public static void TestAllNaN()
{
IDictionary <int, List <Modification> > mods = new Dictionary <int, List <Modification> >();
var prot = new Protein("XMMM", null, null, null, mods);
DigestionParams digestionParams = new DigestionParams(minPeptideLength: 1);
var thePep = prot.Digest(digestionParams, new List <Modification>(), new List <Modification>()).First();
var frags = new List <Product>();
thePep.Fragment(DissociationType.HCD, FragmentationTerminus.Both, frags);
var massArray = frags.Select(p => p.NeutralMass).ToArray();
Array.Sort(massArray);
double[] intensities = new double[] { 1, 1, 1, 1 };
double[] mz = new double[] { 1, 2, 3, 4 };
MzSpectrum massSpectrum = new MzSpectrum(mz, intensities, false);
MsDataScan scan = new MsDataScan(massSpectrum, 1, 1, true, Polarity.Positive, 1, new MzRange(300, 2000), "", MZAnalyzerType.Unknown, massSpectrum.SumOfAllY, null, null, "scan=1", 0, null, null, 0, null, DissociationType.Unknown, 1, null);
PeptideSpectralMatch[] globalPsms = new PeptideSpectralMatch[1];
Ms2ScanWithSpecificMass[] arrayOfSortedMS2Scans = { new Ms2ScanWithSpecificMass(scan, 0, 0, null, new CommonParameters()) };
CommonParameters CommonParameters = new CommonParameters(productMassTolerance: new PpmTolerance(5), scoreCutoff: 1, digestionParams: new DigestionParams(maxMissedCleavages: 0, minPeptideLength: 1, maxModificationIsoforms: int.MaxValue, initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain));
ClassicSearchEngine cse = new ClassicSearchEngine(globalPsms, arrayOfSortedMS2Scans, new List <Modification>(), new List <Modification>(), null, null, null, new List <Protein> {
prot
}, new OpenSearchMode(), CommonParameters, null, new List <string>());
cse.Run();
Assert.IsNull(globalPsms[0]);
}
public static void TestIdenticalPeaks()
{
IDictionary <int, List <Modification> > mods = new Dictionary <int, List <Modification> >();
ModificationMotif.TryGetMotif("M", out ModificationMotif motif);
mods.Add(1, new List <Modification> {
new ModificationWithMass("Hehe", null, motif, TerminusLocalization.NProt, 18.010565, null, null, null, null)
});
var prot = new Protein("MMMM", null, null, null, mods);
DigestionParams digestionParams = new DigestionParams
{
MinPeptideLength = 1,
};
var ye = prot.Digest(digestionParams, new List <ModificationWithMass>(), new List <ModificationWithMass>()).First();
var massArray = ye.CompactPeptide(TerminusType.None).ProductMassesMightHaveDuplicatesAndNaNs(new List <ProductType> {
ProductType.B, ProductType.Y
});
Array.Sort(massArray);
double[] intensities = new double[] { 1, 1, 1, 1 };
double[] mz = new double[] { massArray[0].ToMz(1), massArray[2].ToMz(1), massArray[4].ToMz(1), 10000 };
MzmlMzSpectrum massSpectrum = new MzmlMzSpectrum(mz, intensities, false);
IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> > scan = new MzmlScanWithPrecursor(1, massSpectrum, 1, true, Polarity.Positive, 1, new MzRange(300, 2000), "", MZAnalyzerType.Unknown, massSpectrum.SumOfAllY, 0, null, null, 0, null, DissociationType.Unknown, 1, null, null, "scan=1");
PeptideSpectralMatch[] globalPsms = new PeptideSpectralMatch[1];
Ms2ScanWithSpecificMass[] arrayOfSortedMS2Scans = { new Ms2ScanWithSpecificMass(scan, 0, 0, null) };
CommonParameters CommonParameters = new CommonParameters
{
DigestionParams = new DigestionParams
{
MaxMissedCleavages = 0,
MinPeptideLength = null,
MaxModificationIsoforms = int.MaxValue,
InitiatorMethionineBehavior = InitiatorMethionineBehavior.Retain,
},
ProductMassTolerance = new PpmTolerance(5),
ConserveMemory = false,
ScoreCutoff = 1
};
ClassicSearchEngine cse = new ClassicSearchEngine(globalPsms, arrayOfSortedMS2Scans, new List <ModificationWithMass>(), new List <ModificationWithMass>(), new List <Protein> {
prot
