public void testFindRawNeuCodePairsMethod()
{
//reading in test excel file, process raw components before testing neucode pairs.
Sweet.lollipop = new Lollipop();
Func <InputFile, IEnumerable <Component> > componentReader = c => new ComponentReader().read_components_from_xlsx(c, true);
InputFile noisy = new InputFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "noisy.xlsx"), Labeling.NeuCode, Purpose.Identification);
Sweet.lollipop.input_files.Add(noisy);
string inFileId = noisy.UniqueId.ToString();
Sweet.lollipop.neucode_labeled = true;
Sweet.lollipop.process_raw_components(Sweet.lollipop.input_files, Sweet.lollipop.raw_experimental_components, Purpose.Identification, true);
Assert.AreEqual(223, Sweet.lollipop.raw_experimental_components.Count);
//Check the validity of one component read from the Excel file
Component c1 = Sweet.lollipop.raw_experimental_components[0];
Component c2 = Sweet.lollipop.raw_experimental_components[6]; // this one doesn't have the same number of charge states, which makes for a good example
List <int> c1_charges = c1.charge_states.Select(charge_state => charge_state.charge_count).ToList();
List <int> c2_charges = c2.charge_states.Select(charge_states => charge_states.charge_count).ToList();
HashSet <int> overlapping_charge_states = new HashSet <int>(c1_charges.Intersect(c2_charges));
Assert.AreEqual(9, c1.charge_states.Count);
Assert.AreEqual(8, overlapping_charge_states.Count);
Assert.AreEqual(Sweet.lollipop.input_files.Where(f => f.filename == "noisy").FirstOrDefault().UniqueId + "_1", c1.id); //this line behaving strangely.
Assert.AreEqual(Math.Round(8982.7258, 4), Math.Round(c1.reported_monoisotopic_mass, 4));
Assert.AreEqual(Math.Round(2868299.6, 1), Math.Round(c1.intensity_sum, 1)); //charge state normalized
Assert.AreEqual(Math.Round(2836046.31, 2), Math.Round(NeuCodePair.calculate_sum_intensity_olcs(c1.charge_states, overlapping_charge_states), 2));
Assert.AreEqual(9, c1.charge_states.Count);
Assert.AreEqual("413-415", c1.min_scan + "-" + c1.max_scan);
Assert.AreEqual("56.25-56.51", c1.min_rt + "-" + c1.max_rt);
Assert.AreEqual(Math.Round(56.3809775, 7), Math.Round(c1.rt_apex, 7));
Assert.AreEqual(8981.69, Math.Round(c1.charge_states.OrderBy(s => s.charge_count).First().reported_mass, 2));
//testing intensity ratio
NeuCodePair neucode_pair = Sweet.lollipop.raw_neucode_pairs.Where(i => i.neuCodeHeavy.id == inFileId + "_5" && i.neuCodeLight.id == inFileId + "_1").First();
Assert.AreEqual(2.0695212171812423d, neucode_pair.intensity_ratio); //intensities are charge state normalized
//testing K-count
Assert.AreEqual(7, neucode_pair.lysine_count);
//testing that only overlapping charge states go into intensity ratio
neucode_pair = Sweet.lollipop.raw_neucode_pairs.Where(i => i.neuCodeHeavy.id == inFileId + "_122" && i.neuCodeLight.id == inFileId + "_57").First();
Assert.AreEqual(1.7301034510740836, neucode_pair.intensity_ratio);
}
