Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
FinderTest	42	150	9	0	1.0100%	Show methods

Class FinderTest

Class FinderTest	Line # 42	Total Statements 150	Complexity 9	Uncovered Elements 0	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4444	2.02	1.01	0.00	1.0 1.0100%
setUp() : void   setUp() : void	5555	3.03	1.01	0.00	1.0 1.0100%
testFindAll_regex() : void   testFindAll_regex() : void	6868	12.012	1.01	0.00	1.0 1.0100%
testFind_residueNumber() : void   testFind_residueNumber() : void	9090	12.012	1.01	0.00	1.0 1.0100%
testFindNext() : void   testFindNext() : void	112112	20.020	1.01	0.00	1.0 1.0100%
testFindAll_inDescription() : void   testFindAll_inDescription() : void	152152	38.038	1.01	0.00	1.0 1.0100%
testFindAll_sequenceIds() : void   testFindAll_sequenceIds() : void	213213	27.027	1.01	0.00	1.0 1.0100%
testFindAll_simpleMatch() : void   testFindAll_simpleMatch() : void	260260	27.027	1.01	0.00	1.0 1.0100%
testFind_maximalResultOnly() : void   testFind_maximalResultOnly() : void	304304	9.09	1.01	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.24528302	jalview.analysis.FinderTest.testFindAll_inDescriptionjalview.analysis.FinderTest.testFindAll_inDescription	1PASS
	0.17610063	jalview.analysis.FinderTest.testFindAll_sequenceIdsjalview.analysis.FinderTest.testFindAll_sequenceIds	1PASS
	0.17610063	jalview.analysis.FinderTest.testFindAll_simpleMatchjalview.analysis.FinderTest.testFindAll_simpleMatch	1PASS
	0.13207547	jalview.analysis.FinderTest.testFindNextjalview.analysis.FinderTest.testFindNext	1PASS
	0.08176101	jalview.analysis.FinderTest.testFind_residueNumberjalview.analysis.FinderTest.testFind_residueNumber	1PASS
	0.08176101	jalview.analysis.FinderTest.testFindAll_regexjalview.analysis.FinderTest.testFindAll_regex	1PASS
	0.062893085	jalview.analysis.FinderTest.testFind_maximalResultOnlyjalview.analysis.FinderTest.testFind_maximalResultOnly	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.Assert.assertEquals;
24		import static org.testng.Assert.assertSame;
25		import static org.testng.Assert.assertTrue;
26
27		import jalview.datamodel.Alignment;
28		import jalview.datamodel.AlignmentI;
29		import jalview.datamodel.SearchResultMatchI;
30		import jalview.datamodel.SearchResultsI;
31		import jalview.datamodel.Sequence;
32		import jalview.gui.AlignFrame;
33		import jalview.gui.JvOptionPane;
34		import jalview.io.DataSourceType;
35		import jalview.io.FileLoader;
36
37		import java.util.List;
38
39		import org.testng.annotations.BeforeClass;
40		import org.testng.annotations.Test;
41
		100% Uncovered Elements: 0 (159) Complexity: 9 Complexity Density: 0.06
42		public class FinderTest
43		{
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
44	1	@BeforeClass(alwaysRun = true)...
45		public void setUpJvOptionPane()
46		{
47	1	JvOptionPane.setInteractiveMode(false);
48	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
49		}
50
51		private AlignFrame af;
52
53		private AlignmentI al;
54
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
55	1	@BeforeClass(groups = "Functional")...
56		public void setUp()
57		{
58	1	String seqData = "seq1 ABCD--EF-GHI\n" + "seq2 A--BCDefHI\n"
59		+ "seq3 --bcdEFH\n" + "seq4 aa---aMMMMMaaa\n";
60	1	af = new FileLoader().LoadFileWaitTillLoaded(seqData,
61		DataSourceType.PASTE);
62	1	al = af.getViewport().getAlignment();
63		}
64
65		/**
66		* Test for find all matches of a regular expression
67		*/
		100% Uncovered Elements: 0 (12) Complexity: 1 Complexity Density: 0.08 1PASS
68	1	@Test(groups = "Functional")...