}, new List <ProductType> {
ProductType.B, ProductType.Y
}, new OpenSearchMode(), false, CommonParameters, CommonParameters.ProductMassTolerance, new List <string>());
cse.Run();
Assert.Less(globalPsms[0].Score, 4);
Assert.Greater(globalPsms[0].Score, 3);
}
public static void TestIdenticalPeaks()
{
IDictionary <int, List <Modification> > mods = new Dictionary <int, List <Modification> >();
ModificationMotif.TryGetMotif("M", out ModificationMotif motif);
mods.Add(1, new List <Modification> {
new Modification(_originalId: "Hehe", _target: motif, _locationRestriction: "Anywhere.", _monoisotopicMass: 18.010565)
});
var prot = new Protein("MMMM", null, null, null, mods);
DigestionParams digestionParams = new DigestionParams(minPeptideLength: 1);
var ye = prot.Digest(digestionParams, new List <Modification>(), new List <Modification>()).First();
var frags = new List <Product>();
ye.Fragment(DissociationType.HCD, FragmentationTerminus.Both, frags);
var massArray = frags.Select(p => p.NeutralMass).ToArray();
Array.Sort(massArray);
double[] intensities = new double[] { 1, 1, 1, 1 };
double[] mz = new double[] { massArray[0].ToMz(1), massArray[2].ToMz(1), massArray[4].ToMz(1), 10000 };
MzSpectrum massSpectrum = new MzSpectrum(mz, intensities, false);
MsDataScan scan = new MsDataScan(massSpectrum, 1, 1, true, Polarity.Positive, 1, new MzRange(300, 2000), "", MZAnalyzerType.Unknown, massSpectrum.SumOfAllY, null, null, "scan=1", 0, null, null, 0, null, DissociationType.Unknown, 1, null);
PeptideSpectralMatch[] globalPsms = new PeptideSpectralMatch[1];
Ms2ScanWithSpecificMass[] arrayOfSortedMS2Scans = { new Ms2ScanWithSpecificMass(scan, 0, 1, null, new CommonParameters()) };
CommonParameters CommonParameters = new CommonParameters(
productMassTolerance: new PpmTolerance(5),
scoreCutoff: 1,
digestionParams: new DigestionParams(
maxMissedCleavages: 0,
minPeptideLength: 1,
initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain));
bool writeSpectralLibrary = false;
ClassicSearchEngine cse = new ClassicSearchEngine(globalPsms, arrayOfSortedMS2Scans, new List <Modification>(), new List <Modification>(), null, null, null,
new List <Protein> {
prot
}, new OpenSearchMode(), CommonParameters, null, null, new List <string>(), writeSpectralLibrary);
cse.Run();
Assert.AreEqual(3, globalPsms[0].MatchedFragmentIons.Count);
}
public static void TestIdenticalPeaks()
{
IDictionary <int, List <Modification> > mods = new Dictionary <int, List <Modification> >();
ModificationMotif.TryGetMotif("M", out ModificationMotif motif);
mods.Add(1, new List <Modification> {
new ModificationWithMass("Hehe", null, motif, TerminusLocalization.NProt, 18.010565, null, null, null, null)
});
var prot = new Protein("MMMM", null, null, null, mods);
DigestionParams digestionParams = new DigestionParams(minPeptideLength: 1);
var ye = prot.Digest(digestionParams, new List <ModificationWithMass>(), new List <ModificationWithMass>()).First();
var massArray = ye.CompactPeptide(TerminusType.None).ProductMassesMightHaveDuplicatesAndNaNs(new List <ProductType> {
ProductType.B, ProductType.Y
});
Array.Sort(massArray);
double[] intensities = new double[] { 1, 1, 1, 1 };
double[] mz = new double[] { massArray[0].ToMz(1), massArray[2].ToMz(1), massArray[4].ToMz(1), 10000 };
MzSpectrum massSpectrum = new MzSpectrum(mz, intensities, false);
MsDataScan scan = new MsDataScan(massSpectrum, 1, 1, true, Polarity.Positive, 1, new MzRange(300, 2000), "", MZAnalyzerType.Unknown, massSpectrum.SumOfAllY, null, null, "scan=1", 0, null, null, 0, null, DissociationType.Unknown, 1, null);
PeptideSpectralMatch[] globalPsms = new PeptideSpectralMatch[1];
Ms2ScanWithSpecificMass[] arrayOfSortedMS2Scans = { new Ms2ScanWithSpecificMass(scan, 0, 0, null) };
