public ISpectrum GetSpectrum(int scanNum)
{
try
{
if (reader.GetMSnOrder(scanNum) == 1)
{
GeneralSpectrum spectrum = new GeneralSpectrum(1, scanNum);
List <IPeak> peaks = reader.Read(scanNum);
spectrum.SetPeaks(peaks);
return(spectrum);
}
else
{
int msOrder = reader.GetMSnOrder(scanNum);
TypeOfMSActivation type = reader.GetActivation(scanNum);
double[] mzCharge = reader.GetParentMZCharge(scanNum);
ISpectrum spectrum = new GeneralSpectrumMSn(msOrder, scanNum, type, mzCharge[0], (int)mzCharge[1]);
List <IPeak> peaks = reader.Read(scanNum);
spectrum.SetPeaks(peaks);
return(spectrum);
}
}
catch (Exception e)
{
Console.WriteLine(e.Message);
return(null);
}
}
public GeneralSpectrumMSn(int msOrder, int scanNum, TypeOfMSActivation type, double mz, int charge)
{
activationType = type;
parentMZ = mz;
parentCharge = charge;
this.msOrder = msOrder;
this.scanNum = scanNum;
peaks = new List <IPeak>();
}
public ISpectrum GetSpectrum(int scanNum)
{
int msOrder = getter.GetMSnOrder(scanNum);
TypeOfMSActivation type = (TypeOfMSActivation)getter.GetTypeofActivation(scanNum);
double[] mzCharge = getter.GetParentMZCharge(scanNum);
ISpectrum spectrum = new GeneralSpectrumMSn(msOrder, scanNum, type, mzCharge[0], (int)mzCharge[1]);
List <IPeak> peaks = getter.GetPeaks(scanNum);
spectrum.SetPeaks(peaks);
return(spectrum);
}
public static Component.CVParam ActivationCVParam(TypeOfMSActivation activationType)
{
if (activationType == TypeOfMSActivation.CID)
{
return(new Component.CVParam()
{
cvRef = "MS",
accession = "MS:1000133",
name = "collision-induced dissociation",
value = ""
});
}
else if (activationType == TypeOfMSActivation.HCD)
{
return(new Component.CVParam()
{
cvRef = "MS",
accession = "MS:1002481",
name = "higher energy beam-type collision-induced dissociation",
value = ""
});
}
else if (activationType == TypeOfMSActivation.ETD)
{
return(new Component.CVParam()
{
cvRef = "MS",
accession = "MS:1000598",
name = "electron transfer dissociation",
value = ""
});
}
else
{
return(new Component.CVParam()
{
cvRef = "MS",
accession = "MS:1002631",
name = "Electron-Transfer/Higher-Energy Collision Dissociation (EThcD)",
value = ""
});
}
}
public void WriteMGF(StreamWriter writer, string title,
double mz, int charge, int scan, double retention,
TypeOfMSActivation type,
List <IPeak> majorPeaks)
{
writer.WriteLine("BEGIN IONS");
writer.WriteLine("TITLE=" + title);
writer.WriteLine("SCANS=" + scan.ToString());
writer.WriteLine("RTINSECONDS=" + retention.ToString());
writer.WriteLine("CHARGE=" + charge.ToString() + "+");
writer.WriteLine("PEPMASS=" + mz.ToString());
switch (type)
{
case TypeOfMSActivation.CID:
writer.WriteLine("INSTRUMENT=CID");
break;
case TypeOfMSActivation.ETD:
writer.WriteLine("INSTRUMENT=ETD");
break;
case TypeOfMSActivation.HCD:
writer.WriteLine("INSTRUMENT=HCD");
break;
default:
writer.WriteLine("INSTRUMENT=Default");
break;
}
foreach (IPeak pk in majorPeaks)
{
writer.WriteLine(pk.GetMZ().ToString() + " " + pk.GetIntensity().ToString());
}
writer.WriteLine("END IONS");
writer.WriteLine();
writer.Flush();
}
public GeneralSpectrumMSn(int msOrder, int scanNum, TypeOfMSActivation type, double mz, int charge) : base(msOrder, scanNum)
{
activationType = type;
parentMZ = mz;
parentCharge = charge;
}