69		public void testFindAll_regex()
70		{
71	1	Finder f = new Finder(al, null);
72	1	f.setFindAll(true);
73	1	f.find("E.H"); // 'E, any character, H'
74
75		// should match seq2 efH and seq3 EFH
76	1	SearchResultsI sr = f.getSearchResults();
77	1	assertEquals(sr.getSize(), 2);
78	1	List<SearchResultMatchI> matches = sr.getResults();
79	1	assertSame(al.getSequenceAt(1), matches.get(0).getSequence());
80	1	assertSame(al.getSequenceAt(2), matches.get(1).getSequence());
81	1	assertEquals(matches.get(0).getStart(), 5);
82	1	assertEquals(matches.get(0).getEnd(), 7);
83	1	assertEquals(matches.get(1).getStart(), 4);
84	1	assertEquals(matches.get(1).getEnd(), 6);
85		}
86
87		/**
88		* Test for (undocumented) find residue by position
89		*/
		100% Uncovered Elements: 0 (12) Complexity: 1 Complexity Density: 0.08 1PASS
90	1	@Test(groups = "Functional")...
91		public void testFind_residueNumber()
92		{
93	1	Finder f = new Finder(al, null);
94	1	f.setFindAll(true);
95	1	f.find("9");
96
97		// seq1 and seq4 have 9 residues; no match in other sequences
98	1	SearchResultsI sr = f.getSearchResults();
99	1	assertEquals(sr.getSize(), 2);
100	1	List<SearchResultMatchI> matches = sr.getResults();
101	1	assertSame(al.getSequenceAt(0), matches.get(0).getSequence());
102	1	assertSame(al.getSequenceAt(3), matches.get(1).getSequence());
103	1	assertEquals(matches.get(0).getStart(), 9);
104	1	assertEquals(matches.get(0).getEnd(), 9);
105	1	assertEquals(matches.get(1).getStart(), 9);
106	1	assertEquals(matches.get(1).getEnd(), 9);
107		}
108
109		/**
110		* Test for find next action
111		*/
		100% Uncovered Elements: 0 (20) Complexity: 1 Complexity Density: 0.05 1PASS
112	1	@Test(groups = "Functional")...
113		public void testFindNext()
114		{
115		/*
116		* start at second sequence; resIndex of -1
117		* means sequence id / description is searched
118		*/
119	1	Finder f = new Finder(al, null, 1, -1);
120	1	f.find("e"); // matches id
121
122	1	assertTrue(f.getSearchResults().isEmpty());
123	1	assertEquals(f.getIdMatch().size(), 1);
124	1	assertSame(f.getIdMatch().get(0), al.getSequenceAt(1));
125
126		// resIndex is now 0 - for use in next find next
127	1	assertEquals(f.getResIndex(), 0);
128	1	f = new Finder(al, null, 1, 0);
129	1	f.find("e"); // matches in sequence
130	1	assertTrue(f.getIdMatch().isEmpty());
131	1	assertEquals(f.getSearchResults().getSize(), 1);
132	1	List<SearchResultMatchI> matches = f.getSearchResults().getResults();
133	1	assertEquals(matches.get(0).getStart(), 5);
134	1	assertEquals(matches.get(0).getEnd(), 5);
135	1	assertSame(matches.get(0).getSequence(), al.getSequenceAt(1));
136		// still in the second sequence
137	1	assertEquals(f.getSeqIndex(), 1);
138		// next residue position to search from is 5
139		// (used as base 0 by RegEx so the same as 6 if base 1)
140	1	assertEquals(f.getResIndex(), 5);
141
142		// find next from end of sequence - finds next sequence id
143	1	f = new Finder(al, null, 1, 5);
144	1	f.find("e");
145	1	assertEquals(f.getIdMatch().size(), 1);
146	1	assertSame(f.getIdMatch().get(0), al.getSequenceAt(2));
147		}
148
149		/**
150		* Test for matching within sequence descriptions
151		*/
		100% Uncovered Elements: 0 (38) Complexity: 1 Complexity Density: 0.03 1PASS
152	1	@Test(groups = "Functional")...
