Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
RnaTest	40	121	81	0.970588297.1%	Show methods

Class RnaTest

Class RnaTest	Line # 40	Total Statements 121	Complexity 81	TOTAL Coverage 0.970588297.1%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4343	2.02	1.01	1.0 1.0100%
testGetSimpleBPs() : void   testGetSimpleBPs() : void	5050	9.09	1.01	1.0 1.0100%
testGetSimpleBPs_unmatchedOpener() : void   testGetSimpleBPs_unmatchedOpener() : void	6969	5.05	2.02	0.8 0.880%
testGetSimpleBPs_unmatchedCloser() : void   testGetSimpleBPs_unmatchedCloser() : void	8484	10.010	3.03	0.8 0.880%
testGetRNASecStrucState() : void   testGetRNASecStrucState() : void	113113	8.08	7.07	1.0 1.0100%
testIsClosingParenthesis() : void   testIsClosingParenthesis() : void	147147	10.010	8.08	1.0 1.0100%
testIsCanonicalOrWobblePair() : void   testIsCanonicalOrWobblePair() : void	176176	10.010	13.013	1.0 1.0100%
testIsCanonicalPair() : void   testIsCanonicalPair() : void	205205	10.010	9.09	1.0 1.0100%
testIsOpeningParenthesis() : void   testIsOpeningParenthesis() : void	235235	9.09	8.08	1.0 1.0100%
testGetMatchingOpeningParenthesis() : void   testGetMatchingOpeningParenthesis() : void	261261	8.08	13.013	0.875 0.87587.5%
testIsRnaSecondaryStructureSymbol() : void   testIsRnaSecondaryStructureSymbol() : void	291291	10.010	14.014	1.0 1.0100%
testGetHelixMap_oneHelix() : void   testGetHelixMap_oneHelix() : void	321321	15.015	1.01	1.0 1.0100%
testGetHelixMap_twoHelices() : void   testGetHelixMap_twoHelices() : void	346346	15.015	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.1	jalview.analysis.RnaTest.testIsCanonicalPairjalview.analysis.RnaTest.testIsCanonicalPair	1PASS
	0.1	jalview.analysis.RnaTest.testIsCanonicalOrWobblePairjalview.analysis.RnaTest.testIsCanonicalOrWobblePair	1PASS
	0.09411765	jalview.analysis.RnaTest.testGetHelixMap_oneHelixjalview.analysis.RnaTest.testGetHelixMap_oneHelix	1PASS
	0.09411765	jalview.analysis.RnaTest.testGetHelixMap_twoHelicesjalview.analysis.RnaTest.testGetHelixMap_twoHelices	1PASS
	0.0882353	jalview.analysis.RnaTest.testIsClosingParenthesisjalview.analysis.RnaTest.testIsClosingParenthesis	1PASS
	0.0882353	jalview.analysis.RnaTest.testIsRnaSecondaryStructureSymboljalview.analysis.RnaTest.testIsRnaSecondaryStructureSymbol	1PASS
	0.0882353	jalview.analysis.RnaTest.testGetMatchingOpeningParenthesisjalview.analysis.RnaTest.testGetMatchingOpeningParenthesis	1PASS
	0.08235294	jalview.analysis.RnaTest.testIsOpeningParenthesisjalview.analysis.RnaTest.testIsOpeningParenthesis	1PASS
	0.07647059	jalview.analysis.RnaTest.testGetRNASecStrucStatejalview.analysis.RnaTest.testGetRNASecStrucState	1PASS
	0.05882353	jalview.analysis.RnaTest.testGetSimpleBPsjalview.analysis.RnaTest.testGetSimpleBPs	1PASS
	0.052941177	jalview.analysis.RnaTest.testGetSimpleBPs_unmatchedCloserjalview.analysis.RnaTest.testGetSimpleBPs_unmatchedCloser	1PASS
	0.029411765	jalview.analysis.RnaTest.testGetSimpleBPs_unmatchedOpenerjalview.analysis.RnaTest.testGetSimpleBPs_unmatchedOpener	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 java.util.Locale;
24
25		import static org.testng.AssertJUnit.assertEquals;
26		import static org.testng.AssertJUnit.assertFalse;
27		import static org.testng.AssertJUnit.assertNull;
28		import static org.testng.AssertJUnit.assertTrue;
29		import static org.testng.AssertJUnit.fail;
30
31		import jalview.analysis.SecStrConsensus.SimpleBP;
32		import jalview.datamodel.SequenceFeature;
33		import jalview.gui.JvOptionPane;
34
35		import java.util.List;
36
37		import org.testng.annotations.BeforeClass;
38		import org.testng.annotations.Test;
39
		97.1% Uncovered Elements: 5 (170) Complexity: 81 Complexity Density: 0.67
40		public class RnaTest
41		{
42
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
43	1	@BeforeClass(alwaysRun = true)...
