/// <summary>
/// Retrieve a run of raw spectra with common retention time and changing ion mobility, or a single raw spectrum if no drift info
/// </summary>
/// <param name="internalScanIndex">an index in pwiz.Skyline.Model.Results space</param>
/// <returns>Array of spectra with the same retention time (potentially different ion mobility values for IMS, or just one spectrum)</returns>
public MsDataSpectrum[] GetMsDataFileSpectraWithCommonRetentionTime(int internalScanIndex)
{
var spectra = new List <MsDataSpectrum>();
if (_getMsDataFileScanIds != null)
{
_msDataFileScanIds = _getMsDataFileScanIds();
_getMsDataFileScanIds = null;
}
int dataFileSpectrumStartIndex = internalScanIndex;
// For backward compatibility support SKYD files that did not store scan ID bytes
if (_msDataFileScanIds != null)
{
var scanIdText = _msDataFileScanIds.GetMsDataFileSpectrumId(internalScanIndex);
dataFileSpectrumStartIndex = GetDataFile().GetSpectrumIndex(scanIdText);
if (dataFileSpectrumStartIndex == -1)
{
// try without combining ion mobility (if it's turned on)
dataFileSpectrumStartIndex = GetDataFile(false).GetSpectrumIndex(scanIdText);
if (dataFileSpectrumStartIndex == -1)
{
throw new IOException(string.Format(Resources.ScanProvider_GetScans_The_scan_ID__0__was_not_found_in_the_file__1__, scanIdText, DataFilePath.GetFileName()));
}
}
}
var currentSpectrum = GetDataFile().GetSpectrum(dataFileSpectrumStartIndex);
spectra.Add(currentSpectrum);
if (currentSpectrum.IonMobility.HasValue)
{
// Look for spectra with identical retention time and changing ion mobility values
while (true)
{
dataFileSpectrumStartIndex++;
var nextSpectrum = GetDataFile().GetSpectrum(dataFileSpectrumStartIndex);
if (!nextSpectrum.IonMobility.HasValue ||
nextSpectrum.RetentionTime != currentSpectrum.RetentionTime)
{
break;
}
spectra.Add(nextSpectrum);
currentSpectrum = nextSpectrum;
}
}
return(spectra.ToArray());
}
/// <summary>
/// Retrieve a run of raw spectra with common retention time and changing ion mobility, or a single raw spectrum if no drift info
/// </summary>
/// <param name="internalScanIndex">an index in pwiz.Skyline.Model.Results space</param>
/// <param name="ignoreZeroIntensityPoints">display uses want zero intensity points, data processing uses typically do not</param>
/// <returns>Array of spectra with the same retention time (potentially different ion mobility values for IMS, or just one spectrum)</returns>
public MsDataSpectrum[] GetMsDataFileSpectraWithCommonRetentionTime(int internalScanIndex, bool ignoreZeroIntensityPoints)
{
var spectra = new List <MsDataSpectrum>();
if (_measuredResults != null)
{
_msDataFileScanIds = _measuredResults.LoadMSDataFileScanIds(DataFilePath, out _cachedFile);
_measuredResults = null;
}
int dataFileSpectrumStartIndex = internalScanIndex;
// For backward compatibility support SKYD files that did not store scan ID bytes
if (_msDataFileScanIds != null)
{
var scanIdText = _msDataFileScanIds.GetMsDataFileSpectrumId(internalScanIndex);
dataFileSpectrumStartIndex = GetDataFile(ignoreZeroIntensityPoints).GetSpectrumIndex(scanIdText);
// TODO(brendanx): Improve this error message post-UI freeze
// if (dataFileSpectrumStartIndex == -1)
// throw new ArgumentException(string.Format("The stored scan ID {0} was not found in the file {1}.", scanIdText, DataFilePath));
}
var currentSpectrum = GetDataFile(ignoreZeroIntensityPoints).GetSpectrum(dataFileSpectrumStartIndex);
spectra.Add(currentSpectrum);
if (currentSpectrum.IonMobilities != null) // Sort combined IMS spectra by m/z order
{
ArrayUtil.Sort(currentSpectrum.Mzs, currentSpectrum.Intensities, currentSpectrum.IonMobilities);
}
else if (currentSpectrum.IonMobility.HasValue) // Look ahead for uncombined IMS spectra
{
// Look for spectra with identical retention time and changing ion mobility values
while (true)
{
dataFileSpectrumStartIndex++;
var nextSpectrum = GetDataFile(ignoreZeroIntensityPoints).GetSpectrum(dataFileSpectrumStartIndex);
if (!nextSpectrum.IonMobility.HasValue ||
nextSpectrum.RetentionTime != currentSpectrum.RetentionTime)
{
break;
}
spectra.Add(nextSpectrum);
currentSpectrum = nextSpectrum;
}
}
return(spectra.ToArray());
}
/// <summary>
/// Retrieve a run of raw spectra with common retention time and changing ion mobility, or a single raw spectrum if no drift info
/// </summary>
/// <param name="internalScanIndex">an index in pwiz.Skyline.Model.Results space</param>
/// <param name="ignoreZeroIntensityPoints">display uses want zero intensity points, data processing uses typically do not</param>
/// <returns>Array of spectra with the same retention time (potentially different ion mobility values for IMS, or just one spectrum)</returns>
public MsDataSpectrum[] GetMsDataFileSpectraWithCommonRetentionTime(int internalScanIndex, bool ignoreZeroIntensityPoints)
{
var spectra = new List <MsDataSpectrum>();
if (_getMsDataFileScanIds != null)
{
_msDataFileScanIds = _getMsDataFileScanIds();
_getMsDataFileScanIds = null;
}
int dataFileSpectrumStartIndex = internalScanIndex;
// For backward compatibility support SKYD files that did not store scan ID bytes
if (_msDataFileScanIds != null)
{
var scanIdText = _msDataFileScanIds.GetMsDataFileSpectrumId(internalScanIndex);
dataFileSpectrumStartIndex = GetDataFile(ignoreZeroIntensityPoints).GetSpectrumIndex(scanIdText);
}
var currentSpectrum = GetDataFile(ignoreZeroIntensityPoints).GetSpectrum(dataFileSpectrumStartIndex);
if (currentSpectrum.IonMobilities != null)
{
ArrayUtil.Sort(currentSpectrum.Mzs, currentSpectrum.Intensities, currentSpectrum.IonMobilities); // Sort in m/z order
}
spectra.Add(currentSpectrum);
if (currentSpectrum.IonMobilities == null && // No need to look ahead for 3-array IMS representation
currentSpectrum.IonMobility.HasValue)
{
// Look for spectra with identical retention time and changing ion mobility values
while (true)
{
dataFileSpectrumStartIndex++;
var nextSpectrum = GetDataFile(ignoreZeroIntensityPoints).GetSpectrum(dataFileSpectrumStartIndex);
if (!nextSpectrum.IonMobility.HasValue ||
nextSpectrum.RetentionTime != currentSpectrum.RetentionTime)
{
break;
}
spectra.Add(nextSpectrum);
currentSpectrum = nextSpectrum;
}
}
return(spectra.ToArray());
}
