b9ccfe58b6859ca839c2aef74c190c39948d306e,src/test/java/com/compomics/util/test/experiment/FragmentFactoryTest.java,FragmentFactoryTest,testTagFragmentation,#,375

Before Change


                        }
                    }

                } else if (tagFragmentIon.getNeutralLosses().size() == 1
                        && tagFragmentIon.getNeutralLosses().get(0).isSameAs(NeutralLoss.H2O)) {
                    if (tagFragmentIon.getNumber() == 3) {
                        if (tagFragmentIon.getSubType() == PeptideFragmentIon.B_ION) {
                            Assert.assertTrue(
                                    Math.abs(tagFragmentIon.getTheoreticMass() + protonMass - 272.0700) < tolerance);
                        }
                    } else if (tagFragmentIon.getNumber() == 4) {
                        if (tagFragmentIon.getSubType() == PeptideFragmentIon.B_ION) {
                            Assert.assertTrue(
                                    Math.abs(tagFragmentIon.getTheoreticMass() + protonMass - 401.1125) < tolerance);
                        } else if (tagFragmentIon.getSubType() == PeptideFragmentIon.Y_ION) {
                            Assert.assertTrue(
                                    Math.abs(tagFragmentIon.getTheoreticMass() + protonMass - 550.2660) < tolerance);
                        }
                    } else if (tagFragmentIon.getNumber() == 5) {
                        if (tagFragmentIon.getSubType() == PeptideFragmentIon.B_ION) {
                            Assert.assertTrue(
                                    Math.abs(tagFragmentIon.getTheoreticMass() + protonMass - 548.1810) < tolerance);
                        } else if (tagFragmentIon.getSubType() == PeptideFragmentIon.Y_ION) {
                            Assert.assertTrue(
                                    Math.abs(tagFragmentIon.getTheoreticMass() + protonMass - 637.2980) < tolerance);
                        }
                    } else if (tagFragmentIon.getNumber() == 6) {
                        if (tagFragmentIon.getSubType() == PeptideFragmentIon.B_ION) {
                            Assert.assertTrue(
                                    Math.abs(tagFragmentIon.getTheoreticMass() + protonMass - 605.2024) < tolerance);
                        } else if (tagFragmentIon.getSubType() == PeptideFragmentIon.Y_ION) {
                            Assert.assertTrue(
                                    Math.abs(tagFragmentIon.getTheoreticMass() + protonMass - 793.3991) < tolerance);
                        }
                    } else if (tagFragmentIon.getNumber() == 7) {
                        if (tagFragmentIon.getSubType() == PeptideFragmentIon.B_ION) {
                            Assert.assertTrue(
                                    Math.abs(tagFragmentIon.getTheoreticMass() + protonMass - 742.2613) < tolerance);
                        } else if (tagFragmentIon.getSubType() == PeptideFragmentIon.Y_ION) {
                            Assert.assertTrue(
                                    Math.abs(tagFragmentIon.getTheoreticMass() + protonMass - 921.4517) < tolerance);
                        }
                    } else if (tagFragmentIon.getNumber() == 8) {
                        if (tagFragmentIon.getSubType() == PeptideFragmentIon.B_ION) {
                            Assert.assertTrue(
                                    Math.abs(tagFragmentIon.getTheoreticMass() + protonMass - 855.3454) < tolerance);
                        } else if (tagFragmentIon.getSubType() == PeptideFragmentIon.Y_ION) {
                            Assert.assertTrue(
                                    Math.abs(tagFragmentIon.getTheoreticMass() + protonMass - 1018.5105) < tolerance);
                        }
                    } else if (tagFragmentIon.getNumber() == 9) {
                        if (tagFragmentIon.getSubType() == PeptideFragmentIon.B_ION) {
                            Assert.assertTrue(
                                    Math.abs(tagFragmentIon.getTheoreticMass() + protonMass - 983.4404) < tolerance);
                        } else if (tagFragmentIon.getSubType() == PeptideFragmentIon.Y_ION) {
                            Assert.assertTrue(
                                    Math.abs(tagFragmentIon.getTheoreticMass() + protonMass - 1132.5534) < tolerance);
                        }
                    } else if (tagFragmentIon.getNumber() == 10) {
                        if (tagFragmentIon.getSubType() == PeptideFragmentIon.B_ION) {
                            Assert.assertTrue(
                                    Math.abs(tagFragmentIon.getTheoreticMass() + protonMass - 1096.5244) < tolerance);
                        } else if (tagFragmentIon.getSubType() == PeptideFragmentIon.Y_ION) {
                            Assert.assertTrue(
                                    Math.abs(tagFragmentIon.getTheoreticMass() + protonMass - 1263.5939) < tolerance);
                        }
                    }
                } else if (tagFragmentIon.getNeutralLosses().size() == 1
                        && tagFragmentIon.getNeutralLosses().get(0).isSameAs(NeutralLoss.NH3)) {
                    if (tagFragmentIon.getNumber() == 6) {
                        if (tagFragmentIon.getSubType() == PeptideFragmentIon.Y_ION) {
                            Assert.assertTrue(

