public PeptideSpectrumMatch(TandemMassSpectrum spectrum, Peptide peptide, MassTolerance productMassTolerance)
{
Spectrum = spectrum;
Peptide = peptide;
PrecursorMassErrorDa = spectrum.PrecursorMass - (precursorMassType == MassType.Average ? peptide.AverageMass : peptide.MonoisotopicMass);
PrecursorMassErrorPpm = PrecursorMassErrorDa / (precursorMassType == MassType.Average ? peptide.AverageMass : peptide.MonoisotopicMass) * 1e6;
ScoreMatch(productMassTolerance);
}
public PeptideSpectrumMatch(TandemMassSpectrum spectrum, Peptide peptide, MassTolerance productMassTolerance)
{
Spectrum = spectrum;
Peptide = peptide;
PrecursorMassErrorDa = spectrum.PrecursorMass - (precursorMassType == MassType.Average ? peptide.AverageMass : peptide.MonoisotopicMass);
PrecursorMassErrorPpm = PrecursorMassErrorDa / (precursorMassType == MassType.Average ? peptide.AverageMass : peptide.MonoisotopicMass) * 1e6;
ScoreMatch(productMassTolerance);
}
// This Init method needs to be called before this object can be used.
// For more info, see how we use these objects in DatabaseSearcher.
//
// We copy the peptide parameter deeply (because these sometimes come
// from reusable buffers) but not the spectrum parameter (because these
// are not reused).
//
// The array product_masses_buf is used for temporary internal storage
// and may be resized. It needs to be local to the current thread; no
// locking is performed. Its contents are not of interest to the
// caller.
//
// The fast_q_sorter object also need to be local to the current
// thread, as its internal state will be modified.
public void Init(TandemMassSpectrum spectrum, Peptide peptide, MassTolerance productMassTolerance,
ref double[] product_masses_buf, FastQSorter fast_q_sorter)
{
Spectrum = spectrum;
if(Peptide == null)
Peptide = new Peptide();
Peptide.CopyFrom(peptide);
PrecursorMassErrorDa = spectrum.PrecursorMass - (precursorMassType == MassType.Average ? peptide.AverageMass : peptide.MonoisotopicMass);
PrecursorMassErrorPpm = PrecursorMassErrorDa / (precursorMassType == MassType.Average ? peptide.AverageMass : peptide.MonoisotopicMass) * 1e6;
ScoreMatch(productMassTolerance, ref product_masses_buf, fast_q_sorter);
}
public void Load(string rawFilepath, int minimumAssumedPrecursorChargeState, int maximumAssumedPrecursorChargeState,
double absoluteThreshold, double relativeThresholdPercent, int maximumNumberOfPeaks,
bool assignChargeStates, int maximumThreads)
{
OnReportTaskWithoutProgress(new EventArgs());
IXRawfile2 raw = (IXRawfile2)new MSFileReader_XRawfile();
raw.Open(rawFilepath);
raw.SetCurrentController(0, 1);
Dictionary<int, double[,]> ms1s;
if(GET_PRECURSOR_MZ_AND_INTENSITY_FROM_MS1)
{
ms1s = new Dictionary<int, double[,]>();
}
int first_scan_number = -1;
raw.GetFirstSpectrumNumber(ref first_scan_number);
int last_scan_number = -1;
raw.GetLastSpectrumNumber(ref last_scan_number);
OnReportTaskWithProgress(new EventArgs());
object progress_lock = new object();
int spectra_processed = 0;
int old_progress = 0;
ParallelOptions parallel_options = new ParallelOptions();
parallel_options.MaxDegreeOfParallelism = maximumThreads;
Parallel.For(first_scan_number, last_scan_number + 1, scan_number =>
{
string scan_filter = null;
raw.GetFilterForScanNum(scan_number, ref scan_filter);
if(!scan_filter.Contains(" ms "))
{
string spectrum_id = "controllerType=0 controllerNumber=1 scan=" + scan_number.ToString();
double retention_time_minutes = double.NaN;
raw.RTFromScanNum(scan_number, ref retention_time_minutes);
int polarity = DeterminePolarity(scan_filter);
string fragmentation_method = GetFragmentationMethod(scan_filter);
double precursor_mz;
double precursor_intensity;
GetPrecursor(ms1s, raw, scan_number, scan_filter, first_scan_number, out precursor_mz, out precursor_intensity);
int charge = DeterminePrecursorCharge(raw, scan_number);
if(polarity < 0)
{
charge = -charge;
}
double[,] label_data = GetFragmentationData(raw, scan_number, scan_filter);
List<MSPeak> peaks = new List<MSPeak>(label_data.GetLength(1));
for(int peak_index = label_data.GetLowerBound(1); peak_index <= label_data.GetUpperBound(1); peak_index++)
{
peaks.Add(new MSPeak(label_data[(int)RawLabelDataColumn.MZ, peak_index],
label_data[(int)RawLabelDataColumn.Intensity, peak_index],
assignChargeStates && (int)RawLabelDataColumn.Charge < label_data.GetLength(0) ? (int)label_data[(int)RawLabelDataColumn.Charge, peak_index] : 0, polarity));
}
peaks = FilterPeaks(peaks, absoluteThreshold, relativeThresholdPercent, maximumNumberOfPeaks);
if(peaks.Count > 0)
{
for(int c = (ALWAYS_USE_PRECURSOR_CHARGE_STATE_RANGE || charge == 0 ? minimumAssumedPrecursorChargeState : charge);
