Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
TestAlignSeq	46	75	13	0.977777897.8%	Show methods

Class TestAlignSeq

Class TestAlignSeq	Line # 46	Total Statements 75	Complexity 13	TOTAL Coverage 0.977777897.8%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4949	2.02	1.01	1.0 1.0100%
setUp() : void   setUp() : void	6161	7.07	1.01	1.0 1.0100%
testGetMappingForS1_1() : void   testGetMappingForS1_1() : void	7474	9.09	1.01	1.0 1.0100%
testGetMappingForS1_2() : void   testGetMappingForS1_2() : void	9494	15.015	1.01	1.0 1.0100%
testGetMappingForS1_complex() : void   testGetMappingForS1_complex() : void	116116	11.011	1.01	1.0 1.0100%
checkMapping(Mapping,SequenceI,SequenceI) : void   checkMapping(Mapping,SequenceI,SequenceI) : void	143143	9.09	3.03	1.0 1.0100%
testGetMappingForS1_withLowerCase() : void   testGetMappingForS1_withLowerCase() : void	164164	10.010	1.01	1.0 1.0100%
testExtractGaps() : void   testExtractGaps() : void	187187	4.04	1.01	1.0 1.0100%
print(String) : void   print(String) : void	204204	1.01	1.01	1.0 1.0100%
println() : void   println() : void	210210	1.01	1.01	0.0 0.00%
testPrintAlignment() : void   testPrintAlignment() : void	197197	6.06	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.33333334	jalview.analysis.TestAlignSeq.testGetMappingForS1_2jalview.analysis.TestAlignSeq.testGetMappingForS1_2	1PASS
	0.2888889	jalview.analysis.TestAlignSeq.testGetMappingForS1_complexjalview.analysis.TestAlignSeq.testGetMappingForS1_complex	1PASS
	0.25555557	jalview.analysis.TestAlignSeq.testGetMappingForS1_withLowerCasejalview.analysis.TestAlignSeq.testGetMappingForS1_withLowerCase	1PASS
	0.24444444	jalview.analysis.TestAlignSeq.testGetMappingForS1_1jalview.analysis.TestAlignSeq.testGetMappingForS1_1	1PASS
	0.1	jalview.analysis.TestAlignSeq.testPrintAlignmentjalview.analysis.TestAlignSeq.testPrintAlignment	1PASS
	0.055555556	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		import jalview.util.MapList;
31
32		import java.io.PrintStream;
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
40		/**
41		* Test the alignment -> Mapping routines
42		*
43		* @author jimp
44		*
45		*/
		97.8% Uncovered Elements: 2 (90) Complexity: 13 Complexity Density: 0.17
46		public class TestAlignSeq
47		{
48
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
49	1	@BeforeClass(alwaysRun = true)...
50		public void setUpJvOptionPane()
51		{
52	1	JvOptionPane.setInteractiveMode(false);
53	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
54		}
55
56		SequenceI s1, s2, s3;
57
58		/**
59		* @throws java.lang.Exception
60		*/
		100% Uncovered Elements: 0 (7) Complexity: 1 Complexity Density: 0.14
61	6	@BeforeMethod(alwaysRun = true)...
62		public void setUp() throws Exception
63		{
64	6	s1 = new Sequence("Seq1", "ASDFAQQQRRRSSS");
65	6	s1.setStart(3);
66	6	s1.setEnd(18);
67	6	s2 = new Sequence("Seq2", "ASDFA");
68	6	s2.setStart(5);
69	6	s2.setEnd(9);
70	6	s3 = new Sequence("Seq3", "SDFAQQQSSS");
71
72		}
73
		100% Uncovered Elements: 0 (9) Complexity: 1 Complexity Density: 0.11 1PASS
74	1	@Test(groups = { "Functional" })...
75		/**
76		* test Mappings from alignments correspond to identical positions (for structure & sequence:sequence mappings)
77		*/
78		public void testGetMappingForS1_1()
79		{
80	1	AlignSeq as = AlignSeq.doGlobalNWAlignment(s1, s2, AlignSeq.PEP);
81	1	System.out.println("s1: " + as.getAStr1());
82	1	System.out.println("s2: " + as.getAStr2());
83
84		// aligned results match
85	1	assertEquals("ASDFA", as.getAStr1());
86	1	assertEquals(as.getAStr1(), as.getAStr2());
87
88	1	Mapping s1tos2 = as.getMappingFromS1(false);
89		// ASDFA = 5aa
90	1	assertEquals(s2.getStart(),s1tos2.getMappedPosition(s1.getStart()));
91	1	assertEquals(s2.getStart()+4,s1tos2.getMappedPosition(s1.getStart()+4));
92	1	checkMapping(s1tos2, s1, s2);
93		}
		100% Uncovered Elements: 0 (15) Complexity: 1 Complexity Density: 0.07 1PASS
94	1	@Test(groups = { "Functional" })...
95		/**
96		* test Mappings from alignments correspond to identical positions (for structure & sequence:sequence mappings)
97		*/
98		public void testGetMappingForS1_2()
99		{
100		// simple version of full pathological case
101	1	String s1str="MSNATGVVRSPFEYP";
102	1	String s2str="MSNKTGVPFEAP";
103	1	SequenceI ns1 = new Sequence("S1",s1str);SequenceI ns2 = new Sequence("S2",s2str);
104	1	AlignSeq as = AlignSeq.doGlobalNWAlignment(ns1, ns2, AlignSeq.PEP);
105	1	String astr1="MSNATGVVRSPFEYP";
106	1	String astr2="MSNKTGV---PFEAP";
107	1	int[] mstr1 = new int[] { 1,3, 5,7, 11,13,15,15};
108	1	int[] mstr2 = new int[] { 1,3, 5,7, 8,10, 12,12};
109	1	assertEquals(as.getAStr1(),astr1);
110	1	assertEquals(as.getAStr2(),astr2);
111	1	Mapping as1toas2 = as.getMappingFromS1(false);
112	1	checkMapping(as1toas2,ns1,ns2);
113	1	MapList maplist= new MapList(mstr1, mstr2, 1,1);
114	1	assertEquals(maplist,as.getMappingFromS1(false).getMap());
115		}
		100% Uncovered Elements: 0 (11) Complexity: 1 Complexity Density: 0.09 1PASS
116	1	@Test(groups = { "Functional" })...
