private MSScan GetMSScan(int argScanNo)
{
MSScan msScan = new MSScan(argScanNo);
// GlypID.Readers.clsRawData rawData = new GlypID.Readers.clsRawData() ;
GlypID.HornTransform.clsHornTransform massTransform = new GlypID.HornTransform.clsHornTransform();
GlypID.Peaks.clsPeakProcessor peakProcessor = new GlypID.Peaks.clsPeakProcessor();
GlypID.HornTransform.clsHornTransformParameters transform_parameters = new GlypID.HornTransform.clsHornTransformParameters();
GlypID.Peaks.clsPeakProcessorParameters peak_parameters = new GlypID.Peaks.clsPeakProcessorParameters();
// Declarations
float[] _mzs = null;
float[] _intensities = null;
GlypID.Peaks.clsPeak[] peaks;
GlypID.HornTransform.clsHornTransformResults[] _transformResults;
// Settings
peak_parameters.SignalToNoiseThreshold = 3.0;
peak_parameters.PeakBackgroundRatio = 5.0;
peakProcessor.SetOptions(peak_parameters);
peakProcessor.ProfileType = GlypID.enmProfileType.PROFILE;
transform_parameters.PeptideMinBackgroundRatio = 5.0;
transform_parameters.MaxCharge = 10;
massTransform.TransformParameters = transform_parameters;
// Load
Raw = new GlypID.Readers.clsRawData(_fullFilePath, GlypID.Readers.FileType.FINNIGAN);
if (Raw.GetMSLevel(argScanNo) == 1)
{
// Get spectra
Raw.GetSpectrum(argScanNo, ref _mzs, ref _intensities);
// Get peaks
peaks = new GlypID.Peaks.clsPeak[1];
peakProcessor.DiscoverPeaks(ref _mzs, ref _intensities, ref peaks, Convert.ToSingle(transform_parameters.MinMZ), Convert.ToSingle(transform_parameters.MaxMZ), true);
// Deisotope
double min_background_intensity = peakProcessor.GetBackgroundIntensity(ref _intensities);
double min_peptide_intensity = min_background_intensity * transform_parameters.PeptideMinBackgroundRatio;
_transformResults = new GlypID.HornTransform.clsHornTransformResults[1];
massTransform.PerformTransform(Convert.ToSingle(min_background_intensity), Convert.ToSingle(min_peptide_intensity), ref _mzs, ref _intensities, ref peaks, ref _transformResults);
Array.Clear(_transformResults, 0, _transformResults.Length);
Array.Clear(peaks, 0, peaks.Length);
}
return msScan;
}
public XRawReader(string argFullFilePath)
{
_fullFilePath = argFullFilePath;
Raw = new GlypID.Readers.clsRawData(_fullFilePath, GlypID.Readers.FileType.FINNIGAN);
mobjTransform = new GlypID.HornTransform.clsHornTransform(); //12KB
mobjTransformParameters = new GlypID.HornTransform.clsHornTransformParameters(); //4KB
_transformResult = new GlypID.HornTransform.clsHornTransformResults[1];
cidPeakProcessor = new GlypID.Peaks.clsPeakProcessor(); //68KB
cidPeakParameters = new GlypID.Peaks.clsPeakProcessorParameters();
parentPeakProcessor = new GlypID.Peaks.clsPeakProcessor();
parentPeakParameters = new GlypID.Peaks.clsPeakProcessorParameters();
}
/// <summary>
///
/// </summary>
/// <param name="argFullPath"></param>
/// <param name="argFileType">raw or mzxml</param>
public RawReader(string argFullPath, string argFileType)
{
_fullFilePath = argFullPath;
_fileType = argFileType;
if (_fileType.ToLower() == "raw")
{
Raw = new GlypID.Readers.clsRawData(_fullFilePath, GlypID.Readers.FileType.FINNIGAN);
}
else
{
Raw = new GlypID.Readers.clsRawData(_fullFilePath, GlypID.Readers.FileType.MZXMLRAWDATA);
}
}
public XRawReader(string argFullFilePath)
{
_fullFilePath = argFullFilePath;
Raw = new GlypID.Readers.clsRawData(_fullFilePath, GlypID.Readers.FileType.FINNIGAN);
mobjTransform = new GlypID.HornTransform.clsHornTransform(); //12KB
mobjTransformParameters = new GlypID.HornTransform.clsHornTransformParameters(); //4KB
_transformResult = new GlypID.HornTransform.clsHornTransformResults[1];
cidPeakProcessor = new GlypID.Peaks.clsPeakProcessor(); //68KB
cidPeakParameters = new GlypID.Peaks.clsPeakProcessorParameters();
parentPeakProcessor = new GlypID.Peaks.clsPeakProcessor();
parentPeakParameters = new GlypID.Peaks.clsPeakProcessorParameters();
}
/// <summary>
///
/// </summary>
/// <param name="argFullPath"></param>
/// <param name="argFileType">raw or mzxml</param>
public RawReader(string argFullPath, string argFileType)
{
_fullFilePath = argFullPath;
_fileType = argFileType;
if (_fileType.ToLower() == "raw")
{
Raw = new GlypID.Readers.clsRawData(_fullFilePath, GlypID.Readers.FileType.FINNIGAN);
}
else
{
Raw = new GlypID.Readers.clsRawData(_fullFilePath, GlypID.Readers.FileType.MZXMLRAWDATA);
}
}
// Protected implementation of Dispose pattern.
protected virtual void Dispose(bool disposing)
{
if (disposed)
{
return;
}
if (disposing)
{
// Free any other managed objects here.
Raw = null;
}
// Free any unmanaged objects here.
