public HCDInfo GetHCDInfo(int argScanNum)
{
HCDScoring Scoring = new HCDScoring();
MSScan scan = ReadScan(argScanNum);
double HCDScore = Scoring.CalculateHCDScore(scan.MSPeaks);
enumGlycanType GType = Scoring.DetermineGlycanType(scan.MSPeaks);
HCDInfo HInfo = new HCDInfo(argScanNum, GType, HCDScore);
return(HInfo);
}
public HCDInfo GetHCDInfo(int argScanNum)
{
_usagecountter++;
if (_usagecountter == 100)
{
GlypIDReader.Close();
GlypIDReader.Start();
_usagecountter = 1;
}
GlypIDReader.StandardInput.WriteLine("h");
GlypIDReader.StandardInput.WriteLine(_fullFilePath);
GlypIDReader.StandardInput.WriteLine(_fileType);
GlypIDReader.StandardInput.WriteLine(argScanNum.ToString());
string output = "";
do
{
output = GlypIDReader.StandardOutput.ReadLine();
} while (!output.StartsWith("ANS:"));
Console.WriteLine(output);
output = output.Substring(4);
if (output == "false")
{
return(null);
}
string HCDString = output;
int ScanNum = Convert.ToInt32(HCDString.Split(';')[0]);
string StrType = HCDString.Split(';')[1];
double Score = Convert.ToDouble(HCDString.Split(';')[2]);
enumGlycanType GType = enumGlycanType.NA;
// CA = 1, CS, HM, HY, NA
if (StrType == "CA")
{
GType = enumGlycanType.CA;
}
else if (StrType == "CS")
{
GType = enumGlycanType.CS;
}
else if (StrType == "HM")
{
GType = enumGlycanType.HM;
}
else if (StrType == "HY")
{
GType = enumGlycanType.HY;
}
return(new HCDInfo(ScanNum, GType, Score));
}
public HCDInfo HCDInfo()
{
string HCDString = "";
Process GlypIDReader = new Process();
GlypIDReader.StartInfo.FileName = System.IO.Path.GetDirectoryName(System.Reflection.Assembly.GetEntryAssembly().Location) + "\\GlypIDWrapper.exe";
GlypIDReader.StartInfo.Arguments = "\"" + _FullRawPath + "\" " + _RawType + " H " + _ScanNum.ToString();
GlypIDReader.StartInfo.RedirectStandardOutput = true;
GlypIDReader.StartInfo.RedirectStandardError = true;
GlypIDReader.StartInfo.UseShellExecute = false;
GlypIDReader.StartInfo.CreateNoWindow = true;
GlypIDReader.OutputDataReceived += new DataReceivedEventHandler(
(s, e) =>
{
HCDString += e.Data + "\n";
}
);
GlypIDReader.Start();
GlypIDReader.BeginOutputReadLine();
GlypIDReader.WaitForExit();
_ExitCode = GlypIDReader.ExitCode;
if (_ExitCode == -1)
{
return(null);
}
HCDString = HCDString.Split('\n')[1];
int ScanNum = Convert.ToInt32(HCDString.Split(';')[0]);
string StrType = HCDString.Split(';')[1];
double Score = Convert.ToDouble(HCDString.Split(';')[2]);
enumGlycanType GType = enumGlycanType.NA;
// CA = 1, CS, HM, HY, NA
if (StrType == "CA")
{
GType = enumGlycanType.CA;
}
else if (StrType == "CS")
{
GType = enumGlycanType.CS;
}
else if (StrType == "HM")
{
GType = enumGlycanType.HM;
}
else if (StrType == "HY")
{
GType = enumGlycanType.HY;
}
return(new HCDInfo(ScanNum, GType, Score));
//autoResetEvt = new AutoResetEvent(false);
//Thread WrapperThread = new Thread(StartWrapper);
//WrapperThread.Start();
//WrapperThread.Join();
//autoResetEvt.WaitOne();
//HCDInfo hcdinfo = null;
//if (_ExitCode==1)
//{
// System.Runtime.Serialization.IFormatter f = new System.Runtime.Serialization.Formatters.Binary.BinaryFormatter();
// System.IO.MemoryStream memStream = new System.IO.MemoryStream(RecivedScan);
// hcdinfo = (HCDInfo)f.Deserialize(memStream);
//}
//return hcdinfo;
}
public enumGlycanType DetermineGlycanType(List <MSPeak> argPeaks)
{
enumGlycanType GType = enumGlycanType.NA;
