Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AlignmentAnnotationUtilsTest	47	192	10	1.0100%	Show methods

Class AlignmentAnnotationUtilsTest

Class AlignmentAnnotationUtilsTest	Line # 47	Total Statements 192	Complexity 10	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	5050	2.02	1.01	1.0 1.0100%
testAsList() : void   testAsList() : void	7979	12.012	1.01	1.0 1.0100%
consoleDebug(Map<String, List<List<String>>>,Map<String, List<List<String>>>) : void   consoleDebug(Map<String, List<List<String>>>,Map<String, List<List<String>>>) : void	108108	8.08	1.01	1.0 1.0100%
selectSequences(int) : List<SequenceI>   selectSequences(int) : List<SequenceI>	136136	5.05	1.01	1.0 1.0100%
setUp() : void   setUp() : void	152152	7.07	2.02	1.0 1.0100%
testGetShownHiddenTypes_forSelectionGroup() : void   testGetShownHiddenTypes_forSelectionGroup() : void	176176	47.047	1.01	1.0 1.0100%
testGetShownHiddenTypes_withGraphGroups() : void   testGetShownHiddenTypes_withGraphGroups() : void	254254	79.079	1.01	1.0 1.0100%
testGetVisibleGraphGroups() : void   testGetVisibleGraphGroups() : void	379379	22.022	1.01	1.0 1.0100%
testGetShownHiddenTypes_noSequenceSelected() : void   testGetShownHiddenTypes_noSequenceSelected() : void	425425	10.010	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.4679803	jalview.analysis.AlignmentAnnotationUtilsTest.testGetShownHiddenTypes_withGraphGroupsjalview.analysis.AlignmentAnnotationUtilsTest.testGetShownHiddenTypes_withGraphGroups	1PASS
	0.31034482	jalview.analysis.AlignmentAnnotationUtilsTest.testGetShownHiddenTypes_forSelectionGroupjalview.analysis.AlignmentAnnotationUtilsTest.testGetShownHiddenTypes_forSelectionGroup	1PASS
	0.113300495	jalview.analysis.AlignmentAnnotationUtilsTest.testGetVisibleGraphGroupsjalview.analysis.AlignmentAnnotationUtilsTest.testGetVisibleGraphGroups	1PASS
	0.06403941	jalview.analysis.AlignmentAnnotationUtilsTest.testAsListjalview.analysis.AlignmentAnnotationUtilsTest.testAsList	1PASS
	0.054187194	jalview.analysis.AlignmentAnnotationUtilsTest.testGetShownHiddenTypes_noSequenceSelectedjalview.analysis.AlignmentAnnotationUtilsTest.testGetShownHiddenTypes_noSequenceSelected	1PASS

 

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.analysis;
22
23		import static org.testng.AssertJUnit.assertEquals;
24		import static org.testng.AssertJUnit.assertFalse;
25		import static org.testng.AssertJUnit.assertTrue;
26
27		import jalview.datamodel.AlignmentAnnotation;
28		import jalview.datamodel.AlignmentI;
29		import jalview.datamodel.Annotation;
30		import jalview.datamodel.SequenceI;
31		import jalview.gui.JvOptionPane;
32		import jalview.io.DataSourceType;
33		import jalview.io.FileFormat;
34
35		import java.io.IOException;
36		import java.util.ArrayList;
37		import java.util.BitSet;
38		import java.util.Collection;
39		import java.util.HashMap;
40		import java.util.List;
41		import java.util.Map;
42
43		import org.testng.annotations.BeforeClass;
44		import org.testng.annotations.BeforeMethod;
45		import org.testng.annotations.Test;
46
		100% Uncovered Elements: 0 (203) Complexity: 10 Complexity Density: 0.05
47		public class AlignmentAnnotationUtilsTest
48		{
49
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
50	1	@BeforeClass(alwaysRun = true)...
51		public void setUpJvOptionPane()
52		{
53	1	JvOptionPane.setInteractiveMode(false);
54	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
55		}
56
57		// 4 sequences x 13 positions
58		final static String EOL = "\n";
59
60		// @formatter:off
61		final static String TEST_DATA =
62		">FER_CAPAA Ferredoxin" + EOL +
63		"TIETHKEAELVG-" + EOL +
64		">FER_CAPAN Ferredoxin, chloroplast precursor" + EOL +
65		"TIETHKEAELVG-" + EOL +
66		">FER1_SOLLC Ferredoxin-1, chloroplast precursor" + EOL +
67		"TIETHKEEELTA-" + EOL +
68		">Q93XJ9_SOLTU Ferredoxin I precursor" + EOL +
69		"TIETHKEEELTA-" + EOL;
70		// @formatter:on
71
72		private static final int SEQ_ANN_COUNT = 12;
73
74		private AlignmentI alignment;
75
76		/**
77		* Test method that converts a (possibly null) array to a list.