disposed = true;
}
/// <summary>
///
/// </summary>
/// <param name="argFullPath"></param>
/// <param name="argFileType"></param>
public RawReader(string argFullPath, enumRawDataType argRawType)
{
_fullFilePath = argFullPath;
if (argRawType == enumRawDataType.raw)
{
_fileType = "raw";
Raw = new GlypID.Readers.clsRawData(_fullFilePath, GlypID.Readers.FileType.FINNIGAN);
}
else
{
_fileType = "mzxml";
Raw = new GlypID.Readers.clsRawData(_fullFilePath, GlypID.Readers.FileType.MZXMLRAWDATA);
}
}
/// <summary>
///
/// </summary>
/// <param name="argFullPath"></param>
/// <param name="argFileType"></param>
public RawReader(string argFullPath, enumRawDataType argRawType)
{
_fullFilePath = argFullPath;
if (argRawType == enumRawDataType.raw)
{
_fileType = "raw";
Raw = new GlypID.Readers.clsRawData(_fullFilePath, GlypID.Readers.FileType.FINNIGAN);
}
else
{
_fileType = "mzxml";
Raw = new GlypID.Readers.clsRawData(_fullFilePath, GlypID.Readers.FileType.MZXMLRAWDATA);
}
}
public RawReader(string argFullPath, string argFileType, double argSingleToNoise, double argPeakBackground, double argPeptideBackground, short argMaxCharge)
{
_fullFilePath = argFullPath;
_fileType = argFullPath;
_singleToNoiseRatio=argSingleToNoise;
_peakBackgroundRatio=argPeakBackground;
_peptideMinBackgroundRatio=argPeptideBackground;
_maxCharge = argMaxCharge;
if (_fileType.ToLower() == "raw")
{
Raw = new GlypID.Readers.clsRawData(_fullFilePath, GlypID.Readers.FileType.FINNIGAN);
}
else
{
Raw = new GlypID.Readers.clsRawData(_fullFilePath, GlypID.Readers.FileType.MZXMLRAWDATA);
}
}
public RawReader(string argFullPath, string argFileType, double argSingleToNoise, double argPeakBackground, double argPeptideBackground, short argMaxCharge)
{
_fullFilePath = argFullPath;
_fileType = argFullPath;
_singleToNoiseRatio = argSingleToNoise;
_peakBackgroundRatio = argPeakBackground;
_peptideMinBackgroundRatio = argPeptideBackground;
_maxCharge = argMaxCharge;
if (_fileType.ToLower() == "raw")
{
Raw = new GlypID.Readers.clsRawData(_fullFilePath, GlypID.Readers.FileType.FINNIGAN);
}
else
{
Raw = new GlypID.Readers.clsRawData(_fullFilePath, GlypID.Readers.FileType.MZXMLRAWDATA);
}
}
public RawReader(string argFullPath, enumRawDataType argRawType, double argSingleToNoise, double argPeakBackground, double argPeptideBackground, short argMaxCharge)
{
_fullFilePath = argFullPath;
_singleToNoiseRatio = argSingleToNoise;
_peakBackgroundRatio = argPeakBackground;
_peptideMinBackgroundRatio = argPeptideBackground;
_maxCharge = argMaxCharge;
if (argRawType == enumRawDataType.raw)
{
_fileType = "raw";
Raw = new GlypID.Readers.clsRawData(_fullFilePath, GlypID.Readers.FileType.FINNIGAN);
}
else
{
_fileType = "mzxml";
Raw = new GlypID.Readers.clsRawData(_fullFilePath, GlypID.Readers.FileType.MZXMLRAWDATA);
}
}
/// <summary>
///
/// </summary>
/// <param name="args">
/// Arg0: FilePath
/// Arg1: FileType switch
/// raw
/// mzxml
/// Arg2: Function switch
/// R:ReadScan
/// N:Number of Scan
/// H: Get HCD info
/// C: Checked if it is CID scan
/// S: Scan header Description
/// M: Get MS Level
/// Arg3:
/// Switch R: int scan number
/// Switch N: none
///
/// Arg4: PeakProcessorParameter _singleToNoiseRatio
/// Arg5: PeakProcessorParameter _peakBackgroundRatio
/// Arg6: TransformParameter _peptideMinBackgroundRatio
/// Arg7: TransformParameter _maxCharge
/// </param>
///
static int Main(string[] args)
{
string FunctionSwitch;// = args[2].ToLower();
GlypID.Readers.clsRawData Raw;
//Debug
//End Debug
try
{
do
{
Console.WriteLine(
"@@\nR:ReadScan\n" +
"N:Number of Scan\n" +
"H: Get HCD info\n" +
"C: Checked if it is CID scan\n" +
"S: Scan header Description\n" +
"M: Get MS Level\n" +
"Q: Quit\n" +
"Please select function:");
FunctionSwitch = Console.In.ReadLine().ToLower().Substring(0, 1);
if (FunctionSwitch == "q")
{
return 0;
}
else
{
Console.WriteLine("Please input file location:");
string _fullFilePath = Console.In.ReadLine();
Console.WriteLine("FIle Type(r: Raw, x:mzXML)");
if (Console.In.ReadLine().ToLower().StartsWith("x"))
{
Raw = new GlypID.Readers.clsRawData(_fullFilePath, GlypID.Readers.FileType.MZXMLRAWDATA);
}
else
{
Raw = new GlypID.Readers.clsRawData(_fullFilePath, GlypID.Readers.FileType.FINNIGAN);
}
//PipeClient pipeClt = new PipeClient();
//pipeClt.Connect("\\\\.\\pipe\\GlypIDPipe");
if (FunctionSwitch == "r")//Read Scan
{
Console.WriteLine("Please input scan num:");
int ScanNo = Convert.ToInt32(Console.In.ReadLine());
Console.WriteLine("Please input Single to Noise ratio (default:3.0):");
double parsedResult = 3.0;
double _singleToNoiseRatio = 3.0;
if (double.TryParse(Console.In.ReadLine(), out parsedResult))
{
_singleToNoiseRatio = parsedResult;
}
Console.WriteLine("Please input Peak background ratio (default:5.0):");
parsedResult = 5.0;
double _peakBackgroundRatio = 5.0;
if (double.TryParse(Console.In.ReadLine(), out parsedResult))
{
_peakBackgroundRatio = parsedResult;
}
Console.WriteLine("Please input Minimum background ratio (default:5.0):");
parsedResult = 5.0;
double _peptideMinBackgroundRatio = 5.0;
if (double.TryParse(Console.In.ReadLine(), out parsedResult))
{
_peptideMinBackgroundRatio = parsedResult;
}
Console.WriteLine("Please input Max charge (defatlt:10):");
short paredCharge = 10;
short _maxCharge = 10;
if (short.TryParse(Console.In.ReadLine(), out paredCharge))
{
_maxCharge = paredCharge;
}
Console.WriteLine("Reading Scan");
MSScan scan = GetScanFromFile(ScanNo, _singleToNoiseRatio, _peakBackgroundRatio, _peptideMinBackgroundRatio, _maxCharge , Raw);
string responseMsg = SendScanViaNamedPipe(scan);
//scan = null;
//if (pipeClt.Connected)
//{
// while (!pipeClt.SendMessage(memStream.ToArray())) ;
// Console.WriteLine("Named pipe sent");
// pipeClt.Disconnect();
//}
//else
//{
// throw new Exception("Named Pipe not found");
//}
Console.WriteLine("ANS:Read Scan: " + ScanNo + " finish;MSScan bytes-" + responseMsg);
}
else if (FunctionSwitch == "n") //Get total scans
{
Console.WriteLine("ANS:" + Raw.GetNumScans().ToString());
}
else if (FunctionSwitch == "h") //Check HCD
{
Console.WriteLine("Please input scan num:");
int ScanNo = Convert.ToInt32(Console.In.ReadLine());
HCDInfo HCDinfo = GetHCDInfo(Raw, ScanNo);
if (HCDinfo != null)
{
Console.WriteLine("ANS:" + HCDinfo.ScanNum.ToString() + ";" +
HCDinfo.GlycanType.ToString() + ";" +
HCDinfo.HCDScore.ToString());
}
else
{
Console.WriteLine("ANS:" + "false");
}
}
else if (FunctionSwitch == "c") //Check CID
{
Console.WriteLine("Please input scan num:");
int ScanNo = Convert.ToInt32(Console.In.ReadLine());
if (Raw.IsCIDScan(ScanNo) == true)
{
Console.WriteLine("ANS:" + "true");
}
else
{
Console.WriteLine("ANS:" + "false");
}
}
else if (FunctionSwitch == "s") //Check description
{
Console.WriteLine("Please input scan num:");
int ScanNo = Convert.ToInt32(Console.In.ReadLine());
string description = Raw.GetScanDescription(ScanNo);
Console.WriteLine("ANS:" + description);
}
else if (FunctionSwitch == "m")//Get MS Level
{
Console.WriteLine("Please input scan num:");
