public override XYData GetMassSpectrum(DeconTools.Backend.Core.ScanSet scanset, double minMZ, double maxMZ)
{
//TODO: Update upon error fix.... the YAFMS library is throwing an error if I give an m/z outside it's expected range. So until that is fixed, I'll go get all the m/z values and trim them myself
double[] xvals = null;
float[] yvals = null;
if (scanset.IndexValues.Count <= 1)
{
m_reader.GetSpectrum(this.SpectraID, scanset.PrimaryScanNumber, ref xvals, ref yvals);
}
else
{
xvals = new double[0];
yvals = new float[0];
this.getSummedSpectrum(scanset, ref xvals, ref yvals, minMZ, maxMZ);
}
var xydata = new XYData();
xydata.Xvalues = xvals;
xydata.Yvalues = yvals.Select(p => (double)p).ToArray();
return(xydata);
}
public virtual void AddSelectedChromPeakAndScanSet(ChromPeak bestPeak, ScanSet scanSet, Globals.IsotopicProfileType isotopicProfileType)
{
if (isotopicProfileType == Globals.IsotopicProfileType.UNLABELED)
{
ChromPeakSelected = bestPeak;
ScanSet = scanSet;
if (ScanSet != null)
{
NumMSScansSummed = ScanSet.IndexValues.Count;
}
var failedChromPeakSelection = (ChromPeakSelected == null || Math.Abs(ChromPeakSelected.XValue) < double.Epsilon);
if (failedChromPeakSelection)
{
FailedResult = true;
FailureType = Globals.TargetedResultFailureType.ChrompeakNotFoundWithinTolerances;
}
else
{
FailedResult = false;
FailureType = Globals.TargetedResultFailureType.None;
}
}
else
{
throw new NotSupportedException("Cannot add data for a labeled result in this base class");
}
}
//NOTE: code duplication here... see BrukerRun too
public override void GetMassSpectrum(DeconTools.Backend.Core.ScanSet scanSet, double minMZ, double maxMZ)
{
Check.Require(scanSet != null, "Can't get mass spectrum; inputted set of scans is null");
Check.Require(scanSet.IndexValues.Count > 0, "Can't get mass spectrum; no scan numbers inputted");
int totScans = this.GetNumMSScans();
double[] xvals = new double[0];
double[] yvals = new double[0];
if (scanSet.IndexValues.Count == 1) //this is the case of only wanting one MS spectrum
{
this.RawData.GetSpectrum(scanSet.IndexValues[0], ref xvals, ref yvals);
}
else // need to sum spectra
{
//assume: each scan has exactly same x values
//get first spectrum
this.RawData.GetSpectrum(scanSet.IndexValues[0], ref xvals, ref yvals);
//
double[] summedYvals = new double[xvals.Length];
yvals.CopyTo(summedYvals, 0);
for (int i = 1; i < scanSet.IndexValues.Count; i++)
{
this.RawData.GetSpectrum(scanSet.IndexValues[i], ref xvals, ref yvals);
for (int n = 0; n < xvals.Length; n++)
{
summedYvals[n] += yvals[n];
}
}
yvals = summedYvals;
}
this.XYData.SetXYValues(ref xvals, ref yvals);
if (this.XYData.Xvalues == null || this.XYData.Xvalues.Length == 0)
{
return;
}
bool needsFiltering = (minMZ > this.XYData.Xvalues[0] || maxMZ < this.XYData.Xvalues[this.XYData.Xvalues.Length - 1]);
if (needsFiltering)
{
this.FilterXYPointsByMZRange(minMZ, maxMZ);
}
}
public override void AddSelectedChromPeakAndScanSet(ChromPeak bestPeak, ScanSet scanset, Globals.IsotopicProfileType isotopicProfileType)
{
//if result was not previously processed, will do a standard add of selected chrom peak and scanset
//if result was previously processed, add new data to the Labelled results
if (isotopicProfileType == Globals.IsotopicProfileType.UNLABELLED)
{
