private void shift_masses() { List <DeltaMassPeak> peaks_to_shift = Sweet.lollipop.et_peaks.Where(p => p.mass_shifter != "0" && p.mass_shifter != "").ToList(); if (peaks_to_shift.Count > 0) { //before making shifts, make sure all mass shifters are integers foreach (DeltaMassPeak peak in peaks_to_shift) { if (!Int32.TryParse(peak.mass_shifter, out int ok)) { MessageBox.Show("Could not convert mass shift for peak at delta mass " + peak.DeltaMass + ". Please enter an integer."); return; } } foreach (DeltaMassPeak peak in peaks_to_shift) { int int_mass_shifter = Convert.ToInt32(peak.mass_shifter); peak.shift_experimental_masses(int_mass_shifter, Sweet.lollipop.neucode_labeled); Sweet.shift_peak_action(peak); } ((ProteoformSweet)this.MDIParent).rawExperimentalComponents.FillTablesAndCharts(); if (Sweet.lollipop.neucode_labeled) { Sweet.lollipop.raw_neucode_pairs.Clear(); Sweet.lollipop.process_neucode_components(Sweet.lollipop.raw_neucode_pairs); ((ProteoformSweet)this.MDIParent).neuCodePairs.FillTablesAndCharts(); } ((ProteoformSweet)this.MDIParent).aggregatedProteoforms.RunTheGamut(false); //RunTheGamut(false); //will need to rerun the Gamut if peaks shifted from preset. } }
public void shift_et_peak_neucode_from_actions() { Sweet.lollipop = new Lollipop(); ProteoformCommunity test_community = new ProteoformCommunity(); Sweet.lollipop.target_proteoform_community = test_community; //Make a few experimental proteoforms List <IAggregatable> n1 = TestExperimentalProteoform.generate_neucode_components(100); List <IAggregatable> n2 = TestExperimentalProteoform.generate_neucode_components(100); List <IAggregatable> n3 = TestExperimentalProteoform.generate_neucode_components(200); List <IAggregatable> n4 = TestExperimentalProteoform.generate_neucode_components(200); ExperimentalProteoform pf1 = ConstructorsForTesting.ExperimentalProteoform("E1"); pf1.aggregated = n1; ExperimentalProteoform pf2 = ConstructorsForTesting.ExperimentalProteoform("E2"); pf2.aggregated = n2; ExperimentalProteoform pf3 = ConstructorsForTesting.ExperimentalProteoform("E3"); pf3.aggregated = n3; ExperimentalProteoform pf4 = ConstructorsForTesting.ExperimentalProteoform("E4"); pf4.aggregated = n4; Sweet.lollipop.target_proteoform_community.experimental_proteoforms = new List <ExperimentalProteoform> { pf1, pf2, pf3, pf4 }.ToArray(); //Connect them to theoreticals to form two peaks ProteoformComparison comparison14 = ProteoformComparison.ExperimentalTheoretical; ProteoformComparison comparison25 = ProteoformComparison.ExperimentalTheoretical; ProteoformComparison comparison36 = ProteoformComparison.ExperimentalTheoretical; ProteoformComparison comparison47 = ProteoformComparison.ExperimentalTheoretical; TheoreticalProteoform pf5 = ConstructorsForTesting.make_a_theoretical(); TheoreticalProteoform pf6 = ConstructorsForTesting.make_a_theoretical(); TheoreticalProteoform pf7 = ConstructorsForTesting.make_a_theoretical(); TheoreticalProteoform pf8 = ConstructorsForTesting.make_a_theoretical(); ProteoformRelation pr1 = new ProteoformRelation(pf1, pf5, comparison14, 0, TestContext.CurrentContext.TestDirectory); ProteoformRelation pr2 = new ProteoformRelation(pf2, pf6, comparison25, 0, TestContext.CurrentContext.TestDirectory); ProteoformRelation pr3 = new ProteoformRelation(pf3, pf7, comparison36, 1, TestContext.CurrentContext.TestDirectory); ProteoformRelation pr4 = new ProteoformRelation(pf4, pf8, comparison47, 1, TestContext.CurrentContext.TestDirectory); List <ProteoformRelation> prs = new List <ProteoformRelation> { pr1, pr2, pr3, pr4 }; foreach (ProteoformRelation pr in prs) { pr.set_nearby_group(prs, prs.Select(r => r.InstanceId).ToList()); } test_community.accept_deltaMass_peaks(prs, new List <ProteoformRelation>()); Assert.AreEqual(2, Sweet.lollipop.et_peaks.Count); //Shift the peaks, which shifts all of the proteoforms DeltaMassPeak d2 = Sweet.lollipop.et_peaks[1]; d2.mass_shifter = "-1"; Sweet.shift_peak_action(d2); d2.mass_shifter = null; using (StreamWriter file = new StreamWriter(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"))) file.WriteLine(Sweet.save_method()); Sweet.open_method(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"), string.Join(Environment.NewLine, File.ReadAllLines(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"))), true, out string warning); Sweet.mass_shifts_from_presets(); d2.shift_experimental_masses(Convert.ToInt32(d2.mass_shifter), true); foreach (Component c in n3.OfType <NeuCodePair>().Select(n => n.neuCodeLight). Concat(n4.OfType <NeuCodePair>().Select(n => n.neuCodeLight))) { Assert.AreEqual(-1.0 * Lollipop.MONOISOTOPIC_UNIT_MASS, c.manual_mass_shift); Assert.AreEqual(200 - 1.0 * Lollipop.MONOISOTOPIC_UNIT_MASS, c.weighted_monoisotopic_mass); } foreach (Component c in n3.OfType <NeuCodePair>().Select(n => n.neuCodeHeavy). Concat(n4.OfType <NeuCodePair>().Select(n => n.neuCodeHeavy))) { Assert.AreEqual(-1.0 * Lollipop.MONOISOTOPIC_UNIT_MASS, c.manual_mass_shift); Assert.AreEqual(200 + TestExperimentalProteoform.starter_lysine_count * Lollipop.NEUCODE_LYSINE_MASS_SHIFT - 1.0 * Lollipop.MONOISOTOPIC_UNIT_MASS, c.weighted_monoisotopic_mass); } }