public unsafe Dataset(float[][] data,
int numCol,
CommonParameters cp,
DatasetParameters dp,
float[] labels = null,
float[] weights = null,
int[] groups = null,
Dataset reference = null)
{
CommonParameters = cp;
DatasetParameters = dp;
var pmString = ParamsToString(cp, dp);
_handle = IntPtr.Zero;
var gcHandles = new List <GCHandle>(data.Length);
try
{
float *[] dataPtrs = new float *[data.Length];
int[] nRows = new int[data.Length];
for (int i = 0; i < data.Length; i++)
{
var hdl = GCHandle.Alloc(data[i], GCHandleType.Pinned);
gcHandles.Add(hdl);
dataPtrs[i] = (float *)hdl.AddrOfPinnedObject().ToPointer();
nRows[i] = 1;
}
;
fixed(float **dataPtr = dataPtrs)
fixed(int *nRowsPtr = nRows)
{
PInvokeException.Check(PInvoke.DatasetCreateFromMats(
data.Length,
dataPtr,
nRowsPtr,
numCol,
/*isRowMajor*/ true,
pmString,
reference?._handle ?? IntPtr.Zero,
ref _handle
), nameof(PInvoke.DatasetCreateFromMats));
}
}
finally
{
foreach (var hdl in gcHandles)
{
if (hdl.IsAllocated)
{
hdl.Free();
}
}
;
}
if (labels != null)
{
SetLabels(labels);
}
if (weights != null)
{
SetWeights(weights);
}
if (groups != null)
{
SetGroups(groups);
}
if (NumFeatures != numCol)
{
throw new Exception("Expected GetNumCols to be equal to numCol");
}
if (NumRows != data.Length)
{
throw new Exception("Expected GetNumRows to be equal to numTotalRow");
}
}
/// <summary>
/// Specifies if the x5c claim (public key of the certificate) should be sent to the STS.
/// Sending the x5c enables application developers to achieve easy certificate roll-over in Azure AD:
/// this method will send the public certificate to Azure AD along with the token request,
/// so that Azure AD can use it to validate the subject name based on a trusted issuer policy.
/// This saves the application admin from the need to explicitly manage the certificate rollover
/// (either via portal or powershell/CLI operation)
/// </summary>
/// <param name="withSendX5C"><c>true</c> if the x5c should be sent. Otherwise <c>false</c>.
/// The default is <c>false</c></param>
/// <returns>The builder to chain the .With methods</returns>
public AcquireTokenSilentParameterBuilder WithSendX5C(bool withSendX5C)
{
CommonParameters.AddApiTelemetryFeature(ApiTelemetryFeature.WithSendX5C);
Parameters.SendX5C = withSendX5C;
return(this);
}
private AcquireTokenSilentParameterBuilder WithLoginHint(string loginHint)
{
CommonParameters.AddApiTelemetryFeature(ApiTelemetryFeature.WithLoginHint);
Parameters.LoginHint = loginHint;
return(this);
}
public static void TestCoIsolation()
{
List <DigestionMotif> motifs = new List <DigestionMotif> {
new DigestionMotif("K", null, 1, null)
};
Protease protease = new Protease("CustProtease", CleavageSpecificity.Full, null, null, motifs);
ProteaseDictionary.Dictionary.Add(protease.Name, protease);
CommonParameters CommonParameters = new CommonParameters(scoreCutoff: 1, deconvolutionIntensityRatio: 50, digestionParams: new DigestionParams(protease.Name, minPeptideLength: 1));
var fsp = new List <(string fileName, CommonParameters fileSpecificParameters)>();
fsp.Add(("", CommonParameters));
var variableModifications = new List <Modification>();
var fixedModifications = new List <Modification>();
var proteinList = new List <Protein> {
new Protein("MNNNKNDNK", null)
};
var searchModes = new SinglePpmAroundZeroSearchMode(5);
Proteomics.AminoAcidPolymer.Peptide pep1 = new Proteomics.AminoAcidPolymer.Peptide("NNNK");
Proteomics.AminoAcidPolymer.Peptide pep2 = new Proteomics.AminoAcidPolymer.Peptide("NDNK");
var dist1 = IsotopicDistribution.GetDistribution(pep1.GetChemicalFormula(), 0.1, 0.01);
var dist2 = IsotopicDistribution.GetDistribution(pep2.GetChemicalFormula(), 0.1, 0.01);
MsDataScan[] Scans = new MsDataScan[2];
double[] ms1intensities = new double[] { 0.8, 0.8, 0.2, 0.02, 0.2, 0.02 };
double[] ms1mzs = dist1.Masses.Concat(dist2.Masses).OrderBy(b => b).Select(b => b.ToMz(1)).ToArray();
double selectedIonMz = ms1mzs[1];
MzSpectrum MS1 = new MzSpectrum(ms1mzs, ms1intensities, false);
Scans[0] = new MsDataScan(MS1, 1, 1, false, Polarity.Positive, 1.0, new MzRange(300, 2000), "first spectrum", MZAnalyzerType.Unknown, MS1.SumOfAllY, null, null, "scan=1");
