private void AddToCache(int timePoint)
{
BinaryData xValues = new BinaryData();
BinaryData yValues = new BinaryData();
for (int i = 0; i < XYDataHelper.XValueTestSet1.Length; i++)
{
xValues.Add(XYDataHelper.XValueTestSet1[i]);
yValues.Add(XYDataHelper.YValueTestSet1[i]);
}
cache.Add(timePoint, new BinarySpectrum(1.5, xValues, yValues));
}
public Domain.ISpectrum GetSpectrum(int timePoint, TimeUnit timeUnits, double mzLower, double mzUpper)
{
if (spectrumCache.IsInCache(timePoint))
{
Domain.ISpectrum spectrum = spectrumCache.Read(timePoint);
if (mzLower == 0 && mzUpper == double.MaxValue)
{
return spectrum;
}
else
{
IList<double> xVals = spectrum.XValues;
IList<double> yVals = spectrum.YValues;
BinaryData xValues = new BinaryData();
BinaryData yValues = new BinaryData();
for (int i = 0; i < xVals.Count; i++)
{
if (xVals[i] >= mzLower && xVals[i] <= mzUpper)
{
xValues.Add(xVals[i]);
yValues.Add(yVals[i]);
}
}
return new BinarySpectrum(spectrum.StartRT, xValues, yValues);
}
}
else
{
pwiz.CLI.msdata.Spectrum spectrumFromFile = run.spectrumList.spectrum(timePoint, true);
string level = (string)spectrumFromFile.cvParam(pwiz.CLI.CVID.MS_ms_level).value;
if (level == "1")
{
double rt = RtToTimePointConverter.CalculateRT(spectrumFromFile, timeUnits);
BinaryDataArray mzArray = spectrumFromFile.getMZArray();
BinaryDataArray intensityArray = spectrumFromFile.getIntensityArray();
BinaryData mzData = mzArray.data;
BinaryData intensityData = intensityArray.data;
int totalDataPoints = mzData.Count;
AddSpectrumToCacheIfNotPresent(timePoint, new BinarySpectrum(rt, mzData, intensityData));
return FilterMassList(rt, mzData, intensityData, mzLower, mzUpper);
}
}
return new Domain.Spectrum(0, new List<XYPoint>());
}
public override Spectrum spectrum(int index, bool getBinaryData)
{
Spectrum s = base.spectrum(index, true);
if (s.cvParam(CVID.MS_MSn_spectrum).empty() ||
(int)s.cvParam(CVID.MS_ms_level).value == 1)
{
if (!getBinaryData)
{
s.binaryDataArrays.Clear();
}
return(s);
}
PrecursorList pl = s.precursors;
BinaryData mzArray = s.getMZArray().data;
BinaryData intensityArray = s.getIntensityArray().data;
PointDataMap <double> mziMap = new PointDataMap <double>();
for (int i = 0; i < (int)s.defaultArrayLength; ++i)
{
mziMap.Insert(mzArray[i], intensityArray[i]);
}
Set <double> pointsToRemove = new Set <double>();
foreach (Precursor p in pl)
{
foreach (SelectedIon si in p.selectedIons)
{
double mz = (double)si.cvParam(CVID.MS_selected_ion_m_z).value;
PointDataMap <double> .Enumerator itr = mziMap.LowerBound(mz - 4.0);
if (itr != null && itr.IsValid)
{
while (itr.IsValid && itr.Current.Key - mz < 4.0)
{
pointsToRemove.Add(itr.Current.Key);
itr.MoveNext();
}
}
CVParam chargeParam = si.cvParam(CVID.MS_charge_state);
if (!chargeParam.empty())
{
int z = (int)chargeParam.value;
for (int i = 1; i < z; ++i)
{
double strippedMz = (mz * z) / (z - i);
itr = mziMap.LowerBound(strippedMz - 4.0);
if (itr != null && itr.IsValid)
{
while (itr.IsValid && itr.Current.Key - strippedMz < 4.0)
{
pointsToRemove.Add(itr.Current.Key);
itr.MoveNext();
}
}
}
}
}
}
if (getBinaryData)
{
mzArray.Clear();
intensityArray.Clear();
foreach (PointDataMap <double> .MapPair pair in mziMap)
{
if (pointsToRemove.Contains(pair.Key))
{
continue;
}
mzArray.Add(pair.Key);
intensityArray.Add(pair.Value);
}
s.defaultArrayLength = (ulong)mzArray.Count;
}
else
{
s.binaryDataArrays.Clear();
s.defaultArrayLength -= (ulong)pointsToRemove.Count;
}
return(s);
}
private IXYData ExtractTicByManuallyLookingAtEachSpectrumInTheFile(TimeUnit timeUnits)
{
if (ticCache.IsInCache())
{
return ticCache.Read();
}
else
{
BinaryData xVals = new BinaryData();
BinaryData yVals = new BinaryData();
pwiz.CLI.msdata.SpectrumList spectrumList = run.spectrumList;
int timePoints = spectrumList.size();
for (int i = 0; i < timePoints; i++)
{
pwiz.CLI.msdata.Spectrum s = spectrumList.spectrum(i);
Scan scan = null;
if (s.scanList.scans.Count > 0)
{
scan = s.scanList.scans[0];
}
CVParam param;
param = s.cvParam(pwiz.CLI.CVID.MS_ms_level);
int msLevel = !param.empty() ? (int)param.value : 0;
if (msLevel <= 1)
{
param = scan != null ? scan.cvParam(pwiz.CLI.CVID.MS_scan_start_time) : new CVParam();
double scanTime = !param.empty() ? (double)param.value : 0;
// TODO: Duplicated with CalculateRT, reuse RtToTimePointConverter.
if (timeUnits == TimeUnit.Seconds)
{
xVals.Add(scanTime / 60);
}
param = s.cvParam(pwiz.CLI.CVID.MS_total_ion_current);
yVals.Add(!param.empty() ? (double)param.value : 0);
}
}
IXYData tic = new XYBinaryData(xVals, yVals);
ticCache.Set(tic);
return tic;
}
}
private IXYData ExtractTicNativelyFromFile()
{
Chromatogram chromatogram = run.chromatogramList.chromatogram(0, true);
IList<double> xVals = chromatogram.binaryDataArrays[0].data;
IList<double> yVals = chromatogram.binaryDataArrays[1].data;
BinaryData xValues = new BinaryData();
BinaryData yValues = new BinaryData();
for (int i = 0; i < xVals.Count; i++)
{
xValues.Add(xVals[i]);
yValues.Add(yVals[i]);
}
return new XYBinaryData(xValues, yValues);
}
private BinarySpectrum FilterMassList(double rt, IList<double> mzData, IList<double> intensityData, double mzLower, double mzUpper)
{
BinaryData filteredMzData = new BinaryData();
BinaryData filteredIntensityData = new BinaryData();
if (mzLower != 0 && mzUpper != double.MaxValue)
{
for (int i = 0; i < mzData.Count; i++)
{
if (mzData[i] >= mzLower && mzData[i] <= mzUpper)
{
filteredMzData.Add(mzData[i]);
filteredIntensityData.Add(intensityData[i]);
}
}
}
else
{
return new BinarySpectrum(rt, mzData as BinaryData, intensityData as BinaryData);
}
return new BinarySpectrum(rt, filteredMzData, filteredIntensityData);
}