CommonParameters CommonParameters = new CommonParameters(
productMassTolerance: new PpmTolerance(5),
scoreCutoff: 1,
digestionParams: new DigestionParams(
maxMissedCleavages: 0,
minPeptideLength: 1,
initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain));
ClassicSearchEngine cse = new ClassicSearchEngine(globalPsms, arrayOfSortedMS2Scans, new List <ModificationWithMass>(), new List <ModificationWithMass>(), new List <Protein> {
prot
}, new List <ProductType> {
ProductType.B, ProductType.Y
}, new OpenSearchMode(), CommonParameters, new List <string>());
cse.Run();
Assert.AreEqual(globalPsms[0].MatchedFragmentIons.Count, 3);
}
public static void TestVeryCloseExperimentalsClassic()
{
IDictionary <int, List <Modification> > mods = new Dictionary <int, List <Modification> >();
ModificationMotif.TryGetMotif("M", out ModificationMotif motif);
var prot = new Protein("MMMM", null, null, null, mods);
DigestionParams digestionParams = new DigestionParams(minPeptideLength: 1);
var thePep = prot.Digest(digestionParams, new List <ModificationWithMass>(), new List <ModificationWithMass>()).First();
var massArray = thePep.CompactPeptide(TerminusType.None).ProductMassesMightHaveDuplicatesAndNaNs(new List <ProductType> {
ProductType.B, ProductType.Y
});
Array.Sort(massArray);
double[] intensities = new double[] { 1, 1, 1, 1 };
double[] mz = new double[] { 1, 2, massArray[4].ToMz(1), massArray[4].ToMz(1) + 1e-9 };
MzSpectrum massSpectrum = new MzSpectrum(mz, intensities, false);
MsDataScan scan = new MsDataScan(massSpectrum, 1, 1, true, Polarity.Positive, 1, new MzRange(300, 2000), "", MZAnalyzerType.Unknown, massSpectrum.SumOfAllY, null, null, "scan=1", 0, null, null, 0, null, DissociationType.Unknown, 1, null);
PeptideSpectralMatch[] globalPsms = new PeptideSpectralMatch[1];
Ms2ScanWithSpecificMass[] arrayOfSortedMS2Scans = { new Ms2ScanWithSpecificMass(scan, 0, 0, null) };
CommonParameters CommonParameters = new CommonParameters(
productMassTolerance: new PpmTolerance(5),
scoreCutoff: 1,
digestionParams: new DigestionParams(
maxMissedCleavages: 0,
minPeptideLength: 1,
maxModificationIsoforms: int.MaxValue,
initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain));
ClassicSearchEngine cse = new ClassicSearchEngine(globalPsms, arrayOfSortedMS2Scans, new List <ModificationWithMass>(), new List <ModificationWithMass>(), new List <Protein> {
prot
}, new List <ProductType> {
ProductType.B, ProductType.Y
}, new OpenSearchMode(), CommonParameters, new List <string>());
cse.Run();
Assert.Less(globalPsms[0].Score, 2);
Assert.Greater(globalPsms[0].Score, 1);
}
protected override MyTaskResults RunSpecific(string OutputFolder, List <DbForTask> dbFilenameList, List <string> currentRawFileList, string taskId, FileSpecificParameters[] fileSettingsList)
{
if (SearchParameters.DoQuantification)
{
// disable quantification if a .mgf is being used
if (currentRawFileList.Any(x => Path.GetExtension(x).Equals(".mgf", StringComparison.OrdinalIgnoreCase)))
{
SearchParameters.DoQuantification = false;
}
//if we're doing SILAC, assign and add the silac labels to the residue dictionary
else if (SearchParameters.SilacLabels != null || SearchParameters.StartTurnoverLabel != null || SearchParameters.EndTurnoverLabel != null)
{
char heavyLabel = 'a'; //char to assign
//add the Turnoverlabels to the silacLabels list. They weren't there before just to prevent duplication in the tomls
if (SearchParameters.StartTurnoverLabel != null || SearchParameters.EndTurnoverLabel != null)
{
//original silacLabels object is null, so we need to initialize it
SearchParameters.SilacLabels = new List <SilacLabel>();
if (SearchParameters.StartTurnoverLabel != null)
{
var updatedLabel = SilacConversions.UpdateAminoAcidLabel(SearchParameters.StartTurnoverLabel, heavyLabel);
