package jalview.io; import static org.testng.Assert.assertEquals; import static org.testng.Assert.assertFalse; import static org.testng.Assert.assertNotNull; import static org.testng.Assert.assertNull; import static org.testng.Assert.assertTrue; import static org.testng.Assert.fail; import jalview.analysis.scoremodels.ScoreMatrix; import jalview.analysis.scoremodels.ScoreModels; import java.io.IOException; import java.net.MalformedURLException; import org.testng.annotations.Test; public class ScoreMatrixFileTest { /** * Test a successful parse of a (small) score matrix file * * @throws IOException * @throws MalformedURLException */ @Test(groups = "Functional") public void testParseMatrix_ncbiMixedDelimiters() throws MalformedURLException, IOException { /* * some messy but valid input data, with comma, space * or tab (or combinations) as score value delimiters * this example includes 'guide' symbols on score rows */ String data = "ScoreMatrix MyTest (example)\n" + "A\tT\tU\tt\tx\t-\n" + "A,1.1,1.2,1.3,1.4, 1.5, 1.6\n" + "T,2.1 2.2 2.3 2.4 2.5 2.6\n" + "U\t3.1\t3.2\t3.3\t3.4\t3.5\t3.6\t\n" + "t, 5.1,5.3,5.3,5.4,5.5, 5.6\n" + "x\t6.1, 6.2 6.3 6.4 6.5 6.6\n" + "-, \t7.1\t7.2 7.3, 7.4, 7.5\t,7.6\n"; FileParse fp = new FileParse(data, DataSourceType.PASTE); ScoreMatrixFile parser = new ScoreMatrixFile(fp); ScoreMatrix sm = parser.parseMatrix(); assertNotNull(sm); assertEquals(sm.getName(), "MyTest (example)"); assertEquals(sm.getSize(), 6); assertNull(sm.getDescription()); assertTrue(sm.isDNA()); assertFalse(sm.isProtein()); assertEquals(sm.getMinimumScore(), 1.1f); assertEquals(sm.getPairwiseScore('A', 'A'), 1.1f); assertEquals(sm.getPairwiseScore('A', 'T'), 1.2f); assertEquals(sm.getPairwiseScore('a', 'T'), 1.2f); // A/a equivalent assertEquals(sm.getPairwiseScore('A', 't'), 1.4f); // T/t not equivalent assertEquals(sm.getPairwiseScore('a', 't'), 1.4f); assertEquals(sm.getPairwiseScore('U', 'x'), 3.5f); assertEquals(sm.getPairwiseScore('u', 'x'), 3.5f); // X (upper) and '.' unmapped - get minimum score assertEquals(sm.getPairwiseScore('U', 'X'), 1.1f); assertEquals(sm.getPairwiseScore('A', '.'), 1.1f); assertEquals(sm.getPairwiseScore('-', '-'), 7.6f); assertEquals(sm.getPairwiseScore('A', (char) 128), 0f); // out of range } @Test(groups = "Functional") public void testParseMatrix_headerMissing() { String data; data = "X Y\n1 2\n3 4\n"; try { new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE)) .parseMatrix(); fail("expected exception"); } catch (IOException e) { assertEquals(e.getMessage(), "Format error: 'ScoreMatrix ' should be the first non-comment line"); } } @Test(groups = "Functional") public void testParseMatrix_ncbiNotEnoughRows() { String data = "ScoreMatrix MyTest\nX Y Z\n1 2 3\n4 5 6\n"; try { new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE)) .parseMatrix(); fail("expected exception"); } catch (IOException e) { assertEquals(e.getMessage(), "Expected 3 rows of score data in score matrix but only found 2"); } } @Test(groups = "Functional") public void testParseMatrix_ncbiNotEnoughColumns() { String data = "ScoreMatrix MyTest\nX Y Z\n1 2 3\n4 5\n7 8 9\n"; try { new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE)) .parseMatrix(); fail("expected exception"); } catch (IOException e) { assertEquals(e.getMessage(), "Expected 3 scores at line 4: '4 5' but found 2"); } } @Test(groups = "Functional") public void testParseMatrix_ncbiTooManyColumns() { /* * with two too many columns: */ String data = "ScoreMatrix MyTest\nX\tY\tZ\n1 2 3\n4 5 6 7\n8 9 10\n"; try { new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE)) .parseMatrix(); fail("expected exception"); } catch (IOException e) { assertEquals(e.getMessage(), "Expected 3 scores at line 4: '4 5 6 7' but found 4"); } /* * with guide character and one too many columns: */ data = "ScoreMatrix MyTest\nX Y\nX 1 2\nY 3 4 5\n"; try { new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE)) .parseMatrix(); fail("expected exception"); } catch (IOException e) { assertEquals(e.getMessage(), "Expected 2 scores at line 4: 'Y 3 4 5' but found 3"); } /* * with no guide character and one too many columns */ data = "ScoreMatrix MyTest\nX Y\n1 2\n3 4 5\n"; try { new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE)) .parseMatrix(); fail("expected exception"); } catch (IOException e) { assertEquals(e.getMessage(), "Expected 2 scores at line 4: '3 4 5' but found 3"); } } @Test(groups = "Functional") public void testParseMatrix_ncbiTooManyRows() { String data = "ScoreMatrix MyTest\n\tX\tY\tZ\n1 2 3\n4 5 6\n7 8 9\n10 11 12\n"; try { new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE)) .parseMatrix(); fail("expected exception"); } catch (IOException e) { assertEquals(e.getMessage(), "Unexpected extra input line in score model file: '10 11 12'"); } } @Test(groups = "Functional") public void testParseMatrix_ncbiBadDelimiter() { String data = "ScoreMatrix MyTest\n X Y Z\n1|2|3\n4|5|6\n"; try { new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE)) .parseMatrix(); fail("expected exception"); } catch (IOException e) { assertEquals(e.getMessage(), "Invalid score value '1|2|3' at line 3 column 0"); } } @Test(groups = "Functional") public void testParseMatrix_ncbiBadFloat() { String data = "ScoreMatrix MyTest\n\tX\tY\tZ\n1 2 3\n4 five 6\n7 8 9\n"; try { new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE)) .parseMatrix(); fail("expected exception"); } catch (IOException e) { assertEquals(e.getMessage(), "Invalid score value 'five' at line 4 column 1"); } } @Test(groups = "Functional") public void testParseMatrix_ncbiBadGuideCharacter() { String data = "ScoreMatrix MyTest\n\tX Y\nX 1 2\ny 3 4\n"; try { new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE)) .parseMatrix(); fail("expected exception"); } catch (IOException e) { assertEquals(e.getMessage(), "Error parsing score matrix at line 4, expected 'Y' but found 'y'"); } data = "ScoreMatrix MyTest\n\tX Y\nXX 1 2\nY 3 4\n"; try { new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE)) .parseMatrix(); fail("expected exception"); } catch (IOException e) { assertEquals(e.getMessage(), "Error parsing score matrix at line 3, expected 'X' but found 'XX'"); } } @Test(groups = "Functional") public void testParseMatrix_ncbiNameMissing() { /* * Name missing on ScoreMatrix header line */ String data = "ScoreMatrix\nX Y\n1 2\n3 4\n"; try { new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE)) .parseMatrix(); fail("expected exception"); } catch (IOException e) { assertEquals( e.getMessage(), "Format error: expected 'ScoreMatrix ', found 'ScoreMatrix' at line 1"); } } /** * Test a successful parse of a (small) score matrix file * * @throws IOException * @throws MalformedURLException */ @Test(groups = "Functional") public void testParseMatrix_ncbiFormat() throws MalformedURLException, IOException { // input including comment and blank lines String data = "ScoreMatrix MyTest\n#comment\n\n" + "\tA\tB\tC\n" + "A\t1.0\t2.0\t3.0\n" + "B\t4.0\t5.0\t6.0\n" + "C\t7.0\t8.0\t9.0\n"; FileParse fp = new FileParse(data, DataSourceType.PASTE); ScoreMatrixFile parser = new ScoreMatrixFile(fp); ScoreMatrix sm = parser.parseMatrix(); assertNotNull(sm); assertEquals(sm.getName(), "MyTest"); assertEquals(parser.getMatrixName(), "MyTest"); assertEquals(sm.getPairwiseScore('A', 'A'), 1.0f); assertEquals(sm.getPairwiseScore('B', 'c'), 6.0f); assertEquals(sm.getSize(), 3); } /** * Test a successful parse of a (small) score matrix file * * @throws IOException * @throws MalformedURLException */ @Test(groups = "Functional") public void testParseMatrix_aaIndexBlosum80() throws MalformedURLException, IOException { FileParse fp = new FileParse("resources/scoreModel/blosum80.scm", DataSourceType.FILE); ScoreMatrixFile parser = new ScoreMatrixFile(fp); ScoreMatrix sm = parser.parseMatrix(); assertNotNull(sm); assertEquals(sm.getName(), "HENS920103"); assertEquals(sm.getDescription(), "BLOSUM80 substitution matrix (Henikoff-Henikoff, 1992)"); assertFalse(sm.isDNA()); assertTrue(sm.isProtein()); assertEquals(20, sm.getSize()); assertEquals(sm.getPairwiseScore('A', 'A'), 7f); assertEquals(sm.getPairwiseScore('A', 'R'), -3f); assertEquals(sm.getPairwiseScore('r', 'a'), -3f); // A/a equivalent } /** * Test a successful parse of a (small) score matrix file * * @throws IOException * @throws MalformedURLException */ @Test(groups = "Functional") public void testParseMatrix_aaindexFormat() throws MalformedURLException, IOException { /* * aaindex format has scores for diagonal and below only */ String data = "H MyTest\n" + "D My description\n" + "R PMID:1438297\n" + "A Authors, names\n" + "T Journal title\n" + "J Journal reference\n" + "* matrix in 1/3 Bit Units\n" + "M rows = ABC, cols = ABC\n" + "A\t1.0\n" + "B\t4.0\t5.0\n" + "C\t7.0\t8.0\t9.0\n"; FileParse fp = new FileParse(data, DataSourceType.PASTE); ScoreMatrixFile parser = new ScoreMatrixFile(fp); ScoreMatrix sm = parser.parseMatrix(); assertNotNull(sm); assertEquals(sm.getSize(), 3); assertEquals(sm.getName(), "MyTest"); assertEquals(sm.getDescription(), "My description"); assertEquals(sm.getPairwiseScore('A', 'A'), 1.0f); assertEquals(sm.getPairwiseScore('A', 'B'), 4.0f); assertEquals(sm.getPairwiseScore('A', 'C'), 7.0f); assertEquals(sm.getPairwiseScore('B', 'A'), 4.0f); assertEquals(sm.getPairwiseScore('B', 'B'), 5.0f); assertEquals(sm.getPairwiseScore('B', 'C'), 8.0f); assertEquals(sm.getPairwiseScore('C', 'C'), 9.0f); assertEquals(sm.getPairwiseScore('C', 'B'), 8.0f); assertEquals(sm.getPairwiseScore('C', 'A'), 7.0f); } @Test(groups = "Functional") public void testParseMatrix_aaindex_mMissing() throws MalformedURLException, IOException { /* * aaindex format but M cols=, rows= is missing */ String data = "H MyTest\n" + "A\t1.0\n" + "B\t4.0\t5.0\n" + "C\t7.0\t8.0\t9.0\n"; FileParse fp = new FileParse(data, DataSourceType.PASTE); ScoreMatrixFile parser = new ScoreMatrixFile(fp); try { parser.parseMatrix(); fail("Expected exception"); } catch (FileFormatException e) { assertEquals(e.getMessage(), "No alphabet specified in matrix file"); } } @Test(groups = "Functional") public