/** * A unit test suite for JUnit. * * @return The test suite */ @Test public void testClone() throws Exception { IsotopeContainer isoC = new IsotopeContainer(); IMolecularFormula formula = builder.newInstance(IMolecularFormula.class); isoC.setFormula(formula); double mass = 130.00; isoC.setMass(mass); double intensity = 130.00; isoC.setIntensity(intensity); IsotopeContainer clone = (IsotopeContainer) isoC.clone(); Assert.assertEquals(mass, clone.getMass(), 0.001); Assert.assertEquals(intensity, clone.getIntensity(), 0.001); Assert.assertEquals(formula, clone.getFormula()); }
/** * Clones this IsotopeContainer object and its content. * * @return The cloned object */ @Override public Object clone() throws CloneNotSupportedException { IsotopeContainer isoClone = new IsotopeContainer(); isoClone.forms.addAll(getFormulas()); isoClone.setIntensity(getIntensity()); isoClone.setMass(getMass()); return isoClone; }
private void addDistinctFormula(IsotopeContainer container, IMolecularFormula mf) { for (IMolecularFormula curr : container.getFormulas()) if (MolecularFormulaManipulator.compare(curr, mf)) return; container.addFormula(mf); }
/** * Gets the parameters attribute of the IsotopePatternRule object. * * @return The parameters value * @see #setParameters */ @Override public Object[] getParameters() { // return the parameters as used for the rule validation Object[] params = new Object[2]; if (pattern == null) params[0] = null; else { List<double[]> params0 = new ArrayList<double[]>(); for (IsotopeContainer isotope : pattern.getIsotopes()) { params0.add(new double[] { isotope.getMass(), isotope.getIntensity() }); } params[0] = params0; } params[1] = toleranceMass; return params; }
/** * A unit test suite for JUnit. * * @return The test suite */ @Test public void testIsotopeContainer_double_double() { double mass = 130.00; double intensity = 500000.00; IsotopeContainer isoC = new IsotopeContainer(mass, intensity); Assert.assertNotNull(isoC); Assert.assertEquals(mass, isoC.getMass(), 0.001); Assert.assertEquals(intensity, isoC.getIntensity(), 0.001); }
for (IsotopeContainer other : additional) { double abundance = container.getIntensity() * other.getIntensity() * 0.01; double mass = container.getMass() + other.getMass(); double newIntensity = existing.getIntensity() + abundance; existing.setMass((existing.getMass()*existing.getIntensity() + mass*abundance) / newIntensity); existing.setIntensity(newIntensity); if (storeFormula) { for (IMolecularFormula mf : container.getFormulas()) addDistinctFormula(existing, union(mf, other.getFormula())); IsotopeContainer newcontainer = new IsotopeContainer(mass, abundance); if (storeFormula) { for (IMolecularFormula mf : container.getFormulas()) newcontainer.addFormula(union(mf, other.getFormula()));
/** * A unit test suite for JUnit. * * @return The test suite */ @Test public void testGetIntensity() { IsotopeContainer isoC = new IsotopeContainer(); double intensity = 130.00; isoC.setIntensity(intensity); Assert.assertEquals(intensity, isoC.getIntensity(), 0.001); }
double mass = isoC.getMass(); isoC.setMass(mass + chargeToAdd); factor = isoContainer.getIntensity(); totalFactor += factor; if (closestDp == -1) continue; diffMass = isoContainer.getMass() - iso2.getIsotopes().get(closestDp).getMass(); diffMass = Math.abs(diffMass); diffAbun = 1.0d - (isoContainer.getIntensity() / iso2.getIsotopes().get(closestDp).getIntensity()); diffAbun = Math.abs(diffAbun);
/** * A unit test suite for JUnit. * * @return The test suite */ @Test public void testGetMass() { IsotopeContainer isoC = new IsotopeContainer(); double mass = 130.00; isoC.setMass(mass); Assert.assertEquals(mass, isoC.getMass(), 0.001); }
double abundance = isoContainer.getIntensity(); if (biggestAbundance < abundance) { biggestAbundance = abundance; double inten = isoContainer.getIntensity() / isoHighest.getIntensity(); IsotopeContainer icClone; try { icClone = (IsotopeContainer) isoContainer.clone(); icClone.setIntensity(inten); if (isoHighest.equals(isoContainer)) isoNormalized.setMonoIsotope(icClone);
/** * A unit test suite for JUnit. * * @return The test suite */ @Test public void testIsotopeContainer_IMolecularFormula_double() { IMolecularFormula formula = builder.newInstance(IMolecularFormula.class); double intensity = 130.00; IsotopeContainer isoC = new IsotopeContainer(formula, intensity); Assert.assertNotNull(isoC); Assert.assertEquals(formula, isoC.getFormula()); Assert.assertEquals(intensity, isoC.getIntensity(), 0.001); }
/** * A unit test suite for JUnit. * * @return The test suite */ @Test public void testGetFormula() { IsotopeContainer isoC = new IsotopeContainer(); IMolecularFormula formula = builder.newInstance(IMolecularFormula.class); isoC.setFormula(formula); Assert.assertEquals(formula, isoC.getFormula()); }
/** * A unit test suite for JUnit. * * @return The test suite */ @Test public void testIsotopeContainer() { IsotopeContainer isoC = new IsotopeContainer(); Assert.assertNotNull(isoC); }
/** * A unit test suite for JUnit. * * @return The test suite */ @Test public void testSetFormula_IMolecularFormula() { IsotopeContainer isoC = new IsotopeContainer(); IMolecularFormula formula = builder.newInstance(IMolecularFormula.class); isoC.setFormula(formula); Assert.assertNotNull(isoC); }
@Override public int compare(IsotopeContainer o1, IsotopeContainer o2) { return Double.compare(o2.getIntensity(),o1.getIntensity()); } });
/** * A unit test suite for JUnit. * * @return The test suite */ @Test public void testSetIntensity_double() { IsotopeContainer isoC = new IsotopeContainer(); isoC.setIntensity(5000000.0); Assert.assertNotNull(isoC); }
/** * A unit test suite for JUnit. * * @return The test suite */ @Test public void testSetMass_double() { IsotopeContainer isoC = new IsotopeContainer(); isoC.setMass(130.00); Assert.assertNotNull(isoC); }
/** * Pretty-print the MFs of this isotope container. * @return the MFs */ String getFormulasString() { StringBuilder sb = new StringBuilder(); for (IMolecularFormula mf : getFormulas()) { if (sb.length() != 0) sb.append(", "); sb.append(MolecularFormulaManipulator.getString(mf, false, true)); } return sb.toString(); }
/** * Clones this IsotopePattern object and its content. * * @return The cloned object */ @Override public Object clone() throws CloneNotSupportedException { IsotopePattern isoClone = new IsotopePattern(); IsotopeContainer isoHighest = getMonoIsotope(); for (IsotopeContainer isoContainer : isotopeCList) { if (isoHighest.equals(isoContainer)) isoClone.setMonoIsotope((IsotopeContainer) isoContainer.clone()); else isoClone.addIsotope((IsotopeContainer) isoContainer.clone()); } isoClone.setCharge(getCharge()); return isoClone; } }