public PeakChromatogramGenerator(double tolerance, Globals.ChromatogramGeneratorMode chromMode,
Globals.IsotopicProfileType isotopicProfileTarget, Globals.ToleranceUnit toleranceUnit = Globals.ToleranceUnit.PPM)
{
Tolerance = tolerance;
ChromatogramGeneratorMode = chromMode;
IsotopicProfileTarget = isotopicProfileTarget;
TopNPeaksLowerCutOff = 0.3;
ChromWindowWidthForNonAlignedData = 0.4f;
ChromWindowWidthForAlignedData = 0.1f;
ToleranceUnit = toleranceUnit;
_chromGen = new ChromatogramGenerator();
}
protected ChromatogramCorrelatorBase(int numPointsInSmoother, double minRelativeIntensityForChromCorr,
double chromTolerance, Globals.ToleranceUnit toleranceUnit = Globals.ToleranceUnit.PPM)
{
SavitzkyGolaySmoothingOrder = 2;
NumPointsInSmoother = numPointsInSmoother;
ChromTolerance = chromTolerance;
MinimumRelativeIntensityForChromCorr = minRelativeIntensityForChromCorr;
ChromToleranceUnit = toleranceUnit;
PeakChromGen = new PeakChromatogramGenerator(ChromTolerance, Globals.ChromatogramGeneratorMode.MOST_ABUNDANT_PEAK,
Globals.IsotopicProfileType.UNLABELLED, toleranceUnit);
Smoother = new SavitzkyGolaySmoother(NumPointsInSmoother, SavitzkyGolaySmoothingOrder, false);
}
public XYData GenerateChromatogram(Run run, IsotopicProfile theorProfile, int lowerScan, int upperScan, double tolerance, Globals.ToleranceUnit toleranceUnit = Globals.ToleranceUnit.PPM)
{
if (ChromatogramGeneratorMode == Globals.ChromatogramGeneratorMode.MZ_BASED)
{
throw new NotSupportedException("Don't use this method for MZ_BASED chromatogram generation. Use a different overload");
}
var targetMZList = GetTargetMzList(theorProfile);
return(GenerateChromatogram(run, targetMZList, lowerScan, upperScan, tolerance, toleranceUnit));
}
public XYData GenerateChromatogram(Run run, List <double> targetMzList, int lowerScan, int upperScan, double tolerance, Globals.ToleranceUnit toleranceUnit = Globals.ToleranceUnit.PPM)
{
var midScan = (int)((lowerScan + (double)upperScan) / 2);
if (run.MassIsAligned)
{
for (var i = 0; i < targetMzList.Count; i++)
{
targetMzList[i] = getAlignedMZValue(targetMzList[i], run, midScan);
}
}
var chromValues = _chromGen.GenerateChromatogram(run.ResultCollection.GetMsPeakResultsGroupedAndMzOrdered(), lowerScan, upperScan, targetMzList, tolerance, toleranceUnit);
chromValues = FilterOutDataBasedOnMsMsLevel(run, chromValues, 1, false);
return(chromValues);
}
public XYData GenerateChromatogram(Run run, int scanStart, int scanStop, double targetMz, double tolerance, Globals.ToleranceUnit toleranceUnit = Globals.ToleranceUnit.PPM)
{
var targetMzList = new List <double> {
targetMz
};
return(GenerateChromatogram(run, targetMzList, scanStart, scanStop, tolerance, toleranceUnit));
}
//TODO: make a ChromatogramObject that will help handle my MSPeakResults, etc.
public XYData GenerateChromatogram(Dictionary <int, List <MSPeakResult> > groupedMsPeakList, int minScan, int maxScan, List <double> targetMZList, double tolerance, int chromIDToAssign, Globals.ToleranceUnit toleranceUnit = Globals.ToleranceUnit.PPM)
{
Check.Require(groupedMsPeakList != null && groupedMsPeakList.Count > 0, "Cannot generate chromatogram. Source msPeakList is empty or hasn't been defined.");
var scanTolerance = 5; // TODO: keep an eye on this
// PNNLOmics.Generic.AnonymousComparer<MSPeakResult> comparer = new PNNLOmics.Generic.AnonymousComparer<MSPeakResult>((x, y) => x.MSPeak.XValue.CompareTo(y.MSPeak.XValue));
var comparer = new MSPeakResultComparer();
var tempPeakList = new List <MSPeakResult>();
for (var i = minScan - scanTolerance; i < maxScan + scanTolerance; i++)
{
if (groupedMsPeakList == null || !groupedMsPeakList.TryGetValue(i, out var msPeakResultList))
{
continue;
}
foreach (var targetMZ in targetMZList)
{
double lowerMZ;
double upperMZ;
if (toleranceUnit == Globals.ToleranceUnit.PPM)
{
lowerMZ = targetMZ - tolerance * targetMZ / 1e6;
upperMZ = targetMZ + tolerance * targetMZ / 1e6;
}
else if (toleranceUnit == Globals.ToleranceUnit.MZ)
{
lowerMZ = targetMZ - tolerance;
upperMZ = targetMZ + tolerance;
}
else
{
throw new ArgumentOutOfRangeException("Trying to create chromatogram, but the " + toleranceUnit +
" unit isn't supported");
}
var lowMsPeak = new MSPeak(lowerMZ);
var lowMsPeakResult = new MSPeakResult {
MSPeak = lowMsPeak
};
var binarySearchResult = msPeakResultList.BinarySearch(lowMsPeakResult, comparer);
var nearestSearchResult = binarySearchResult >= 0 ? binarySearchResult : ~binarySearchResult;
for (var j = nearestSearchResult; j < msPeakResultList.Count; j++)
{
var msPeakResult = msPeakResultList[j];
if (msPeakResult.MSPeak.XValue <= upperMZ)
{
tempPeakList.Add(msPeakResult);
}
}
}
}
XYData chromData = null;
if (!tempPeakList.Any())
{
//TODO: we want to return 0 intensity values. But need to make sure there are no downstream problems with this change.
