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  1. Project Clover database Tue Nov 18 2025 10:51:49 GMT
  2. Package jalview.io

File ScoreMatrixFileTest.java

 

Code metrics

0
175
21
1
520
407
39
0.22
8.33
21
1.86

Classes

Class Line # Actions
ScoreMatrixFileTest 39 175 39
0.9081632590.8%
 

Contributing tests

This file is covered by 20 tests. .

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 static org.testng.Assert.assertEquals;
24    import static org.testng.Assert.assertFalse;
25    import static org.testng.Assert.assertNotNull;
26    import static org.testng.Assert.assertNull;
27    import static org.testng.Assert.assertTrue;
28    import static org.testng.Assert.fail;
29   
30    import jalview.analysis.scoremodels.ScoreMatrix;
31    import jalview.analysis.scoremodels.ScoreModels;
32   
33    import java.io.IOException;
34    import java.net.MalformedURLException;
35   
36    import org.testng.annotations.AfterMethod;
37    import org.testng.annotations.Test;
38   
 
39    public class ScoreMatrixFileTest
40    {
41   
 
42  20 toggle @AfterMethod(alwaysRun = true)
43    public void tearDownAfterTest()
44    {
45  20 ScoreModels.getInstance().reset();
46    }
47   
48    /**
49    * Test a successful parse of a (small) score matrix file
50    *
51    * @throws IOException
52    * @throws MalformedURLException
53    */
 
54  1 toggle @Test(groups = "Functional")
55    public void testParseMatrix_ncbiMixedDelimiters()
56    throws MalformedURLException, IOException
57    {
58    /*
59    * some messy but valid input data, with comma, space
60    * or tab (or combinations) as score value delimiters
61    * this example includes 'guide' symbols on score rows
62    */
63  1 String data = "ScoreMatrix MyTest (example)\n" + "A\tT\tU\tt\tx\t-\n"
64    + "A,1.1,1.2,1.3,1.4, 1.5, 1.6\n"
65    + "T,2.1 2.2 2.3 2.4 2.5 2.6\n"
66    + "U\t3.1\t3.2\t3.3\t3.4\t3.5\t3.6\t\n"
67    + "t, 5.1,5.3,5.3,5.4,5.5, 5.6\n"
68    + "x\t6.1, 6.2 6.3 6.4 6.5 6.6\n"
69    + "-, \t7.1\t7.2 7.3, 7.4, 7.5\t,7.6\n";
70  1 FileParse fp = new FileParse(data, DataSourceType.PASTE);
71  1 ScoreMatrixFile parser = new ScoreMatrixFile(fp);
72  1 ScoreMatrix sm = parser.parseMatrix();
73   
74  1 assertNotNull(sm);
75  1 assertEquals(sm.getName(), "MyTest (example)");
76  1 assertEquals(sm.getSize(), 6);
77  1 assertNull(sm.getDescription());
78  1 assertTrue(sm.isDNA());
79  1 assertFalse(sm.isProtein());
80  1 assertEquals(sm.getMinimumScore(), 1.1f);
81  1 assertEquals(sm.getPairwiseScore('A', 'A'), 1.1f);
82  1 assertEquals(sm.getPairwiseScore('A', 'T'), 1.2f);
83  1 assertEquals(sm.getPairwiseScore('a', 'T'), 1.2f); // A/a equivalent
84  1 assertEquals(sm.getPairwiseScore('A', 't'), 1.4f); // T/t not equivalent
85  1 assertEquals(sm.getPairwiseScore('a', 't'), 1.4f);
86  1 assertEquals(sm.getPairwiseScore('U', 'x'), 3.5f);
87  1 assertEquals(sm.getPairwiseScore('u', 'x'), 3.5f);
88    // X (upper) and '.' unmapped - get minimum score
89  1 assertEquals(sm.getPairwiseScore('U', 'X'), 1.1f);
90  1 assertEquals(sm.getPairwiseScore('A', '.'), 1.1f);
91  1 assertEquals(sm.getPairwiseScore('-', '-'), 7.6f);
92  1 assertEquals(sm.getPairwiseScore('A', (char) 128), 0f); // out of range
93    }
94   
 
