Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
PhylipFileTests	47	31	8	0	1.0100%	Show methods

Class PhylipFileTests

Class PhylipFileTests	Line # 47	Total Statements 31	Complexity 8	Uncovered Elements 0	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	5050	2.02	1.01	0.00	1.0 1.0100%
getTestData() : Map<String, String>   getTestData() : Map<String, String>	6969	12.012	1.01	0.00	1.0 1.0100%
testSequentialDataExtraction() : void   testSequentialDataExtraction() : void	111111	1.01	1.01	0.00	1.0 1.0100%
testInterleavedDataExtraction() : void   testInterleavedDataExtraction() : void	123123	1.01	1.01	0.00	1.0 1.0100%
testDataExtraction(String) : void   testDataExtraction(String) : void	135135	6.06	1.01	0.00	1.0 1.0100%
testSequentialIO() : void   testSequentialIO() : void	156156	1.01	1.01	0.00	1.0 1.0100%
testInterleavedIO() : void   testInterleavedIO() : void	168168	1.01	1.01	0.00	1.0 1.0100%
testIO(String) : void   testIO(String) : void	180180	7.07	1.01	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.5641026	jalview.io.PhylipFileTests.testInterleavedDataExtractionjalview.io.PhylipFileTests.testInterleavedDataExtraction	1PASS
	0.5641026	jalview.io.PhylipFileTests.testSequentialDataExtractionjalview.io.PhylipFileTests.testSequentialDataExtraction	1PASS
	0.25641027	jalview.io.PhylipFileTests.testInterleavedIOjalview.io.PhylipFileTests.testInterleavedIO	1PASS
	0.25641027	jalview.io.PhylipFileTests.testSequentialIOjalview.io.PhylipFileTests.testSequentialIO	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.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 <a
41		* href="http://www.molecularevolution.org/resources/fileformats"
42		* >molecularrevolution.org<a>.
43		*
44		* @author David Corsar
45		*
46		*/
		100% Uncovered Elements: 0 (39) Complexity: 8 Complexity Density: 0.26
47		public class PhylipFileTests
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		// 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		*/
		100% Uncovered Elements: 0 (12) Complexity: 1 Complexity Density: 0.08
69	2	private static Map<String, String> getTestData()...
70		{
71	2	Map<String, String> data = new HashMap<String, String>();
72	2	data.put(
73		"Cow",
