JAL-1988 JAL-3130 New jlinked JRE in jalview_java2 with modules. Still needs jaxws...
[jalview.git] / test / jalview / io / TCoffeeScoreFileTest.java
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   @BeforeClass(alwaysRun = true)
40   public void setUpJvOptionPane()
41   {
42     JvOptionPane.setInteractiveMode(false);
43     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   @Test(groups = { "Functional" })
53   public void testReadHeader() throws IOException
54   {
55
56     TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),
57             DataSourceType.FILE);
58     AssertJUnit.assertTrue(scoreFile.getWarningMessage(),
59             scoreFile.isValid());
60
61     Header header = scoreFile.header;
62     AssertJUnit.assertNotNull(header);
63     AssertJUnit
64             .assertEquals(
65                     "T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)",
66                     header.head);
67     AssertJUnit.assertEquals(90, header.score);
68     AssertJUnit.assertEquals(89, header.getScoreFor("1PHT"));
69     AssertJUnit.assertEquals(90, header.getScoreFor("1BB9"));
70     AssertJUnit.assertEquals(94, header.getScoreFor("1UHC"));
71     AssertJUnit.assertEquals(94, header.getScoreFor("1YCS"));
72     AssertJUnit.assertEquals(93, header.getScoreFor("1OOT"));
73     AssertJUnit.assertEquals(94, header.getScoreFor("1ABO"));
74     AssertJUnit.assertEquals(94, header.getScoreFor("1FYN"));
75     AssertJUnit.assertEquals(94, header.getScoreFor("1QCF"));
76     AssertJUnit.assertEquals(90, header.getScoreFor("cons"));
77   }
78
79   @Test(groups = { "Functional" })
80   public void testWrongFile()
81   {
82     try
83     {
84       TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(),
85               DataSourceType.FILE);
86       AssertJUnit.assertFalse(result.isValid());
87     } catch (IOException x)
88     {
89       AssertJUnit.assertTrue("File not found exception thrown",
90               x instanceof FileNotFoundException);
91     }
92   }
93
94   @Test(groups = { "Functional" })
95   public void testHeightAndWidth() throws IOException
96   {
97     TCoffeeScoreFile result = new TCoffeeScoreFile(SCORE_FILE.getPath(),
98             DataSourceType.FILE);
99     AssertJUnit.assertTrue(result.isValid());
100     AssertJUnit.assertEquals(8, result.getHeight());
101     AssertJUnit.assertEquals(83, result.getWidth());
102   }
103
104   @Test(groups = { "Functional" })
105   public void testReadBlock() throws IOException
106   {
107
108     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     FileParse source = new FileParse(BLOCK, DataSourceType.PASTE);
120     Block block = TCoffeeScoreFile.readBlock(source, 0);
121
122     AssertJUnit.assertNotNull(block);
123     AssertJUnit.assertEquals(
124             "999999999999999999999999998762112222543211112134",
125             block.getScoresFor("1PHT"));
126     AssertJUnit.assertEquals(
127             "99999999999999999999999999987-------4322----2234",
128             block.getScoresFor("1BB9"));
129     AssertJUnit.assertEquals(
130             "99999999999999999999999999987-------5321----2246",
131             block.getScoresFor("1UHC"));
132     AssertJUnit.assertEquals(
133             "99999999999999999999999999986-------4321----1-35",
134             block.getScoresFor("1YCS"));
135     AssertJUnit.assertEquals(
136             "999999999999999999999999999861-------3------1135",
137             block.getScoresFor("1OOT"));
138     AssertJUnit.assertEquals(
139             "99999999999999999999999999986-------422-------34",
140             block.getScoresFor("1ABO"));
141     AssertJUnit.assertEquals(
142             "99999999999999999999999999985-------32--------35",
143             block.getScoresFor("1FYN"));
144     AssertJUnit.assertEquals(
145             "99999999999999999999999999974-------2---------24",
146             block.getScoresFor("1QCF"));
147     AssertJUnit.assertEquals(
148             "999999999999999999999999999851000110321100001134",
149             block.getConsensus());
150   }
151
152   @Test(groups = { "Functional" })
153   public void testParse() throws IOException
154   {
155
156     TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
157             DataSourceType.FILE);
158
159     AssertJUnit
160             .assertEquals(
161                     "999999999999999999999999998762112222543211112134----------5666642367889999999999889",
162                     parser.getScoresFor("1PHT"));
163     AssertJUnit
164             .assertEquals(
165                     "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889",
166                     parser.getScoresFor("1BB9"));
167     AssertJUnit
168             .assertEquals(
169                     "99999999999999999999999999987-------5321----2246----------788774--66789999999999889",
170                     parser.getScoresFor("1UHC"));
171     AssertJUnit
172             .assertEquals(
173                     "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889",
