private void ExecuteAttestButton_Click(object sender, EventArgs e)
{
btnAttestPTMs.Enabled = false;
btnCancelAttestaion.Enabled = true;
_bgWorkerAttestation = new BackgroundWorker();
//_bgWorkerClustering.WorkerReportsProgress = true;
_bgWorkerAttestation.WorkerSupportsCancellation = true;
_bgWorkerCancelled = false;
var config = new PhosphoRSConfig();
config.setSpectrumType(dissociationTypeComboBox.SelectedItem.ToString());
config.fragmentMassTolerance = Double.Parse(FragmentMZToleranceTextBox.Text);
_bgWorkerAttestation.DoWork += _bgWorkerClustering_DoWork;
_bgWorkerAttestation.RunWorkerCompleted += _bgWorkerClustering_RunWorkerCompleted;
_bgWorkerAttestation.RunWorkerAsync(config);
}
private void ExecuteAttestButton_Click(object sender, EventArgs e)
{
btnAttestPTMs.Enabled = false;
btnCancelAttestaion.Enabled = true;
_bgWorkerAttestation = new BackgroundWorker();
//_bgWorkerClustering.WorkerReportsProgress = true;
_bgWorkerAttestation.WorkerSupportsCancellation = true;
_bgWorkerCancelled = false;
var config = new PhosphoRSConfig();
config.setSpectrumType(dissociationTypeComboBox.SelectedItem.ToString());
config.fragmentMassTolerance = Double.Parse(FragmentMZToleranceTextBox.Text);
_bgWorkerAttestation.DoWork += _bgWorkerClustering_DoWork;
_bgWorkerAttestation.RunWorkerCompleted += _bgWorkerClustering_RunWorkerCompleted;
_bgWorkerAttestation.RunWorkerAsync(config);
}
private void ExecutePhosphoRS(PhosphoRSConfig config)
{
// Set up the cancel token.
cancelAttestation = new CancellationTokenSource();
// Initialize time stamps and status reporting variables.
DateTime startTime = DateTime.Now;
Invoke(new MethodInvoker(() =>
{
progressBar.ProgressBar.Visible = true;
progressBar.Maximum = 100;
//tbStatus.Font = new Font(FontFamily.GenericMonospace, 10.0f);
}));
//session.CreateSQLQuery("CREATE TABLE IF NOT EXISTS PeptideModificationProbability (PeptideModification INTEGER PRIMARY KEY, Probability NUMERIC)").ExecuteUpdate();
session.CreateSQLQuery("DELETE FROM PeptideModificationProbability").ExecuteUpdate();
var insertSiteProbabilityCommand = session.Connection.CreateCommand();
var PepModParameter = insertSiteProbabilityCommand.CreateParameter();
var ProbParameter = insertSiteProbabilityCommand.CreateParameter();
insertSiteProbabilityCommand.Parameters.Add(PepModParameter);
insertSiteProbabilityCommand.Parameters.Add(ProbParameter);
insertSiteProbabilityCommand.CommandText = "INSERT INTO PeptideModificationProbability VALUES (?,?)";
// Init the variables used by phosphoRS. Clear its internal variables also.
items = new List<System.Tuple<phosphoRS.PeptideSpectrumMatch, List<System.Tuple<int, List<int>>>>>();
var distinctSources = session.Query<SpectrumSource>().ToList();
var sourceFilepaths = new Dictionary<string, string>();
distinctSources.ForEach(source => sourceFilepaths[source.Name] = IDPickerForm.LocateSpectrumSource(source.Name, session.Connection.GetDataSource()));
if (distinctSources.Any(source => sourceFilepaths[source.Name].IsNullOrEmpty()))
setStatus("Cancelled attestation: some sources are a missing source file");
// group the spectra by source and run each source as a batch
int totalSources = distinctSources.Count;
int currentSource = 0;
//This task listen to this collection and takes any message that is send...