74		"ATGGCATATCCCATACAACTAGGATTCCAAGATGCAACATCACCAATCATAGAAGAACTACTTCACTTTCATGACCACACGCTAATAATTGTCTTCTTAATTAGCTCATTAGTACTTTACATTATTTCACTAATACTAACGACAAAGCTGACCCATACAAGCACGATAGATGCACAAGAAGTAGAGACAATCTGAACCATTCTGCCCGCCATCATCTTAATTCTAATTGCTCTTCCTTCTTTACGAATTCTATACATAATAGATGAAATCAATAACCCATCTCTTACAGTAAAAACCATAGGACATCAGTGATACTGAAGCTATGAGTATACAGATTATGAGGACTTAAGCTTCGACTCCTACATAATTCCAACATCAGAATTAAAGCCAGGGGAGCTACGACTATTAGAAGTCGATAATCGAGTTGTACTACCAATAGAAATAACAATCCGAATGTTAGTCTCCTCTGAAGACGTATTACACTCATGAGCTGTGCCCTCTCTAGGACTAAAAACAGACGCAATCCCAGGCCGTCTAAACCAAACAACCCTTATATCGTCCCGTCCAGGCTTATATTACGGTCAATGCTCAGAAATTTGCGGGTCAAACCACAGTTTCATACCCATTGTCCTTGAGTTAGTCCCACTAAAGTACTTTGAAAAATGATCTGCGTCAATATTA---------------------TAA");
75	2	data.put(
76		"Carp",
77		"ATGGCACACCCAACGCAACTAGGTTTCAAGGACGCGGCCATACCCGTTATAGAGGAACTTCTTCACTTCCACGACCACGCATTAATAATTGTGCTCCTAATTAGCACTTTAGTTTTATATATTATTACTGCAATGGTATCAACTAAACTTACTAATAAATATATTCTAGACTCCCAAGAAATCGAAATCGTATGAACCATTCTACCAGCCGTCATTTTAGTACTAATCGCCCTGCCCTCCCTACGCATCCTGTACCTTATAGACGAAATTAACGACCCTCACCTGACAATTAAAGCAATAGGACACCAATGATACTGAAGTTACGAGTATACAGACTATGAAAATCTAGGATTCGACTCCTATATAGTACCAACCCAAGACCTTGCCCCCGGACAATTCCGACTTCTGGAAACAGACCACCGAATAGTTGTTCCAATAGAATCCCCAGTCCGTGTCCTAGTATCTGCTGAAGACGTGCTACATTCTTGAGCTGTTCCATCCCTTGGCGTAAAAATGGACGCAGTCCCAGGACGACTAAATCAAGCCGCCTTTATTGCCTCACGCCCAGGGGTCTTTTACGGACAATGCTCTGAAATTTGTGGAGCTAATCACAGCTTTATACCAATTGTAGTTGAAGCAGTACCTCTCGAACACTTCGAAAACTGATCCTCATTAATACTAGAAGACGCCTCGCTAGGAAGCTAA");
78	2	data.put(
79		"Chicken",
80		"ATGGCCAACCACTCCCAACTAGGCTTTCAAGACGCCTCATCCCCCATCATAGAAGAGCTCGTTGAATTCCACGACCACGCCCTGATAGTCGCACTAGCAATTTGCAGCTTAGTACTCTACCTTCTAACTCTTATACTTATAGAAAAACTATCA---TCAAACACCGTAGATGCCCAAGAAGTTGAACTAATCTGAACCATCCTACCCGCTATTGTCCTAGTCCTGCTTGCCCTCCCCTCCCTCCAAATCCTCTACATAATAGACGAAATCGACGAACCTGATCTCACCCTAAAAGCCATCGGACACCAATGATACTGAACCTATGAATACACAGACTTCAAGGACCTCTCATTTGACTCCTACATAACCCCAACAACAGACCTCCCCCTAGGCCACTTCCGCCTACTAGAAGTCGACCATCGCATTGTAATCCCCATAGAATCCCCCATTCGAGTAATCATCACCGCTGATGACGTCCTCCACTCATGAGCCGTACCCGCCCTCGGGGTAAAAACAGACGCAATCCCTGGACGACTAAATCAAACCTCCTTCATCACCACTCGACCAGGAGTGTTTTACGGACAATGCTCAGAAATCTGCGGAGCTAACCACAGCTACATACCCATTGTAGTAGAGTCTACCCCCCTAAAACACTTTGAAGCCTGATCCTCACTA------------------CTGTCATCTTAA");
81	2	data.put(
82		"Human",
83		"ATGGCACATGCAGCGCAAGTAGGTCTACAAGACGCTACTTCCCCTATCATAGAAGAGCTTATCACCTTTCATGATCACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTCCTGTATGCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAACATCTCAGACGCTCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATCATCCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTACATAACAGACGAGGTCAACGATCCCTCCCTTACCATCAAATCAATTGGCCACCAATGGTACTGAACCTACGAGTACACCGACTACGGCGGACTAATCTTCAACTCCTACATACTTCCCCCATTATTCCTAGAACCAGGCGACCTGCGACTCCTTGACGTTGACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGTATAATAATTACATCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGCTTAAAAACAGATGCAATTCCCGGACGTCTAAACCAAACCACTTTCACCGCTACACGACCGGGGGTATACTACGGTCAATGCTCTGAAATCTGTGGAGCAAACCACAGTTTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAAATA---------------------GGGCCCGTATTTACCCTATAG");
