private phosphoRS.PTMResultClass RunOnSource(string sourceFilepath, int currentSource, int totalSources, PhosphoRSConfig config, IDictionary<long, PhosphoPeptideAttestationRow> phosphoRows)
{
var msd = new pwiz.CLI.msdata.MSDataFile(sourceFilepath);
var spectrumList = msd.run.spectrumList;
int rowNumber = 0;
int totalRows = phosphoRows.Count();
items.Clear();
var spectrumTypes = new Set<CVID>();
foreach (var row in phosphoRows)
{
if (rowNumber == 0 || (rowNumber % 100) == 0)
{
if (cancelAttestation.IsCancellationRequested)
{
this.progressBar.ProgressBar.Visible = false;
_bgWorkerCancelled = true;
setProgress(-1, "Cancelled.");
return null;
}
else
{
if (rowNumber == 0)
setStatus(String.Format("Reading peaks and creating PhosphoRS objects for source {0} of {1} ({2}): {3} spectra\r\n", currentSource, totalSources, Path.GetFileName(sourceFilepath), totalRows));
setProgress((rowNumber + 1) / totalRows * 100, String.Format("Reading peaks and creating PhosphoRS objects for source {0} of {1} ({2}): {3}/{4} spectra", currentSource, totalSources, Path.GetFileName(sourceFilepath), rowNumber + 1, totalRows));
}
}
var pwizSpectrum = spectrumList.spectrum(spectrumList.find(row.Value.SpectrumNativeID), true); //may create indexoutofrange error if no spectrum nativeID
var OriginalMZs = pwizSpectrum.getMZArray().data; //getMZArray().data returns IList<double>
var OriginalIntensities = pwizSpectrum.getIntensityArray().data;
row.Value.Peaks = new phosphoRS.Peak[OriginalMZs.Count];
for (int i = 0; i < OriginalMZs.Count; ++i)
row.Value.Peaks[i] = new phosphoRS.Peak(OriginalMZs[i], OriginalIntensities[i]);
if (config.spectrumType == phosphoRS.SpectrumType.None)
{
row.Value.SpectrumType = phosphoRS.SpectrumType.None;
foreach (var precursor in pwizSpectrum.precursors)
foreach (var method in precursor.activation.cvParamChildren(CVID.MS_dissociation_method))
{
// if dissociation method is set to "Auto" but could not be determined from the file, alert the user
if (!spectrumTypeByDissociationMethod.Contains(method.cvid))
throw new InvalidDataException("cannot handle unmapped dissociation method \"" + CV.cvTermInfo(method.cvid).shortName() + "\" for spectrum \"" + row.Value.SourceName + "/" + row.Value.SpectrumNativeID + "\"; please override the method manually");
else if (row.Value.SpectrumType != phosphoRS.SpectrumType.ECD_ETD) // don't override ETD (e.g. if there is also supplemental CID)
{
row.Value.SpectrumType = spectrumTypeByDissociationMethod[method.cvid];
spectrumTypes.Add(method.cvid);
}
}
if (row.Value.SpectrumType == phosphoRS.SpectrumType.None)
throw new InvalidDataException("cannot find a dissociation method for spectrum \"" + row.Value.SourceName + "/" + row.Value.SpectrumNativeID + "\"; please set the method manually");
}
else
row.Value.SpectrumType = config.spectrumType;
var psm = getPhosphoRS_PSM(config, row.Value);
// DEBUG
//tbStatus.AppendText(PeptideToString(phosphoPeptide) + "," + AAS.ToOneLetterCodeString() + "," + ptmRepresentation.ToString() + "\n");
// Init the mod map of original variant for this PSM.
var id2ModMap = new List<System.Tuple<int, List<int>>> { new System.Tuple<int, List<int>>((int) row.Value.PSMId, row.Value.OriginalPhosphoSites.Keys.ToList<int>()) };
items.Add(new System.Tuple<phosphoRS.PeptideSpectrumMatch, List<System.Tuple<int, List<int>>>>(psm, id2ModMap));
++rowNumber;
}
// report automatically found fragmentation method
if (config.spectrumType == phosphoRS.SpectrumType.None)
setStatus(String.Format("Found {0} fragmentation types: {1}\r\n", spectrumTypes.Count, String.Join(", ", spectrumTypes.Keys.Select(o => CV.cvTermInfo(o).shortName()))));
setProgress(currentSource / totalSources * 100, String.Format("Running PhosphoRS on source {0} of {1} ({2})...", currentSource, totalSources, Path.GetFileName(sourceFilepath)));
// Initialize the localization.
currentNr = 0;
var phosphoRS_Context = new phosphoRS.ThreadManagement(this, cancelAttestation, config.maxIsoformCount, config.maxPTMCount, config.scoreNLToo, config.fragmentMassTolerance, config.scoredAA, items.Count);
// Start the site localization (takes advantage of multi-threading)
try
{
phosphoRS_Context.StartPTMLocalisation();
// Safety if the attestation module doesn't throw the exception.
