public void full_agg()
{
double max_monoisotopic_mass = TestExperimentalProteoform.starter_mass + TestExperimentalProteoform.missed_monoisotopics * Lollipop.MONOISOTOPIC_UNIT_MASS;
double min_monoisotopic_mass = TestExperimentalProteoform.starter_mass - TestExperimentalProteoform.missed_monoisotopics * Lollipop.MONOISOTOPIC_UNIT_MASS;
IEnumerable <NeuCodePair> neucodes = TestExperimentalProteoform.generate_neucode_components(TestExperimentalProteoform.starter_mass).OfType <NeuCodePair>();
List <Component> components = neucodes.Select(nc => nc.neuCodeLight).Concat(neucodes.Select(nc => nc.neuCodeHeavy)).ToList();
List <Component> quant_components = TestExperimentalProteoform.generate_neucode_quantitative_components();
//Must use Sweet.lol.remaining_components because ThreadStart only uses void methods
//Must use Sweet.lol.remaining_components because ThreadStart only uses void methods
Sweet.lollipop.neucode_labeled = true;
Sweet.lollipop.input_files = new List <InputFile> {
new InputFile("fake.txt", Purpose.Quantification)
};
List <ExperimentalProteoform> vetted_quant = Sweet.lollipop.aggregate_proteoforms(true, neucodes, components, quant_components, 0);
Assert.AreEqual(1, vetted_quant.Count);
Assert.AreEqual(2, vetted_quant[0].aggregated.Count);
Assert.AreEqual(2, vetted_quant[0].lt_verification_components.Count);
Assert.AreEqual(2, vetted_quant[0].hv_verification_components.Count);
Assert.AreEqual(1, vetted_quant[0].lt_quant_components.Count);
Assert.AreEqual(1, vetted_quant[0].hv_quant_components.Count);
Assert.AreEqual(2, quant_components.Count);
Assert.AreEqual(0, Sweet.lollipop.remaining_quantification_components.Count);
}
public void create_proteoforms_in_bounds_monoisotopic_tolerance()
{
double max_monoisotopic_mass = TestExperimentalProteoform.starter_mass + TestExperimentalProteoform.missed_monoisotopics * Lollipop.MONOISOTOPIC_UNIT_MASS;
double min_monoisotopic_mass = TestExperimentalProteoform.starter_mass - TestExperimentalProteoform.missed_monoisotopics * Lollipop.MONOISOTOPIC_UNIT_MASS;
List <IAggregatable> components = TestExperimentalProteoform.generate_neucode_components(TestExperimentalProteoform.starter_mass);
Sweet.lollipop.neucode_labeled = true;
List <ExperimentalProteoform> pfs = Sweet.lollipop.createProteoforms(components.OfType <NeuCodePair>(), components.OfType <Component>(), 0);
Assert.AreEqual(1, pfs.Count);
Assert.AreEqual(2, pfs[0].aggregated.Count);
Assert.AreEqual(2, components.Count);
Assert.AreEqual(0, Sweet.lollipop.remaining_to_aggregate.Count);
}
public void assign_quant_components_in_bounds_monoisotopic_tolerance()
{
double max_monoisotopic_mass = TestExperimentalProteoform.starter_mass + TestExperimentalProteoform.missed_monoisotopics * Lollipop.MONOISOTOPIC_UNIT_MASS;
double min_monoisotopic_mass = TestExperimentalProteoform.starter_mass - TestExperimentalProteoform.missed_monoisotopics * Lollipop.MONOISOTOPIC_UNIT_MASS;
IEnumerable <NeuCodePair> neucodes = TestExperimentalProteoform.generate_neucode_components(TestExperimentalProteoform.starter_mass).OfType <NeuCodePair>();
List <Component> quant_components = TestExperimentalProteoform.generate_neucode_quantitative_components();
// in bounds lowest monoisotopic error
SaveState.lollipop.neucode_labeled = true;
List <ExperimentalProteoform> pfs = SaveState.lollipop.createProteoforms(neucodes, neucodes, 0);
List <ExperimentalProteoform> vetted_quant = SaveState.lollipop.assignQuantificationComponents(pfs, quant_components);