c <= (ALWAYS_USE_PRECURSOR_CHARGE_STATE_RANGE || charge == 0 ? maximumAssumedPrecursorChargeState : charge); c++)
{
double precursor_mass = MSPeak.MassFromMZ(precursor_mz, c);
TandemMassSpectrum spectrum = new TandemMassSpectrum(rawFilepath, scan_number, spectrum_id, null, retention_time_minutes, fragmentation_method, precursor_mz, precursor_intensity, c, precursor_mass, peaks);
lock(this)
{
Add(spectrum);
}
}
}
}
lock(progress_lock)
{
spectra_processed++;
int new_progress = (int)((double)spectra_processed / (last_scan_number - first_scan_number + 1) * 100);
if(new_progress > old_progress)
{
OnUpdateProgress(new ProgressEventArgs(new_progress));
old_progress = new_progress;
}
}
});
raw.Close();
}
public void Load(string mzmlFilepath, int minimumAssumedPrecursorChargeState, int maximumAssumedPrecursorChargeState,
double absoluteThreshold, double relativeThresholdPercent, int maximumNumberOfPeaks,
bool assignChargeStates, bool deisotope, MassTolerance isotopicMZTolerance, int maximumThreads)
{
OnReportTaskWithoutProgress(EventArgs.Empty);
XmlDocument mzML_temp = new XmlDocument();
mzML_temp.Load(mzmlFilepath);
XPathNavigator mzML = mzML_temp.CreateNavigator();
XmlNamespaceManager xnm = new XmlNamespaceManager(mzML.NameTable);
xnm.AddNamespace("mzML", mzML_temp.DocumentElement.NamespaceURI);
Dictionary<string, XPathNodeIterator> referenceable_param_groups = new Dictionary<string, XPathNodeIterator>();
foreach(XPathNavigator referenceable_param_group in mzML.Select("//mzML:mzML/mzML:referenceableParamGroupList/mzML:referenceableParamGroup", xnm))
{
referenceable_param_groups.Add(referenceable_param_group.GetAttribute("id", string.Empty), referenceable_param_group.SelectChildren(XPathNodeType.All));
}
ParallelOptions parallel_options = new ParallelOptions();
parallel_options.MaxDegreeOfParallelism = maximumThreads;
Dictionary<string, SpectrumNavigator> ms1s = null;
if(GET_PRECURSOR_MZ_AND_INTENSITY_FROM_MS1)
{
ms1s = new Dictionary<string, SpectrumNavigator>();
#if NON_MULTITHREADED
foreach(XPathNavigator spectrum_navigator in mzML.Select("//mzML:mzML/mzML:run/mzML:spectrumList/mzML:spectrum", xnm).Cast<XPathNavigator>())
#else
Parallel.ForEach(mzML.Select("//mzML:mzML/mzML:run/mzML:spectrumList/mzML:spectrum", xnm).Cast<XPathNavigator>(), parallel_options, spectrum_navigator =>
#endif
{
string scan_id = spectrum_navigator.GetAttribute("id", string.Empty);
int ms_level = -1;
foreach(XPathNavigator spectrum_child_navigator in spectrum_navigator.SelectChildren(XPathNodeType.All))
{
if(spectrum_child_navigator.Name.Equals("cvParam", StringComparison.OrdinalIgnoreCase))
{
if(spectrum_child_navigator.GetAttribute("name", string.Empty).Equals("ms level", StringComparison.OrdinalIgnoreCase))
{
ms_level = int.Parse(spectrum_child_navigator.GetAttribute("value", string.Empty));
}
}
else if(spectrum_child_navigator.Name.Equals("referenceableParamGroupRef", StringComparison.OrdinalIgnoreCase))
{
foreach(XPathNavigator navigator in referenceable_param_groups[spectrum_child_navigator.GetAttribute("ref", string.Empty)])
{
if(navigator.Name.Equals("cvParam", StringComparison.OrdinalIgnoreCase))
{
if(navigator.GetAttribute("name", string.Empty).Equals("ms level", StringComparison.OrdinalIgnoreCase))
{
ms_level = int.Parse(navigator.GetAttribute("value", string.Empty));
break;
}
}
}
}
}
if(ms_level == 1)
{
lock(ms1s)
{
ms1s.Add(scan_id, new SpectrumNavigator(spectrum_navigator, xnm));
}
}
}
#if !NON_MULTITHREADED
);
#endif
}
int num_spectra = int.Parse(mzML.SelectSingleNode("//mzML:mzML/mzML:run/mzML:spectrumList", xnm).GetAttribute("count", string.Empty));
OnReportTaskWithProgress(EventArgs.Empty);
object progress_lock = new object();
int spectra_processed = 0;
int old_progress = 0;
#if NON_MULTITHREADED
foreach(XPathNavigator spectrum_navigator in mzML.Select("//mzML:mzML/mzML:run/mzML:spectrumList/mzML:spectrum", xnm).Cast<XPathNavigator>())
#else
Parallel.ForEach(mzML.Select("//mzML:mzML/mzML:run/mzML:spectrumList/mzML:spectrum", xnm).Cast<XPathNavigator>(), parallel_options, spectrum_navigator =>
#endif
{
int spectrum_index = int.Parse(spectrum_navigator.GetAttribute("index", string.Empty));
int spectrum_number = spectrum_index + 1;
string spectrum_id = spectrum_navigator.GetAttribute("id", string.Empty);
string spectrum_title = null;
int ms_level = -1;
int polarity = 0;
double retention_time_minutes = double.NaN;
string precursor_scan_id = null;
double precursor_mz = double.NaN;
int charge = 0;
double precursor_intensity = double.NaN;
string fragmentation_method = "collision-induced dissociation";
double[] mz = null;
double[] intensity = null;
foreach(XPathNavigator spectrum_child_navigator in spectrum_navigator.SelectChildren(XPathNodeType.All))
{