78		*/
		100% Uncovered Elements: 0 (12) Complexity: 1 Complexity Density: 0.08 1PASS
79	1	@Test(groups = { "Functional" })...
80		public void testAsList()
81		{
82		// null array
83	1	Collection<AlignmentAnnotation> c1 = AlignmentAnnotationUtils
84		.asList(null);
85	1	assertTrue(c1.isEmpty());
86
87		// empty array
88	1	AlignmentAnnotation[] anns = new AlignmentAnnotation[0];
89	1	c1 = AlignmentAnnotationUtils.asList(anns);
90	1	assertTrue(c1.isEmpty());
91
92		// non-empty array
93	1	anns = new AlignmentAnnotation[2];
94	1	anns[0] = new AlignmentAnnotation("label0", "desc0", 0.0f);
95	1	anns[1] = new AlignmentAnnotation("label1", "desc1", 1.0f);
96	1	c1 = AlignmentAnnotationUtils.asList(anns);
97	1	assertEquals(2, c1.size());
98	1	assertTrue(c1.contains(anns[0]));
99	1	assertTrue(c1.contains(anns[1]));
100		}
101
102		/**
103		* This output is not part of the test but may help make sense of it...
104		*
105		* @param shownTypes
106		* @param hiddenTypes
107		*/
		100% Uncovered Elements: 0 (8) Complexity: 1 Complexity Density: 0.12
108	2	protected void consoleDebug(Map<String, List<List<String>>> shownTypes,...
109		Map<String, List<List<String>>> hiddenTypes)
110		{
111	2	for (String calcId : shownTypes.keySet())
112		{
113	3	System.out.println("Visible annotation types for calcId=" + calcId);
114	3	for (List<String> type : shownTypes.get(calcId))
115		{
116	3	System.out.println(" " + type);
117		}
118		}
119	2	for (String calcId : hiddenTypes.keySet())
120		{
121	4	System.out.println("Hidden annotation types for calcId=" + calcId);
122	4	for (List<String> type : hiddenTypes.get(calcId))
123		{
124	5	System.out.println(" " + type);
125		}
126		}
127		}
128
129		/**
130		* Add a sequence group to the alignment with the specified sequences (base 0)
131		* in it
132		*
133		* @param i
134		* @param more
135		*/
		100% Uncovered Elements: 0 (5) Complexity: 1 Complexity Density: 0.2
136	2	private List<SequenceI> selectSequences(int... selected)...
137		{
138	2	List<SequenceI> result = new ArrayList<SequenceI>();
139	2	SequenceI[] seqs = alignment.getSequencesArray();
140	2	for (int i : selected)
141		{
142	4	result.add(seqs[i]);
143		}
144	2	return result;
145		}
146
147		/**
148		* Load the test alignment and generate annotations on it
149		*
150		* @throws IOException
151		*/
		100% Uncovered Elements: 0 (9) Complexity: 2 Complexity Density: 0.29
152	5	@BeforeMethod(alwaysRun = true)...
153		public void setUp() throws IOException
154		{
155	5	alignment = new jalview.io.FormatAdapter().readFile(TEST_DATA,
156		DataSourceType.PASTE, FileFormat.Fasta);
157
158	5	AlignmentAnnotation[] anns = new AlignmentAnnotation[SEQ_ANN_COUNT];
159	65	for (int i = 0; i < anns.length; i++)
160		{
161		/*
162		* Use the constructor for a positional annotation (with an Annotation
163		* array)
164		*/
165	60	anns[i] = new AlignmentAnnotation("Label" + i, "Desc " + i,
166		new Annotation[] {});
167	60	anns[i].setCalcId("CalcId" + i);
168	60	anns[i].visible = true;
169	60	alignment.addAnnotation(anns[i]);
170		}
171		}
172
173		/**
174		* Test a mixture of show/hidden annotations in/outside selection group.
175		*/
		100% Uncovered Elements: 0 (47) Complexity: 1 Complexity Density: 0.02 1PASS
176	1	@Test(groups = { "Functional" })...