Assert.AreEqual(1, vetted_quant.Count);
Assert.AreEqual(2, vetted_quant[0].aggregated_components.Count);
Assert.AreEqual(1, vetted_quant[0].lt_quant_components.Count);
Assert.AreEqual(1, vetted_quant[0].hv_quant_components.Count);
Assert.AreEqual(2, quant_components.Count);
Assert.AreEqual(0, SaveState.lollipop.remaining_quantification_components.Count);
}
public void vet_proteoforms_in_bounds_monoisotopic_tolerance()
{
double max_monoisotopic_mass = TestExperimentalProteoform.starter_mass + TestExperimentalProteoform.missed_monoisotopics * Lollipop.MONOISOTOPIC_UNIT_MASS;
double min_monoisotopic_mass = TestExperimentalProteoform.starter_mass - TestExperimentalProteoform.missed_monoisotopics * Lollipop.MONOISOTOPIC_UNIT_MASS;
IEnumerable <NeuCodePair> neucodes = TestExperimentalProteoform.generate_neucode_components(TestExperimentalProteoform.starter_mass).OfType <NeuCodePair>();
List <Component> components = neucodes.Select(nc => nc.neuCodeLight).Concat(neucodes.Select(nc => nc.neuCodeHeavy)).ToList();
// in bounds lowest monoisotopic error
Sweet.lollipop.neucode_labeled = true;
List <ExperimentalProteoform> pfs = Sweet.lollipop.createProteoforms(neucodes, components, 0);
List <ExperimentalProteoform> vetted = Sweet.lollipop.vetExperimentalProteoforms(pfs, components, new List <ExperimentalProteoform>());
Assert.AreEqual(1, vetted.Count);
Assert.AreEqual(2, vetted[0].aggregated.Count);
Assert.AreEqual(2, vetted[0].lt_verification_components.Count);
Assert.AreEqual(2, vetted[0].hv_verification_components.Count);
Assert.AreEqual(4, components.Count);
Assert.AreEqual(0, Sweet.lollipop.remaining_verification_components.Count);
}
public void unlabeled_agg()
{
double max_monoisotopic_mass = TestExperimentalProteoform.starter_mass + TestExperimentalProteoform.missed_monoisotopics * Lollipop.MONOISOTOPIC_UNIT_MASS;
double min_monoisotopic_mass = TestExperimentalProteoform.starter_mass - TestExperimentalProteoform.missed_monoisotopics * Lollipop.MONOISOTOPIC_UNIT_MASS;
List <IAggregatable> components = TestExperimentalProteoform.generate_unlabeled_components(TestExperimentalProteoform.starter_mass);
Sweet.lollipop.neucode_labeled = false;
Sweet.lollipop.remaining_to_aggregate = new List <IAggregatable>(components);
Sweet.lollipop.remaining_verification_components = new HashSet <Component>(components.OfType <Component>());
Sweet.lollipop.missed_monoisotopics_range = Enumerable.Range(-3, 3 * 2 + 1).ToList();
ExperimentalProteoform e = ConstructorsForTesting.ExperimentalProteoform("E");
e.root = components[0];
e.aggregate();
e.verify();
Assert.AreEqual(2, e.aggregated.Count);
Assert.AreEqual(2, e.lt_verification_components.Count);
Assert.AreEqual(0, e.hv_verification_components.Count); // everything goes into light with unlabeled
Assert.AreEqual(0, e.lt_quant_components.Count); // no quantitation for unlabeled, yet
Assert.AreEqual(0, e.hv_quant_components.Count);
}
public void unlabeled_agg()
{
SaveState.lollipop.min_num_bioreps = 0;
double max_monoisotopic_mass = TestExperimentalProteoform.starter_mass + TestExperimentalProteoform.missed_monoisotopics * Lollipop.MONOISOTOPIC_UNIT_MASS;
double min_monoisotopic_mass = TestExperimentalProteoform.starter_mass - TestExperimentalProteoform.missed_monoisotopics * Lollipop.MONOISOTOPIC_UNIT_MASS;
List <Component> components = TestExperimentalProteoform.generate_unlabeled_components(TestExperimentalProteoform.starter_mass);
SaveState.lollipop.neucode_labeled = false;