if(spectrum_child_navigator.Name.Equals("cvParam", StringComparison.OrdinalIgnoreCase))
{
if(spectrum_child_navigator.GetAttribute("name", string.Empty).Equals("ms level", StringComparison.OrdinalIgnoreCase))
{
ms_level = int.Parse(spectrum_child_navigator.GetAttribute("value", string.Empty));
}
else if(spectrum_child_navigator.GetAttribute("name", string.Empty).Equals("positive scan", StringComparison.OrdinalIgnoreCase))
{
polarity = 1;
}
else if(spectrum_child_navigator.GetAttribute("name", string.Empty).Equals("negative scan", StringComparison.OrdinalIgnoreCase))
{
polarity = -1;
}
else if(spectrum_child_navigator.GetAttribute("name", string.Empty).Equals("spectrum title", StringComparison.OrdinalIgnoreCase))
{
spectrum_title = spectrum_child_navigator.GetAttribute("value", string.Empty);
}
}
else if(spectrum_child_navigator.Name.Equals("referenceableParamGroupRef", StringComparison.OrdinalIgnoreCase))
{
foreach(XPathNavigator navigator in referenceable_param_groups[spectrum_child_navigator.GetAttribute("ref", string.Empty)])
{
if(navigator.Name.Equals("cvParam", StringComparison.OrdinalIgnoreCase))
{
if(navigator.GetAttribute("name", string.Empty).Equals("ms level", StringComparison.OrdinalIgnoreCase))
{
ms_level = int.Parse(navigator.GetAttribute("value", string.Empty));
}
else if(navigator.GetAttribute("name", string.Empty).Equals("positive scan", StringComparison.OrdinalIgnoreCase))
{
polarity = 1;
}
else if(navigator.GetAttribute("name", string.Empty).Equals("negative scan", StringComparison.OrdinalIgnoreCase))
{
polarity = -1;
}
}
}
}
else if(spectrum_child_navigator.Name.Equals("scanList", StringComparison.OrdinalIgnoreCase))
{
foreach(XPathNavigator navigator in spectrum_child_navigator.Select("mzML:scan/mzML:cvParam", xnm))
{
if(navigator.GetAttribute("name", string.Empty).Equals("scan start time", StringComparison.OrdinalIgnoreCase))
{
retention_time_minutes = double.Parse(navigator.GetAttribute("value", string.Empty), CultureInfo.InvariantCulture);
if(navigator.GetAttribute("unitName", string.Empty).StartsWith("s", StringComparison.OrdinalIgnoreCase))
{
retention_time_minutes = TimeSpan.FromSeconds(retention_time_minutes).TotalMinutes;
}
}
}
}
else if(spectrum_child_navigator.Name.Equals("precursorList", StringComparison.OrdinalIgnoreCase))
{
XPathNavigator precursor_node = spectrum_child_navigator.SelectSingleNode("mzML:precursor", xnm);
precursor_scan_id = precursor_node.GetAttribute("spectrumRef", string.Empty);
foreach(XPathNavigator navigator in precursor_node.Select("mzML:selectedIonList/mzML:selectedIon/mzML:cvParam", xnm))
{
if(navigator.GetAttribute("name", string.Empty).Equals("selected ion m/z", StringComparison.OrdinalIgnoreCase))
{
precursor_mz = double.Parse(navigator.GetAttribute("value", string.Empty), CultureInfo.InvariantCulture);
}
else if(navigator.GetAttribute("name", string.Empty).Equals("charge state", StringComparison.OrdinalIgnoreCase))
{
charge = int.Parse(navigator.GetAttribute("value", string.Empty));
if(polarity < 0)
{
charge = -charge;
}
}
else if(navigator.GetAttribute("name", string.Empty).Equals("peak intensity", StringComparison.OrdinalIgnoreCase))
{
precursor_intensity = double.Parse(navigator.GetAttribute("value", string.Empty), CultureInfo.InvariantCulture);
}
}
XPathNavigator navigator2 = spectrum_child_navigator.SelectSingleNode("mzML:precursor/mzML:activation/mzML:cvParam", xnm);
if(navigator2 != null)
{
fragmentation_method = navigator2.GetAttribute("name", string.Empty);
}
}
else if(spectrum_child_navigator.Name.Equals("binaryDataArrayList", StringComparison.OrdinalIgnoreCase))
{
ReadDataFromSpectrumNavigator(spectrum_child_navigator.Select("mzML:binaryDataArray/*", xnm), out mz, out intensity);
}
if(ms_level == 1)
{
break;
}
}
if(ms_level >= 2)
{
if(GET_PRECURSOR_MZ_AND_INTENSITY_FROM_MS1 && precursor_scan_id != null)
{
SpectrumNavigator ms1;
if(ms1s.TryGetValue(precursor_scan_id, out ms1))
{
double[] ms1_mz;
double[] ms1_intensity;
ms1.GetSpectrum(out ms1_mz, out ms1_intensity);
int index = -1;
for(int i = ms1_mz.GetLowerBound(0); i <= ms1_mz.GetUpperBound(0); i++)
{
if(index < 0 || Math.Abs(ms1_mz[i] - precursor_mz) < Math.Abs(ms1_mz[index] - precursor_mz))
{
index = i;
}
}
precursor_mz = ms1_mz[index];
precursor_intensity = ms1_intensity[index];
}
}
if(mz != null && intensity != null && mz.Length > 0 && intensity.Length > 0)
{
List<MSPeak> peaks = new List<MSPeak>(mz.Length);
for(int i = 0; i < mz.Length; i++)
{
peaks.Add(new MSPeak(mz[i], intensity[i], 0, polarity));
}
peaks = FilterPeaks(peaks, absoluteThreshold, relativeThresholdPercent, maximumNumberOfPeaks);
if(peaks.Count > 0)
{
peaks.Sort(MSPeak.AscendingMZComparison);