Action progressListenerAction = () =>
{
try
{
phosphoRS.ThreadManagement.progressMessage msg;
double lastProgress = -1;
while (!progressMessageQueue.IsCompleted)
{
msg = progressMessageQueue.Take();
if (msg.type == phosphoRS.ThreadManagement.progressMessage.typeOfMessage.stringMessage && !msg.message.IsNullOrEmpty())
{
//setStatus(String.Format("PhosphoRS message: {0}\r\n", msg.message));
}
else
{
if (msg.spectraProcessed == 1.0 || msg.spectraProcessed > lastProgress + 0.01)
{
lastProgress = msg.spectraProcessed;
double baseProgress = (double) currentSource / totalSources;
int currentProgress = Math.Min(100, (int) Math.Round((baseProgress + msg.spectraProcessed * 1.0 / totalSources) * 100));
setProgress(currentProgress, String.Format("Running PhosphoRS on source {0} of {1}...", currentSource, totalSources));
}
}
}
}
catch (Exception)
{
}
};
foreach (var source in distinctSources)
{
Task progressListener = Task.Factory.StartNew(progressListenerAction);
progressMessageQueue = new BlockingCollection<phosphoRS.ThreadManagement.progressMessage>(new ConcurrentQueue<phosphoRS.ThreadManagement.progressMessage>());
// get phospho peptide-spectrum matches for the source
setStatus(String.Format("Finding phosphopeptides in \"{0}\"... ", source.Name));
setProgress(-1, String.Format("Finding phosphopeptides in \"{0}\"... ", source.Name));
DateTime findTime = DateTime.Now;
var phosphoPSMs = getPhosphoPSMs(source.Id.Value);
setStatus(String.Format("found {0} phosphopeptides ({1} seconds elapsed).\r\n", phosphoPSMs.Count, (DateTime.Now - findTime).TotalSeconds));
if (phosphoPSMs.Count == 0)
continue;
phosphoRS.PTMResultClass result = RunOnSource(sourceFilepaths[source.Name], ++currentSource, totalSources, config, phosphoPSMs);
if (cancelAttestation.IsCancellationRequested)
return;
if (result == null)
throw new Exception("Error running PhosphoRS on source " + source.Name);
IDictionary<int, double> propMap;
IDictionary<int, double> peptideScoreMap;
IDictionary<int, string> sitepropMap;
// peptide ID to site probabilities map
sitepropMap = result.PeptideIdPrsSiteProbabilitiesMap;
// peptid ID to isoform confidence probability map
propMap = result.PeptideIdPrsProbabilityMap;
// peptide ID to binomial score map
peptideScoreMap = result.PeptideIdPrsScoreMap;
//setProgress(4, "(4/4) Injecting results into the database...");
// A map of PSMId to localization representation in string format.
//Dictionary<long, string> localizationStrings = new Dictionary<long, string>();
var transaction = session.BeginTransaction();
foreach (var isoform in result.IsoformGroupList)
{
if (isoform.Count == 0)
continue;
PhosphoPeptideAttestationRow row;
if (isoform.Error)
{
long PSMId = (long) isoform.PeptideIDs[0];
row = phosphoPSMs[PSMId];
setStatus(String.Format("Error running on {0} ({1}): {2}\r\n", PSMId, phosphoPSMs[PSMId].Peptide.sequence, isoform.Message));
continue;
}
else
{
long PSMId = (long) isoform.Peptides.First().ID;
row = phosphoPSMs[PSMId];
}
long pmId = -1;
foreach(var site in isoform.SiteProbabilities)
{
bool gotSite = row.OriginalPhosphoSites.TryGetValue(site.SequencePosition - 1, out pmId);
if (!gotSite)
continue;
PepModParameter.Value = pmId;
ProbParameter.Value = site.Probability;
insertSiteProbabilityCommand.ExecuteNonQuery();
}
if (pmId == -1)
throw new InvalidDataException("no PhosphoRS site probability matches to an original phospho site");
}
transaction.Commit();
}
Invoke(new MethodInvoker(() =>
{
progressBar.ProgressBar.Visible = false;
setProgress(-1, "Finished.");
}));
}
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.PeptideSpectrumMatch getPhosphoRS_PSM(PhosphoRSConfig config, PhosphoPeptideAttestationRow variant)
{
// Get the phosphorylated peptide and add all modifications to the base sequence.
proteome.Peptide phosphoPeptide = new proteome.Peptide(variant.UnphosphorylatedSequence, proteome.ModificationParsing.ModificationParsing_Auto, proteome.ModificationDelimiter.ModificationDelimiter_Brackets);
proteome.ModificationMap variantPeptideMods = phosphoPeptide.modifications();
variant.OriginalPhosphoSites.Keys.ToList().ForEach(location => { variantPeptideMods[location].Add(config.pwizMod); });
// This modification ID is used to tell phosphoRS how to modify the sequence.