84	2	data.put(
85		"Loach",
86		"ATGGCACATCCCACACAATTAGGATTCCAAGACGCGGCCTCACCCGTAATAGAAGAACTTCTTCACTTCCATGACCATGCCCTAATAATTGTATTTTTGATTAGCGCCCTAGTACTTTATGTTATTATTACAACCGTCTCAACAAAACTCACTAACATATATATTTTGGACTCACAAGAAATTGAAATCGTATGAACTGTGCTCCCTGCCCTAATCCTCATTTTAATCGCCCTCCCCTCACTACGAATTCTATATCTTATAGACGAGATTAATGACCCCCACCTAACAATTAAGGCCATGGGGCACCAATGATACTGAAGCTACGAGTATACTGATTATGAAAACTTAAGTTTTGACTCCTACATAATCCCCACCCAGGACCTAACCCCTGGACAATTCCGGCTACTAGAGACAGACCACCGAATGGTTGTTCCCATAGAATCCCCTATTCGCATTCTTGTTTCCGCCGAAGATGTACTACACTCCTGGGCCCTTCCAGCCATGGGGGTAAAGATAGACGCGGTCCCAGGACGCCTTAACCAAACCGCCTTTATTGCCTCCCGCCCCGGGGTATTCTATGGGCAATGCTCAGAAATCTGTGGAGCAAACCACAGCTTTATACCCATCGTAGTAGAAGCGGTCCCACTATCTCACTTCGAAAACTGGTCCACCCTTATACTAAAAGACGCCTCACTAGGAAGCTAA");
87	2	data.put(
88		"Mouse",
89		"ATGGCCTACCCATTCCAACTTGGTCTACAAGACGCCACATCCCCTATTATAGAAGAGCTAATAAATTTCCATGATCACACACTAATAATTGTTTTCCTAATTAGCTCCTTAGTCCTCTATATCATCTCGCTAATATTAACAACAAAACTAACACATACAAGCACAATAGATGCACAAGAAGTTGAAACCATTTGAACTATTCTACCAGCTGTAATCCTTATCATAATTGCTCTCCCCTCTCTACGCATTCTATATATAATAGACGAAATCAACAACCCCGTATTAACCGTTAAAACCATAGGGCACCAATGATACTGAAGCTACGAATATACTGACTATGAAGACCTATGCTTTGATTCATATATAATCCCAACAAACGACCTAAAACCTGGTGAACTACGACTGCTAGAAGTTGATAACCGAGTCGTTCTGCCAATAGAACTTCCAATCCGTATATTAATTTCATCTGAAGACGTCCTCCACTCATGAGCAGTCCCCTCCCTAGGACTTAAAACTGATGCCATCCCAGGCCGACTAAATCAAGCAACAGTAACATCAAACCGACCAGGGTTATTCTATGGCCAATGCTCTGAAATTTGTGGATCTAACCATAGCTTTATGCCCATTGTCCTAGAAATGGTTCCACTAAAATATTTCGAAAACTGATCTGCTTCAATAATT---------------------TAA");
90	2	data.put(
91		"Rat",
92		"ATGGCTTACCCATTTCAACTTGGCTTACAAGACGCTACATCACCTATCATAGAAGAACTTACAAACTTTCATGACCACACCCTAATAATTGTATTCCTCATCAGCTCCCTAGTACTTTATATTATTTCACTAATACTAACAACAAAACTAACACACACAAGCACAATAGACGCCCAAGAAGTAGAAACAATTTGAACAATTCTCCCAGCTGTCATTCTTATTCTAATTGCCCTTCCCTCCCTACGAATTCTATACATAATAGACGAGATTAATAACCCAGTTCTAACAGTAAAAACTATAGGACACCAATGATACTGAAGCTATGAATATACTGACTATGAAGACCTATGCTTTGACTCCTACATAATCCCAACCAATGACCTAAAACCAGGTGAACTTCGTCTATTAGAAGTTGATAATCGGGTAGTCTTACCAATAGAACTTCCAATTCGTATACTAATCTCATCCGAAGACGTCCTGCACTCATGAGCCATCCCTTCACTAGGGTTAAAAACCGACGCAATCCCCGGCCGCCTAAACCAAGCTACAGTCACATCAAACCGACCAGGTCTATTCTATGGCCAATGCTCTGAAATTTGCGGCTCAAATCACAGCTTCATACCCATTGTACTAGAAATAGTGCCTCTAAAATATTTCGAAAACTGATCAGCTTCTATAATT---------------------TAA");
