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  1. Project Clover database Thu Nov 7 2024 17:01:39 GMT
  2. Package jalview.io

File TCoffeeScoreFileTest.java

 

Code metrics

0
86
9
1
267
219
10
0.12
9.56
9
1.11

Classes

Class Line # Actions
TCoffeeScoreFileTest 36 86 10
0.00%
 

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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 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   
 
36    public class TCoffeeScoreFileTest
37    {
38   
 
39  0 toggle @BeforeClass(alwaysRun = true)
40    public void setUpJvOptionPane()
41    {
42  0 JvOptionPane.setInteractiveMode(false);
43  0 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   
 
52  0 toggle @Test(groups = { "Functional" })
53    public void testReadHeader() throws IOException
54    {
55   
56  0 TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),
57    DataSourceType.FILE);
58  0 AssertJUnit.assertTrue(scoreFile.getWarningMessage(),
59    scoreFile.isValid());
60   
61  0 Header header = scoreFile.header;
62  0 AssertJUnit.assertNotNull(header);
63  0 AssertJUnit.assertEquals(
64    "T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)",
65    header.head);
66  0 AssertJUnit.assertEquals(90, header.score);
67  0 AssertJUnit.assertEquals(89, header.getScoreFor("1PHT"));
68  0 AssertJUnit.assertEquals(90, header.getScoreFor("1BB9"));
69  0 AssertJUnit.assertEquals(94, header.getScoreFor("1UHC"));
70  0 AssertJUnit.assertEquals(94, header.getScoreFor("1YCS"));
71  0 AssertJUnit.assertEquals(93, header.getScoreFor("1OOT"));
72  0 AssertJUnit.assertEquals(94, header.getScoreFor("1ABO"));
73  0 AssertJUnit.assertEquals(94, header.getScoreFor("1FYN"));
74  0 AssertJUnit.assertEquals(94, header.getScoreFor("1QCF"));
75  0 AssertJUnit.assertEquals(90, header.getScoreFor("cons"));
76    }
77   
 
78  0 toggle @Test(groups = { "Functional" })
79    public void testWrongFile()
80    {
81  0 try
82    {
83  0 TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(),
84    DataSourceType.FILE);
85  0 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   
 
93  0 toggle @Test(groups = { "Functional" })
94    public void testHeightAndWidth() throws IOException
95    {
96  0 TCoffeeScoreFile result = new TCoffeeScoreFile(SCORE_FILE.getPath(),
97    DataSourceType.FILE);
98  0 AssertJUnit.assertTrue(result.isValid());
99  0 AssertJUnit.assertEquals(8, result.getHeight());
100  0 AssertJUnit.assertEquals(83, result.getWidth());
101    }
102   
 
103  0 toggle @Test(groups = { "Functional" })
104    public void testReadBlock() throws IOException
105    {
106   
107  0 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  0 FileParse source = new FileParse(BLOCK, DataSourceType.PASTE);
119  0 Block block = TCoffeeScoreFile.readBlock(source, 0);
120   
121  0 AssertJUnit.assertNotNull(block);
122  0 AssertJUnit.assertEquals(
123    "999999999999999999999999998762112222543211112134",
124    block.getScoresFor("1PHT"));
125  0 AssertJUnit.assertEquals(
126    "99999999999999999999999999987-------4322----2234",
127    block.getScoresFor("1BB9"));
128  0 AssertJUnit.assertEquals(
129    "99999999999999999999999999987-------5321----2246",
130    block.getScoresFor("1UHC"));
131  0 AssertJUnit.assertEquals(
132    "99999999999999999999999999986-------4321----1-35",
133    block.getScoresFor("1YCS"));
134  0 AssertJUnit.assertEquals(
135    "999999999999999999999999999861-------3------1135",
136    block.getScoresFor("1OOT"));
137  0 AssertJUnit.assertEquals(
138    "99999999999999999999999999986-------422-------34",
139    block.getScoresFor("1ABO"));
140  0 AssertJUnit.assertEquals(
141    "99999999999999999999999999985-------32--------35",
142    block.getScoresFor("1FYN"));
143  0 AssertJUnit.assertEquals(
144    "99999999999999999999999999974-------2---------24",
145    block.getScoresFor("1QCF"));
146  0 AssertJUnit.assertEquals(
147    "999999999999999999999999999851000110321100001134",
148    block.getConsensus());
149    }
150   
 