int modificationID = config.phosphorylationSymbol + 1;
// Build a string representation of all modificaitons in a peptide for phospoRS
// "0.00011000000000.0" : 1 is the ID of the modification. All phosphos in a data
// set need to have one ID. This ID is used by the PhosphoRS to figure out which
// mods need to be scored.
var ptmRepresentation = new StringBuilder();
// Store all modifications in phosphoRS modification objects
var modifications = new List<phosphoRS.AminoAcidModification>();
// Get the n-terminal modifications.
if (variantPeptideMods.ContainsKey(proteome.ModificationMap.NTerminus()))
{
phosphoRS.AminoAcidModification otherMod = new phosphoRS.AminoAcidModification('2', "unknown", "unk", "none", variantPeptideMods[proteome.ModificationMap.NTerminus()].monoisotopicDeltaMass(), 0.0, null);
modifications.Add(otherMod);
ptmRepresentation.Append(modificationID.ToString() + ".");
//++modificationID;
}
else
{
ptmRepresentation.Append("0.");
}
// Process all other modifications.
for (int aaIndex = 0; aaIndex < phosphoPeptide.sequence.Length; ++aaIndex)
{
// If phosphorylation, use the existing scoredAA variable.
if (variantPeptideMods.ContainsKey(aaIndex))
{
if (variant.OriginalPhosphoSites.Keys.Contains(aaIndex))
{
modifications.Add(config.scoredAA);
ptmRepresentation.Append(config.phosphorylationSymbol.ToString()[0]);
}
else
{
// Otherwise, make an "unknown" modification with a separate modification ID.
var otherMod = new phosphoRS.AminoAcidModification(modificationID.ToString()[0], "unknown", "unk", "none", variantPeptideMods[aaIndex].monoisotopicDeltaMass(), 0.0, phosphoRS.AminoAcidSequence.ParseAASequence("" + phosphoPeptide.sequence[aaIndex]));
modifications.Add(otherMod);
ptmRepresentation.Append(modificationID.ToString());
//++modificationID;
}
}
else
{
ptmRepresentation.Append("0");
}
}
// Process any c-terminal modifications.
if (variantPeptideMods.ContainsKey(proteome.ModificationMap.CTerminus()))
{
var otherMod = new phosphoRS.AminoAcidModification(modificationID.ToString()[0], "unknown", "unk", "none", variantPeptideMods[proteome.ModificationMap.CTerminus()].monoisotopicDeltaMass(), 0.0, null);
modifications.Add(otherMod);
ptmRepresentation.Append("." + modificationID.ToString());
}
else
{
ptmRepresentation.Append(".0");
}
// Get the phosphoRS peptide sequence.
// Assign spectrum ID, amino acid sequence, list of all modifications, a so-called 'modification position string' (here every digit represents an amino acid within the peptide sequence
// '0' indicates not modified, values != '0' indicate the unique identifier of the amino acid's modification the first digit represents the n-terminus the last digit represents the c-terminus)
var AAS = phosphoRS.AminoAcidSequence.Create((int)variant.SpectrumId, phosphoPeptide.sequence, modifications, ptmRepresentation.ToString());
// Make a phosphoRS peptide-spectrum match.
