public static void TestSeparateIonsByTerminus()
{
List <ProductType> allIonTypes = new List <ProductType> {
ProductType.B, ProductType.C, ProductType.Zdot, ProductType.Y
};
List <List <ProductType> > separated = ProductTypeMethods.SeparateIonsByTerminus(allIonTypes);
Assert.IsTrue(separated.Count == 2);
Assert.IsTrue(separated[0].Count == 2);
Assert.IsTrue(separated[1].Count == 2);
Assert.IsTrue(separated[0].Contains(ProductType.B));
Assert.IsTrue(separated[0].Contains(ProductType.C));
Assert.IsTrue(separated[1].Contains(ProductType.Y));
Assert.IsTrue(separated[1].Contains(ProductType.Zdot));
List <List <ProductType> > nOnly = ProductTypeMethods.SeparateIonsByTerminus(separated[0]);
Assert.IsTrue(nOnly.Count == 1);
Assert.IsTrue(nOnly[0].Count == 2);
Assert.IsTrue(nOnly[0].Contains(ProductType.B));
Assert.IsTrue(nOnly[0].Contains(ProductType.C));
List <List <ProductType> > cOnly = ProductTypeMethods.SeparateIonsByTerminus(separated[1]);
Assert.IsTrue(cOnly.Count == 1);
Assert.IsTrue(cOnly[0].Count == 2);
Assert.IsTrue(cOnly[0].Contains(ProductType.Y));
Assert.IsTrue(cOnly[0].Contains(ProductType.Zdot));
}
public static void TestSeparateIonsByTerminus()
{
List <ProductType> allIonTypes = new List <ProductType> {
ProductType.b, ProductType.c, ProductType.zPlusOne, ProductType.y
};
List <List <ProductType> > separated = ProductTypeMethods.SeparateIonsByTerminus(allIonTypes);
Assert.IsTrue(separated.Count == 2);
Assert.IsTrue(separated[0].Count == 2);
Assert.IsTrue(separated[1].Count == 2);
Assert.IsTrue(separated[0].Contains(ProductType.b));
Assert.IsTrue(separated[0].Contains(ProductType.c));
Assert.IsTrue(separated[1].Contains(ProductType.y));
Assert.IsTrue(separated[1].Contains(ProductType.zPlusOne));
List <List <ProductType> > nOnly = ProductTypeMethods.SeparateIonsByTerminus(separated[0]);
Assert.IsTrue(nOnly.Count == 1);
Assert.IsTrue(nOnly[0].Count == 2);
Assert.IsTrue(nOnly[0].Contains(ProductType.b));
Assert.IsTrue(nOnly[0].Contains(ProductType.c));
List <List <ProductType> > cOnly = ProductTypeMethods.SeparateIonsByTerminus(separated[1]);
Assert.IsTrue(cOnly.Count == 1);
Assert.IsTrue(cOnly[0].Count == 2);
Assert.IsTrue(cOnly[0].Contains(ProductType.y));
Assert.IsTrue(cOnly[0].Contains(ProductType.zPlusOne));
}
protected override MyTaskResults RunSpecific(string OutputFolder, List <DbForTask> dbFilenameList, List <string> currentRawFileList, string taskId, FileSpecificParameters[] fileSettingsList)
{
// disable quantification if a .mgf is being used
if (SearchParameters.DoQuantification && currentRawFileList.Any(x => Path.GetExtension(x).Equals(".mgf", StringComparison.OrdinalIgnoreCase)))
{
SearchParameters.DoQuantification = false;
}
// load modifications
Status("Loading modifications...", taskId);
List <ModificationWithMass> variableModifications = GlobalVariables.AllModsKnown.OfType <ModificationWithMass>().Where(b => CommonParameters.ListOfModsVariable.Contains((b.modificationType, b.id))).ToList();
List <ModificationWithMass> fixedModifications = GlobalVariables.AllModsKnown.OfType <ModificationWithMass>().Where(b => CommonParameters.ListOfModsFixed.Contains((b.modificationType, b.id))).ToList();
List <string> localizeableModificationTypes = GlobalVariables.AllModTypesKnown.ToList();
// what types of fragment ions to search for
List <ProductType> ionTypes = new List <ProductType>();
if (CommonParameters.BIons && CommonParameters.AddCompIons)
{
ionTypes.Add(ProductType.B);
}
else if (CommonParameters.BIons)
{
ionTypes.Add(ProductType.BnoB1ions);
}
if (CommonParameters.YIons)
{
ionTypes.Add(ProductType.Y);
}
if (CommonParameters.ZdotIons)
