/** * 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; } }
/** * A unit test suite for JUnit. * * @return The test suite */ @Test public void testGetMonoIsotope() { IsotopePattern isoP = new IsotopePattern(); IsotopeContainer isoC = new IsotopeContainer(); isoP.setMonoIsotope(isoC); Assert.assertEquals(isoC, isoP.getMonoIsotope()); }
/** * Junit test * * @throws Exception */ @Test public void testSortByIntensity_IsotopePattern() { IsotopePattern spExp = new IsotopePattern(); spExp.setMonoIsotope(new IsotopeContainer(157.07503, 0.0001)); spExp.addIsotope(new IsotopeContainer(156.07770, 1)); spExp.addIsotope(new IsotopeContainer(157.08059, 0.0003)); spExp.addIsotope(new IsotopeContainer(158.08135, 0.002)); spExp.setCharge(1); IsotopePattern isoNorma = IsotopePatternManipulator.sortByIntensity(spExp); List<IsotopeContainer> listISO = isoNorma.getIsotopes(); Assert.assertEquals(156.07770, isoNorma.getMonoIsotope().getMass(), 0.00001); Assert.assertEquals(156.07770, listISO.get(0).getMass(), 0.00001); Assert.assertEquals(158.08135, listISO.get(1).getMass(), 0.00001); Assert.assertEquals(157.08059, listISO.get(2).getMass(), 0.00001); Assert.assertEquals(157.07503, listISO.get(3).getMass(), 0.00001); Assert.assertEquals(1, isoNorma.getMonoIsotope().getIntensity(), 0.00001); Assert.assertEquals(1, listISO.get(0).getIntensity(), 0.00001); Assert.assertEquals(0.002, listISO.get(1).getIntensity(), 0.00001); Assert.assertEquals(0.0003, listISO.get(2).getIntensity(), 0.001); Assert.assertEquals(0.0001, listISO.get(3).getIntensity(), 0.00001); Assert.assertEquals(1, isoNorma.getCharge(), 0.00001); }
Assert.assertEquals(156.07770, isoNorma.getMonoIsotope().getMass(), 0.001); Assert.assertEquals(156.07770, listISO.get(0).getMass(), 0.00001); Assert.assertEquals(157.07503, listISO.get(1).getMass(), 0.00001); Assert.assertEquals(158.08135, listISO.get(3).getMass(), 0.00001); Assert.assertEquals(2, isoNorma.getMonoIsotope().getIntensity(), 0.001); Assert.assertEquals(2, listISO.get(0).getIntensity(), 0.001); Assert.assertEquals(0.0002, listISO.get(1).getIntensity(), 0.00001);
/** * Junit test * * @throws Exception */ @Test public void testSortAndNormalizedByIntensity_IsotopePattern() { IsotopePattern spExp = new IsotopePattern(); spExp.addIsotope(new IsotopeContainer(157.07503, 0.0002)); spExp.setMonoIsotope(new IsotopeContainer(156.07770, 2)); spExp.addIsotope(new IsotopeContainer(158.08135, 0.004)); spExp.addIsotope(new IsotopeContainer(157.08059, 0.0006)); spExp.setCharge(1); IsotopePattern isoNorma = IsotopePatternManipulator.sortAndNormalizedByIntensity(spExp); List<IsotopeContainer> listISO = isoNorma.getIsotopes(); Assert.assertEquals(156.07770, isoNorma.getMonoIsotope().getMass(), 0.00001); Assert.assertEquals(156.07770, listISO.get(0).getMass(), 0.00001); Assert.assertEquals(158.08135, listISO.get(1).getMass(), 0.00001); Assert.assertEquals(157.08059, listISO.get(2).getMass(), 0.00001); Assert.assertEquals(157.07503, listISO.get(3).getMass(), 0.00001); Assert.assertEquals(1, isoNorma.getMonoIsotope().getIntensity(), 0.00001); Assert.assertEquals(1, listISO.get(0).getIntensity(), 0.00001); Assert.assertEquals(0.002, listISO.get(1).getIntensity(), 0.00001); Assert.assertEquals(0.0003, listISO.get(2).getIntensity(), 0.00001); Assert.assertEquals(0.0001, listISO.get(3).getIntensity(), 0.00001); Assert.assertEquals(1, isoNorma.getCharge(), 0.001); }
/** * Junit test * * @throws Exception */ @Test public void testNormalize_IsotopePattern() { IsotopePattern spExp = new IsotopePattern(); spExp.setMonoIsotope(new IsotopeContainer(156.07770, 2)); spExp.addIsotope(new IsotopeContainer(157.08059, 0.0006)); spExp.addIsotope(new IsotopeContainer(157.07503, 0.0002)); spExp.addIsotope(new IsotopeContainer(158.08135, 0.004)); spExp.setCharge(1); IsotopePattern isoNorma = IsotopePatternManipulator.normalize(spExp); List<IsotopeContainer> listISO = isoNorma.getIsotopes(); Assert.assertEquals(1, isoNorma.getMonoIsotope().getIntensity(), 0.00001); Assert.assertEquals(1, listISO.get(0).getIntensity(), 0.00001); Assert.assertEquals(0.0003, listISO.get(1).getIntensity(), 0.00001); Assert.assertEquals(0.0001, listISO.get(2).getIntensity(), 0.00001); Assert.assertEquals(0.002, listISO.get(3).getIntensity(), 0.00001); Assert.assertEquals(156.07770, isoNorma.getMonoIsotope().getMass(), 0.00001); Assert.assertEquals(156.07770, listISO.get(0).getMass(), 0.00001); Assert.assertEquals(157.08059, listISO.get(1).getMass(), 0.00001); Assert.assertEquals(157.07503, listISO.get(2).getMass(), 0.00001); Assert.assertEquals(158.08135, listISO.get(3).getMass(), 0.00001); Assert.assertEquals(1, isoNorma.getCharge(), 0.00001); }
/** * A unit test suite for JUnit. * * @return The test suite */ @Test public void testClone() throws Exception { IsotopePattern spExp = new IsotopePattern(); spExp.setMonoIsotope(new IsotopeContainer(156.07770, 1)); spExp.addIsotope(new IsotopeContainer(157.07503, 0.0004)); spExp.addIsotope(new IsotopeContainer(157.08059, 0.0003)); spExp.addIsotope(new IsotopeContainer(158.08135, 0.002)); spExp.setCharge(1); IsotopePattern clone = (IsotopePattern) spExp.clone(); Assert.assertEquals(156.07770, clone.getMonoIsotope().getMass(), 0.001); Assert.assertEquals(156.07770, clone.getIsotopes().get(0).getMass(), 0.001); Assert.assertEquals(157.07503, clone.getIsotopes().get(1).getMass(), 0.001); Assert.assertEquals(157.08059, clone.getIsotopes().get(2).getMass(), 0.001); Assert.assertEquals(158.08135, clone.getIsotopes().get(3).getMass(), 0.001); Assert.assertEquals(1, clone.getMonoIsotope().getIntensity(), 0.001); Assert.assertEquals(1, clone.getIsotopes().get(0).getIntensity(), 0.001); Assert.assertEquals(0.0004, clone.getIsotopes().get(1).getIntensity(), 0.001); Assert.assertEquals(0.0003, clone.getIsotopes().get(2).getIntensity(), 0.001); Assert.assertEquals(0.002, clone.getIsotopes().get(3).getIntensity(), 0.001); Assert.assertEquals(1, clone.getCharge(), 0.001); }