SaveState.lollipop.remaining_components = new List <Component>(components);
SaveState.lollipop.remaining_verification_components = new List <Component>(components);
ExperimentalProteoform e = ConstructorsForTesting.ExperimentalProteoform("E");
e.root = components[0];
e.aggregate();
e.verify();
Assert.AreEqual(2, e.aggregated_components.Count);
Assert.AreEqual(2, e.lt_verification_components.Count);
Assert.AreEqual(0, e.hv_verification_components.Count); // everything goes into light with unlabeled
Assert.AreEqual(0, e.lt_quant_components.Count); // no quantitation for unlabeled, yet
Assert.AreEqual(0, e.hv_quant_components.Count);
}
public void full_agg_without_validation()
{
double max_monoisotopic_mass = TestExperimentalProteoform.starter_mass + TestExperimentalProteoform.missed_monoisotopics * Lollipop.MONOISOTOPIC_UNIT_MASS;
double min_monoisotopic_mass = TestExperimentalProteoform.starter_mass - TestExperimentalProteoform.missed_monoisotopics * Lollipop.MONOISOTOPIC_UNIT_MASS;
IEnumerable <NeuCodePair> neucodes = TestExperimentalProteoform.generate_neucode_components(TestExperimentalProteoform.starter_mass).OfType <NeuCodePair>();
List <Component> components = neucodes.Select(nc => nc.neuCodeLight).Concat(neucodes.Select(nc => nc.neuCodeHeavy)).ToList();
List <Component> quant_components = TestExperimentalProteoform.generate_neucode_quantitative_components();
//Must use Sweet.lol.remaining_components because ThreadStart only uses void methods
Sweet.lollipop.neucode_labeled = true;
Sweet.lollipop.decoy_proteoform_communities = new Dictionary <string, ProteoformCommunity> {
{ "1", new ProteoformCommunity() }
};
Sweet.lollipop.input_files = new List <InputFile> {
new InputFile("fake.txt", Purpose.Quantification)
};
List <ExperimentalProteoform> vetted_quant = Sweet.lollipop.aggregate_proteoforms(false, neucodes, components, quant_components, 0);
Assert.AreEqual(1, vetted_quant.Count);
Assert.AreEqual(1, Sweet.lollipop.decoy_proteoform_communities.First().Value.experimental_proteoforms.Length);
Assert.AreEqual(2, vetted_quant[0].aggregated.Count);
Assert.AreEqual(0, vetted_quant[0].lt_verification_components.Count);
Assert.AreEqual(0, vetted_quant[0].hv_verification_components.Count);
Assert.AreEqual(1, vetted_quant[0].lt_quant_components.Count);
Assert.AreEqual(1, vetted_quant[0].hv_quant_components.Count);
Assert.AreEqual(2, quant_components.Count);
Assert.AreEqual(0, Sweet.lollipop.remaining_quantification_components.Count);
Sweet.lollipop.clear_aggregation();
Assert.True(Sweet.lollipop.decoy_proteoform_communities.All(x => x.Value.experimental_proteoforms.Length == 0));
Assert.IsEmpty(Sweet.lollipop.target_proteoform_community.experimental_proteoforms);
Assert.IsEmpty(Sweet.lollipop.remaining_to_aggregate);
Assert.IsEmpty(Sweet.lollipop.remaining_quantification_components);
Assert.IsEmpty(Sweet.lollipop.remaining_verification_components);
}
public void shift_et_peak_unlabeled()
{
Sweet.lollipop = new Lollipop();
ProteoformCommunity test_community = new ProteoformCommunity();
Sweet.lollipop.target_proteoform_community = test_community;
Sweet.lollipop.neucode_labeled = false;
//Make a few experimental proteoforms
List <IAggregatable> n1 = TestExperimentalProteoform.generate_neucode_components(100);
List <IAggregatable> n2 = TestExperimentalProteoform.generate_neucode_components(200);
List <IAggregatable> n3 = TestExperimentalProteoform.generate_neucode_components(200);
