Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
TCoffeeScoreFileTest	36	86	10	0.989473798.9%	Show methods

Class TCoffeeScoreFileTest

Class TCoffeeScoreFileTest	Line # 36	Total Statements 86	Complexity 10	TOTAL Coverage 0.989473798.9%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	3939	2.02	1.01	1.0 1.0100%
testReadHeader() : void   testReadHeader() : void	5252	15.015	1.01	1.0 1.0100%
testWrongFile() : void   testWrongFile() : void	7878	4.04	2.02	0.75 0.7575%
testHeightAndWidth() : void   testHeightAndWidth() : void	9393	4.04	1.01	1.0 1.0100%
testReadBlock() : void   testReadBlock() : void	103103	13.013	1.01	1.0 1.0100%
testParse() : void   testParse() : void	151151	10.010	1.01	1.0 1.0100%
testGetAsList() : void   testGetAsList() : void	187187	12.012	1.01	1.0 1.0100%
testGetAsArray() : void   testGetAsArray() : void	225225	21.021	1.01	1.0 1.0100%
testHeightAndWidthWithResidueNumbers() : void   testHeightAndWidthWithResidueNumbers() : void	256256	5.05	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.23157895	jalview.io.TCoffeeScoreFileTest.testGetAsArrayjalview.io.TCoffeeScoreFileTest.testGetAsArray	1PASS
	0.16842106	jalview.io.TCoffeeScoreFileTest.testReadHeaderjalview.io.TCoffeeScoreFileTest.testReadHeader	1PASS
	0.14736842	jalview.io.TCoffeeScoreFileTest.testReadBlockjalview.io.TCoffeeScoreFileTest.testReadBlock	1PASS
	0.1368421	jalview.io.TCoffeeScoreFileTest.testGetAsListjalview.io.TCoffeeScoreFileTest.testGetAsList	1PASS
	0.11578947	jalview.io.TCoffeeScoreFileTest.testParsejalview.io.TCoffeeScoreFileTest.testParse	1PASS
	0.06315789	jalview.io.TCoffeeScoreFileTest.testHeightAndWidthWithResidueNumbersjalview.io.TCoffeeScoreFileTest.testHeightAndWidthWithResidueNumbers	1PASS
	0.05263158	jalview.io.TCoffeeScoreFileTest.testHeightAndWidthjalview.io.TCoffeeScoreFileTest.testHeightAndWidth	1PASS
	0.042105265	jalview.io.TCoffeeScoreFileTest.testWrongFilejalview.io.TCoffeeScoreFileTest.testWrongFile	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 jalview.gui.JvOptionPane;
24		import jalview.io.TCoffeeScoreFile.Block;
25		import jalview.io.TCoffeeScoreFile.Header;
26
27		import java.io.File;
28		import java.io.FileNotFoundException;
29		import java.io.IOException;
30		import java.util.List;
31
32		import org.testng.AssertJUnit;
33		import org.testng.annotations.BeforeClass;
34		import org.testng.annotations.Test;
35
		98.9% Uncovered Elements: 1 (95) Complexity: 10 Complexity Density: 0.12
36		public class TCoffeeScoreFileTest
37		{
38
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
39	1	@BeforeClass(alwaysRun = true)...
40		public void setUpJvOptionPane()
41		{
42	1	JvOptionPane.setInteractiveMode(false);
43	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
44		}
45
46		final static File SCORE_FILE = new File(
47		"test/jalview/io/tcoffee.score_ascii");
48
49		final static File ALIGN_FILE = new File(
50		"test/jalview/io/tcoffee.fasta_aln");
51
		100% Uncovered Elements: 0 (15) Complexity: 1 Complexity Density: 0.07 1PASS
52	1	@Test(groups = { "Functional" })...
53		public void testReadHeader() throws IOException
54		{
55
56	1	TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),
57		DataSourceType.FILE);
58	1	AssertJUnit.assertTrue(scoreFile.getWarningMessage(),
59		scoreFile.isValid());
60
61	1	Header header = scoreFile.header;
62	1	AssertJUnit.assertNotNull(header);
63	1	AssertJUnit.assertEquals(
64		"T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)",
65		header.head);
66	1	AssertJUnit.assertEquals(90, header.score);
67	1	AssertJUnit.assertEquals(89, header.getScoreFor("1PHT"));
68	1	AssertJUnit.assertEquals(90, header.getScoreFor("1BB9"));
69	1	AssertJUnit.assertEquals(94, header.getScoreFor("1UHC"));
70	1	AssertJUnit.assertEquals(94, header.getScoreFor("1YCS"));
71	1	AssertJUnit.assertEquals(93, header.getScoreFor("1OOT"));
72	1	AssertJUnit.assertEquals(94, header.getScoreFor("1ABO"));
73	1	AssertJUnit.assertEquals(94, header.getScoreFor("1FYN"));
74	1	AssertJUnit.assertEquals(94, header.getScoreFor("1QCF"));
75	1	AssertJUnit.assertEquals(90, header.getScoreFor("cons"));
76		}
77
		75% Uncovered Elements: 1 (4) Complexity: 2 Complexity Density: 0.5 1PASS
78	1	@Test(groups = { "Functional" })...
