/// <summary>
/// Open the given file and import scans into the reader.
/// </summary>
/// <returns></returns>
public System.Collections.IEnumerator GetEnumerator()
{
rawFile.SelectInstrument(ThermoBiz.Device.MS, 1);
// Get the first and last scan from the RAW file
int FirstScan = rawFile.RunHeaderEx.FirstSpectrum;
int LastScan = rawFile.RunHeaderEx.LastSpectrum;
for (int iScanNumber = FirstScan; iScanNumber <= LastScan; iScanNumber++)
{
ThermoBiz.Scan thermoScan = ThermoBiz.Scan.FromFile(rawFile, iScanNumber);
IScanFilter scanFilter = rawFile.GetFilterForScanNumber(iScanNumber);
IScanEvent scanEvent = rawFile.GetScanEventForScanNumber(iScanNumber);
if ((int)scanFilter.MSOrder == 1)
{
LastMS1 = iScanNumber;
}
Data.Scan scan = new Data.Scan()
{
ScanNumber = iScanNumber,
ScanEvent = (iScanNumber - LastMS1) + 1,
BasePeakIntensity = thermoScan.ScanStatistics.BasePeakIntensity,
BasePeakMz = thermoScan.ScanStatistics.BasePeakMass,
TotalIonCurrent = thermoScan.ScanStatistics.TIC,
LowestMz = thermoScan.ScanStatistics.LowMass,
HighestMz = thermoScan.ScanStatistics.HighMass,
StartMz = scanFilter.GetMassRange(0).Low,
EndMz = scanFilter.GetMassRange(0).High,
ScanType = ReadScanType(scanFilter.ToString()),
MsOrder = (int)scanFilter.MSOrder,
Polarity = (scanFilter.Polarity == PolarityType.Positive) ? Data.Polarity.Positive : Data.Polarity.Negative,
FilterLine = scanFilter.ToString(),
DetectorType = readDetectorType(scanFilter.MassAnalyzer),
RetentionTime = rawFile.RetentionTimeFromScanNumber(iScanNumber)
};
if (scan.MsOrder > 1)
{
// Get the current scan's activation method while ignoring upstream activation
scan.PrecursorActivationMethod = ConvertActivationType(scanFilter.GetActivation(scan.MsOrder - 2));
// handle dependent scans and not SPS (processed below)
scan.Precursors.Clear();
for (int i = 0; i < scanEvent.MassCount; ++i)
{
var reaction = scanEvent.GetReaction(i);
scan.CollisionEnergy = reaction.CollisionEnergy;
var precursor = new Data.Precursor
{
IsolationWidth = reaction.IsolationWidth,
IsolationMz = reaction.PrecursorMass,
Mz = reaction.PrecursorMass,
OriginalMz = reaction.PrecursorMass
};
scan.Precursors.Add(precursor);
}
}
ThermoBiz.RunHeader runHeader = rawFile.RunHeader;
ThermoBiz.LogEntry trailer = rawFile.GetTrailerExtraInformation(iScanNumber);
for (int i = 0; i < trailer.Length; i++)
{
var value = trailer.Values[i];
if (value == null)
{
continue;
}
switch (trailer.Labels[i])
{
case "Access ID":
int access_id = Convert.ToInt32(value);
if (access_id > 0)
{
scan.PrecursorMasterScanNumber = access_id;
}
break;
case "Scan Description:":
scan.Description = value.Trim();
break;
case "Ion Injection Time (ms):":
scan.IonInjectionTime = double.Parse(value);
break;
case "Elapsed Scan Time (sec):":
scan.ElapsedScanTime = double.Parse(value);
break;
case "Charge State:":
int charge = int.Parse(value);
foreach (var precursor in scan.Precursors)
{
precursor.Charge = charge;
precursor.OriginalCharge = precursor.Charge;
}
break;
case "Master Scan Number:":
scan.PrecursorMasterScanNumber = int.Parse(value);
break;
case "Master Index:":
scan.MasterIndex = int.Parse(value);
break;
case "Monoisotopic M/Z:":
if (Options.RawMonoMz && scan.Precursors.Count > 0)
{
double mz = double.Parse(value);
if (mz > 0)
{
scan.Precursors[0].Mz = mz;
}
}
break;
case "FAIMS CV:":
scan.FaimsCV = (int)double.Parse(value);
break;
case "FAIMS Voltage On:":
scan.FaimsState = (value == "No") ? Data.TriState.Off : Data.TriState.On;
break;
case "SPS Masses:":
string[] spsIonStringArray = value.TrimEnd(',').Split(',');
if (!string.IsNullOrWhiteSpace(spsIonStringArray[0]) && spsIonStringArray.Length > 0)
{
scan.Precursors.Clear();
for (int spsIndex = 0; spsIndex < spsIonStringArray.Length; spsIndex++)
{
if (double.TryParse(spsIonStringArray[spsIndex], out double spsIon))
{
scan.Precursors.Add(new Data.Precursor(spsIon, 0, 1));
}
}
}
break;
}
}
if (scan.PrecursorMasterScanNumber <= 0 && scan.MsOrder > 1)
{
// Try again to set the precursor scan.