{
ionTypes.Add(ProductType.Zdot);
}
if (CommonParameters.CIons)
{
ionTypes.Add(ProductType.C);
}
// load proteins
List <Protein> proteinList = LoadProteins(taskId, dbFilenameList, SearchParameters.SearchTarget, SearchParameters.DecoyType, localizeableModificationTypes, CommonParameters);
// write prose settings
ProseCreatedWhileRunning.Append("The following search settings were used: ");
ProseCreatedWhileRunning.Append("protease = " + CommonParameters.DigestionParams.Protease + "; ");
ProseCreatedWhileRunning.Append("maximum missed cleavages = " + CommonParameters.DigestionParams.MaxMissedCleavages + "; ");
ProseCreatedWhileRunning.Append("minimum peptide length = " + CommonParameters.DigestionParams.MinPeptideLength + "; ");
ProseCreatedWhileRunning.Append(CommonParameters.DigestionParams.MaxPeptideLength == int.MaxValue ?
"maximum peptide length = unspecified; " :
"maximum peptide length = " + CommonParameters.DigestionParams.MaxPeptideLength + "; ");
ProseCreatedWhileRunning.Append("initiator methionine behavior = " + CommonParameters.DigestionParams.InitiatorMethionineBehavior + "; ");
ProseCreatedWhileRunning.Append("fixed modifications = " + string.Join(", ", fixedModifications.Select(m => m.id)) + "; ");
ProseCreatedWhileRunning.Append("variable modifications = " + string.Join(", ", variableModifications.Select(m => m.id)) + "; ");
ProseCreatedWhileRunning.Append("max mods per peptide = " + CommonParameters.DigestionParams.MaxModsForPeptide + "; ");
ProseCreatedWhileRunning.Append("max modification isoforms = " + CommonParameters.DigestionParams.MaxModificationIsoforms + "; ");
ProseCreatedWhileRunning.Append("precursor mass tolerance = " + CommonParameters.PrecursorMassTolerance + "; ");
ProseCreatedWhileRunning.Append("product mass tolerance = " + CommonParameters.ProductMassTolerance + "; ");
ProseCreatedWhileRunning.Append("report PSM ambiguity = " + CommonParameters.ReportAllAmbiguity + ". ");
ProseCreatedWhileRunning.Append("The combined search database contained " + proteinList.Count(p => !p.IsDecoy) + " non-decoy protein entries including " + proteinList.Count(p => p.IsContaminant) + " contaminant sequences. ");
// start the search task
MyTaskResults = new MyTaskResults(this);
List <PeptideSpectralMatch> allPsms = new List <PeptideSpectralMatch>();
FlashLFQResults flashLfqResults = null;
MyFileManager myFileManager = new MyFileManager(SearchParameters.DisposeOfFileWhenDone);
var fileSpecificCommonParams = fileSettingsList.Select(b => SetAllFileSpecificCommonParams(CommonParameters, b));
HashSet <DigestionParams> ListOfDigestionParams = new HashSet <DigestionParams>(fileSpecificCommonParams.Select(p => p.DigestionParams));
int completedFiles = 0;
object indexLock = new object();
object psmLock = new object();
Status("Searching files...", taskId);
Status("Searching files...", new List <string> {
taskId, "Individual Spectra Files"
});
Dictionary <string, int[]> numMs2SpectraPerFile = new Dictionary <string, int[]>();
for (int spectraFileIndex = 0; spectraFileIndex < currentRawFileList.Count; spectraFileIndex++)
{
if (GlobalVariables.StopLoops)
{
break;
}
var origDataFile = currentRawFileList[spectraFileIndex];
// mark the file as in-progress
StartingDataFile(origDataFile, new List <string> {
taskId, "Individual Spectra Files", origDataFile
});
CommonParameters combinedParams = SetAllFileSpecificCommonParams(CommonParameters, fileSettingsList[spectraFileIndex]);
MassDiffAcceptor massDiffAcceptor = GetMassDiffAcceptor(combinedParams.PrecursorMassTolerance, SearchParameters.MassDiffAcceptorType, SearchParameters.CustomMdac);
