/// <summary>
/// Illustrate how to make calls to deisotope a spectrum.
/// </summary>
/// <param name="dataAccess"></param>
private void DeisotopeTest(IMsdrDataReader dataAccess)
{
IMsdrPeakFilter filter1 = new MsdrPeakFilter();
filter1.AbsoluteThreshold = 10;
filter1.RelativeThreshold = 0.1;
filter1.MaxNumPeaks = 0;//no limit on max number of peaks
IMsdrChargeStateAssignmentFilter csaFilter = new MsdrChargeStateAssignmentFilter();
IBDASpecFilter f = new BDASpecFilter();
f.SpectrumType = SpecType.MassSpectrum;
IBDAMSScanFileInformation msscanFileInfo = dataAccess.MSScanFileInformation;
int numSpectra = (int)msscanFileInfo.TotalScansPresent;
int nNonEmptyCount = 0; // just deisotope the first 10 non-empty spectra
for (int i = 0; i < numSpectra; i++)
{
IBDASpecData spec = dataAccess.GetSpectrum(i, filter1, filter1);//same peak filter used for both MS and MS2 spectra (you can pass in 2 different filters)
println("Original spectrum has " + spec.TotalDataPoints + " points");
if (spec.XArray.Length > 0)
{
++nNonEmptyCount;
}
if (nNonEmptyCount > 10)
{
break;
}
dataAccess.Deisotope(spec, csaFilter);
println(" Deisotoped spectrum has " + spec.TotalDataPoints + " points");
}
}
private void DoSpectrumExtractionTestWithStorage(IMsdrDataReader dataAccess)
{
IMsdrPeakFilter filter1 = new MsdrPeakFilter();
filter1.AbsoluteThreshold = 10;
filter1.RelativeThreshold = 0.1;
filter1.MaxNumPeaks = 0;
IBDAMSScanFileInformation msscanFileInfo = dataAccess.MSScanFileInformation;
int numSpectra = (int)msscanFileInfo.TotalScansPresent;
for (int i = 0; i < numSpectra; i++)
{
IBDASpecData spec = dataAccess.GetSpectrum(i, filter1, filter1, DesiredMSStorageType.PeakElseProfile);
println("Spectrum " + i.ToString() + "has " + spec.TotalDataPoints + " points");
}
}
private List <IonPolarity> GetScanIonPolarities(IDataAccess dataAccess)
{
List <IonPolarity> rv = new List <IonPolarity>();
IonPolarity polaritiesInFile = IonPolarity.Unassigned;
IBDAFileInformation fileInfo = dataAccess.FileInformation;
if (fileInfo.IsMSDataPresent())
{
IBDAMSScanFileInformation msInfo = fileInfo.MSScanFileInformation;
IBDAMSScanTypeInformation scanInfo = msInfo.GetMSScanTypeInformation(MSScanType.Scan);
if (scanInfo != null)
{
polaritiesInFile = scanInfo.IonPolarities;
}
}
if (polaritiesInFile == IonPolarity.Unassigned)
{
UserMessage msg = new UserMessage(0,
string.Empty,
ProgramModule.CoreFacades,
DACoreFacadeMessages.MSG_MFE_NoMsScanData);
throw new MSDAApplicationException(msg as IUserMessage);
}
switch (polaritiesInFile)
{
case IonPolarity.Mixed:
rv.Add(IonPolarity.Positive);
rv.Add(IonPolarity.Negative);
break;
case IonPolarity.Positive:
rv.Add(IonPolarity.Positive);
break;
case IonPolarity.Negative:
rv.Add(IonPolarity.Negative);
break;
default:
break;
}
return(rv);
}
private void PrintMSScanInfo(IMsdrDataReader dataAccess)
{
//////////////////////////////////////
///MSScan.bin information
/////////////////////////////////////////
IBDAMSScanFileInformation msscan = dataAccess.FileInformation.MSScanFileInformation;
//TotalScansPresent
println("Total # of Scans: " + msscan.TotalScansPresent);
//SpectraFormat
println("Spectral Format: " + msscan.SpectraFormat);
//is fixed cycle length?