double[] ms2intensities = new double[] { 1, 1, 1, 1, 1 };
double[] ms2mzs = new double[] { 146.106.ToMz(1), 228.086.ToMz(1), 229.07.ToMz(1), 260.148.ToMz(1), 342.129.ToMz(1) };
MzSpectrum MS2 = new MzSpectrum(ms2mzs, ms2intensities, false);
double isolationMZ = selectedIonMz;
Scans[1] = new MsDataScan(MS2, 2, 2, false, Polarity.Positive, 2.0, new MzRange(100, 1500), "second spectrum", MZAnalyzerType.Unknown, MS2.SumOfAllY, null, null, "scan=2", selectedIonMz, null, null, isolationMZ, 2.5, DissociationType.HCD, 1, null);
var myMsDataFile = new MsDataFile(Scans, null);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, new CommonParameters(deconvolutionIntensityRatio: 50)).OrderBy(b => b.PrecursorMass).ToArray();
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];;
new ClassicSearchEngine(allPsmsArray, listOfSortedms2Scans, variableModifications, fixedModifications, null, null, null,
proteinList, searchModes, CommonParameters, fsp, null, new List <string>()).Run();
// Two matches for this single scan! Corresponding to two co-isolated masses
Assert.AreEqual(2, allPsmsArray.Length);
Assert.IsTrue(allPsmsArray[0].Score > 1);
Assert.AreEqual(2, allPsmsArray[0].ScanNumber);
Assert.AreEqual("NNNK", allPsmsArray[0].BaseSequence);
Assert.AreEqual("NDNK", allPsmsArray[1].BaseSequence);
}
public static void TestIndexEngineLowRes()
{
var proteinList = ProteinDbLoader.LoadProteinFasta(Path.Combine(TestContext.CurrentContext.TestDirectory, @"indexEngineTestFasta.fasta"), true, DecoyType.Reverse, false, ProteinDbLoader.UniprotAccessionRegex, ProteinDbLoader.UniprotFullNameRegex, ProteinDbLoader.UniprotFullNameRegex, ProteinDbLoader.UniprotGeneNameRegex,
ProteinDbLoader.UniprotOrganismRegex, out var dbErrors, -1);
var variableModifications = new List <Modification>();
var fixedModifications = new List <Modification>();
var localizeableModifications = new List <Modification>();
Dictionary <Modification, ushort> modsDictionary = new Dictionary <Modification, ushort>();
foreach (var mod in fixedModifications)
{
modsDictionary.Add(mod, 0);
}
int i = 1;
foreach (var mod in variableModifications)
{
modsDictionary.Add(mod, (ushort)i);
i++;
}
foreach (var mod in localizeableModifications)
{
modsDictionary.Add(mod, (ushort)i);
i++;
}
CommonParameters CommonParameters = new CommonParameters(dissociationType: DissociationType.LowCID, maxThreadsToUsePerFile: 1, scoreCutoff: 1, digestionParams: new DigestionParams(protease: "trypsin", minPeptideLength: 1));
var fsp = new List <(string fileName, CommonParameters fileSpecificParameters)>();
fsp.Add(("", CommonParameters));
var engine = new IndexingEngine(proteinList, variableModifications, fixedModifications, null, null, null, 1, DecoyType.Reverse, CommonParameters,
fsp, 30000, false, new List <FileInfo>(), TargetContaminantAmbiguity.RemoveContaminant, new List <string>());
var results = (IndexingResults)engine.Run();
Assert.AreEqual(10, results.PeptideIndex.Count);
var bubba = results.FragmentIndex;
var tooBubba = results.PrecursorIndex;
var digestedList = proteinList[0].Digest(CommonParameters.DigestionParams, new List <Modification>(), variableModifications).ToList();
digestedList.AddRange(proteinList[1].Digest(CommonParameters.DigestionParams, new List <Modification>(), variableModifications));
Assert.AreEqual(10, digestedList.Count);
foreach (PeptideWithSetModifications peptide in digestedList)
{
Assert.Contains(peptide, results.PeptideIndex);
var fragments = new List <Product>();
peptide.Fragment(CommonParameters.DissociationType, FragmentationTerminus.Both, fragments);
int positionInPeptideIndex = results.PeptideIndex.IndexOf(peptide);
foreach (Product fragment in fragments.Where(f => f.ProductType == ProductType.b || f.ProductType == ProductType.y))
{
// mass of the fragment
double fragmentMass = Math.Round(fragment.NeutralMass / 1.0005079, 0) * 1.0005079;
int integerMassRepresentation = (int)Math.Round(fragmentMass * 1000);
// look up the peptides that have fragments with this mass
// the result of the lookup is a list of peptide IDs that have this fragment mass
List <int> fragmentBin = results.FragmentIndex[integerMassRepresentation];
// this list should contain this peptide!
