// Returns false on cancellation
private bool ProcessFile(MsDataFileUri filePath)
{
var results = _document.Settings.MeasuredResults;
if (!results.MSDataFilePaths.Contains(filePath))
{
return(true); // Nothing to do
}
if (_progressStatus != null)
{
_progressStatus = _progressStatus.ChangeMessage(filePath.GetFileName());
}
_currentDisplayedTransitionGroupDocNode = null;
var tolerance = (float)_document.Settings.TransitionSettings.Instrument.MzMatchTolerance;
foreach (var pair in _document.MoleculePrecursorPairs)
{
var nodePep = pair.NodePep;
var nodeGroup = pair.NodeGroup;
var libKey = nodeGroup.GetLibKey(nodePep);
// Across all replicates for this precursor, note the ion mobility at max intensity for this mz
for (var i = 0; i < results.Chromatograms.Count; i++)
{
if (_progressMonitor != null && _progressMonitor.IsCanceled)
{
return(false);
}
ChromatogramGroupInfo[] chromGroupInfos;
results.TryLoadChromatogram(i, nodePep, nodeGroup, tolerance, true, out chromGroupInfos);
foreach (var chromInfo in chromGroupInfos.Where(c => Equals(filePath, c.FilePath)))
{
if (!ProcessChromInfo(filePath, chromInfo, pair, nodeGroup, tolerance, libKey))
{
return(false); // User cancelled
}
}
}
}
return(true);
}
private bool ProcessMSLevel(MsDataFileUri filePath, int msLevel, IEnumerable <ChromatogramInfo> transitionPointSets,
ChromatogramGroupInfo chromInfo, double?apexRT, TransitionGroupDocNode nodeGroup, LibKey libKey, float tolerance)
{
var transitions = new List <TransitionFullScanInfo>();
var chromSource = (msLevel == 1) ? ChromSource.ms1 : ChromSource.fragment;
IList <float> times = null;
foreach (var tranPointSet in transitionPointSets.Where(t => t.Source == chromSource))
{
transitions.Add(new TransitionFullScanInfo
{
//Name = tranPointSet.Header.,
Source = chromSource,
TimeIntensities = tranPointSet.TimeIntensities,
PrecursorMz = chromInfo.PrecursorMz,
ProductMz = tranPointSet.ProductMz,
ExtractionWidth = tranPointSet.ExtractionWidth,
//Id = nodeTran.Id
});
times = tranPointSet.Times;
}
if (!transitions.Any())
{
return(true); // Nothing to do at this ms level
}
IScanProvider scanProvider = new ScanProvider(_documentFilePath,
filePath,
chromSource, times, transitions.ToArray(),
_document.Settings.MeasuredResults,
() => _document.Settings.MeasuredResults.LoadMSDataFileScanIds(filePath));
// Across all spectra at the peak retention time, find the one with max total
// intensity for the mz's of interest (ie the isotopic distribution) and note its ion mobility.
var scanIndex = MsDataFileScanHelper.FindScanIndex(times, apexRT.Value);
_msDataFileScanHelper.UpdateScanProvider(scanProvider, 0, scanIndex);
_msDataFileScanHelper.MsDataSpectra = null; // Reset
scanIndex = _msDataFileScanHelper.GetScanIndex();
_msDataFileScanHelper.ScanProvider.SetScanForBackgroundLoad(scanIndex);
lock (this)
{
while (_msDataFileScanHelper.MsDataSpectra == null && _dataFileScanHelperException == null)
{
if (_progressMonitor != null && _progressMonitor.IsCanceled)
{
return(false);
}
Monitor.Wait(this, 500); // Let background loader do its thing
}
}
if (_dataFileScanHelperException != null)
{
throw new IOException(TextUtil.LineSeparate(Resources.DriftTimeFinder_HandleLoadScanException_Problem_using_results_to_populate_drift_time_library__, _dataFileScanHelperException.Message), _dataFileScanHelperException);
}
if (_progressMonitor != null && !ReferenceEquals(nodeGroup, _currentDisplayedTransitionGroupDocNode))
{
// Do this after scan load so first group after file switch doesn't seem laggy
_progressStatus = _progressStatus.ChangeMessage(TextUtil.LineSeparate(filePath.GetFileName(), nodeGroup.ToString())).
