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);
}
}