Assert.Contains(positionInPeptideIndex, fragmentBin);
}
}
foreach (var fdfd in digestedList)
{
Assert.Contains(fdfd, results.PeptideIndex);
}
}
public ShaderCompilerResult Compile(ShaderCode shaderCode, ShaderCompilerArguments arguments)
{
var entryPoint = arguments.GetString("EntryPoint");
var targetProfile = arguments.GetString("TargetProfile");
var disableOptimizations = arguments.GetBoolean("DisableOptimizations");
var optimizationLevel = Convert.ToInt32(arguments.GetString("OptimizationLevel"));
using (var tempFile = TempFile.FromShaderCode(shaderCode))
{
var fcPath = $"{tempFile.FilePath}.fc";
var fePath = $"{tempFile.FilePath}.fe";
var foPath = $"{tempFile.FilePath}.fo";
var args = $"--target-profile {targetProfile} --entry-point {entryPoint} --optimization-level {optimizationLevel}";
args += $" --assembly-file \"{fcPath}\" --errors-file \"{fePath}\" --object-file \"{foPath}\"";
args += $" --file \"{tempFile.FilePath}\"";
if (disableOptimizations)
{
args += " --disable-optimizations";
}
var fxcShimPath = CommonParameters.GetBinaryPath("fxc", arguments, "ShaderPlayground.Shims.Fxc.dll");
ProcessHelper.Run(
"dotnet.exe",
$"\"{fxcShimPath}\" {args}",
out var _,
out var stderr);
int?selectedOutputIndex = null;
bool success = true;
var disassembly = FileHelper.ReadAllTextIfExists(fcPath);
if (string.IsNullOrWhiteSpace(disassembly))
{
disassembly = "<Compilation error occurred>";
selectedOutputIndex = 1;
success = false;
}
var binaryOutput = FileHelper.ReadAllBytesIfExists(foPath);
var buildOutput = FileHelper.ReadAllTextIfExists(fePath);
if (string.IsNullOrWhiteSpace(buildOutput))
{
buildOutput = stderr;
}
FileHelper.DeleteIfExists(fcPath);
FileHelper.DeleteIfExists(fePath);
FileHelper.DeleteIfExists(foPath);
return(new ShaderCompilerResult(
success,
new ShaderCode(LanguageNames.Dxbc, binaryOutput),
selectedOutputIndex,
new ShaderCompilerOutput("Disassembly", LanguageNames.Dxbc, disassembly),
new ShaderCompilerOutput("Build output", null, buildOutput)));
}
}
private void SaveButton_Click(object sender, RoutedEventArgs e)
{
string fieldNotUsed = "1";
if (!GlobalGuiSettings.CheckTaskSettingsValidity(PrecursorMassToleranceTextBox.Text, ProductMassToleranceTextBox.Text, MissedCleavagesTextBox.Text,
MaxModificationIsoformsTextBox.Text, MinPeptideLengthTextBox.Text, MaxPeptideLengthTextBox.Text, MaxThreadsTextBox.Text, MinScoreAllowed.Text,
fieldNotUsed, fieldNotUsed, fieldNotUsed, fieldNotUsed, fieldNotUsed, null, null, fieldNotUsed, MaxModsPerPeptideTextBox.Text, fieldNotUsed, fieldNotUsed))
{
return;
}
Protease protease = (Protease)ProteaseComboBox.SelectedItem;
int maxMissedCleavages = string.IsNullOrEmpty(MissedCleavagesTextBox.Text) ? int.MaxValue : (int.Parse(MissedCleavagesTextBox.Text, CultureInfo.InvariantCulture));
int minPeptideLength = int.Parse(MinPeptideLengthTextBox.Text, NumberStyles.Any, CultureInfo.InvariantCulture);
int maxPeptideLength = string.IsNullOrEmpty(MaxPeptideLengthTextBox.Text) ? int.MaxValue : (int.Parse(MaxPeptideLengthTextBox.Text, NumberStyles.Any, CultureInfo.InvariantCulture));
int minVariantDepth = int.Parse(MinVariantDepthTextBox.Text, NumberStyles.Any, CultureInfo.InvariantCulture);
int maxHeterozygousVariants = int.Parse(MaxHeterozygousVariantsTextBox.Text, NumberStyles.Any, CultureInfo.InvariantCulture);
int maxModificationIsoforms = int.Parse(MaxModificationIsoformsTextBox.Text, CultureInfo.InvariantCulture);
int maxModsPerPeptide = int.Parse(MaxModsPerPeptideTextBox.Text, CultureInfo.InvariantCulture);
DissociationType dissociationType = GlobalVariables.AllSupportedDissociationTypes[DissociationTypeComboBox.SelectedItem.ToString()];
CustomFragmentationWindow.Close();
DigestionParams digestionParamsToSave = new DigestionParams(
protease: protease.Name,
maxMissedCleavages: maxMissedCleavages,
minPeptideLength: minPeptideLength,
maxPeptideLength: maxPeptideLength,
maxModificationIsoforms: maxModificationIsoforms,
maxModsForPeptides: maxModsPerPeptide);
var listOfModsVariable = new List <(string, string)>();
foreach (var heh in VariableModTypeForTreeViewObservableCollection)
{
listOfModsVariable.AddRange(heh.Children.Where(b => b.Use).Select(b => (b.Parent.DisplayName, b.ModName)));
}
if (!GlobalGuiSettings.VariableModCheck(listOfModsVariable))
{
return;
}
var listOfModsFixed = new List <(string, string)>();
foreach (var heh in FixedModTypeForTreeViewObservableCollection)
{
listOfModsFixed.AddRange(heh.Children.Where(b => b.Use).Select(b => (b.Parent.DisplayName, b.ModName)));
}
Tolerance productMassTolerance;
if (ProductMassToleranceComboBox.SelectedIndex == 0)
{