int ScanNo = Convert.ToInt32(Console.In.ReadLine());
Console.WriteLine("ANS:" + Raw.GetMSLevel(ScanNo));
}
else
{
Console.WriteLine("Function error");
}
}
} while (true);
}
catch (Exception e)
{
Console.WriteLine(e.Message);
return -1;
}
//if (args == null || args.Length == 0)
//{
// Console.WriteLine("args is null"); // Check for null array
// return -1;
//}
//if (FunctionSwitch == "r" && args.Length != 8)
//{
// Console.WriteLine("args is not enough"); // Check for null array
// return -1;
//}
//else
//{
// string _fullFilePath = Console.In.ReadLine();
// Console.WriteLine("Init GlypID");
// if (args[1].ToLower() == "raw")
// {
// Raw = new GlypID.Readers.clsRawData(_fullFilePath, GlypID.Readers.FileType.FINNIGAN);
// }
// else
// {
// Raw = new GlypID.Readers.clsRawData(_fullFilePath, GlypID.Readers.FileType.MZXMLRAWDATA);
// }
// if (FunctionSwitch == "n") //Get Total scans
// {
// Console.WriteLine(Raw.GetNumScans().ToString());
// return Raw.GetNumScans();
// }
// else if (FunctionSwitch == "m") //Get MS Level
// {
// int ScanNo = Convert.ToInt32(args[3]);
// return Raw.GetMSLevel(ScanNo);
// }
// else if (FunctionSwitch == "c") //IsCID Scan
// {
// int ScanNo = Convert.ToInt32(args[3]);
// if (Raw.IsCIDScan(ScanNo) == true)
// {
// return 1;
// }
// return 0;
// }
// else if (FunctionSwitch == "s") //Get Description
// {
// int ScanNo = Convert.ToInt32(args[3]);
// //Console.WriteLine("Get Description info");
// string description = Raw.GetScanDescription(ScanNo);
// Console.WriteLine(description);
// //System.Runtime.Serialization.IFormatter f = new System.Runtime.Serialization.Formatters.Binary.BinaryFormatter();
// //MemoryStream memStream = new MemoryStream();
// //f.Serialize(memStream, description);
// //PipeClient pipeClt = new PipeClient();
// //pipeClt.Connect("\\\\.\\pipe\\GlypIDPipe");
// //if (pipeClt.Connected)
// //{
// // while (!pipeClt.SendMessage(memStream.ToArray())) ;
// // Console.WriteLine("Named pipe sent");
// //}
// //else
// //{
// // throw new Exception("Named Pipe not found");
// //}
// return 1;
// }
// else if (FunctionSwitch == "h") //Get HCD
// {
// int ScanNo = Convert.ToInt32(args[3]);
// HCDInfo HCDinfo = GetHCDInfo(Raw, ScanNo);
// //Console.WriteLine("Get HCD info");
// //System.Runtime.Serialization.IFormatter f = new System.Runtime.Serialization.Formatters.Binary.BinaryFormatter();
// //PipeClient pipeClt = new PipeClient();
// //pipeClt.Connect("\\\\.\\pipe\\GlypIDPipeHCD");
// if (HCDinfo != null)
// {
// Console.WriteLine(HCDinfo.ScanNum.ToString() + ";" +
// HCDinfo.GlycanType.ToString() + ";" +
// HCDinfo.HCDScore.ToString());
// //MemoryStream memStream = new MemoryStream();
// //f.Serialize(memStream, HCDinfo);
// //if (pipeClt.Connected)
// //{
// // while (!pipeClt.SendMessage(memStream.ToArray())) ;
// // Console.WriteLine("Named pipe sent");
// //}
// //else
// //{
// // throw new Exception("Named Pipe not found");
// //}
// return 1;
// }
// else
// {
// //if (pipeClt.Connected)
// //{
// // while (!pipeClt.SendMessage(Encoding.ASCII.GetBytes("No HCD Info found"))) ;
// // Console.WriteLine("Named pipe sent");
// //}
// //else
// //{
// // throw new Exception("Named Pipe not found");
// //}
// return -1;
// }
// }
// else //ReadScan
// {
// int ScanNo = Convert.ToInt32(args[3]);
// double _singleToNoiseRatio = Convert.ToDouble(args[4]);
// double _peakBackgroundRatio = Convert.ToDouble(args[5]);
// double _peptideMinBackgroundRatio = Convert.ToDouble(args[6]);
// short _maxCharge = Convert.ToInt16(args[7]);
// Console.WriteLine("Read Scan");
// MSScan scan = GetScanFromFile(ScanNo, _singleToNoiseRatio, _peakBackgroundRatio, _peptideMinBackgroundRatio, _maxCharge);
// System.Runtime.Serialization.IFormatter f = new System.Runtime.Serialization.Formatters.Binary.BinaryFormatter();
// MemoryStream memStream = new MemoryStream();
// f.Serialize(memStream, scan);
// PipeClient pipeClt = new PipeClient();
// pipeClt.Connect("\\\\.\\pipe\\GlypIDPipe");
// if (pipeClt.Connected)
// {
// while (!pipeClt.SendMessage(memStream.ToArray())) ;
// Console.WriteLine("Named pipe sent");
// }
// else
// {
// throw new Exception("Named Pipe not found");
// }
// /*NamedPipeClientStream PipeClient = new NamedPipeClientStream(".", "ReadMSScan", PipeDirection.Out);
// PipeClient.Connect();
// f.Serialize(PipeClient, scan);
// PipeClient.Close();*/
// Console.WriteLine("Read Scan: " + args[3] + " finish");
// }
// //End Read Scan
// return 1;
//}
}
private static float[] FindChargeAndMono(GlypID.Peaks.clsPeak[] argPeaks, float argTargetMZ, int argParentScanNo, GlypID.Readers.clsRawData Raw)
{
float[] MonoAndMz = new float[2];
double interval = 9999.9;
int ClosedIdx = 0;
for (int i = 0; i < argPeaks.Length; i++)
{
if (Math.Abs(argPeaks[i].mdbl_mz - argTargetMZ) < interval)
{
interval = Math.Abs(argPeaks[i].mdbl_mz - argTargetMZ);
ClosedIdx = i;
}
}
//Charge
float testMz = 0.0f;
int MaxMatchedPeak = 2;
for (int i = 1; i <= 6; i++)
{
double FirstMonoMz = 0.0;
int ForwardPeak = 0;
int BackardPeak = 0;
//Forward Check
testMz = argTargetMZ - 1.0f / (float)i;
int CheckIdx = ClosedIdx - 1;
for (int j = 1; j <= 10; j++)
{
if (CheckIdx < 0)
{
break;
}
if (Math.Abs(argPeaks[CheckIdx].mdbl_mz - testMz) <= 0.03)
{
ForwardPeak++;
testMz = Convert.ToSingle(argPeaks[CheckIdx].mdbl_mz) - 1.0f / (float)i;
FirstMonoMz = argPeaks[CheckIdx].mdbl_mz;
}
CheckIdx = CheckIdx - 1;
}
//Backward
testMz = argTargetMZ + 1.0f / (float)i;
CheckIdx = ClosedIdx + 1;
for (int j = 1; j <= 10; j++)
{
if (CheckIdx >= argPeaks.Length)
{
break;
}
if (Math.Abs(argPeaks[CheckIdx].mdbl_mz - testMz) <= 0.03)
{
BackardPeak++;
testMz = Convert.ToSingle(argPeaks[CheckIdx].mdbl_mz) + 1.0f / (float)i;
}
CheckIdx = CheckIdx + 1;
}
if (ForwardPeak == 0)
{
FirstMonoMz = argTargetMZ;
}
if (ForwardPeak + BackardPeak >= MaxMatchedPeak)
{
MaxMatchedPeak = ForwardPeak + BackardPeak;
MonoAndMz[0] = Convert.ToSingle(FirstMonoMz);
MonoAndMz[1] = i;
}
}
if (MonoAndMz[1] == 0)
{
if (interval < 0.01)
{
MonoAndMz[0] = argTargetMZ;
}
MonoAndMz[1] = Raw.GetMonoChargeFromHeader(argParentScanNo);
}
return(MonoAndMz);
}
public HCDInfo(GlypID.Readers.clsRawData argReader, int argScanNo)
{
int ParentScan = argReader.GetParentScan(argScanNo);
// Scorers and transforms
GlypID.HCDScoring.clsHCDScoring HCDScoring = new GlypID.HCDScoring.clsHCDScoring();
GlypID.HornTransform.clsHornTransform Transform = new GlypID.HornTransform.clsHornTransform();
// mzs , intensities
float[] hcd_mzs = null;
float[] hcd_intensities = null;
float[] parent_mzs = null;
float[] parent_intensities = null;
// Peaks
GlypID.Peaks.clsPeak[] parent_peaks;
GlypID.Peaks.clsPeak[] hcd_peaks;
// Peak Processors
GlypID.Peaks.clsPeakProcessor hcdPeakProcessor = new GlypID.Peaks.clsPeakProcessor();
GlypID.Peaks.clsPeakProcessor parentPeakProcessor = new GlypID.Peaks.clsPeakProcessor();
// Results
GlypID.HCDScoring.clsHCDScoringScanResults[] hcd_scoring_results;
GlypID.HornTransform.clsHornTransformResults[] transform_results;
// Params