177		public void testGetShownHiddenTypes_forSelectionGroup()
178		{
179	1	Map<String, List<List<String>>> shownTypes = new HashMap<String, List<List<String>>>();
180	1	Map<String, List<List<String>>> hiddenTypes = new HashMap<String, List<List<String>>>();
181	1	AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
182	1	SequenceI[] seqs = alignment.getSequencesArray();
183
184		/*
185		* Configure annotation properties for test
186		*/
187		// not in selection group (should be ignored):
188		// hidden annotation Label4 not in selection group
189	1	anns[4].sequenceRef = seqs[2];
190	1	anns[4].visible = false;
191	1	anns[7].sequenceRef = seqs[1];
192	1	anns[7].visible = true;
193
194		/*
195		* in selection group, hidden:
196		*/
197	1	anns[2].sequenceRef = seqs[3]; // CalcId2/Label2
198	1	anns[2].visible = false;
199	1	anns[3].sequenceRef = seqs[3]; // CalcId3/Label2
200	1	anns[3].visible = false;
201	1	anns[3].label = "Label2";
202	1	anns[4].sequenceRef = seqs[3]; // CalcId2/Label3
203	1	anns[4].visible = false;
204	1	anns[4].label = "Label3";
205	1	anns[4].setCalcId("CalcId2");
206	1	anns[8].sequenceRef = seqs[0]; // CalcId9/Label9
207	1	anns[8].visible = false;
208	1	anns[8].label = "Label9";
209	1	anns[8].setCalcId("CalcId9");
210		/*
211		* in selection group, visible
212		*/
213	1	anns[6].sequenceRef = seqs[0]; // CalcId6/Label6
214	1	anns[6].visible = true;
215	1	anns[9].sequenceRef = seqs[3]; // CalcId9/Label9
216	1	anns[9].visible = true;
217
218	1	List<SequenceI> selected = selectSequences(0, 3);
219	1	AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
220		AlignmentAnnotationUtils.asList(anns), selected);
221
222		// check results; note CalcId9/Label9 is both hidden and shown (for
223		// different sequences) so should be in both
224		// shown: CalcId6/Label6 and CalcId9/Label9
225	1	assertEquals(2, shownTypes.size());
226	1	assertEquals(1, shownTypes.get("CalcId6").size());
227	1	assertEquals(1, shownTypes.get("CalcId6").get(0).size());
228	1	assertEquals("Label6", shownTypes.get("CalcId6").get(0).get(0));
229	1	assertEquals(1, shownTypes.get("CalcId9").size());
230	1	assertEquals(1, shownTypes.get("CalcId9").get(0).size());
231	1	assertEquals("Label9", shownTypes.get("CalcId9").get(0).get(0));
232
233		// hidden: CalcId2/Label2, CalcId2/Label3, CalcId3/Label2, CalcId9/Label9
234	1	assertEquals(3, hiddenTypes.size());
235	1	assertEquals(2, hiddenTypes.get("CalcId2").size());
236	1	assertEquals(1, hiddenTypes.get("CalcId2").get(0).size());
237	1	assertEquals("Label2", hiddenTypes.get("CalcId2").get(0).get(0));
238	1	assertEquals(1, hiddenTypes.get("CalcId2").get(1).size());
239	1	assertEquals("Label3", hiddenTypes.get("CalcId2").get(1).get(0));
240	1	assertEquals(1, hiddenTypes.get("CalcId3").size());
241	1	assertEquals(1, hiddenTypes.get("CalcId3").get(0).size());
242	1	assertEquals("Label2", hiddenTypes.get("CalcId3").get(0).get(0));
243	1	assertEquals(1, hiddenTypes.get("CalcId9").size());
244	1	assertEquals(1, hiddenTypes.get("CalcId9").get(0).size());
245	1	assertEquals("Label9", hiddenTypes.get("CalcId9").get(0).get(0));
246
247	1	consoleDebug(shownTypes, hiddenTypes);
248		}
249
250		/**
251		* Test case where there are 'grouped' annotations, visible and hidden, within
252		* and without the selection group.
253		*/
		100% Uncovered Elements: 0 (79) Complexity: 1 Complexity Density: 0.01 1PASS
254	1	@Test(groups = { "Functional" })...