44		public void setUpJvOptionPane()
45		{
46	1	JvOptionPane.setInteractiveMode(false);
47	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
48		}
49
		100% Uncovered Elements: 0 (9) Complexity: 1 Complexity Density: 0.11 1PASS
50	1	@Test(groups = { "Functional" })...
51		public void testGetSimpleBPs() throws WUSSParseException
52		{
53	1	String rna = "([{})]"; // JAL-1081 example
54	1	List<SimpleBP> bps = Rna.getSimpleBPs(rna);
55	1	assertEquals(3, bps.size());
56
57		/*
58		* the base pairs are added in the order in which the matching base is found
59		* (popping the stack of unmatched opening brackets)
60		*/
61	1	assertEquals(2, bps.get(0).bp5); // {
62	1	assertEquals(3, bps.get(0).bp3); // }
63	1	assertEquals(0, bps.get(1).bp5); // (
64	1	assertEquals(4, bps.get(1).bp3); // )
65	1	assertEquals(1, bps.get(2).bp5); // [
66	1	assertEquals(5, bps.get(2).bp3); // ]
67		}
68
		80% Uncovered Elements: 1 (5) Complexity: 2 Complexity Density: 0.4 1PASS
69	1	@Test(groups = { "Functional" })...
70		public void testGetSimpleBPs_unmatchedOpener()
71		{
72	1	String rna = "(([{})]";
73	1	try
74		{
75	1	Rna.getSimpleBPs(rna);
76	0	fail("expected exception");
77		} catch (WUSSParseException e)
78		{
79		// error reported as after end of input string
80	1	assertEquals(rna.length(), e.getProblemPos());
81		}
82		}
83
		80% Uncovered Elements: 2 (10) Complexity: 3 Complexity Density: 0.3 1PASS
84	1	@Test(groups = { "Functional" })...
85		public void testGetSimpleBPs_unmatchedCloser()
86		{
87	1	String rna = "([{})]]]";
88	1	try
89		{
90	1	Rna.getSimpleBPs(rna);
91	0	fail("expected exception");
92		} catch (WUSSParseException e)
93		{
94		// error reported as at first unmatched close
95	1	assertEquals(6, e.getProblemPos());
96		}
97
98		/*
99		* a variant where we have no opening bracket of the same type
100		* as the unmatched closing bracket (no stack rather than empty stack)
101		*/
102	1	rna = "((()])";
103	1	try
104		{
105	1	Rna.getSimpleBPs(rna);
106	0	fail("expected exception");
107		} catch (WUSSParseException e)
108		{
109	1	assertEquals(4, e.getProblemPos());
110		}
111		}
112
		100% Uncovered Elements: 0 (12) Complexity: 7 Complexity Density: 0.88 1PASS
113	1	@Test(groups = { "Functional" })...
114		public void testGetRNASecStrucState()
115		{
116	1	assertNull(Rna.getRNASecStrucState(null));
117	257	for (int i = 0; i <= 255; i++)
118		{
119	256	String s = String.valueOf((char) i);
120	256	String ss = Rna.getRNASecStrucState(s);
121
122		/*
123		* valid SS chars are a-z, A-Z, and various brackets;
124		* anything else is returned as a space
125		*/
126	256	if ((i >= 'a' && i <= 'z') || (i >= 'A' && i <= 'Z')
127		|| "()[]{}<>".indexOf(s) > -1)
128		{
129	60	assertEquals("" + i, s, ss);
130		}
131		else
132		{
133	196	assertEquals(" ", ss);
134		}
135		}
136
137		/*
138		* a string is processed character by character
139		*/
140	1	assertEquals("a [K ]z} {Q b(w)p><i",
141		Rna.getRNASecStrucState("a.[K-]z}?{Q b(w)p><i"));
142		}
143
144		/**
145		* Tests for isClosingParenthesis with char or String argument
146		*/
		100% Uncovered Elements: 0 (14) Complexity: 8 Complexity Density: 0.8 1PASS
147	1	@Test(groups = { "Functional" })...