95  1 toggle @Test(groups = "Functional")
96    public void testParseMatrix_headerMissing()
97    {
98  1 String data;
99   
100  1 data = "X Y\n1 2\n3 4\n";
101  1 try
102    {
103  1 new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE))
104    .parseMatrix();
105  0 fail("expected exception");
106    } catch (IOException e)
107    {
108  1 assertEquals(e.getMessage(),
109    "Format error: 'ScoreMatrix <name>' should be the first non-comment line");
110    }
111    }
112   
 
113  1 toggle @Test(groups = "Functional")
114    public void testParseMatrix_ncbiNotEnoughRows()
115    {
116  1 String data = "ScoreMatrix MyTest\nX Y Z\n1 2 3\n4 5 6\n";
117  1 try
118    {
119  1 new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE))
120    .parseMatrix();
121  0 fail("expected exception");
122    } catch (IOException e)
123    {
124  1 assertEquals(e.getMessage(),
125    "Expected 3 rows of score data in score matrix but only found 2");
126    }
127    }
128   
 
129  1 toggle @Test(groups = "Functional")
130    public void testParseMatrix_ncbiNotEnoughColumns()
131    {
132  1 String data = "ScoreMatrix MyTest\nX Y Z\n1 2 3\n4 5\n7 8 9\n";
133  1 try
134    {
135  1 new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE))
136    .parseMatrix();
137  0 fail("expected exception");
138    } catch (IOException e)
139    {
140  1 assertEquals(e.getMessage(),
141    "Expected 3 scores at line 4: '4 5' but found 2");
142    }
143    }
144   
 
145  1 toggle @Test(groups = "Functional")
146    public void testParseMatrix_ncbiTooManyColumns()
147    {
148    /*
149    * with two too many columns:
150    */
151  1 String data = "ScoreMatrix MyTest\nX\tY\tZ\n1 2 3\n4 5 6 7\n8 9 10\n";
152  1 try
153    {
154  1 new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE))
155    .parseMatrix();
156  0 fail("expected exception");
157    } catch (IOException e)
158    {
159  1 assertEquals(e.getMessage(),
160    "Expected 3 scores at line 4: '4 5 6 7' but found 4");
161    }
162   
163    /*
164    * with guide character and one too many columns:
165    */
166  1 data = "ScoreMatrix MyTest\nX Y\nX 1 2\nY 3 4 5\n";
167  1 try
168    {
169  1 new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE))
170    .parseMatrix();
171  0 fail("expected exception");
172    } catch (IOException e)
173    {
174  1 assertEquals(e.getMessage(),
175    "Expected 2 scores at line 4: 'Y 3 4 5' but found 3");
176    }
177   
178    /*
179    * with no guide character and one too many columns
180    */
181  1 data = "ScoreMatrix MyTest\nX Y\n1 2\n3 4 5\n";
182  1 try
183    {
184  1 new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE))
185    .parseMatrix();
186  0 fail("expected exception");
187    } catch (IOException e)
188    {
189  1 assertEquals(e.getMessage(),
190    "Expected 2 scores at line 4: '3 4 5' but found 3");
191    }
192    }
193   
 
194  1 toggle @Test(groups = "Functional")
195    public void testParseMatrix_ncbiTooManyRows()
196    {
197  1 String data = "ScoreMatrix MyTest\n\tX\tY\tZ\n1 2 3\n4 5 6\n7 8 9\n10 11 12\n";
198  1 try
199    {
200  1 new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE))
201    .parseMatrix();
202  0 fail("expected exception");
203    } catch (IOException e)
204    {
205  1 assertEquals(e.getMessage(),
206    "Unexpected extra input line in score model file: '10 11 12'");
207    }
208    }
209   
 
210  1 toggle @Test(groups = "Functional")
211    public void testParseMatrix_ncbiBadDelimiter()
212    {
213  1 String data = "ScoreMatrix MyTest\n X Y Z\n1|2|3\n4|5|6\n";
214  1 try
215    {
216  1 new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE))
217    .parseMatrix();
218  0 fail("expected exception");
219    } catch (IOException e)
220    {
221  1 assertEquals(e.getMessage(),
222    "Invalid score value '1|2|3' at line 3 column 0");
223    }
224    }
225   
 
