Merge branch 'JAL-1332_regression' into develop
[jalview.git] / test / jalview / io / TCoffeeScoreFileTest.java
1 /*
2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3  * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
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 of the License, or (at your option) any later version.
10  *  
11  * Jalview is distributed in the hope that it will be useful, but 
12  * WITHOUT ANY WARRANTY; without even the implied warranty 
13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
14  * PURPOSE.  See the GNU General Public License for more details.
15  * 
16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
17  */
18 package jalview.io;
19
20 import static org.junit.Assert.*;
21 import jalview.io.TCoffeeScoreFile.Block;
22 import jalview.io.TCoffeeScoreFile.Header;
23
24 import java.io.File;
25 import java.io.FileNotFoundException;
26 import java.io.IOException;
27 import java.util.List;
28
29 import javax.xml.parsers.ParserConfigurationException;
30
31 import org.junit.Test;
32 import org.xml.sax.SAXException;
33
34 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
35 import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
36 import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
37 import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
38
39 public class TCoffeeScoreFileTest {
40
41         final static File SCORE_FILE = new File("test/jalview/io/tcoffee.score_ascii");
42     final static File ALIGN_FILE = new File("test/jalview/io/tcoffee.fasta_aln");
43         
44         @Test
45         public void testReadHeader() throws IOException {
46
47             TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),AppletFormatAdapter.FILE);
48             assertTrue(scoreFile.getWarningMessage(),scoreFile.isValid());
49                 
50             Header header = scoreFile.header;
51                 assertNotNull(header);
52                 assertEquals( "T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)", header.head );
53                 assertEquals( 90, header.score );
54                 assertEquals( 89, header.getScoreFor("1PHT") );
55                 assertEquals( 90, header.getScoreFor("1BB9") );
56                 assertEquals( 94, header.getScoreFor("1UHC") );
57                 assertEquals( 94, header.getScoreFor("1YCS") );
58                 assertEquals( 93, header.getScoreFor("1OOT") );
59                 assertEquals( 94, header.getScoreFor("1ABO") );
60                 assertEquals( 94, header.getScoreFor("1FYN") );
61                 assertEquals( 94, header.getScoreFor("1QCF") );
62                 assertEquals( 90, header.getScoreFor("cons") );
63         }
64         
65         
66         @Test
67         public void testWrongFile()  {
68             try {
69                         TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(), FormatAdapter.FILE);
70                         assertFalse(result.isValid());
71             } 
72             catch (IOException x)
73             {
74               assertTrue("File not found exception thrown",x instanceof FileNotFoundException);
75             }
76         } 
77
78         @Test
79         public void testHeightAndWidth() throws IOException {
80                 TCoffeeScoreFile result = new TCoffeeScoreFile(SCORE_FILE.getPath(), FormatAdapter.FILE);
81                 assertTrue(result.isValid());
82                 assertEquals( 8, result.getHeight() );
83                 assertEquals( 83, result.getWidth() );
84         }       
85         
86         @Test
87         public void testReadBlock( ) throws IOException {
88                 
89                 String BLOCK = "\n" +
90                                 "\n" +
91                                 "\n" +
92                                 "1PHT   999999999999999999999999998762112222543211112134\n" +
93                                 "1BB9   99999999999999999999999999987-------4322----2234  \n" +
94                                 "1UHC   99999999999999999999999999987-------5321----2246\n" +
95                                 "1YCS   99999999999999999999999999986-------4321----1-35\n" +
96                                 "1OOT   999999999999999999999999999861-------3------1135  \n" +
97                                 "1ABO   99999999999999999999999999986-------422-------34\n" +
98                                 "1FYN   99999999999999999999999999985-------32--------35\n" +
99                                 "1QCF   99999999999999999999999999974-------2---------24\n" +
100                                 "cons   999999999999999999999999999851000110321100001134\n" +
101                                 "\n" +
102                                 "\n";
103                 FileParse source=new FileParse(BLOCK, FormatAdapter.PASTE);
104                 Block block = TCoffeeScoreFile.readBlock(source, 0);
105
106                 assertNotNull(block);
107                 assertEquals( "999999999999999999999999998762112222543211112134", block.getScoresFor("1PHT") );
108                 assertEquals( "99999999999999999999999999987-------4322----2234", block.getScoresFor("1BB9") );
109                 assertEquals( "99999999999999999999999999987-------5321----2246", block.getScoresFor("1UHC") );
110                 assertEquals( "99999999999999999999999999986-------4321----1-35", block.getScoresFor("1YCS") );
111                 assertEquals( "999999999999999999999999999861-------3------1135", block.getScoresFor("1OOT") );
