/// <summary>
/// Constructor
/// </summary>
/// <param name="mzXmlPath"></param>
/// <param name="peptideMassCalculator"></param>
private MzXmlManager(string mzXmlPath, PHRPReader.PeptideMassCalculator peptideMassCalculator)
{
mPeptideMassCalculator = peptideMassCalculator;
try
{
// Note: prior to October 2017 the dataset name was determined by removing the last 4 characters from datasetName
// That logic seemed flawed and has thus been removed
if (mzXmlPath.EndsWith(".gz", StringComparison.OrdinalIgnoreCase))
{
DatasetName = Path.GetFileNameWithoutExtension(Path.GetFileNameWithoutExtension(mzXmlPath));
}
else
{
DatasetName = Path.GetFileNameWithoutExtension(mzXmlPath);
}
mzAccessor = new clsMzXMLFileAccessor();
mzAccessor.OpenFile(mzXmlPath);
}
catch (DirectoryNotFoundException)
{
throw new DirectoryNotFoundException("The specified directory for " +
"the mzXml could not be found!");
}
catch (FileNotFoundException)
{
var filename = Path.GetFileName(mzXmlPath);
throw new FileNotFoundException("The specified mzXml file \"" +
filename + "\" could not be found!");
}
}
public override void Load(string file_name)
{
mstr_file_name = file_name;
Close();
mobj_MzXmlFile = new clsMzXMLFileAccessor();
mobj_MzXmlFile.OpenFile(mstr_file_name);
mobj_MzXmlFile.ReadAndCacheEntireFile();
}
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>
/// Gets the total number of scans for the group id provided
/// </summary>
/// <param name="group"></param>
/// <returns></returns>
public int GetTotalScans(int group)
{
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];
return rawReader.ScanCount;
}