/// <summary>
/// Name: GetParentMZ
/// Description: This function returns the ParentIon of the current experiment (determined by m_experimentCode).
/// </summary>
/// <returns>
/// Output: This function outputs the Parent Ion in the form of a double.
/// </returns>
public double GetParentMZ()
{
clsSpectrumInfo tempInfo = new clsSpectrumInfo();
m_fileToRead.GetSpectrumByScanNumber(this.m_experimentCode, ref tempInfo);
return(tempInfo.ParentIonMZ);
}
// Note that Centroid is ignored by this class
public override bool GetRawData(out List <double> mzs, out List <double> intensities, int scan_num, bool centroid, int num_pts)
{
if (scan_num > mint_num_scans)
{
var mesg = "File only has " + mint_num_scans + " scans. Cannot read to scan number: " + scan_num;
throw new Exception(mesg);
}
mint_current_scan = scan_num;
mobj_MzXmlFile.GetSpectrumHeaderInfoByScanNumber(scan_num, out mobj_CurrentScanData);
mzs = new List <double>();
intensities = new List <double>();
var scanData = new clsSpectrumInfo();
mobj_MzXmlFile.GetSpectrumByScanNumber(scan_num, out scanData);
var num_points = scanData.DataCount;
if (num_pts > 0 && num_pts < num_points)
{
num_points = num_pts;
}
mzs.Capacity = num_points;
intensities.Capacity = num_points;
double fMass;
double fInten;
var max_intensity = -1 * double.MaxValue;
var min_intensity = double.MaxValue;
for (var i = 0; i < scanData.DataCount; i++)
{
fMass = scanData.MZList[i];
fInten = scanData.IntensityList[i];
if (fInten > max_intensity)
{
max_intensity = fInten;
}
if (fInten < min_intensity) //Anoop Jan 08: was > before
{
min_intensity = fInten;
}
mzs.Add(fMass);
intensities.Add(fInten);
}
mdbl_signal_level = max_intensity - min_intensity;
return(true);
}
public override bool IsProfileScan(int scan_num)
{
var scanData = new clsSpectrumInfo();
mobj_MzXmlFile.GetSpectrumHeaderInfoByScanNumber(scan_num, out scanData);
// TODO: Validate this solution
//if (scanData.profileType == 'p')
// return true;
//else if (scanData.profileType == 'c')
// return false;
return(!scanData.Centroided);
//default
//return true;
}
public override double GetScanTime(int scan_num)
{
if (mint_current_scan == scan_num)
{
return(mobj_CurrentScanData.RetentionTimeMin);
}
else
{
var scanData = new clsSpectrumInfo();
// its time to read in that scan.
mint_current_scan = scan_num;
mobj_MzXmlFile.GetSpectrumHeaderInfoByScanNumber(scan_num, out scanData);
return(scanData.RetentionTimeMin);
}
}
public override int GetParentScan(int scan_num)
{
var scan = scan_num;
var scanData = new clsSpectrumInfo();
mobj_MzXmlFile.GetSpectrumHeaderInfoByScanNumber(scan, out scanData);
for (scan = scan_num - 1;; scan--)
{
mobj_MzXmlFile.GetSpectrumHeaderInfoByScanNumber(scan, out scanData);
if (scanData.MSLevel == 1)
{
break;
}
}
return(scan);
}
public override void GetTicFromFile(out List <double> intensities, out List <double> scan_times,
bool base_peak_tic)
{
intensities = new List <double>();
scan_times = new List <double>();
if (mobj_MzXmlFile == null)
{
return;
}
var nonzero_time_reported = false;
for (var scan_num = 0; scan_num <= mint_num_scans; scan_num++)
{
// its time to read in that scan.
mint_current_scan = scan_num;
var scanData = new clsSpectrumInfo();
mobj_MzXmlFile.GetSpectrumHeaderInfoByScanNumber(scan_num, out scanData);
scan_times.Add(scanData.RetentionTimeMin);
if (scanData.RetentionTimeMin != 0.0)
{
nonzero_time_reported = true;
}
if (base_peak_tic)
{
intensities.Add(scanData.BasePeakIntensity);
}
else
{
intensities.Add(scanData.TotalIonCurrent);
}
}
// for mzxml files in which no retention times were recorded.