93	2	data.put(
94		"Seal",
95		"ATGGCATACCCCCTACAAATAGGCCTACAAGATGCAACCTCTCCCATTATAGAGGAGTTACTACACTTCCATGACCACACATTAATAATTGTGTTCCTAATTAGCTCATTAGTACTCTACATTATCTCACTTATACTAACCACGAAACTCACCCACACAAGTACAATAGACGCACAAGAAGTGGAAACGGTGTGAACGATCCTACCCGCTATCATTTTAATTCTCATTGCCCTACCATCATTACGAATCCTCTACATAATGGACGAGATCAATAACCCTTCCTTGACCGTAAAAACTATAGGACATCAGTGATACTGAAGCTATGAGTACACAGACTACGAAGACCTGAACTTTGACTCATATATGATCCCCACACAAGAACTAAAGCCCGGAGAACTACGACTGCTAGAAGTAGACAATCGAGTAGTCCTCCCAATAGAAATAACAATCCGCATACTAATCTCATCAGAAGATGTACTCCACTCATGAGCCGTACCGTCCCTAGGACTAAAAACTGATGCTATCCCAGGACGACTAAACCAAACAACCCTAATAACCATACGACCAGGACTGTACTACGGTCAATGCTCAGAAATCTGTGGTTCAAACCACAGCTTCATACCTATTGTCCTCGAATTGGTCCCACTATCCCACTTCGAGAAATGATCTACCTCAATGCTT---------------------TAA");
96	2	data.put(
97		"Whale",
98		"ATGGCATATCCATTCCAACTAGGTTTCCAAGATGCAGCATCACCCATCATAGAAGAGCTCCTACACTTTCACGATCATACACTAATAATCGTTTTTCTAATTAGCTCTTTAGTTCTCTACATTATTACCCTAATGCTTACAACCAAATTAACACATACTAGTACAATAGACGCCCAAGAAGTAGAAACTGTCTGAACTATCCTCCCAGCCATTATCTTAATTTTAATTGCCTTGCCTTCATTACGGATCCTTTACATAATAGACGAAGTCAATAACCCCTCCCTCACTGTAAAAACAATAGGTCACCAATGATATTGAAGCTATGAGTATACCGACTACGAAGACCTAAGCTTCGACTCCTATATAATCCCAACATCAGACCTAAAGCCAGGAGAACTACGATTATTAGAAGTAGATAACCGAGTTGTCTTACCTATAGAAATAACAATCCGAATATTAGTCTCATCAGAAGACGTACTCCACTCATGGGCCGTACCCTCCTTGGGCCTAAAAACAGATGCAATCCCAGGACGCCTAAACCAAACAACCTTAATATCAACACGACCAGGCCTATTTTATGGACAATGCTCAGAGATCTGCGGCTCAAACCACAGTTTCATACCAATTGTCCTAGAACTAGTACCCCTAGAAGTCTTTGAAAAATGATCTGTATCAATACTA---------------------TAA");
99	2	data.put(
100		"Frog",
101		"ATGGCACACCCATCACAATTAGGTTTTCAAGACGCAGCCTCTCCAATTATAGAAGAATTACTTCACTTCCACGACCATACCCTCATAGCCGTTTTTCTTATTAGTACGCTAGTTCTTTACATTATTACTATTATAATAACTACTAAACTAACTAATACAAACCTAATGGACGCACAAGAGATCGAAATAGTGTGAACTATTATACCAGCTATTAGCCTCATCATAATTGCCCTTCCATCCCTTCGTATCCTATATTTAATAGATGAAGTTAATGATCCACACTTAACAATTAAAGCAATCGGCCACCAATGATACTGAAGCTACGAATATACTAACTATGAGGATCTCTCATTTGACTCTTATATAATTCCAACTAATGACCTTACCCCTGGACAATTCCGGCTGCTAGAAGTTGATAATCGAATAGTAGTCCCAATAGAATCTCCAACCCGACTTTTAGTTACAGCCGAAGACGTCCTCCACTCGTGAGCTGTACCCTCCTTGGGTGTCAAAACAGATGCAATCCCAGGACGACTTCATCAAACATCATTTATTGCTACTCGTCCGGGAGTATTTTACGGACAATGTTCAGAAATTTGCGGAGCAAACCACAGCTTTATACCAATTGTAGTTGAAGCAGTACCGCTAACCGACTTTGAAAACTGATCTTCATCAATACTA---GAAGCATCACTA------AGA");
102	2	return data;
103		}
104
105		/**
106		* Tests sequential format file is read correctly by comparing read sequence
107		* with that in the test data.