117		/**
118		* test Mappings from alignments correspond to identical positions (for structure & sequence:sequence mappings)
119		*/
120		public void testGetMappingForS1_complex()
121		{
122		// chance encountered a pathological case from JAL-4566
123		// OPSD_MACFA to 7zbc
124	1	String s1str="MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNAEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLFGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEARAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSASIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA";
125	1	String s2str="MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLC";
126	1	SequenceI ns1 = new Sequence("S1",s1str);
127	1	SequenceI ns2 = new Sequence("S2",s2str);
128	1	AlignSeq as = AlignSeq.doGlobalNWAlignment(ns1, ns2, AlignSeq.PEP);
129	1	String astr1="MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNAEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLFGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEARAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSASIYNPVIYIMMNKQFRNCMLTTIC";
130	1	String astr2="MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKP----RFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVF--------------TQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLC";
131	1	assertEquals(as.getAStr1(),astr1);
132	1	assertEquals(as.getAStr2(),astr2);
133	1	Mapping as1toas2 = as.getMappingFromS1(false);
134	1	checkMapping(as1toas2,ns1,ns2);
135		}
136
137		/**
138		* verifies positions in _s2 are either not mapped, or mapped to identical residues in _s1
139		* @param s1tos2
140		* @param _s1
141		* @param _s2
142		*/
		100% Uncovered Elements: 0 (13) Complexity: 3 Complexity Density: 0.33
143	4	public void checkMapping(Mapping s1tos2, SequenceI _s1, SequenceI _s2)...
144		{
145	4	System.out.println(s1tos2.getMap().toString());
146	326	for (int i = _s2.getStart(); i < _s2.getEnd(); i++)
147		{
148	322	int[] mp = s1tos2.locateRange(i, i);
149	322	char s2c = _s2.getCharAt(i - _s2.getStart());
150	322	if (mp == null)
151		{
152	23	System.out.println("Position in s2: " + i + s2c + " is NOT MAPPED");
153		}
154		else
155		{
156	299	char s1c = _s1.getCharAt(mp[0] - _s1.getStart());
157	299	System.out.println("Position in s2: " + i + s2c
158		+ " maps to position in s1: " + mp[0] + s1c);
159	299	assertEquals(s1c, s2c);
160		}
161		}
162		}
163
		100% Uncovered Elements: 0 (10) Complexity: 1 Complexity Density: 0.1 1PASS
164	1	@Test(groups = { "Functional" })...
165		/**
166		* simple test that mapping from alignment corresponds identical positions.
167		*/
168		public void testGetMappingForS1_withLowerCase()
169		{
170		// make one of the sequences lower case
171	1	SequenceI ns2 = new Sequence(s2);
172	1	ns2.replace('D', 'd');
173	1	AlignSeq as = AlignSeq.doGlobalNWAlignment(s1, ns2, AlignSeq.PEP);
174	1	System.out.println("s1: " + as.getAStr1());
175	1	System.out.println("s2: " + as.getAStr2());
176
177		// aligned results match
178	1	assertEquals("ASDFA", as.getAStr1());
179	1	assertEquals(as.getAStr1(), as.getAStr2().toUpperCase(Locale.ROOT));
180
181	1	Mapping s1tos2 = as.getMappingFromS1(false);
182	1	assertEquals("ASdFA", as.getAStr2());
183		// verify mapping is consistent between original all-caps sequences
184	1	checkMapping(s1tos2, s1, s2);
185		}
186
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25 1PASS
187	1	@Test(groups = { "Functional" })...
188		public void testExtractGaps()
189		{
190	1	assertNull(AlignSeq.extractGaps(null, null));
191	1	assertNull(AlignSeq.extractGaps(". -", null));
192	1	assertNull(AlignSeq.extractGaps(null, "AB-C"));
193
194	1	assertEquals("ABCD", AlignSeq.extractGaps(" .-", ". -A-B.C D."));
195		}
196
		100% Uncovered Elements: 0 (6) Complexity: 1 Complexity Density: 0.17 1PASS
197	1	@Test(groups = { "Functional" })...
198		public void testPrintAlignment()
199		{
200	1	AlignSeq as = AlignSeq.doGlobalNWAlignment(s1, s3, AlignSeq.PEP);
201	1	final StringBuilder baos = new StringBuilder();
202	1	PrintStream ps = new PrintStream(System.out)
203		{
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
204	1	@Override...
205		public void print(String x)
206		{
207	1	baos.append(x);
208		}
209
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
210	0	@Override...
211		public void println()
212		{
213	0	baos.append("\n");
214		}
215		};
216
217	1	as.printAlignment(ps);
218	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"
219		+ "Seq1/4-13 SDFAQQQRRR\n" + " ||||||| \n"
220		+ "Seq3/1-10 SDFAQQQSSS\n\n" + "Percentage ID = 70.00\n\n";
221	1	assertEquals(expected, baos.toString());
222		}
223		}