public void TestDisplaySpectra(string rawFile, string idFile)
{
// init
var idFileReader = IdFileReaderFactory.CreateReader(idFile);
var ids = idFileReader.Read();
var lcms = PbfLcMsRun.GetLcMsRun(rawFile);
var idList = ids.ToList();
foreach (var id in idList)
{
id.LcMs = lcms;
id.RawFileName = Path.GetFileNameWithoutExtension(rawFile);
}
idList.Sort(new PrSm.PrSmScoreComparer());
var prsm = idList[0];
// init XicPlotViewModel
var dialogService = new TestableMainDialogService();
var spectrumViewModel = new SpectrumViewModel(dialogService, lcms);
// init test ions
var baseIonTypes = new List <BaseIonType> {
BaseIonType.B, BaseIonType.Y
};
var neutralLosses = new List <NeutralLoss> {
NeutralLoss.NoLoss
};
const int charge = 1;
const int minCharge = 1, maxCharge = 2;
var ionTypeFactory = new IonTypeFactory(maxCharge);
var ionTypes = IonUtils.GetIonTypes(ionTypeFactory, baseIonTypes, neutralLosses, minCharge, maxCharge);
var ions = IonUtils.GetFragmentIonLabels(prsm.Sequence, charge, ionTypes);
var ionVms = ions.Select(label => new LabeledIonViewModel(label.Composition, label.IonType, label.IsFragmentIon, lcms, label.PrecursorIon, label.IsChargeState, label.Index)).ToList();
}
/// <summary>
/// Gets selected ion types based on the selected BaseIonTypes and NeutralLosses.
/// </summary>
/// <returns>Array of IonTypes.</returns>
private IonType[] GetIonTypes()
{
var charge = Math.Min(this.fragmentationSequence.Charge - 1, 100);
charge = Math.Max(charge, 1);
return(IonUtils.GetIonTypes(
IcParameters.Instance.IonTypeFactory,
this.BaseIonTypes.Where(bit => bit.IsSelected).Select(bit => bit.BaseIonType).ToList(),
this.NeutralLosses.Where(nl => nl.IsSelected).Select(nl => nl.NeutralLoss).ToList(),
1,
charge).ToArray());
}
/// <summary>
/// Update ion types based on selected base ion types, selected neutral losses, and charge range.
/// </summary>
private void UpdateIonTypes()
{
// set ion types
var selectedBase = this.SelectedBaseIonTypes.Cast <BaseIonType>().ToList();
var selectedLosses = this.SelectedNeutralLosses.Cast <NeutralLoss>().ToList();
this.IonTypes =
new ReactiveList <IonType>(
IonUtils.GetIonTypes(
IcParameters.Instance.IonTypeFactory,
selectedBase,
selectedLosses,
this.MinCharge,
this.MaxCharge));
}
