("[2, 5, 7]", cs.getSelected().toString());
260   
261  1 cs.invertColumnSelection(1, 9, al);
262  1 assertEquals("[1, 4, 8]", cs.getSelected().toString());
263    }
264   
 
265  1 toggle @Test(groups = { "Functional" })
266    public void testMaxColumnSelection()
267    {
268  1 ColumnSelection cs = new ColumnSelection();
269  1 cs.addElement(0);
270  1 cs.addElement(513);
271  1 cs.addElement(1);
272  1 assertEquals(513, cs.getMax());
273  1 cs.removeElement(513);
274  1 assertEquals(1, cs.getMax());
275  1 cs.removeElement(1);
276  1 assertEquals(0, cs.getMax());
277  1 cs.addElement(512);
278  1 cs.addElement(513);
279  1 assertEquals(513, cs.getMax());
280   
281    }
282   
 
283  1 toggle @Test(groups = { "Functional" })
284    public void testMinColumnSelection()
285    {
286  1 ColumnSelection cs = new ColumnSelection();
287  1 cs.addElement(0);
288  1 cs.addElement(513);
289  1 cs.addElement(1);
290  1 assertEquals(0, cs.getMin());
291  1 cs.removeElement(0);
292  1 assertEquals(1, cs.getMin());
293  1 cs.addElement(0);
294  1 assertEquals(0, cs.getMin());
295    }
296   
 
297  1 toggle @Test(groups = { "Functional" })
298    public void testEquals()
299    {
300  1 ColumnSelection cs = new ColumnSelection();
301  1 cs.addElement(0);
302  1 cs.addElement(513);
303  1 cs.addElement(1);
304   
305    // same selections added in a different order
306  1 ColumnSelection cs2 = new ColumnSelection();
307  1 cs2.addElement(1);
308  1 cs2.addElement(513);
309  1 cs2.addElement(0);
310   
311  1 assertTrue(cs.equals(cs2));
312  1 assertTrue(cs.equals(cs));
313  1 assertTrue(cs2.equals(cs));
314  1 assertTrue(cs2.equals(cs2));
315   
316  1 cs2.addElement(12);
317  1 assertFalse(cs.equals(cs2));
318  1 assertFalse(cs2.equals(cs));
319   
320  1 cs2.removeElement(12);
321  1 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  1 toggle @Test(groups = { "Functional" })
341    public void testGetSelected()
342    {
343  1 ColumnSelection cs = new ColumnSelection();
344  1 int[] sel = { 4, 3, 7, 21 };
345  1 for (int col : sel)
346    {
347  4 cs.addElement(col);
348    }
349   
350  1 List<Integer> selected = cs.getSelected();
351  1 assertEquals(4, selected.size());
352  1 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  1 cs.removeElement(7);
359  1 cs.addElement(1);
360  1 cs.removeElement(4);
361  1 assertEquals("[3, 21, 1]", selected.toString());
362    }
363   
364    /**
365    * Test to verify that the list returned by getSelection cannot be modified
366    */
 
367  1 toggle @Test(groups = { "Functional" })
368    public void testGetSelected_isReadOnly()
369    {
370  1 ColumnSelection cs = new ColumnSelection();
371  1 cs.addElement(3);
372   
373  1 List<Integer> selected = cs.getSelected();
374  1 try
375    {
376  1 selected.clear();
377  0 fail("expected exception");
378    } catch (UnsupportedOperationException e)
379    {
380    // expected
381    }
382  1 try
383    {
384  1 selected.add(1);
385  0 fail("expected exception");
386    } catch (UnsupportedOperationException e)
387    {
388    // expected
389    }
390  1 try
391    {
392  1 selected.remove(3);
393  0 fail("expected exception");
394    } catch (UnsupportedOperationException e)
395    {
396    // expected
397    }
398  1 try
399    {
400  1 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  1 toggle @Test(
413    groups = "Functional",
414    expectedExceptions =
415    { ConcurrentModificationException.class })
416    public void testGetSelected_concurrentModification()
417    {
418  1 ColumnSelection cs = new ColumnSelection();
419  1 cs.addElement(0);
420  1 cs.addElement(1);
421  1 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  1 List<Integer> selected = cs.getSelected();
428  1 for (Integer col : selected)
429    {
430  1 if (col.intValue() == 0)
431    {
432  1 cs.removeElement(1);
433    }
434    }
435    }
436   
 