GlypID.Scoring.clsScoringParameters scoring_parameters = new GlypID.Scoring.clsScoringParameters();
GlypID.HornTransform.clsHornTransformParameters transform_parameters = new GlypID.HornTransform.clsHornTransformParameters();
scoring_parameters.MinNumPeaksToConsider = 2;
scoring_parameters.PPMTolerance = 10;
scoring_parameters.UsePPM = true;
// Init
Transform.TransformParameters = transform_parameters;
// Loading parent
int parent_scan = argReader.GetParentScan(argScanNo);
double parent_mz = argReader.GetParentMz(argScanNo);
int scan_level = argReader.GetMSLevel(argScanNo);
int parent_level = argReader.GetMSLevel(parent_scan);
argReader.GetSpectrum(parent_scan, ref parent_mzs, ref parent_intensities);
// Parent processing
parent_peaks = new GlypID.Peaks.clsPeak[1];
parentPeakProcessor.ProfileType = GlypID.enmProfileType.PROFILE;
parentPeakProcessor.DiscoverPeaks(ref parent_mzs, ref parent_intensities, ref parent_peaks,
Convert.ToSingle(transform_parameters.MinMZ), Convert.ToSingle(transform_parameters.MaxMZ), true);
double bkg_intensity = parentPeakProcessor.GetBackgroundIntensity(ref parent_intensities);
double min_peptide_intensity = bkg_intensity * transform_parameters.PeptideMinBackgroundRatio;
transform_results = new GlypID.HornTransform.clsHornTransformResults[1];
bool found = Transform.FindPrecursorTransform(Convert.ToSingle(bkg_intensity), Convert.ToSingle(min_peptide_intensity), ref parent_mzs, ref parent_intensities, ref parent_peaks, Convert.ToSingle(parent_mz), ref transform_results);
if (!found && (argReader.GetMonoChargeFromHeader(ParentScan) > 0))
{
found = true;
double mono_mz = argReader.GetMonoMzFromHeader(ParentScan);
if (mono_mz == 0)
{
mono_mz = parent_mz;
}
short[] charges = new short[1];
charges[0] = argReader.GetMonoChargeFromHeader(ParentScan);
Transform.AllocateValuesToTransform(Convert.ToSingle(mono_mz), 0, ref charges, ref transform_results); // Change abundance value from 0 to parent_intensity if you wish
}
if (found && transform_results.Length == 1)
{
// Score HCD scan first
argReader.GetSpectrum(argScanNo, ref hcd_mzs, ref hcd_intensities);
double hcd_background_intensity = GlypID.Utils.GetAverage(ref hcd_intensities, ref hcd_mzs, Convert.ToSingle(scoring_parameters.MinHCDMz), Convert.ToSingle(scoring_parameters.MaxHCDMz));
hcdPeakProcessor.SetPeakIntensityThreshold(hcd_background_intensity);
hcd_peaks = new GlypID.Peaks.clsPeak[1];
//Check Header
string Header = argReader.GetScanDescription(argScanNo);
hcdPeakProcessor.ProfileType = GlypID.enmProfileType.PROFILE;
if (Header.Substring(Header.IndexOf("+") + 1).Trim().StartsWith("c"))
{
hcdPeakProcessor.ProfileType = GlypID.enmProfileType.CENTROIDED;
}
hcdPeakProcessor.DiscoverPeaks(ref hcd_mzs, ref hcd_intensities, ref hcd_peaks, Convert.ToSingle
(scoring_parameters.MinHCDMz), Convert.ToSingle(scoring_parameters.MaxHCDMz), false);
hcdPeakProcessor.InitializeUnprocessedData();
hcd_scoring_results = new GlypID.HCDScoring.clsHCDScoringScanResults[1];
HCDScoring.ScoringParameters = scoring_parameters;
_hcd_score = HCDScoring.ScoreHCDSpectra(ref hcd_peaks, ref hcd_mzs, ref hcd_intensities, ref transform_results, ref hcd_scoring_results);
_gType = (GlypID.enmGlycanType)hcd_scoring_results[0].menm_glycan_type;
}
}
private static MSScan GetScanFromFile(int argScanNo, double argSingleToNoise, double argPeakBackground, double argPeptideBackground, short argMaxCharge, GlypID.Readers.clsRawData Raw)
{
float[] _cidMzs = null;
float[] _cidIntensities = null;
GlypID.Peaks.clsPeak[] _cidPeaks = new GlypID.Peaks.clsPeak[1];
GlypID.Peaks.clsPeak[] _parentPeaks = new GlypID.Peaks.clsPeak[1];
GlypID.HornTransform.clsHornTransform mobjTransform = new GlypID.HornTransform.clsHornTransform();
GlypID.HornTransform.clsHornTransformParameters mobjTransformParameters = new GlypID.HornTransform.clsHornTransformParameters();
GlypID.HornTransform.clsHornTransformResults[] _transformResult;
GlypID.Peaks.clsPeakProcessor cidPeakProcessor = new GlypID.Peaks.clsPeakProcessor();
GlypID.Peaks.clsPeakProcessorParameters cidPeakParameters = new GlypID.Peaks.clsPeakProcessorParameters();
GlypID.Peaks.clsPeakProcessor parentPeakProcessor = new GlypID.Peaks.clsPeakProcessor();
GlypID.Peaks.clsPeakProcessorParameters parentPeakParameters = new GlypID.Peaks.clsPeakProcessorParameters();
//Start Read Scan
MSScan scan = new MSScan(argScanNo);
Raw.GetSpectrum(argScanNo, ref _cidMzs, ref _cidIntensities);
scan.MsLevel = Raw.GetMSLevel(Convert.ToInt32(argScanNo));
double min_peptide_intensity = 0;
scan.Time = Raw.GetScanTime(scan.ScanNo);
scan.ScanHeader = Raw.GetScanDescription(scan.ScanNo);
if (scan.MsLevel != 1)
{
float[] _parentRawMzs = null;
float[] _parentRawIntensitys = null;
string Header = Raw.GetScanDescription(argScanNo);
cidPeakProcessor.ProfileType = GlypID.enmProfileType.CENTROIDED;
if (Header.Substring(Header.IndexOf("+") + 1).Trim().StartsWith("p"))
{
cidPeakProcessor.ProfileType = GlypID.enmProfileType.PROFILE;
}
// cidPeakProcessor.DiscoverPeaks(ref _cidMzs, ref _cidIntensities, ref _cidPeaks,
// Convert.ToSingle(mobjTransformParameters.MinMZ), Convert.ToSingle(mobjTransformParameters.MaxMZ), false);
for (int chNum = 0; chNum < _cidMzs.Length; chNum++)
{
scan.MSPeaks.Add(new MSPeak(
Convert.ToSingle(_cidMzs[chNum]),
Convert.ToSingle(_cidIntensities[chNum])));
}
//for (int chNum = 0; chNum < _cidMzs.Length; chNum++)
//{
// scan.MSPeaks.Add(new MSPeak(
// Convert.ToSingle(_cidMzs[chNum]),
// Convert.ToSingle(_cidIntensities[chNum])));
//}
// Get parent information
scan.ParentScanNo = Raw.GetParentScan(scan.ScanNo);
Raw.GetSpectrum(scan.ParentScanNo, ref _parentRawMzs, ref _parentRawIntensitys);
parentPeakProcessor.ProfileType = GlypID.enmProfileType.PROFILE;
parentPeakProcessor.DiscoverPeaks(ref _parentRawMzs, ref _parentRawIntensitys, ref _parentPeaks, Convert.ToSingle(mobjTransformParameters.MinMZ), Convert.ToSingle(mobjTransformParameters.MaxMZ), true);
float _parentBackgroundIntensity = (float)parentPeakProcessor.GetBackgroundIntensity(ref _parentRawIntensitys);
_transformResult = new GlypID.HornTransform.clsHornTransformResults[1];
bool found = false;
if (Raw.IsFTScan(scan.ParentScanNo))
{
// High resolution data
found = mobjTransform.FindPrecursorTransform(Convert.ToSingle(_parentBackgroundIntensity), Convert.ToSingle(min_peptide_intensity), ref _parentRawMzs, ref _parentRawIntensitys, ref _parentPeaks, Convert.ToSingle(scan.ParentMZ), ref _transformResult);
}
if (!found)//de-isotope fail
{
// Low resolution data or bad high res spectra
short cs = Raw.GetMonoChargeFromHeader(scan.ScanNo);
double monoMZ = Raw.GetMonoMzFromHeader(scan.ScanNo);
List <float> ParentMzs = new List <float>(_parentRawMzs);
int CloseIdx = MassUtility.GetClosestMassIdx(ParentMzs, Convert.ToSingle(monoMZ));
if (cs > 0)
{
short[] charges = new short[1];
charges[0] = cs;
mobjTransform.AllocateValuesToTransform(Convert.ToSingle(scan.ParentMZ), Convert.ToInt32(_parentRawIntensitys[CloseIdx]), ref charges, ref _transformResult);
}
else
{
// instrument has no charge just store 2 and 3.
