Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
PhylipFileTests	47	31	8	0.00%	Show methods

Class PhylipFileTests

Class PhylipFileTests	Line # 47	Total Statements 31	Complexity 8	TOTAL Coverage 0.00%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	5050	2.02	1.01	0.0 0.00%
getTestData() : Map<String, String>   getTestData() : Map<String, String>	6969	12.012	1.01	0.0 0.00%
testSequentialDataExtraction() : void   testSequentialDataExtraction() : void	101101	1.01	1.01	0.0 0.00%
testInterleavedDataExtraction() : void   testInterleavedDataExtraction() : void	113113	1.01	1.01	0.0 0.00%
testDataExtraction(String) : void   testDataExtraction(String) : void	125125	6.06	1.01	0.0 0.00%
testSequentialIO() : void   testSequentialIO() : void	146146	1.01	1.01	0.0 0.00%
testInterleavedIO() : void   testInterleavedIO() : void	158158	1.01	1.01	0.0 0.00%
testIO(String) : void   testIO(String) : void	170170	7.07	1.01	0.0 0.00%

 

Contributing tests

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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.io;
22
23		import static org.testng.AssertJUnit.assertNotNull;
24		import static org.testng.AssertJUnit.assertTrue;
25
26		import jalview.datamodel.AlignmentI;
27		import jalview.datamodel.SequenceI;
28		import jalview.gui.JvOptionPane;
29
30		import java.io.IOException;
31		import java.util.HashMap;
32		import java.util.Map;
33
34		import org.testng.annotations.BeforeClass;
35		import org.testng.annotations.Test;
36
37		/**
38		* Test file for {@link PhylipFile}.
39		*
40		* Tests use example data obtained from
41		* <a href="http://www.molecularevolution.org/resources/fileformats"
42		* >molecularrevolution.org<a>.
43		*
44		* @author David Corsar
45		*
46		*/
		0% Uncovered Elements: 39 (39) Complexity: 8 Complexity Density: 0.26
47		public class PhylipFileTests
48		{
49
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
50	0	@BeforeClass(alwaysRun = true)...
51		public void setUpJvOptionPane()
52		{
53	0	JvOptionPane.setInteractiveMode(false);
54	0	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
55		}
56
57		// interleaved file from
58		// http://www.molecularevolution.org/molevolfiles/fileformats/dna.phy.dat
59		// sequential file is the interleave file converted into sequential format
60
61		static String sequentialFile = "examples/dna_sequential.phy",
62		interleavedFile = "examples/dna_interleaved.phy";
63
64		/**
65		* Creates a name:sequence map for the data in the above files
66		*
67		* @return
68		*/
		0% Uncovered Elements: 12 (12) Complexity: 1 Complexity Density: 0.08