255		public void testGetShownHiddenTypes_withGraphGroups()
256		{
257	1	final int GROUP_3 = 3;
258	1	final int GROUP_4 = 4;
259	1	final int GROUP_5 = 5;
260	1	final int GROUP_6 = 6;
261
262	1	Map<String, List<List<String>>> shownTypes = new HashMap<String, List<List<String>>>();
263	1	Map<String, List<List<String>>> hiddenTypes = new HashMap<String, List<List<String>>>();
264	1	AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
265	1	SequenceI[] seqs = alignment.getSequencesArray();
266
267		/*
268		* Annotations for selection group and graph group
269		*
270		* Hidden annotations Label2, Label3, in (hidden) group 5
271		*/
272	1	anns[2].sequenceRef = seqs[3];
273	1	anns[2].visible = false;
274	1	anns[2].graph = AlignmentAnnotation.LINE_GRAPH;
275	1	anns[2].graphGroup = GROUP_5; // not a visible group
276	1	anns[3].sequenceRef = seqs[0];
277	1	anns[3].visible = false;
278	1	anns[3].graph = AlignmentAnnotation.LINE_GRAPH;
279	1	anns[3].graphGroup = GROUP_5;
280		// need to ensure annotations have the same calcId as well
281	1	anns[3].setCalcId("CalcId2");
282		// annotations for a different hidden group generating the same group label
283	1	anns[10].sequenceRef = seqs[0];
284	1	anns[10].visible = false;
285	1	anns[10].graph = AlignmentAnnotation.LINE_GRAPH;
286	1	anns[10].graphGroup = GROUP_3;
287	1	anns[10].label = "Label3";
288	1	anns[10].setCalcId("CalcId2");
289	1	anns[11].sequenceRef = seqs[3];
290	1	anns[11].visible = false;
291	1	anns[11].graph = AlignmentAnnotation.LINE_GRAPH;
292	1	anns[11].graphGroup = GROUP_3;
293	1	anns[11].label = "Label2";
294	1	anns[11].setCalcId("CalcId2");
295
296		// annotations Label1 (hidden), Label5 (visible) in group 6 (visible)
297	1	anns[1].sequenceRef = seqs[3];
298		// being in a visible group should take precedence over this visibility
299	1	anns[1].visible = false;
300	1	anns[1].graph = AlignmentAnnotation.LINE_GRAPH;
301	1	anns[1].graphGroup = GROUP_6;
302	1	anns[5].sequenceRef = seqs[0];
303	1	anns[5].visible = true;
304	1	anns[5].graph = AlignmentAnnotation.LINE_GRAPH;
305	1	anns[5].graphGroup = GROUP_6;
306	1	anns[5].setCalcId("CalcId1");
307		/*
308		* Annotations 0 and 4 are visible, for a different CalcId and graph group.
309		* They produce the same label as annotations 1 and 5, which should not be
310		* duplicated in the results. This case corresponds to (e.g.) many
311		* occurrences of an IUPred Short/Long annotation group, one per sequence.
312		*/
313	1	anns[4].sequenceRef = seqs[0];
314	1	anns[4].visible = false;
315	1	anns[4].graph = AlignmentAnnotation.LINE_GRAPH;
316	1	anns[4].graphGroup = GROUP_4;
317	1	anns[4].label = "Label1";
318	1	anns[4].setCalcId("CalcId1");
319	1	anns[0].sequenceRef = seqs[0];
320	1	anns[0].visible = true;
321	1	anns[0].graph = AlignmentAnnotation.LINE_GRAPH;
322	1	anns[0].graphGroup = GROUP_4;
323	1	anns[0].label = "Label5";
324	1	anns[0].setCalcId("CalcId1");
325
326		/*
327		* Annotations outwith selection group - should be ignored.