437  1 toggle @Test(groups = "Functional")
438    public void testMarkColumns()
439    {
440  1 ColumnSelection cs = new ColumnSelection();
441  1 cs.addElement(5); // this will be cleared
442  1 BitSet toMark = new BitSet();
443  1 toMark.set(1);
444  1 toMark.set(3);
445  1 toMark.set(6);
446  1 toMark.set(9);
447   
448  1 assertTrue(cs.markColumns(toMark, 3, 8, false, false, false));
449  1 List<Integer> selected = cs.getSelected();
450  1 assertEquals(2, selected.size());
451  1 assertTrue(selected.contains(3));
452  1 assertTrue(selected.contains(6));
453    }
454   
 
455  1 toggle @Test(groups = "Functional")
456    public void testMarkColumns_extend()
457    {
458  1 ColumnSelection cs = new ColumnSelection();
459  1 cs.addElement(1);
460  1 cs.addElement(5);
461  1 BitSet toMark = new BitSet();
462  1 toMark.set(1);
463  1 toMark.set(3);
464  1 toMark.set(6);
465  1 toMark.set(9);
466   
467    /*
468    * extending selection of {3, 6} should leave {1, 3, 5, 6} selected
469    */
470  1 assertTrue(cs.markColumns(toMark, 3, 8, false, true, false));
471  1 List<Integer> selected = cs.getSelected();
472  1 assertEquals(4, selected.size());
473  1 assertTrue(selected.contains(1));
474  1 assertTrue(selected.contains(3));
475  1 assertTrue(selected.contains(5));
476  1 assertTrue(selected.contains(6));
477    }
478   
 
479  1 toggle @Test(groups = "Functional")
480    public void testMarkColumns_invert()
481    {
482  1 ColumnSelection cs = new ColumnSelection();
483  1 cs.addElement(5); // this will be cleared
484  1 BitSet toMark = new BitSet();
485  1 toMark.set(1);
486  1 toMark.set(3);
487  1 toMark.set(6);
488  1 toMark.set(9);
489   
490    /*
491    * inverted selection of {3, 6} should select {4, 5, 7, 8}
492    */
493  1 assertTrue(cs.markColumns(toMark, 3, 8, true, false, false));
494  1 List<Integer> selected = cs.getSelected();
495  1 assertEquals(4, selected.size());
496  1 assertTrue(selected.contains(4));
497  1 assertTrue(selected.contains(5));
498  1 assertTrue(selected.contains(7));
499  1 assertTrue(selected.contains(8));
500    }
501   
 
502  1 toggle @Test(groups = "Functional")
503    public void testMarkColumns_toggle()
504    {
505  1 ColumnSelection cs = new ColumnSelection();
506  1 cs.addElement(1); // outside change range
507  1 cs.addElement(3);
508  1 cs.addElement(4);
509  1 cs.addElement(10); // outside change range
510  1 BitSet toMark = new BitSet();
511  1 toMark.set(1);
512  1 toMark.set(3);
513  1 toMark.set(6);
514  1 toMark.set(9);
515   
516    /*
517    * toggling state of {3, 6} should leave {1, 4, 6, 10} selected
518    */
519  1 assertTrue(cs.markColumns(toMark, 3, 8, false, false, true));
520  1 List<Integer> selected = cs.getSelected();
521  1 assertEquals(4, selected.size());
522  1 assertTrue(selected.contains(1));
523  1 assertTrue(selected.contains(4));
524  1 assertTrue(selected.contains(6));
525  1 assertTrue(selected.contains(10));
526    }
527   
 
