public void Init(string path)
{
using (FileStream fileStream = new FileStream(path, FileMode.Open, FileAccess.Read))
{
using (StreamReader sr = new StreamReader(fileStream))
{
string line;
List <IPeak> peaks = new List <IPeak>();
int scan_num = 0;
double rention_time = 0;
double precursor_mz = 0;
int precursor_charge = 0;
// Read lines from the file until end of file (EOD) is reached.
while ((line = sr.ReadLine()) != null)
{
if (line.StartsWith("BEGIN"))
{
peaks = new List <IPeak>();
}
else if (line.StartsWith("END"))
{
MS2Spectrum spectrum = new MS2Spectrum(scan_num, rention_time,
precursor_mz, precursor_charge);
spectrum.SetPeaks(peaks);
spectrumTable[scan_num] = spectrum;
}
else if (scan.IsMatch(line))
{
MatchCollection matches = scan.Matches(line);
foreach (Match match in matches)
{
GroupCollection groups = match.Groups;
scan_num = int.Parse(groups[1].Value);
break;
}
}
else if (rt_second.IsMatch(line))
{
MatchCollection matches = rt_second.Matches(line);
foreach (Match match in matches)
{
GroupCollection groups = match.Groups;
rention_time = double.Parse(groups[1].Value);
break;
}
}
else if (pepmass.IsMatch(line))
{
MatchCollection matches = pepmass.Matches(line);
foreach (Match match in matches)
{
GroupCollection groups = match.Groups;
precursor_mz = double.Parse(groups[1].Value);
break;
}
}
else if (charge.IsMatch(line))
{
MatchCollection matches = charge.Matches(line);
foreach (Match match in matches)
{
GroupCollection groups = match.Groups;
precursor_charge = int.Parse(groups[1].Value);
break;
}
}
else if (mz_intensity.IsMatch(line))
{
MatchCollection matches = mz_intensity.Matches(line);
foreach (Match match in matches)
{
GroupCollection groups = match.Groups;
peaks.Add(new GeneralPeak(double.Parse(groups[1].Value),
double.Parse(groups[2].Value)));
break;
}
}
}
}
}
}
void GenerateTasks()
{
if (Path.GetExtension(msPath) == ".mgf")
{
MGFSpectrumReader reader = new MGFSpectrumReader();
reader.Init(msPath);
Dictionary <int, MS2Spectrum> spectraData = reader.GetSpectrum();
foreach (int scan in spectraData.Keys)
{
MS2Spectrum spectrum = spectraData[scan];
SearchTask searchTask = new SearchTask(spectrum,
spectrum.PrecursorMZ(), spectrum.PrecursorCharge());
tasks.Enqueue(searchTask);
readingCounter.Add(spectraData.Count);
}
}
else
{
ISpectrumReader reader = new ThermoRawSpectrumReader();
LocalMaximaPicking picking = new LocalMaximaPicking();
IProcess process = new WeightedAveraging(new LocalNeighborPicking());
reader.Init(msPath);
int start = reader.GetFirstScan();
int end = reader.GetLastScan();
Dictionary <int, List <int> > scanGroup = new Dictionary <int, List <int> >();
int current = -1;
for (int i = start; i < end; i++)
{
if (reader.GetMSnOrder(i) == 1)
{
current = i;
scanGroup[i] = new List <int>();
}
else if (reader.GetMSnOrder(i) == 2)
{
scanGroup[current].Add(i);
}
}
Parallel.ForEach(scanGroup,
new ParallelOptions {
MaxDegreeOfParallelism = SearchingParameters.Access.ThreadNums
},
(scanPair) =>
{
if (scanPair.Value.Count > 0)
{
ISpectrum ms1 = reader.GetSpectrum(scanPair.Key);
foreach (int i in scanPair.Value)
{
double mz = reader.GetPrecursorMass(i, reader.GetMSnOrder(i));
List <IPeak> ms1Peaks = FilterPeaks(ms1.GetPeaks(), mz, searchRange);
if (ms1Peaks.Count() == 0)
{
continue;
}
ICharger charger = new Patterson();
int charge = charger.Charge(ms1Peaks, mz - searchRange, mz + searchRange);
// insert pseudo peaks for large gap
List <IPeak> peaks = new List <IPeak>();
double precision = 0.02;
double last = ms1Peaks.First().GetMZ();
foreach (IPeak peak in ms1Peaks)
{
if (peak.GetMZ() - last > precision)
{
peaks.Add(new GeneralPeak(last + precision / 2, 0));
peaks.Add(new GeneralPeak(peak.GetMZ() - precision / 2, 0));
}
peaks.Add(peak);
last = peak.GetMZ();
}
List <IPeak> majorPeaks = picking.Process(peaks);
// find evelope cluster
EnvelopeProcess envelope = new EnvelopeProcess();
var cluster = envelope.Cluster(majorPeaks, mz, charge);
if (cluster.Count == 0)
{
continue;
}
// find monopeak
Averagine averagine = new Averagine(AveragineType.GlycoPeptide);
BrainCSharp braincs = new BrainCSharp();
MonoisotopicSearcher searcher = new MonoisotopicSearcher(averagine, braincs);
MonoisotopicScore result = searcher.Search(mz, charge, cluster);
double precursorMZ = result.GetMZ();
// search
ISpectrum ms2 = reader.GetSpectrum(i);
ms2 = process.Process(ms2);
SearchTask searchTask = new SearchTask(ms2, precursorMZ, charge);
tasks.Enqueue(searchTask);
}
}
readingCounter.Add(scanGroup.Count);
});
}
}
