Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
TCoffeeScoreFileTest	36	86	10	1	0.989473798.9%	Show methods

Class TCoffeeScoreFileTest

Class TCoffeeScoreFileTest	Line # 36	Total Statements 86	Complexity 10	Uncovered Elements 1	TOTAL Coverage 0.989473798.9%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	3939	2.02	1.01	0.00	1.0 1.0100%
testReadHeader() : void   testReadHeader() : void	5252	15.015	1.01	0.00	1.0 1.0100%
testWrongFile() : void   testWrongFile() : void	7979	4.04	2.02	1.01	0.75 0.7575%
testHeightAndWidth() : void   testHeightAndWidth() : void	9494	4.04	1.01	0.00	1.0 1.0100%
testReadBlock() : void   testReadBlock() : void	104104	13.013	1.01	0.00	1.0 1.0100%
testParse() : void   testParse() : void	152152	10.010	1.01	0.00	1.0 1.0100%
testGetAsList() : void   testGetAsList() : void	197197	12.012	1.01	0.00	1.0 1.0100%
testGetAsArray() : void   testGetAsArray() : void	244244	21.021	1.01	0.00	1.0 1.0100%
testHeightAndWidthWithResidueNumbers() : void   testHeightAndWidthWithResidueNumbers() : void	275275	5.05	1.01	0.00	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
64		.assertEquals(
65		"T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)",
66		header.head);
67	1	AssertJUnit.assertEquals(90, header.score);
68	1	AssertJUnit.assertEquals(89, header.getScoreFor("1PHT"));
69	1	AssertJUnit.assertEquals(90, header.getScoreFor("1BB9"));
70	1	AssertJUnit.assertEquals(94, header.getScoreFor("1UHC"));
71	1	AssertJUnit.assertEquals(94, header.getScoreFor("1YCS"));
72	1	AssertJUnit.assertEquals(93, header.getScoreFor("1OOT"));
73	1	AssertJUnit.assertEquals(94, header.getScoreFor("1ABO"));
74	1	AssertJUnit.assertEquals(94, header.getScoreFor("1FYN"));
75	1	AssertJUnit.assertEquals(94, header.getScoreFor("1QCF"));
76	1	AssertJUnit.assertEquals(90, header.getScoreFor("cons"));
77		}
78
		75% Uncovered Elements: 1 (4) Complexity: 2 Complexity Density: 0.5 1PASS
79	1	@Test(groups = { "Functional" })...
80		public void testWrongFile()
81		{
82	1	try
83		{
84	1	TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(),
85		DataSourceType.FILE);
86	1	AssertJUnit.assertFalse(result.isValid());
87		} catch (IOException x)
88		{
89	0	AssertJUnit.assertTrue("File not found exception thrown",
90		x instanceof FileNotFoundException);
91		}
92		}
93
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25 1PASS
94	1	@Test(groups = { "Functional" })...
95		public void testHeightAndWidth() throws IOException
96		{
97	1	TCoffeeScoreFile result = new TCoffeeScoreFile(SCORE_FILE.getPath(),
98		DataSourceType.FILE);
99	1	AssertJUnit.assertTrue(result.isValid());
100	1	AssertJUnit.assertEquals(8, result.getHeight());
101	1	AssertJUnit.assertEquals(83, result.getWidth());
102		}
103
		100% Uncovered Elements: 0 (13) Complexity: 1 Complexity Density: 0.08 1PASS
104	1	@Test(groups = { "Functional" })...