226  1 toggle @Test(groups = "Functional")
227    public void testParseMatrix_ncbiBadFloat()
228    {
229  1 String data = "ScoreMatrix MyTest\n\tX\tY\tZ\n1 2 3\n4 five 6\n7 8 9\n";
230  1 try
231    {
232  1 new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE))
233    .parseMatrix();
234  0 fail("expected exception");
235    } catch (IOException e)
236    {
237  1 assertEquals(e.getMessage(),
238    "Invalid score value 'five' at line 4 column 1");
239    }
240    }
241   
 
242  1 toggle @Test(groups = "Functional")
243    public void testParseMatrix_ncbiBadGuideCharacter()
244    {
245  1 String data = "ScoreMatrix MyTest\n\tX Y\nX 1 2\ny 3 4\n";
246  1 try
247    {
248  1 new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE))
249    .parseMatrix();
250  0 fail("expected exception");
251    } catch (IOException e)
252    {
253  1 assertEquals(e.getMessage(),
254    "Error parsing score matrix at line 4, expected 'Y' but found 'y'");
255    }
256   
257  1 data = "ScoreMatrix MyTest\n\tX Y\nXX 1 2\nY 3 4\n";
258  1 try
259    {
260  1 new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE))
261    .parseMatrix();
262  0 fail("expected exception");
263    } catch (IOException e)
264    {
265  1 assertEquals(e.getMessage(),
266    "Error parsing score matrix at line 3, expected 'X' but found 'XX'");
267    }
268    }
269   
 
270  1 toggle @Test(groups = "Functional")
271    public void testParseMatrix_ncbiNameMissing()
272    {
273    /*
274    * Name missing on ScoreMatrix header line
275    */
276  1 String data = "ScoreMatrix\nX Y\n1 2\n3 4\n";
277  1 try
278    {
279  1 new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE))
280    .parseMatrix();
281  0 fail("expected exception");
282    } catch (IOException e)
283    {
284  1 assertEquals(e.getMessage(),
285    "Format error: expected 'ScoreMatrix <name>', found 'ScoreMatrix' at line 1");
286    }
287    }
288   
289    /**
290    * Test a successful parse of a (small) score matrix file
291    *
292    * @throws IOException
293    * @throws MalformedURLException
294    */
 
295  1 toggle @Test(groups = "Functional")
296    public void testParseMatrix_ncbiFormat()
297    throws MalformedURLException, IOException
298    {
299    // input including comment and blank lines
300  1 String data = "ScoreMatrix MyTest\n#comment\n\n" + "\tA\tB\tC\n"
301    + "A\t1.0\t2.0\t3.0\n" + "B\t4.0\t5.0\t6.0\n"
302    + "C\t7.0\t8.0\t9.0\n";
303  1 FileParse fp = new FileParse(data, DataSourceType.PASTE);
304  1 ScoreMatrixFile parser = new ScoreMatrixFile(fp);
305  1 ScoreMatrix sm = parser.parseMatrix();
306   
307  1 assertNotNull(sm);
308  1 assertEquals(sm.getName(), "MyTest");
309  1 assertEquals(parser.getMatrixName(), "MyTest");
310  1 assertEquals(sm.getPairwiseScore('A', 'A'), 1.0f);
311  1 assertEquals(sm.getPairwiseScore('B', 'c'), 6.0f);
312  1 assertEquals(sm.getSize(), 3);
313    }
314   
315    /**
316    * Test a successful parse of a (small) score matrix file
317    *
318    * @throws IOException
319    * @throws MalformedURLException
320    */
 
321  1 toggle @Test(groups = "Functional")
322    public void testParseMatrix_aaIndexBlosum80()
323    throws MalformedURLException, IOException
324    {
325  1 FileParse fp = new FileParse("resources/scoreModel/blosum80.scm",
326    DataSourceType.FILE);
327  1 ScoreMatrixFile parser = new ScoreMatrixFile(fp);
328  1 ScoreMatrix sm = parser.parseMatrix();
329   
330  1 assertNotNull(sm);
331  1 assertEquals(sm.getName(), "HENS920103");
332  1 assertEquals(sm.getDescription(),
333    "BLOSUM80 substitution matrix (Henikoff-Henikoff, 1992)");
334  1 assertFalse(sm.isDNA());
335  1 assertTrue(sm.isProtein());
336  1 assertEquals(20, sm.getSize());
337   
338  1 assertEquals(sm.getPairwiseScore('A', 'A'), 7f);
339  1 assertEquals(sm.getPairwiseScore('A', 'R'), -3f);
340  1 assertEquals(sm.getPairwiseScore('r', 'a'), -3f); // A/a equivalent
341    }
342   
343    /**
344    * Test a successful parse of a (small) score matrix file
345    *
346    * @throws IOException
347    * @throws MalformedURLException
348    */
 