short[] charges = new short[2];
charges[0] = 2;
charges[1] = 3;
mobjTransform.AllocateValuesToTransform(Convert.ToSingle(scan.ParentMZ), Convert.ToInt32(_parentRawIntensitys[CloseIdx]), ref charges, ref _transformResult);
}
}
if (_transformResult[0].mint_peak_index == -1) //De-isotope parent scan
{
//Get parent info
MSScan _parentScan = GetScanFromFile(scan.ParentScanNo, argSingleToNoise, argPeakBackground, argPeptideBackground, argMaxCharge, Raw);
float[] _MSMzs = null;
float[] _MSIntensities = null;
Raw.GetSpectrum(scan.ParentScanNo, ref _MSMzs, ref _MSIntensities);
// Now find peaks
parentPeakParameters.SignalToNoiseThreshold = 0;
parentPeakParameters.PeakBackgroundRatio = 0.01;
parentPeakProcessor.SetOptions(parentPeakParameters);
parentPeakProcessor.ProfileType = GlypID.enmProfileType.PROFILE;
parentPeakProcessor.DiscoverPeaks(ref _MSMzs, ref _MSIntensities, ref _cidPeaks,
Convert.ToSingle(mobjTransformParameters.MinMZ), Convert.ToSingle(mobjTransformParameters.MaxMZ), true);
//Look for charge and mono.
float[] monoandcharge = FindChargeAndMono(_cidPeaks, Convert.ToSingle(Raw.GetParentMz(scan.ScanNo)), scan.ScanNo, Raw);
//scan.ParentMonoMW = _parentScan.MSPeaks[ClosedIdx].MonoMass;
//scan.ParentAVGMonoMW = _parentScan.MSPeaks[ClosedIdx].;
scan.ParentMZ = monoandcharge[0];
if (monoandcharge[1] == 0.0f)
{
scan.ParentCharge = Convert.ToInt32(Raw.GetMonoChargeFromHeader(scan.ParentScanNo));
}
else
{
scan.ParentCharge = Convert.ToInt32(monoandcharge[1]);
}
scan.ParentMonoMW = (monoandcharge[0] - Atoms.ProtonMass) * monoandcharge[1];
}
else
{
scan.ParentMonoMW = (float)_transformResult[0].mdbl_mono_mw;
scan.ParentAVGMonoMW = (float)_transformResult[0].mdbl_average_mw;
scan.ParentMZ = (float)_transformResult[0].mdbl_mz;
scan.ParentCharge = (int)_transformResult[0].mshort_cs;
}
scan.IsCIDScan = Raw.IsCIDScan(argScanNo);
scan.IsFTScan = Raw.IsFTScan(argScanNo);
Array.Clear(_transformResult, 0, _transformResult.Length);
Array.Clear(_cidPeaks, 0, _cidPeaks.Length);
Array.Clear(_cidMzs, 0, _cidMzs.Length);
Array.Clear(_cidIntensities, 0, _cidIntensities.Length);
Array.Clear(_parentRawMzs, 0, _parentRawMzs.Length);
Array.Clear(_parentRawIntensitys, 0, _parentRawIntensitys.Length);
}
else //MS Scan
{
scan.ParentMZ = 0.0f;
double mdbl_current_background_intensity = 0;
// Now find peaks
parentPeakParameters.SignalToNoiseThreshold = argSingleToNoise;
parentPeakParameters.PeakBackgroundRatio = argPeakBackground;
parentPeakProcessor.SetOptions(parentPeakParameters);
parentPeakProcessor.ProfileType = GlypID.enmProfileType.PROFILE;
parentPeakProcessor.DiscoverPeaks(ref _cidMzs, ref _cidIntensities, ref _cidPeaks,
Convert.ToSingle(mobjTransformParameters.MinMZ), Convert.ToSingle(mobjTransformParameters.MaxMZ), true);
mdbl_current_background_intensity = parentPeakProcessor.GetBackgroundIntensity(ref _cidIntensities);
// Settings
min_peptide_intensity = mdbl_current_background_intensity * mobjTransformParameters.PeptideMinBackgroundRatio;
if (mobjTransformParameters.UseAbsolutePeptideIntensity)
{
if (min_peptide_intensity < mobjTransformParameters.AbsolutePeptideIntensity)
{
min_peptide_intensity = mobjTransformParameters.AbsolutePeptideIntensity;
}
}
mobjTransformParameters.PeptideMinBackgroundRatio = argPeptideBackground;
mobjTransformParameters.MaxCharge = argMaxCharge;
mobjTransform.TransformParameters = mobjTransformParameters;
// Now perform deisotoping
_transformResult = new GlypID.HornTransform.clsHornTransformResults[1];
mobjTransform.PerformTransform(Convert.ToSingle(mdbl_current_background_intensity), Convert.ToSingle(min_peptide_intensity), ref _cidMzs, ref _cidIntensities, ref _cidPeaks, ref _transformResult);
// for getting results
for (int chNum = 0; chNum < _transformResult.Length; chNum++)
{
double sumintensity = 0.0;
double mostIntenseIntensity = 0.0;
for (int i = 0; i < _transformResult[chNum].marr_isotope_peak_indices.Length; i++)
{
sumintensity = sumintensity + _cidPeaks[_transformResult[chNum].marr_isotope_peak_indices[i]].mdbl_intensity;
if (Math.Abs(_transformResult[chNum].mdbl_most_intense_mw -
(_cidPeaks[_transformResult[chNum].marr_isotope_peak_indices[i]].mdbl_mz * _transformResult[chNum].mshort_cs - Atoms.ProtonMass * _transformResult[chNum].mshort_cs))
< 1.0 / _transformResult[chNum].mshort_cs)
{
mostIntenseIntensity = _cidPeaks[_transformResult[chNum].mint_peak_index].mdbl_intensity;
}
}
scan.MSPeaks.Add(new MSPeak(
Convert.ToSingle(_transformResult[chNum].mdbl_mono_mw),
_transformResult[chNum].mint_mono_intensity,
_transformResult[chNum].mshort_cs,
Convert.ToSingle(_transformResult[chNum].mdbl_mz),
Convert.ToSingle(_transformResult[chNum].mdbl_fit),
Convert.ToSingle(_transformResult[chNum].mdbl_most_intense_mw),
mostIntenseIntensity,
sumintensity
));
}
Array.Clear(_transformResult, 0, _transformResult.Length);
Array.Clear(_cidPeaks, 0, _cidPeaks.Length);
Array.Clear(_cidMzs, 0, _cidMzs.Length);
Array.Clear(_cidIntensities, 0, _cidIntensities.Length);
}
return(scan);
}
/// <summary>
///
/// </summary>
/// <param name="args">
/// Arg0: FilePath
/// Arg1: FileType switch
/// raw
/// mzxml
/// Arg2: Function switch
/// R:ReadScan
/// N:Number of Scan
/// H: Get HCD info
/// C: Checked if it is CID scan
/// S: Scan header Description
/// M: Get MS Level
/// Arg3:
/// Switch R: int scan number
/// Switch N: none
///
/// Arg4: PeakProcessorParameter _singleToNoiseRatio
/// Arg5: PeakProcessorParameter _peakBackgroundRatio
/// Arg6: TransformParameter _peptideMinBackgroundRatio
/// Arg7: TransformParameter _maxCharge
/// </param>
///
static int Main(string[] args)
{
string FunctionSwitch;// = args[2].ToLower();
GlypID.Readers.clsRawData Raw;
//Debug
//End Debug
try
{
do
{
Console.WriteLine(
"@@\nR:ReadScan\n" +
"N:Number of Scan\n" +
"H: Get HCD info\n" +
"C: Checked if it is CID scan\n" +
"S: Scan header Description\n" +