69	0	private static Map<String, String> getTestData()...
70		{
71	0	Map<String, String> data = new HashMap<String, String>();
72	0	data.put("Cow",
73		"ATGGCATATCCCATACAACTAGGATTCCAAGATGCAACATCACCAATCATAGAAGAACTACTTCACTTTCATGACCACACGCTAATAATTGTCTTCTTAATTAGCTCATTAGTACTTTACATTATTTCACTAATACTAACGACAAAGCTGACCCATACAAGCACGATAGATGCACAAGAAGTAGAGACAATCTGAACCATTCTGCCCGCCATCATCTTAATTCTAATTGCTCTTCCTTCTTTACGAATTCTATACATAATAGATGAAATCAATAACCCATCTCTTACAGTAAAAACCATAGGACATCAGTGATACTGAAGCTATGAGTATACAGATTATGAGGACTTAAGCTTCGACTCCTACATAATTCCAACATCAGAATTAAAGCCAGGGGAGCTACGACTATTAGAAGTCGATAATCGAGTTGTACTACCAATAGAAATAACAATCCGAATGTTAGTCTCCTCTGAAGACGTATTACACTCATGAGCTGTGCCCTCTCTAGGACTAAAAACAGACGCAATCCCAGGCCGTCTAAACCAAACAACCCTTATATCGTCCCGTCCAGGCTTATATTACGGTCAATGCTCAGAAATTTGCGGGTCAAACCACAGTTTCATACCCATTGTCCTTGAGTTAGTCCCACTAAAGTACTTTGAAAAATGATCTGCGTCAATATTA---------------------TAA");
74	0	data.put("Carp",
75		"ATGGCACACCCAACGCAACTAGGTTTCAAGGACGCGGCCATACCCGTTATAGAGGAACTTCTTCACTTCCACGACCACGCATTAATAATTGTGCTCCTAATTAGCACTTTAGTTTTATATATTATTACTGCAATGGTATCAACTAAACTTACTAATAAATATATTCTAGACTCCCAAGAAATCGAAATCGTATGAACCATTCTACCAGCCGTCATTTTAGTACTAATCGCCCTGCCCTCCCTACGCATCCTGTACCTTATAGACGAAATTAACGACCCTCACCTGACAATTAAAGCAATAGGACACCAATGATACTGAAGTTACGAGTATACAGACTATGAAAATCTAGGATTCGACTCCTATATAGTACCAACCCAAGACCTTGCCCCCGGACAATTCCGACTTCTGGAAACAGACCACCGAATAGTTGTTCCAATAGAATCCCCAGTCCGTGTCCTAGTATCTGCTGAAGACGTGCTACATTCTTGAGCTGTTCCATCCCTTGGCGTAAAAATGGACGCAGTCCCAGGACGACTAAATCAAGCCGCCTTTATTGCCTCACGCCCAGGGGTCTTTTACGGACAATGCTCTGAAATTTGTGGAGCTAATCACAGCTTTATACCAATTGTAGTTGAAGCAGTACCTCTCGAACACTTCGAAAACTGATCCTCATTAATACTAGAAGACGCCTCGCTAGGAAGCTAA");
76	0	data.put("Chicken",
77		"ATGGCCAACCACTCCCAACTAGGCTTTCAAGACGCCTCATCCCCCATCATAGAAGAGCTCGTTGAATTCCACGACCACGCCCTGATAGTCGCACTAGCAATTTGCAGCTTAGTACTCTACCTTCTAACTCTTATACTTATAGAAAAACTATCA---TCAAACACCGTAGATGCCCAAGAAGTTGAACTAATCTGAACCATCCTACCCGCTATTGTCCTAGTCCTGCTTGCCCTCCCCTCCCTCCAAATCCTCTACATAATAGACGAAATCGACGAACCTGATCTCACCCTAAAAGCCATCGGACACCAATGATACTGAACCTATGAATACACAGACTTCAAGGACCTCTCATTTGACTCCTACATAACCCCAACAACAGACCTCCCCCTAGGCCACTTCCGCCTACTAGAAGTCGACCATCGCATTGTAATCCCCATAGAATCCCCCATTCGAGTAATCATCACCGCTGATGACGTCCTCCACTCATGAGCCGTACCCGCCCTCGGGGTAAAAACAGACGCAATCCCTGGACGACTAAATCAAACCTCCTTCATCACCACTCGACCAGGAGTGTTTTACGGACAATGCTCAGAAATCTGCGGAGCTAACCACAGCTACATACCCATTGTAGTAGAGTCTACCCCCCTAAAACACTTTGAAGCCTGATCCTCACTA------------------CTGTCATCTTAA");
78	0	data.put("Human",