productMassTolerance = new AbsoluteTolerance(double.Parse(ProductMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
else
{
productMassTolerance = new PpmTolerance(double.Parse(ProductMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
Tolerance precursorMassTolerance;
if (PrecursorMassToleranceComboBox.SelectedIndex == 0)
{
precursorMassTolerance = new AbsoluteTolerance(double.Parse(PrecursorMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
else
{
precursorMassTolerance = new PpmTolerance(double.Parse(PrecursorMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
bool parseMaxThreadsPerFile = int.Parse(MaxThreadsTextBox.Text, CultureInfo.InvariantCulture) <= Environment.ProcessorCount && int.Parse(MaxThreadsTextBox.Text, CultureInfo.InvariantCulture) > 0;
//the below parameters are optimized for top-down but do not exist in the GUI as of Nov. 13, 2019
if (((Protease)ProteaseComboBox.SelectedItem).Name.Contains("top-down"))
{
CommonParameters commonParamsToSave = new CommonParameters(
taskDescriptor: OutputFileNameTextBox.Text != "" ? OutputFileNameTextBox.Text : "CalibrateTask",
maxThreadsToUsePerFile: parseMaxThreadsPerFile ? int.Parse(MaxThreadsTextBox.Text, CultureInfo.InvariantCulture) : new CommonParameters().MaxThreadsToUsePerFile,
digestionParams: digestionParamsToSave,
dissociationType: dissociationType,
scoreCutoff: double.Parse(MinScoreAllowed.Text, CultureInfo.InvariantCulture),
listOfModsFixed: listOfModsFixed,
listOfModsVariable: listOfModsVariable,
productMassTolerance: productMassTolerance,
precursorMassTolerance: precursorMassTolerance,
assumeOrphanPeaksAreZ1Fragments: protease.Name != "top-down",
minVariantDepth: minVariantDepth,
maxHeterozygousVariants: maxHeterozygousVariants,
useProvidedPrecursorInfo: false, //Updated
deconvolutionMaxAssumedChargeState: 60, //Updated
trimMsMsPeaks: false); //Updated
TheTask.CommonParameters = commonParamsToSave;
}
else //bottom-up
{
CommonParameters commonParamsToSave = new CommonParameters(
taskDescriptor: OutputFileNameTextBox.Text != "" ? OutputFileNameTextBox.Text : "CalibrateTask",
maxThreadsToUsePerFile: parseMaxThreadsPerFile ? int.Parse(MaxThreadsTextBox.Text, CultureInfo.InvariantCulture) : new CommonParameters().MaxThreadsToUsePerFile,
digestionParams: digestionParamsToSave,
dissociationType: dissociationType,
scoreCutoff: double.Parse(MinScoreAllowed.Text, CultureInfo.InvariantCulture),
listOfModsFixed: listOfModsFixed,
listOfModsVariable: listOfModsVariable,
productMassTolerance: productMassTolerance,
precursorMassTolerance: precursorMassTolerance,
assumeOrphanPeaksAreZ1Fragments: protease.Name != "top-down",
minVariantDepth: minVariantDepth,
maxHeterozygousVariants: maxHeterozygousVariants);
TheTask.CommonParameters = commonParamsToSave;
}
TheTask.CalibrationParameters.WriteIndexedMzml = writeIndexMzmlCheckbox.IsChecked.Value;
DialogResult = true;
}
public CalibrationEngine(MsDataFile myMSDataFile, DataPointAquisitionResults datapoints, CommonParameters commonParameters, List <string> nestedIds) : base(commonParameters, nestedIds)
{
MyMsDataFile = myMSDataFile;
Datapoints = datapoints;
}
private void SaveButton_Click(object sender, RoutedEventArgs e)
{
string fieldNotUsed = "1";
if (!GlobalGuiSettings.CheckTaskSettingsValidity(XLPrecusorMsTlTextBox.Text, productMassToleranceTextBox.Text, missedCleavagesTextBox.Text,
maxModificationIsoformsTextBox.Text, MinPeptideLengthTextBox.Text, MaxPeptideLengthTextBox.Text, maxThreadsTextBox.Text, minScoreAllowed.Text,
fieldNotUsed, fieldNotUsed, fieldNotUsed, TopNPeaksTextBox.Text, MinRatioTextBox.Text, null, null, numberOfDatabaseSearchesTextBox.Text, fieldNotUsed, fieldNotUsed, fieldNotUsed))
{
return;
}
DissociationType dissociationType = GlobalVariables.AllSupportedDissociationTypes[DissociationTypeComboBox.SelectedItem.ToString()];
DissociationType childDissociationType = DissociationType.Unknown;
if (ChildScanDissociationTypeComboBox.SelectedItem != null)
{
childDissociationType = GlobalVariables.AllSupportedDissociationTypes[ChildScanDissociationTypeComboBox.SelectedItem.ToString()];
}
CustomFragmentationWindow.Close();
//TheTask.XlSearchParameters.SearchGlyco = RbSearchGlyco.IsChecked.Value;
//TheTask.XlSearchParameters.SearchGlycoWithBgYgIndex = CkbSearchGlycoWithBgYgIndex.IsChecked.Value;
TheTask.XlSearchParameters.RestrictToTopNHits = ckbXLTopNum.IsChecked.Value;
TheTask.XlSearchParameters.CrosslinkSearchTopNum = int.Parse(txtXLTopNum.Text, CultureInfo.InvariantCulture);
TheTask.XlSearchParameters.CrosslinkAtCleavageSite = ckbCrosslinkAtCleavageSite.IsChecked.Value;