if (!nonzero_time_reported)
{
for (var scan_num = 0; scan_num <= mint_num_scans; scan_num++)
{
scan_times[scan_num] = scan_num;
}
}
}
public override bool IsFTScan(int scan_num)
{
var scan = scan_num;
var scanData = new clsSpectrumInfo();
mobj_MzXmlFile.GetSpectrumHeaderInfoByScanNumber(scan, out scanData);
string xmlText;
mobj_MzXmlFile.GetSourceXMLByScanNumber(scan_num, out xmlText);
// TODO: Validate this solution
if (xmlText.Contains("FTMS"))
{
return(true);
}
else if (xmlText.Contains("ITMS"))
{
return(false);
}
//default
return(false);
}
public List<MSSpectra> GetMSMSSpectra(int group, Dictionary<int, int> excludeMap, bool loadPeaks)
{
var spectra = new List<MSSpectra>();
if (!m_dataFiles.ContainsKey(group))
{
throw new Exception("The group-dataset ID provided was not found.");
}
// If we dont have a reader, then create one for this group
// next time, it will be available and we won't have to waste time
// opening the file.
if (!m_readers.ContainsKey(group))
{
var path = m_dataFiles[group];
var reader = new clsMzXMLFileAccessor();
m_readers.Add(group, reader);
var opened = reader.OpenFile(path);
if (!opened)
{
throw new IOException("Could not open the mzXML file " + path);
}
}
var rawReader = m_readers[group];
var numberOfScans = rawReader.ScanCount;
var info = new clsSpectrumInfo();
for (var i = 0; i < numberOfScans; i++)
{
// This scan is not to be used.
var isInExcludeMap = excludeMap.ContainsKey(i);
if (isInExcludeMap)
continue;
var header = new clsSpectrumInfo();
rawReader.GetSpectrumHeaderInfoByIndex(i, ref header);
if (header.MSLevel > 1)
{
var spectrum = new MSSpectra();
spectrum.MsLevel = header.MSLevel;
spectrum.RetentionTime = header.RetentionTimeMin;
spectrum.Scan = i;
spectrum.PrecursorMz = header.ParentIonMZ;
spectrum.TotalIonCurrent = header.TotalIonCurrent;
spectrum.CollisionType = CollisionType.Other;
spectra.Add(spectrum);
}
}
return spectra;
}
private clsSpectrumInfo GetScanInfo(int scan, int groupId, out ScanSummary summary)
{
if (!m_dataFiles.ContainsKey(groupId))
{
throw new Exception("The group-dataset ID provided was not found.");
}
// If we dont have a reader, then create one for this group
// next time, it will be available and we won't have to waste time
// opening the file.
if (!m_readers.ContainsKey(groupId))
{
var path = m_dataFiles[groupId];
var reader = new clsMzXMLFileAccessor();
m_readers.Add(groupId, reader);
var opened = reader.OpenFile(path);
if (!opened)
{
throw new IOException("Could not open the mzXML file " + path);
}
}
var rawReader = m_readers[groupId];
var totalScans = rawReader.ScanCount;
var info = new clsSpectrumInfo();
rawReader.GetSpectrumByScanNumber(scan, ref info);
summary = new ScanSummary
{
Bpi = Convert.ToInt64(info.BasePeakIntensity),
BpiMz = info.BasePeakMZ,
MsLevel = info.MSLevel,
PrecursorMz = info.ParentIonMZ,
TotalIonCurrent = Convert.ToInt64(info.TotalIonCurrent)
};
return info;
}
/// <summary>
/// Reads a list of MSMS Spectra header data from the mzXML file.
/// </summary>
/// <param name="file">file to read.</param>
/// <returns>List of MSMS spectra data</returns>
public List<MSSpectra> ReadMSMSSpectra(string file)
{
var spectra = new List<MSSpectra>();
var reader = new clsMzXMLFileReader {SkipBinaryData = true};
var opened = reader.OpenFile(file);
if (!opened)
{
throw new IOException("Could not open the mzXML file " + file);
}
var totalScans = reader.ScanCount;
for (var i = 0; i < totalScans; i++)
{
var info = new clsSpectrumInfo();
reader.GetSpectrumByScanNumber(i, ref info);
if (info.MSLevel > 1)
{
var spectrum = new MSSpectra
{
MsLevel = info.MSLevel,
RetentionTime = info.RetentionTimeMin,
Scan = i,
PrecursorMz = info.ParentIonMZ,
TotalIonCurrent = info.TotalIonCurrent,
CollisionType = CollisionType.Other
};
// Need to make this a standard type of collision based off of the data.
spectra.Add(spectrum);
}
}
reader.CloseFile();
return spectra;
}
/// <summary>
/// Name: CloseFile
/// Description: This function Closes the file and sets the opened flag to false.
/// </summary>
public void CloseFile()
{
this.m_isFileOpened = false;
this.m_fileToRead.CloseFile();
this.m_currentSpectrum = null;
}