79		"ATGGCACATGCAGCGCAAGTAGGTCTACAAGACGCTACTTCCCCTATCATAGAAGAGCTTATCACCTTTCATGATCACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTCCTGTATGCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAACATCTCAGACGCTCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATCATCCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTACATAACAGACGAGGTCAACGATCCCTCCCTTACCATCAAATCAATTGGCCACCAATGGTACTGAACCTACGAGTACACCGACTACGGCGGACTAATCTTCAACTCCTACATACTTCCCCCATTATTCCTAGAACCAGGCGACCTGCGACTCCTTGACGTTGACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGTATAATAATTACATCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGCTTAAAAACAGATGCAATTCCCGGACGTCTAAACCAAACCACTTTCACCGCTACACGACCGGGGGTATACTACGGTCAATGCTCTGAAATCTGTGGAGCAAACCACAGTTTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAAATA---------------------GGGCCCGTATTTACCCTATAG");
80	0	data.put("Loach",
81		"ATGGCACATCCCACACAATTAGGATTCCAAGACGCGGCCTCACCCGTAATAGAAGAACTTCTTCACTTCCATGACCATGCCCTAATAATTGTATTTTTGATTAGCGCCCTAGTACTTTATGTTATTATTACAACCGTCTCAACAAAACTCACTAACATATATATTTTGGACTCACAAGAAATTGAAATCGTATGAACTGTGCTCCCTGCCCTAATCCTCATTTTAATCGCCCTCCCCTCACTACGAATTCTATATCTTATAGACGAGATTAATGACCCCCACCTAACAATTAAGGCCATGGGGCACCAATGATACTGAAGCTACGAGTATACTGATTATGAAAACTTAAGTTTTGACTCCTACATAATCCCCACCCAGGACCTAACCCCTGGACAATTCCGGCTACTAGAGACAGACCACCGAATGGTTGTTCCCATAGAATCCCCTATTCGCATTCTTGTTTCCGCCGAAGATGTACTACACTCCTGGGCCCTTCCAGCCATGGGGGTAAAGATAGACGCGGTCCCAGGACGCCTTAACCAAACCGCCTTTATTGCCTCCCGCCCCGGGGTATTCTATGGGCAATGCTCAGAAATCTGTGGAGCAAACCACAGCTTTATACCCATCGTAGTAGAAGCGGTCCCACTATCTCACTTCGAAAACTGGTCCACCCTTATACTAAAAGACGCCTCACTAGGAAGCTAA");
82	0	data.put("Mouse",
83		"ATGGCCTACCCATTCCAACTTGGTCTACAAGACGCCACATCCCCTATTATAGAAGAGCTAATAAATTTCCATGATCACACACTAATAATTGTTTTCCTAATTAGCTCCTTAGTCCTCTATATCATCTCGCTAATATTAACAACAAAACTAACACATACAAGCACAATAGATGCACAAGAAGTTGAAACCATTTGAACTATTCTACCAGCTGTAATCCTTATCATAATTGCTCTCCCCTCTCTACGCATTCTATATATAATAGACGAAATCAACAACCCCGTATTAACCGTTAAAACCATAGGGCACCAATGATACTGAAGCTACGAATATACTGACTATGAAGACCTATGCTTTGATTCATATATAATCCCAACAAACGACCTAAAACCTGGTGAACTACGACTGCTAGAAGTTGATAACCGAGTCGTTCTGCCAATAGAACTTCCAATCCGTATATTAATTTCATCTGAAGACGTCCTCCACTCATGAGCAGTCCCCTCCCTAGGACTTAAAACTGATGCCATCCCAGGCCGACTAAATCAAGCAACAGTAACATCAAACCGACCAGGGTTATTCTATGGCCAATGCTCTGAAATTTGTGGATCTAACCATAGCTTTATGCCCATTGTCCTAGAAATGGTTCCACTAAAATATTTCGAAAACTGATCTGCTTCAATAATT---------------------TAA");
84	0	data.put("Rat",
85		"ATGGCTTACCCATTTCAACTTGGCTTACAAGACGCTACATCACCTATCATAGAAGAACTTACAAACTTTCATGACCACACCCTAATAATTGTATTCCTCATCAGCTCCCTAGTACTTTATATTATTTCACTAATACTAACAACAAAACTAACACACACAAGCACAATAGACGCCCAAGAAGTAGAAACAATTTGAACAATTCTCCCAGCTGTCATTCTTATTCTAATTGCCCTTCCCTCCCTACGAATTCTATACATAATAGACGAGATTAATAACCCAGTTCTAACAGTAAAAACTATAGGACACCAATGATACTGAAGCTATGAATATACTGACTATGAAGACCTATGCTTTGACTCCTACATAATCCCAACCAATGACCTAAAACCAGGTGAACTTCGTCTATTAGAAGTTGATAATCGGGTAGTCTTACCAATAGAACTTCCAATTCGTATACTAATCTCATCCGAAGACGTCCTGCACTCATGAGCCATCCCTTCACTAGGGTTAAAAACCGACGCAATCCCCGGCCGCCTAAACCAAGCTACAGTCACATCAAACCGACCAGGTCTATTCTATGGCCAATGCTCTGAAATTTGCGGCTCAAATCACAGCTTCATACCCATTGTACTAGAAATAGTGCCTCTAAAATATTTCGAAAACTGATCAGCTTCTATAATT---------------------TAA");
