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  1. Project Clover database Thu Aug 13 2020 12:04:21 BST
  2. Package jalview.io

File ScoreMatrixFileTest.java

 

Code metrics

0
175
21
1
513
420
39
0.22
8.33
21
1.86

Classes

Class Line # Actions
ScoreMatrixFileTest 19 175 39
0.9081632590.8%
 

Contributing tests

This file is covered by 20 tests. .

Source view

1    package jalview.io;
2   
3    import static org.testng.Assert.assertEquals;
4    import static org.testng.Assert.assertFalse;
5    import static org.testng.Assert.assertNotNull;
6    import static org.testng.Assert.assertNull;
7    import static org.testng.Assert.assertTrue;
8    import static org.testng.Assert.fail;
9   
10    import jalview.analysis.scoremodels.ScoreMatrix;
11    import jalview.analysis.scoremodels.ScoreModels;
12   
13    import java.io.IOException;
14    import java.net.MalformedURLException;
15   
16    import org.testng.annotations.AfterMethod;
17    import org.testng.annotations.Test;
18   
 
19    public class ScoreMatrixFileTest
20    {
21   
 
22  20 toggle @AfterMethod(alwaysRun=true)
23    public void tearDownAfterTest()
24    {
25  20 ScoreModels.getInstance().reset();
26    }
27   
28    /**
29    * Test a successful parse of a (small) score matrix file
30    *
31    * @throws IOException
32    * @throws MalformedURLException
33    */
 
34  1 toggle @Test(groups = "Functional")
35    public void testParseMatrix_ncbiMixedDelimiters()
36    throws MalformedURLException,
37    IOException
38    {
39    /*
40    * some messy but valid input data, with comma, space
41    * or tab (or combinations) as score value delimiters
42    * this example includes 'guide' symbols on score rows
43    */
44  1 String data = "ScoreMatrix MyTest (example)\n" + "A\tT\tU\tt\tx\t-\n"
45    + "A,1.1,1.2,1.3,1.4, 1.5, 1.6\n"
46    + "T,2.1 2.2 2.3 2.4 2.5 2.6\n"
47    + "U\t3.1\t3.2\t3.3\t3.4\t3.5\t3.6\t\n"
48    + "t, 5.1,5.3,5.3,5.4,5.5, 5.6\n"
49    + "x\t6.1, 6.2 6.3 6.4 6.5 6.6\n"
50    + "-, \t7.1\t7.2 7.3, 7.4, 7.5\t,7.6\n";
51  1 FileParse fp = new FileParse(data, DataSourceType.PASTE);
52  1 ScoreMatrixFile parser = new ScoreMatrixFile(fp);
53  1 ScoreMatrix sm = parser.parseMatrix();
54   
55  1 assertNotNull(sm);
56  1 assertEquals(sm.getName(), "MyTest (example)");
57  1 assertEquals(sm.getSize(), 6);
58  1 assertNull(sm.getDescription());
59  1 assertTrue(sm.isDNA());
60  1 assertFalse(sm.isProtein());
61  1 assertEquals(sm.getMinimumScore(), 1.1f);
62  1 assertEquals(sm.getPairwiseScore('A', 'A'), 1.1f);
63  1 assertEquals(sm.getPairwiseScore('A', 'T'), 1.2f);
64  1 assertEquals(sm.getPairwiseScore('a', 'T'), 1.2f); // A/a equivalent
65  1 assertEquals(sm.getPairwiseScore('A', 't'), 1.4f); // T/t not equivalent
66  1 assertEquals(sm.getPairwiseScore('a', 't'), 1.4f);
67  1 assertEquals(sm.getPairwiseScore('U', 'x'), 3.5f);
68  1 assertEquals(sm.getPairwiseScore('u', 'x'), 3.5f);
69    // X (upper) and '.' unmapped - get minimum score
70  1 assertEquals(sm.getPairwiseScore('U', 'X'), 1.1f);
71  1 assertEquals(sm.getPairwiseScore('A', '.'), 1.1f);
72  1 assertEquals(sm.getPairwiseScore('-', '-'), 7.6f);
73  1 assertEquals(sm.getPairwiseScore('A', (char) 128), 0f); // out of range
74    }
75   
 
