# Scores are not symbol case sensitive, unless column(s) are provided for lower case characters
# The 'guide symbol' at the start of each row of score values is optional
#
-# Comment header line with symbols is provided as a guide
+# Header line with symbols may be provided as a guide
# Values may be integer or floating point, delimited by tab, space, comma or combinations
#
-# A R N D C Q E G H I L K M F P S T W Y V B Z X *
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
#
A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 0 -4 -4
R -1 5 0 -2 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -4 -4
# Scores are not case sensitive, unless column(s) are provided for lower case characters
#
#
-# Comment line with symbols is provided as a guide
+# Header line with symbols is provided as a guide
# Values may be integer or floating point, delimited by tab, space, comma or combinations
#
-# A C G T U I X R Y N -
-#
+ A C G T U I X R Y N -
10 -8 -8 -8 -8 1 1 1 -8 1 1 1
-8 10 -8 -8 -8 1 1 -8 1 1 1 1
-8 -8 10 -8 -8 1 1 1 -8 1 1 1
# Scores are not case sensitive, unless column(s) are provided for lower case characters
#
#
-# Comment line with symbols is provided as a guide
+# Header line with symbols is provided as a guide
# Values may be integer or floating point, delimited by tab, space, comma or combinations
#
# A R N D C Q E G H I L K M F P S T W Y V B Z X *
-#
2 -2 0 0 -2 0 0 1 -1 -1 -2 -1 -1 -3 1 1 1 -6 -3 0 0 0 0 -8 -8
-2 6 0 -1 -4 1 -1 -3 2 -2 -3 3 0 -4 0 0 -1 2 -4 -2 -1 0 -1 -8 -8
0 0 2 2 -4 1 1 0 2 -2 -3 1 -2 -3 0 1 0 -4 -2 -2 2 1 0 -8 -8
}
/**
- * Print the score matrix, optionally formatted as html, with the alphabet symbols as column headings and at the start of each row
+ * Print the score matrix, optionally formatted as html, with the alphabet
+ * symbols as column headings and at the start of each row.
+ * <p>
+ * The non-html format should give an output which can be parsed as a score
+ * matrix file
+ *
* @param html
* @return
*/
sb.append("<table border=\"1\">");
sb.append(html ? "<tr><th></th>" : "");
}
+ else
+ {
+ sb.append("ScoreMatrix ").append(getName()).append("\n");
+ sb.append(symbols).append("\n");
+ }
for (char sym : symbols)
{
if (html)
}
return new Matrix(values);
}
+
+ /**
+ * Answers a hashcode computed from the symbol alphabet and the matrix score
+ * values
+ */
+ @Override
+ public int hashCode()
+ {
+ int hs = Arrays.hashCode(symbols);
+ for (float[] row : matrix)
+ {
+ hs = hs * 31 + Arrays.hashCode(row);
+ }
+ return hs;
+ }
+
+ /**
+ * Answers true if the argument is a ScoreMatrix with the same symbol alphabet
+ * and score values, else false
+ */
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (!(obj instanceof ScoreMatrix))
+ {
+ return false;
+ }
+ ScoreMatrix sm = (ScoreMatrix) obj;
+ if (Arrays.equals(symbols, sm.symbols)
+ && Arrays.deepEquals(matrix, sm.matrix))
+ {
+ return true;
+ }
+ return false;
+ }
}
}
/*
+ * permit an uncommented line with delimited residue headings
+ */
+ if (isHeaderLine(data, alphabet))
+ {
+ continue;
+ }
+
+ /*
* subsequent lines should be the symbol scores
* optionally with the symbol as the first column for readability
*/
return sm;
}
+ /**
+ * Answers true if the data line consists of the alphabet characters,
+ * delimited (as to provide a heading row). Otherwise returns false (e.g. if
+ * the data is a row of score values).
+ *
+ * @param data
+ * @param alphabet
+ * @return
+ */
+ private boolean isHeaderLine(String data, String alphabet)
+ {
+ StringTokenizer scoreLine = new StringTokenizer(data, DELIMITERS);
+ int i = 0;
+ while (scoreLine.hasMoreElements())
+ {
+ /*
+ * skip over characters in the alphabet that are
+ * also a delimiter (e.g. space)
+ */
+ char symbol = alphabet.charAt(i++);
+ if (!DELIMITERS.contains(String.valueOf(symbol)))
+ {
+ if (!String.valueOf(symbol).equals(scoreLine.nextToken()))
+ {
+ return false;
+ }
+ }
+ }
+ return true;
+ }
+
public String getMatrixName()
{
return matrixName;
package jalview.analysis.scoremodels;
+
import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertTrue;
import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
+import jalview.io.DataSourceType;
+import jalview.io.FileParse;
+import jalview.io.ScoreMatrixFile;
import jalview.math.MatrixI;
+import java.io.IOException;
+import java.net.MalformedURLException;
+
import org.testng.annotations.Test;
public class ScoreMatrixTest
// Q.G + I.W + A.C = -2 + -3 + 0 = -5
assertEquals(pairwise.getValue(2, 3), -5d);
}
+
+ /**
+ * Test that the result of outputMatrix can be reparsed to give an identical
+ * ScoreMatrix
+ *
+ * @throws IOException
+ * @throws MalformedURLException
+ */
+ @Test(groups = "Functional")
+ public void testOutputMatrix_roundTrip() throws MalformedURLException,
+ IOException
+ {
+ ScoreMatrix sm = ScoreModels.getInstance().getBlosum62();
+ String output = sm.outputMatrix(false);
+ FileParse fp = new FileParse(output, DataSourceType.PASTE);
+ ScoreMatrixFile parser = new ScoreMatrixFile(fp);
+ ScoreMatrix sm2 = parser.parseMatrix();
+ assertNotNull(sm2);
+ assertTrue(sm2.equals(sm));
+ }
}
if (psm instanceof ScoreMatrix)
{
ScoreMatrix sm = (ScoreMatrix) psm;
- System.out.println("ScoreMatrix " + sm.getName());
System.out.println(sm.outputMatrix(asHtml));
}
}
"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 testParse_withResidueHeading() throws MalformedURLException,
+ IOException
+ {
+ String data = "ScoreMatrix MyTest\n" + "ABC\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(sm.getPairwiseScore('A', 'A'), 1.0f);
+ assertEquals(sm.getPairwiseScore('B', 'c'), 6.0f);
+ assertEquals(sm.getSize(), 3);
+ }
}
git://source.jalview.org / jalview.git / commitdiff