528  1 toggle @Test(groups = "Functional")
529    public void testCopyConstructor()
530    {
531  1 ColumnSelection cs = new ColumnSelection();
532  1 cs.addElement(3);
533  1 cs.addElement(1);
534   
535  1 ColumnSelection cs2 = new ColumnSelection(cs);
536  1 assertTrue(cs2.hasSelectedColumns());
537   
538    // order of column selection is preserved
539  1 assertEquals("[3, 1]", cs2.getSelected().toString());
540    }
541   
 
542  1 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  1 ColumnSelection cs = new ColumnSelection();
550  1 cs.addElement(4);
551  1 SequenceGroup sg = new SequenceGroup();
552  1 sg.setStartRes(4);
553  1 sg.setEndRes(4);
554  1 cs.stretchGroup(5, sg, 4, 4);
555  1 assertEquals(cs.getSelected().size(), 2);
556  1 assertTrue(cs.contains(4));
557  1 assertTrue(cs.contains(5));
558  1 assertEquals(sg.getStartRes(), 4);
559  1 assertEquals(sg.getEndRes(), 5);
560   
561    /*
562    * emulate drag right with columns 10-20 already selected
563    */
564  1 cs.clear();
565  12 for (int i = 10; i <= 20; i++)
566    {
567  11 cs.addElement(i);
568    }
569  1 assertEquals(cs.getSelected().size(), 11);
570  1 sg = new SequenceGroup();
571  1 sg.setStartRes(10);
572  1 sg.setEndRes(20);
573  1 cs.stretchGroup(21, sg, 10, 20);
574  1 assertEquals(cs.getSelected().size(), 12);
575  1 assertTrue(cs.contains(10));
576  1 assertTrue(cs.contains(21));
577  1 assertEquals(sg.getStartRes(), 10);
578  1 assertEquals(sg.getEndRes(), 21);
579    }
580   
 
581  1 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  1 ColumnSelection cs = new ColumnSelection();
588  12 for (int i = 10; i <= 20; i++)
589    {
590  11 cs.addElement(i);
591    }
592  1 assertEquals(cs.getSelected().size(), 11);
593  1 SequenceGroup sg = new SequenceGroup();
594  1 sg.setStartRes(10);
595  1 sg.setEndRes(20);
596  1 cs.stretchGroup(19, sg, 10, 20);
597  1 assertEquals(cs.getSelected().size(), 10);
598  1 assertTrue(cs.contains(10));
599  1 assertTrue(cs.contains(19));
600  1 assertFalse(cs.contains(20));
601  1 assertEquals(sg.getStartRes(), 10);
602  1 assertEquals(sg.getEndRes(), 19);
603    }
604   
 
