public object Convert(object value, Type targetType, object parameter, CultureInfo culture)
{
SpectrumViewModel spectrum = value as SpectrumViewModel;
if (spectrum != null)
{
_Spectrum.DataContext = spectrum;
return(_Spectrum);
}
ScreenCaptureViewModel screenCapture = value as ScreenCaptureViewModel;
if (screenCapture != null)
{
_ScreenCapture.DataContext = screenCapture;
return(_ScreenCapture);
}
CustomEffectViewModel custom = value as CustomEffectViewModel;
if (custom != null)
{
_Custom.DataContext = custom;
return(_Custom);
}
return(null);
}
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>
/// Initializes a new instance of the <see cref="DataSetViewModel"/> class.
/// </summary>
/// <param name="dialogService">A dialog service for opening dialogs from the view model</param>
public DataSetViewModel(IMainDialogService dialogService)
{
this.dialogService = dialogService;
ReadyToClose = false;
IdFileOpen = false;
SelectedPrSm = new PrSm();
ScanViewModel = new ScanViewModel(dialogService, new List <PrSm>());
CreateSequenceViewModel = new CreateSequenceViewModel(dialogService)
{
SelectedDataSetViewModel = this
};
CreateSequenceViewModel.CreateAndAddPrSmCommand.Subscribe(
_ => ScanViewModel.Data.Add(CreateSequenceViewModel.SelectedPrSm));
// Remove filter by raw file name from ScanViewModel filters
ScanViewModel.Filters.Remove(ScanViewModel.Filters.FirstOrDefault(f => f.Name == "Raw File Name"));
// When a PrSm is selected from the ScanViewModel, update the SelectedPrSm for this data set
ScanViewModel.WhenAnyValue(x => x.SelectedPrSm).Where(prsm => prsm != null).Subscribe(x => SelectedPrSm = x);
// When the scan number in the selected prsm changes, the selected scan in the xic plots should update
this.WhenAnyValue(x => x.SelectedPrSm)
.Where(_ => SelectedPrSm != null && SpectrumViewModel != null && XicViewModel != null)
.Subscribe(prsm =>
{
SpectrumViewModel.UpdateSpectra(prsm.Scan, SelectedPrSm.PrecursorMz);
XicViewModel.SetSelectedScan(prsm.Scan);
XicViewModel.ZoomToScan(prsm.Scan);
});
var prsmObservable = this.WhenAnyValue(x => x.SelectedPrSm).Where(prsm => prsm != null);
prsmObservable
.Select(prsm => prsm.GetFragmentationSequence()).Where(fragSeq => fragSeq != null)
.Subscribe(fragSeq =>
{
SpectrumViewModel.FragmentationSequence = fragSeq;
XicViewModel.FragmentationSequence = fragSeq;
});
// When the prsm changes, update the Scan View Model.
prsmObservable.Subscribe(prsm => ScanViewModel.SelectedPrSm = prsm);
// When the prsm updates, update the prsm in the sequence creator
prsmObservable.Subscribe(prsm => CreateSequenceViewModel.SelectedPrSm = prsm);
// When the prsm updates, update the feature map
prsmObservable.Where(_ => FeatureMapViewModel != null).Subscribe(prsm => FeatureMapViewModel.FeatureMapViewModel.SelectedPrSm = prsm);
// When prsm updates, subscribe to scan updates
prsmObservable.Subscribe(prsm =>
{
prsm.WhenAnyValue(x => x.Scan, x => x.PrecursorMz)
.Where(x => x.Item1 > 0 && x.Item2 > 0 && SpectrumViewModel != null)
.Subscribe(x => SpectrumViewModel.UpdateSpectra(x.Item1, x.Item2));
prsm.WhenAnyValue(x => x.Scan).Where(scan => scan > 0 && XicViewModel != null)
.Subscribe(scan => XicViewModel.SetSelectedScan(scan));
});
// When a new prsm is created by CreateSequenceViewModel, update SelectedPrSm
CreateSequenceViewModel.WhenAnyValue(x => x.SelectedPrSm).Subscribe(prsm => SelectedPrSm = prsm);
// When IDs are filtered in the ScanViewModel, update feature map with new IDs
ScanViewModel.WhenAnyValue(x => x.FilteredData).Where(_ => FeatureMapViewModel != null).Subscribe(data => FeatureMapViewModel.UpdateIds(data));
// Toggle instrument data when ShowInstrumentData setting is changed.
IcParameters.Instance.WhenAnyValue(x => x.ShowInstrumentData).Select(async x => await ScanViewModel.ToggleShowInstrumentDataAsync(x, (PbfLcMsRun)LcMs)).Subscribe();
// When product ion tolerance or ion correlation threshold change, update scorer factory
IcParameters.Instance.WhenAnyValue(x => x.ProductIonTolerancePpm, x => x.IonCorrelationThreshold)
.Subscribe(
x =>
{
var scorer = new ScorerFactory(x.Item1, Constants.MinCharge, Constants.MaxCharge, x.Item2);
CreateSequenceViewModel.ScorerFactory = scorer;
ScanViewModel.ScorerFactory = scorer;
});
// When an ID file has been opened, turn on the unidentified scan filter
this.WhenAnyValue(x => x.IdFileOpen)
.Where(idFileOpen => idFileOpen)
.Select(_ => ScanViewModel.Filters.FirstOrDefault(f => f.Name == "Hide Unidentified Scans"))
.Where(f => f != null)
.Subscribe(f => f.Selected = true);
// Start MsPf Search Command
StartMsPfSearchCommand = ReactiveCommand.Create(StartMsPfSearchImplementation);
// Close command verifies that the user wants to close the dataset, then sets ReadyToClose to true if they are
CloseCommand = ReactiveCommand.Create(() =>
{
ReadyToClose =
dialogService.ConfirmationBox(
string.Format("Are you sure you would like to close {0}?", Title), string.Empty);
});
}