105		public void testReadBlock() throws IOException
106		{
107
108	1	String BLOCK = "\n" + "\n" + "\n"
109		+ "1PHT 999999999999999999999999998762112222543211112134\n"
110		+ "1BB9 99999999999999999999999999987-------4322----2234 \n"
111		+ "1UHC 99999999999999999999999999987-------5321----2246\n"
112		+ "1YCS 99999999999999999999999999986-------4321----1-35\n"
113		+ "1OOT 999999999999999999999999999861-------3------1135 \n"
114		+ "1ABO 99999999999999999999999999986-------422-------34\n"
115		+ "1FYN 99999999999999999999999999985-------32--------35\n"
116		+ "1QCF 99999999999999999999999999974-------2---------24\n"
117		+ "cons 999999999999999999999999999851000110321100001134\n"
118		+ "\n" + "\n";
119	1	FileParse source = new FileParse(BLOCK, DataSourceType.PASTE);
120	1	Block block = TCoffeeScoreFile.readBlock(source, 0);
121
122	1	AssertJUnit.assertNotNull(block);
123	1	AssertJUnit.assertEquals(
124		"999999999999999999999999998762112222543211112134",
125		block.getScoresFor("1PHT"));
126	1	AssertJUnit.assertEquals(
127		"99999999999999999999999999987-------4322----2234",
128		block.getScoresFor("1BB9"));
129	1	AssertJUnit.assertEquals(
130		"99999999999999999999999999987-------5321----2246",
131		block.getScoresFor("1UHC"));
132	1	AssertJUnit.assertEquals(
133		"99999999999999999999999999986-------4321----1-35",
134		block.getScoresFor("1YCS"));
135	1	AssertJUnit.assertEquals(
136		"999999999999999999999999999861-------3------1135",
137		block.getScoresFor("1OOT"));
138	1	AssertJUnit.assertEquals(
139		"99999999999999999999999999986-------422-------34",
140		block.getScoresFor("1ABO"));
141	1	AssertJUnit.assertEquals(
142		"99999999999999999999999999985-------32--------35",
143		block.getScoresFor("1FYN"));
144	1	AssertJUnit.assertEquals(
145		"99999999999999999999999999974-------2---------24",
146		block.getScoresFor("1QCF"));
147	1	AssertJUnit.assertEquals(
148		"999999999999999999999999999851000110321100001134",
149		block.getConsensus());
150		}
151
		100% Uncovered Elements: 0 (10) Complexity: 1 Complexity Density: 0.1 1PASS
152	1	@Test(groups = { "Functional" })...
153		public void testParse() throws IOException
154		{
155
156	1	TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
157		DataSourceType.FILE);
158
159	1	AssertJUnit
160		.assertEquals(
161		"999999999999999999999999998762112222543211112134----------5666642367889999999999889",
162		parser.getScoresFor("1PHT"));
163	1	AssertJUnit
164		.assertEquals(
165		"99999999999999999999999999987-------4322----22341111111111676653-355679999999999889",
166		parser.getScoresFor("1BB9"));
167	1	AssertJUnit
168		.assertEquals(
169		"99999999999999999999999999987-------5321----2246----------788774--66789999999999889",
170		parser.getScoresFor("1UHC"));
171	1	AssertJUnit
172		.assertEquals(
173		"99999999999999999999999999986-------4321----1-35----------78777--356789999999999889",
174		parser.getScoresFor("1YCS"));
175	1	AssertJUnit
176		.assertEquals(
177		"999999999999999999999999999861-------3------1135----------78877--356789999999997-67",
178		parser.getScoresFor("1OOT"));
179	1	AssertJUnit
180		.assertEquals(
181		"99999999999999999999999999986-------422-------34----------687774--56779999999999889",
182		parser.getScoresFor("1ABO"));
183	1	AssertJUnit
184		.assertEquals(
185		"99999999999999999999999999985-------32--------35----------6888842356789999999999889",
186		parser.getScoresFor("1FYN"));
187	1	AssertJUnit
188		.assertEquals(
189		"99999999999999999999999999974-------2---------24----------6878742356789999999999889",
190		parser.getScoresFor("1QCF"));
191	1	AssertJUnit
192		.assertEquals(
193		"99999999999999999999999999985100011032110000113400100000006877641356789999999999889",
194		parser.getScoresFor("cons"));
195		}
196
		100% Uncovered Elements: 0 (12) Complexity: 1 Complexity Density: 0.08 1PASS
197	1	@Test(groups = { "Functional" })...