heavyLabel = updatedLabel.nextHeavyLabel;
SearchParameters.StartTurnoverLabel = updatedLabel.updatedLabel;
SearchParameters.SilacLabels.Add(SearchParameters.StartTurnoverLabel);
}
if (SearchParameters.EndTurnoverLabel != null)
{
var updatedLabel = SilacConversions.UpdateAminoAcidLabel(SearchParameters.EndTurnoverLabel, heavyLabel);
heavyLabel = updatedLabel.nextHeavyLabel;
SearchParameters.EndTurnoverLabel = updatedLabel.updatedLabel;
SearchParameters.SilacLabels.Add(SearchParameters.EndTurnoverLabel);
}
}
else
{
//change the silac residues to lower case amino acids (currently null)
List <SilacLabel> updatedLabels = new List <SilacLabel>();
for (int i = 0; i < SearchParameters.SilacLabels.Count; i++)
{
var updatedLabel = SilacConversions.UpdateAminoAcidLabel(SearchParameters.SilacLabels[i], heavyLabel);
heavyLabel = updatedLabel.nextHeavyLabel;
updatedLabels.Add(updatedLabel.updatedLabel);
}
SearchParameters.SilacLabels = updatedLabels;
}
}
}
//if no quant, remove any silac labels that may have been added, because they screw up downstream analysis
if (!SearchParameters.DoQuantification) //using "if" instead of "else", because DoQuantification can change if it's an mgf
{
SearchParameters.SilacLabels = null;
}
LoadModifications(taskId, out var variableModifications, out var fixedModifications, out var localizeableModificationTypes);
// load proteins
List <Protein> proteinList = LoadProteins(taskId, dbFilenameList, SearchParameters.SearchTarget, SearchParameters.DecoyType, localizeableModificationTypes, CommonParameters);
SanitizeProteinDatabase(proteinList, SearchParameters.TCAmbiguity);
// load spectral libraries
var spectralLibrary = LoadSpectralLibraries(taskId, dbFilenameList);
// 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.IdWithMotif)) + "; ");
ProseCreatedWhileRunning.Append("variable modifications = " + string.Join(", ", variableModifications.Select(m => m.IdWithMotif)) + "; ");
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>();
//generate an array to store category specific fdr values (for speedy semi/nonspecific searches)
int numFdrCategories = (int)(Enum.GetValues(typeof(FdrCategory)).Cast <FdrCategory>().Last() + 1); //+1 because it starts at zero
List <PeptideSpectralMatch>[] allCategorySpecificPsms = new List <PeptideSpectralMatch> [numFdrCategories];
for (int i = 0; i < numFdrCategories; i++)
{
allCategorySpecificPsms[i] = new List <PeptideSpectralMatch>();
}
FlashLfqResults flashLfqResults = null;
MyFileManager myFileManager = new MyFileManager(SearchParameters.DisposeOfFileWhenDone);
var fileSpecificCommonParams = fileSettingsList.Select(b => SetAllFileSpecificCommonParams(CommonParameters, b));
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);
Status("Getting ms2 scans...", thisId);
Ms2ScanWithSpecificMass[] arrayOfMs2ScansSortedByMass = GetMs2Scans(myMsDataFile, origDataFile, combinedParams).OrderBy(b => b.PrecursorMass).ToArray();
numMs2SpectraPerFile.Add(Path.GetFileNameWithoutExtension(origDataFile), new int[] { myMsDataFile.GetAllScansList().Count(p => p.MsnOrder == 2), arrayOfMs2ScansSortedByMass.Length });
myFileManager.DoneWithFile(origDataFile);
PeptideSpectralMatch[] fileSpecificPsms = new PeptideSpectralMatch[arrayOfMs2ScansSortedByMass.Length];
// modern search
if (SearchParameters.SearchType == SearchType.Modern)
{
for (int currentPartition = 0; currentPartition < combinedParams.TotalPartitions; currentPartition++)
{
List <PeptideWithSetModifications> 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, SearchParameters.SilacLabels,
SearchParameters.StartTurnoverLabel, SearchParameters.EndTurnoverLabel, currentPartition, SearchParameters.DecoyType, combinedParams, FileSpecificParameters,
