/**
* A unit test suite for JUnit.
*
* @return The test suite
*/
@Test
public void testContains_IMolecularFormulaSet_IMolecularFormula() {
IMolecularFormula mf1 = new MolecularFormula();
mf1.addIsotope(builder.newIsotope("C"), 4);
mf1.addIsotope(builder.newIsotope("H"), 12);
mf1.addIsotope(builder.newIsotope("N"), 1);
mf1.addIsotope(builder.newIsotope("O"), 4);
IMolecularFormula mf3 = new MolecularFormula();
mf3.addIsotope(builder.newIsotope("C"), 9);
mf3.addIsotope(builder.newIsotope("H"), 5);
mf3.addIsotope(builder.newIsotope("O"), 7);
IMolecularFormulaSet formulaSet = new MolecularFormulaSet();
formulaSet.addMolecularFormula(mf1);
formulaSet.addMolecularFormula(mf3);
IMolecularFormula mf2 = new MolecularFormula();
mf2.addIsotope(builder.newIsotope("C"), 4);
mf2.addIsotope(builder.newIsotope("H"), 12);
mf2.addIsotope(builder.newIsotope("N"), 1);
mf2.addIsotope(builder.newIsotope("O"), 4);
IMolecularFormula mf4 = new MolecularFormula();
mf4.addIsotope(builder.newIsotope("C"), 4);
IIsotope hyd = builder.newIsotope("H");
hyd.setExactMass(2.0032342);
mf4.addIsotope(hyd, 12);
mf4.addIsotope(builder.newIsotope("N"), 1);
mf4.addIsotope(builder.newIsotope("O"), 4);
Assert.assertTrue(MolecularFormulaSetManipulator.contains(formulaSet, mf2));
Assert.assertFalse(MolecularFormulaSetManipulator.contains(formulaSet, mf4));
}
/**
* A unit test suite for JUnit.
*
* @return The test suite
*/
@Test
public void testRemove_IMolecularFormulaSet_MolecularFormulaRange() {
MolecularFormulaRange formulaRange = new MolecularFormulaRange();
formulaRange.addIsotope(builder.newIsotope("C"), 0, 4);
formulaRange.addIsotope(builder.newIsotope("H"), 0, 12);
formulaRange.addIsotope(builder.newIsotope("N"), 0, 2);
IMolecularFormula mf2 = new MolecularFormula();
mf2.addIsotope(builder.newIsotope("C"), 1);
mf2.addIsotope(builder.newIsotope("H"), 11);
mf2.addIsotope(builder.newIsotope("N"), 1);
IMolecularFormula mf1 = new MolecularFormula();
mf1.addIsotope(builder.newIsotope("C"), 3);
mf1.addIsotope(builder.newIsotope("H"), 10);
IMolecularFormulaSet formulaSet = new MolecularFormulaSet();
formulaSet.addMolecularFormula(mf1);
formulaSet.addMolecularFormula(mf2);
IMolecularFormulaSet newMFSet = MolecularFormulaSetManipulator.remove(formulaSet, formulaRange);
/*the mf2 is excluded from the limits. It doesn't contain N*/
Assert.assertEquals(2, newMFSet.size());
}
/**
* A unit test suite for JUnit.
*
* @return The test suite
*/
@Test
public void testRemove_2() {
IMolecularFormula formulaMin = new MolecularFormula();
formulaMin.addIsotope(builder.newIsotope("C"), 1);
formulaMin.addIsotope(builder.newIsotope("H"), 1);
formulaMin.addIsotope(builder.newIsotope("N"), 1);
IMolecularFormula formulaMax = new MolecularFormula();
formulaMax.addIsotope(builder.newIsotope("C"), 4);
formulaMax.addIsotope(builder.newIsotope("H"), 12);
formulaMax.addIsotope(builder.newIsotope("N"), 2);
IMolecularFormula mf1 = new MolecularFormula();
mf1.addIsotope(builder.newIsotope("C"), 3);
mf1.addIsotope(builder.newIsotope("H"), 10);
mf1.addIsotope(builder.newIsotope("N"), 1);
IMolecularFormula mf2 = new MolecularFormula();
mf2.addIsotope(builder.newIsotope("C"), 1);
mf2.addIsotope(builder.newIsotope("H"), 1);
IMolecularFormulaSet formulaSet = new MolecularFormulaSet();
formulaSet.addMolecularFormula(mf1);
formulaSet.addMolecularFormula(mf2);
IMolecularFormulaSet newMFSet =
MolecularFormulaSetManipulator.remove(formulaSet, formulaMin, formulaMax);
/*the mf2 is excluded from the limits. It doesn't contain N*/
Assert.assertEquals(1, newMFSet.size());
Assert.assertEquals(
MolecularFormulaManipulator.getString(mf1),
MolecularFormulaManipulator.getString(newMFSet.getMolecularFormula(0)));
}
/**
* A unit test suite for JUnit.