var thisId = new List <string> {
taskId, "Individual Spectra Files", origDataFile
};
NewCollection(Path.GetFileName(origDataFile), thisId);
Status("Loading spectra file...", thisId);
MsDataFile myMsDataFile = myFileManager.LoadFile(origDataFile, combinedParams.TopNpeaks, combinedParams.MinRatio, combinedParams.TrimMs1Peaks, combinedParams.TrimMsMsPeaks, combinedParams);
Status("Getting ms2 scans...", thisId);
Ms2ScanWithSpecificMass[] arrayOfMs2ScansSortedByMass = GetMs2Scans(myMsDataFile, origDataFile, combinedParams.DoPrecursorDeconvolution, combinedParams.UseProvidedPrecursorInfo, combinedParams.DeconvolutionIntensityRatio, combinedParams.DeconvolutionMaxAssumedChargeState, combinedParams.DeconvolutionMassTolerance).OrderBy(b => b.PrecursorMass).ToArray();
numMs2SpectraPerFile.Add(Path.GetFileNameWithoutExtension(origDataFile), new int[] { myMsDataFile.GetAllScansList().Count(p => p.MsnOrder == 2), arrayOfMs2ScansSortedByMass.Length });
myFileManager.DoneWithFile(origDataFile);
var fileSpecificPsms = new PeptideSpectralMatch[arrayOfMs2ScansSortedByMass.Length];
// modern search
if (SearchParameters.SearchType == SearchType.Modern)
{
for (int currentPartition = 0; currentPartition < combinedParams.TotalPartitions; currentPartition++)
{
List <CompactPeptide> peptideIndex = null;
List <Protein> proteinListSubset = proteinList.GetRange(currentPartition * proteinList.Count() / combinedParams.TotalPartitions, ((currentPartition + 1) * proteinList.Count() / combinedParams.TotalPartitions) - (currentPartition * proteinList.Count() / combinedParams.TotalPartitions));
Status("Getting fragment dictionary...", new List <string> {
taskId
});
var indexEngine = new IndexingEngine(proteinListSubset, variableModifications, fixedModifications, ionTypes, currentPartition, SearchParameters.DecoyType, ListOfDigestionParams, combinedParams, SearchParameters.MaxFragmentSize, new List <string> {
taskId
});
List <int>[] fragmentIndex = null;
lock (indexLock)
{
GenerateIndexes(indexEngine, dbFilenameList, ref peptideIndex, ref fragmentIndex, taskId);
}
Status("Searching files...", taskId);
new ModernSearchEngine(fileSpecificPsms, arrayOfMs2ScansSortedByMass, peptideIndex, fragmentIndex, ionTypes, currentPartition, combinedParams, massDiffAcceptor, SearchParameters.MaximumMassThatFragmentIonScoreIsDoubled, thisId).Run();
ReportProgress(new ProgressEventArgs(100, "Done with search " + (currentPartition + 1) + "/" + combinedParams.TotalPartitions + "!", thisId));
}
}
// nonspecific search
else if (SearchParameters.SearchType == SearchType.NonSpecific)
{
List <List <ProductType> > terminusSeparatedIons = ProductTypeMethods.SeparateIonsByTerminus(ionTypes);
foreach (List <ProductType> terminusSpecificIons in terminusSeparatedIons)
{
for (int currentPartition = 0; currentPartition < combinedParams.TotalPartitions; currentPartition++)
{
List <CompactPeptide> peptideIndex = null;
List <Protein> proteinListSubset = proteinList.GetRange(currentPartition * proteinList.Count() / combinedParams.TotalPartitions, ((currentPartition + 1) * proteinList.Count() / combinedParams.TotalPartitions) - (currentPartition * proteinList.Count() / combinedParams.TotalPartitions));
List <int>[] fragmentIndex = new List <int> [1];
Status("Getting fragment dictionary...", new List <string> {
taskId
});
var indexEngine = new IndexingEngine(proteinListSubset, variableModifications, fixedModifications, terminusSpecificIons, currentPartition, SearchParameters.DecoyType, ListOfDigestionParams, combinedParams, SearchParameters.MaxFragmentSize, new List <string> {
taskId
});
lock (indexLock)