"M: Get MS Level\n" +
"Q: Quit\n" +
"Please select function:");
FunctionSwitch = Console.In.ReadLine().ToLower().Substring(0, 1);
if (FunctionSwitch == "q")
{
return(0);
}
else
{
Console.WriteLine("Please input file location:");
string _fullFilePath = Console.In.ReadLine();
Console.WriteLine("FIle Type(r: Raw, x:mzXML)");
if (Console.In.ReadLine().ToLower().StartsWith("x"))
{
Raw = new GlypID.Readers.clsRawData(_fullFilePath, GlypID.Readers.FileType.MZXMLRAWDATA);
}
else
{
Raw = new GlypID.Readers.clsRawData(_fullFilePath, GlypID.Readers.FileType.FINNIGAN);
}
//PipeClient pipeClt = new PipeClient();
//pipeClt.Connect("\\\\.\\pipe\\GlypIDPipe");
if (FunctionSwitch == "r")//Read Scan
{
Console.WriteLine("Please input scan num:");
int ScanNo = Convert.ToInt32(Console.In.ReadLine());
Console.WriteLine("Please input Single to Noise ratio (default:3.0):");
double parsedResult = 3.0;
double _singleToNoiseRatio = 3.0;
if (double.TryParse(Console.In.ReadLine(), out parsedResult))
{
_singleToNoiseRatio = parsedResult;
}
Console.WriteLine("Please input Peak background ratio (default:5.0):");
parsedResult = 5.0;
double _peakBackgroundRatio = 5.0;
if (double.TryParse(Console.In.ReadLine(), out parsedResult))
{
_peakBackgroundRatio = parsedResult;
}
Console.WriteLine("Please input Minimum background ratio (default:5.0):");
parsedResult = 5.0;
double _peptideMinBackgroundRatio = 5.0;
if (double.TryParse(Console.In.ReadLine(), out parsedResult))
{
_peptideMinBackgroundRatio = parsedResult;
}
Console.WriteLine("Please input Max charge (defatlt:10):");
short paredCharge = 10;
short _maxCharge = 10;
if (short.TryParse(Console.In.ReadLine(), out paredCharge))
{
_maxCharge = paredCharge;
}
Console.WriteLine("Reading Scan");
MSScan scan = GetScanFromFile(ScanNo, _singleToNoiseRatio, _peakBackgroundRatio, _peptideMinBackgroundRatio, _maxCharge, Raw);
string responseMsg = SendScanViaNamedPipe(scan);
//scan = null;
//if (pipeClt.Connected)
//{
// while (!pipeClt.SendMessage(memStream.ToArray())) ;
// Console.WriteLine("Named pipe sent");
// pipeClt.Disconnect();
//}
//else
//{
// throw new Exception("Named Pipe not found");
//}
Console.WriteLine("ANS:Read Scan: " + ScanNo + " finish;MSScan bytes-" + responseMsg);
}
else if (FunctionSwitch == "n") //Get total scans
{
Console.WriteLine("ANS:" + Raw.GetNumScans().ToString());
}
else if (FunctionSwitch == "h") //Check HCD
{
Console.WriteLine("Please input scan num:");
int ScanNo = Convert.ToInt32(Console.In.ReadLine());
HCDInfo HCDinfo = GetHCDInfo(Raw, ScanNo);
if (HCDinfo != null)
{
Console.WriteLine("ANS:" + HCDinfo.ScanNum.ToString() + ";" +
HCDinfo.GlycanType.ToString() + ";" +
HCDinfo.HCDScore.ToString());
}
else
{
Console.WriteLine("ANS:" + "false");
}
}
else if (FunctionSwitch == "c") //Check CID
{
Console.WriteLine("Please input scan num:");
int ScanNo = Convert.ToInt32(Console.In.ReadLine());
if (Raw.IsCIDScan(ScanNo) == true)
{
Console.WriteLine("ANS:" + "true");
}
else
{
Console.WriteLine("ANS:" + "false");
}
}
else if (FunctionSwitch == "s") //Check description
{
Console.WriteLine("Please input scan num:");
int ScanNo = Convert.ToInt32(Console.In.ReadLine());
string description = Raw.GetScanDescription(ScanNo);
Console.WriteLine("ANS:" + description);
}
else if (FunctionSwitch == "m")//Get MS Level
{
Console.WriteLine("Please input scan num:");
int ScanNo = Convert.ToInt32(Console.In.ReadLine());
Console.WriteLine("ANS:" + Raw.GetMSLevel(ScanNo));
}
else
{
Console.WriteLine("Function error");
}
}
} while (true);
}
catch (Exception e)
{
Console.WriteLine(e.Message);
return(-1);
}
//if (args == null || args.Length == 0)
//{
// Console.WriteLine("args is null"); // Check for null array
// return -1;
//}
//if (FunctionSwitch == "r" && args.Length != 8)
//{
// Console.WriteLine("args is not enough"); // Check for null array
// return -1;
//}
//else
//{
// string _fullFilePath = Console.In.ReadLine();
// Console.WriteLine("Init GlypID");
// if (args[1].ToLower() == "raw")
// {
// Raw = new GlypID.Readers.clsRawData(_fullFilePath, GlypID.Readers.FileType.FINNIGAN);
// }
// else
// {
// Raw = new GlypID.Readers.clsRawData(_fullFilePath, GlypID.Readers.FileType.MZXMLRAWDATA);
// }
// if (FunctionSwitch == "n") //Get Total scans
// {
// Console.WriteLine(Raw.GetNumScans().ToString());
// return Raw.GetNumScans();
// }
// else if (FunctionSwitch == "m") //Get MS Level
// {
// int ScanNo = Convert.ToInt32(args[3]);
// return Raw.GetMSLevel(ScanNo);
// }
// else if (FunctionSwitch == "c") //IsCID Scan
// {
// int ScanNo = Convert.ToInt32(args[3]);
// if (Raw.IsCIDScan(ScanNo) == true)
// {
// return 1;
// }
// return 0;
// }
// else if (FunctionSwitch == "s") //Get Description
// {
// int ScanNo = Convert.ToInt32(args[3]);
// //Console.WriteLine("Get Description info");
// string description = Raw.GetScanDescription(ScanNo);
// Console.WriteLine(description);
// //System.Runtime.Serialization.IFormatter f = new System.Runtime.Serialization.Formatters.Binary.BinaryFormatter();
// //MemoryStream memStream = new MemoryStream();
// //f.Serialize(memStream, description);
// //PipeClient pipeClt = new PipeClient();
// //pipeClt.Connect("\\\\.\\pipe\\GlypIDPipe");
// //if (pipeClt.Connected)
// //{
// // while (!pipeClt.SendMessage(memStream.ToArray())) ;
// // Console.WriteLine("Named pipe sent");
// //}
// //else
// //{
// // throw new Exception("Named Pipe not found");
// //}
// return 1;
// }
// else if (FunctionSwitch == "h") //Get HCD
// {
// int ScanNo = Convert.ToInt32(args[3]);
// HCDInfo HCDinfo = GetHCDInfo(Raw, ScanNo);
// //Console.WriteLine("Get HCD info");
// //System.Runtime.Serialization.IFormatter f = new System.Runtime.Serialization.Formatters.Binary.BinaryFormatter();
// //PipeClient pipeClt = new PipeClient();
// //pipeClt.Connect("\\\\.\\pipe\\GlypIDPipeHCD");
// if (HCDinfo != null)
// {