76  1 toggle @Test(groups = "Functional")
77    public void testParseMatrix_headerMissing()
78    {
79  1 String data;
80   
81  1 data = "X Y\n1 2\n3 4\n";
82  1 try
83    {
84  1 new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE))
85    .parseMatrix();
86  0 fail("expected exception");
87    } catch (IOException e)
88    {
89  1 assertEquals(e.getMessage(),
90    "Format error: 'ScoreMatrix <name>' should be the first non-comment line");
91    }
92    }
93   
 
94  1 toggle @Test(groups = "Functional")
95    public void testParseMatrix_ncbiNotEnoughRows()
96    {
97  1 String data = "ScoreMatrix MyTest\nX Y Z\n1 2 3\n4 5 6\n";
98  1 try
99    {
100  1 new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE))
101    .parseMatrix();
102  0 fail("expected exception");
103    } catch (IOException e)
104    {
105  1 assertEquals(e.getMessage(),
106    "Expected 3 rows of score data in score matrix but only found 2");
107    }
108    }
109   
 
110  1 toggle @Test(groups = "Functional")
111    public void testParseMatrix_ncbiNotEnoughColumns()
112    {
113  1 String data = "ScoreMatrix MyTest\nX Y Z\n1 2 3\n4 5\n7 8 9\n";
114  1 try
115    {
116  1 new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE))
117    .parseMatrix();
118  0 fail("expected exception");
119    } catch (IOException e)
120    {
121  1 assertEquals(e.getMessage(),
122    "Expected 3 scores at line 4: '4 5' but found 2");
123    }
124    }
125   
 
126  1 toggle @Test(groups = "Functional")
127    public void testParseMatrix_ncbiTooManyColumns()
128    {
129    /*
130    * with two too many columns:
131    */
132  1 String data = "ScoreMatrix MyTest\nX\tY\tZ\n1 2 3\n4 5 6 7\n8 9 10\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 6 7' but found 4");
142    }
143   
144    /*
145    * with guide character and one too many columns:
146    */
147  1 data = "ScoreMatrix MyTest\nX Y\nX 1 2\nY 3 4 5\n";
148  1 try
149    {
150  1 new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE))
151    .parseMatrix();
152  0 fail("expected exception");
153    } catch (IOException e)
154    {
155  1 assertEquals(e.getMessage(),
156    "Expected 2 scores at line 4: 'Y 3 4 5' but found 3");
157    }
158   
159    /*
160    * with no guide character and one too many columns
161    */
162  1 data = "ScoreMatrix MyTest\nX Y\n1 2\n3 4 5\n";
163  1 try
164    {
165  1 new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE))
166    .parseMatrix();
167  0 fail("expected exception");
168    } catch (IOException e)
169    {
170  1 assertEquals(e.getMessage(),
171    "Expected 2 scores at line 4: '3 4 5' but found 3");
172    }
173    }
174   
 
175  1 toggle @Test(groups = "Functional")
176    public void testParseMatrix_ncbiTooManyRows()
177    {
178  1 String data = "ScoreMatrix MyTest\n\tX\tY\tZ\n1 2 3\n4 5 6\n7 8 9\n10 11 12\n";
179  1 try
180    {
181  1 new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE))
182    .parseMatrix();
183  0 fail("expected exception");
184    } catch (IOException e)
185    {
186  1 assertEquals(e.getMessage(),
187    "Unexpected extra input line in score model file: '10 11 12'");
188    }
189    }
190   
 
191  1 toggle @Test(groups = "Functional")
192    public void testParseMatrix_ncbiBadDelimiter()
193    {
194  1 String data = "ScoreMatrix MyTest\n X Y Z\n1|2|3\n4|5|6\n";
195  1 try
196    {
197  1 new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE))
198    .parseMatrix();
199  0 fail("expected exception");
200    } catch (IOException e)
201    {
202  1 assertEquals(e.getMessage(),
203    "Invalid score value '1|2|3' at line 3 column 0");
204    }
205    }
206   
 
207  1 toggle @Test(groups = "Functional")
208    public void testParseMatrix_ncbiBadFloat()
209    {
210  1 String data = "ScoreMatrix MyTest\n\tX\tY\tZ\n1 2 3\n4 five 6\n7 8 9\n";
211  1 try
212    {
213  1 new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE))
214    .parseMatrix();
215  0 fail("expected exception");
216    } catch (IOException e)
217    {
218  1 assertEquals(e.getMessage(),
219    "Invalid score value 'five' at line 4 column 1");
220    }
221    }
222   
 
