/// <summary>
/// Creates an Xic for a feature based on individual charge states.
/// </summary>
/// <param name="rawPath">Path to the raw file.</param>
/// <param name="peaksPath">Path to the peaks file.</param>
/// <param name="feature">Feature to target</param>
public Dictionary <int, Chromatogram> CreateXicForChargeStates(UMCLight feature, bool shouldSmooth)
{
Dictionary <int, Chromatogram> chromatograms = new Dictionary <int, Chromatogram>();
Dictionary <int, List <XYZData> > charges = feature.CreateChargeSIC();
XicFinder finder = new XicFinder();
feature.ChargeStateChromatograms.Clear();
//
foreach (int charge in charges.Keys)
{
// This is the current XIC - but it's not that great
List <XYZData> xicMz = charges[charge];
// Finds the maximum point in the XIC, we'll use this as our target, it most likely contains
// the exact point that we'll want to use to help identify the feature.
var maxPoint = xicMz.Where(u => u.Y == xicMz.Max(x => x.Y)).Select(u => new { u.X, u.Y, u.Z }).FirstOrDefault();
int targetScan = Convert.ToInt32(maxPoint.X);
double targetMz = maxPoint.Z;
// Find the Xic based on the target point, this may include other peaks
List <XYData> totalXic = null;
try
{
totalXic = FindXic(targetMz, targetScan, shouldSmooth);
if (totalXic.Count > 1)
{
// Then find a specific Xic based on the target scan.
List <XYData> specificXic = finder.FindTarget(totalXic, targetScan);
// Add the targeted Xic to the charge state map so that we can create Xic's for each charge state.
Chromatogram gram = new Chromatogram(specificXic, maxPoint.Z, charge);
chromatograms.Add(charge, gram);
}
}
catch (PreconditionException)
{
// This would mean that the charge state didnt have enough features in it.
}
}
return(chromatograms);
}
/// <summary>
/// Creates an Xic for a feature based on individual charge states.
/// </summary>
/// <param name="rawPath">Path to the raw file.</param>
/// <param name="peaksPath">Path to the peaks file.</param>
/// <param name="feature">Feature to target</param>
public Dictionary <int, List <Chromatogram> > CreateXicForIsotopes(UMCLight feature, bool shouldSmooth)
{
Dictionary <int, List <Chromatogram> > chromatograms = new Dictionary <int, List <Chromatogram> >();
Dictionary <int, List <XYZData> > charges = feature.CreateChargeSIC();
XicFinder finder = new XicFinder();
feature.IsotopeChromatograms.Clear();
foreach (int charge in charges.Keys)
{
/// Creates a list of Xic's for a given chromatogram.
List <Chromatogram> grams = new List <Chromatogram>();
chromatograms.Add(charge, grams);
// This is the current XIC - but it's not that great
List <XYZData> xicMz = charges[charge];
// Finds the maximum point in the XIC, we'll use this as our target, it most likely contains
// the exact point that we'll want to use to help identify the feature.
var maxPoint = xicMz.Where(u => u.Y == xicMz.Max(x => x.Y)).Select(u => new { u.X, u.Y, u.Z }).FirstOrDefault();
int targetScan = Convert.ToInt32(maxPoint.X);
double targetMz = maxPoint.Z;
List <XYData> isotopicProfile = CreateIsotopicProfile(targetMz, targetScan, charge);
foreach (XYData isotope in isotopicProfile)
{
// Find the Xic based on the target point, this may include other peaks
List <XYData> totalXic = FindXic(targetMz, targetScan, shouldSmooth);
// Then find a specific Xic based on the target scan.
List <XYData> targetIsotopeXic = finder.FindTarget(totalXic, targetScan);
// Add the targeted Xic to the charge state map so that we can create Xic's for each charge state.
Chromatogram gram = new Chromatogram(targetIsotopeXic, maxPoint.Z, charge);
grams.Add(gram);
}
chromatograms[charge] = grams;
}
feature.IsotopeChromatograms = chromatograms;
return(chromatograms);
}
/// <summary>
/// Creates an Xic for a feature based on individual charge states.