println("Is fixed cycle length data present? " + msscan.IsFixedCycleLengthDataPresent());
//is multiple spectra per scan present?
println("Is multiple spectra per scan present? " + msscan.IsMultipleSpectraPerScanPresent());
//IonPolarity
println("Ion Polarity: " + msscan.IonPolarity);
//MSLevel
println("MS Level: " + msscan.MSLevel);
//IonModes
println("Ionization Mode: " + msscan.IonModes);
//DeviceType
println("Device Type: " + msscan.DeviceType);
//CollisionEnergy
print("Collision Energies: ");
double[] collisionEnergy = msscan.CollisionEnergy;
if (collisionEnergy.Length == 0)
{
println("None");
}
else
{
for (int i = 0; i < collisionEnergy.Length; i++)
{
if (i == collisionEnergy.Length - 1)//last one
{
println(Convert.ToString(collisionEnergy[i]));
}
else
{
print(Convert.ToString(collisionEnergy[i]) + ", ");
}
}
}
//FragmentorVoltages
print("Fragmentor Voltages: ");
double[] fragVolt = msscan.FragmentorVoltage;
if (fragVolt.Length == 0)
{
println("None");
}
else
{
for (int i = 0; i < fragVolt.Length; i++)
{
if (i == fragVolt.Length - 1)//last one
{
println(Convert.ToString(fragVolt[i]));
}
else
{
print(Convert.ToString(fragVolt[i] + ", "));
}
}
}
//MRMTransitions
print("MRM transitions: ");
IRange[] mrmTrans = msscan.MRMTransitions;
if (mrmTrans.Length == 0)
{
println("None");
}
else
{
for (int i = 0; i < mrmTrans.Length; i++)
{
if (i == mrmTrans.Length - 1)//last one
{
println(Convert.ToString(mrmTrans[i].Start) + "->" + Convert.ToString(mrmTrans[i].End));
}
else
{
print(Convert.ToString(mrmTrans[i].Start) + "->" + Convert.ToString(mrmTrans[i].End) + ", ");
}
}
}
//SIMIons
double[] simIons = msscan.SIMIons;
print("SIM ions: ");
if (simIons.Length == 0)
{
println("None");
}
else
{
for (int i = 0; i < simIons.Length; i++)
{
if (i == simIons.Length - 1)
{
println(Convert.ToString(simIons[i]));
}
else
{
print(Convert.ToString(simIons[i]) + ", ");
}
}
}
//ScanMethodNumbers
print("Scan Method Numbers: ");
int[] scanMethodNums = msscan.ScanMethodNumbers;
if (scanMethodNums.Length == 0)
{
println("None");
}
else
{
for (int i = 0; i < scanMethodNums.Length; i++)
{
if (i == scanMethodNums.Length - 1)//last one
{
println(Convert.ToString(scanMethodNums[i]));
}
else
{
print(Convert.ToString(scanMethodNums[i]) + ", ");
}
}
}
//ScanTypesInformationCount
println("Scan Type Count: " + msscan.ScanTypesInformationCount);
//ScanTypes
println("Scan types: " + msscan.ScanTypes);
StringBuilder buf = new StringBuilder();
IBDAMSScanTypeInformation[] types = msscan.GetMSScanTypeInformation();
foreach (IBDAMSScanTypeInformation type in types)
{
double[] mz = type.MzOfInterest;
buf.Append("MS scan type: " + type.MSScanType + ", " + type.IonPolarities);
if (mz != null && mz.Length > 0)
{
buf.Append(", m/z of interest = ");
for (int i = 0; i < mz.Length; i++)
{
if (i == mz.Length - 1)//last one
{
buf.Append(mz[i]);
}
else
{
buf.Append(mz[i] + ", ");
}
}
}
buf.AppendLine();
}
print(buf.ToString());
}