174                     parser.getScoresFor("1YCS"));
175     AssertJUnit
176             .assertEquals(
177                     "999999999999999999999999999861-------3------1135----------78877--356789999999997-67",
178                     parser.getScoresFor("1OOT"));
179     AssertJUnit
180             .assertEquals(
181                     "99999999999999999999999999986-------422-------34----------687774--56779999999999889",
182                     parser.getScoresFor("1ABO"));
183     AssertJUnit
184             .assertEquals(
185                     "99999999999999999999999999985-------32--------35----------6888842356789999999999889",
186                     parser.getScoresFor("1FYN"));
187     AssertJUnit
188             .assertEquals(
189                     "99999999999999999999999999974-------2---------24----------6878742356789999999999889",
190                     parser.getScoresFor("1QCF"));
191     AssertJUnit
192             .assertEquals(
193                     "99999999999999999999999999985100011032110000113400100000006877641356789999999999889",
194                     parser.getScoresFor("cons"));
195   }
196
197   @Test(groups = { "Functional" })
198   public void testGetAsList() throws IOException
199   {
200
201     TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
202             DataSourceType.FILE);
203     AssertJUnit.assertTrue(parser.getWarningMessage(), parser.isValid());
204     List<String> scores = parser.getScoresList();
205     AssertJUnit
206             .assertEquals(
207                     "999999999999999999999999998762112222543211112134----------5666642367889999999999889",
208                     scores.get(0));
209     AssertJUnit
210             .assertEquals(
211                     "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889",
212                     scores.get(1));
213     AssertJUnit
214             .assertEquals(
215                     "99999999999999999999999999987-------5321----2246----------788774--66789999999999889",
216                     scores.get(2));
217     AssertJUnit
218             .assertEquals(
219                     "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889",
220                     scores.get(3));
221     AssertJUnit
222             .assertEquals(
223                     "999999999999999999999999999861-------3------1135----------78877--356789999999997-67",
224                     scores.get(4));
225     AssertJUnit
226             .assertEquals(
227                     "99999999999999999999999999986-------422-------34----------687774--56779999999999889",
228                     scores.get(5));
229     AssertJUnit
230             .assertEquals(
231                     "99999999999999999999999999985-------32--------35----------6888842356789999999999889",
232                     scores.get(6));
233     AssertJUnit
234             .assertEquals(
235                     "99999999999999999999999999974-------2---------24----------6878742356789999999999889",
236                     scores.get(7));
237     AssertJUnit
238             .assertEquals(
239                     "99999999999999999999999999985100011032110000113400100000006877641356789999999999889",
240                     scores.get(8));
241
242   }
243
244   @Test(groups = { "Functional" })
245   public void testGetAsArray() throws IOException
246   {
247
248     TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
249             DataSourceType.FILE);
250     AssertJUnit.assertTrue(parser.getWarningMessage(), parser.isValid());
251     byte[][] scores = parser.getScoresArray();
252
253     AssertJUnit.assertEquals(9, scores[0][0]);
254     AssertJUnit.assertEquals(9, scores[1][0]);
255     AssertJUnit.assertEquals(9, scores[2][0]);
256     AssertJUnit.assertEquals(9, scores[3][0]);
257     AssertJUnit.assertEquals(9, scores[4][0]);
258     AssertJUnit.assertEquals(9, scores[5][0]);
259     AssertJUnit.assertEquals(9, scores[6][0]);
260     AssertJUnit.assertEquals(9, scores[7][0]);
261     AssertJUnit.assertEquals(9, scores[8][0]);
262
263     AssertJUnit.assertEquals(5, scores[0][36]);
264     AssertJUnit.assertEquals(4, scores[1][36]);
265     AssertJUnit.assertEquals(5, scores[2][36]);
266     AssertJUnit.assertEquals(4, scores[3][36]);
267     AssertJUnit.assertEquals(-1, scores[4][36]);
268     AssertJUnit.assertEquals(4, scores[5][36]);
269     AssertJUnit.assertEquals(3, scores[6][36]);
270     AssertJUnit.assertEquals(2, scores[7][36]);
271     AssertJUnit.assertEquals(3, scores[8][36]);
272
273   }
274
275   @Test(groups = { "Functional" })
276   public void testHeightAndWidthWithResidueNumbers() throws Exception
277   {
278     String file = "test/jalview/io/tcoffee.score_ascii_with_residue_numbers";
279     TCoffeeScoreFile result = new TCoffeeScoreFile(file, DataSourceType.FILE);
280     AssertJUnit.assertTrue(result.isValid());
281     AssertJUnit.assertEquals(5, result.getHeight());
282     AssertJUnit.assertEquals(84, result.getWidth());
283   }
284
285 }