public MassSpectrum GetMassSpectrum(MassSpectrum metaSpectrum, SpectrumList spectrumList)
{
MassSpectrum spectrum = new MassSpectrum(metaSpectrum, spectrumList.spectrum(metaSpectrum.Index, true));
//MassSpectrum realMetaSpectrum = ( metaSpectrum.Tag as DataGridViewRow ).Tag as MassSpectrum;
//realMetaSpectrum.Element.dataProcessing = spectrum.Element.dataProcessing;
//realMetaSpectrum.Element.defaultArrayLength = spectrum.Element.defaultArrayLength;
return(spectrum);
}
public ParseSpectraFile(string mzmlPath, HashSet <int> scanNumSet, string ext)
{
int currentScanNum = -1;
try
{
MSDataFile msd = new MSDataFile(mzmlPath);
SpectrumList spectrumList = msd.run.spectrumList;
for (int i = 0; i < spectrumList.size(); ++i)
{
Spectrum spectrum = spectrumList.spectrum(i, true);
if (int.Parse(spectrum.cvParams[0].value) == 2)
{
Match match = scanNumPattern.Match(spectrum.id);
currentScanNum = int.Parse(match.Groups[1].Value);
if (scanNumSet.Contains(currentScanNum))
{
MZIntensityPairList mzIntensityPairs = new MZIntensityPairList();
spectrum.getMZIntensityPairs(ref mzIntensityPairs);
Dictionary <float, int> originalPeakList = new Dictionary <float, int>(mzIntensityPairs.Count);
foreach (MZIntensityPair mzIntensity in mzIntensityPairs)
{
originalPeakList[(float)mzIntensity.mz] = (int)mzIntensity.intensity;
}
spectraMap[currentScanNum] = originalPeakList;
}
}
}
}
catch (Exception ex)
{
MessageBox.Show(ex.Message + ": " + currentScanNum, "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
Application.Exit();
}
}
public MassSpectrum GetMassSpectrum( MassSpectrum metaSpectrum, SpectrumList spectrumList )
{
MassSpectrum spectrum = new MassSpectrum( metaSpectrum, spectrumList.spectrum( metaSpectrum.Index, true ) );
//MassSpectrum realMetaSpectrum = ( metaSpectrum.Tag as DataGridViewRow ).Tag as MassSpectrum;
//realMetaSpectrum.Element.dataProcessing = spectrum.Element.dataProcessing;
//realMetaSpectrum.Element.defaultArrayLength = spectrum.Element.defaultArrayLength;
return spectrum;
}
public MassSpectrum GetMassSpectrum( MassSpectrum metaSpectrum, SpectrumList spectrumList )
{
MassSpectrum spectrum = new MassSpectrum( this, spectrumList.spectrum( metaSpectrum.Index, true ) );
spectrum.Tag = metaSpectrum.Tag;
return spectrum;
}
public MassSpectrum GetMassSpectrum( int index, bool getBinaryData, SpectrumList spectrumList )
{
return new MassSpectrum( this, spectrumList.spectrum( index, getBinaryData ) );
}
private static bool HasDriftTimeSpectraInList(SpectrumList spectrumList)
{
if (spectrumList == null || spectrumList.size() == 0)
return false;
// Assume that if any spectra have drift times, all do
using (var spectrum = spectrumList.spectrum(0, false))
{
return GetDriftTimeMsec(spectrum).HasValue;
}
}
private static bool HasSrmSpectraInList(SpectrumList spectrumList)
{
if (spectrumList == null || spectrumList.size() == 0)
return false;
// If the first spectrum is not SRM, the others will not be either
using (var spectrum = spectrumList.spectrum(0, false))
{
return IsSrmSpectrum(spectrum);
}
}
public Tuple <List <Point3D>, BoundingBox> Get3dSpectrum()
{
var result = new Tuple <List <Point3D>, BoundingBox>(new List <Point3D>(),
new BoundingBox
{
MinX = Double.MaxValue, MaxX = Double.MinValue, MinY = Double.MaxValue, MaxY = Double.MinValue
});
var bounds = result.Item2;
if (StartIndex == EndIndex)
{
var s = SpectrumList.spectrum(StartIndex, true);
var mzArray = s.getMZArray().data.Storage();
var intensityArray = s.getIntensityArray().data.Storage();
var mobilityArray = s.GetIonMobilityArray();
if (mobilityArray == null)
{
throw new NullReferenceException("mobilityBDA");
}
for (int j = 0, end = mzArray.Length; j < end; ++j)
{
double mz = mzArray[j];
double intensity = intensityArray[j];
double mobility = mobilityArray[j];
bounds.MinX = Math.Min(bounds.MinX, mz);
bounds.MinY = Math.Min(bounds.MinY, mobility);
bounds.MaxX = Math.Max(bounds.MaxX, mz);
bounds.MaxY = Math.Max(bounds.MaxY, mobility);
result.Item1.Add(new Point3D(mz, mobility, intensity));
}
}
else
{
for (int i = StartIndex, end = EndIndex; i <= end; ++i)
{
var s = SpectrumList.spectrum(i, true);
var mzArray = s.getMZArray().data.Storage();
var intensityArray = s.getIntensityArray().data.Storage();
var mobilityArray = s.GetIonMobilityArray();
for (int j = 0; j < mzArray.Length; ++j)
{
double mz = mzArray[j];
double intensity = intensityArray[j];
double mobility = mobilityArray?.ElementAt(j) ?? (double)s.scanList.scans[0].cvParamChild(CVID.MS_ion_mobility_attribute).value;
bounds.MinX = Math.Min(bounds.MinX, mz);
bounds.MinY = Math.Min(bounds.MinY, mobility);
bounds.MaxX = Math.Max(bounds.MaxX, mz);
bounds.MaxY = Math.Max(bounds.MaxY, mobility);
result.Item1.Add(new Point3D(mz, mobility, intensity));
}
}
}
return(result);
}
protected string parseMsLevel(int index)
{
return(spectrumList.spectrum(index).cvParamChild(CVID.MS_ms_level).value.ToString());
}