public static int[] ExtractMsm(string filename, IPeakList peakList, IRawFile rawFile, string msmName,
string msmNameBinary, string msmNameIndex, int topx,
double isotopeCorrelationThreshold, SilacType type, out long[] pointers)
{
StreamWriter sw = new StreamWriter(msmName);
BinaryWriter writer = FileUtil.GetBinaryWriter(msmNameBinary);
List <long> filePointers = new List <long>();
List <int> fileScanNumbers = new List <int>();
long filePos = 0;
for (int i = 0; i < rawFile.MS2Count; i++)
{
Spectrum s = rawFile.GetMS2Spectrum(i);
int scanNumber = rawFile.GetScanNumberFromMs2Index(i);
double simpleMz = rawFile.GetMS2MonoisotopicMz(i);
if (double.IsNaN(simpleMz) || simpleMz < 1)
{
simpleMz = peakList.GetMs2Mz(i);
if (double.IsNaN(simpleMz) || simpleMz < 1)
{
simpleMz = 1;
}
}
int charge;
double mz;
double mass;
GetPrecursorInfo(out charge, out mz, out mass, peakList, scanNumber, type, isotopeCorrelationThreshold, simpleMz);
if (rawFile.GetMS2SignalType(i) != SignalType.Centroid)
{
double[] specMasses;
float[] specIntensities;
T01PeakDetection.DetectPeaks(s, false, 3, CentroidPosition.gaussian, out specMasses, out specIntensities);
s = new Spectrum(specMasses, specIntensities);
}
if (topx > 0)
{
s = s.TopX(topx, 100);
}
int sn = rawFile.GetScanNumberFromMs2Index(i);
if (s.Count == 0)
{
continue;
}
StringBuilder sb = new StringBuilder();
writer.Write(s.Count);
for (int j = 0; j < s.Count; j++)
{
sb.AppendFormat("{0:F3}\t{1:F2}\n", s.GetMass(j), s.GetIntensity(j));
writer.Write(s.GetMass(j));
writer.Write(1.0 * s.GetIntensity(j));
}
filePointers.Add(filePos);
fileScanNumbers.Add(sn);
filePos += 16 * s.Count + 4;
sw.WriteLine("BEGIN IONS");
sw.WriteLine("PEPMASS={0:F6}", mz);
if (charge > 0)
{
sw.WriteLine("CHARGE={0}+", charge);
}
else
{
sw.WriteLine("CHARGE=2+ and 3+");
}
sw.WriteLine("TITLE=RawFile: {0} FinneganScanNumber: {1}", filename, sn);
sw.Write(sb.ToString());
sw.WriteLine("END IONS");
sw.WriteLine();
}
writer.Close();
sw.Close();
pointers = filePointers.ToArray();
return(fileScanNumbers.ToArray());
}