SearchParameters.MaxFragmentSize, false, dbFilenameList.Select(p => new FileInfo(p.FilePath)).ToList(), SearchParameters.TCAmbiguity, new List <string> {
taskId
});
List <int>[] fragmentIndex = null;
List <int>[] precursorIndex = null;
lock (indexLock)
{
GenerateIndexes(indexEngine, dbFilenameList, ref peptideIndex, ref fragmentIndex, ref precursorIndex, proteinList, taskId);
}
Status("Searching files...", taskId);
new ModernSearchEngine(fileSpecificPsms, arrayOfMs2ScansSortedByMass, peptideIndex, fragmentIndex, currentPartition,
combinedParams, this.FileSpecificParameters, massDiffAcceptor, SearchParameters.MaximumMassThatFragmentIonScoreIsDoubled, thisId).Run();
ReportProgress(new ProgressEventArgs(100, "Done with search " + (currentPartition + 1) + "/" + combinedParams.TotalPartitions + "!", thisId));
if (GlobalVariables.StopLoops)
{
break;
}
}
}
// nonspecific search
else if (SearchParameters.SearchType == SearchType.NonSpecific)
{
PeptideSpectralMatch[][] fileSpecificPsmsSeparatedByFdrCategory = new PeptideSpectralMatch[numFdrCategories][]; //generate an array of all possible locals
for (int i = 0; i < numFdrCategories; i++) //only add if we're using for FDR, else ignore it as null.
{
fileSpecificPsmsSeparatedByFdrCategory[i] = new PeptideSpectralMatch[arrayOfMs2ScansSortedByMass.Length];
}
//create params for N, C, or both if semi
List <CommonParameters> paramsToUse = new List <CommonParameters> {
combinedParams
};
if (combinedParams.DigestionParams.SearchModeType == CleavageSpecificity.Semi) //if semi, we need to do both N and C to hit everything
{
paramsToUse.Clear();
List <FragmentationTerminus> terminiToUse = new List <FragmentationTerminus> {
FragmentationTerminus.N, FragmentationTerminus.C
};
foreach (FragmentationTerminus terminus in terminiToUse) //set both termini
{
paramsToUse.Add(combinedParams.CloneWithNewTerminus(terminus));
}
}
//Compress array of deconvoluted ms2 scans to avoid searching the same ms2 multiple times while still identifying coisolated peptides
List <int>[] coisolationIndex = new List <int>[] { new List <int>() };
if (arrayOfMs2ScansSortedByMass.Length != 0)
{
int maxScanNumber = arrayOfMs2ScansSortedByMass.Max(x => x.OneBasedScanNumber);
coisolationIndex = new List <int> [maxScanNumber + 1];
for (int i = 0; i < arrayOfMs2ScansSortedByMass.Length; i++)
{
int scanNumber = arrayOfMs2ScansSortedByMass[i].OneBasedScanNumber;
if (coisolationIndex[scanNumber] == null)
{
coisolationIndex[scanNumber] = new List <int> {
i
};
}
else
{
coisolationIndex[scanNumber].Add(i);
}
}
coisolationIndex = coisolationIndex.Where(x => x != null).ToArray();
}
//foreach terminus we're going to look at
foreach (CommonParameters paramToUse in paramsToUse)
{
//foreach database partition
for (int currentPartition = 0; currentPartition < paramToUse.TotalPartitions; currentPartition++)
{
List <PeptideWithSetModifications> peptideIndex = null;
List <Protein> proteinListSubset = proteinList.GetRange(currentPartition * proteinList.Count / paramToUse.TotalPartitions,
((currentPartition + 1) * proteinList.Count / paramToUse.TotalPartitions) - (currentPartition * proteinList.Count / paramToUse.TotalPartitions));
List <int>[] fragmentIndex = null;
List <int>[] precursorIndex = null;
Status("Getting fragment dictionary...", new List <string> {
taskId
});
var indexEngine = new IndexingEngine(proteinListSubset, variableModifications, fixedModifications, SearchParameters.SilacLabels,
SearchParameters.StartTurnoverLabel, SearchParameters.EndTurnoverLabel, currentPartition, SearchParameters.DecoyType, paramToUse, FileSpecificParameters,
SearchParameters.MaxFragmentSize, true, dbFilenameList.Select(p => new FileInfo(p.FilePath)).ToList(), SearchParameters.TCAmbiguity, new List <string> {
