@Test
public void testSetDescription() {
SubstitutionMatrix<AminoAcidCompound> matrix = SimpleSubstitutionMatrix.getBlosum62();
assertEquals(matrix.getDescription().substring(0, 2), "# ");
matrix.setDescription("blah");
assertEquals(matrix.getDescription().substring(0, 2), "bl");
}
@Test
public void testSetName() {
SubstitutionMatrix<AminoAcidCompound> matrix = SimpleSubstitutionMatrix.getBlosum62();
assertEquals(matrix.getName(), "blosum62");
matrix.setName("blah");
assertEquals(matrix.getName(), "blah");
}
@Test
public void testSimpleSubstitutionMatrixCompoundSetOfCShortShort() {
SubstitutionMatrix<AminoAcidCompound> matrix =
new SimpleSubstitutionMatrix<AminoAcidCompound>(
AminoAcidCompoundSet.getAminoAcidCompoundSet(), (short) 5, (short) 1);
assertEquals(matrix.getName(), "IDENTITY_5_1");
}
@Test()
public void testSimpleSubstitutionMatrix() {
SubstitutionMatrix<AminoAcidCompound> matrix = SimpleSubstitutionMatrix.getBlosum62();
assertEquals(matrix.getCompoundSet(), AminoAcidCompoundSet.getAminoAcidCompoundSet());
assertEquals(matrix.getName(), "blosum62");
assertEquals(matrix.getMaxValue(), 11);
assertEquals(matrix.getMinValue(), -4);
}
@Test
public void testToString() {
SubstitutionMatrix<NucleotideCompound> matrix =
new SimpleSubstitutionMatrix<NucleotideCompound>(
DNACompoundSet.getDNACompoundSet(),
"# Test\nA C G T\nA 5 0 0 0\nC 0 5 0 0 \nG 0 0 5 0\n T 0 0 0 1\n",
"DNAtest");
assertEquals(matrix.toString().substring(0, 6), "# Test");
assertEquals(
matrix.toString(),
String.format("# Test%n A C G T%nA 5 0 0 0%nC 0 5 0 0%nG 0 0 5 0%nT 0 0 0 1%n"));
}
@Test
public void test() throws CompoundNotFoundException {
NucleotideCompound A = new DNASequence("A").getCompoundAt(1);
NucleotideCompound a = new DNASequence("a").getCompoundAt(1);
NucleotideCompound c = new DNASequence("c").getCompoundAt(1);
SubstitutionMatrix<NucleotideCompound> matrix =
new SimpleSubstitutionMatrix<NucleotideCompound>(
DNACompoundSet.getDNACompoundSet(), (short) 1, (short) 0);
assertEquals(1, (matrix.getValue(A, A)));
assertEquals(1, (matrix.getValue(a, a)));
assertEquals(1, (matrix.getValue(A, a)));
assertEquals(0, (matrix.getValue(a, c)));
}
@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);
}