86	0	data.put("Seal",
87		"ATGGCATACCCCCTACAAATAGGCCTACAAGATGCAACCTCTCCCATTATAGAGGAGTTACTACACTTCCATGACCACACATTAATAATTGTGTTCCTAATTAGCTCATTAGTACTCTACATTATCTCACTTATACTAACCACGAAACTCACCCACACAAGTACAATAGACGCACAAGAAGTGGAAACGGTGTGAACGATCCTACCCGCTATCATTTTAATTCTCATTGCCCTACCATCATTACGAATCCTCTACATAATGGACGAGATCAATAACCCTTCCTTGACCGTAAAAACTATAGGACATCAGTGATACTGAAGCTATGAGTACACAGACTACGAAGACCTGAACTTTGACTCATATATGATCCCCACACAAGAACTAAAGCCCGGAGAACTACGACTGCTAGAAGTAGACAATCGAGTAGTCCTCCCAATAGAAATAACAATCCGCATACTAATCTCATCAGAAGATGTACTCCACTCATGAGCCGTACCGTCCCTAGGACTAAAAACTGATGCTATCCCAGGACGACTAAACCAAACAACCCTAATAACCATACGACCAGGACTGTACTACGGTCAATGCTCAGAAATCTGTGGTTCAAACCACAGCTTCATACCTATTGTCCTCGAATTGGTCCCACTATCCCACTTCGAGAAATGATCTACCTCAATGCTT---------------------TAA");
88	0	data.put("Whale",
89		"ATGGCATATCCATTCCAACTAGGTTTCCAAGATGCAGCATCACCCATCATAGAAGAGCTCCTACACTTTCACGATCATACACTAATAATCGTTTTTCTAATTAGCTCTTTAGTTCTCTACATTATTACCCTAATGCTTACAACCAAATTAACACATACTAGTACAATAGACGCCCAAGAAGTAGAAACTGTCTGAACTATCCTCCCAGCCATTATCTTAATTTTAATTGCCTTGCCTTCATTACGGATCCTTTACATAATAGACGAAGTCAATAACCCCTCCCTCACTGTAAAAACAATAGGTCACCAATGATATTGAAGCTATGAGTATACCGACTACGAAGACCTAAGCTTCGACTCCTATATAATCCCAACATCAGACCTAAAGCCAGGAGAACTACGATTATTAGAAGTAGATAACCGAGTTGTCTTACCTATAGAAATAACAATCCGAATATTAGTCTCATCAGAAGACGTACTCCACTCATGGGCCGTACCCTCCTTGGGCCTAAAAACAGATGCAATCCCAGGACGCCTAAACCAAACAACCTTAATATCAACACGACCAGGCCTATTTTATGGACAATGCTCAGAGATCTGCGGCTCAAACCACAGTTTCATACCAATTGTCCTAGAACTAGTACCCCTAGAAGTCTTTGAAAAATGATCTGTATCAATACTA---------------------TAA");
90	0	data.put("Frog",
91		"ATGGCACACCCATCACAATTAGGTTTTCAAGACGCAGCCTCTCCAATTATAGAAGAATTACTTCACTTCCACGACCATACCCTCATAGCCGTTTTTCTTATTAGTACGCTAGTTCTTTACATTATTACTATTATAATAACTACTAAACTAACTAATACAAACCTAATGGACGCACAAGAGATCGAAATAGTGTGAACTATTATACCAGCTATTAGCCTCATCATAATTGCCCTTCCATCCCTTCGTATCCTATATTTAATAGATGAAGTTAATGATCCACACTTAACAATTAAAGCAATCGGCCACCAATGATACTGAAGCTACGAATATACTAACTATGAGGATCTCTCATTTGACTCTTATATAATTCCAACTAATGACCTTACCCCTGGACAATTCCGGCTGCTAGAAGTTGATAATCGAATAGTAGTCCCAATAGAATCTCCAACCCGACTTTTAGTTACAGCCGAAGACGTCCTCCACTCGTGAGCTGTACCCTCCTTGGGTGTCAAAACAGATGCAATCCCAGGACGACTTCATCAAACATCATTTATTGCTACTCGTCCGGGAGTATTTTACGGACAATGTTCAGAAATTTGCGGAGCAAACCACAGCTTTATACCAATTGTAGTTGAAGCAGTACCGCTAACCGACTTTGAAAACTGATCTTCATCAATACTA---GAAGCATCACTA------AGA");
92	0	return data;
93		}
94
95		/**
96		* Tests sequential format file is read correctly by comparing read sequence
97		* with that in the test data.