349  1 toggle @Test(groups = "Functional")
350    public void testParseMatrix_aaindexFormat()
351    throws MalformedURLException, IOException
352    {
353    /*
354    * aaindex format has scores for diagonal and below only
355    */
356  1 String data = "H MyTest\n" + "D My description\n" + "R PMID:1438297\n"
357    + "A Authors, names\n" + "T Journal title\n"
358    + "J Journal reference\n" + "* matrix in 1/3 Bit Units\n"
359    + "M rows = ABC, cols = ABC\n" + "A\t1.0\n" + "B\t4.0\t5.0\n"
360    + "C\t7.0\t8.0\t9.0\n";
361  1 FileParse fp = new FileParse(data, DataSourceType.PASTE);
362  1 ScoreMatrixFile parser = new ScoreMatrixFile(fp);
363  1 ScoreMatrix sm = parser.parseMatrix();
364   
365  1 assertNotNull(sm);
366  1 assertEquals(sm.getSize(), 3);
367  1 assertEquals(sm.getName(), "MyTest");
368  1 assertEquals(sm.getDescription(), "My description");
369  1 assertEquals(sm.getPairwiseScore('A', 'A'), 1.0f);
370  1 assertEquals(sm.getPairwiseScore('A', 'B'), 4.0f);
371  1 assertEquals(sm.getPairwiseScore('A', 'C'), 7.0f);
372  1 assertEquals(sm.getPairwiseScore('B', 'A'), 4.0f);
373  1 assertEquals(sm.getPairwiseScore('B', 'B'), 5.0f);
374  1 assertEquals(sm.getPairwiseScore('B', 'C'), 8.0f);
375  1 assertEquals(sm.getPairwiseScore('C', 'C'), 9.0f);
376  1 assertEquals(sm.getPairwiseScore('C', 'B'), 8.0f);
377  1 assertEquals(sm.getPairwiseScore('C', 'A'), 7.0f);
378    }
379   
 
380  1 toggle @Test(groups = "Functional")
381    public void testParseMatrix_aaindex_mMissing()
382    throws MalformedURLException, IOException
383    {
384    /*
385    * aaindex format but M cols=, rows= is missing
386    */
387  1 String data = "H MyTest\n" + "A\t1.0\n" + "B\t4.0\t5.0\n"
388    + "C\t7.0\t8.0\t9.0\n";
389  1 FileParse fp = new FileParse(data, DataSourceType.PASTE);
390  1 ScoreMatrixFile parser = new ScoreMatrixFile(fp);
391  1 try
392    {
393  1 parser.parseMatrix();
394  0 fail("Expected exception");
395    } catch (FileFormatException e)
396    {
397  1 assertEquals(e.getMessage(), "No alphabet specified in matrix file");
398    }
399    }
400   
 
401  1 toggle @Test(groups = "Functional")
402    public void testParseMatrix_aaindex_rowColMismatch()
403    throws MalformedURLException, IOException
404    {
405  1 String data = "H MyTest\n" + "M rows=ABC, cols=ABD\n" + "A\t1.0\n"
406    + "B\t4.0\t5.0\n" + "C\t7.0\t8.0\t9.0\n";
407  1 FileParse fp = new FileParse(data, DataSourceType.PASTE);
408  1 ScoreMatrixFile parser = new ScoreMatrixFile(fp);
409  1 try
410    {
411  1 parser.parseMatrix();
412  0 fail("Expected exception");
413    } catch (FileFormatException e)
414    {
415  1 assertEquals(e.getMessage(),
416    "Unexpected aaIndex score matrix data at line 2: M rows=ABC, cols=ABD rows != cols");
417    }
418    }
419   
 
420  1 toggle @Test(groups = "Functional")
421    public void testParseMatrix_ncbiHeaderRepeated()
422    {
423  1 String data = "ScoreMatrix BLOSUM\nScoreMatrix PAM250\nX Y\n1 2\n3 4\n";
424  1 try
425    {
426  1 new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE))
427    .parseMatrix();
428  0 fail("expected exception");
429    } catch (IOException e)
430    {
431  1 assertEquals(e.getMessage(),
432    "Error: 'ScoreMatrix' repeated in file at line 2");
433    }
434    }
435   
 
