/// <summary>
/// Step through the MZ values in array dblMZs and compute the ppm-based mass difference between adjacent points
/// </summary>
/// <param name="ionCount">Number of items in dblMZs; if -1, then parses all data in dblMZs</param>
/// <param name="dblMZs"></param>
/// <param name="msLevel"></param>
/// <param name="centroidingStatus"></param>
/// <remarks>Assumes the ions are sorted</remarks>
public void CheckSpectrum(int ionCount, double[] dblMZs, int msLevel, eCentroidStatusConstants centroidingStatus = eCentroidStatusConstants.Unknown)
{
if (ionCount < 0)
{
ionCount = dblMZs.Length;
}
// Possibly sort dblMZs
for (var i = 1; i <= ionCount - 1; i++)
{
if (dblMZs[i] < dblMZs[i - 1])
{
// Sort required
Array.Sort(dblMZs);
break; // TODO: might not be correct. Was : Exit For
}
}
var lstPpmDiffs = new List <double>(ionCount);
for (var i = 1; i <= ionCount - 1; i++)
{
var dblMZ = dblMZs[i];
var dblPreviousMZ = dblMZs[i - 1];
if (dblPreviousMZ > 0 && dblMZ > dblPreviousMZ)
{
var delMppm = 1000000.0 * (dblMZ - dblPreviousMZ) / dblMZ;
lstPpmDiffs.Add(delMppm);
}
}
CheckPPMDiffs(lstPpmDiffs, msLevel, centroidingStatus);
}
/// <summary>
/// Examines lstPpmDiffs to determine if the data is centroided data
/// </summary>
/// <param name="lstPpmDiffs"></param>
/// <param name="msLevel">1 for MS1, 2 for MS2, etc.</param>
/// <param name="centroidingStatus"></param>
/// <remarks>Increments class property TotalSpectra if lstPpmDiffs is not empty; increments class property CentroidedSpectra if the data is centroided</remarks>
protected void CheckPPMDiffs(List <double> lstPpmDiffs, int msLevel, eCentroidStatusConstants centroidingStatus)
{
if (lstPpmDiffs.Count > 0)
{
IncrementDictionaryByMSLevel(ref mTotalSpectra, msLevel);
var empiricalCentroidStatus = eCentroidStatusConstants.Profile;
if (IsDataCentroided(lstPpmDiffs))
{
empiricalCentroidStatus = eCentroidStatusConstants.Centroid;
}
if (centroidingStatus == eCentroidStatusConstants.Centroid & empiricalCentroidStatus == eCentroidStatusConstants.Profile)
{
// The empirical algorithm has classified a centroid spectrum as profile
// Change it back to centroid
empiricalCentroidStatus = eCentroidStatusConstants.Centroid;
IncrementDictionaryByMSLevel(ref mCentroidedSpectraClassifiedAsProfile, msLevel);
}
if (empiricalCentroidStatus == eCentroidStatusConstants.Centroid)
{
IncrementDictionaryByMSLevel(ref mCentroidedSpectra, msLevel);
}
}
}
/// <summary>
/// Examines lstPpmDiffs to determine if the data is centroided data
/// </summary>
/// <param name="lstMZs"></param>
/// <param name="lstPpmDiffs"></param>
/// <param name="msLevel">1 for MS1, 2 for MS2, etc.</param>
/// <param name="centroidingStatus">Expected centroid mode</param>
/// <param name="spectrumTitle">Optional spectrum title (e.g. scan number)</param>
/// <remarks>
/// Increments class property TotalSpectra if lstPpmDiffs is not empty
/// Increments class property CentroidedSpectra if the data is centroided
/// </remarks>
private void CheckPPMDiffs(
ICollection <double> lstMZs,
IList <double> lstPpmDiffs,
int msLevel,
eCentroidStatusConstants centroidingStatus,
string spectrumTitle = "")
{
if (lstPpmDiffs.Count <= 0)
{
return;
}
IncrementDictionaryByMSLevel(mTotalSpectra, msLevel);
if (RaiseDebugEvents)
{
if (string.IsNullOrWhiteSpace(spectrumTitle))
{
OnDebugEvent(string.Format("Examining MS{0} spectrum", msLevel));
}
else
{
OnDebugEvent("Examining " + spectrumTitle);
}
}
var empiricalCentroidStatus = eCentroidStatusConstants.Profile;
if (IsDataCentroided(lstPpmDiffs, spectrumTitle))
{
empiricalCentroidStatus = eCentroidStatusConstants.Centroid;
}
else
{
// Data appears profile
// Examine the data by region to confirm that at least two thirds of the regions have profile mode data
if (IsDataCentroidedInRegions(lstMZs, DEFAULT_REGION_COUNT, spectrumTitle))
{
// When examining regions, the data appears centroided
empiricalCentroidStatus = eCentroidStatusConstants.Centroid;
}
}
if (centroidingStatus == eCentroidStatusConstants.Centroid && empiricalCentroidStatus == eCentroidStatusConstants.Profile)
{
// The empirical algorithm has classified a centroid spectrum as profile
// Change it back to centroid
empiricalCentroidStatus = eCentroidStatusConstants.Centroid;