79		public void testWrongFile()
80		{
81	1	try
82		{
83	1	TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(),
84		DataSourceType.FILE);
85	1	AssertJUnit.assertFalse(result.isValid());
86		} catch (IOException x)
87		{
88	0	AssertJUnit.assertTrue("File not found exception thrown",
89		x instanceof FileNotFoundException);
90		}
91		}
92
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25 1PASS
93	1	@Test(groups = { "Functional" })...
94		public void testHeightAndWidth() throws IOException
95		{
96	1	TCoffeeScoreFile result = new TCoffeeScoreFile(SCORE_FILE.getPath(),
97		DataSourceType.FILE);
98	1	AssertJUnit.assertTrue(result.isValid());
99	1	AssertJUnit.assertEquals(8, result.getHeight());
100	1	AssertJUnit.assertEquals(83, result.getWidth());
101		}
102
		100% Uncovered Elements: 0 (13) Complexity: 1 Complexity Density: 0.08 1PASS
103	1	@Test(groups = { "Functional" })...
104		public void testReadBlock() throws IOException
105		{
106
107	1	String BLOCK = "\n" + "\n" + "\n"
108		+ "1PHT 999999999999999999999999998762112222543211112134\n"
109		+ "1BB9 99999999999999999999999999987-------4322----2234 \n"
110		+ "1UHC 99999999999999999999999999987-------5321----2246\n"
111		+ "1YCS 99999999999999999999999999986-------4321----1-35\n"
112		+ "1OOT 999999999999999999999999999861-------3------1135 \n"
113		+ "1ABO 99999999999999999999999999986-------422-------34\n"
114		+ "1FYN 99999999999999999999999999985-------32--------35\n"
115		+ "1QCF 99999999999999999999999999974-------2---------24\n"
116		+ "cons 999999999999999999999999999851000110321100001134\n"
117		+ "\n" + "\n";
118	1	FileParse source = new FileParse(BLOCK, DataSourceType.PASTE);
119	1	Block block = TCoffeeScoreFile.readBlock(source, 0);
120
121	1	AssertJUnit.assertNotNull(block);
122	1	AssertJUnit.assertEquals(
123		"999999999999999999999999998762112222543211112134",
124		block.getScoresFor("1PHT"));
125	1	AssertJUnit.assertEquals(
126		"99999999999999999999999999987-------4322----2234",
127		block.getScoresFor("1BB9"));
128	1	AssertJUnit.assertEquals(
129		"99999999999999999999999999987-------5321----2246",
130		block.getScoresFor("1UHC"));
131	1	AssertJUnit.assertEquals(
132		"99999999999999999999999999986-------4321----1-35",
133		block.getScoresFor("1YCS"));
134	1	AssertJUnit.assertEquals(
135		"999999999999999999999999999861-------3------1135",
136		block.getScoresFor("1OOT"));
137	1	AssertJUnit.assertEquals(
138		"99999999999999999999999999986-------422-------34",
139		block.getScoresFor("1ABO"));
140	1	AssertJUnit.assertEquals(
141		"99999999999999999999999999985-------32--------35",
142		block.getScoresFor("1FYN"));
143	1	AssertJUnit.assertEquals(
144		"99999999999999999999999999974-------2---------24",
145		block.getScoresFor("1QCF"));
146	1	AssertJUnit.assertEquals(
147		"999999999999999999999999999851000110321100001134",
148		block.getConsensus());
149		}
150
		100% Uncovered Elements: 0 (10) Complexity: 1 Complexity Density: 0.1 1PASS
151	1	@Test(groups = { "Functional" })...
152		public void testParse() throws IOException
153		{
154
155	1	TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
156		DataSourceType.FILE);
157
158	1	AssertJUnit.assertEquals(
159		"999999999999999999999999998762112222543211112134----------5666642367889999999999889",
160		parser.getScoresFor("1PHT"));
161	1	AssertJUnit.assertEquals(
162		"99999999999999999999999999987-------4322----22341111111111676653-355679999999999889",
163		parser.getScoresFor("1BB9"));
164	1	AssertJUnit.assertEquals(
165		"99999999999999999999999999987-------5321----2246----------788774--66789999999999889",
166		parser.getScoresFor("1UHC"));
167	1	AssertJUnit.assertEquals(
168		"99999999999999999999999999986-------4321----1-35----------78777--356789999999999889",
169		parser.getScoresFor("1YCS"));
170	1	AssertJUnit.assertEquals(
171		"999999999999999999999999999861-------3------1135----------78877--356789999999997-67",
172		parser.getScoresFor("1OOT"));
173	1	AssertJUnit.assertEquals(
174		"99999999999999999999999999986-------422-------34----------687774--56779999999999889",
175		parser.getScoresFor("1ABO"));
176	1	AssertJUnit.assertEquals(
177		"99999999999999999999999999985-------32--------35----------6888842356789999999999889",
178		parser.getScoresFor("1FYN"));
179	1	AssertJUnit.assertEquals(
180		"99999999999999999999999999974-------2---------24----------6878742356789999999999889",
181		parser.getScoresFor("1QCF"));
182	1	AssertJUnit.assertEquals(
183		"99999999999999999999999999985100011032110000113400100000006877641356789999999999889",
184		parser.getScoresFor("cons"));
185		}
186
		100% Uncovered Elements: 0 (12) Complexity: 1 Complexity Density: 0.08 1PASS
187	1	@Test(groups = { "Functional" })...
