Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
TestAlignSeq	47	45	10	0.9642857396.4%	Show methods

Class TestAlignSeq

Class TestAlignSeq	Line # 47	Total Statements 45	Complexity 10	TOTAL Coverage 0.9642857396.4%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	5050	2.02	1.01	1.0 1.0100%
setUp() : void   setUp() : void	6262	7.07	1.01	1.0 1.0100%
testGetMappingForS1() : void   testGetMappingForS1() : void	7575	7.07	1.01	1.0 1.0100%
checkMapping(Mapping,SequenceI,SequenceI) : void   checkMapping(Mapping,SequenceI,SequenceI) : void	9393	7.07	2.02	1.0 1.0100%
testGetMappingForS1_withLowerCase() : void   testGetMappingForS1_withLowerCase() : void	107107	10.010	1.01	1.0 1.0100%
testExtractGaps() : void   testExtractGaps() : void	130130	4.04	1.01	1.0 1.0100%
print(String) : void   print(String) : void	147147	1.01	1.01	1.0 1.0100%
println() : void   println() : void	153153	1.01	1.01	0.0 0.00%
testPrintAlignment() : void   testPrintAlignment() : void	140140	6.06	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.375	jalview.analysis.TestAlignSeq.testGetMappingForS1_withLowerCasejalview.analysis.TestAlignSeq.testGetMappingForS1_withLowerCase	1PASS
	0.32142857	jalview.analysis.TestAlignSeq.testGetMappingForS1jalview.analysis.TestAlignSeq.testGetMappingForS1	1PASS
	0.16071428	jalview.analysis.TestAlignSeq.testPrintAlignmentjalview.analysis.TestAlignSeq.testPrintAlignment	1PASS
	0.08928572	jalview.analysis.TestAlignSeq.testExtractGapsjalview.analysis.TestAlignSeq.testExtractGaps	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.assertNull;
25
26		import jalview.datamodel.Mapping;
27		import jalview.datamodel.Sequence;
28		import jalview.datamodel.SequenceI;
29		import jalview.gui.JvOptionPane;
30
31		import java.io.PrintStream;
32		import java.nio.charset.Charset;
33		import java.util.Locale;
34
35		import org.testng.annotations.BeforeClass;
36		import org.testng.annotations.BeforeMethod;
37		import org.testng.annotations.Test;
38
39		import com.google.common.base.Charsets;
40
41		/**
42		* Test the alignment -> Mapping routines
43		*
44		* @author jimp
45		*
46		*/
		96.4% Uncovered Elements: 2 (56) Complexity: 10 Complexity Density: 0.22
47		public class TestAlignSeq
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		SequenceI s1, s2, s3;
58
59		/**
60		* @throws java.lang.Exception
61		*/
		100% Uncovered Elements: 0 (7) Complexity: 1 Complexity Density: 0.14
62	4	@BeforeMethod(alwaysRun = true)...
63		public void setUp() throws Exception
64		{
65	4	s1 = new Sequence("Seq1", "ASDFAQQQRRRSSS");
66	4	s1.setStart(3);
67	4	s1.setEnd(18);
68	4	s2 = new Sequence("Seq2", "ASDFA");
69	4	s2.setStart(5);
70	4	s2.setEnd(9);
71	4	s3 = new Sequence("Seq3", "SDFAQQQSSS");
72
73		}
74
		100% Uncovered Elements: 0 (7) Complexity: 1 Complexity Density: 0.14 1PASS
75	1	@Test(groups = { "Functional" })...
76		/**
77		* simple test that mapping from alignment corresponds identical positions.