return new phosphoRS.PeptideSpectrumMatch((int)variant.PSMId, variant.SpectrumType, variant.Charge, variant.PrecursorMZ, variant.Peaks, AAS);
}
private string PeptideToString(proteome.Peptide peptide, IList<phosphoRS.PTMSiteProbability> localizationProbabilities, PhosphoRSConfig config)
{
var probabilityMap = localizationProbabilities.ToDictionary(o => o.SequencePosition, o => o.Probability);
string format = String.Format("[{{0:f{0}}}]", 0);
StringBuilder sb = new StringBuilder();
if (peptide.modifications().ContainsKey(proteome.ModificationMap.NTerminus()))
sb.AppendFormat(format, peptide.modifications()[proteome.ModificationMap.NTerminus()].monoisotopicDeltaMass());
for (int i = 0; i < peptide.sequence.Length; ++i)
{
sb.Append(peptide.sequence[i]);
if (probabilityMap.ContainsKey(i + 1))
{
if (probabilityMap[i + 1] > 0)
sb.AppendFormat("[{0:f0}({1:f0}%)]", config.scoredAA.MassDelta, probabilityMap[i + 1] * 100);
//else
// sb.AppendFormat("({0:f0})", config.scoredAA.MassDelta, probabilityMap[i + 1]);
}
else if (peptide.modifications().ContainsKey(i))
{
double modMass = peptide.modifications()[i].monoisotopicDeltaMass();
sb.AppendFormat(format, modMass);
}
}
if (peptide.modifications().ContainsKey(proteome.ModificationMap.CTerminus()))
sb.AppendFormat(format, peptide.modifications()[proteome.ModificationMap.CTerminus()].monoisotopicDeltaMass());
return sb.ToString();
}
private void ExecutePhosphoRS(PhosphoRSConfig config)
{
// Set up the cancel token.
cancelAttestation = new CancellationTokenSource();
// Initialize time stamps and status reporting variables.
DateTime startTime = DateTime.Now;
Invoke(new MethodInvoker(() =>
{
progressBar.ProgressBar.Visible = true;
progressBar.Maximum = 100;
//tbStatus.Font = new Font(FontFamily.GenericMonospace, 10.0f);
}));
//session.CreateSQLQuery("CREATE TABLE IF NOT EXISTS PeptideModificationProbability (PeptideModification INTEGER PRIMARY KEY, Probability NUMERIC)").ExecuteUpdate();
session.CreateSQLQuery("DELETE FROM PeptideModificationProbability").ExecuteUpdate();
var insertSiteProbabilityCommand = session.Connection.CreateCommand();
var PepModParameter = insertSiteProbabilityCommand.CreateParameter();
var ProbParameter = insertSiteProbabilityCommand.CreateParameter();
insertSiteProbabilityCommand.Parameters.Add(PepModParameter);
insertSiteProbabilityCommand.Parameters.Add(ProbParameter);
insertSiteProbabilityCommand.CommandText = "INSERT INTO PeptideModificationProbability VALUES (?,?)";
// Init the variables used by phosphoRS. Clear its internal variables also.
items = new List <System.Tuple <phosphoRS.PeptideSpectrumMatch, List <System.Tuple <int, List <int> > > > >();
var distinctSources = session.Query <SpectrumSource>().ToList();
var sourceFilepaths = new Dictionary <string, string>();
distinctSources.ForEach(source => sourceFilepaths[source.Name] = IDPickerForm.LocateSpectrumSource(source.Name, session.Connection.GetDataSource()));
if (distinctSources.Any(source => sourceFilepaths[source.Name].IsNullOrEmpty()))
{
setStatus("Cancelled attestation: some sources are a missing source file");
}
// group the spectra by source and run each source as a batch
int totalSources = distinctSources.Count;
int currentSource = 0;
//This task listen to this collection and takes any message that is send...
Action progressListenerAction = () =>
{
try
{
phosphoRS.ThreadManagement.progressMessage msg;
double lastProgress = -1;
while (!progressMessageQueue.IsCompleted)
{
msg = progressMessageQueue.Take();
if (msg.type == phosphoRS.ThreadManagement.progressMessage.typeOfMessage.stringMessage && !msg.message.IsNullOrEmpty())
{
//setStatus(String.Format("PhosphoRS message: {0}\r\n", msg.message));
}
else
{
if (msg.spectraProcessed == 1.0 || msg.spectraProcessed > lastProgress + 0.01)
{
lastProgress = msg.spectraProcessed;
double baseProgress = (double)currentSource / totalSources;
int currentProgress = Math.Min(100, (int)Math.Round((baseProgress + msg.spectraProcessed * 1.0 / totalSources) * 100));