TheTask.XlSearchParameters.Crosslinker = (Crosslinker)cbCrosslinkers.SelectedItem;
TheTask.XlSearchParameters.XlQuench_H2O = ckbQuenchH2O.IsChecked.Value;
TheTask.XlSearchParameters.XlQuench_NH2 = ckbQuenchNH2.IsChecked.Value;
TheTask.XlSearchParameters.XlQuench_Tris = ckbQuenchTris.IsChecked.Value;
TheTask.XlSearchParameters.DecoyType = checkBoxDecoy.IsChecked.Value ? DecoyType.Reverse : DecoyType.None;
Protease protease = (Protease)proteaseComboBox.SelectedItem;
int MaxMissedCleavages = string.IsNullOrEmpty(missedCleavagesTextBox.Text) ? int.MaxValue : (int.Parse(missedCleavagesTextBox.Text, NumberStyles.Any, CultureInfo.InvariantCulture));
int MinPeptideLength = (int.Parse(MinPeptideLengthTextBox.Text, NumberStyles.Any, CultureInfo.InvariantCulture));
int MaxPeptideLength = string.IsNullOrEmpty(MaxPeptideLengthTextBox.Text) ? int.MaxValue : (int.Parse(MaxPeptideLengthTextBox.Text, NumberStyles.Any, CultureInfo.InvariantCulture));
int MaxModificationIsoforms = (int.Parse(maxModificationIsoformsTextBox.Text, CultureInfo.InvariantCulture));
InitiatorMethionineBehavior InitiatorMethionineBehavior = ((InitiatorMethionineBehavior)initiatorMethionineBehaviorComboBox.SelectedIndex);
DigestionParams digestionParamsToSave = new DigestionParams(
protease: protease.Name,
maxMissedCleavages: MaxMissedCleavages,
minPeptideLength: MinPeptideLength,
maxPeptideLength: MaxPeptideLength,
maxModificationIsoforms: MaxModificationIsoforms,
initiatorMethionineBehavior: InitiatorMethionineBehavior);
Tolerance ProductMassTolerance;
if (productMassToleranceComboBox.SelectedIndex == 0)
{
ProductMassTolerance = new AbsoluteTolerance(double.Parse(productMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
else
{
ProductMassTolerance = new PpmTolerance(double.Parse(productMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
Tolerance PrecursorMassTolerance;
if (cbbXLprecusorMsTl.SelectedIndex == 0)
{
PrecursorMassTolerance = new AbsoluteTolerance(double.Parse(XLPrecusorMsTlTextBox.Text, CultureInfo.InvariantCulture));
}
else
{
PrecursorMassTolerance = new PpmTolerance(double.Parse(XLPrecusorMsTlTextBox.Text, CultureInfo.InvariantCulture));
}
TheTask.XlSearchParameters.WriteOutputForPercolator = ckbPercolator.IsChecked.Value;
TheTask.XlSearchParameters.WritePepXml = ckbPepXML.IsChecked.Value;
var listOfModsVariable = new List <(string, string)>();
foreach (var heh in VariableModTypeForTreeViewObservableCollection)
{
listOfModsVariable.AddRange(heh.Children.Where(b => b.Use).Select(b => (b.Parent.DisplayName, b.ModName)));
}
var listOfModsFixed = new List <(string, string)>();
foreach (var heh in FixedModTypeForTreeViewObservableCollection)
{
listOfModsFixed.AddRange(heh.Children.Where(b => b.Use).Select(b => (b.Parent.DisplayName, b.ModName)));
}
CommonParameters commonParamsToSave = new CommonParameters(
precursorMassTolerance: PrecursorMassTolerance,
taskDescriptor: OutputFileNameTextBox.Text != "" ? OutputFileNameTextBox.Text : "XLSearchTask",
productMassTolerance: ProductMassTolerance,
doPrecursorDeconvolution: deconvolutePrecursors.IsChecked.Value,
useProvidedPrecursorInfo: useProvidedPrecursor.IsChecked.Value,
digestionParams: digestionParamsToSave,
trimMs1Peaks: trimMs1.IsChecked.Value,
trimMsMsPeaks: trimMsMs.IsChecked.Value,
numberOfPeaksToKeepPerWindow: int.Parse(TopNPeaksTextBox.Text),
minimumAllowedIntensityRatioToBasePeak: double.Parse(MinRatioTextBox.Text, CultureInfo.InvariantCulture),
dissociationType: dissociationType,
childScanDissociationType: childDissociationType,
scoreCutoff: double.Parse(minScoreAllowed.Text, CultureInfo.InvariantCulture),
totalPartitions: int.Parse(numberOfDatabaseSearchesTextBox.Text, CultureInfo.InvariantCulture),
listOfModsVariable: listOfModsVariable,
listOfModsFixed: listOfModsFixed,
assumeOrphanPeaksAreZ1Fragments: protease.Name != "top-down");
TheTask.CommonParameters = commonParamsToSave;
DialogResult = true;
}
private static Tuple <List <PeptideSpectralMatch>, Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> >, MassDiffAcceptor, bool, CompactPeptideBase, CompactPeptideBase> GetInfo(bool localizeable)
{
CommonParameters CommonParameters = new CommonParameters
{
DigestionParams = new DigestionParams
{
MinPeptideLength = null,
MaxMissedCleavages = 0,
InitiatorMethionineBehavior = InitiatorMethionineBehavior.Retain,
MaxModsForPeptide = 1,
MaxModificationIsoforms = 2,
},
ScoreCutoff = 1
};
// Alanine = Glycine + CH2
Protein protein1 = new Protein("MA", "protein1");
Protein protein2 = new Protein("MG", "protein2");
Protein protein3;
double monoisotopicMass = Chemistry.ChemicalFormula.ParseFormula("CH2").MonoisotopicMass;