// Console.WriteLine(HCDinfo.ScanNum.ToString() + ";" +
// HCDinfo.GlycanType.ToString() + ";" +
// HCDinfo.HCDScore.ToString());
// //MemoryStream memStream = new MemoryStream();
// //f.Serialize(memStream, HCDinfo);
// //if (pipeClt.Connected)
// //{
// // while (!pipeClt.SendMessage(memStream.ToArray())) ;
// // Console.WriteLine("Named pipe sent");
// //}
// //else
// //{
// // throw new Exception("Named Pipe not found");
// //}
// return 1;
// }
// else
// {
// //if (pipeClt.Connected)
// //{
// // while (!pipeClt.SendMessage(Encoding.ASCII.GetBytes("No HCD Info found"))) ;
// // Console.WriteLine("Named pipe sent");
// //}
// //else
// //{
// // throw new Exception("Named Pipe not found");
// //}
// return -1;
// }
// }
// else //ReadScan
// {
// int ScanNo = Convert.ToInt32(args[3]);
// double _singleToNoiseRatio = Convert.ToDouble(args[4]);
// double _peakBackgroundRatio = Convert.ToDouble(args[5]);
// double _peptideMinBackgroundRatio = Convert.ToDouble(args[6]);
// short _maxCharge = Convert.ToInt16(args[7]);
// Console.WriteLine("Read Scan");
// MSScan scan = GetScanFromFile(ScanNo, _singleToNoiseRatio, _peakBackgroundRatio, _peptideMinBackgroundRatio, _maxCharge);
// System.Runtime.Serialization.IFormatter f = new System.Runtime.Serialization.Formatters.Binary.BinaryFormatter();
// MemoryStream memStream = new MemoryStream();
// f.Serialize(memStream, scan);
// PipeClient pipeClt = new PipeClient();
// pipeClt.Connect("\\\\.\\pipe\\GlypIDPipe");
// if (pipeClt.Connected)
// {
// while (!pipeClt.SendMessage(memStream.ToArray())) ;
// Console.WriteLine("Named pipe sent");
// }
// else
// {
// throw new Exception("Named Pipe not found");
// }
// /*NamedPipeClientStream PipeClient = new NamedPipeClientStream(".", "ReadMSScan", PipeDirection.Out);
// PipeClient.Connect();
// f.Serialize(PipeClient, scan);
// PipeClient.Close();*/
// Console.WriteLine("Read Scan: " + args[3] + " finish");
// }
// //End Read Scan
// return 1;
//}
}
public RawReader(string argFullPath, enumRawDataType argRawType, double argSingleToNoise, double argPeakBackground, double argPeptideBackground, short argMaxCharge)
{
_fullFilePath = argFullPath;
_singleToNoiseRatio = argSingleToNoise;
_peakBackgroundRatio = argPeakBackground;
_peptideMinBackgroundRatio = argPeptideBackground;
_maxCharge = argMaxCharge;
if (argRawType == enumRawDataType.raw)
{
_fileType = "raw";
Raw = new GlypID.Readers.clsRawData(_fullFilePath, GlypID.Readers.FileType.FINNIGAN);
}
else
{
_fileType = "mzxml";
Raw = new GlypID.Readers.clsRawData(_fullFilePath, GlypID.Readers.FileType.MZXMLRAWDATA);
}
}
// Protected implementation of Dispose pattern.
protected virtual void Dispose(bool disposing)
{
if (disposed)
return;
if (disposing)
{
// Free any other managed objects here.
Raw=null;
}
// Free any unmanaged objects here.
disposed = true;
}
public Class1(string argFileName, int argScanNo)
{
_scanNum = argScanNo;
_filename = argFileName;
GlypID.HornTransform.clsHornTransform Transform = new GlypID.HornTransform.clsHornTransform();
GlypID.Peaks.clsPeakProcessor cidPeakProcessor = new GlypID.Peaks.clsPeakProcessor();
GlypID.Peaks.clsPeakProcessor parentPeakProcessor = new GlypID.Peaks.clsPeakProcessor();
GlypID.HornTransform.clsHornTransformParameters transform_parameters = new GlypID.HornTransform.clsHornTransformParameters();
GlypID.Peaks.clsPeakProcessorParameters peak_parameters = new GlypID.Peaks.clsPeakProcessorParameters();
Raw = new GlypID.Readers.clsRawData(_filename, GlypID.Readers.FileType.FINNIGAN);
Raw.GetSpectrum(_scanNum, ref _cidMzs, ref _cidIntensities);
Transform.TransformParameters = transform_parameters;
_msLevel = Raw.GetMSLevel(_scanNum);
if (_msLevel > 1)
{
_parentScanNum = Raw.GetParentScan(_scanNum);
_parentMz = (float)Raw.GetParentMz(_scanNum);
}
else
{
return; //MS scan
}
Raw.GetSpectrum(_parentScanNum, ref _parentRawMzs, ref _parentRawIntensitys);
_cidPeaks = new GlypID.Peaks.clsPeak[1];
cidPeakProcessor.ProfileType = GlypID.enmProfileType.CENTROIDED;
cidPeakProcessor.DiscoverPeaks(ref _cidMzs, ref _cidIntensities, ref _cidPeaks,
Convert.ToSingle(transform_parameters.MinMZ), Convert.ToSingle(transform_parameters.MaxMZ), false);
_parentPeaks = new GlypID.Peaks.clsPeak[1];
parentPeakProcessor.ProfileType = GlypID.enmProfileType.PROFILE;
parentPeakProcessor.DiscoverPeaks(ref _parentRawMzs, ref _parentRawIntensitys, ref _parentPeaks,
Convert.ToSingle(transform_parameters.MinMZ), Convert.ToSingle(transform_parameters.MaxMZ), true);
_parentBackgroundIntensity = (float)parentPeakProcessor.GetBackgroundIntensity(ref _parentRawIntensitys);
double min_peptide_intensity = _parentBackgroundIntensity * transform_parameters.PeptideMinBackgroundRatio;
if (transform_parameters.UseAbsolutePeptideIntensity)
{
if (min_peptide_intensity < transform_parameters.AbsolutePeptideIntensity)
{
min_peptide_intensity = transform_parameters.AbsolutePeptideIntensity;
}
}
_transformResult = new GlypID.HornTransform.clsHornTransformResults[1];
bool found = Transform.FindPrecursorTransform(Convert.ToSingle(_parentBackgroundIntensity), Convert.ToSingle(min_peptide_intensity), ref _parentRawMzs, ref _parentRawIntensitys, ref _parentPeaks, Convert.ToSingle(_parentMz), ref _transformResult);
if (Raw.IsFTScan(_parentScanNum))
{
// High resolution data
found = Transform.FindPrecursorTransform(Convert.ToSingle(_parentBackgroundIntensity), Convert.ToSingle(min_peptide_intensity), ref _parentRawMzs, ref _parentRawIntensitys, ref _parentPeaks, Convert.ToSingle(_parentMz), ref _transformResult);
}
if (!found)
{
// Low resolution data or bad high res spectra
short cs = Raw.GetMonoChargeFromHeader(_scanNum);
if (cs > 0)
{
short[] charges = new short[1];
charges[0] = cs;
Transform.AllocateValuesToTransform(Convert.ToSingle(_parentMz), 500, ref charges, ref _transformResult);
}
else
{
// instrument has no charge just store 2 and 3.