112                 assertEquals( "99999999999999999999999999986-------422-------34", block.getScoresFor("1ABO") );
113                 assertEquals( "99999999999999999999999999985-------32--------35", block.getScoresFor("1FYN") );
114                 assertEquals( "99999999999999999999999999974-------2---------24", block.getScoresFor("1QCF") );
115                 assertEquals( "999999999999999999999999999851000110321100001134", block.getConsensus() );
116         }
117
118         @Test
119         public void testParse() throws IOException {
120
121                 TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(), FormatAdapter.FILE);
122
123                 assertEquals( "999999999999999999999999998762112222543211112134----------5666642367889999999999889", parser.getScoresFor("1PHT") );
124                 assertEquals( "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889", parser.getScoresFor("1BB9") );
125                 assertEquals( "99999999999999999999999999987-------5321----2246----------788774--66789999999999889", parser.getScoresFor("1UHC") );
126                 assertEquals( "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889", parser.getScoresFor("1YCS") );
127                 assertEquals( "999999999999999999999999999861-------3------1135----------78877--356789999999997-67", parser.getScoresFor("1OOT") );
128                 assertEquals( "99999999999999999999999999986-------422-------34----------687774--56779999999999889", parser.getScoresFor("1ABO") );
129                 assertEquals( "99999999999999999999999999985-------32--------35----------6888842356789999999999889", parser.getScoresFor("1FYN") );
130                 assertEquals( "99999999999999999999999999974-------2---------24----------6878742356789999999999889", parser.getScoresFor("1QCF") );
131                 assertEquals( "99999999999999999999999999985100011032110000113400100000006877641356789999999999889", parser.getScoresFor("cons") );             
132         }
133
134         
135         @Test
136         public void testGetAsList() throws IOException {
137                 
138           TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),FormatAdapter.FILE);
139           assertTrue(parser.getWarningMessage(),parser.isValid());
140                 List<String> scores = parser.getScoresList();
141                 assertEquals( "999999999999999999999999998762112222543211112134----------5666642367889999999999889", scores.get(0) );
142                 assertEquals( "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889", scores.get(1) );
143                 assertEquals( "99999999999999999999999999987-------5321----2246----------788774--66789999999999889", scores.get(2) );
144                 assertEquals( "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889", scores.get(3) );
145                 assertEquals( "999999999999999999999999999861-------3------1135----------78877--356789999999997-67", scores.get(4) );
146                 assertEquals( "99999999999999999999999999986-------422-------34----------687774--56779999999999889", scores.get(5) );
147                 assertEquals( "99999999999999999999999999985-------32--------35----------6888842356789999999999889", scores.get(6) );
148                 assertEquals( "99999999999999999999999999974-------2---------24----------6878742356789999999999889", scores.get(7) );
149                 assertEquals( "99999999999999999999999999985100011032110000113400100000006877641356789999999999889", scores.get(8) );           
150                 
151         } 
152         
153         
154         @Test
155         public void testGetAsArray() throws IOException {
156                 
157           TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),FormatAdapter.FILE);
158           assertTrue(parser.getWarningMessage(),parser.isValid());
159                 byte[][] scores = parser.getScoresArray();
160         
161                 assertEquals( 9, scores[0][0] );
162                 assertEquals( 9, scores[1][0] );
163                 assertEquals( 9, scores[2][0] );
164                 assertEquals( 9, scores[3][0] );
165                 assertEquals( 9, scores[4][0] );
166                 assertEquals( 9, scores[5][0] );
167                 assertEquals( 9, scores[6][0] );
168                 assertEquals( 9, scores[7][0] );
169                 assertEquals( 9, scores[8][0] );
170                 
171                 assertEquals( 5, scores[0][36] );
172                 assertEquals( 4, scores[1][36] );
173                 assertEquals( 5, scores[2][36] );
174                 assertEquals( 4, scores[3][36] );
175                 assertEquals( -1, scores[4][36] );
176                 assertEquals( 4, scores[5][36] );
177                 assertEquals( 3, scores[6][36] );
178                 assertEquals( 2, scores[7][36] );
179                 assertEquals( 3, scores[8][36] );
180                 
181         } 
182         
183         @Test
184         public void testHeightAndWidthWithResidueNumbers() throws Exception {
185                 String file = "test/jalview/io/tcoffee.score_ascii_with_residue_numbers";
186                 TCoffeeScoreFile result = new TCoffeeScoreFile(file, FormatAdapter.FILE);
187                 assertTrue(result.isValid());
188                 assertEquals( 5, result.getHeight() );
189                 assertEquals( 84, result.getWidth() );
190         }       
191         
192         
193         
194 }