void ComposedElementTest::testOperatorNotEqual() {
// initializes alphabet
Alphabet cho;
cho.push_back(*hydrogen);
cho.push_back(*carbon);
cho.push_back(*oxygen);
// initializes elements
Element elementH(*hydrogen);
Element elementO(*oxygen);
Element elementC(*carbon);
elements_container elements;
elements[elementH] = 4;
elements[elementO] = 2;
elements[elementC] = 2;
// checks case with different elements
composed_element_type molecule1(elements);
elements[elementH] = 5;
composed_element_type molecule1_not_equal(elements);
CPPUNIT_ASSERT(molecule1 != molecule1_not_equal);
// checks case with different sequences
composed_element_type molecule3("C2H4O2", cho),
molecule3_not_equal("C2H3O2", cho);
CPPUNIT_ASSERT(molecule3 != molecule3_not_equal);
}
void ComposedElementTest::testOperatorMinus() {
// initializes alphabet
Alphabet cho;
cho.push_back(*hydrogen);
cho.push_back(*carbon);
cho.push_back(*oxygen);
composed_element_type molecule1("H10O6", cho), molecule2("O4H4", cho);
molecule1 -= molecule2;
CPPUNIT_ASSERT_EQUAL(molecule1.getElements().size(),
static_cast<elements_container::size_type>(2));
CPPUNIT_ASSERT_EQUAL(molecule1.getElementAbundance("O"),
static_cast<elements_container::mapped_type>(2));
CPPUNIT_ASSERT_EQUAL(molecule1.getElementAbundance("H"),
static_cast<elements_container::mapped_type>(6));
composed_element_type molecule3("O8H2", cho), molecule4("O6H7C5", cho);
molecule3 -= molecule4;
CPPUNIT_ASSERT_EQUAL(molecule3.getElements().size(),
static_cast<elements_container::size_type>(1));
CPPUNIT_ASSERT_EQUAL(molecule3.getElementAbundance("O"),
static_cast<elements_container::mapped_type>(2));
}
void ComposedElementTest::testOperatorEqual() {
// checks for type of constructors with sequence
Alphabet cho;
cho.push_back(*hydrogen);
cho.push_back(*carbon);
cho.push_back(*oxygen);
composed_element_type molecule1("H4C2O2", cho);
composed_element_type molecule1_equal("H4C2O2", cho);
CPPUNIT_ASSERT(molecule1 == molecule1_equal);
// checks for type of constructors with elements
Element elementH(*hydrogen);
Element elementO(*oxygen);
Element elementC(*carbon);
elements_container elements;
elements[elementH] = 4;
elements[elementO] = 2;
elements[elementC] = 2;
// checks for type of constructors with elements and random sequence order
composed_element_type molecule2(elements);
composed_element_type molecule2_equal(elements);
CPPUNIT_ASSERT(molecule2 == molecule2_equal);
}
void ComposedElementTest::testUpdateIsotopeDistribution() {
Alphabet cho;
cho.push_back(*hydrogen);
cho.push_back(*carbon);
cho.push_back(*oxygen);
std::vector<unsigned int> decomposition;
decomposition.push_back(static_cast<unsigned int>(4));
decomposition.push_back(static_cast<unsigned int>(2));
decomposition.push_back(static_cast<unsigned int>(2));
// initializes molecule without setting isotope distribution and sequence
composed_element_type molecule(decomposition, cho);
molecule.updateIsotopeDistribution();
isotopes_type isodistr = molecule.getIsotopeDistribution();
CPPUNIT_ASSERT_DOUBLES_EQUAL(isodistr.getMass(0), static_cast<mass_type>(60.02113), 1.0e-6);
CPPUNIT_ASSERT_DOUBLES_EQUAL(isodistr.getMass(1), static_cast<mass_type>(61.0245862), 1.0e-6);