148		public void testIsClosingParenthesis()
149		{
150	1	assertFalse(Rna.isClosingParenthesis(null));
151
152		/*
153		* only a-z, )]}> are closing bracket symbols
154		*/
155	257	for (int i = 0; i <= 255; i++)
156		{
157	256	boolean isClosingChar = Rna.isClosingParenthesis((char) i);
158	256	boolean isClosingString = Rna
159		.isClosingParenthesis(String.valueOf((char) i));
160	256	if ((i >= 'a' && i <= 'z') || i == ')' || i == '}' || i == ']'
161		|| i == '>')
162		{
163	30	assertTrue(String.format("close base pair %c", i), isClosingChar);
164	30	assertTrue(String.format("close base pair %c", i), isClosingString);
165		}
166		else
167		{
168	226	assertFalse(String.format("close base pair %c", i), isClosingChar);
169	226	assertFalse(String.format("close base pair %c", i),
170		isClosingString);
171		}
172	256	assertFalse(Rna.isClosingParenthesis(String.valueOf((char) i) + " "));
173		}
174		}
175
		100% Uncovered Elements: 0 (16) Complexity: 13 Complexity Density: 1.3 1PASS
176	1	@Test(groups = { "Functional" })...
177		public void testIsCanonicalOrWobblePair()
178		{
179	1	String bases = "acgtuACGTU";
180	11	for (int i = 0; i < bases.length(); i++)
181		{
182	110	for (int j = 0; j < bases.length(); j++)
183		{
184	100	char first = bases.charAt(i);
185	100	char second = bases.charAt(j);
186	100	boolean result = Rna.isCanonicalOrWobblePair(first, second);
187	100	String pair = new String(new char[] { first, second })
188		.toUpperCase(Locale.ROOT);
189	100	if (pair.equals("AT") || pair.equals("TA") || pair.equals("AU")
190		|| pair.equals("UA") || pair.equals("GC")
191		|| pair.equals("CG") || pair.equals("GT")
192		|| pair.equals("TG") || pair.equals("GU")
193		|| pair.equals("UG"))
194		{
195	40	assertTrue(pair + " should be valid", result);
196		}
197		else
198		{
199	60	assertFalse(pair + " should be invalid", result);
200		}
201		}
202		}
203		}
204
		100% Uncovered Elements: 0 (16) Complexity: 9 Complexity Density: 0.9 1PASS
205	1	@Test(groups = { "Functional" })...
206		public void testIsCanonicalPair()
207		{
208	1	String bases = "acgtuACGTU";
209	11	for (int i = 0; i < bases.length(); i++)
210		{
211	110	for (int j = 0; j < bases.length(); j++)
212		{
213	100	char first = bases.charAt(i);
214	100	char second = bases.charAt(j);
215	100	boolean result = Rna.isCanonicalPair(first, second);
216	100	String pair = new String(new char[] { first, second })
217		.toUpperCase(Locale.ROOT);
218	100	if (pair.equals("AT") || pair.equals("TA") || pair.equals("AU")
219		|| pair.equals("UA") || pair.equals("GC")
220		|| pair.equals("CG"))
221		{
222	24	assertTrue(pair + " should be valid", result);
223		}
224		else
225		{
226	76	assertFalse(pair + " should be invalid", result);
227		}
228		}
229		}
230		}
231
232		/**
233		* Tests for isOpeningParenthesis with char or String argument
234		*/
		100% Uncovered Elements: 0 (13) Complexity: 8 Complexity Density: 0.89 1PASS
235	1	@Test(groups = { "Functional" })...
236		public void testIsOpeningParenthesis()
237		{
238		/*
239		* only A-Z, ([{< are opening bracket symbols
240		*/
241	257	for (int i = 0; i <= 255; i++)
242		{
243	256	boolean isOpeningChar = Rna.isOpeningParenthesis((char) i);
244	256	boolean isOpeningString = Rna
245		.isOpeningParenthesis(String.valueOf((char) i));
246	256	if ((i >= 'A' && i <= 'Z') || i == '(' || i == '{' || i == '['
247		|| i == '<')
248		{
249	30	assertTrue(String.format("Open base pair %c", i), isOpeningChar);
250	30	assertTrue(String.format("Open base pair %c", i), isOpeningString);
251		}
252		else
253		{
254	226	assertFalse(String.format("Open base pair %c", i), isOpeningChar);
255	226	assertFalse(String.format("Open base pair %c", i), isOpeningString);
256		}
257	256	assertFalse(Rna.isOpeningParenthesis(String.valueOf((char) i) + " "));
258		}
259		}
260
		87.5% Uncovered Elements: 2 (16) Complexity: 13 Complexity Density: 1.62 1PASS
261	1	@Test(groups = { "Functional" })...