}
else
{
chromData = GetChromDataAndFillInZerosAndAssignChromID(tempPeakList, chromIDToAssign);
}
return(chromData);
}
/// <summary>
/// Will generate a chromatogram that is in fact a combination of chromatograms based on user-supplied target m/z values.
/// This is geared for producing a chromatogram for an isotopic profile, but only using narrow mass ranges
/// that encompass individual peaks of an isotopic profile.
/// </summary>
/// <param name="groupedMsPeakList"></param>
/// <param name="minScan"></param>
/// <param name="maxScan"></param>
/// <param name="targetMZList"></param>
/// <param name="tolerance"></param>
/// <param name="toleranceUnit"></param>
/// <returns></returns>
public XYData GenerateChromatogram(Dictionary <int, List <MSPeakResult> > groupedMsPeakList, int minScan, int maxScan, List <double> targetMZList, double tolerance, Globals.ToleranceUnit toleranceUnit = Globals.ToleranceUnit.PPM)
{
var defaultChromID = 0;
return(GenerateChromatogram(groupedMsPeakList, minScan, maxScan, targetMZList, tolerance, defaultChromID, toleranceUnit));
}
public XYData GenerateChromatogram(List <MSPeakResult> msPeakList, int minScan, int maxScan, double targetMZ, double tolerance, int chromIDToAssign, Globals.ToleranceUnit toleranceUnit = Globals.ToleranceUnit.PPM)
{
var targetMZList = new List <double>
{
targetMZ
};
return(GenerateChromatogram(msPeakList, minScan, maxScan, targetMZList, tolerance, chromIDToAssign, toleranceUnit));
}
public XYData GenerateChromatogram(List <MSPeakResult> msPeakList, int minScan, int maxScan, List <double> targetMZList, double tolerance, int chromIDToAssign, Globals.ToleranceUnit toleranceUnit = Globals.ToleranceUnit.PPM)
{
Check.Require(msPeakList != null && msPeakList.Count > 0, "Cannot generate chromatogram. Source msPeakList is empty or hasn't been defined.");
if (msPeakList == null)
{
return(null);
}
var scanTolerance = 5; // TODO: keep an eye on this
var indexOfLowerScan = GetIndexOfClosestScanValue(msPeakList, minScan, 0, msPeakList.Count - 1, scanTolerance);
var indexOfUpperScan = GetIndexOfClosestScanValue(msPeakList, maxScan, 0, msPeakList.Count - 1, scanTolerance);
XYData chromData = null;
foreach (var targetMZ in targetMZList)
{
double lowerMZ;
double upperMZ;
if (toleranceUnit == Globals.ToleranceUnit.PPM)
{
lowerMZ = targetMZ - tolerance * targetMZ / 1e6;
upperMZ = targetMZ + tolerance * targetMZ / 1e6;
}
else if (toleranceUnit == Globals.ToleranceUnit.MZ)
{
lowerMZ = targetMZ - tolerance;
upperMZ = targetMZ + tolerance;
}
else
{
throw new ArgumentOutOfRangeException("Trying to create chromatogram, but the " + toleranceUnit + " unit isn't supported");
}
var tempPeakList = new List <MSPeakResult>();
for (var i = indexOfLowerScan; i <= indexOfUpperScan; i++)
{
var msPeakResult = msPeakList[i];
var xValue = msPeakResult.MSPeak.XValue;
if (xValue >= lowerMZ && xValue <= upperMZ)
{
tempPeakList.Add(msPeakResult);
}
}
if (!tempPeakList.Any())
{
//TODO: we want to return 0 intensity values. But need to make sure there are no downstream problems with this change.
}
else
{
var currentChromData = GetChromDataAndFillInZerosAndAssignChromID(tempPeakList, chromIDToAssign);
chromData = AddCurrentXYDataToBaseXYData(chromData, currentChromData);
}
}
return(chromData);
}
public ChromatogramCorrelator(int numPointsInSmoother, double minRelativeIntensityForChromCorr = 0.01, double chromToleranceInPPM = 20, Globals.ToleranceUnit chromToleranceUnit = Globals.ToleranceUnit.PPM)
: base(numPointsInSmoother, minRelativeIntensityForChromCorr, chromToleranceInPPM, chromToleranceUnit)
{
}
