Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
TestAlignSeq	43	30	8	2	0.9487179594.9%	Show methods

Class TestAlignSeq

Class TestAlignSeq	Line # 43	Total Statements 30	Complexity 8	Uncovered Elements 2	TOTAL Coverage 0.9487179594.9%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4646	2.02	1.01	0.00	1.0 1.0100%
setUp() : void   setUp() : void	5858	7.07	1.01	0.00	1.0 1.0100%
testGetMappingForS1() : void   testGetMappingForS1() : void	7171	9.09	2.02	0.00	1.0 1.0100%
testExtractGaps() : void   testExtractGaps() : void	9797	4.04	1.01	0.00	1.0 1.0100%
print(String) : void   print(String) : void	114114	1.01	1.01	0.00	1.0 1.0100%
println() : void   println() : void	120120	1.01	1.01	1.01	0.0 0.00%
testPrintAlignment() : void   testPrintAlignment() : void	107107	6.06	1.01	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.30769232	jalview.analysis.TestAlignSeq.testGetMappingForS1jalview.analysis.TestAlignSeq.testGetMappingForS1	1PASS
	0.23076923	jalview.analysis.TestAlignSeq.testPrintAlignmentjalview.analysis.TestAlignSeq.testPrintAlignment	1PASS
	0.12820514	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
33		import org.testng.annotations.BeforeClass;
34		import org.testng.annotations.BeforeMethod;
35		import org.testng.annotations.Test;
36
37		/**
38		* Test the alignment -> Mapping routines
39		*
40		* @author jimp
41		*
42		*/
		94.9% Uncovered Elements: 2 (39) Complexity: 8 Complexity Density: 0.27
43		public class TestAlignSeq
44		{
45
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
46	1	@BeforeClass(alwaysRun = true)...
47		public void setUpJvOptionPane()
48		{
49	1	JvOptionPane.setInteractiveMode(false);
50	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
51		}
52
53		SequenceI s1, s2, s3;
54
55		/**
56		* @throws java.lang.Exception
57		*/
		100% Uncovered Elements: 0 (7) Complexity: 1 Complexity Density: 0.14
58	3	@BeforeMethod(alwaysRun = true)...
59		public void setUp() throws Exception
60		{
61	3	s1 = new Sequence("Seq1", "ASDFAQQQRRRSSS");
62	3	s1.setStart(3);
63	3	s1.setEnd(18);
64	3	s2 = new Sequence("Seq2", "ASDFA");
65	3	s2.setStart(5);
66	3	s2.setEnd(9);
67	3	s3 = new Sequence("Seq3", "SDFAQQQSSS");
68
69		}
70
		100% Uncovered Elements: 0 (11) Complexity: 2 Complexity Density: 0.22 1PASS
71	1	@Test(groups = { "Functional" })...
72		/**
73		* simple test that mapping from alignment corresponds identical positions.
74		*/
75		public void testGetMappingForS1()
76		{
77	1	AlignSeq as = AlignSeq.doGlobalNWAlignment(s1, s2, AlignSeq.PEP);
78	1	System.out.println("s1: " + as.getAStr1());
79	1	System.out.println("s2: " + as.getAStr2());
80
81		// aligned results match
82	1	assertEquals("ASDFA", as.getAStr1());
83	1	assertEquals(as.getAStr1(), as.getAStr2());
84
85	1	Mapping s1tos2 = as.getMappingFromS1(false);
86	1	System.out.println(s1tos2.getMap().toString());
87	5	for (int i = s2.getStart(); i < s2.getEnd(); i++)
88		{
89	4	System.out.println("Position in s2: " + i
90		+ " maps to position in s1: " + s1tos2.getPosition(i));
91		// TODO fails: getCharAt doesn't allow for the start position??
92		// assertEquals(String.valueOf(s2.getCharAt(i)),
93		// String.valueOf(s1.getCharAt(s1tos2.getPosition(i))));
94		}
95		}
96
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25 1PASS
97	1	@Test(groups = { "Functional" })...
98		public void testExtractGaps()
99		{
100	1	assertNull(AlignSeq.extractGaps(null, null));
101	1	assertNull(AlignSeq.extractGaps(". -", null));
102	1	assertNull(AlignSeq.extractGaps(null, "AB-C"));
103
104	1	assertEquals("ABCD", AlignSeq.extractGaps(" .-", ". -A-B.C D."));
105		}
106
		100% Uncovered Elements: 0 (6) Complexity: 1 Complexity Density: 0.17 1PASS
107	1	@Test(groups = { "Functional" })...
108		public void testPrintAlignment()
109		{
110	1	AlignSeq as = AlignSeq.doGlobalNWAlignment(s1, s3, AlignSeq.PEP);
111	1	final StringBuilder baos = new StringBuilder();
112	1	PrintStream ps = new PrintStream(System.out)
113		{
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
114	1	@Override...
115		public void print(String x)
116		{
117	1	baos.append(x);
118		}
119
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
120	0	@Override...
121		public void println()
122		{
123	0	baos.append("\n");
124		}
125		};
126
127	1	as.printAlignment(ps);
128	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"
129		+ "Seq1/4-13 SDFAQQQRRR\n"
130		+ " ||||||| \n"
131		+ "Seq3/1-10 SDFAQQQSSS\n\n" + "Percentage ID = 70.00\n\n";
132	1	assertEquals(expected, baos.toString());
133		}
134		}