/// </summary>
/// <param name="rawPath">Path to the raw file.</param>
/// <param name="peaksPath">Path to the peaks file.</param>
/// <param name="feature">Feature to target</param>
public Dictionary<int, Chromatogram> CreateXicForChargeStates(UMCLight feature, bool shouldSmooth)
{
Dictionary<int, Chromatogram> chromatograms = new Dictionary<int, Chromatogram>();
Dictionary<int, List<XYZData>> charges = feature.CreateChargeSIC();
XicFinder finder = new XicFinder();
feature.ChargeStateChromatograms.Clear();
//
foreach (int charge in charges.Keys)
{
// This is the current XIC - but it's not that great
List<XYZData> xicMz = charges[charge];
// Finds the maximum point in the XIC, we'll use this as our target, it most likely contains
// the exact point that we'll want to use to help identify the feature.
var maxPoint = xicMz.Where( u => u.Y == xicMz.Max(x=>x.Y)).Select(u=> new { u.X, u.Y, u.Z}).FirstOrDefault();
int targetScan = Convert.ToInt32(maxPoint.X);
double targetMz = maxPoint.Z;
// Find the Xic based on the target point, this may include other peaks
List<PNNLOmics.Data.XYData> totalXic = null;
try
{
totalXic = FindXic(targetMz, targetScan, shouldSmooth);
if (totalXic.Count > 1)
{
// Then find a specific Xic based on the target scan.
List<PNNLOmics.Data.XYData> specificXic = finder.FindTarget(totalXic, targetScan);
// Add the targeted Xic to the charge state map so that we can create Xic's for each charge state.
Chromatogram gram = new Chromatogram(specificXic, maxPoint.Z, charge);
chromatograms.Add(charge, gram);
}
}
catch (PreconditionException)
{
// This would mean that the charge state didnt have enough features in it.
}
}
return chromatograms;
}
/// <summary>
/// Creates an Xic for a feature based on individual charge states.
/// </summary>
/// <param name="rawPath">Path to the raw file.</param>
/// <param name="peaksPath">Path to the peaks file.</param>
/// <param name="feature">Feature to target</param>
public Dictionary<int, List<Chromatogram>> CreateXicForIsotopes(UMCLight feature, bool shouldSmooth)
{
Dictionary<int, List<Chromatogram>> chromatograms = new Dictionary<int, List<Chromatogram>>();
Dictionary<int, List<XYZData>> charges = feature.CreateChargeSIC();
XicFinder finder = new XicFinder();
feature.IsotopeChromatograms.Clear();
foreach (int charge in charges.Keys)
{
/// Creates a list of Xic's for a given chromatogram.
List<Chromatogram> grams = new List<Chromatogram>();
chromatograms.Add(charge, grams);
// This is the current XIC - but it's not that great
List<XYZData> xicMz = charges[charge];
// Finds the maximum point in the XIC, we'll use this as our target, it most likely contains
// the exact point that we'll want to use to help identify the feature.
var maxPoint = xicMz.Where(u => u.Y == xicMz.Max(x => x.Y)).Select(u => new { u.X, u.Y, u.Z }).FirstOrDefault();
int targetScan = Convert.ToInt32(maxPoint.X);
double targetMz = maxPoint.Z;
List<PNNLOmics.Data.XYData> isotopicProfile = CreateIsotopicProfile(targetMz, targetScan, charge);
foreach (PNNLOmics.Data.XYData isotope in isotopicProfile)
{
// Find the Xic based on the target point, this may include other peaks
List<PNNLOmics.Data.XYData> totalXic = FindXic(targetMz, targetScan, shouldSmooth);
// Then find a specific Xic based on the target scan.
List<PNNLOmics.Data.XYData> targetIsotopeXic = finder.FindTarget(totalXic, targetScan);
// Add the targeted Xic to the charge state map so that we can create Xic's for each charge state.
Chromatogram gram = new Chromatogram(targetIsotopeXic, maxPoint.Z, charge);
grams.Add(gram);
}
chromatograms[charge] = grams;
}
feature.IsotopeChromatograms = chromatograms;
return chromatograms;
}