108		*
109		* @throws Exception
110		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1 1PASS
111	1	@Test(groups = { "Functional" })...
112		public void testSequentialDataExtraction() throws Exception
113		{
114	1	testDataExtraction(sequentialFile);
115		}
116
117		/**
118		* Tests interleaved format file is read correctly by comparing read sequence
119		* with that in the test data.
120		*
121		* @throws Exception
122		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1 1PASS
123	1	@Test(groups = { "Functional" })...
124		public void testInterleavedDataExtraction() throws Exception
125		{
126	1	testDataExtraction(interleavedFile);
127		}
128
129		/**
130		* Tests a PHYLIP file is read correctly by comparing read sequence with that
131		* in the test data.
132		*
133		* @throws Exception
134		*/
		100% Uncovered Elements: 0 (6) Complexity: 1 Complexity Density: 0.17
135	2	private void testDataExtraction(String file) throws IOException...
136		{
137	2	AppletFormatAdapter rf = new AppletFormatAdapter();
138	2	AlignmentI al = rf.readFile(file, DataSourceType.FILE,
139		FileFormat.Phylip);
140	2	assertNotNull("Couldn't read supplied alignment data.", al);
141
142	2	Map<String, String> data = PhylipFileTests.getTestData();
143	2	for (SequenceI s : al.getSequencesArray())
144		{
145	20	assertTrue(s.getName() + " sequence did not match test data.", data
146		.get(s.getName()).equals(s.getSequenceAsString()));
147		}
148		}
149
150		/**
151		* Tests sequential format file reading and writing without data lose using
152		* similar approach to {@link StockholmFileTest}
153		*
154		* @throws Exception
155		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1 1PASS
156	1	@Test(groups = { "Functional" })...
157		public void testSequentialIO() throws Exception
158		{
159	1	testIO(sequentialFile);
160		}
161
162		/**
163		* Tests interleaved format file reading and writing without data lose using
164		* similar approach to {@link StockholmFileTest}
165		*
166		* @throws Exception
167		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1 1PASS
168	1	@Test(groups = { "Functional" })...
169		public void testInterleavedIO() throws Exception
170		{
171	1	testIO(interleavedFile);
172		}
173
174		/**
175		* Uses {@link StockholmFileTest} to test read/write/read
176		*
177		* @param file
178		* @throws IOException
179		*/
		100% Uncovered Elements: 0 (7) Complexity: 1 Complexity Density: 0.14
180	2	public void testIO(String file) throws IOException...
181		{
182	2	AppletFormatAdapter rf = new AppletFormatAdapter();
183	2	AlignmentI al = rf.readFile(file, DataSourceType.FILE,
184		FileFormat.Phylip);
185	2	assertNotNull("Couldn't read supplied alignment data.", al);
186
187	2	String outputfile = rf.formatSequences(FileFormat.Phylip, al, true);
188
189	2	AlignmentI al_input = new AppletFormatAdapter().readFile(outputfile,
190		DataSourceType.PASTE, FileFormat.Phylip);
191	2	assertNotNull("Couldn't parse reimported alignment data.", al_input);
192
193	2	StockholmFileTest.testAlignmentEquivalence(al, al_input, false, false,
194		false);
195
196		}
197		}