for(int c = (ALWAYS_USE_PRECURSOR_CHARGE_STATE_RANGE || charge == 0 ? minimumAssumedPrecursorChargeState : charge);
c <= (ALWAYS_USE_PRECURSOR_CHARGE_STATE_RANGE || charge == 0 ? maximumAssumedPrecursorChargeState : charge); c++)
{
List<MSPeak> new_peaks = peaks;
if(assignChargeStates)
{
new_peaks = AssignChargeStates(new_peaks, c, polarity, isotopicMZTolerance);
if(deisotope)
{
new_peaks = Deisotope(new_peaks, c, polarity, isotopicMZTolerance);
}
}
double precursor_mass = MSPeak.MassFromMZ(precursor_mz, c);
TandemMassSpectrum spectrum = new TandemMassSpectrum(mzmlFilepath, spectrum_number, spectrum_id, spectrum_title, retention_time_minutes, fragmentation_method, precursor_mz, precursor_intensity, c, precursor_mass, new_peaks);
lock(this)
{
Add(spectrum);
}
}
}
}
}
lock(progress_lock)
{
spectra_processed++;
int new_progress = (int)((double)spectra_processed / num_spectra * 100);
if(new_progress > old_progress)
{
OnUpdateProgress(new ProgressEventArgs(new_progress));
old_progress = new_progress;
}
}
}
#if !NON_MULTITHREADED
);
#endif
}
public void Load(string mzmlFilepath, int minimumAssumedPrecursorChargeState, int maximumAssumedPrecursorChargeState,
double absoluteThreshold, double relativeThresholdPercent, int maximumNumberOfPeaks,
bool assignChargeStates, bool deisotope, MassTolerance isotopicMZTolerance, int maximumThreads)
{
OnReportTaskWithoutProgress(EventArgs.Empty);
XmlDocument mzML_temp = new XmlDocument();
mzML_temp.Load(mzmlFilepath);
XPathNavigator mzML = mzML_temp.CreateNavigator();
XmlNamespaceManager xnm = new XmlNamespaceManager(mzML.NameTable);
xnm.AddNamespace("mzML", mzML_temp.DocumentElement.NamespaceURI);
Dictionary<string, XPathNodeIterator> referenceable_param_groups = new Dictionary<string, XPathNodeIterator>();
foreach(XPathNavigator referenceable_param_group in mzML.Select("//mzML:mzML/mzML:referenceableParamGroupList/mzML:referenceableParamGroup", xnm))
{
referenceable_param_groups.Add(referenceable_param_group.GetAttribute("id", string.Empty), referenceable_param_group.SelectChildren(XPathNodeType.All));
}
ParallelOptions parallel_options = new ParallelOptions();
parallel_options.MaxDegreeOfParallelism = maximumThreads;
Dictionary<string, SpectrumNavigator> ms1s = null;
if(GET_PRECURSOR_MZ_AND_INTENSITY_FROM_MS1)
{
ms1s = new Dictionary<string, SpectrumNavigator>();
#if NON_MULTITHREADED
foreach(XPathNavigator spectrum_navigator in mzML.Select("//mzML:mzML/mzML:run/mzML:spectrumList/mzML:spectrum", xnm).Cast<XPathNavigator>())
#else
Parallel.ForEach(mzML.Select("//mzML:mzML/mzML:run/mzML:spectrumList/mzML:spectrum", xnm).Cast<XPathNavigator>(), parallel_options, spectrum_navigator =>
#endif
{
string scan_id = spectrum_navigator.GetAttribute("id", string.Empty);
int ms_level = -1;
foreach(XPathNavigator spectrum_child_navigator in spectrum_navigator.SelectChildren(XPathNodeType.All))
{
if(spectrum_child_navigator.Name.Equals("cvParam", StringComparison.OrdinalIgnoreCase))
{
if(spectrum_child_navigator.GetAttribute("name", string.Empty).Equals("ms level", StringComparison.OrdinalIgnoreCase))
{
ms_level = int.Parse(spectrum_child_navigator.GetAttribute("value", string.Empty));
}
}
else if(spectrum_child_navigator.Name.Equals("referenceableParamGroupRef", StringComparison.OrdinalIgnoreCase))
{
foreach(XPathNavigator navigator in referenceable_param_groups[spectrum_child_navigator.GetAttribute("ref", string.Empty)])
{
if(navigator.Name.Equals("cvParam", StringComparison.OrdinalIgnoreCase))
{
if(navigator.GetAttribute("name", string.Empty).Equals("ms level", StringComparison.OrdinalIgnoreCase))
{
ms_level = int.Parse(navigator.GetAttribute("value", string.Empty));
break;
}
}
}
}
}
if(ms_level == 1)
{
lock(ms1s)
{
ms1s.Add(scan_id, new SpectrumNavigator(spectrum_navigator, xnm));
}
}
}
#if !NON_MULTITHREADED
);
#endif
}
int num_spectra = int.Parse(mzML.SelectSingleNode("//mzML:mzML/mzML:run/mzML:spectrumList", xnm).GetAttribute("count", string.Empty));
OnReportTaskWithProgress(EventArgs.Empty);
object progress_lock = new object();
int spectra_processed = 0;
int old_progress = 0;
#if NON_MULTITHREADED
foreach(XPathNavigator spectrum_navigator in mzML.Select("//mzML:mzML/mzML:run/mzML:spectrumList/mzML:spectrum", xnm).Cast<XPathNavigator>())
#else
Parallel.ForEach(mzML.Select("//mzML:mzML/mzML:run/mzML:spectrumList/mzML:spectrum", xnm).Cast<XPathNavigator>(), parallel_options, spectrum_navigator =>
#endif
{
int spectrum_index = int.Parse(spectrum_navigator.GetAttribute("index", string.Empty));
int spectrum_number = spectrum_index + 1;
string spectrum_id = spectrum_navigator.GetAttribute("id", string.Empty);
string spectrum_title = null;
int ms_level = -1;
int polarity = 0;
double retention_time_minutes = double.NaN;