151  0 toggle @Test(groups = { "Functional" })
152    public void testParse() throws IOException
153    {
154   
155  0 TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
156    DataSourceType.FILE);
157   
158  0 AssertJUnit.assertEquals(
159    "999999999999999999999999998762112222543211112134----------5666642367889999999999889",
160    parser.getScoresFor("1PHT"));
161  0 AssertJUnit.assertEquals(
162    "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889",
163    parser.getScoresFor("1BB9"));
164  0 AssertJUnit.assertEquals(
165    "99999999999999999999999999987-------5321----2246----------788774--66789999999999889",
166    parser.getScoresFor("1UHC"));
167  0 AssertJUnit.assertEquals(
168    "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889",
169    parser.getScoresFor("1YCS"));
170  0 AssertJUnit.assertEquals(
171    "999999999999999999999999999861-------3------1135----------78877--356789999999997-67",
172    parser.getScoresFor("1OOT"));
173  0 AssertJUnit.assertEquals(
174    "99999999999999999999999999986-------422-------34----------687774--56779999999999889",
175    parser.getScoresFor("1ABO"));
176  0 AssertJUnit.assertEquals(
177    "99999999999999999999999999985-------32--------35----------6888842356789999999999889",
178    parser.getScoresFor("1FYN"));
179  0 AssertJUnit.assertEquals(
180    "99999999999999999999999999974-------2---------24----------6878742356789999999999889",
181    parser.getScoresFor("1QCF"));
182  0 AssertJUnit.assertEquals(
183    "99999999999999999999999999985100011032110000113400100000006877641356789999999999889",
184    parser.getScoresFor("cons"));
185    }
186   
 
187  0 toggle @Test(groups = { "Functional" })
188    public void testGetAsList() throws IOException
189    {
190   
191  0 TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
192    DataSourceType.FILE);
193  0 AssertJUnit.assertTrue(parser.getWarningMessage(), parser.isValid());
194  0 List<String> scores = parser.getScoresList();
195  0 AssertJUnit.assertEquals(
196    "999999999999999999999999998762112222543211112134----------5666642367889999999999889",
197    scores.get(0));
198  0 AssertJUnit.assertEquals(
199    "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889",
200    scores.get(1));
201  0 AssertJUnit.assertEquals(
202    "99999999999999999999999999987-------5321----2246----------788774--66789999999999889",
203    scores.get(2));
204  0 AssertJUnit.assertEquals(
205    "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889",
206    scores.get(3));
207  0 AssertJUnit.assertEquals(
208    "999999999999999999999999999861-------3------1135----------78877--356789999999997-67",
209    scores.get(4));
210  0 AssertJUnit.assertEquals(
211    "99999999999999999999999999986-------422-------34----------687774--56779999999999889",
212    scores.get(5));
213  0 AssertJUnit.assertEquals(
214    "99999999999999999999999999985-------32--------35----------6888842356789999999999889",
215    scores.get(6));
216  0 AssertJUnit.assertEquals(
217    "99999999999999999999999999974-------2---------24----------6878742356789999999999889",
218    scores.get(7));
219  0 AssertJUnit.assertEquals(
220    "99999999999999999999999999985100011032110000113400100000006877641356789999999999889",
221    scores.get(8));
222   
223    }
224   
 
225  0 toggle @Test(groups = { "Functional" })
226    public void testGetAsArray() throws IOException
227    {
228   
229  0 TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
230    DataSourceType.FILE);
231  0 AssertJUnit.assertTrue(parser.getWarningMessage(), parser.isValid());
232  0 byte[][] scores = parser.getScoresArray();
233   
234  0 AssertJUnit.assertEquals(9, scores[0][0]);
235  0 AssertJUnit.assertEquals(9, scores[1][0]);
236  0 AssertJUnit.assertEquals(9, scores[2][0]);
237  0 AssertJUnit.assertEquals(9, scores[3][0]);
238  0 AssertJUnit.assertEquals(9, scores[4][0]);
239  0 AssertJUnit.assertEquals(9, scores[5][0]);
240  0 AssertJUnit.assertEquals(9, scores[6][0]);
241  0 AssertJUnit.assertEquals(9, scores[7][0]);
242  0 AssertJUnit.assertEquals(9, scores[8][0]);
243   
244  0 AssertJUnit.assertEquals(5, scores[0][36]);
245  0 AssertJUnit.assertEquals(4, scores[1][36]);
246  0 AssertJUnit.assertEquals(5, scores[2][36]);
247  0 AssertJUnit.assertEquals(4, scores[3][36]);
248  0 AssertJUnit.assertEquals(-1, scores[4][36]);
249  0 AssertJUnit.assertEquals(4, scores[5][36]);
250  0 AssertJUnit.assertEquals(3, scores[6][36]);
251  0 AssertJUnit.assertEquals(2, scores[7][36]);
252  0 AssertJUnit.assertEquals(3, scores[8][36]);
253   
254    }
255   
 
256  0 toggle @Test(groups = { "Functional" })
257    public void testHeightAndWidthWithResidueNumbers() throws Exception
258    {
259  0 String file = "test/jalview/io/tcoffee.score_ascii_with_residue_numbers";
260  0 TCoffeeScoreFile result = new TCoffeeScoreFile(file,
261    DataSourceType.FILE);
262  0 AssertJUnit.assertTrue(result.isValid());
263  0 AssertJUnit.assertEquals(5, result.getHeight());
264  0 AssertJUnit.assertEquals(84, result.getWidth());
265    }
266   
267    }
  • Report generated by OpenClover v 4.4.1 on Thu Nov 7 2024 17:02:19 GMT using coverage data from Thu Jan 1 1970 01:00:00 GMT.
  • OpenClover is free and open-source software.