SetPrecursorScanNumber(scan);
}
if (scan.MsOrder > 1 && scan.PrecursorMasterScanNumber > rawFile.RunHeader.FirstSpectrum && scan.PrecursorMasterScanNumber < rawFile.RunHeader.LastSpectrum)
{
// Fill precursor information
var parentScan = ThermoBiz.Scan.FromFile(rawFile, scan.PrecursorMasterScanNumber);
if (parentScan != null)
{
foreach (var precursor in scan.Precursors)
{
precursor.Intensity = GetMaxIntensity(parentScan, precursor.IsolationMz, precursor.IsolationWidth);
}
}
}
if (thermoScan.HasCentroidStream)
{
// High res data
CentroidsFromArrays(scan, thermoScan.CentroidScan.Masses, thermoScan.CentroidScan.Intensities, thermoScan.CentroidScan.Baselines, thermoScan.CentroidScan.Noises);
}
else
{
// Low res data
CentroidsFromArrays(scan, thermoScan.PreferredMasses, thermoScan.PreferredIntensities);
}
if (scan.PeakCount > 0)
{
scan.LowestMz = scan.Centroids[0].Mz;
scan.HighestMz = scan.Centroids[scan.PeakCount - 1].Mz;
}
yield return(scan);
}
}
/// <summary>
/// Gets the max intensity found by looking through the peaks in the parent scan.
/// </summary>
///
/// <returns>The max intensity.</returns>
/// <param name="number">the scan number.</param>
/// <param name="targetMz">Target mz.</param>
private double GetMaxIntensity(ThermoBiz.Scan scan, double targetMz, double isolationWidth)
{
bool hasCentroidStream = scan.ScanStatistics.IsCentroidScan && (scan.ScanStatistics.SpectrumPacketType == ThermoBiz.SpectrumPacketType.FtCentroid);
double tolerance = 0.5;
if (isolationWidth > 0.01)
{
tolerance = isolationWidth / 2;
}
else if (hasCentroidStream)
{
tolerance = 0.05;
}
double precursorIntensity = 0;
double[] mzs = null;
double[] intensities = null;
if (hasCentroidStream)
{
var centroidStream = scan.CentroidScan;
mzs = centroidStream.Masses;
intensities = centroidStream.Intensities;
}
else
{
var segmentedScan = scan.SegmentedScan;
mzs = segmentedScan.Positions;
intensities = segmentedScan.Intensities;
}
// Find the nearest peak to the low end.
int low = 0;
int mid = 0;
int hi = 0;
double lowerMz = targetMz - tolerance;
while (hi > low)
{
mid = (int)System.Math.Ceiling((hi - low) / 2.0) + low;
if (mzs[mid] > lowerMz)
{
hi = mid - 1;
}
else
{
low = mid;
}
}
// Iterate until it reaches the upper bound.
for (int i = mid; i < mzs.Length; i++)
{
double mz = mzs[i];
double intensity = intensities[i];
if (System.Math.Abs(targetMz - mz) < tolerance)
{
if (intensity > precursorIntensity)
{
precursorIntensity = intensity;
}
}
// stop if we've gone too far
if (mz - targetMz > tolerance)
{
break;
}
}
return(precursorIntensity);
}