string precursor_scan_id = null;
double precursor_mz = double.NaN;
int charge = 0;
double precursor_intensity = double.NaN;
string fragmentation_method = "collision-induced dissociation";
double[] mz = null;
double[] intensity = null;
foreach(XPathNavigator spectrum_child_navigator in spectrum_navigator.SelectChildren(XPathNodeType.All))
{
if(spectrum_child_navigator.Name.Equals("cvParam", StringComparison.OrdinalIgnoreCase))
{
if(spectrum_child_navigator.GetAttribute("name", string.Empty).Equals("ms level", StringComparison.OrdinalIgnoreCase))
{
ms_level = int.Parse(spectrum_child_navigator.GetAttribute("value", string.Empty));
}
else if(spectrum_child_navigator.GetAttribute("name", string.Empty).Equals("positive scan", StringComparison.OrdinalIgnoreCase))
{
polarity = 1;
}
else if(spectrum_child_navigator.GetAttribute("name", string.Empty).Equals("negative scan", StringComparison.OrdinalIgnoreCase))
{
polarity = -1;
}
else if(spectrum_child_navigator.GetAttribute("name", string.Empty).Equals("spectrum title", StringComparison.OrdinalIgnoreCase))
{
spectrum_title = spectrum_child_navigator.GetAttribute("value", string.Empty);
}
}
else if(spectrum_child_navigator.Name.Equals("referenceableParamGroupRef", StringComparison.OrdinalIgnoreCase))
{
foreach(XPathNavigator navigator in referenceable_param_groups[spectrum_child_navigator.GetAttribute("ref", string.Empty)])
{
if(navigator.Name.Equals("cvParam", StringComparison.OrdinalIgnoreCase))
{
if(navigator.GetAttribute("name", string.Empty).Equals("ms level", StringComparison.OrdinalIgnoreCase))
{
ms_level = int.Parse(navigator.GetAttribute("value", string.Empty));
}
else if(navigator.GetAttribute("name", string.Empty).Equals("positive scan", StringComparison.OrdinalIgnoreCase))
{
polarity = 1;
}
else if(navigator.GetAttribute("name", string.Empty).Equals("negative scan", StringComparison.OrdinalIgnoreCase))
{
polarity = -1;
}
}
}
}
else if(spectrum_child_navigator.Name.Equals("scanList", StringComparison.OrdinalIgnoreCase))
{
foreach(XPathNavigator navigator in spectrum_child_navigator.Select("mzML:scan/mzML:cvParam", xnm))
{
if(navigator.GetAttribute("name", string.Empty).Equals("scan start time", StringComparison.OrdinalIgnoreCase))
{
retention_time_minutes = double.Parse(navigator.GetAttribute("value", string.Empty), CultureInfo.InvariantCulture);
if(navigator.GetAttribute("unitName", string.Empty).StartsWith("s", StringComparison.OrdinalIgnoreCase))
{
retention_time_minutes = TimeSpan.FromSeconds(retention_time_minutes).TotalMinutes;
}
}
}
}
else if(spectrum_child_navigator.Name.Equals("precursorList", StringComparison.OrdinalIgnoreCase))
{
XPathNavigator precursor_node = spectrum_child_navigator.SelectSingleNode("mzML:precursor", xnm);
precursor_scan_id = precursor_node.GetAttribute("spectrumRef", string.Empty);
foreach(XPathNavigator navigator in precursor_node.Select("mzML:selectedIonList/mzML:selectedIon/mzML:cvParam", xnm))
{
if(navigator.GetAttribute("name", string.Empty).Equals("selected ion m/z", StringComparison.OrdinalIgnoreCase))
{
precursor_mz = double.Parse(navigator.GetAttribute("value", string.Empty), CultureInfo.InvariantCulture);
}
else if(navigator.GetAttribute("name", string.Empty).Equals("charge state", StringComparison.OrdinalIgnoreCase))
{
charge = int.Parse(navigator.GetAttribute("value", string.Empty));
if(polarity < 0)
{
charge = -charge;
}
}
else if(navigator.GetAttribute("name", string.Empty).Equals("peak intensity", StringComparison.OrdinalIgnoreCase))
{
precursor_intensity = double.Parse(navigator.GetAttribute("value", string.Empty), CultureInfo.InvariantCulture);
}
}
XPathNavigator navigator2 = spectrum_child_navigator.SelectSingleNode("mzML:precursor/mzML:activation/mzML:cvParam", xnm);
if(navigator2 != null)
{
fragmentation_method = navigator2.GetAttribute("name", string.Empty);
}
}
else if(spectrum_child_navigator.Name.Equals("binaryDataArrayList", StringComparison.OrdinalIgnoreCase))
{
ReadDataFromSpectrumNavigator(spectrum_child_navigator.Select("mzML:binaryDataArray/*", xnm), out mz, out intensity);
}
if(ms_level == 1)
{
break;
}
}
if(ms_level >= 2)
{
if(GET_PRECURSOR_MZ_AND_INTENSITY_FROM_MS1 && precursor_scan_id != null)
{
SpectrumNavigator ms1;
if(ms1s.TryGetValue(precursor_scan_id, out ms1))
{
double[] ms1_mz;
double[] ms1_intensity;
ms1.GetSpectrum(out ms1_mz, out ms1_intensity);
int index = -1;
for(int i = ms1_mz.GetLowerBound(0); i <= ms1_mz.GetUpperBound(0); i++)
{
if(index < 0 || Math.Abs(ms1_mz[i] - precursor_mz) < Math.Abs(ms1_mz[index] - precursor_mz))
{
index = i;
}
}
precursor_mz = ms1_mz[index];
precursor_intensity = ms1_intensity[index];
}
}
if(mz != null && intensity != null && mz.Length > 0 && intensity.Length > 0)