short[] charges = new short[2];
charges[0] = 2;
charges[1] = 3;
Transform.AllocateValuesToTransform(Convert.ToSingle(_parentMz), 500, ref charges, ref _transformResult);
}
}
_parentMonoMW = (float)_transformResult[0].mdbl_mono_mw;
_parentCharge = (int)_transformResult[0].mshort_cs;
MaxIntensityPeak();
Raw.Close();
}
private MSScan GetMSScan(int argScanNo)
{
MSScan msScan = new MSScan(argScanNo);
// GlypID.Readers.clsRawData rawData = new GlypID.Readers.clsRawData() ;
GlypID.HornTransform.clsHornTransform massTransform = new GlypID.HornTransform.clsHornTransform();
GlypID.Peaks.clsPeakProcessor peakProcessor = new GlypID.Peaks.clsPeakProcessor();
GlypID.HornTransform.clsHornTransformParameters transform_parameters = new GlypID.HornTransform.clsHornTransformParameters();
GlypID.Peaks.clsPeakProcessorParameters peak_parameters = new GlypID.Peaks.clsPeakProcessorParameters();
// Declarations
float[] _mzs = null;
float[] _intensities = null;
GlypID.Peaks.clsPeak[] peaks;
GlypID.HornTransform.clsHornTransformResults[] _transformResults;
// Settings
peak_parameters.SignalToNoiseThreshold = 3.0;
peak_parameters.PeakBackgroundRatio = 5.0;
peakProcessor.SetOptions(peak_parameters);
peakProcessor.ProfileType = GlypID.enmProfileType.PROFILE;
transform_parameters.PeptideMinBackgroundRatio = 5.0;
transform_parameters.MaxCharge = 10;
massTransform.TransformParameters = transform_parameters;
// Load
Raw = new GlypID.Readers.clsRawData(_fullFilePath, GlypID.Readers.FileType.FINNIGAN);
if (Raw.GetMSLevel(argScanNo) == 1)
{
// Get spectra
Raw.GetSpectrum(argScanNo, ref _mzs, ref _intensities);
// Get peaks
peaks = new GlypID.Peaks.clsPeak[1];
peakProcessor.DiscoverPeaks(ref _mzs, ref _intensities, ref peaks, Convert.ToSingle(transform_parameters.MinMZ), Convert.ToSingle(transform_parameters.MaxMZ), true);
// Deisotope
double min_background_intensity = peakProcessor.GetBackgroundIntensity(ref _intensities);
double min_peptide_intensity = min_background_intensity * transform_parameters.PeptideMinBackgroundRatio;
_transformResults = new GlypID.HornTransform.clsHornTransformResults[1];
massTransform.PerformTransform(Convert.ToSingle(min_background_intensity), Convert.ToSingle(min_peptide_intensity), ref _mzs, ref _intensities, ref peaks, ref _transformResults);
Array.Clear(_transformResults, 0, _transformResults.Length);
Array.Clear(peaks, 0, peaks.Length);
}
return msScan;
}
public Class1(string argFileName,int argScanNo)
{
_scanNum = argScanNo;
_filename = argFileName;
GlypID.HornTransform.clsHornTransform Transform = new GlypID.HornTransform.clsHornTransform();
GlypID.Peaks.clsPeakProcessor cidPeakProcessor = new GlypID.Peaks.clsPeakProcessor();
GlypID.Peaks.clsPeakProcessor parentPeakProcessor = new GlypID.Peaks.clsPeakProcessor();
GlypID.HornTransform.clsHornTransformParameters transform_parameters = new GlypID.HornTransform.clsHornTransformParameters();
GlypID.Peaks.clsPeakProcessorParameters peak_parameters = new GlypID.Peaks.clsPeakProcessorParameters();
Raw = new GlypID.Readers.clsRawData(_filename, GlypID.Readers.FileType.FINNIGAN);
Raw.GetSpectrum(_scanNum, ref _cidMzs, ref _cidIntensities);
Transform.TransformParameters = transform_parameters;
_msLevel = Raw.GetMSLevel(_scanNum);
if (_msLevel > 1)
{
_parentScanNum = Raw.GetParentScan(_scanNum);
_parentMz = (float)Raw.GetParentMz(_scanNum);
}
else
{
return; //MS scan
}
Raw.GetSpectrum(_parentScanNum, ref _parentRawMzs, ref _parentRawIntensitys);
_cidPeaks = new GlypID.Peaks.clsPeak[1];
cidPeakProcessor.ProfileType = GlypID.enmProfileType.CENTROIDED;
cidPeakProcessor.DiscoverPeaks(ref _cidMzs, ref _cidIntensities, ref _cidPeaks,
Convert.ToSingle(transform_parameters.MinMZ), Convert.ToSingle(transform_parameters.MaxMZ), false);
_parentPeaks = new GlypID.Peaks.clsPeak[1];
parentPeakProcessor.ProfileType = GlypID.enmProfileType.PROFILE;
parentPeakProcessor.DiscoverPeaks(ref _parentRawMzs, ref _parentRawIntensitys, ref _parentPeaks,
Convert.ToSingle(transform_parameters.MinMZ), Convert.ToSingle(transform_parameters.MaxMZ), true);
_parentBackgroundIntensity = (float)parentPeakProcessor.GetBackgroundIntensity(ref _parentRawIntensitys);
double min_peptide_intensity = _parentBackgroundIntensity * transform_parameters.PeptideMinBackgroundRatio;
if (transform_parameters.UseAbsolutePeptideIntensity)
{
if (min_peptide_intensity < transform_parameters.AbsolutePeptideIntensity)
min_peptide_intensity = transform_parameters.AbsolutePeptideIntensity;
}
_transformResult = new GlypID.HornTransform.clsHornTransformResults[1];
bool found = Transform.FindPrecursorTransform(Convert.ToSingle(_parentBackgroundIntensity), Convert.ToSingle(min_peptide_intensity), ref _parentRawMzs, ref _parentRawIntensitys, ref _parentPeaks, Convert.ToSingle(_parentMz), ref _transformResult);
if (Raw.IsFTScan(_parentScanNum))
{
// High resolution data
found = Transform.FindPrecursorTransform(Convert.ToSingle(_parentBackgroundIntensity), Convert.ToSingle(min_peptide_intensity), ref _parentRawMzs, ref _parentRawIntensitys, ref _parentPeaks, Convert.ToSingle(_parentMz), ref _transformResult);
}
if (!found)
{
// Low resolution data or bad high res spectra
short cs = Raw.GetMonoChargeFromHeader(_scanNum);
if (cs > 0)
{
short[] charges = new short[1];
charges[0] = cs;
Transform.AllocateValuesToTransform(Convert.ToSingle(_parentMz),500, ref charges, ref _transformResult);
}
else
{
// instrument has no charge just store 2 and 3.
short[] charges = new short[2];
charges[0] = 2;
charges[1] = 3;
Transform.AllocateValuesToTransform(Convert.ToSingle(_parentMz), 500,ref charges, ref _transformResult);
}
}
_parentMonoMW = (float)_transformResult[0].mdbl_mono_mw;
_parentCharge = (int)_transformResult[0].mshort_cs;
MaxIntensityPeak();
Raw.Close();
}