setProgress(currentProgress, String.Format("Running PhosphoRS on source {0} of {1}...", currentSource, totalSources));
}
}
}
}
catch (Exception)
{
}
};
foreach (var source in distinctSources)
{
Task progressListener = Task.Factory.StartNew(progressListenerAction);
progressMessageQueue = new BlockingCollection <phosphoRS.ThreadManagement.progressMessage>(new ConcurrentQueue <phosphoRS.ThreadManagement.progressMessage>());
// get phospho peptide-spectrum matches for the source
setStatus(String.Format("Finding phosphopeptides in \"{0}\"... ", source.Name));
setProgress(-1, String.Format("Finding phosphopeptides in \"{0}\"... ", source.Name));
DateTime findTime = DateTime.Now;
var phosphoPSMs = getPhosphoPSMs(source.Id.Value);
setStatus(String.Format("found {0} phosphopeptides ({1} seconds elapsed).\r\n", phosphoPSMs.Count, (DateTime.Now - findTime).TotalSeconds));
if (phosphoPSMs.Count == 0)
{
continue;
}
phosphoRS.PTMResultClass result = RunOnSource(sourceFilepaths[source.Name], ++currentSource, totalSources, config, phosphoPSMs);
if (cancelAttestation.IsCancellationRequested)
{
return;
}
if (result == null)
{
throw new Exception("Error running PhosphoRS on source " + source.Name);
}
IDictionary <int, double> propMap;
IDictionary <int, double> peptideScoreMap;
IDictionary <int, string> sitepropMap;
// peptide ID to site probabilities map
sitepropMap = result.PeptideIdPrsSiteProbabilitiesMap;
// peptid ID to isoform confidence probability map
propMap = result.PeptideIdPrsProbabilityMap;
// peptide ID to binomial score map
peptideScoreMap = result.PeptideIdPrsScoreMap;
//setProgress(4, "(4/4) Injecting results into the database...");
// A map of PSMId to localization representation in string format.
//Dictionary<long, string> localizationStrings = new Dictionary<long, string>();
var transaction = session.BeginTransaction();
foreach (var isoform in result.IsoformGroupList)
{
if (isoform.Count == 0)
{
continue;
}
PhosphoPeptideAttestationRow row;
if (isoform.Error)
{
long PSMId = (long)isoform.PeptideIDs[0];
row = phosphoPSMs[PSMId];
setStatus(String.Format("Error running on {0} ({1}): {2}\r\n", PSMId, phosphoPSMs[PSMId].Peptide.sequence, isoform.Message));
continue;
}
else
{
long PSMId = (long)isoform.Peptides.First().ID;
row = phosphoPSMs[PSMId];
}
long pmId = -1;
foreach (var site in isoform.SiteProbabilities)
{
bool gotSite = row.OriginalPhosphoSites.TryGetValue(site.SequencePosition - 1, out pmId);
if (!gotSite)
{
continue;
}
PepModParameter.Value = pmId;
ProbParameter.Value = site.Probability;
insertSiteProbabilityCommand.ExecuteNonQuery();
}
if (pmId == -1)
{
throw new InvalidDataException("no PhosphoRS site probability matches to an original phospho site");
}
}
transaction.Commit();
}
Invoke(new MethodInvoker(() =>
{
progressBar.ProgressBar.Visible = false;
setProgress(-1, "Finished.");
}));
}
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.PeptideSpectrumMatch getPhosphoRS_PSM(PhosphoRSConfig config, PhosphoPeptideAttestationRow variant)
{
// Get the phosphorylated peptide and add all modifications to the base sequence.
proteome.Peptide phosphoPeptide = new proteome.Peptide(variant.UnphosphorylatedSequence, proteome.ModificationParsing.ModificationParsing_Auto, proteome.ModificationDelimiter.ModificationDelimiter_Brackets);
proteome.ModificationMap variantPeptideMods = phosphoPeptide.modifications();
variant.OriginalPhosphoSites.Keys.ToList().ForEach(location => { variantPeptideMods[location].Add(config.pwizMod); });
// This modification ID is used to tell phosphoRS how to modify the sequence.
int modificationID = config.phosphorylationSymbol + 1;
// Build a string representation of all modificaitons in a peptide for phospoRS
// "0.00011000000000.0" : 1 is the ID of the modification. All phosphos in a data
// set need to have one ID. This ID is used by the PhosphoRS to figure out which
// mods need to be scored.
var ptmRepresentation = new StringBuilder();
// Store all modifications in phosphoRS modification objects
var modifications = new List <phosphoRS.AminoAcidModification>();
// Get the n-terminal modifications.