After Change


                        }
                    }

                } else if (tagFragmentIon.getNeutralLosses().length == 1
                        && tagFragmentIon.getNeutralLosses()[0].isSameAs(NeutralLoss.H2O)) {
                    if (tagFragmentIon.getNumber() == 3) {
                        if (tagFragmentIon.getSubType() == PeptideFragmentIon.B_ION) {
                            Assert.assertTrue(
                                    Math.abs(tagFragmentIon.getTheoreticMass() + protonMass - 272.0700) < tolerance);
                        }
                    } else if (tagFragmentIon.getNumber() == 4) {
                        if (tagFragmentIon.getSubType() == PeptideFragmentIon.B_ION) {
                            Assert.assertTrue(
                                    Math.abs(tagFragmentIon.getTheoreticMass() + protonMass - 401.1125) < tolerance);
                        } else if (tagFragmentIon.getSubType() == PeptideFragmentIon.Y_ION) {
                            Assert.assertTrue(
                                    Math.abs(tagFragmentIon.getTheoreticMass() + protonMass - 550.2660) < tolerance);
                        }
                    } else if (tagFragmentIon.getNumber() == 5) {
                        if (tagFragmentIon.getSubType() == PeptideFragmentIon.B_ION) {
                            Assert.assertTrue(
                                    Math.abs(tagFragmentIon.getTheoreticMass() + protonMass - 548.1810) < tolerance);
                        } else if (tagFragmentIon.getSubType() == PeptideFragmentIon.Y_ION) {
                            Assert.assertTrue(
                                    Math.abs(tagFragmentIon.getTheoreticMass() + protonMass - 637.2980) < tolerance);
                        }
                    } else if (tagFragmentIon.getNumber() == 6) {
                        if (tagFragmentIon.getSubType() == PeptideFragmentIon.B_ION) {
                            Assert.assertTrue(
                                    Math.abs(tagFragmentIon.getTheoreticMass() + protonMass - 605.2024) < tolerance);
                        } else if (tagFragmentIon.getSubType() == PeptideFragmentIon.Y_ION) {
                            Assert.assertTrue(
                                    Math.abs(tagFragmentIon.getTheoreticMass() + protonMass - 793.3991) < tolerance);
                        }
                    } else if (tagFragmentIon.getNumber() == 7) {
                        if (tagFragmentIon.getSubType() == PeptideFragmentIon.B_ION) {
                            Assert.assertTrue(
                                    Math.abs(tagFragmentIon.getTheoreticMass() + protonMass - 742.2613) < tolerance);
                        } else if (tagFragmentIon.getSubType() == PeptideFragmentIon.Y_ION) {
                            Assert.assertTrue(
                                    Math.abs(tagFragmentIon.getTheoreticMass() + protonMass - 921.4517) < tolerance);
                        }
                    } else if (tagFragmentIon.getNumber() == 8) {
                        if (tagFragmentIon.getSubType() == PeptideFragmentIon.B_ION) {
                            Assert.assertTrue(
                                    Math.abs(tagFragmentIon.getTheoreticMass() + protonMass - 855.3454) < tolerance);
                        } else if (tagFragmentIon.getSubType() == PeptideFragmentIon.Y_ION) {
                            Assert.assertTrue(
                                    Math.abs(tagFragmentIon.getTheoreticMass() + protonMass - 1018.5105) < tolerance);
                        }
                    } else if (tagFragmentIon.getNumber() == 9) {
                        if (tagFragmentIon.getSubType() == PeptideFragmentIon.B_ION) {
                            Assert.assertTrue(
                                    Math.abs(tagFragmentIon.getTheoreticMass() + protonMass - 983.4404) < tolerance);
                        } else if (tagFragmentIon.getSubType() == PeptideFragmentIon.Y_ION) {
                            Assert.assertTrue(
                                    Math.abs(tagFragmentIon.getTheoreticMass() + protonMass - 1132.5534) < tolerance);
                        }
                    } else if (tagFragmentIon.getNumber() == 10) {
                        if (tagFragmentIon.getSubType() == PeptideFragmentIon.B_ION) {
                            Assert.assertTrue(
                                    Math.abs(tagFragmentIon.getTheoreticMass() + protonMass - 1096.5244) < tolerance);
                        } else if (tagFragmentIon.getSubType() == PeptideFragmentIon.Y_ION) {
                            Assert.assertTrue(
                                    Math.abs(tagFragmentIon.getTheoreticMass() + protonMass - 1263.5939) < tolerance);
                        }
                    }
                } else if (tagFragmentIon.getNeutralLosses().length == 1
                        && tagFragmentIon.getNeutralLosses()[0].isSameAs(NeutralLoss.NH3)) {
                    if (tagFragmentIon.getNumber() == 6) {
                        if (tagFragmentIon.getSubType() == PeptideFragmentIon.Y_ION) {
                            Assert.assertTrue(