153		public void testFindAll_inDescription()
154		{
155	1	AlignmentI al2 = new Alignment(al);
156	1	al2.getSequenceAt(0).setDescription("BRAF");
157	1	al2.getSequenceAt(1).setDescription("braf");
158	1	Finder f = new Finder(al2, null);
159	1	f.setFindAll(true);
160	1	f.setIncludeDescription(true);
161
162	1	f.find("rAF");
163	1	assertEquals(f.getIdMatch().size(), 2);
164	1	assertSame(f.getIdMatch().get(0), al2.getSequenceAt(0));
165	1	assertSame(f.getIdMatch().get(1), al2.getSequenceAt(1));
166	1	assertTrue(f.getSearchResults().isEmpty());
167
168		/*
169		* case sensitive
170		*/
171	1	f = new Finder(al2, null);
172	1	f.setFindAll(true);
173	1	f.setCaseSensitive(true);
174	1	f.setIncludeDescription(true);
175
176	1	f.find("RAF");
177	1	assertEquals(f.getIdMatch().size(), 1);
178	1	assertSame(f.getIdMatch().get(0), al2.getSequenceAt(0));
179	1	assertTrue(f.getSearchResults().isEmpty());
180
181		/*
182		* match sequence id, description and sequence!
183		*/
184	1	al2.getSequenceAt(0).setDescription("the efh sequence");
185	1	al2.getSequenceAt(0).setName("mouseEFHkinase");
186	1	al2.getSequenceAt(1).setName("humanEFHkinase");
187	1	f = new Finder(al2, null);
188	1	f.setFindAll(true);
189	1	f.setIncludeDescription(true);
190
191		/*
192		* sequence matches should have no duplicates
193		*/
194	1	f.find("EFH");
195	1	assertEquals(f.getIdMatch().size(), 2);
196	1	assertSame(f.getIdMatch().get(0), al2.getSequenceAt(0));
197	1	assertSame(f.getIdMatch().get(1), al2.getSequenceAt(1));
198
199	1	assertEquals(f.getSearchResults().getSize(), 2);
200	1	SearchResultMatchI match = f.getSearchResults().getResults().get(0);
201	1	assertSame(al2.getSequenceAt(1), match.getSequence());
202	1	assertEquals(5, match.getStart());
203	1	assertEquals(7, match.getEnd());
204	1	match = f.getSearchResults().getResults().get(1);
205	1	assertSame(al2.getSequenceAt(2), match.getSequence());
206	1	assertEquals(4, match.getStart());
207	1	assertEquals(6, match.getEnd());
208		}
209
210		/**
211		* Test for matching within sequence ids
212		*/
		100% Uncovered Elements: 0 (27) Complexity: 1 Complexity Density: 0.04 1PASS
213	1	@Test(groups = "Functional")...