// Function that attempts to categorize the glycan type by calculating cross correlation
//First find peaks and get p value
int num_hcd_present = 0;
double hcd_score = 0;
double del_mz_bin = 0.015;
double del_mz_range = mdbl_max_mz - mdbl_min_mz;
double p = (2 * del_mz_bin) / del_mz_range;
double p_value = 0;
double[] mzs = new double[argPeaks.Count];
double[] intensities = new double[argPeaks.Count];
List <int> mint_peak_indices = new List <int>();
for (int i = 0; i < argPeaks.Count; i++)
{
mzs[i] = argPeaks[i].MonoisotopicMZ;
intensities[i] = argPeaks[i].MonoIntensity;
}
float[] obs_intensities = new float[7];
double maxintensity = 0;
for (int j = 0; j < 7; j++)
{
obs_intensities[j] = 0;
}
mint_peak_indices.Clear();
for (int j = 0; j < 7; j++)
{
double this_mz = marr_theoretical_peaks[j];
int ClosedIdx = MassUtility.GetClosestMassIdx(argPeaks, Convert.ToSingle(mzs[j]));
if (Math.Abs(mzs[ClosedIdx] - this_mz) < del_mz_bin)
{
if (intensities[ClosedIdx] > obs_intensities[j]) //Anoop jan 2011, make sure you get teh highest intensity
{
num_hcd_present++;
mint_peak_indices.Add(ClosedIdx);
obs_intensities[j] = (float)intensities[ClosedIdx];
if (intensities[ClosedIdx] > maxintensity)
{
maxintensity = intensities[ClosedIdx];
}
}
}
}
// Normalizing
for (int j = 0; j < 7; j++)
{
obs_intensities[j] = (float)(obs_intensities[j] / maxintensity);
}
if (num_hcd_present >= mint_min_number_peaks)
{
for (int i = 0; i < mint_peak_indices.Count; i++)
{
identified_peak_indices.Add(mint_peak_indices[i]);
}
// Start calculating p value
long N_factorial = Factorial(7);
if (num_hcd_present > 7)
{
num_hcd_present = 7;
}
for (int x = num_hcd_present; x <= 7; x++)
{
long x_factorial = Factorial(x);
long N_x_factorial = Factorial(7 - x);
double N_choose_x = (double)(N_factorial / (x_factorial * N_x_factorial));
double pX = N_choose_x * Math.Pow(p, x) * Math.Pow(1 - p, 7 - x);
p_value += pX;
}
//Now do a correlation with each class
float corr_HM = 0;
float corr_CA = 0;
float corr_CS = 0;
float corr_Hybrid = 0;
float max_corr = 0;
//Anoop Jan 2011, performing the glycan type detection in two stages,
//if NeuAc peak (or its water equivalent) is present, a distinction between hybrid and sialylated structures is made
// else only look for high mannose and complex_asialylated
if ((obs_intensities[4] > 0) || (obs_intensities[3] > 0))
{
corr_CS = Correlation(obs_intensities, marr_theoretical_cs, 0);
corr_Hybrid = Correlation(obs_intensities, marr_theoretical_hybrid, 0);
corr_HM = 0;
corr_CA = 0;
}
else
{
corr_CS = 0;
corr_Hybrid = 0;
corr_HM = Correlation(obs_intensities, marr_theoretical_hm, 0);
corr_CA = Correlation(obs_intensities, marr_theoretical_ca, 0);
}
max_corr = Math.Max(Math.Max(Math.Max(corr_HM, corr_CA), corr_CS), corr_Hybrid);
if (max_corr == corr_HM)
{
GType = enumGlycanType.HM;
}
if (max_corr == corr_CA)
{
GType = enumGlycanType.CA;
}
if (max_corr == corr_CS)
{
GType = enumGlycanType.CS;
}
if (max_corr == corr_Hybrid)
{
GType = enumGlycanType.HY;
}
}
else
{
p_value = 1;
GType = enumGlycanType.NA;
}
return(GType);
}
public HCDInfo(int argScanNum, enumGlycanType argGType, double argHCDScore)
{
_scanNum = argScanNum;
_type = argGType;
_hcdscore = argHCDScore;
}
public HCDInfo(int argScanNum, enumGlycanType argGType, double argHCDScore)
{
_scanNum = argScanNum;
_type = argGType;
_hcdscore = argHCDScore;
}