262		public void testGetMatchingOpeningParenthesis() throws WUSSParseException
263		{
264	257	for (int i = 0; i <= 255; i++)
265		{
266	256	boolean isClosing = Rna.isClosingParenthesis((char) i);
267	256	if (isClosing)
268		{
269	30	char opening = Rna.getMatchingOpeningParenthesis((char) i);
270	30	if (i >= 'a' && i <= 'z')
271		{
272	26	assertEquals(i + 'A' - 'a', opening);
273		}
274	4	else if (i == ')' && opening == '(' || i == ']' && opening == '['
275		|| i == '}' && opening == '{' || i == '>' && opening == '<')
276		{
277		// ok
278		}
279		else
280		{
281	0	fail("Got " + opening + " as opening bracket pair for "
282		+ ((char) i));
283		}
284		}
285		}
286		}
287
288		/**
289		* Tests for isRnaSecondaryStructureSymbol with char or String argument
290		*/
		100% Uncovered Elements: 0 (14) Complexity: 14 Complexity Density: 1.4 1PASS
291	1	@Test(groups = { "Functional" })...
292		public void testIsRnaSecondaryStructureSymbol()
293		{
294	1	assertFalse(Rna.isRnaSecondaryStructureSymbol(null));
295
296		/*
297		* only A-Z, a-z, ()[]{}<> are valid symbols
298		*/
299	257	for (int i = 0; i <= 255; i++)
300		{
301	256	boolean isValidChar = Rna.isRnaSecondaryStructureSymbol((char) i);
302	256	boolean isValidString = Rna
303		.isRnaSecondaryStructureSymbol(String.valueOf((char) i));
304	256	if ((i >= 'A' && i <= 'Z') || (i >= 'a' && i <= 'z') || i == '('
305		|| i == ')' || i == '{' || i == '}' || i == '[' || i == ']'
306		|| i == '<' || i == '>')
307		{
308	60	assertTrue(String.format("close base pair %c", i), isValidChar);
309	60	assertTrue(String.format("close base pair %c", i), isValidString);
310		}
311		else
312		{
313	196	assertFalse(String.format("close base pair %c", i), isValidChar);
314	196	assertFalse(String.format("close base pair %c", i), isValidString);
315		}
316	256	assertFalse(Rna.isRnaSecondaryStructureSymbol(
317		String.valueOf((char) i) + " "));
318		}
319		}
320
		100% Uncovered Elements: 0 (15) Complexity: 1 Complexity Density: 0.07 1PASS
321	1	@Test(groups = "Functional")...
322		public void testGetHelixMap_oneHelix() throws WUSSParseException
323		{
324	1	String rna = ".(..[{.<..>}..].)";
325	1	SequenceFeature[] sfs = Rna.getHelixMap(rna);
326	1	assertEquals(4, sfs.length);
327
328		/*
329		* pairs are added in the order in which the closing bracket is found
330		* (see testGetSimpleBPs)
331		*/
332	1	assertEquals(7, sfs[0].getBegin());
333	1	assertEquals(10, sfs[0].getEnd());
334	1	assertEquals("0", sfs[0].getFeatureGroup());
335	1	assertEquals(5, sfs[1].getBegin());
336	1	assertEquals(11, sfs[1].getEnd());
337	1	assertEquals("0", sfs[1].getFeatureGroup());
338	1	assertEquals(4, sfs[2].getBegin());
339	1	assertEquals(14, sfs[2].getEnd());
340	1	assertEquals("0", sfs[2].getFeatureGroup());
341	1	assertEquals(1, sfs[3].getBegin());
342	1	assertEquals(16, sfs[3].getEnd());
343	1	assertEquals("0", sfs[3].getFeatureGroup());
344		}
345
		100% Uncovered Elements: 0 (15) Complexity: 1 Complexity Density: 0.07 1PASS
346	1	@Test(groups = "Functional")...
347		public void testGetHelixMap_twoHelices() throws WUSSParseException
348		{
349	1	String rna = ".([.)]..{.<}.>";
350	1	SequenceFeature[] sfs = Rna.getHelixMap(rna);
351	1	assertEquals(4, sfs.length);
352
353		/*
354		* pairs are added in the order in which the closing bracket is found
355		* (see testGetSimpleBPs)
356		*/
357	1	assertEquals(1, sfs[0].getBegin());
358	1	assertEquals(4, sfs[0].getEnd());
359	1	assertEquals("0", sfs[0].getFeatureGroup());
360	1	assertEquals(2, sfs[1].getBegin());
361	1	assertEquals(5, sfs[1].getEnd());
362	1	assertEquals("0", sfs[1].getFeatureGroup());
363	1	assertEquals(8, sfs[2].getBegin());
364	1	assertEquals(11, sfs[2].getEnd());
365	1	assertEquals("1", sfs[2].getFeatureGroup());
366	1	assertEquals(10, sfs[3].getBegin());
367	1	assertEquals(13, sfs[3].getEnd());
368	1	assertEquals("1", sfs[3].getFeatureGroup());
369		}
370		}