78		*/
79		public void testGetMappingForS1()
80		{
81	1	AlignSeq as = AlignSeq.doGlobalNWAlignment(s1, s2, AlignSeq.PEP);
82	1	System.out.println("s1: " + as.getAStr1());
83	1	System.out.println("s2: " + as.getAStr2());
84
85		// aligned results match
86	1	assertEquals("ASDFA", as.getAStr1());
87	1	assertEquals(as.getAStr1(), as.getAStr2());
88
89	1	Mapping s1tos2 = as.getMappingFromS1(false);
90	1	checkMapping(s1tos2, s1, s2);
91		}
92
		100% Uncovered Elements: 0 (9) Complexity: 2 Complexity Density: 0.29
93	2	public void checkMapping(Mapping s1tos2, SequenceI _s1, SequenceI _s2)...
94		{
95	2	System.out.println(s1tos2.getMap().toString());
96	10	for (int i = _s2.getStart(); i < _s2.getEnd(); i++)
97		{
98	8	int p = s1tos2.getPosition(i);
99	8	char s2c = _s2.getCharAt(i - _s2.getStart());
100	8	char s1c = _s1.getCharAt(p - _s1.getStart());
101	8	System.out.println("Position in s2: " + i + s2c
102		+ " maps to position in s1: " + p + s1c);
103	8	assertEquals(s1c, s2c);
104		}
105		}
106
		100% Uncovered Elements: 0 (10) Complexity: 1 Complexity Density: 0.1 1PASS
107	1	@Test(groups = { "Functional" })...
108		/**
109		* simple test that mapping from alignment corresponds identical positions.
110		*/
111		public void testGetMappingForS1_withLowerCase()
112		{
113		// make one of the sequences lower case
114	1	SequenceI ns2 = new Sequence(s2);
115	1	ns2.replace('D', 'd');
116	1	AlignSeq as = AlignSeq.doGlobalNWAlignment(s1, ns2, AlignSeq.PEP);
117	1	System.out.println("s1: " + as.getAStr1());
118	1	System.out.println("s2: " + as.getAStr2());
119
120		// aligned results match
121	1	assertEquals("ASDFA", as.getAStr1());
122	1	assertEquals(as.getAStr1(), as.getAStr2().toUpperCase(Locale.ROOT));
123
124	1	Mapping s1tos2 = as.getMappingFromS1(false);
125	1	assertEquals("ASdFA", as.getAStr2());
126		// verify mapping is consistent between original all-caps sequences
127	1	checkMapping(s1tos2, s1, s2);
128		}
129
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25 1PASS
130	1	@Test(groups = { "Functional" })...
131		public void testExtractGaps()
132		{
133	1	assertNull(AlignSeq.extractGaps(null, null));
134	1	assertNull(AlignSeq.extractGaps(". -", null));
135	1	assertNull(AlignSeq.extractGaps(null, "AB-C"));
136
137	1	assertEquals("ABCD", AlignSeq.extractGaps(" .-", ". -A-B.C D."));
138		}
139
		100% Uncovered Elements: 0 (6) Complexity: 1 Complexity Density: 0.17 1PASS
140	1	@Test(groups = { "Functional" })...
141		public void testPrintAlignment()
142		{
143	1	AlignSeq as = AlignSeq.doGlobalNWAlignment(s1, s3, AlignSeq.PEP);
144	1	final StringBuilder baos = new StringBuilder();
145	1	PrintStream ps = new PrintStream(System.out)
146		{
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
147	1	@Override...
148		public void print(String x)
149		{
150	1	baos.append(x);
151		}
152
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
153	0	@Override...
154		public void println()
155		{
156	0	baos.append("\n");
157		}
158		};
159
160	1	as.printAlignment(ps);
161	1	String expected = "Score = 320.0\nLength of alignment = 10\nSequence Seq1/4-13 (Sequence length = 14)\nSequence Seq3/1-10 (Sequence length = 10)\n\n"
162		+ "Seq1/4-13 SDFAQQQRRR\n" + " ||||||| \n"
163		+ "Seq3/1-10 SDFAQQQSSS\n\n" + "Percentage ID = 70.00\n\n";
164	1	assertEquals(expected, baos.toString());
165		}
166		}