List <IAggregatable> n4 = TestExperimentalProteoform.generate_neucode_components(200);
ExperimentalProteoform pf1 = ConstructorsForTesting.ExperimentalProteoform("E1");
pf1.aggregated = n1.Select(n => (n as NeuCodePair).neuCodeLight).ToList <IAggregatable>();
ExperimentalProteoform pf2 = ConstructorsForTesting.ExperimentalProteoform("E2");
pf2.aggregated = n2.Select(n => (n as NeuCodePair).neuCodeLight).ToList <IAggregatable>();
ExperimentalProteoform pf3 = ConstructorsForTesting.ExperimentalProteoform("E3");
pf3.aggregated = n3.Select(n => (n as NeuCodePair).neuCodeLight).ToList <IAggregatable>();
ExperimentalProteoform pf4 = ConstructorsForTesting.ExperimentalProteoform("E4");
pf4.aggregated = n4.Select(n => (n as NeuCodePair).neuCodeLight).ToList <IAggregatable>();
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.shift_experimental_masses(-1, false);
foreach (Component c in pf3.aggregated.Concat(pf4.aggregated).OfType <Component>())
{
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);
}
Sweet.lollipop.clear_et();
Assert.AreEqual(0, Sweet.lollipop.et_peaks.Count);
//don't double shift E if it's in two peaks...
pr1 = new ProteoformRelation(pf1, pf5, comparison14, 1, TestContext.CurrentContext.TestDirectory);
pr2 = new ProteoformRelation(pf1, pf6, comparison14, 1, TestContext.CurrentContext.TestDirectory);
prs = new List <ProteoformRelation> {
pr1, pr2
};
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(1, Sweet.lollipop.et_peaks.Count);
//Shift the peaks, which shifts all of the proteoforms
d2 = Sweet.lollipop.et_peaks[0];
d2.shift_experimental_masses(-1, false);
foreach (Component c in pf3.aggregated.Concat(pf4.aggregated).OfType <Component>())
{
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);
}
}
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);
}
}
public void shift_et_peak_neucode()
{
SaveState.lollipop = new Lollipop();
ProteoformCommunity test_community = new ProteoformCommunity();
SaveState.lollipop.target_proteoform_community = test_community;
//Make a few experimental proteoforms
List <Component> n1 = TestExperimentalProteoform.generate_neucode_components(100);
List <Component> n2 = TestExperimentalProteoform.generate_neucode_components(100);
List <Component> n3 = TestExperimentalProteoform.generate_neucode_components(200);
List <Component> n4 = TestExperimentalProteoform.generate_neucode_components(200);
ExperimentalProteoform pf1 = ConstructorsForTesting.ExperimentalProteoform("E1");
pf1.aggregated_components = n1;
ExperimentalProteoform pf2 = ConstructorsForTesting.ExperimentalProteoform("E2");
pf2.aggregated_components = n2;
ExperimentalProteoform pf3 = ConstructorsForTesting.ExperimentalProteoform("E3");
pf3.aggregated_components = n3;
ExperimentalProteoform pf4 = ConstructorsForTesting.ExperimentalProteoform("E4");
pf4.aggregated_components = n4;
SaveState.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, SaveState.lollipop.et_peaks.Count);
//Shift the peaks, which shifts all of the proteoforms
DeltaMassPeak d2 = SaveState.lollipop.et_peaks[1];
d2.shift_experimental_masses(-1, true);
Assert.IsTrue(pf3.mass_shifted);
Assert.IsTrue(pf4.mass_shifted);
foreach (Component c in
n3.
Concat(n4).
Concat(n3.Select(n => ((NeuCodePair)n).neuCodeLight)).
Concat(n4.Select(n => ((NeuCodePair)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.Select(n => ((NeuCodePair)n).neuCodeHeavy).
Concat(n4.Select(n => ((NeuCodePair)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);
}
}