214		public void testFindAll_sequenceIds()
215		{
216	1	Finder f = new Finder(al, null);
217	1	f.setFindAll(true);
218
219		/*
220		* case insensitive
221		*/
222	1	f.find("SEQ1");
223	1	assertEquals(f.getIdMatch().size(), 1);
224	1	assertSame(f.getIdMatch().get(0), al.getSequenceAt(0));
225	1	assertTrue(f.getSearchResults().isEmpty());
226
227		/*
228		* case sensitive
229		*/
230	1	f = new Finder(al, null);
231	1	f.setFindAll(true);
232	1	f.setCaseSensitive(true);
233	1	f.find("SEQ1");
234	1	assertTrue(f.getSearchResults().isEmpty());
235
236		/*
237		* match both sequence id and sequence
238		*/
239	1	AlignmentI al2 = new Alignment(al);
240	1	al2.addSequence(new Sequence("aBz", "xyzabZpqrAbZ"));
241	1	f = new Finder(al2, null);
242	1	f.setFindAll(true);
243	1	f.find("ABZ");
244	1	assertEquals(f.getIdMatch().size(), 1);
245	1	assertSame(f.getIdMatch().get(0), al2.getSequenceAt(4));
246	1	assertEquals(f.getSearchResults().getSize(), 2);
247	1	SearchResultMatchI match = f.getSearchResults().getResults().get(0);
248	1	assertSame(al2.getSequenceAt(4), match.getSequence());
249	1	assertEquals(4, match.getStart());
250	1	assertEquals(6, match.getEnd());
251	1	match = f.getSearchResults().getResults().get(1);
252	1	assertSame(al2.getSequenceAt(4), match.getSequence());
253	1	assertEquals(10, match.getStart());
254	1	assertEquals(12, match.getEnd());
255		}
256
257		/**
258		* Test finding all matches of a sequence pattern in an alignment
259		*/
		100% Uncovered Elements: 0 (27) Complexity: 1 Complexity Density: 0.04 1PASS
260	1	@Test(groups = "Functional")...
261		public void testFindAll_simpleMatch()
262		{
263	1	Finder f = new Finder(al, null);
264	1	f.setFindAll(true);
265
266		/*
267		* case insensitive first
268		*/
269	1	f.find("EfH");
270	1	SearchResultsI searchResults = f.getSearchResults();
271	1	assertEquals(searchResults.getSize(), 2);
272	1	SearchResultMatchI match = searchResults.getResults().get(0);
273	1	assertSame(al.getSequenceAt(1), match.getSequence());
274	1	assertEquals(5, match.getStart());
275	1	assertEquals(7, match.getEnd());
276	1	match = searchResults.getResults().get(1);
277	1	assertSame(al.getSequenceAt(2), match.getSequence());
278	1	assertEquals(4, match.getStart());
279	1	assertEquals(6, match.getEnd());
280
281		/*
282		* case sensitive
283		*/
284	1	f = new Finder(al, null);
285	1	f.setFindAll(true);
286	1	f.setCaseSensitive(true);
287	1	f.find("BC");
288	1	searchResults = f.getSearchResults();
289	1	assertEquals(searchResults.getSize(), 2);
290	1	match = searchResults.getResults().get(0);
291	1	assertSame(al.getSequenceAt(0), match.getSequence());
292	1	assertEquals(2, match.getStart());
293	1	assertEquals(3, match.getEnd());
294	1	match = searchResults.getResults().get(1);
295	1	assertSame(al.getSequenceAt(1), match.getSequence());
296	1	assertEquals(2, match.getStart());
297	1	assertEquals(3, match.getEnd());
298		}
299
300		/**
301		* Test for JAL-2302 to verify that sub-matches are not included in a find all
302		* result
303		*/
		100% Uncovered Elements: 0 (9) Complexity: 1 Complexity Density: 0.11 1PASS
304	1	@Test(groups = "Functional")...
305		public void testFind_maximalResultOnly()
306		{
307	1	Finder f = new Finder(al, null);
308	1	f.setFindAll(true);
309	1	f.find("M+");
310	1	SearchResultsI searchResults = f.getSearchResults();
311	1	assertEquals(searchResults.getSize(), 1);
312	1	SearchResultMatchI match = searchResults.getResults().get(0);
313	1	assertSame(al.getSequenceAt(3), match.getSequence());
314	1	assertEquals(4, match.getStart()); // dataset sequence positions
315	1	assertEquals(8, match.getEnd()); // base 1
316		}
317		}