@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);
}