436  1 toggle @Test(groups = "Functional")
437    public void testParseMatrix_aaindex_tooManyRows()
438    throws MalformedURLException, IOException
439    {
440  1 String data = "H MyTest\n" + "M rows=ABC, cols=ABC\n" + "A\t1.0\n"
441    + "B\t4.0\t5.0\n" + "C\t7.0\t8.0\t9.0\n" + "C\t7.0\t8.0\t9.0\n";
442  1 FileParse fp = new FileParse(data, DataSourceType.PASTE);
443  1 ScoreMatrixFile parser = new ScoreMatrixFile(fp);
444  1 try
445    {
446  1 parser.parseMatrix();
447  0 fail("Expected exception");
448    } catch (FileFormatException e)
449    {
450  1 assertEquals(e.getMessage(), "Too many data rows in matrix file");
451    }
452    }
453   
 
454  1 toggle @Test(groups = "Functional")
455    public void testParseMatrix_aaindex_extraDataLines()
456    throws MalformedURLException, IOException
457    {
458  1 String data = "H MyTest\n" + "M rows=ABC, cols=ABC\n" + "A\t1.0\n"
459    + "B\t4.0\t5.0\n" + "C\t7.0\t8.0\t9.0\n" + "something extra\n";
460  1 FileParse fp = new FileParse(data, DataSourceType.PASTE);
461  1 ScoreMatrixFile parser = new ScoreMatrixFile(fp);
462  1 try
463    {
464  1 parser.parseMatrix();
465  0 fail("Expected exception");
466    } catch (FileFormatException e)
467    {
468  1 assertEquals(e.getMessage(), "Too many data rows in matrix file");
469    }
470    }
471   
 
472  1 toggle @Test(groups = "Functional")
473    public void testParseMatrix_aaindex_tooFewColumns()
474    throws MalformedURLException, IOException
475    {
476  1 String data = "H MyTest\n" + "M rows=ABC, cols=ABC\n" + "A\t1.0\n"
477    + "B\t4.0\t5.0\n" + "C\t7.0\t8.0\n";
478  1 FileParse fp = new FileParse(data, DataSourceType.PASTE);
479  1 ScoreMatrixFile parser = new ScoreMatrixFile(fp);
480  1 try
481    {
482  1 parser.parseMatrix();
483  0 fail("Expected exception");
484    } catch (FileFormatException e)
485    {
486  1 assertEquals(e.getMessage(),
487    "Expected 3 scores at line 5: 'C\t7.0\t8.0' but found 2");
488    }
489    }
490   
491    /**
492    * Test a successful parse and register of a score matrix file
493    *
494    * @throws IOException
495    * @throws MalformedURLException
496    */
 
497  1 toggle @Test(groups = "Functional")
498    public void testParse_ncbiFormat()
499    throws MalformedURLException, IOException
500    {
501  1 assertNull(ScoreModels.getInstance().getScoreModel("MyNewTest", null));
502   
503  1 String data = "ScoreMatrix MyNewTest\n" + "\tA\tB\tC\n"
504    + "A\t1.0\t2.0\t3.0\n" + "B\t4.0\t5.0\t6.0\n"
505    + "C\t7.0\t8.0\t9.0\n";
506  1 FileParse fp = new FileParse(data, DataSourceType.PASTE);
507  1 ScoreMatrixFile parser = new ScoreMatrixFile(fp);
508   
509  1 parser.parse();
510   
511  1 ScoreMatrix sm = (ScoreMatrix) ScoreModels.getInstance()
512    .getScoreModel("MyNewTest", null);
513  1 assertNotNull(sm);
514  1 assertEquals(sm.getName(), "MyNewTest");
515  1 assertEquals(parser.getMatrixName(), "MyNewTest");
516  1 assertEquals(sm.getPairwiseScore('A', 'A'), 1.0f);
517  1 assertEquals(sm.getPairwiseScore('B', 'c'), 6.0f);
518  1 assertEquals(sm.getSize(), 3);
519    }
520    }
  • Report generated by OpenClover v 4.4.1 on Tue Nov 18 2025 11:02:12 GMT using coverage data from Tue Nov 18 2025 11:01:58 GMT.
  • OpenClover is free and open-source software.