ModificationMotif.TryGetMotif("G", out ModificationMotif motif1);
ModificationMotif.TryGetMotif("A", out ModificationMotif motif2);
TerminusLocalization modificationSites = TerminusLocalization.Any;
List <ModificationWithMass> allKnownFixedModifications = new List <ModificationWithMass>
{
new ModificationWithMass("CH2 on Glycine", null, motif1, modificationSites, monoisotopicMass)
};
List <ModificationWithMass> variableModifications;
ModificationWithMass alanineMod = new ModificationWithMass("CH2 on Alanine", null, motif2, modificationSites, monoisotopicMass);
if (localizeable)
{
variableModifications = new List <ModificationWithMass>();
IDictionary <int, List <Modification> > oneBasedModifications = new Dictionary <int, List <Modification> >
{
{ 2, new List <Modification> {
alanineMod
} }
};
protein3 = new Protein("MA", "protein3", oneBasedModifications: oneBasedModifications);
}
else
{
variableModifications = new List <ModificationWithMass>();
variableModifications = new List <ModificationWithMass> {
alanineMod
};
protein3 = new Protein("MA", "protein3");
}
var pepWithSetModifications1 = protein1.Digest(CommonParameters.DigestionParams, allKnownFixedModifications, variableModifications).First();
var pepWithSetModifications2 = protein2.Digest(CommonParameters.DigestionParams, allKnownFixedModifications, variableModifications).First();
var pepWithSetModifications3 = protein3.Digest(CommonParameters.DigestionParams, allKnownFixedModifications, variableModifications).Last();
CompactPeptide compactPeptide1 = new CompactPeptide(pepWithSetModifications1, TerminusType.None);
CompactPeptide compactPeptideDuplicate = new CompactPeptide(pepWithSetModifications2, TerminusType.None);
Assert.AreEqual(compactPeptide1, compactPeptideDuplicate);
CompactPeptide compactPeptide2 = new CompactPeptide(pepWithSetModifications3, TerminusType.None);
string fullFilePath = null;
int precursorCharge = 0;
TestDataFile testDataFile = new TestDataFile();
IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> > mzLibScan = testDataFile.GetOneBasedScan(2) as IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> >;
Ms2ScanWithSpecificMass scan = new Ms2ScanWithSpecificMass(mzLibScan, 0, precursorCharge, fullFilePath);
int scanIndex = 0;
double score = 0;
int notch = 0;
PeptideSpectralMatch psm1 = new PeptideSpectralMatch(compactPeptide1, notch, score, scanIndex, scan);
psm1.SetFdrValues(0, 0, 0, 0, 0, 0, 0, 0, 0, false);
PeptideSpectralMatch psm2 = new PeptideSpectralMatch(compactPeptide1, notch, score, scanIndex, scan);
psm2.SetFdrValues(0, 0, 0, 0, 0, 0, 0, 0, 0, false);
PeptideSpectralMatch psm3 = new PeptideSpectralMatch(compactPeptide2, notch, score, scanIndex, scan);
psm3.SetFdrValues(0, 0, 0, 0, 0, 0, 0, 0, 0, false);
var newPsms = new List <PeptideSpectralMatch>
{
psm1,
psm2,
psm3
};
MassDiffAcceptor massDiffAcceptors = new SinglePpmAroundZeroSearchMode(5);
SequencesToActualProteinPeptidesEngine stappe = new SequencesToActualProteinPeptidesEngine(newPsms, new List <Protein> {
protein1, protein2, protein3
}, allKnownFixedModifications, variableModifications, new List <ProductType> {
ProductType.B, ProductType.Y
}, new List <IDigestionParams> {
CommonParameters.DigestionParams
}, CommonParameters.ReportAllAmbiguity, new List <string>());
var haha = (SequencesToActualProteinPeptidesEngineResults)stappe.Run();
var compactPeptideToProteinPeptideMatching = haha.CompactPeptideToProteinPeptideMatching;
Assert.AreEqual(2, compactPeptideToProteinPeptideMatching.Count);
psm1.MatchToProteinLinkedPeptides(compactPeptideToProteinPeptideMatching);
bool noOneHitWonders = false;
return(new Tuple <List <PeptideSpectralMatch>, Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> >, MassDiffAcceptor, bool, CompactPeptideBase, CompactPeptideBase>
(
newPsms, compactPeptideToProteinPeptideMatching, massDiffAcceptors, noOneHitWonders, compactPeptide1, compactPeptide2
));
}
private void SaveButton_Click(object sender, RoutedEventArgs e)
{
string fieldNotUsed = "1";
if (!GlobalGuiSettings.CheckTaskSettingsValidity(precursorMassToleranceTextBox.Text, productMassToleranceTextBox.Text, missedCleavagesTextBox.Text,
maxModificationIsoformsTextBox.Text, MinPeptideLengthTextBox.Text, MaxPeptideLengthTextBox.Text, maxThreadsTextBox.Text, minScoreAllowed.Text,
fieldNotUsed, fieldNotUsed, fieldNotUsed, fieldNotUsed, fieldNotUsed, null, null, fieldNotUsed, fieldNotUsed, fieldNotUsed, fieldNotUsed))
{
return;
}
Protease protease = (Protease)proteaseComboBox.SelectedItem;
int MaxMissedCleavages = string.IsNullOrEmpty(missedCleavagesTextBox.Text) ? int.MaxValue : (int.Parse(missedCleavagesTextBox.Text, CultureInfo.InvariantCulture));
