public IDictionary <int, IList <MSFeatureLight> > CreateXic(UMCLight feature, double massError, ISpectraProvider provider)
{
var features = new Dictionary <int, IList <MSFeatureLight> >();
var chargeFeatures = feature.CreateChargeMap();
// For each UMC...
foreach (var charge in chargeFeatures.Keys)
{
// Find the mininmum and maximum features
var msFeatures = CreateXic(chargeFeatures[charge],
massError,
provider);
features.Add(charge, new List <MSFeatureLight>());
foreach (var newFeature in msFeatures)
{
// Here we ask if this is a new MS Feature or old...
if (!chargeFeatures.ContainsKey(newFeature.Scan))
{
// Otherwise add the new feature
newFeature.MassMonoisotopic = feature.MassMonoisotopic;
newFeature.DriftTime = feature.DriftTime;
newFeature.GroupId = feature.GroupId;
}
features[charge].Add(newFeature);
}
}
return(features);
}
private void UpdateCharges(UMCLight feature)
{
Charges.Clear();
m_scanMaps = feature.CreateChargeMap();
foreach (var charge in m_scanMaps.Keys)
{
double mz = 0;
var minScan = int.MaxValue;
var maxScan = int.MinValue;
double maxIntensity = 0;
foreach (var msFeature in m_scanMaps[charge])
{
minScan = Math.Min(minScan, msFeature.Scan);
maxScan = Math.Max(maxScan, msFeature.Scan);
if (maxIntensity >= msFeature.Abundance)
{
continue;
}
maxIntensity = msFeature.Abundance;
mz = msFeature.Mz;
}
Charges.Add(new ChargeStateViewModel(charge, mz, minScan, maxScan));
}
if (Charges.Count <= 0)
{
return;
}
SelectedCharge = Charges[0];
}
/// <summary>
/// Creates SIC's mapped by charge state for the MS Features in the feature.
/// </summary>
/// <param name="feature"></param>
/// <returns></returns>
public static Dictionary <int, List <XYZData> > CreateChargeSICForMonoMass(this UMCLight feature)
{
var chargeMap = feature.CreateChargeMap();
var sicMap = new Dictionary <int, List <XYZData> >();
foreach (var charge in chargeMap.Keys)
{
chargeMap[charge].Sort(delegate(MSFeatureLight x, MSFeatureLight y) { return(x.Scan.CompareTo(y.Scan)); }
);
var data = chargeMap[charge].ConvertAll(x => new XYZData(x.Scan, x.Abundance, x.MassMonoisotopicAligned));
sicMap.Add(charge, data);
}
return(sicMap);
}
/// <summary>
/// Creates SIC's mapped by charge state for the MS Features in the feature.
/// </summary>
/// <param name="feature"></param>
/// <param name="provider">Object that can read data from a raw file or data source.</param>
/// <returns></returns>
public static Dictionary <int, List <XYZData> > CreateChargeSIC(this UMCLight feature, ISpectraProvider provider)
{
var chargeMap = feature.CreateChargeMap();
var sicMap = new Dictionary <int, List <XYZData> >();
foreach (var charge in chargeMap.Keys)
{
chargeMap[charge].Sort(delegate(MSFeatureLight x, MSFeatureLight y) { return(x.Scan.CompareTo(y.Scan)); }
);
var data = chargeMap[charge].ConvertAll(x => new XYZData(x.Scan, x.Abundance, x.Mz));
sicMap.Add(charge, data);
}
if (provider != null)
{
// Creates an SIC map for a given charge state of the feature.
foreach (var charge in sicMap.Keys)
{
var data = sicMap[charge];
// The data is alread sorted.
var minScan = int.MaxValue;
var maxScan = int.MinValue;
var mzValues = new List <double>();
foreach (var x in data)
{
mzValues.Add(x.Z);
minScan = Math.Min(minScan, Convert.ToInt32(x.X));
maxScan = Math.Max(maxScan, Convert.ToInt32(x.X));
}
mzValues.Sort();
double mz = 0;
var mid = Convert.ToInt32(mzValues.Count / 2);
mz = mzValues[mid];
minScan -= 20;
maxScan += 20;
// Build the SIC
var intensities = new List <XYZData>();
for (var scan = minScan; scan < maxScan; scan++)
{
var summary = new ScanSummary();
var spectrum = provider.GetRawSpectra(scan, 1, out summary);
double intensity = 0;
var minDistance = double.MaxValue;
var index = -1;
for (var i = 0; i < spectrum.Count; i++)
{
var distance = spectrum[i].X - mz;
if (distance < minDistance)
{
index = i;
minDistance = distance;
}
}
if (index >= 0)
{
intensity = spectrum[index].Y;
}
var newPoint = new XYZData(scan, intensity, mz);
intensities.Add(newPoint);
}
sicMap[charge] = intensities;
}
}
return(sicMap);
}
private void UpdateCharges(UMCLight feature)
{
Charges.Clear();
m_scanMaps = feature.CreateChargeMap();
foreach (var charge in m_scanMaps.Keys)
{
double mz = 0;
var minScan = int.MaxValue;
var maxScan = int.MinValue;
double maxIntensity = 0;
foreach (var msFeature in m_scanMaps[charge])
{
minScan = Math.Min(minScan, msFeature.Scan);
maxScan = Math.Max(maxScan, msFeature.Scan);
if (maxIntensity >= msFeature.Abundance)
continue;
maxIntensity = msFeature.Abundance;
mz = msFeature.Mz;
}
Charges.Add(new ChargeStateViewModel(charge, mz, minScan, maxScan));
}
if (Charges.Count <= 0)
return;
SelectedCharge = Charges[0];
}
