// second instance method is for ITMS data
public static QuantData QuantifyOneScan(SegmentedScanData segmentedScan, string labelingReagent)
{
(string[] Labels, double[] Masses)reporters = new LabelingReagents().Reagents[labelingReagent];
QuantData quantData = new QuantData();
int index;
for (int i = 0; i < reporters.Masses.Length; i++)
{
double mass = reporters.Masses[i];
int[] indices = segmentedScan.Positions.FindAllIndex1((x) =>
{
if (Math.Abs(x - mass) / mass * 1e6 < 10)
{
return(true);
}
else
{
return(false);
}
});
if (indices.Length > 1)
{
double[] massDiff = new double[indices.Length];
for (int ix = 0; ix < indices.Length; ix++)
{
massDiff[ix] = Math.Abs(segmentedScan.Positions[indices[ix]] - mass);
}
index = Array.Find(indices, (x) => { return(massDiff[x] == massDiff.Min()); });
quantData.Add(reporters.Labels[i], new ReporterIon(segmentedScan.Positions[index],
segmentedScan.Intensities[index], massDiff[index] / mass * 1e6));
}
else
{
if (indices.Length == 1)
{
index = indices[0];
var diff = Math.Abs(segmentedScan.Positions[index] - mass);
quantData.Add(reporters.Labels[i], new ReporterIon(segmentedScan.Positions[index],
segmentedScan.Intensities[index], diff / mass * 1e6));
}
else
{
quantData.Add(reporters.Labels[i], new ReporterIon(0, 0, 0));
}
}
}
return(quantData);
}
public static (CentroidStreamCollection centroids, SegmentScanCollection segments) MsData(IRawDataPlus rawFile, ScanIndex index)
{
rawFile.SelectInstrument(Device.MS, 1);
CentroidStreamCollection centroids = new CentroidStreamCollection();
SegmentScanCollection segments = new SegmentScanCollection();
CentroidStream centroid;
SegmentedScan segment;
var scans = index.allScans;
//var lockTarget = new object(); // this is so we can keep track of progress in the parallel loop
ProgressIndicator P = new ProgressIndicator(scans.Count(), "Extracting scan data");
P.Start();
foreach (int scan in scans.Keys)
{
// first get out the mass spectrum
if (index.allScans[scan].MassAnalyzer == MassAnalyzerType.MassAnalyzerFTMS)
{
centroid = rawFile.GetCentroidStream(scan, false);
centroids[scan] = new CentroidStreamData(centroid);
}
else
{
segment = rawFile.GetSegmentedScanFromScanNumber(scan, null);
segments[scan] = new SegmentedScanData(segment);
}
//lock (lockTarget)
//{
// P.Update();
//}
P.Update();
}
P.Done();
return(centroids, segments);
}
public static void WriteMGF(RawDataCollection rawData, IRawDataPlus rawFile, string outputDirectory, double cutoff = 0, int[] scans = null, double intensityCutoff = 0.01)
{
double intCutoff = 0;
string fileName = ReadWrite.GetPathToFile(outputDirectory, rawData.rawFileName, ".mgf");
MassAnalyzerType ms2MassAnalyzer = rawData.methodData.MassAnalyzers[MSOrderType.Ms2];
List <Operations> operations = new List <Operations> {
Operations.ScanIndex, Operations.MethodData, Operations.TrailerExtras, Operations.RetentionTimes
};
if (ms2MassAnalyzer == MassAnalyzerType.MassAnalyzerFTMS)
{
operations.Add(Operations.Ms2CentroidStreams);
}
else
{
operations.Add(Operations.Ms2SegmentedScans);
}
CheckIfDone.Check(rawData, rawFile, operations);
const int BufferSize = 65536; // 64 Kilobytes
using (StreamWriter f = new StreamWriter(fileName, false, Encoding.UTF8, BufferSize)) //Open a new file, the MGF file
{
// if the scans argument is null, use all scans
if (scans == null)
{
scans = rawData.scanIndex.ScanEnumerators[MSOrderType.Ms2];
}
ProgressIndicator progress = new ProgressIndicator(scans.Count(), String.Format("Writing MGF file"));
foreach (int i in scans)
{
f.WriteLine("\nBEGIN IONS");
f.WriteLine("RAWFILE={0}", rawData.rawFileName);
f.WriteLine("TITLE=Spectrum_{0}", i);
f.WriteLine("SCAN={0}", i);
f.WriteLine("RTINSECONDS={0}", rawData.retentionTimes[i]);
f.WriteLine("PEPMASS={0}", rawData.trailerExtras[i].MonoisotopicMZ);
f.WriteLine("CHARGE={0}", rawData.trailerExtras[i].ChargeState);
if (ms2MassAnalyzer == MassAnalyzerType.MassAnalyzerFTMS)
{
CentroidStreamData centroid = rawData.centroidStreams[i];
if (centroid.Intensities.Length > 0)
{
intCutoff = centroid.Intensities.Max() * intensityCutoff;
}
else
{
intCutoff = 0;
}
for (int j = 0; j < centroid.Masses.Length; j++)
{
//f.WriteLine(Math.Round(centroid.Masses[j], 4).ToString() + " " + Math.Round(centroid.Intensities[j], 4).ToString());
if (centroid.Masses[j] > cutoff & centroid.Intensities[j] > intCutoff)
{
f.WriteLine("{0} {1}", Math.Round(centroid.Masses[j], 5), Math.Round(centroid.Intensities[j], 4));
}
}
}
else
{
SegmentedScanData segments = rawData.segmentedScans[i];
if (segments.Intensities.Length > 0)
{
intCutoff = segments.Intensities.Max() * intensityCutoff;
}
else
{
intCutoff = 0;
}
for (int j = 0; j < segments.Positions.Length; j++)
{
if (segments.Positions[j] > cutoff & segments.Intensities[j] > intCutoff)
{
f.WriteLine("{0} {1}", Math.Round(segments.Positions[j], 5), Math.Round(segments.Intensities[j], 4));
}
}
}
f.WriteLine("END IONS");
progress.Update();
}
progress.Done();
}
Utilities.ConsoleUtils.ClearLastLine();
}