98		*
99		* @throws Exception
100		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1 4-
101	0	@Test(groups = { "Functional" })...
102		public void testSequentialDataExtraction() throws Exception
103		{
104	0	testDataExtraction(sequentialFile);
105		}
106
107		/**
108		* Tests interleaved format file is read correctly by comparing read sequence
109		* with that in the test data.
110		*
111		* @throws Exception
112		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1 4-
113	0	@Test(groups = { "Functional" })...
114		public void testInterleavedDataExtraction() throws Exception
115		{
116	0	testDataExtraction(interleavedFile);
117		}
118
119		/**
120		* Tests a PHYLIP file is read correctly by comparing read sequence with that
121		* in the test data.
122		*
123		* @throws Exception
124		*/
		0% Uncovered Elements: 6 (6) Complexity: 1 Complexity Density: 0.17
125	0	private void testDataExtraction(String file) throws IOException...
126		{
127	0	AppletFormatAdapter rf = new AppletFormatAdapter();
128	0	AlignmentI al = rf.readFile(file, DataSourceType.FILE,
129		FileFormat.Phylip);
130	0	assertNotNull("Couldn't read supplied alignment data.", al);
131
132	0	Map<String, String> data = PhylipFileTests.getTestData();
133	0	for (SequenceI s : al.getSequencesArray())
134		{
135	0	assertTrue(s.getName() + " sequence did not match test data.",
136		data.get(s.getName()).equals(s.getSequenceAsString()));
137		}
138		}
139
140		/**
141		* Tests sequential format file reading and writing without data lose using
142		* similar approach to {@link StockholmFileTest}
143		*
144		* @throws Exception
145		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1 4-
146	0	@Test(groups = { "Functional" })...
147		public void testSequentialIO() throws Exception
148		{
149	0	testIO(sequentialFile);
150		}
151
152		/**
153		* Tests interleaved format file reading and writing without data lose using
154		* similar approach to {@link StockholmFileTest}
155		*
156		* @throws Exception
157		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1 4-
158	0	@Test(groups = { "Functional" })...
159		public void testInterleavedIO() throws Exception
160		{
161	0	testIO(interleavedFile);
162		}
163
164		/**
165		* Uses {@link StockholmFileTest} to test read/write/read
166		*
167		* @param file
168		* @throws IOException
169		*/
		0% Uncovered Elements: 7 (7) Complexity: 1 Complexity Density: 0.14
170	0	public void testIO(String file) throws IOException...
171		{
172	0	AppletFormatAdapter rf = new AppletFormatAdapter();
173	0	AlignmentI al = rf.readFile(file, DataSourceType.FILE,
174		FileFormat.Phylip);
175	0	assertNotNull("Couldn't read supplied alignment data.", al);
176
177	0	String outputfile = rf.formatSequences(FileFormat.Phylip, al, true);
178
179	0	AlignmentI al_input = new AppletFormatAdapter().readFile(outputfile,
180		DataSourceType.PASTE, FileFormat.Phylip);
181	0	assertNotNull("Couldn't parse reimported alignment data.", al_input);
182
183	0	StockholmFileTest.testAlignmentEquivalence(al, al_input, false, false,
184		false);
185
186		}
187		}