CPPUNIT_ASSERT_DOUBLES_EQUAL(isodistr.getMass(2), static_cast<mass_type>(62.0254827), 1.0e-6);
CPPUNIT_ASSERT_DOUBLES_EQUAL(isodistr.getMass(3), static_cast<mass_type>(63.0288285), 1.0e-6);
CPPUNIT_ASSERT_DOUBLES_EQUAL(isodistr.getAbundance(0), static_cast<abundance_type>(0.972690002), 1.0e-6);
CPPUNIT_ASSERT_DOUBLES_EQUAL(isodistr.getAbundance(1), static_cast<abundance_type>(0.0231608083), 1.0e-6);
CPPUNIT_ASSERT_DOUBLES_EQUAL(isodistr.getAbundance(2), static_cast<abundance_type>(0.00405304857), 1.0e-6);
CPPUNIT_ASSERT_DOUBLES_EQUAL(isodistr.getAbundance(3), static_cast<abundance_type>(9.1561898e-05), 1.0e-6);
}
void ComposedElementTest::testConstructorDecompositionAlphabet() {
Alphabet cho;
cho.push_back(*hydrogen);
cho.push_back(*carbon);
cho.push_back(*oxygen);
std::vector<unsigned int> decomposition;
decomposition.push_back(static_cast<unsigned int>(3));
decomposition.push_back(static_cast<unsigned int>(2));
decomposition.push_back(static_cast<unsigned int>(1));
composed_element_type molecule(decomposition, cho);
CPPUNIT_ASSERT_EQUAL(molecule.getElementAbundance("C"),
static_cast<elements_container::mapped_type>(2));
CPPUNIT_ASSERT_EQUAL(molecule.getElementAbundance("H"),
static_cast<elements_container::mapped_type>(3));
CPPUNIT_ASSERT_EQUAL(molecule.getElementAbundance("O"),
static_cast<elements_container::mapped_type>(1));
// checks if isotope distribution is not yet initialized
CPPUNIT_ASSERT(molecule.getIsotopeDistribution().empty());
// checks if sequence is not yet initialized
CPPUNIT_ASSERT(molecule.getSequence().empty());
}
void ComposedElementTest::testConstructorTexNotationSequenceAlphabet() {
Alphabet cho;
cho.push_back(*hydrogen);
cho.push_back(*carbon);
cho.push_back(*oxygen);
composed_element_type molecule("C_{2}H_{4}O_{2}", cho, composed_element_type::TEX_NOTATION_MOLECULE_SEQUENCE_TYPE);
CPPUNIT_ASSERT_EQUAL(molecule.getSequence(), static_cast<name_type>("C_{2}H_{4}O_{2}"));
CPPUNIT_ASSERT_EQUAL(molecule.getElementAbundance("C"),
static_cast<elements_container::mapped_type>(2));
CPPUNIT_ASSERT_EQUAL(molecule.getElementAbundance("H"),
static_cast<elements_container::mapped_type>(4));
CPPUNIT_ASSERT_EQUAL(molecule.getElementAbundance("O"),
static_cast<elements_container::mapped_type>(2));
// checks if isotope distribution is not yet initialized
CPPUNIT_ASSERT(molecule.getIsotopeDistribution().empty());
}
void ComposedElementTest::testConstructorSequenceAlphabet() {
Alphabet cho;
cho.push_back(*hydrogen);
cho.push_back(*carbon);
cho.push_back(*oxygen);
composed_element_type molecule("C2H4O2", cho);
CPPUNIT_ASSERT_EQUAL(molecule.getSequence(), static_cast<name_type>("C2H4O2"));
CPPUNIT_ASSERT_EQUAL(molecule.getElements().size(),
static_cast<elements_container::size_type>(3));
CPPUNIT_ASSERT_EQUAL(molecule.getElementAbundance("C"),
static_cast<elements_container::mapped_type>(2));
CPPUNIT_ASSERT_EQUAL(molecule.getElementAbundance("H"),
static_cast<elements_container::mapped_type>(4));
CPPUNIT_ASSERT_EQUAL(molecule.getElementAbundance("O"),
static_cast<elements_container::mapped_type>(2));
// checks if isotope distribution is not yet initialized
CPPUNIT_ASSERT(molecule.getIsotopeDistribution().empty());
}