223  1 toggle @Test(groups = "Functional")
224    public void testParseMatrix_ncbiBadGuideCharacter()
225    {
226  1 String data = "ScoreMatrix MyTest\n\tX Y\nX 1 2\ny 3 4\n";
227  1 try
228    {
229  1 new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE))
230    .parseMatrix();
231  0 fail("expected exception");
232    } catch (IOException e)
233    {
234  1 assertEquals(e.getMessage(),
235    "Error parsing score matrix at line 4, expected 'Y' but found 'y'");
236    }
237   
238  1 data = "ScoreMatrix MyTest\n\tX Y\nXX 1 2\nY 3 4\n";
239  1 try
240    {
241  1 new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE))
242    .parseMatrix();
243  0 fail("expected exception");
244    } catch (IOException e)
245    {
246  1 assertEquals(e.getMessage(),
247    "Error parsing score matrix at line 3, expected 'X' but found 'XX'");
248    }
249    }
250   
 
251  1 toggle @Test(groups = "Functional")
252    public void testParseMatrix_ncbiNameMissing()
253    {
254    /*
255    * Name missing on ScoreMatrix header line
256    */
257  1 String data = "ScoreMatrix\nX Y\n1 2\n3 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(
266    e.getMessage(),
267    "Format error: expected 'ScoreMatrix <name>', found 'ScoreMatrix' at line 1");
268    }
269    }
270   
271    /**
272    * Test a successful parse of a (small) score matrix file
273    *
274    * @throws IOException
275    * @throws MalformedURLException
276    */
 
277  1 toggle @Test(groups = "Functional")
278    public void testParseMatrix_ncbiFormat() throws MalformedURLException,
279    IOException
280    {
281    // input including comment and blank lines
282  1 String data = "ScoreMatrix MyTest\n#comment\n\n" + "\tA\tB\tC\n"
283    + "A\t1.0\t2.0\t3.0\n" + "B\t4.0\t5.0\t6.0\n"
284    + "C\t7.0\t8.0\t9.0\n";
285  1 FileParse fp = new FileParse(data, DataSourceType.PASTE);
286  1 ScoreMatrixFile parser = new ScoreMatrixFile(fp);
287  1 ScoreMatrix sm = parser.parseMatrix();
288   
289  1 assertNotNull(sm);
290  1 assertEquals(sm.getName(), "MyTest");
291  1 assertEquals(parser.getMatrixName(), "MyTest");
292  1 assertEquals(sm.getPairwiseScore('A', 'A'), 1.0f);
293  1 assertEquals(sm.getPairwiseScore('B', 'c'), 6.0f);
294  1 assertEquals(sm.getSize(), 3);
295    }
296   
297    /**
298    * Test a successful parse of a (small) score matrix file
299    *
300    * @throws IOException
301    * @throws MalformedURLException
302    */
 
303  1 toggle @Test(groups = "Functional")
304    public void testParseMatrix_aaIndexBlosum80()
305    throws MalformedURLException,
306    IOException
307    {
308  1 FileParse fp = new FileParse("resources/scoreModel/blosum80.scm",
309    DataSourceType.FILE);
310  1 ScoreMatrixFile parser = new ScoreMatrixFile(fp);
311  1 ScoreMatrix sm = parser.parseMatrix();
312   
313  1 assertNotNull(sm);
314  1 assertEquals(sm.getName(), "HENS920103");
315  1 assertEquals(sm.getDescription(),
316    "BLOSUM80 substitution matrix (Henikoff-Henikoff, 1992)");
317  1 assertFalse(sm.isDNA());
318  1 assertTrue(sm.isProtein());
319  1 assertEquals(20, sm.getSize());
320   
321  1 assertEquals(sm.getPairwiseScore('A', 'A'), 7f);
322  1 assertEquals(sm.getPairwiseScore('A', 'R'), -3f);
323  1 assertEquals(sm.getPairwiseScore('r', 'a'), -3f); // A/a equivalent
324    }
325   
326    /**
327    * Test a successful parse of a (small) score matrix file
328    *
329    * @throws IOException
330    * @throws MalformedURLException
331    */
 