IncrementDictionaryByMSLevel(mCentroidedSpectraClassifiedAsProfile, msLevel);
}
if (empiricalCentroidStatus == eCentroidStatusConstants.Centroid)
{
IncrementDictionaryByMSLevel(mCentroidedSpectra, msLevel);
}
}
/// <summary>
/// Step through the MZ values in array dblMZs and compute the ppm-based mass difference between adjacent points
/// </summary>
/// <param name="ionCount">Number of items in dblMZs; if -1, then parses all data in dblMZs</param>
/// <param name="dblMZs"></param>
/// <param name="msLevel"></param>
/// <param name="centroidingStatus"></param>
/// <param name="spectrumTitle">Optional spectrum title (e.g. scan number)</param>
public void CheckSpectrum(
int ionCount,
double[] dblMZs,
int msLevel,
eCentroidStatusConstants centroidingStatus = eCentroidStatusConstants.Unknown,
string spectrumTitle = "")
{
if (ionCount < 0)
{
ionCount = dblMZs.Length;
}
// Possibly sort dblMZs
for (var i = 1; i <= ionCount - 1; i++)
{
if (dblMZs[i] < dblMZs[i - 1])
{
// Sort required
Array.Sort(dblMZs);
break;
}
}
var lstPpmDiffs = new List <double>(ionCount);
for (var i = 1; i <= ionCount - 1; i++)
{
var mz = dblMZs[i];
var previousMz = dblMZs[i - 1];
if (previousMz > 0 && mz > previousMz)
{
var delMassPPM = 1000000.0 * (mz - previousMz) / mz;
lstPpmDiffs.Add(delMassPPM);
}
}
CheckPPMDiffs(dblMZs.ToList(), lstPpmDiffs, msLevel, centroidingStatus, spectrumTitle);
}
/// <summary>
/// Step through the MZ values in array dblMZs and compute the ppm-based mass difference between adjacent points
/// </summary>
/// <param name="lstMZs"></param>
/// <param name="msLevel"></param>
/// <param name="assumeSorted"></param>
/// <param name="centroidingStatus"></param>
/// <param name="spectrumTitle">Optional spectrum title (e.g. scan number)</param>
/// <remarks>
/// Increments class property TotalSpectra if lstMZs is not empty
/// Increments class property CentroidedSpectra if the data is centroided
/// </remarks>
public void CheckSpectrum(
List <double> lstMZs,
int msLevel,
bool assumeSorted,
eCentroidStatusConstants centroidingStatus = eCentroidStatusConstants.Unknown,
string spectrumTitle = "")
{
if (!assumeSorted)
{
// Check whether sorting is required
for (var i = 1; i <= lstMZs.Count - 1; i++)
{
if (lstMZs[i] < lstMZs[i - 1])
{
lstMZs.Sort();
break;
}
}
}
var lstPpmDiffs = new List <double>(lstMZs.Count);
for (var i = 1; i <= lstMZs.Count - 1; i++)
{
var mz = lstMZs[i];
var previousMz = lstMZs[i - 1];
if (previousMz > 0 && mz > previousMz)
{
var delMassPPM = 1000000.0 * (mz - previousMz) / mz;
lstPpmDiffs.Add(delMassPPM);
}
}
CheckPPMDiffs(lstMZs, lstPpmDiffs, msLevel, centroidingStatus, spectrumTitle);
}
public void CheckSpectrum(List <double> lstMZs, int msLevel, bool assumeSorted, eCentroidStatusConstants centroidingStatus = eCentroidStatusConstants.Unknown)
{
if (!assumeSorted)
{
// Check whether sorting is required
for (var i = 1; i <= lstMZs.Count - 1; i++)
{
if (lstMZs[i] < lstMZs[i - 1])
{
lstMZs.Sort();
break;
}
}
}
var lstPpmDiffs = new List <double>(lstMZs.Count);
for (var i = 1; i <= lstMZs.Count - 1; i++)
{
var dblMZ = lstMZs[i];
var dblPreviousMZ = lstMZs[i - 1];
if (dblPreviousMZ > 0 && dblMZ > dblPreviousMZ)
{
var delMppm = 1000000.0 * (dblMZ - dblPreviousMZ) / dblMZ;
lstPpmDiffs.Add(delMppm);
}
}
CheckPPMDiffs(lstPpmDiffs, msLevel, centroidingStatus);
}
public void CheckSpectrum(List <double> lstMZs, int msLevel, eCentroidStatusConstants centroidingStatus)
{
CheckSpectrum(lstMZs, msLevel, assumeSorted: false, centroidingStatus: centroidingStatus);
}
/// <summary>
/// Step through the MZ values in array dblMZs and compute the ppm-based mass difference between adjacent points
/// </summary>
/// <param name="lstMZs"></param>
/// <param name="msLevel"></param>
/// <param name="centroidingStatus"></param>
/// <param name="spectrumTitle">Optional spectrum title (e.g. scan number)</param>
/// <remarks>
/// Increments class property TotalSpectra if lstMZs is not empty
/// Increments class property CentroidedSpectra if the data is centroided
/// </remarks>
public void CheckSpectrum(List <double> lstMZs, int msLevel, eCentroidStatusConstants centroidingStatus, string spectrumTitle = "")
{
CheckSpectrum(lstMZs, msLevel, false, centroidingStatus, spectrumTitle);
}
