/**
   * 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);
  }
Exemple #5
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 /**
  * 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")));
  }