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.AfterMethod;
import org.testng.annotations.Test;
public class ScoreMatrixFileTest
{
+ @AfterMethod(alwaysRun = true)
+ public void tearDownAfterTest()
+ {
+ ScoreModels.getInstance().reset();
+ }
+
/**
* Test a successful parse of a (small) score matrix file
*
* @throws MalformedURLException
*/
@Test(groups = "Functional")
- public void testParse() throws MalformedURLException, IOException
+ 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\n" + "ATU tx-\n"
- + "A,1.1,1.2,1.3,1.4, 1.5, 1.6, 1.7\n"
- + "T,2.1 2.2 2.3 2.4 2.5 2.6 2.7\n"
- + "U\t3.1\t3.2\t3.3\t3.4\t3.5\t3.6\t3.7\n"
- + " 4.1 ,4.2,\t,4.3 ,\t4.4\t, \4.5,4.6 4.7\n"
- + "t, 5.1,5.3,5.3,5.4,5.5, 5.6, 5.7\n"
- + "x\t6.1, 6.2 6.3 6.4 6.5 6.6 6.7\n"
- + "-, \t7.1\t7.2 7.3, 7.4, 7.5\t,7.6,7.7\n";
+ 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");
+ 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'), 1.5f); // T/t not equivalent
- assertEquals(sm.getPairwiseScore('a', 't'), 1.5f);
- assertEquals(sm.getPairwiseScore('T', ' '), 2.4f);
- assertEquals(sm.getPairwiseScore('U', 'x'), 3.6f);
- assertEquals(sm.getPairwiseScore('u', 'x'), 3.6f);
- assertEquals(sm.getPairwiseScore('U', 'X'), 0f); // X (upper) unmapped
- assertEquals(sm.getPairwiseScore('A', '.'), 0f); // . unmapped
- assertEquals(sm.getPairwiseScore('-', '-'), 7.7f);
+ 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
-
- /*
- * without guide symbols on score rows
- */
- data = "ScoreMatrix MyTest\nXY\n1 2\n3 4\n";
- fp = new FileParse(data, DataSourceType.PASTE);
- parser = new ScoreMatrixFile(fp);
- sm = parser.parseMatrix();
- assertNotNull(sm);
- assertEquals(sm.getPairwiseScore('X', 'X'), 1f);
- assertEquals(sm.getPairwiseScore('X', 'y'), 2f);
- assertEquals(sm.getPairwiseScore('y', 'x'), 3f);
- assertEquals(sm.getPairwiseScore('y', 'Y'), 4f);
- assertEquals(sm.getPairwiseScore('D', 'R'), 0f);
}
@Test(groups = "Functional")
- public void testParse_headerMissing()
+ public void testParseMatrix_headerMissing()
{
String data;
- data = "XY\n1 2\n3 4\n";
+ data = "X Y\n1 2\n3 4\n";
try
{
new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE))
}
@Test(groups = "Functional")
- public void testParse_notEnoughRows()
+ public void testParseMatrix_ncbiNotEnoughRows()
{
- String data = "ScoreMatrix MyTest\nXY\n1 2\n";
+ String data = "ScoreMatrix MyTest\nX Y Z\n1 2 3\n4 5 6\n";
try
{
new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE))
} catch (IOException e)
{
assertEquals(e.getMessage(),
- "Expected 2 rows of score data in score matrix but only found 1");
+ "Expected 3 rows of score data in score matrix but only found 2");
}
}
@Test(groups = "Functional")
- public void testParse_notEnoughColumns()
+ public void testParseMatrix_ncbiNotEnoughColumns()
{
- String data = "ScoreMatrix MyTest\nXY\n1 2\n3\n";
+ String data = "ScoreMatrix MyTest\nX Y Z\n1 2 3\n4 5\n7 8 9\n";
try
{
new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE))
} catch (IOException e)
{
assertEquals(e.getMessage(),
- "Expected 2 scores at line 4 but found 1");
+ "Expected 3 scores at line 4: '4 5' but found 2");
}
}
@Test(groups = "Functional")
- public void testParse_tooManyColumns()
+ public void testParseMatrix_ncbiTooManyColumns()
{
/*
* with two too many columns:
*/
- String data = "ScoreMatrix MyTest\nXY\n1 2\n3 4 5 6\n";