332  1 toggle @Test(groups = "Functional")
333    public void testParseMatrix_aaindexFormat() throws MalformedURLException,
334    IOException
335    {
336    /*
337    * aaindex format has scores for diagonal and below only
338    */
339  1 String data = "H MyTest\n" + "D My description\n" + "R PMID:1438297\n"
340    + "A Authors, names\n" + "T Journal title\n"
341    + "J Journal reference\n" + "* matrix in 1/3 Bit Units\n"
342    + "M rows = ABC, cols = ABC\n" + "A\t1.0\n"
343    + "B\t4.0\t5.0\n"
344    + "C\t7.0\t8.0\t9.0\n";
345  1 FileParse fp = new FileParse(data, DataSourceType.PASTE);
346  1 ScoreMatrixFile parser = new ScoreMatrixFile(fp);
347  1 ScoreMatrix sm = parser.parseMatrix();
348   
349  1 assertNotNull(sm);
350  1 assertEquals(sm.getSize(), 3);
351  1 assertEquals(sm.getName(), "MyTest");
352  1 assertEquals(sm.getDescription(), "My description");
353  1 assertEquals(sm.getPairwiseScore('A', 'A'), 1.0f);
354  1 assertEquals(sm.getPairwiseScore('A', 'B'), 4.0f);
355  1 assertEquals(sm.getPairwiseScore('A', 'C'), 7.0f);
356  1 assertEquals(sm.getPairwiseScore('B', 'A'), 4.0f);
357  1 assertEquals(sm.getPairwiseScore('B', 'B'), 5.0f);
358  1 assertEquals(sm.getPairwiseScore('B', 'C'), 8.0f);
359  1 assertEquals(sm.getPairwiseScore('C', 'C'), 9.0f);
360  1 assertEquals(sm.getPairwiseScore('C', 'B'), 8.0f);
361  1 assertEquals(sm.getPairwiseScore('C', 'A'), 7.0f);
362    }
363   
 
364  1 toggle @Test(groups = "Functional")
365    public void testParseMatrix_aaindex_mMissing()
366    throws MalformedURLException,
367    IOException
368    {
369    /*
370    * aaindex format but M cols=, rows= is missing
371    */
372  1 String data = "H MyTest\n" + "A\t1.0\n"
373    + "B\t4.0\t5.0\n"
374    + "C\t7.0\t8.0\t9.0\n";
375  1 FileParse fp = new FileParse(data, DataSourceType.PASTE);
376  1 ScoreMatrixFile parser = new ScoreMatrixFile(fp);
377  1 try
378    {
379  1 parser.parseMatrix();
380  0 fail("Expected exception");
381    } catch (FileFormatException e)
382    {
383  1 assertEquals(e.getMessage(), "No alphabet specified in matrix file");
384    }
385    }
386   
 
387  1 toggle @Test(groups = "Functional")
388    public void testParseMatrix_aaindex_rowColMismatch()
389    throws MalformedURLException,
390    IOException
391    {
392  1 String data = "H MyTest\n" + "M rows=ABC, cols=ABD\n" + "A\t1.0\n"
393    + "B\t4.0\t5.0\n"
394    + "C\t7.0\t8.0\t9.0\n";
395  1 FileParse fp = new FileParse(data, DataSourceType.PASTE);
396  1 ScoreMatrixFile parser = new ScoreMatrixFile(fp);
397  1 try
398    {
399  1 parser.parseMatrix();
400  0 fail("Expected exception");
401    } catch (FileFormatException e)
402    {
403  1 assertEquals(
404    e.getMessage(),
405    "Unexpected aaIndex score matrix data at line 2: M rows=ABC, cols=ABD rows != cols");
406    }
407    }
408   
 
409  1 toggle @Test(groups = "Functional")
410    public void testParseMatrix_ncbiHeaderRepeated()
411    {
412  1 String data = "ScoreMatrix BLOSUM\nScoreMatrix PAM250\nX Y\n1 2\n3 4\n";
413  1 try
414    {
415  1 new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE))
416    .parseMatrix();
417  0 fail("expected exception");
418    } catch (IOException e)
419    {
420  1 assertEquals(e.getMessage(),
421    "Error: 'ScoreMatrix' repeated in file at line 2");
422    }
423    }
424   
 