605  1 toggle @Test(groups = { "Functional" })
606    public void testFilterAnnotations()
607    {
608  1 ColumnSelection cs = new ColumnSelection();
609  1 AlignmentAnnotation alann = new AlignmentAnnotation("dummy",
610    "dummyDesc", null);
611   
612    /*
613    * filter with no conditions clears the selection
614    */
615  1 Annotation[] anns = new Annotation[] { null };
616  1 AnnotationFilterParameter filter = new AnnotationFilterParameter();
617  1 cs.addElement(3);
618  1 alann.annotations = anns;
619  1 int added = cs.filterAnnotations(alann, filter);
620  1 assertEquals(0, added);
621  1 assertTrue(cs.isEmpty());
622   
623    /*
624    * select on description (regex)
625    */
626  1 filter.setRegexString("w.rld");
627  1 filter.addRegexSearchField(SearchableAnnotationField.DESCRIPTION);
628  1 Annotation helix = new Annotation("(", "hello", '<', 2f);
629  1 Annotation sheet = new Annotation("(", "world", '<', 2f);
630  1 alann.annotations = new Annotation[] { null, helix, sheet };
631  1 added = cs.filterAnnotations(alann, filter);
632  1 assertEquals(1, added);
633  1 assertTrue(cs.contains(2));
634   
635    /*
636    * select on label (invalid regex, exact match)
637    */
638  1 filter = new AnnotationFilterParameter();
639  1 filter.setRegexString("(");
640  1 filter.addRegexSearchField(SearchableAnnotationField.DISPLAY_STRING);
641  1 alann.annotations = new Annotation[] { null, helix, sheet };
642  1 added = cs.filterAnnotations(alann, filter);
643  1 assertEquals(2, added);
644  1 assertTrue(cs.contains(1));
645  1 assertTrue(cs.contains(2));
646   
647    /*
648    * select Helix (secondary structure symbol H)
649    */
650  1 filter = new AnnotationFilterParameter();
651  1 filter.setFilterAlphaHelix(true);
652  1 helix = new Annotation("x", "desc", 'H', 0f);
653  1 sheet = new Annotation("x", "desc", 'E', 1f);
654  1 Annotation turn = new Annotation("x", "desc", 'S', 2f);
655  1 Annotation ann4 = new Annotation("x", "desc", 'Y', 3f);
656  1 alann.annotations = new Annotation[] { null, helix, sheet, turn, ann4 };
657  1 added = cs.filterAnnotations(alann, filter);
658  1 assertEquals(1, added);
659  1 assertTrue(cs.contains(1));
660   
661    /*
662    * select Helix and Sheet (E)
663    */
664  1 filter.setFilterBetaSheet(true);
665  1 alann.annotations = new Annotation[] { null, helix, sheet, turn, ann4 };
666  1 added = cs.filterAnnotations(alann, filter);
667  1 assertEquals(2, added);
668  1 assertTrue(cs.contains(1));
669  1 assertTrue(cs.contains(2));
670   
671    /*
672    * select Sheet and Turn (S)
673    */
674  1 filter.setFilterAlphaHelix(false);
675  1 filter.setFilterTurn(true);
676  1 alann.annotations = new Annotation[] { null, helix, sheet, turn, ann4 };
677  1 added = cs.filterAnnotations(alann, filter);
678  1 assertEquals(2, added);
679  1 assertTrue(cs.contains(2));
680  1 assertTrue(cs.contains(3));
681   
682    /*
683    * select value < 2f (ann1, ann2)
684    */
685  1 filter = new AnnotationFilterParameter();
686  1 filter.setThresholdType(ThresholdType.BELOW_THRESHOLD);
687  1 filter.setThresholdValue(2f);
688  1 alann.annotations = new Annotation[] { null, helix, sheet, turn, ann4 };
689  1 added = cs.filterAnnotations(alann, filter);
690  1 assertEquals(2, added);
691  1 assertTrue(cs.contains(1));
692  1 assertTrue(cs.contains(2));
693   
694    /*
695    * select value > 2f (ann4 only)
696    */
697  1 filter.setThresholdType(ThresholdType.ABOVE_THRESHOLD);
698  1 alann.annotations = new Annotation[] { null, helix, sheet, turn, ann4 };
699  1 added = cs.filterAnnotations(alann, filter);
700  1 assertEquals(1, added);
701  1 assertTrue(cs.contains(4));
702   
703    /*
704    * select >2f or Helix
705    */
706  1 filter.setFilterAlphaHelix(true);
707  1 alann.annotations = new Annotation[] { null, helix, sheet, turn, ann4 };
708  1 added = cs.filterAnnotations(alann, filter);
709  1 assertEquals(2, added);
710  1 assertTrue(cs.contains(1));
711  1 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  1 filter.setThresholdType(ThresholdType.BELOW_THRESHOLD);
718  1 filter.setThresholdValue(1f);
719  1 alann.annotations = new Annotation[] { null, helix, sheet, turn, ann4 };
720  1 added = cs.filterAnnotations(alann, filter);
721  1 assertEquals(1, added);
722  1 assertTrue(cs.contains(1));
723    }
724    }
  • Report generated by OpenClover v 4.4.1 on Thu Nov 7 2024 10:19:08 GMT using coverage data from Thu Nov 7 2024 10:18:53 GMT.
  • OpenClover is free and open-source software.