UpdatePercentCompleteProgress(_progressMonitor, _currentStep++, _totalSteps);
_currentDisplayedTransitionGroupDocNode = nodeGroup;
}
EvaluateBestIonMobilityValue(msLevel, libKey, tolerance, transitions);
return(true);
}
public bool ImportResultsFile(MsDataFileUri replicateFile, string replicateName, DateTime? importBefore, DateTime? importOnOrAfter,
OptimizableRegression optimize, bool disableJoining = false)
{
// Skip if file write time is after importBefore or before importAfter
try
{
var fileLastWriteTime = replicateFile.GetFileLastWriteTime();
if (importBefore != null && importBefore < fileLastWriteTime)
{
_out.WriteLine(Resources.CommandLine_ImportResultsFile_File_write_date__0__is_after___import_before_date__1___Ignoring___,
fileLastWriteTime, importBefore);
return true;
}
else if (importOnOrAfter != null && importOnOrAfter >= fileLastWriteTime)
{
_out.WriteLine(Resources.CommandLine_ImportResultsFile_File_write_date__0__is_before___import_on_or_after_date__1___Ignoring___, fileLastWriteTime, importOnOrAfter);
return true;
}
}
catch (Exception e)
{
_out.WriteLine(Resources.CommandLine_ImportResultsInDir_Error__Could_not_get_last_write_time_for_file__0__, replicateFile);
_out.WriteLine(e);
return false;
}
_out.WriteLine(Resources.CommandLine_ImportResultsFile_Adding_results___);
// Hack for un-readable RAW files from Thermo instruments.
if(!CanReadFile(replicateFile))
{
_out.WriteLine(Resources.CommandLine_ImportResultsFile_Warning__Cannot_read_file__0____Ignoring___, replicateFile);
return true;
}
//This function will also detect whether the replicate exists in the document
ProgressStatus status;
SrmDocument newDoc;
IProgressMonitor progressMonitor = new CommandProgressMonitor(_out, new ProgressStatus(string.Empty));
try
{
if (disableJoining)
_doc = _doc.ChangeSettingsNoDiff(_doc.Settings.ChangeIsResultsJoiningDisabled(true));
newDoc = ImportResults(_doc,_skylineFile, replicateName, replicateFile, optimize, progressMonitor, out status);
}
catch (Exception x)
{
_out.WriteLine(Resources.CommandLine_ImportResultsFile_Error__Failed_importing_the_results_file__0__, replicateFile);
_out.WriteLine(x.Message);
return false;
}
status = status ?? new ProgressStatus(string.Empty).Complete();
if (status.IsError && status.ErrorException != null)
{
if (status.ErrorException is MissingDataException)
{
_out.WriteLine(Resources.CommandLine_ImportResultsFile_Warning__Failed_importing_the_results_file__0____Ignoring___, replicateFile);
_out.WriteLine(status.ErrorException.Message);
return true;
}
_out.WriteLine(Resources.CommandLine_ImportResultsFile_Error__Failed_importing_the_results_file__0__, replicateFile);
_out.WriteLine(status.ErrorException.Message);
return false;
}
if (!status.IsComplete || ReferenceEquals(_doc, newDoc))
{
_out.WriteLine(Resources.CommandLine_ImportResultsFile_Error__Failed_importing_the_results_file__0__, replicateFile);
return false;
}
_doc = newDoc;
_out.WriteLine(Resources.CommandLine_ImportResultsFile_Results_added_from__0__to_replicate__1__, replicateFile.GetFileName(), replicateName);
//the file was imported successfully
_importCount++;
return true;
}
public static string GetFileName(MsDataFileUri msDataFileUri)
{
return msDataFileUri.GetFileName();
}
private bool ProcessMSLevel(MsDataFileUri filePath, int msLevel, IEnumerable<ChromatogramInfo> transitionPointSets,
ChromatogramGroupInfo chromInfo, double? apexRT, TransitionGroupDocNode nodeGroup, LibKey libKey, float tolerance)
{
var transitions = new List<TransitionFullScanInfo>();
var chromSource = (msLevel == 1) ? ChromSource.ms1 : ChromSource.fragment;
foreach (var tranPointSet in transitionPointSets.Where(t => t.Source == chromSource))
{
transitions.Add(new TransitionFullScanInfo
{
//Name = tranPointSet.Header.,
Source = chromSource,
ScanIndexes = chromInfo.ScanIndexes,
PrecursorMz = chromInfo.PrecursorMz,
ProductMz = tranPointSet.ProductMz,
ExtractionWidth = tranPointSet.ExtractionWidth,
//Id = nodeTran.Id
});
}
var chorusUrl = filePath as ChorusUrl;
IScanProvider scanProvider;
if (null == chorusUrl)
{
scanProvider = new ScanProvider(_documentFilePath,
filePath,
chromSource, chromInfo.Times, transitions.ToArray(),
() => _document.Settings.MeasuredResults.LoadMSDataFileScanIds(filePath));
}
else
{
scanProvider = new ChorusScanProvider(_documentFilePath,
chorusUrl,
chromSource, chromInfo.Times, transitions.ToArray());
}
// Across all spectra at the peak retention time, find the one with max total
// intensity for the mz's of interest (ie the isotopic distribution) and note its drift time.