425  1 toggle @Test(groups = "Functional")
426    public void testParseMatrix_aaindex_tooManyRows()
427    throws MalformedURLException,
428    IOException
429    {
430  1 String data = "H MyTest\n" + "M rows=ABC, cols=ABC\n" + "A\t1.0\n"
431    + "B\t4.0\t5.0\n" + "C\t7.0\t8.0\t9.0\n" + "C\t7.0\t8.0\t9.0\n";
432  1 FileParse fp = new FileParse(data, DataSourceType.PASTE);
433  1 ScoreMatrixFile parser = new ScoreMatrixFile(fp);
434  1 try
435    {
436  1 parser.parseMatrix();
437  0 fail("Expected exception");
438    } catch (FileFormatException e)
439    {
440  1 assertEquals(e.getMessage(), "Too many data rows in matrix file");
441    }
442    }
443   
 
444  1 toggle @Test(groups = "Functional")
445    public void testParseMatrix_aaindex_extraDataLines()
446    throws MalformedURLException,
447    IOException
448    {
449  1 String data = "H MyTest\n" + "M rows=ABC, cols=ABC\n" + "A\t1.0\n"
450    + "B\t4.0\t5.0\n" + "C\t7.0\t8.0\t9.0\n" + "something extra\n";
451  1 FileParse fp = new FileParse(data, DataSourceType.PASTE);
452  1 ScoreMatrixFile parser = new ScoreMatrixFile(fp);
453  1 try
454    {
455  1 parser.parseMatrix();
456  0 fail("Expected exception");
457    } catch (FileFormatException e)
458    {
459  1 assertEquals(e.getMessage(), "Too many data rows in matrix file");
460    }
461    }
462   
 
463  1 toggle @Test(groups = "Functional")
464    public void testParseMatrix_aaindex_tooFewColumns()
465    throws MalformedURLException,
466    IOException
467    {
468  1 String data = "H MyTest\n" + "M rows=ABC, cols=ABC\n" + "A\t1.0\n"
469    + "B\t4.0\t5.0\n" + "C\t7.0\t8.0\n";
470  1 FileParse fp = new FileParse(data, DataSourceType.PASTE);
471  1 ScoreMatrixFile parser = new ScoreMatrixFile(fp);
472  1 try
473    {
474  1 parser.parseMatrix();
475  0 fail("Expected exception");
476    } catch (FileFormatException e)
477    {
478  1 assertEquals(
479    e.getMessage(),
480    "Expected 3 scores at line 5: 'C\t7.0\t8.0' but found 2");
481    }
482    }
483   
484    /**
485    * Test a successful parse and register of a score matrix file
486    *
487    * @throws IOException
488    * @throws MalformedURLException
489    */
 
490  1 toggle @Test(groups = "Functional")
491    public void testParse_ncbiFormat() throws MalformedURLException,
492    IOException
493    {
494  1 assertNull(ScoreModels.getInstance().getScoreModel("MyNewTest", null));
495   
496  1 String data = "ScoreMatrix MyNewTest\n" + "\tA\tB\tC\n"
497    + "A\t1.0\t2.0\t3.0\n" + "B\t4.0\t5.0\t6.0\n"
498    + "C\t7.0\t8.0\t9.0\n";
499  1 FileParse fp = new FileParse(data, DataSourceType.PASTE);
500  1 ScoreMatrixFile parser = new ScoreMatrixFile(fp);
501   
502  1 parser.parse();
503   
504  1 ScoreMatrix sm = (ScoreMatrix) ScoreModels.getInstance().getScoreModel(
505    "MyNewTest", null);
506  1 assertNotNull(sm);
507  1 assertEquals(sm.getName(), "MyNewTest");
508  1 assertEquals(parser.getMatrixName(), "MyNewTest");
509  1 assertEquals(sm.getPairwiseScore('A', 'A'), 1.0f);
510  1 assertEquals(sm.getPairwiseScore('B', 'c'), 6.0f);
511  1 assertEquals(sm.getSize(), 3);
512    }
513    }
  • Report generated by OpenClover v 4.4.1 on Thu Aug 13 2020 12:06:48 BST using coverage data from Thu Aug 13 2020 12:06:40 BST.
  • OpenClover is free and open-source software.