198		public void testGetAsList() throws IOException
199		{
200
201	1	TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
202		DataSourceType.FILE);
203	1	AssertJUnit.assertTrue(parser.getWarningMessage(), parser.isValid());
204	1	List<String> scores = parser.getScoresList();
205	1	AssertJUnit
206		.assertEquals(
207		"999999999999999999999999998762112222543211112134----------5666642367889999999999889",
208		scores.get(0));
209	1	AssertJUnit
210		.assertEquals(
211		"99999999999999999999999999987-------4322----22341111111111676653-355679999999999889",
212		scores.get(1));
213	1	AssertJUnit
214		.assertEquals(
215		"99999999999999999999999999987-------5321----2246----------788774--66789999999999889",
216		scores.get(2));
217	1	AssertJUnit
218		.assertEquals(
219		"99999999999999999999999999986-------4321----1-35----------78777--356789999999999889",
220		scores.get(3));
221	1	AssertJUnit
222		.assertEquals(
223		"999999999999999999999999999861-------3------1135----------78877--356789999999997-67",
224		scores.get(4));
225	1	AssertJUnit
226		.assertEquals(
227		"99999999999999999999999999986-------422-------34----------687774--56779999999999889",
228		scores.get(5));
229	1	AssertJUnit
230		.assertEquals(
231		"99999999999999999999999999985-------32--------35----------6888842356789999999999889",
232		scores.get(6));
233	1	AssertJUnit
234		.assertEquals(
235		"99999999999999999999999999974-------2---------24----------6878742356789999999999889",
236		scores.get(7));
237	1	AssertJUnit
238		.assertEquals(
239		"99999999999999999999999999985100011032110000113400100000006877641356789999999999889",
240		scores.get(8));
241
242		}
243
		100% Uncovered Elements: 0 (21) Complexity: 1 Complexity Density: 0.05 1PASS
244	1	@Test(groups = { "Functional" })...
245		public void testGetAsArray() throws IOException
246		{
247
248	1	TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
249		DataSourceType.FILE);
250	1	AssertJUnit.assertTrue(parser.getWarningMessage(), parser.isValid());
251	1	byte[][] scores = parser.getScoresArray();
252
253	1	AssertJUnit.assertEquals(9, scores[0][0]);
254	1	AssertJUnit.assertEquals(9, scores[1][0]);
255	1	AssertJUnit.assertEquals(9, scores[2][0]);
256	1	AssertJUnit.assertEquals(9, scores[3][0]);
257	1	AssertJUnit.assertEquals(9, scores[4][0]);
258	1	AssertJUnit.assertEquals(9, scores[5][0]);
259	1	AssertJUnit.assertEquals(9, scores[6][0]);
260	1	AssertJUnit.assertEquals(9, scores[7][0]);
261	1	AssertJUnit.assertEquals(9, scores[8][0]);
262
263	1	AssertJUnit.assertEquals(5, scores[0][36]);
264	1	AssertJUnit.assertEquals(4, scores[1][36]);
265	1	AssertJUnit.assertEquals(5, scores[2][36]);
266	1	AssertJUnit.assertEquals(4, scores[3][36]);
267	1	AssertJUnit.assertEquals(-1, scores[4][36]);
268	1	AssertJUnit.assertEquals(4, scores[5][36]);
269	1	AssertJUnit.assertEquals(3, scores[6][36]);
270	1	AssertJUnit.assertEquals(2, scores[7][36]);
271	1	AssertJUnit.assertEquals(3, scores[8][36]);
272
273		}
274
		100% Uncovered Elements: 0 (5) Complexity: 1 Complexity Density: 0.2 1PASS
275	1	@Test(groups = { "Functional" })...
276		public void testHeightAndWidthWithResidueNumbers() throws Exception
277		{
278	1	String file = "test/jalview/io/tcoffee.score_ascii_with_residue_numbers";
279	1	TCoffeeScoreFile result = new TCoffeeScoreFile(file, DataSourceType.FILE);
280	1	AssertJUnit.assertTrue(result.isValid());
281	1	AssertJUnit.assertEquals(5, result.getHeight());
282	1	AssertJUnit.assertEquals(84, result.getWidth());
283		}
284
285		}