public void Close()
{
Raw.Close();
}
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();
}
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();
}