{
List<MSPeak> peaks = new List<MSPeak>(mz.Length);
for(int i = 0; i < mz.Length; i++)
{
peaks.Add(new MSPeak(mz[i], intensity[i], 0, polarity));
}
peaks = FilterPeaks(peaks, absoluteThreshold, relativeThresholdPercent, maximumNumberOfPeaks);
if(peaks.Count > 0)
{
peaks.Sort(MSPeak.AscendingMZComparison);
for(int c = (ALWAYS_USE_PRECURSOR_CHARGE_STATE_RANGE || charge == 0 ? minimumAssumedPrecursorChargeState : charge);
c <= (ALWAYS_USE_PRECURSOR_CHARGE_STATE_RANGE || charge == 0 ? maximumAssumedPrecursorChargeState : charge); c++)
{
List<MSPeak> new_peaks = peaks;
if(assignChargeStates)
{
new_peaks = AssignChargeStates(new_peaks, c, polarity, isotopicMZTolerance);
if(deisotope)
{
new_peaks = Deisotope(new_peaks, c, polarity, isotopicMZTolerance);
}
}
double precursor_mass = MSPeak.MassFromMZ(precursor_mz, c);
TandemMassSpectrum spectrum = new TandemMassSpectrum(mzmlFilepath, spectrum_number, spectrum_id, spectrum_title, retention_time_minutes, fragmentation_method, precursor_mz, precursor_intensity, c, precursor_mass, new_peaks);
lock(this)
{
Add(spectrum);
}
}
}
}
}
lock(progress_lock)
{
spectra_processed++;
int new_progress = (int)((double)spectra_processed / num_spectra * 100);
if(new_progress > old_progress)
{
OnUpdateProgress(new ProgressEventArgs(new_progress));
old_progress = new_progress;
}
}
}
#if !NON_MULTITHREADED
);
#endif
}
public static int AscendingPrecursorMassComparison(TandemMassSpectrum left, TandemMassSpectrum right)
{
return(left.PrecursorMass.CompareTo(right.PrecursorMass));
}
public void Load(string rawFilepath, int minimumAssumedPrecursorChargeState, int maximumAssumedPrecursorChargeState,
double absoluteThreshold, double relativeThresholdPercent, int maximumNumberOfPeaks,
bool assignChargeStates, int maximumThreads)
{
OnReportTaskWithoutProgress(new EventArgs());
IXRawfile2 raw = (IXRawfile2) new MSFileReader_XRawfile();
raw.Open(rawFilepath);
raw.SetCurrentController(0, 1);
Dictionary <int, double[, ]> ms1s;
if (GET_PRECURSOR_MZ_AND_INTENSITY_FROM_MS1)
{
ms1s = new Dictionary <int, double[, ]>();
}
int first_scan_number = -1;
raw.GetFirstSpectrumNumber(ref first_scan_number);
int last_scan_number = -1;
raw.GetLastSpectrumNumber(ref last_scan_number);
OnReportTaskWithProgress(new EventArgs());
object progress_lock = new object();
int spectra_processed = 0;
int old_progress = 0;
ParallelOptions parallel_options = new ParallelOptions();
parallel_options.MaxDegreeOfParallelism = maximumThreads;
Parallel.For(first_scan_number, last_scan_number + 1, scan_number =>
{
string scan_filter = null;
raw.GetFilterForScanNum(scan_number, ref scan_filter);
if (!scan_filter.Contains(" ms "))
{
string spectrum_id = "controllerType=0 controllerNumber=1 scan=" + scan_number.ToString();
double retention_time_minutes = double.NaN;
raw.RTFromScanNum(scan_number, ref retention_time_minutes);
int polarity = DeterminePolarity(scan_filter);
string fragmentation_method = GetFragmentationMethod(scan_filter);
double precursor_mz;
double precursor_intensity;
GetPrecursor(ms1s, raw, scan_number, scan_filter, first_scan_number, out precursor_mz, out precursor_intensity);
int charge = DeterminePrecursorCharge(raw, scan_number);
if (polarity < 0)
{
charge = -charge;
}
double[,] label_data = GetFragmentationData(raw, scan_number, scan_filter);
List <MSPeak> peaks = new List <MSPeak>(label_data.GetLength(1));
for (int peak_index = label_data.GetLowerBound(1); peak_index <= label_data.GetUpperBound(1); peak_index++)
{
peaks.Add(new MSPeak(label_data[(int)RawLabelDataColumn.MZ, peak_index],
label_data[(int)RawLabelDataColumn.Intensity, peak_index],
assignChargeStates && (int)RawLabelDataColumn.Charge < label_data.GetLength(0) ? (int)label_data[(int)RawLabelDataColumn.Charge, peak_index] : 0, polarity));
}
peaks = FilterPeaks(peaks, absoluteThreshold, relativeThresholdPercent, maximumNumberOfPeaks);
if (peaks.Count > 0)
{
for (int c = (ALWAYS_USE_PRECURSOR_CHARGE_STATE_RANGE || charge == 0 ? minimumAssumedPrecursorChargeState : charge);
c <= (ALWAYS_USE_PRECURSOR_CHARGE_STATE_RANGE || charge == 0 ? maximumAssumedPrecursorChargeState : charge); c++)
{
double precursor_mass = MSPeak.MassFromMZ(precursor_mz, c);
TandemMassSpectrum spectrum = new TandemMassSpectrum(rawFilepath, scan_number, spectrum_id, null, retention_time_minutes, fragmentation_method, precursor_mz, precursor_intensity, c, precursor_mass, peaks);
lock (this)
{
Add(spectrum);
}
}
}
}
lock (progress_lock)
{
spectra_processed++;
int new_progress = (int)((double)spectra_processed / (last_scan_number - first_scan_number + 1) * 100);
if (new_progress > old_progress)
{
OnUpdateProgress(new ProgressEventArgs(new_progress));
old_progress = new_progress;
}