taskId
});
lock (indexLock)
{
GenerateIndexes(indexEngine, dbFilenameList, ref peptideIndex, ref fragmentIndex, ref precursorIndex, proteinList, taskId);
}
Status("Searching files...", taskId);
new NonSpecificEnzymeSearchEngine(fileSpecificPsmsSeparatedByFdrCategory, arrayOfMs2ScansSortedByMass, coisolationIndex, peptideIndex, fragmentIndex,
precursorIndex, currentPartition, paramToUse, this.FileSpecificParameters, variableModifications, massDiffAcceptor,
SearchParameters.MaximumMassThatFragmentIonScoreIsDoubled, thisId).Run();
ReportProgress(new ProgressEventArgs(100, "Done with search " + (currentPartition + 1) + "/" + paramToUse.TotalPartitions + "!", thisId));
if (GlobalVariables.StopLoops)
{
break;
}
}
}
lock (psmLock)
{
for (int i = 0; i < allCategorySpecificPsms.Length; i++)
{
if (allCategorySpecificPsms[i] != null)
{
allCategorySpecificPsms[i].AddRange(fileSpecificPsmsSeparatedByFdrCategory[i]);
}
}
}
}
// classic search
else
{
Status("Starting search...", thisId);
var newClassicSearchEngine = new ClassicSearchEngine(fileSpecificPsms, arrayOfMs2ScansSortedByMass, variableModifications, fixedModifications, SearchParameters.SilacLabels,
SearchParameters.StartTurnoverLabel, SearchParameters.EndTurnoverLabel, proteinList, massDiffAcceptor, combinedParams, this.FileSpecificParameters, spectralLibrary, thisId, SearchParameters.WriteSpectralLibrary);
newClassicSearchEngine.Run();
ReportProgress(new ProgressEventArgs(100, "Done with search!", thisId));
}
//look for internal fragments
if (SearchParameters.MinAllowedInternalFragmentLength != 0)
{
MatchInternalFragmentIons(fileSpecificPsms, arrayOfMs2ScansSortedByMass, combinedParams, SearchParameters.MinAllowedInternalFragmentLength);
}
// calculate/set spectral angles if there is a spectral library being used
if (spectralLibrary != null)
{
Status("Calculating spectral library similarity...", thisId);
}
SpectralLibrarySearchFunction.CalculateSpectralAngles(spectralLibrary, fileSpecificPsms, arrayOfMs2ScansSortedByMass, combinedParams);
lock (psmLock)
{
allPsms.AddRange(fileSpecificPsms);
}
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"
}));
}
if (spectralLibrary != null)
{
spectralLibrary.CloseConnections();
}
ReportProgress(new ProgressEventArgs(100, "Done with all searches!", new List <string> {
taskId, "Individual Spectra Files"
}));
int numNotches = GetNumNotches(SearchParameters.MassDiffAcceptorType, SearchParameters.CustomMdac);
//resolve category specific fdrs (for speedy semi and nonspecific
if (SearchParameters.SearchType == SearchType.NonSpecific)
{
allPsms = NonSpecificEnzymeSearchEngine.ResolveFdrCategorySpecificPsms(allCategorySpecificPsms, numNotches, taskId, CommonParameters, FileSpecificParameters);
}
PostSearchAnalysisParameters parameters = new PostSearchAnalysisParameters
{
SearchTaskResults = MyTaskResults,
SearchTaskId = taskId,
SearchParameters = SearchParameters,
ProteinList = proteinList,
AllPsms = allPsms,
VariableModifications = variableModifications,
FixedModifications = fixedModifications,
ListOfDigestionParams = new HashSet <DigestionParams>(fileSpecificCommonParams.Select(p => p.DigestionParams)),
CurrentRawFileList = currentRawFileList,
MyFileManager = myFileManager,
NumNotches = numNotches,
OutputFolder = OutputFolder,
IndividualResultsOutputFolder = Path.Combine(OutputFolder, "Individual File Results"),
FlashLfqResults = flashLfqResults,
FileSettingsList = fileSettingsList,
NumMs2SpectraPerFile = numMs2SpectraPerFile,
DatabaseFilenameList = dbFilenameList
};
PostSearchAnalysisTask postProcessing = new PostSearchAnalysisTask
{
Parameters = parameters,
FileSpecificParameters = this.FileSpecificParameters,
CommonParameters = CommonParameters
};
return(postProcessing.Run());
}