328		*/
329		// Hidden grouped annotations
330	1	anns[6].sequenceRef = seqs[2];
331	1	anns[6].visible = false;
332	1	anns[6].graph = AlignmentAnnotation.LINE_GRAPH;
333	1	anns[6].graphGroup = GROUP_4;
334	1	anns[8].sequenceRef = seqs[1];
335	1	anns[8].visible = false;
336	1	anns[8].graph = AlignmentAnnotation.LINE_GRAPH;
337	1	anns[8].graphGroup = GROUP_4;
338
339		// visible grouped annotations Label7, Label9
340	1	anns[7].sequenceRef = seqs[2];
341	1	anns[7].visible = true;
342	1	anns[7].graph = AlignmentAnnotation.LINE_GRAPH;
343	1	anns[7].graphGroup = GROUP_4;
344	1	anns[9].sequenceRef = seqs[1];
345	1	anns[9].visible = true;
346	1	anns[9].graph = AlignmentAnnotation.LINE_GRAPH;
347	1	anns[9].graphGroup = GROUP_4;
348
349		/*
350		* Generate annotations[] arrays to match aligned columns
351		*/
352		// adjustForAlignment(anns);
353
354	1	List<SequenceI> selected = selectSequences(0, 3);
355	1	AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
356		AlignmentAnnotationUtils.asList(anns), selected);
357
358	1	consoleDebug(shownTypes, hiddenTypes);
359
360		// CalcId1 / Label1, Label5 (only) should be 'shown', once, as a compound
361		// type
362	1	assertEquals(1, shownTypes.size());
363	1	assertEquals(1, shownTypes.get("CalcId1").size());
364	1	assertEquals(2, shownTypes.get("CalcId1").get(0).size());
365	1	assertEquals("Label1", shownTypes.get("CalcId1").get(0).get(0));
366	1	assertEquals("Label5", shownTypes.get("CalcId1").get(0).get(1));
367
368		// CalcId2 / Label2, Label3 (only) should be 'hidden'
369	1	assertEquals(1, hiddenTypes.size());
370	1	assertEquals(1, hiddenTypes.get("CalcId2").size());
371	1	assertEquals(2, hiddenTypes.get("CalcId2").get(0).size());
372	1	assertEquals("Label2", hiddenTypes.get("CalcId2").get(0).get(0));
373	1	assertEquals("Label3", hiddenTypes.get("CalcId2").get(0).get(1));
374		}
375
376		/**
377		* Test method that determines visible graph groups.
378		*/
		100% Uncovered Elements: 0 (22) Complexity: 1 Complexity Density: 0.05 1PASS
379	1	@Test(groups = { "Functional" })...
380		public void testGetVisibleGraphGroups()
381		{
382	1	AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
383		/*
384		* a bar graph group is not included
385		*/
386	1	anns[0].graph = AlignmentAnnotation.BAR_GRAPH;
387	1	anns[0].graphGroup = 1;
388	1	anns[0].visible = true;
389
390		/*
391		* a line graph group is included as long as one of its members is visible
392		*/
393	1	anns[1].graph = AlignmentAnnotation.LINE_GRAPH;
394	1	anns[1].graphGroup = 5;
395	1	anns[1].visible = false;
396	1	anns[2].graph = AlignmentAnnotation.LINE_GRAPH;
397	1	anns[2].graphGroup = 5;
398	1	anns[2].visible = true;
399
400		/*
401		* a line graph group with no visible rows is not included
402		*/
403	1	anns[3].graph = AlignmentAnnotation.LINE_GRAPH;
404	1	anns[3].graphGroup = 3;
405	1	anns[3].visible = false;
406
407		// a visible line graph with no graph group is not included
408	1	anns[4].graph = AlignmentAnnotation.LINE_GRAPH;
409	1	anns[4].graphGroup = -1;
410	1	anns[4].visible = true;
411
412	1	BitSet result = AlignmentAnnotationUtils.getVisibleLineGraphGroups(
413		AlignmentAnnotationUtils.asList(anns));
414	1	assertTrue(result.get(5));
415	1	assertFalse(result.get(0));
416	1	assertFalse(result.get(1));
417	1	assertFalse(result.get(2));
418	1	assertFalse(result.get(3));
419		}
420
421		/**
422		* Test for case where no sequence is selected. Shouldn't normally arise but
423		* check it handles it gracefully.
424		*/
		100% Uncovered Elements: 0 (10) Complexity: 1 Complexity Density: 0.1 1PASS
425	1	@Test(groups = { "Functional" })...
426		public void testGetShownHiddenTypes_noSequenceSelected()
427		{
428	1	Map<String, List<List<String>>> shownTypes = new HashMap<String, List<List<String>>>();
429	1	Map<String, List<List<String>>> hiddenTypes = new HashMap<String, List<List<String>>>();
430	1	AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
431		// selected sequences null
432	1	AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
433		AlignmentAnnotationUtils.asList(anns), null);
434	1	assertTrue(shownTypes.isEmpty());
435	1	assertTrue(hiddenTypes.isEmpty());
436
437	1	List<SequenceI> sequences = new ArrayList<SequenceI>();
438		// selected sequences empty list
439	1	AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
440		AlignmentAnnotationUtils.asList(anns), sequences);
441	1	assertTrue(shownTypes.isEmpty());
442	1	assertTrue(hiddenTypes.isEmpty());
443		}
444		}