void testParseMatrix_aaindex_rowColMismatch() throws MalformedURLException, IOException { String data = "H MyTest\n" + "M rows=ABC, cols=ABD\n" + "A\t1.0\n" + "B\t4.0\t5.0\n" + "C\t7.0\t8.0\t9.0\n"; FileParse fp = new FileParse(data, DataSourceType.PASTE); ScoreMatrixFile parser = new ScoreMatrixFile(fp); try { parser.parseMatrix(); fail("Expected exception"); } catch (FileFormatException e) { assertEquals( e.getMessage(), "Unexpected aaIndex score matrix data at line 2: M rows=ABC, cols=ABD rows != cols"); } } @Test(groups = "Functional") public void testParseMatrix_ncbiHeaderRepeated() { String data = "ScoreMatrix BLOSUM\nScoreMatrix PAM250\nX Y\n1 2\n3 4\n"; try { new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE)) .parseMatrix(); fail("expected exception"); } catch (IOException e) { assertEquals(e.getMessage(), "Error: 'ScoreMatrix' repeated in file at line 2"); } } @Test(groups = "Functional") public void testParseMatrix_aaindex_tooManyRows() throws MalformedURLException, IOException { String data = "H MyTest\n" + "M rows=ABC, cols=ABC\n" + "A\t1.0\n" + "B\t4.0\t5.0\n" + "C\t7.0\t8.0\t9.0\n" + "C\t7.0\t8.0\t9.0\n"; FileParse fp = new FileParse(data, DataSourceType.PASTE); ScoreMatrixFile parser = new ScoreMatrixFile(fp); try { parser.parseMatrix(); fail("Expected exception"); } catch (FileFormatException e) { assertEquals(e.getMessage(), "Too many data rows in matrix file"); } } @Test(groups = "Functional") public void testParseMatrix_aaindex_extraDataLines() throws MalformedURLException, IOException { String data = "H MyTest\n" + "M rows=ABC, cols=ABC\n" + "A\t1.0\n" + "B\t4.0\t5.0\n" + "C\t7.0\t8.0\t9.0\n" + "something extra\n"; FileParse fp = new FileParse(data, DataSourceType.PASTE); ScoreMatrixFile parser = new ScoreMatrixFile(fp); try { parser.parseMatrix(); fail("Expected exception"); } catch (FileFormatException e) { assertEquals(e.getMessage(), "Too many data rows in matrix file"); } } @Test(groups = "Functional") public void testParseMatrix_aaindex_tooFewColumns() throws MalformedURLException, IOException { String data = "H MyTest\n" + "M rows=ABC, cols=ABC\n" + "A\t1.0\n" + "B\t4.0\t5.0\n" + "C\t7.0\t8.0\n"; FileParse fp = new FileParse(data, DataSourceType.PASTE); ScoreMatrixFile parser = new ScoreMatrixFile(fp); try { parser.parseMatrix(); fail("Expected exception"); } catch (FileFormatException e) { assertEquals( e.getMessage(), "Expected 3 scores at line 5: 'C\t7.0\t8.0' but found 2"); } } /** * Test a successful parse and register of a score matrix file * * @throws IOException * @throws MalformedURLException */ @Test(groups = "Functional") public void testParse_ncbiFormat() throws MalformedURLException, IOException { assertNull(ScoreModels.getInstance().getScoreModel("MyNewTest", null)); String data = "ScoreMatrix MyNewTest\n" + "\tA\tB\tC\n" + "A\t1.0\t2.0\t3.0\n" + "B\t4.0\t5.0\t6.0\n" + "C\t7.0\t8.0\t9.0\n"; FileParse fp = new FileParse(data, DataSourceType.PASTE); ScoreMatrixFile parser = new ScoreMatrixFile(fp); parser.parse(); ScoreMatrix sm = (ScoreMatrix) ScoreModels.getInstance().getScoreModel( "MyNewTest", null); assertNotNull(sm); assertEquals(sm.getName(), "MyNewTest"); assertEquals(parser.getMatrixName(), "MyNewTest"); assertEquals(sm.getPairwiseScore('A', 'A'), 1.0f); assertEquals(sm.getPairwiseScore('B', 'c'), 6.0f); assertEquals(sm.getSize(), 3); } }