+ 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))
} catch (IOException e)
{
assertEquals(e.getMessage(),
- "Expected 2 scores at line 4 but found 4");
+ "Expected 3 scores at line 4: '4 5 6 7' but found 4");
}
/*
* with guide character and one too many columns:
*/
- data = "ScoreMatrix MyTest\nXY\nX 1 2\nY 3 4 5\n";
+ data = "ScoreMatrix MyTest\nX Y\nX 1 2\nY 3 4 5\n";
try
{
new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE))
} catch (IOException e)
{
assertEquals(e.getMessage(),
- "Expected 2 scores at line 4 but found 4");
+ "Expected 2 scores at line 4: 'Y 3 4 5' but found 3");
}
/*
- * with no guide character and one too many columns:
- * parser guesses the first column is the guide character
+ * with no guide character and one too many columns
*/
- data = "ScoreMatrix MyTest\nXY\n1 2\n3 4 5\n";
+ data = "ScoreMatrix MyTest\nX Y\n1 2\n3 4 5\n";
try
{
new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE))
} catch (IOException e)
{
assertEquals(e.getMessage(),
- "Error parsing score matrix at line 4, expected 'Y' but found '3'");
+ "Expected 2 scores at line 4: '3 4 5' but found 3");
}
}
@Test(groups = "Functional")
- public void testParse_tooManyRows()
+ public void testParseMatrix_ncbiTooManyRows()
{
- String data = "ScoreMatrix MyTest\nXY\n1 2\n3 4\n6 7";
+ 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))
} catch (IOException e)
{
assertEquals(e.getMessage(),
- "Unexpected extra input line in score model file: '6 7'");
+ "Unexpected extra input line in score model file: '10 11 12'");
}
}
@Test(groups = "Functional")
- public void testParse_badDelimiter()
+ public void testParseMatrix_ncbiBadDelimiter()
{
- String data = "ScoreMatrix MyTest\nXY\n1|2\n3|4\n";
+ String data = "ScoreMatrix MyTest\n X Y Z\n1|2|3\n4|5|6\n";
try
{
new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE))
} catch (IOException e)
{
assertEquals(e.getMessage(),
- "Expected 2 scores at line 3 but found 1");
+ "Invalid score value '1|2|3' at line 3 column 0");
}
}
@Test(groups = "Functional")
- public void testParse_badFloat()
+ public void testParseMatrix_ncbiBadFloat()
{
- String data = "ScoreMatrix MyTest\nXY\n1 2\n3 four\n";
+ 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))
} catch (IOException e)
{
assertEquals(e.getMessage(),
- "Invalid score value 'four' at line 4 column 1");
+ "Invalid score value 'five' at line 4 column 1");
}
}
@Test(groups = "Functional")
- public void testParse_badGuideCharacter()
+ public void testParseMatrix_ncbiBadGuideCharacter()
{
- String data = "ScoreMatrix MyTest\nXY\nX 1 2\ny 3 4\n";
+ String data = "ScoreMatrix MyTest\n\tX Y\nX 1 2\ny 3 4\n";
try
{
new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE))
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 testParse_nameMissing()
+ public void testParseMatrix_ncbiNameMissing()
{
/*
- * Name missing
+ * Name missing on ScoreMatrix header line
*/
- String data = "ScoreMatrix\nXY\n1 2\n3 4\n";
+ String data = "ScoreMatrix\nX Y\n1 2\n3 4\n";
try
{
new ScoreMatrixFile(new FileParse(data, DataSourceType.PASTE))
fail("expected exception");
} catch (IOException e)
{
- assertEquals(
- e.getMessage(),
+ assertEquals(e.getMessage(),
"Format error: expected 'ScoreMatrix <name>', 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);
+ }
}
git://source.jalview.org / jalview.git / blobdiff