*
* @return The test suite
*/
@Test
public void testRemove_IMolecularFormulaSet_IMolecularFormula_IMolecularFormula() {
IMolecularFormula formulaMin = new MolecularFormula();
formulaMin.addIsotope(builder.newIsotope("C"), 1);
formulaMin.addIsotope(builder.newIsotope("H"), 1);
formulaMin.addIsotope(builder.newIsotope("O"), 1);
IMolecularFormula formulaMax = new MolecularFormula();
formulaMax.addIsotope(builder.newIsotope("C"), 4);
formulaMax.addIsotope(builder.newIsotope("H"), 12);
formulaMax.addIsotope(builder.newIsotope("N"), 2);
IMolecularFormula mf1 = new MolecularFormula();
mf1.addIsotope(builder.newIsotope("C"), 3);
mf1.addIsotope(builder.newIsotope("H"), 10);
mf1.addIsotope(builder.newIsotope("N"), 1);
IMolecularFormulaSet formulaSet = new MolecularFormulaSet();
formulaSet.addMolecularFormula(mf1);
IMolecularFormulaSet newMFSet =
MolecularFormulaSetManipulator.remove(formulaSet, formulaMin, formulaMax);
Assert.assertNull(newMFSet);
}
/**
* Adds all molecularFormulas in the MolecularFormulaSet to this chemObject.
*
* @param formulaSet The MolecularFormulaSet
*/
@TestMethod("testAdd_IMolecularFormulaSet")
public void add(IMolecularFormulaSet formulaSet) {
for (IMolecularFormula mf : formulaSet.molecularFormulas()) {
addMolecularFormula(mf);
}
/*
* notifyChanged() is called by addAtomContainer()
*/
}
/**
* A unit test suite for JUnit.
*
* @return The test suite
*/
@Test
public void testGetMinOccurrenceElements_IMolecularFormulaSet() {
IMolecularFormula mf1 = new MolecularFormula(); /*C4H12NO4*/
mf1.addIsotope(builder.newIsotope("C"), 4);
mf1.addIsotope(builder.newIsotope("H"), 12);
mf1.addIsotope(builder.newIsotope("N"), 1);
mf1.addIsotope(builder.newIsotope("O"), 4);
IMolecularFormula mf2 = new MolecularFormula(); /*C7H20N4O2*/
mf2.addIsotope(builder.newIsotope("C"), 7);
mf2.addIsotope(builder.newIsotope("H"), 20);
mf2.addIsotope(builder.newIsotope("N"), 4);
mf2.addIsotope(builder.newIsotope("O"), 2);
IMolecularFormula mf3 = new MolecularFormula(); /*C9H5O7*/
mf3.addIsotope(builder.newIsotope("C"), 9);
mf3.addIsotope(builder.newIsotope("H"), 5);
mf3.addIsotope(builder.newIsotope("O"), 7);
IMolecularFormulaSet mfSet = new MolecularFormulaSet();
mfSet.addMolecularFormula(mf1);
mfSet.addMolecularFormula(mf2);
mfSet.addMolecularFormula(mf3);
IMolecularFormula molecularFormula =
MolecularFormulaSetManipulator.getMinOccurrenceElements(mfSet);
/* Result: C4H5NO2 */
Assert.assertEquals(12, MolecularFormulaManipulator.getAtomCount(molecularFormula));
Assert.assertEquals(4, molecularFormula.getIsotopeCount());
Assert.assertEquals(4, molecularFormula.getIsotopeCount(builder.newIsotope("C")));
Assert.assertEquals(5, molecularFormula.getIsotopeCount(builder.newIsotope("H")));
Assert.assertEquals(1, molecularFormula.getIsotopeCount(builder.newIsotope("N")));
Assert.assertEquals(2, molecularFormula.getIsotopeCount(builder.newIsotope("O")));
}