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jalviewX

  1. Project Clover database Wed Oct 31 2018 15:13:58 GMT
  2. Package jalview.datamodel

File ColumnSelectionTest.java

 

Code metrics

6
357
22
1
729
515
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0.08
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Classes

Class Line # Actions
ColumnSelectionTest 44 357 29 5
0.98701398.7%
 

Contributing tests

This file is covered by 21 tests. .

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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 jalview.analysis.AlignmentGenerator;
29    import jalview.gui.JvOptionPane;
30    import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
31    import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField;
32    import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.ThresholdType;
33   
34    import java.util.Arrays;
35    import java.util.BitSet;
36    import java.util.Collections;
37    import java.util.ConcurrentModificationException;
38    import java.util.Iterator;
39    import java.util.List;
40   
41    import org.testng.annotations.BeforeClass;
42    import org.testng.annotations.Test;
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(new Integer(2), sel.get(0));
107  1 assertEquals(new Integer(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(new Integer(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 = { ConcurrentModificationException.class })
415    public void testGetSelected_concurrentModification()
416    {
417  1 ColumnSelection cs = new ColumnSelection();
418  1 cs.addElement(0);
419  1 cs.addElement(1);
420  1 cs.addElement(2);
421   
422    /*
423    * simulate changing the list under us (e.g. in a separate
424    * thread) while iterating over it -> ConcurrentModificationException
425    */
426  1 List<Integer> selected = cs.getSelected();
427  1 for (Integer col : selected)
428    {
429  1 if (col.intValue() == 0)
430    {
431  1 cs.removeElement(1);
432    }
433    }
434    }
435   
 
436  1 toggle @Test(groups = "Functional")
437    public void testMarkColumns()
438    {
439  1 ColumnSelection cs = new ColumnSelection();
440  1 cs.addElement(5); // this will be cleared
441  1 BitSet toMark = new BitSet();
442  1 toMark.set(1);
443  1 toMark.set(3);
444  1 toMark.set(6);
445  1 toMark.set(9);
446   
447  1 assertTrue(cs.markColumns(toMark, 3, 8, false, false, false));
448  1 List<Integer> selected = cs.getSelected();
449  1 assertEquals(2, selected.size());
450  1 assertTrue(selected.contains(3));
451  1 assertTrue(selected.contains(6));
452    }
453   
 
454  1 toggle @Test(groups = "Functional")
455    public void testMarkColumns_extend()
456    {
457  1 ColumnSelection cs = new ColumnSelection();
458  1 cs.addElement(1);
459  1 cs.addElement(5);
460  1 BitSet toMark = new BitSet();
461  1 toMark.set(1);
462  1 toMark.set(3);
463  1 toMark.set(6);
464  1 toMark.set(9);
465   
466    /*
467    * extending selection of {3, 6} should leave {1, 3, 5, 6} selected
468    */
469  1 assertTrue(cs.markColumns(toMark, 3, 8, false, true, false));
470  1 List<Integer> selected = cs.getSelected();
471  1 assertEquals(4, selected.size());
472  1 assertTrue(selected.contains(1));
473  1 assertTrue(selected.contains(3));
474  1 assertTrue(selected.contains(5));
475  1 assertTrue(selected.contains(6));
476    }
477   
 
478  1 toggle @Test(groups = "Functional")
479    public void testMarkColumns_invert()
480    {
481  1 ColumnSelection cs = new ColumnSelection();
482  1 cs.addElement(5); // this will be cleared
483  1 BitSet toMark = new BitSet();
484  1 toMark.set(1);
485  1 toMark.set(3);
486  1 toMark.set(6);
487  1 toMark.set(9);
488   
489    /*
490    * inverted selection of {3, 6} should select {4, 5, 7, 8}
491    */
492  1 assertTrue(cs.markColumns(toMark, 3, 8, true, false, false));
493  1 List<Integer> selected = cs.getSelected();
494  1 assertEquals(4, selected.size());
495  1 assertTrue(selected.contains(4));
496  1 assertTrue(selected.contains(5));
497  1 assertTrue(selected.contains(7));
498  1 assertTrue(selected.contains(8));
499    }
500   
 
501  1 toggle @Test(groups = "Functional")
502    public void testMarkColumns_toggle()
503    {
504  1 ColumnSelection cs = new ColumnSelection();
505  1 cs.addElement(1); // outside change range
506  1 cs.addElement(3);
507  1 cs.addElement(4);
508  1 cs.addElement(10); // outside change range
509  1 BitSet toMark = new BitSet();
510  1 toMark.set(1);
511  1 toMark.set(3);
512  1 toMark.set(6);
513  1 toMark.set(9);
514   
515    /*
516    * toggling state of {3, 6} should leave {1, 4, 6, 10} selected
517    */
518  1 assertTrue(cs.markColumns(toMark, 3, 8, false, false, true));
519  1 List<Integer> selected = cs.getSelected();
520  1 assertEquals(4, selected.size());
521  1 assertTrue(selected.contains(1));
522  1 assertTrue(selected.contains(4));
523  1 assertTrue(selected.contains(6));
524  1 assertTrue(selected.contains(10));
525    }
526   
 