if (cancelAttestation.IsCancellationRequested)
{
this.progressBar.ProgressBar.Visible = false;
_bgWorkerCancelled = true;
setProgress(-1, "Cancelled.");
return null;
}
return phosphoRS_Context.PTMResult;
}
catch (OperationCanceledException)
{
this.progressBar.ProgressBar.Visible = false;
_bgWorkerCancelled = true;
setProgress(-1, "Cancelled.");
return null;
}
finally
{
msd.Dispose();
}
}
private phosphoRS.PTMResultClass RunOnSource(string sourceFilepath, int currentSource, int totalSources, PhosphoRSConfig config, IDictionary <long, PhosphoPeptideAttestationRow> phosphoRows)
{
var msd = new pwiz.CLI.msdata.MSDataFile(sourceFilepath);
var spectrumList = msd.run.spectrumList;
int rowNumber = 0;
int totalRows = phosphoRows.Count();
items.Clear();
var spectrumTypes = new Set <CVID>();
foreach (var row in phosphoRows)
{
if (rowNumber == 0 || (rowNumber % 100) == 0)
{
if (cancelAttestation.IsCancellationRequested)
{
this.progressBar.ProgressBar.Visible = false;
_bgWorkerCancelled = true;
setProgress(-1, "Cancelled.");
return(null);
}
else
{
if (rowNumber == 0)
{
setStatus(String.Format("Reading peaks and creating PhosphoRS objects for source {0} of {1} ({2}): {3} spectra\r\n", currentSource, totalSources, Path.GetFileName(sourceFilepath), totalRows));
}
setProgress((rowNumber + 1) / totalRows * 100, String.Format("Reading peaks and creating PhosphoRS objects for source {0} of {1} ({2}): {3}/{4} spectra", currentSource, totalSources, Path.GetFileName(sourceFilepath), rowNumber + 1, totalRows));
}
}
var pwizSpectrum = spectrumList.spectrum(spectrumList.find(row.Value.SpectrumNativeID), true); //may create indexoutofrange error if no spectrum nativeID
var OriginalMZs = pwizSpectrum.getMZArray().data; //getMZArray().data returns IList<double>
var OriginalIntensities = pwizSpectrum.getIntensityArray().data;
row.Value.Peaks = new phosphoRS.Peak[OriginalMZs.Count];
for (int i = 0; i < OriginalMZs.Count; ++i)
{
row.Value.Peaks[i] = new phosphoRS.Peak(OriginalMZs[i], OriginalIntensities[i]);
}
if (config.spectrumType == phosphoRS.SpectrumType.None)
{
row.Value.SpectrumType = phosphoRS.SpectrumType.None;
foreach (var precursor in pwizSpectrum.precursors)
{
foreach (var method in precursor.activation.cvParamChildren(CVID.MS_dissociation_method))
{
// if dissociation method is set to "Auto" but could not be determined from the file, alert the user
if (!spectrumTypeByDissociationMethod.Contains(method.cvid))
{
throw new InvalidDataException("cannot handle unmapped dissociation method \"" + CV.cvTermInfo(method.cvid).shortName() + "\" for spectrum \"" + row.Value.SourceName + "/" + row.Value.SpectrumNativeID + "\"; please override the method manually");
}
else if (row.Value.SpectrumType != phosphoRS.SpectrumType.ECD_ETD) // don't override ETD (e.g. if there is also supplemental CID)
{
row.Value.SpectrumType = spectrumTypeByDissociationMethod[method.cvid];
spectrumTypes.Add(method.cvid);
}
}
}
if (row.Value.SpectrumType == phosphoRS.SpectrumType.None)
{
throw new InvalidDataException("cannot find a dissociation method for spectrum \"" + row.Value.SourceName + "/" + row.Value.SpectrumNativeID + "\"; please set the method manually");
}
}
else
{
row.Value.SpectrumType = config.spectrumType;
}
var psm = getPhosphoRS_PSM(config, row.Value);
// DEBUG
//tbStatus.AppendText(PeptideToString(phosphoPeptide) + "," + AAS.ToOneLetterCodeString() + "," + ptmRepresentation.ToString() + "\n");
// Init the mod map of original variant for this PSM.
var id2ModMap = new List <System.Tuple <int, List <int> > > {
new System.Tuple <int, List <int> >((int)row.Value.PSMId, row.Value.OriginalPhosphoSites.Keys.ToList <int>())
};
items.Add(new System.Tuple <phosphoRS.PeptideSpectrumMatch, List <System.Tuple <int, List <int> > > >(psm, id2ModMap));
++rowNumber;
}
// report automatically found fragmentation method
if (config.spectrumType == phosphoRS.SpectrumType.None)
{
setStatus(String.Format("Found {0} fragmentation types: {1}\r\n", spectrumTypes.Count, String.Join(", ", spectrumTypes.Keys.Select(o => CV.cvTermInfo(o).shortName()))));
}
setProgress(currentSource / totalSources * 100, String.Format("Running PhosphoRS on source {0} of {1} ({2})...", currentSource, totalSources, Path.GetFileName(sourceFilepath)));
// Initialize the localization.
currentNr = 0;
var phosphoRS_Context = new phosphoRS.ThreadManagement(this, cancelAttestation, config.maxIsoformCount, config.maxPTMCount, config.scoreNLToo, config.fragmentMassTolerance, config.scoredAA, items.Count);
// Start the site localization (takes advantage of multi-threading)
try
{
phosphoRS_Context.StartPTMLocalisation();
// Safety if the attestation module doesn't throw the exception.
if (cancelAttestation.IsCancellationRequested)
{
this.progressBar.ProgressBar.Visible = false;
_bgWorkerCancelled = true;
setProgress(-1, "Cancelled.");
return(null);
}
return(phosphoRS_Context.PTMResult);
}
catch (OperationCanceledException)
{
this.progressBar.ProgressBar.Visible = false;
_bgWorkerCancelled = true;
setProgress(-1, "Cancelled.");
return(null);
}
finally
{
msd.Dispose();
}
}