int MinPeptideLength = int.Parse(MinPeptideLengthTextBox.Text, NumberStyles.Any, CultureInfo.InvariantCulture);
int MaxPeptideLength = string.IsNullOrEmpty(MaxPeptideLengthTextBox.Text) ? int.MaxValue : (int.Parse(MaxPeptideLengthTextBox.Text, NumberStyles.Any, CultureInfo.InvariantCulture));
int MinVariantDepth = int.Parse(MinVariantDepthTextBox.Text, NumberStyles.Any, CultureInfo.InvariantCulture);
int MaxHeterozygousVariants = int.Parse(MaxHeterozygousVariantsTextBox.Text, NumberStyles.Any, CultureInfo.InvariantCulture);
int MaxModificationIsoforms = int.Parse(maxModificationIsoformsTextBox.Text, CultureInfo.InvariantCulture);
DissociationType dissociationType = GlobalVariables.AllSupportedDissociationTypes[DissociationTypeComboBox.SelectedItem.ToString()];
CustomFragmentationWindow.Close();
DigestionParams digestionParamsToSave = new DigestionParams(
protease: protease.Name,
maxMissedCleavages: MaxMissedCleavages,
minPeptideLength: MinPeptideLength,
maxPeptideLength: MaxPeptideLength,
maxModificationIsoforms: MaxModificationIsoforms);
var listOfModsVariable = new List <(string, string)>();
foreach (var heh in VariableModTypeForTreeViewObservableCollection)
{
listOfModsVariable.AddRange(heh.Children.Where(b => b.Use).Select(b => (b.Parent.DisplayName, b.ModName)));
}
if (!GlobalGuiSettings.VariableModCheck(listOfModsVariable))
{
return;
}
var listOfModsFixed = new List <(string, string)>();
foreach (var heh in FixedModTypeForTreeViewObservableCollection)
{
listOfModsFixed.AddRange(heh.Children.Where(b => b.Use).Select(b => (b.Parent.DisplayName, b.ModName)));
}
Tolerance ProductMassTolerance;
if (productMassToleranceComboBox.SelectedIndex == 0)
{
ProductMassTolerance = new AbsoluteTolerance(double.Parse(productMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
else
{
ProductMassTolerance = new PpmTolerance(double.Parse(productMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
Tolerance PrecursorMassTolerance;
if (precursorMassToleranceComboBox.SelectedIndex == 0)
{
PrecursorMassTolerance = new AbsoluteTolerance(double.Parse(precursorMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
else
{
PrecursorMassTolerance = new PpmTolerance(double.Parse(precursorMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
bool parseMaxThreadsPerFile = int.Parse(maxThreadsTextBox.Text, CultureInfo.InvariantCulture) <= Environment.ProcessorCount && int.Parse(maxThreadsTextBox.Text, CultureInfo.InvariantCulture) > 0;
CommonParameters commonParamsToSave = new CommonParameters(
taskDescriptor: OutputFileNameTextBox.Text != "" ? OutputFileNameTextBox.Text : "CalibrateTask",
maxThreadsToUsePerFile: parseMaxThreadsPerFile ? int.Parse(maxThreadsTextBox.Text, CultureInfo.InvariantCulture) : new CommonParameters().MaxThreadsToUsePerFile,
digestionParams: digestionParamsToSave,
dissociationType: dissociationType,
scoreCutoff: double.Parse(minScoreAllowed.Text, CultureInfo.InvariantCulture),
listOfModsFixed: listOfModsFixed,
listOfModsVariable: listOfModsVariable,
productMassTolerance: ProductMassTolerance,
precursorMassTolerance: PrecursorMassTolerance,
assumeOrphanPeaksAreZ1Fragments: protease.Name != "top-down",
minVariantDepth: MinVariantDepth,
maxHeterozygousVariants: MaxHeterozygousVariants);
TheTask.CommonParameters = commonParamsToSave;
DialogResult = true;
}
public ModernSearchEngine(PeptideSpectralMatch[] globalPsms, Ms2ScanWithSpecificMass[] listOfSortedms2Scans, List <CompactPeptide> peptideIndex, List <int>[] fragmentIndex, List <ProductType> lp, int currentPartition, CommonParameters commonParameters, MassDiffAcceptor massDiffAcceptor, double maximumMassThatFragmentIonScoreIsDoubled, List <string> nestedIds) : base(commonParameters, nestedIds)
{
PeptideSpectralMatches = globalPsms;
ListOfSortedms2Scans = listOfSortedms2Scans;
PeptideIndex = peptideIndex;
FragmentIndex = fragmentIndex;
ProductTypes = lp;
CurrentPartition = currentPartition + 1;
MassDiffAcceptor = massDiffAcceptor;
DissociationTypes = DetermineDissociationType(lp);
MaxMassThatFragmentIonScoreIsDoubled = maximumMassThatFragmentIonScoreIsDoubled;
}
public unsafe Dataset(double[][] sampleValuePerColumn,
int[][] sampleIndicesPerColumn,
int numCol,
int[] sampleNonZeroCntPerColumn,
int numSampleRow,
int numTotalRow,
CommonParameters cp,
DatasetParameters dp,
float[] labels = null,
float[] weights = null,
int[] groups = null)
{
CommonParameters = cp;
DatasetParameters = dp;
var pmString = ParamsToString(cp, dp);
_handle = IntPtr.Zero;
// Use GCHandle to pin the memory, avoid the memory relocation.
