public MapParser()
{
_utils = new GlycoFragworkDLL.Utils.Utilities();
_ScoringParameters = new GlypID.Scoring.clsScoringParameters();
_CIDSpectralUtilities = new SpectralUtilities();
_HCDSpectralUtilities = new SpectralUtilities();
_ETDSpectralUtilities = new SpectralUtilities();
_params = new Params();
}
public MapParserOld()
{
_GlycoMap = new GlycoFragworkDLL.Classes.MapRecord();
_utils = new GlycoFragworkDLL.Utils.Utilities();
_ScoringParameters = new GlypID.Scoring.clsScoringParameters();
_TransformParameters = new GlypID.HornTransform.clsHornTransformParameters();
_binSize = 0.05;
_PPMDiff = 20;
}
public MapCreator()
{
_GlycoMap = new Classes.MapRecord() ;
_utils = new Utilities();
_glycopeptides = new List<GlycopeptideRecord> ();
_TransformParameters = new GlypID.HornTransform.clsHornTransformParameters() ;
_ParentPeakProcessorParams = new GlypID.Peaks.clsPeakProcessorParameters() ;
_MSMSPeakProcessorParams = new GlypID.Peaks.clsPeakProcessorParameters() ;
_ScoringParameters = new GlypID.Scoring.clsScoringParameters();
_HornTransform = new GlypID.HornTransform.clsHornTransform() ;
_ParentPeakProcessor = new GlypID.Peaks.clsPeakProcessor() ;
_MSMSPeakProcessor = new GlypID.Peaks.clsPeakProcessor() ;
_ParentPeaks = new GlypID.Peaks.clsPeak[1] ;
_MSMSPeaks = new GlypID.Peaks.clsPeak[1];
_ParentTransformResults = new GlypID.HornTransform.clsHornTransformResults[1];
_dGlycopeptides = new Dictionary<int, List<GlycopeptideRecord>>();
_CIDScoring = new GlypID.CIDScoring.clsCIDScoring();
_HCDScoring = new GlypID.HCDScoring.clsHCDScoring();
_ETDScoring = new GlypID.ETDScoring.clsETDScoring();
}
/// <summary>
/// No HCD info the return will be null
/// </summary>
/// <param name="argReader"></param>
/// <param name="argScanNo"></param>
/// <returns></returns>
private static HCDInfo GetHCDInfo(GlypID.Readers.clsRawData argReader, int argScanNo)
{
if(!argReader.IsHCDScan(argScanNo))
{
return null;
}
HCDInfo HCDinfo = null;
double _hcd_score;
GlypID.enmGlycanType _gType;
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;
enumGlycanType GType; //Convert from GlypID.enumGlycanType to MassLib.enumGlycanType;
if (_gType == GlypID.enmGlycanType.CA)
{
GType = enumGlycanType.CA;
}
else if (_gType == GlypID.enmGlycanType.CS)
{
GType = enumGlycanType.CS;
}
else if (_gType == GlypID.enmGlycanType.HM)
{
GType = enumGlycanType.HM;
}
else if (_gType == GlypID.enmGlycanType.HY)
{
GType = enumGlycanType.HY;
}
else
{
GType = enumGlycanType.NA;
}
HCDinfo = new HCDInfo(argScanNo, GType, _hcd_score);
}
return HCDinfo;
}
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;
}
}
