public MyScanContainer(IEnumerable <SimpleSpectrum> spectra)
{
SimpleSpectrum[] allSpectra = spectra.ToArray();
SimpleSpectrum previous = null;
for (int i = 0; i < allSpectra.Length; i++)
{
SimpleSpectrum current = allSpectra[i];
if (current.MsLevel == 1)
{
originalMs1Spectra.Add(current);
}
else
{
originalMsnSpectra.Add(current);
}
// compute the scan duration of the previous scan
if (i == 0)
{
previous = current;
}
else
{
double previousDuration = (current.ScanStartTime - previous.ScanStartTime) * 60;
scanDurations.Add(previous.ScanNumber, previousDuration);
previous = current;
}
}
}
// Use this for initialization
void Start()
{
spectrumAnalyzer = spectrumAsset.GetComponent <SimpleSpectrum>();
//ps = GetComponent<ParticleSystem>();
pShape = ps.shape;
pMain = ps.main;
vMain = ps.velocityOverLifetime;
}
public bool SetCustomScan(ICustomScan cs)
{
// select whether to generate ms1 or msn spectra from the read mzML data
List <SimpleSpectrum> spectraList = null;
if (cs.Values["ScanType"] == "Full")
{
// if empty, copy ms1 spectra from the original list
if (this.myScanContainer.ms1Spectra.Count == 0)
{
this.myScanContainer.ms1Spectra = new List <SimpleSpectrum>(this.myScanContainer.originalMs1Spectra);
}
spectraList = this.myScanContainer.ms1Spectra;
}
else if (cs.Values["ScanType"] == "MSn")
{
// if empty, copy msn spectra from the original list
if (this.myScanContainer.msnSpectra.Count == 0)
{
this.myScanContainer.msnSpectra = new List <SimpleSpectrum>(this.myScanContainer.originalMsnSpectra);
}
spectraList = this.myScanContainer.msnSpectra;
}
// if we can actually generate a custom scan ...
if (spectraList.Count > 0)
{
// pop a spectrum from the list
SimpleSpectrum current = spectraList[0];
spectraList.RemoveAt(0);
// pretend to do a scan for some time
double scanDuration = this.myScanContainer.scanDurations.ContainsKey(current.ScanNumber) ?
this.myScanContainer.scanDurations[current.ScanNumber] : 0.25;
//Console.WriteLine("Scan number={0} duration={1}", current.ScanNumber, scanDuration);
// delay for scan duration + half of single processing delay
//double spdDelay = cs.SingleProcessingDelay / 2;
//double totalDelay = scanDuration + spdDelay;
// delay for scan duration only
double totalDelay = scanDuration;
// send the scan and trigger canAcceptNextCustomScan event some time later
int milliSecondDelay = ((int)totalDelay) * 1000;
IMsScan msScan = new MyMsScan(current, cs.RunningNumber, this.startTime);
Task.Delay(milliSecondDelay).ContinueWith(t => OnSingleProcessingDelay(msScan));
return(true);
}
return(false);
}
private bool disposedValue = false; // To detect redundant calls
public MyMsScan(SimpleSpectrum scan, long runningNumber, DateTime startTime)
{
// obtained from checking the dumps of scan header from the actual instrument
this.Header["MassAnalyzer"] = "";
this.Header["IonizationMode"] = "";
this.Header["ScanRate"] = "";
this.Header["ScanMode"] = "";
double elapsedTime = DateTime.Now.Subtract(startTime).TotalSeconds;
this.Header["StartTime"] = elapsedTime.ToString();
this.Header["Scan"] = scan.ScanNumber.ToString();
this.Header["TIC"] = scan.TotalIonCurrent.ToString();
this.Header["BasePeakIntensity"] = "";
this.Header["BasePeakMass"] = "";
this.Header["CycleNumber"] = "";
this.Header["Polarity"] = "0";
this.Header["Microscans"] = "";
this.Header["InjectTime"] = "";
this.Header["ScanData"] = "";
this.Header["Segments"] = "";
this.Header["Monoisotopic"] = "";
this.Header["MasterScan"] = runningNumber.ToString();
this.Header["FirstMass"] = "";
this.Header["LastMass"] = "";
this.Header["Checksum"] = "";
this.Header["MSOrder"] = scan.MsLevel.ToString();
this.Header["Average"] = "";
this.Header["Dependent"] = "";
this.Header["MSX"] = "";
this.Header["SourceFragmentaiton"] = ""; // the spelling is correct here, "SourceFragmentaiton"
this.Header["SourceFragmentationEnergy"] = "";
this.Trailer = new MyTrailer(runningNumber);
List <ICentroid> myList = new List <ICentroid>();
if (scan.Centroided)
{
this.CentroidCount = scan.Mzs.Length;
foreach (Peak p in scan.Peaks)
{
ICentroid centroid = new MyCentroid(p);
myList.Add(centroid);
}
this.Centroids = myList;
}
}