}
});
raw.Close();
}
public static int AscendingPrecursorMassComparison(TandemMassSpectrum left, TandemMassSpectrum right)
{
return left.PrecursorMass.CompareTo(right.PrecursorMass);
}
public void Load(string agilentDFolderPath, int minimumAssumedPrecursorChargeState, int maximumAssumedPrecursorChargeState,
double absoluteThreshold, double relativeThresholdPercent, int maximumNumberOfPeaks,
bool assignChargeStates, bool deisotope, int maximumThreads)
{
OnReportTaskWithoutProgress(new EventArgs());
IMsdrDataReader agilent_d = new MassSpecDataReader();
agilent_d.OpenDataFile(agilentDFolderPath);
Dictionary <int, IBDASpecData> ms1s;
if (GET_PRECURSOR_MZ_AND_INTENSITY_FROM_MS1)
{
ms1s = new Dictionary <int, IBDASpecData>();
}
IMsdrPeakFilter ms1_peak_filter = new MsdrPeakFilter();
IMsdrPeakFilter ms2_peak_filter = new MsdrPeakFilter();
ms2_peak_filter.AbsoluteThreshold = absoluteThreshold;
ms2_peak_filter.RelativeThreshold = relativeThresholdPercent;
ms2_peak_filter.MaxNumPeaks = maximumNumberOfPeaks;
ChargeStateAssignmentWrapper csaw = new ChargeStateAssignmentWrapper();
OnReportTaskWithProgress(new EventArgs());
object progress_lock = new object();
int spectra_processed = 0;
int old_progress = 0;
ParallelOptions parallel_options = new ParallelOptions();
parallel_options.MaxDegreeOfParallelism = maximumThreads;
Parallel.For(0, (int)agilent_d.MSScanFileInformation.TotalScansPresent, parallel_options, row_number =>
{
IMSScanRecord scan_record;
lock (agilent_d)
{
scan_record = agilent_d.GetScanRecord(row_number);
}
if (scan_record.MSLevel == MSLevel.MSMS)
{
IBDASpecData agilent_spectrum;
lock (agilent_d)
{
agilent_spectrum = agilent_d.GetSpectrum(row_number, ms1_peak_filter, ms2_peak_filter);
}
if (agilent_spectrum.TotalDataPoints > 0)
{
int polarity = 0;
if (agilent_spectrum.IonPolarity == IonPolarity.Positive)
{
polarity = 1;
}
else if (agilent_spectrum.IonPolarity == IonPolarity.Negative)
{
polarity = -1;
}
int spectrum_number = row_number + 1;
string scan_id = "scanId=" + agilent_spectrum.ScanId.ToString();
double precursor_mz = agilent_spectrum.MZOfInterest[0].Start;
double precursor_intensity;
if (GET_PRECURSOR_MZ_AND_INTENSITY_FROM_MS1)
{
GetAccurateMZAndIntensity(ms1s, agilent_d, agilent_spectrum.ParentScanId, ref precursor_mz, out precursor_intensity);
}
else
{
agilent_spectrum.GetPrecursorIntensity(out precursor_intensity);
}
int charge;
agilent_spectrum.GetPrecursorCharge(out charge);
if (polarity < 0)
{
charge = -charge;
}
List <MSPeak> peaks = null;
if (!assignChargeStates)
{
peaks = new List <MSPeak>(agilent_spectrum.TotalDataPoints);
for (int i = 0; i < agilent_spectrum.TotalDataPoints; i++)
{
peaks.Add(new MSPeak(agilent_spectrum.XArray[i], agilent_spectrum.YArray[i], 0, polarity));
}
}
for (int c = (ALWAYS_USE_PRECURSOR_CHARGE_STATE_RANGE || charge == 0 ? minimumAssumedPrecursorChargeState : charge);
c <= (ALWAYS_USE_PRECURSOR_CHARGE_STATE_RANGE || charge == 0 ? maximumAssumedPrecursorChargeState : charge); c++)
{
if (assignChargeStates)
{
int[] peak_ids = new int[agilent_spectrum.TotalDataPoints];
double[] peak_mzs = new double[agilent_spectrum.TotalDataPoints];
double[] peak_intensities = new double[agilent_spectrum.TotalDataPoints];
for (int i = 0; i < agilent_spectrum.TotalDataPoints; i++)
{
peak_ids[i] = i;
peak_mzs[i] = agilent_spectrum.XArray[i];
peak_intensities[i] = agilent_spectrum.YArray[i];
}
int[] peak_charge_states = new int[agilent_spectrum.TotalDataPoints];
int[] peak_clusters = new int[agilent_spectrum.TotalDataPoints];
int num_peaks;
lock (csaw)
{
csaw.SetParameters(IsotopeModel.Peptidic, 1, (short)c, false, ACCURACY_C0, ACCURACY_C1);
num_peaks = csaw.AssignChargeStates(peak_ids, peak_mzs, peak_intensities, peak_charge_states, peak_clusters);
}
peaks = new List <MSPeak>(num_peaks);
HashSet <int> observed_peak_clusters = new HashSet <int>();
for (int i = 0; i < num_peaks; i++)
{
bool isotopic_peak = observed_peak_clusters.Contains(peak_clusters[i]);
if (!deisotope || !isotopic_peak)
{
peaks.Add(new MSPeak(peak_mzs[i], peak_intensities[i], peak_charge_states[i], polarity));
if (peak_clusters[i] > 0 && !isotopic_peak)
{
observed_peak_clusters.Add(peak_clusters[i]);
}
}
}
}
double precursor_mass = MSPeak.MassFromMZ(precursor_mz, c);
TandemMassSpectrum spectrum = new TandemMassSpectrum(agilentDFolderPath, spectrum_number, scan_id, null, scan_record.RetentionTime, FRAGMENTATION_METHOD, precursor_mz, precursor_intensity, c, precursor_mass, peaks);
lock (this)
{
Add(spectrum);
}
}
}
}
lock (progress_lock)
{
spectra_processed++;
int new_progress = (int)((double)spectra_processed / agilent_d.MSScanFileInformation.TotalScansPresent * 100);
if (new_progress > old_progress)
{
