/// <summary>
/// Build plot for observed/theoretical isotope envelopes.
/// </summary>
/// <param name="selectedFeaturePoint">The selected Feature Point.</param>
private void BuildIsotopePlots(Feature.FeaturePoint selectedFeaturePoint)
{
if (selectedFeaturePoint == null || selectedFeaturePoint.Isotopes.Length == 0)
{
return;
}
this.IsotopicEnvelope.BuildPlot(
selectedFeaturePoint.Isotopes,
selectedFeaturePoint.Mass,
selectedFeaturePoint.Charge);
this.IsotopicEnvelopeExpanded = true;
}
/// <summary>
/// Read a line from the feature file containing a single feature.
/// </summary>
/// <param name="line">The line from the feature file.</param>
/// <param name="delimeter">The delimiter used in feature file.</param>
/// <param name="headers">The headers of the feature file columns.</param>
/// <returns>Parsed feature.</returns>
private static Feature ReadFeature(string line, char delimeter, IReadOnlyDictionary <string, int> headers)
{
var expectedHeaders = new List <string>
{
"MonoMass",
"Abundance",
"LikelihoodRatio",
"Envelope",
"MinCharge",
"MaxCharge",
////"SummedCorr",
"MinScan",
"MaxScan"
};
string likelihoodVarHeader = "LikelihoodRatio";
foreach (var header in expectedHeaders.Where(header => !headers.ContainsKey(header)))
{
if (header == "LikelihoodRatio" && headers.ContainsKey("Probability"))
{
likelihoodVarHeader = "Probability";
}
else
{
throw new KeyNotFoundException(string.Format("Missing expected column header \"{0}\" in feature file.", header));
}
}
var parts = line.Split(delimeter);
var mass = Convert.ToDouble(parts[headers["MonoMass"]]);
var abundance = Convert.ToDouble(parts[headers["Abundance"]]);
var score = Convert.ToDouble(parts[headers[likelihoodVarHeader]]);
var isotopes = ReadIsotopicEnvelope(parts[headers["Envelope"]]);
var minCharge = Convert.ToInt32(parts[headers["MinCharge"]]);
var maxCharge = Convert.ToInt32(parts[headers["MaxCharge"]]);
int id = -1;
if (headers.ContainsKey("FeatureID"))
{
id = Convert.ToInt32(parts[headers["FeatureID"]]);
}
var summedCorr = headers.ContainsKey("SummedCorr") ? Convert.ToDouble(parts[headers["SummedCorr"]]) : 0.0;
int mostAbundantIsotopeIndex = Averagine.GetIsotopomerEnvelope(mass).MostAbundantIsotopeIndex;
List <Peak> minIsotopicProfile = Averagine.GetTheoreticalIsotopeProfile(mass, minCharge, 0);
List <Peak> maxIsotopicProfile = Averagine.GetTheoreticalIsotopeProfile(mass, maxCharge, 0);
var minPoint = new Feature.FeaturePoint
{
Id = id,
Mass = mass,
Scan = Convert.ToInt32(parts[headers["MinScan"]]),
Mz = minIsotopicProfile[mostAbundantIsotopeIndex].Mz,
Charge = minCharge,
Abundance = abundance,
Score = score,
Isotopes = isotopes,
Correlation = summedCorr
};
var maxPoint = new Feature.FeaturePoint
{
Id = id,
Mass = mass,
Scan = Convert.ToInt32(parts[headers["MaxScan"]]),
Mz = maxIsotopicProfile[mostAbundantIsotopeIndex].Mz,
Charge = maxCharge,
Abundance = abundance,
Score = score,
Isotopes = isotopes,
Correlation = summedCorr,
};
return(new Feature(minPoint, maxPoint)
{
Id = id
});
}
/// <summary>
/// Event handler for mouse click event to set SelectedDataPoint
/// </summary>
/// <param name="sender">The sender PlotView</param>
/// <param name="args">The event arguments.</param>
private void FeatureMapMouseDown(object sender, OxyMouseEventArgs args)
{
this.selectedFeaturePoint = null;
this.selectedPrSmPoint = null;
var series = this.FeatureMap.GetSeriesFromPoint(args.Position, 10);
if (series is LineSeries)
{ // Was a feature clicked?
var result = series.GetNearestPoint(args.Position, false);
if (result == null)
{
return;
}
var featurePoint = result.Item as Feature.FeaturePoint;
if (featurePoint != null)
{
// See if there is a ms2 point closer than this feature point
PrSm closestPrSm = null;
if (this.showFoundIdMs2 || this.showFoundUnIdMs2)
{
var feature = featurePoint.Feature;
var prsms = feature.AssociatedPrSms;
var minDist = result.Position.DistanceToSquared(args.Position);
foreach (var prsm in prsms)
{
if ((prsm.Sequence.Count == 0 && !this.showFoundUnIdMs2) ||
(prsm.Sequence.Count > 0 && !this.showFoundIdMs2))
{
continue;
}
var sp = this.xaxis.Transform(prsm.RetentionTime, featurePoint.Mass, this.yaxis);
var distSq = sp.DistanceToSquared(args.Position);
if (closestPrSm == null || distSq < minDist)
{
closestPrSm = prsm;
minDist = distSq;
}
}
}
if (closestPrSm != null)
{
this.selectedPrSmPoint = closestPrSm;
}
this.selectedFeaturePoint = featurePoint;
}
}
else if (series is ScatterSeries)
{ // Was a ms2 cross clicked?
var result = series.GetNearestPoint(args.Position, false);
if (result == null)
{
return;
}
this.selectedPrSmPoint = result.Item as PrSm;
}
}