base.AddSelectedChromPeakAndScanSet(bestPeak, scanset, isotopicProfileType);
}
else
{
ChromPeakSelectedN15 = bestPeak;
ScanSetForN15Profile = scanset;
}
}
//NOTE: code duplication here... see BrukerRun too
public override XYData GetMassSpectrum(DeconTools.Backend.Core.ScanSet scanSet, double minMZ, double maxMZ)
{
Check.Require(scanSet != null, "Can't get mass spectrum; inputted set of scans is null");
Check.Require(scanSet.IndexValues.Count > 0, "Can't get mass spectrum; no scan numbers inputted");
var totScans = this.GetNumMSScans();
var xvals = new double[0];
var yvals = new double[0];
if (scanSet.IndexValues.Count == 1) //this is the case of only wanting one MS spectrum
{
this.RawData.GetSpectrum(scanSet.IndexValues[0], ref xvals, ref yvals, false);
}
else // need to sum spectra
{
//assume: each scan has exactly same x values
//get first spectrum
this.RawData.GetSpectrum(scanSet.IndexValues[0], ref xvals, ref yvals, false);
//
var summedYvals = new double[xvals.Length];
yvals.CopyTo(summedYvals, 0);
for (var i = 1; i < scanSet.IndexValues.Count; i++)
{
this.RawData.GetSpectrum(scanSet.IndexValues[i], ref xvals, ref yvals, false);
for (var n = 0; n < xvals.Length; n++)
{
summedYvals[n] += yvals[n];
}
}
yvals = summedYvals;
}
var xydata = new XYData();
xydata.Xvalues = xvals;
xydata.Yvalues = yvals;
xydata = xydata.TrimData(minMZ, maxMZ);
return(xydata);
}
public void TrimScans(ScanSet scanSet, int maxScansAllowed)
{
Check.Require(maxScansAllowed > 0, "Scans cannot be trimmed to fewer than one");
if (scanSet.IndexValues.Count > maxScansAllowed)
{
var numScansToBeRemoved = (scanSet.IndexValues.Count - maxScansAllowed + 1) / 2;
var newScans = new List <int>();
for (var i = numScansToBeRemoved; i < (scanSet.IndexValues.Count - numScansToBeRemoved); i++) //this loop will cleave off the first n scans and the last n scans
{
newScans.Add(scanSet.IndexValues[i]);
}
scanSet.IndexValues = newScans;
}
}
protected ScanResult(ScanSet scanSet)
{
ScanSet = scanSet;
}
public StandardScanResult(ScanSet scanSet) : base(scanSet)
{
}
/// <summary>
/// Constructor that takes run, LC scan set, and an IMS scan set
/// </summary>
/// <param name="run"></param>
/// <param name="lcScanSet"></param>
/// <param name="scanSet"></param>
public UIMFIsosResult(Run run, ScanSet lcScanSet, IMSScanSet scanSet)
{
Run = run;
ScanSet = lcScanSet;
IMSScanSet = scanSet;
}
public UimfScanResult(ScanSet frameSet)
{
ScanSet = frameSet;
}
public UimfScanResult(ScanSet frameset)
{
this.ScanSet = frameset;
}
public UserState(Run currentRun, ScanSet scanSet, FrameSet frameset)
{
this.currentRun = currentRun;
this.currentScanSet = scanSet;
this.currentFrameSet = frameset;
}
public ScanResult(ScanSet scanset)
{
ScanSet = scanset;
}
public UIMFIsosResult(Run run, ScanSet lcScanset, IMSScanSet scanset)
{
this.Run = run;
this.ScanSet = lcScanset;
this.IMSScanSet = scanset;
}
public virtual XYData GetMassSpectrum(ScanSet lcScanset, ScanSet imsScanset, double minMZ, double maxMZ)
{
throw new NotSupportedException("This overload of GetMassSpectrum is only supported in IMS dataset types");
}
public abstract XYData GetMassSpectrum(ScanSet scanset, double minMZ, double maxMZ);
public virtual XYData GetMassSpectrum(ScanSet scanset)
{
//set a wide mz range so we get everything
return(GetMassSpectrum(scanset, 0, 100000));
}