188		public void testGetAsList() throws IOException
189		{
190
191	1	TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
192		DataSourceType.FILE);
193	1	AssertJUnit.assertTrue(parser.getWarningMessage(), parser.isValid());
194	1	List<String> scores = parser.getScoresList();
195	1	AssertJUnit.assertEquals(
196		"999999999999999999999999998762112222543211112134----------5666642367889999999999889",
197		scores.get(0));
198	1	AssertJUnit.assertEquals(
199		"99999999999999999999999999987-------4322----22341111111111676653-355679999999999889",
200		scores.get(1));
201	1	AssertJUnit.assertEquals(
202		"99999999999999999999999999987-------5321----2246----------788774--66789999999999889",
203		scores.get(2));
204	1	AssertJUnit.assertEquals(
205		"99999999999999999999999999986-------4321----1-35----------78777--356789999999999889",
206		scores.get(3));
207	1	AssertJUnit.assertEquals(
208		"999999999999999999999999999861-------3------1135----------78877--356789999999997-67",
209		scores.get(4));
210	1	AssertJUnit.assertEquals(
211		"99999999999999999999999999986-------422-------34----------687774--56779999999999889",
212		scores.get(5));
213	1	AssertJUnit.assertEquals(
214		"99999999999999999999999999985-------32--------35----------6888842356789999999999889",
215		scores.get(6));
216	1	AssertJUnit.assertEquals(
217		"99999999999999999999999999974-------2---------24----------6878742356789999999999889",
218		scores.get(7));
219	1	AssertJUnit.assertEquals(
220		"99999999999999999999999999985100011032110000113400100000006877641356789999999999889",
221		scores.get(8));
222
223		}
224
		100% Uncovered Elements: 0 (21) Complexity: 1 Complexity Density: 0.05 1PASS
225	1	@Test(groups = { "Functional" })...
226		public void testGetAsArray() throws IOException
227		{
228
229	1	TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
230		DataSourceType.FILE);
231	1	AssertJUnit.assertTrue(parser.getWarningMessage(), parser.isValid());
232	1	byte[][] scores = parser.getScoresArray();
233
234	1	AssertJUnit.assertEquals(9, scores[0][0]);
235	1	AssertJUnit.assertEquals(9, scores[1][0]);
236	1	AssertJUnit.assertEquals(9, scores[2][0]);
237	1	AssertJUnit.assertEquals(9, scores[3][0]);
238	1	AssertJUnit.assertEquals(9, scores[4][0]);
239	1	AssertJUnit.assertEquals(9, scores[5][0]);
240	1	AssertJUnit.assertEquals(9, scores[6][0]);
241	1	AssertJUnit.assertEquals(9, scores[7][0]);
242	1	AssertJUnit.assertEquals(9, scores[8][0]);
243
244	1	AssertJUnit.assertEquals(5, scores[0][36]);
245	1	AssertJUnit.assertEquals(4, scores[1][36]);
246	1	AssertJUnit.assertEquals(5, scores[2][36]);
247	1	AssertJUnit.assertEquals(4, scores[3][36]);
248	1	AssertJUnit.assertEquals(-1, scores[4][36]);
249	1	AssertJUnit.assertEquals(4, scores[5][36]);
250	1	AssertJUnit.assertEquals(3, scores[6][36]);
251	1	AssertJUnit.assertEquals(2, scores[7][36]);
252	1	AssertJUnit.assertEquals(3, scores[8][36]);
253
254		}
255
		100% Uncovered Elements: 0 (5) Complexity: 1 Complexity Density: 0.2 1PASS
256	1	@Test(groups = { "Functional" })...
257		public void testHeightAndWidthWithResidueNumbers() throws Exception
258		{
259	1	String file = "test/jalview/io/tcoffee.score_ascii_with_residue_numbers";
260	1	TCoffeeScoreFile result = new TCoffeeScoreFile(file,
261		DataSourceType.FILE);
262	1	AssertJUnit.assertTrue(result.isValid());
263	1	AssertJUnit.assertEquals(5, result.getHeight());
264	1	AssertJUnit.assertEquals(84, result.getWidth());
265		}
266
267		}