var scanIndex = chromInfo.ScanIndexes != null
? MsDataFileScanHelper.FindScanIndex(chromInfo, apexRT.Value)
: -1;
_msDataFileScanHelper.UpdateScanProvider(scanProvider, 0, scanIndex);
_msDataFileScanHelper.MsDataSpectra = null; // Reset
scanIndex = _msDataFileScanHelper.GetScanIndex();
_msDataFileScanHelper.ScanProvider.SetScanForBackgroundLoad(scanIndex);
lock (this)
{
while (_msDataFileScanHelper.MsDataSpectra == null && _dataFileScanHelperException == null)
{
if (_progressMonitor != null && _progressMonitor.IsCanceled)
return false;
Monitor.Wait(this, 500); // Let background loader do its thing
}
}
if (_dataFileScanHelperException != null)
{
throw new IOException(TextUtil.LineSeparate(Resources.DriftTimeFinder_HandleLoadScanException_Problem_using_results_to_populate_drift_time_library__, _dataFileScanHelperException.Message), _dataFileScanHelperException);
}
if (_progressMonitor != null && !ReferenceEquals(nodeGroup, _currentDisplayedTransitionGroupDocNode))
{
// Do this after scan load so first group after file switch doesn't seem laggy
_progressStatus = _progressStatus.ChangeMessage(TextUtil.LineSeparate(filePath.GetFileName(), nodeGroup.ToString())).
UpdatePercentCompleteProgress(_progressMonitor, _currentStep++, _totalSteps);
_currentDisplayedTransitionGroupDocNode = nodeGroup;
}
EvaluateBestDriftTime(msLevel, libKey, tolerance, transitions);
return true;
}
// Returns false on cancellation
private bool ProcessFile(MsDataFileUri filePath)
{
var results = _document.Settings.MeasuredResults;
if (!results.MSDataFilePaths.Contains(filePath))
return true; // Nothing to do
if (_progressStatus != null)
{
_progressStatus = _progressStatus.ChangeMessage(filePath.GetFileName());
}
_currentDisplayedTransitionGroupDocNode = null;
var tolerance = (float)_document.Settings.TransitionSettings.Instrument.MzMatchTolerance;
foreach (var pair in _document.MoleculePrecursorPairs)
{
var nodePep = pair.NodePep;
var nodeGroup = pair.NodeGroup;
var libKey = new LibKey(nodePep.RawTextId, nodeGroup.PrecursorCharge);
// Across all replicates for this precursor, note the drift time at max intensity for this mz
for (var i = 0; i < results.Chromatograms.Count; i++)
{
if (_progressMonitor != null && _progressMonitor.IsCanceled)
return false;
ChromatogramGroupInfo[] chromGroupInfos;
results.TryLoadChromatogram(i, nodePep, nodeGroup, tolerance, true, out chromGroupInfos);
foreach (var chromInfo in chromGroupInfos.Where(c => filePath == c.FilePath))
{
if (!ProcessChromInfo(filePath, chromInfo, pair, nodeGroup, tolerance, libKey))
return false; // User cancelled
}
}
}
return true;
}
public static string GetFileName(MsDataFileUri msDataFileUri)
{
return(msDataFileUri.GetFileName());
}