GenerateIndexes(indexEngine, dbFilenameList, ref peptideIndex, ref fragmentIndex, taskId);
Status("Getting precursor dictionary...", new List <string> {
taskId
});
List <CompactPeptide> peptideIndexPrecursor = null;
List <Protein> proteinListSubsetPrecursor = proteinList.GetRange(currentPartition * proteinList.Count() / combinedParams.TotalPartitions, ((currentPartition + 1) * proteinList.Count() / combinedParams.TotalPartitions) - (currentPartition * proteinList.Count() / combinedParams.TotalPartitions));
List <int>[] fragmentIndexPrecursor = new List <int> [1];
var indexEnginePrecursor = new PrecursorIndexingEngine(proteinListSubsetPrecursor, variableModifications, fixedModifications, terminusSpecificIons, currentPartition, SearchParameters.DecoyType, ListOfDigestionParams, combinedParams, 0, new List <string> {
taskId
});
lock (indexLock)
GenerateIndexes(indexEnginePrecursor, dbFilenameList, ref peptideIndexPrecursor, ref fragmentIndexPrecursor, taskId);
if (peptideIndex.Count != peptideIndexPrecursor.Count)
{
throw new MetaMorpheusException("peptideIndex not identical between indexing engines");
}
Status("Searching files...", taskId);
new NonSpecificEnzymeSearchEngine(fileSpecificPsms, arrayOfMs2ScansSortedByMass, peptideIndex, fragmentIndex, fragmentIndexPrecursor, terminusSpecificIons, currentPartition, combinedParams, massDiffAcceptor, SearchParameters.MaximumMassThatFragmentIonScoreIsDoubled, thisId).Run();
ReportProgress(new ProgressEventArgs(100, "Done with search " + (currentPartition + 1) + "/" + combinedParams.TotalPartitions + "!", thisId));
}
}
}
// classic search
else
{
Status("Starting search...", thisId);
new ClassicSearchEngine(fileSpecificPsms, arrayOfMs2ScansSortedByMass, variableModifications, fixedModifications, proteinList, ionTypes, massDiffAcceptor, combinedParams, thisId).Run();
ReportProgress(new ProgressEventArgs(100, "Done with search!", thisId));
}
lock (psmLock)
{
allPsms.AddRange(fileSpecificPsms.Where(p => p != null));
}
completedFiles++;
FinishedDataFile(origDataFile, new List <string> {
taskId, "Individual Spectra Files", origDataFile
});
ReportProgress(new ProgressEventArgs(completedFiles / currentRawFileList.Count, "Searching...", new List <string> {
taskId, "Individual Spectra Files"
}));
}
ReportProgress(new ProgressEventArgs(100, "Done with all searches!", new List <string> {
taskId, "Individual Spectra Files"
}));
PostSearchAnalysisParameters parameters = new PostSearchAnalysisParameters();
parameters.SearchTaskResults = MyTaskResults;
parameters.SearchTaskId = taskId;
parameters.SearchParameters = SearchParameters;
parameters.ProteinList = proteinList;
parameters.IonTypes = ionTypes;
parameters.AllPsms = allPsms;
parameters.FixedModifications = fixedModifications;
parameters.VariableModifications = variableModifications;
parameters.ListOfDigestionParams = ListOfDigestionParams;
parameters.CurrentRawFileList = currentRawFileList;
parameters.MyFileManager = myFileManager;
parameters.NumNotches = GetNumNotches(SearchParameters.MassDiffAcceptorType, SearchParameters.CustomMdac);
parameters.OutputFolder = OutputFolder;
parameters.IndividualResultsOutputFolder = Path.Combine(OutputFolder, "Individual File Results");
parameters.FlashLfqResults = flashLfqResults;
parameters.FileSettingsList = fileSettingsList;
parameters.NumMs2SpectraPerFile = numMs2SpectraPerFile;
parameters.DatabaseFilenameList = dbFilenameList;
PostSearchAnalysisTask postProcessing = new PostSearchAnalysisTask();
postProcessing.Parameters = parameters;
postProcessing.CommonParameters = CommonParameters;
return(postProcessing.Run());
}