if (variantPeptideMods.ContainsKey(proteome.ModificationMap.NTerminus()))
{
phosphoRS.AminoAcidModification otherMod = new phosphoRS.AminoAcidModification('2', "unknown", "unk", "none", variantPeptideMods[proteome.ModificationMap.NTerminus()].monoisotopicDeltaMass(), 0.0, null);
modifications.Add(otherMod);
ptmRepresentation.Append(modificationID.ToString() + ".");
//++modificationID;
}
else
{
ptmRepresentation.Append("0.");
}
// Process all other modifications.
for (int aaIndex = 0; aaIndex < phosphoPeptide.sequence.Length; ++aaIndex)
{
// If phosphorylation, use the existing scoredAA variable.
if (variantPeptideMods.ContainsKey(aaIndex))
{
if (variant.OriginalPhosphoSites.Keys.Contains(aaIndex))
{
modifications.Add(config.scoredAA);
ptmRepresentation.Append(config.phosphorylationSymbol.ToString()[0]);
}
else
{
// Otherwise, make an "unknown" modification with a separate modification ID.
var otherMod = new phosphoRS.AminoAcidModification(modificationID.ToString()[0], "unknown", "unk", "none", variantPeptideMods[aaIndex].monoisotopicDeltaMass(), 0.0, phosphoRS.AminoAcidSequence.ParseAASequence("" + phosphoPeptide.sequence[aaIndex]));
modifications.Add(otherMod);
ptmRepresentation.Append(modificationID.ToString());
//++modificationID;
}
}
else
{
ptmRepresentation.Append("0");
}
}
// Process any c-terminal modifications.
if (variantPeptideMods.ContainsKey(proteome.ModificationMap.CTerminus()))
{
var otherMod = new phosphoRS.AminoAcidModification(modificationID.ToString()[0], "unknown", "unk", "none", variantPeptideMods[proteome.ModificationMap.CTerminus()].monoisotopicDeltaMass(), 0.0, null);
modifications.Add(otherMod);
ptmRepresentation.Append("." + modificationID.ToString());
}
else
{
ptmRepresentation.Append(".0");
}
// Get the phosphoRS peptide sequence.
// Assign spectrum ID, amino acid sequence, list of all modifications, a so-called 'modification position string' (here every digit represents an amino acid within the peptide sequence
// '0' indicates not modified, values != '0' indicate the unique identifier of the amino acid's modification the first digit represents the n-terminus the last digit represents the c-terminus)
var AAS = phosphoRS.AminoAcidSequence.Create((int)variant.SpectrumId, phosphoPeptide.sequence, modifications, ptmRepresentation.ToString());
// Make a phosphoRS peptide-spectrum match.
return(new phosphoRS.PeptideSpectrumMatch((int)variant.PSMId, variant.SpectrumType, variant.Charge, variant.PrecursorMZ, variant.Peaks, AAS));
}
private string PeptideToString(proteome.Peptide peptide, IList <phosphoRS.PTMSiteProbability> localizationProbabilities, PhosphoRSConfig config)
{
var probabilityMap = localizationProbabilities.ToDictionary(o => o.SequencePosition, o => o.Probability);
string format = String.Format("[{{0:f{0}}}]", 0);
StringBuilder sb = new StringBuilder();
if (peptide.modifications().ContainsKey(proteome.ModificationMap.NTerminus()))
{
sb.AppendFormat(format, peptide.modifications()[proteome.ModificationMap.NTerminus()].monoisotopicDeltaMass());
}
for (int i = 0; i < peptide.sequence.Length; ++i)
{
sb.Append(peptide.sequence[i]);
if (probabilityMap.ContainsKey(i + 1))
{
if (probabilityMap[i + 1] > 0)
{
sb.AppendFormat("[{0:f0}({1:f0}%)]", config.scoredAA.MassDelta, probabilityMap[i + 1] * 100);
}
//else
// sb.AppendFormat("({0:f0})", config.scoredAA.MassDelta, probabilityMap[i + 1]);
}
else if (peptide.modifications().ContainsKey(i))
{
double modMass = peptide.modifications()[i].monoisotopicDeltaMass();
sb.AppendFormat(format, modMass);
}
}
if (peptide.modifications().ContainsKey(proteome.ModificationMap.CTerminus()))
{
sb.AppendFormat(format, peptide.modifications()[proteome.ModificationMap.CTerminus()].monoisotopicDeltaMass());
}
return(sb.ToString());
}
