@Test
public void testSimpleSubstitutionMatrixCompoundSetOfCStringString() {
DNACompoundSet dnacs = DNACompoundSet.getDNACompoundSet();
SubstitutionMatrix<NucleotideCompound> dnaTest =
new SimpleSubstitutionMatrix<NucleotideCompound>(
dnacs, "# Test\nA C G T\nA 5 0 0 0\nC 0 5 0 0\nG 0 0 5 0\nT 0 0 0 1\n", "DNA Test");
short[][] matrix = dnaTest.getMatrix();
assertEquals(matrix[1][1], 5);
assertEquals(matrix[3][3], 1);
assertEquals(matrix[3][1], 0);
assertEquals(dnaTest.getMatrixAsString().substring(2, 9), "A C G T");
assertEquals(
dnaTest.getValue(dnacs.getCompoundForString("G"), dnacs.getCompoundForString("G")), 5);
assertEquals(
dnaTest.getValue(dnacs.getCompoundForString("A"), dnacs.getCompoundForString("G")), 0);
}
/*
* Author: Daniel Cameron
*/
@Test
public void testCaseEquivalence() {
DNACompoundSet dnacs = DNACompoundSet.getDNACompoundSet();
SubstitutionMatrix<NucleotideCompound> dnaTest =
new SimpleSubstitutionMatrix<NucleotideCompound>(
dnacs, "# Test\nA C G T\nA 5 0 0 0\nC 0 5 0 0\nG 0 0 5 0\nT 0 0 0 1\n", "DNA Test");
@SuppressWarnings("unused")
short[][] matrix = dnaTest.getMatrix();
assertEquals(
dnaTest.getValue(dnacs.getCompoundForString("G"), dnacs.getCompoundForString("g")), 5);
assertEquals(
dnaTest.getValue(dnacs.getCompoundForString("A"), dnacs.getCompoundForString("g")), 0);
assertEquals(
dnaTest.getValue(dnacs.getCompoundForString("g"), dnacs.getCompoundForString("G")), 5);
assertEquals(
dnaTest.getValue(dnacs.getCompoundForString("g"), dnacs.getCompoundForString("A")), 0);
}