OnUpdateProgress(new ProgressEventArgs(new_progress));
old_progress = new_progress;
}
}
});
agilent_d.CloseDataFile();
}
public void Load(string agilentDFolderPath, int minimumAssumedPrecursorChargeState, int maximumAssumedPrecursorChargeState,
double absoluteThreshold, double relativeThresholdPercent, int maximumNumberOfPeaks,
bool assignChargeStates, bool deisotope, int maximumThreads)
{
OnReportTaskWithoutProgress(new EventArgs());
IMsdrDataReader agilent_d = new MassSpecDataReader();
agilent_d.OpenDataFile(agilentDFolderPath);
Dictionary<int, IBDASpecData> ms1s;
if(GET_PRECURSOR_MZ_AND_INTENSITY_FROM_MS1)
{
ms1s = new Dictionary<int, IBDASpecData>();
}
IMsdrPeakFilter ms1_peak_filter = new MsdrPeakFilter();
IMsdrPeakFilter ms2_peak_filter = new MsdrPeakFilter();
ms2_peak_filter.AbsoluteThreshold = absoluteThreshold;
ms2_peak_filter.RelativeThreshold = relativeThresholdPercent;
ms2_peak_filter.MaxNumPeaks = maximumNumberOfPeaks;
ChargeStateAssignmentWrapper csaw = new ChargeStateAssignmentWrapper();
OnReportTaskWithProgress(new EventArgs());
object progress_lock = new object();
int spectra_processed = 0;
int old_progress = 0;
ParallelOptions parallel_options = new ParallelOptions();
parallel_options.MaxDegreeOfParallelism = maximumThreads;
Parallel.For(0, (int)agilent_d.MSScanFileInformation.TotalScansPresent, parallel_options, row_number =>
{
IMSScanRecord scan_record;
lock(agilent_d)
{
scan_record = agilent_d.GetScanRecord(row_number);
}
if(scan_record.MSLevel == MSLevel.MSMS)
{
IBDASpecData agilent_spectrum;
lock(agilent_d)
{
agilent_spectrum = agilent_d.GetSpectrum(row_number, ms1_peak_filter, ms2_peak_filter);
}
if(agilent_spectrum.TotalDataPoints > 0)
{
int polarity = 0;
if(agilent_spectrum.IonPolarity == IonPolarity.Positive)
{
polarity = 1;
}
else if(agilent_spectrum.IonPolarity == IonPolarity.Negative)
{
polarity = -1;
}
int spectrum_number = row_number + 1;
string scan_id = "scanId=" + agilent_spectrum.ScanId.ToString();
double precursor_mz = agilent_spectrum.MZOfInterest[0].Start;
double precursor_intensity;
if(GET_PRECURSOR_MZ_AND_INTENSITY_FROM_MS1)
{
GetAccurateMZAndIntensity(ms1s, agilent_d, agilent_spectrum.ParentScanId, ref precursor_mz, out precursor_intensity);
}
else
{
agilent_spectrum.GetPrecursorIntensity(out precursor_intensity);
}
int charge;
agilent_spectrum.GetPrecursorCharge(out charge);
if(polarity < 0)
{
charge = -charge;
}
List<MSPeak> peaks = null;
if(!assignChargeStates)
{
peaks = new List<MSPeak>(agilent_spectrum.TotalDataPoints);
for(int i = 0; i < agilent_spectrum.TotalDataPoints; i++)
{
peaks.Add(new MSPeak(agilent_spectrum.XArray[i], agilent_spectrum.YArray[i], 0, polarity));
}
}
for(int c = (ALWAYS_USE_PRECURSOR_CHARGE_STATE_RANGE || charge == 0 ? minimumAssumedPrecursorChargeState : charge);
c <= (ALWAYS_USE_PRECURSOR_CHARGE_STATE_RANGE || charge == 0 ? maximumAssumedPrecursorChargeState : charge); c++)
{
if(assignChargeStates)
{
int[] peak_ids = new int[agilent_spectrum.TotalDataPoints];
double[] peak_mzs = new double[agilent_spectrum.TotalDataPoints];
double[] peak_intensities = new double[agilent_spectrum.TotalDataPoints];
for(int i = 0; i < agilent_spectrum.TotalDataPoints; i++)
{
peak_ids[i] = i;
peak_mzs[i] = agilent_spectrum.XArray[i];
peak_intensities[i] = agilent_spectrum.YArray[i];
}
int[] peak_charge_states = new int[agilent_spectrum.TotalDataPoints];
int[] peak_clusters = new int[agilent_spectrum.TotalDataPoints];
int num_peaks;
lock(csaw)
{
csaw.SetParameters(IsotopeModel.Peptidic, 1, (short)c, false, ACCURACY_C0, ACCURACY_C1);
num_peaks = csaw.AssignChargeStates(peak_ids, peak_mzs, peak_intensities, peak_charge_states, peak_clusters);
}
peaks = new List<MSPeak>(num_peaks);
HashSet<int> observed_peak_clusters = new HashSet<int>();
for(int i = 0; i < num_peaks; i++)
{
bool isotopic_peak = observed_peak_clusters.Contains(peak_clusters[i]);
if(!deisotope || !isotopic_peak)
{
peaks.Add(new MSPeak(peak_mzs[i], peak_intensities[i], peak_charge_states[i], polarity));
if(peak_clusters[i] > 0 && !isotopic_peak)
{
observed_peak_clusters.Add(peak_clusters[i]);
}
}
}
}
double precursor_mass = MSPeak.MassFromMZ(precursor_mz, c);
TandemMassSpectrum spectrum = new TandemMassSpectrum(agilentDFolderPath, spectrum_number, scan_id, null, scan_record.RetentionTime, FRAGMENTATION_METHOD, precursor_mz, precursor_intensity, c, precursor_mass, peaks);
lock(this)
{
Add(spectrum);
}
}
}
}
lock(progress_lock)
{
spectra_processed++;
int new_progress = (int)((double)spectra_processed / agilent_d.MSScanFileInformation.TotalScansPresent * 100);
if(new_progress > old_progress)
{
OnUpdateProgress(new ProgressEventArgs(new_progress));
old_progress = new_progress;
}
}
});
agilent_d.CloseDataFile();
}