527  1 toggle @Test(groups = "Functional")
528    public void testCopyConstructor()
529    {
530  1 ColumnSelection cs = new ColumnSelection();
531  1 cs.addElement(3);
532  1 cs.addElement(1);
533   
534  1 ColumnSelection cs2 = new ColumnSelection(cs);
535  1 assertTrue(cs2.hasSelectedColumns());
536   
537    // order of column selection is preserved
538  1 assertEquals("[3, 1]", cs2.getSelected().toString());
539    }
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   
610    /*
611    * filter with no conditions clears the selection
612    */
613  1 Annotation[] anns = new Annotation[] { null };
614  1 AnnotationFilterParameter filter = new AnnotationFilterParameter();
615  1 cs.addElement(3);
616  1 int added = cs.filterAnnotations(anns, filter);
617  1 assertEquals(0, added);
618  1 assertTrue(cs.isEmpty());
619   
620    /*
621    * select on description (regex)
622    */
623  1 filter.setRegexString("w.rld");
624  1 filter.addRegexSearchField(SearchableAnnotationField.DESCRIPTION);
625  1 Annotation helix = new Annotation("(", "hello", '<', 2f);
626  1 Annotation sheet = new Annotation("(", "world", '<', 2f);
627  1 added = cs.filterAnnotations(new Annotation[] { null, helix, sheet },
628    filter);
629  1 assertEquals(1, added);
630  1 assertTrue(cs.contains(2));
631   
632    /*
633    * select on label (invalid regex, exact match)
634    */
635  1 filter = new AnnotationFilterParameter();
636  1 filter.setRegexString("(");
637  1 filter.addRegexSearchField(SearchableAnnotationField.DISPLAY_STRING);
638  1 added = cs.filterAnnotations(new Annotation[] { null, helix, sheet },
639    filter);
640  1 assertEquals(2, added);
641  1 assertTrue(cs.contains(1));
642  1 assertTrue(cs.contains(2));
643   
644    /*
645    * select Helix (secondary structure symbol H)
646    */
647  1 filter = new AnnotationFilterParameter();
648  1 filter.setFilterAlphaHelix(true);
649  1 helix = new Annotation("x", "desc", 'H', 0f);
650  1 sheet = new Annotation("x", "desc", 'E', 1f);
651  1 Annotation turn = new Annotation("x", "desc", 'S', 2f);
652  1 Annotation ann4 = new Annotation("x", "desc", 'Y', 3f);
653  1 added = cs
654    .filterAnnotations(new Annotation[]
655    { null, helix, sheet, turn, ann4 },
656    filter);
657  1 assertEquals(1, added);
658  1 assertTrue(cs.contains(1));
659   
660    /*
661    * select Helix and Sheet (E)
662    */
663  1 filter.setFilterBetaSheet(true);
664  1 added = cs
665    .filterAnnotations(new Annotation[]
666    { null, helix, sheet, turn, ann4 }, 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 added = cs
677    .filterAnnotations(new Annotation[]
678    { null, helix, sheet, turn, ann4 }, filter);
679  1 assertEquals(2, added);
680  1 assertTrue(cs.contains(2));
681  1 assertTrue(cs.contains(3));
682   
683    /*
684    * select value < 2f (ann1, ann2)
685    */
686  1 filter = new AnnotationFilterParameter();
687  1 filter.setThresholdType(ThresholdType.BELOW_THRESHOLD);
688  1 filter.setThresholdValue(2f);
689  1 added = cs
690    .filterAnnotations(new Annotation[]
691    { null, helix, sheet, turn, ann4 }, filter);
692  1 assertEquals(2, added);
693  1 assertTrue(cs.contains(1));
694  1 assertTrue(cs.contains(2));
695   
696    /*
697    * select value > 2f (ann4 only)
698    */
699  1 filter.setThresholdType(ThresholdType.ABOVE_THRESHOLD);
700  1 added = cs
701    .filterAnnotations(new Annotation[]
702    { null, helix, sheet, turn, ann4 }, filter);
703  1 assertEquals(1, added);
704  1 assertTrue(cs.contains(4));
705   
706    /*
707    * select >2f or Helix
708    */
709  1 filter.setFilterAlphaHelix(true);
710  1 added = cs
711    .filterAnnotations(new Annotation[]
712    { null, helix, sheet, turn, ann4 }, filter);
713  1 assertEquals(2, added);
714  1 assertTrue(cs.contains(1));
715  1 assertTrue(cs.contains(4));
716   
717    /*
718    * select < 1f or Helix; one annotation matches both
719    * return value should only count it once
720    */
721  1 filter.setThresholdType(ThresholdType.BELOW_THRESHOLD);
722  1 filter.setThresholdValue(1f);
723  1 added = cs
724    .filterAnnotations(new Annotation[]
725    { null, helix, sheet, turn, ann4 }, filter);
726  1 assertEquals(1, added);
727  1 assertTrue(cs.contains(1));
728    }
729    }
  • Report generated by OpenClover v 4.2.1 on Wed Oct 31 2018 15:15:54 GMT using coverage data from Wed Oct 31 2018 15:15:47 GMT.
  • Clover free edition.