Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AlignSeqTest	33	24	5	1.0100%	Show methods

Class AlignSeqTest

Class AlignSeqTest	Line # 33	Total Statements 24	Complexity 5	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	3636	2.02	1.01	1.0 1.0100%
testExtractGaps() : void   testExtractGaps() : void	4343	9.09	1.01	1.0 1.0100%
testIndexEncode_nucleotide() : void   testIndexEncode_nucleotide() : void	5858	4.04	1.01	1.0 1.0100%
testIndexEncode_peptide() : void   testIndexEncode_peptide() : void	6969	4.04	1.01	1.0 1.0100%
testGlobalAlignment() : void   testGlobalAlignment() : void	8080	5.05	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.3448276	jalview.analysis.AlignSeqTest.testExtractGapsjalview.analysis.AlignSeqTest.testExtractGaps	1PASS
	0.20689656	jalview.analysis.AlignSeqTest.testGlobalAlignmentjalview.analysis.AlignSeqTest.testGlobalAlignment	1PASS
	0.1724138	jalview.analysis.AlignSeqTest.testIndexEncode_peptidejalview.analysis.AlignSeqTest.testIndexEncode_peptide	1PASS
	0.1724138	jalview.analysis.AlignSeqTest.testIndexEncode_nucleotidejalview.analysis.AlignSeqTest.testIndexEncode_nucleotide	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.assertNull;
25		import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
26
27		import jalview.datamodel.Sequence;
28		import jalview.gui.JvOptionPane;
29
30		import org.testng.annotations.BeforeClass;
31		import org.testng.annotations.Test;
32
		100% Uncovered Elements: 0 (29) Complexity: 5 Complexity Density: 0.21
33		public class AlignSeqTest
34		{
35
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
36	1	@BeforeClass(alwaysRun = true)...
37		public void setUpJvOptionPane()
38		{
39	1	JvOptionPane.setInteractiveMode(false);
40	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
41		}
42
		100% Uncovered Elements: 0 (9) Complexity: 1 Complexity Density: 0.11 1PASS
43	1	@Test(groups = { "Functional" })...
44		public void testExtractGaps()
45		{
46	1	assertNull(AlignSeq.extractGaps(null, null));
47	1	assertNull(AlignSeq.extractGaps(null, "ACG"));
48	1	assertNull(AlignSeq.extractGaps("-. ", null));
49
50	1	assertEquals(AlignSeq.extractGaps("", " AC-G.T"), " AC-G.T");
51	1	assertEquals(AlignSeq.extractGaps(" ", " AC-G.T"), "AC-G.T");
52	1	assertEquals(AlignSeq.extractGaps(" -", " AC-G.T"), "ACG.T");
53	1	assertEquals(AlignSeq.extractGaps(" -.", " AC-G.T ."), "ACGT");
54	1	assertEquals(AlignSeq.extractGaps("-", " AC-G.T"), " ACG.T");
55	1	assertEquals(AlignSeq.extractGaps("-. ", " -. .-"), "");
56		}
57
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25 1PASS
58	1	@Test(groups = { "Functional" })...
59		public void testIndexEncode_nucleotide()
60		{
61	1	AlignSeq as = new AlignSeq(new Sequence("s1", "TTAG"),
62		new Sequence("s2", "ACGT"), AlignSeq.DNA);
63	1	int[] expected = new int[] { 0, 0, 1, 1, 2, 2, 3, 3, 4, 4, 5, 5, 6, 6,
64		7, 7, 8, 8, 9, 9, -1, -1, 10, -1 };
65	1	String s = "aAcCgGtTuUiIxXrRyYnN .-?";
66	1	assertArrayEquals(expected, as.indexEncode(s));
67		}
68
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25 1PASS
69	1	@Test(groups = { "Functional" })...
70		public void testIndexEncode_peptide()
71		{
72	1	AlignSeq as = new AlignSeq(new Sequence("s1", "PFY"),
73		new Sequence("s2", "RQW"), AlignSeq.PEP);
74	1	int[] expected = new int[] { 0, 0, 1, 1, 2, 2, 21, 21, 22, 22, -1, 23,
75		-1, -1, -1 };
76	1	String s = "aArRnNzZxX *.-?";
77	1	assertArrayEquals(expected, as.indexEncode(s));
78		}
79
		100% Uncovered Elements: 0 (5) Complexity: 1 Complexity Density: 0.2 1PASS
80	1	@Test(groups = { "Functional" })...
81		public void testGlobalAlignment()
82		{
83	1	String seq1 = "CAGCTAGCG", seq2 = "CCATACGA";
84	1	Sequence sq1 = new Sequence("s1", seq1), sq2 = new Sequence("s2", seq2);
85		// AlignSeq doesn't report the unaligned regions at either end of sequences
86		// String alseq1="-CAGCTAGCG-",alseq2="CCA--TA-CGA";
87		// so we check we have the aligned segment correct only
88	1	String alseq1 = "CAGCTAGCG", alseq2 = "CA--TA-CG";
89	1	AlignSeq as = AlignSeq.doGlobalNWAlignment(sq1, sq2, AlignSeq.DNA);
90	1	assertEquals(as.getAStr1() + "\n" + as.getAStr2(),
91		alseq1 + "\n" + alseq2);
92		}
93		}