GCHandle[] gcValues = new GCHandle[numCol];
GCHandle[] gcIndices = new GCHandle[numCol];
try
{
double *[] ptrArrayValues = new double *[numCol];
int *[] ptrArrayIndices = new int *[numCol];
for (int i = 0; i < numCol; i++)
{
gcValues[i] = GCHandle.Alloc(sampleValuePerColumn[i], GCHandleType.Pinned);
ptrArrayValues[i] = (double *)gcValues[i].AddrOfPinnedObject().ToPointer();
gcIndices[i] = GCHandle.Alloc(sampleIndicesPerColumn[i], GCHandleType.Pinned);
ptrArrayIndices[i] = (int *)gcIndices[i].AddrOfPinnedObject().ToPointer();
}
;
fixed(double **ptrValues = ptrArrayValues)
fixed(int **ptrIndices = ptrArrayIndices)
fixed(int *ptrSampleNonZeroCntPerColumn = sampleNonZeroCntPerColumn)
{
PInvokeException.Check(PInvoke.DatasetCreateFromSampledColumn(
(IntPtr)ptrValues, (IntPtr)ptrIndices, numCol, ptrSampleNonZeroCntPerColumn, numSampleRow, numTotalRow,
pmString, ref _handle), nameof(PInvoke.DatasetCreateFromSampledColumn));
}
}
finally
{
for (int i = 0; i < numCol; i++)
{
if (gcValues[i].IsAllocated)
{
gcValues[i].Free();
}
if (gcIndices[i].IsAllocated)
{
gcIndices[i].Free();
}
}
;
}
if (labels != null)
{
SetLabels(labels);
}
if (weights != null)
{
SetWeights(weights);
}
if (groups != null)
{
SetGroups(groups);
}
if (NumFeatures != numCol)
{
throw new Exception("Expected GetNumCols to be equal to numCol");
}
if (NumRows != numTotalRow)
{
throw new Exception("Expected GetNumRows to be equal to numTotalRow");
}
}
private Dataset(IntPtr h, CommonParameters cp, DatasetParameters dp)
{
_handle = h;
CommonParameters = cp;
DatasetParameters = dp;
}
public static void TestCompIons_ModernSearch()
{
var myMsDataFile = new TestDataFile();
var variableModifications = new List <Modification>();
var fixedModifications = new List <Modification>();
var localizeableModifications = new List <Modification>();
Dictionary <Modification, ushort> modsDictionary = new Dictionary <Modification, ushort>();
foreach (var mod in fixedModifications)
{
modsDictionary.Add(mod, 0);
}
int ii = 1;
foreach (var mod in variableModifications)
{
modsDictionary.Add(mod, (ushort)ii);
ii++;
}
foreach (var mod in localizeableModifications)
{
modsDictionary.Add(mod, (ushort)ii);
ii++;
}
var proteinList = new List <Protein> {
new Protein("MNNNKQQQ", null)
};
SearchParameters SearchParameters = new SearchParameters
{
MassDiffAcceptorType = MassDiffAcceptorType.Exact,
SearchTarget = true,
};
List <DigestionMotif> motifs = new List <DigestionMotif> {
new DigestionMotif("K", null, 1, null)
};
Protease protease = new Protease("singleN4", CleavageSpecificity.Full, null, null, motifs);
ProteaseDictionary.Dictionary.Add(protease.Name, protease);
CommonParameters CommonParameters = new CommonParameters(digestionParams: new DigestionParams(protease: protease.Name, minPeptideLength: 1), scoreCutoff: 1);
var fsp = new List <(string fileName, CommonParameters fileSpecificParameters)>();
fsp.Add(("", CommonParameters));
CommonParameters withCompIons = new CommonParameters(digestionParams: new DigestionParams(protease: protease.Name, minPeptideLength: 1), scoreCutoff: 1, addCompIons: true);
var fspComp = new List <(string fileName, CommonParameters fileSpecificParameters)>();
fspComp.Add(("", CommonParameters));
var indexEngine = new IndexingEngine(proteinList, variableModifications, fixedModifications, null, null, null,
1, DecoyType.Reverse, CommonParameters, fsp, SearchParameters.MaxFragmentSize, false, new List <FileInfo>(), TargetContaminantAmbiguity.RemoveContaminant, new List <string>());
var indexResults = (IndexingResults)indexEngine.Run();
Tolerance DeconvolutionMassTolerance = new PpmTolerance(5);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, new CommonParameters()).OrderBy(b => b.PrecursorMass).ToArray();
MassDiffAcceptor massDiffAcceptor = SearchTask.GetMassDiffAcceptor(CommonParameters.PrecursorMassTolerance, SearchParameters.MassDiffAcceptorType, SearchParameters.CustomMdac);
// without complementary ions
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ModernSearchEngine(allPsmsArray, listOfSortedms2Scans, indexResults.PeptideIndex, indexResults.FragmentIndex, 0, CommonParameters, fsp, massDiffAcceptor, SearchParameters.MaximumMassThatFragmentIonScoreIsDoubled, new List <string>()).Run();
// with complementary ions
PeptideSpectralMatch[] allPsmsArray2 = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ModernSearchEngine(allPsmsArray2, listOfSortedms2Scans, indexResults.PeptideIndex, indexResults.FragmentIndex, 0, withCompIons, fspComp, massDiffAcceptor, SearchParameters.MaximumMassThatFragmentIonScoreIsDoubled, new List <string>()).Run();
// Single search mode
Assert.AreEqual(allPsmsArray.Length, allPsmsArray2.Length);
// Single ms2 scan
Assert.AreEqual(allPsmsArray.Length, allPsmsArray2.Length);
Assert.That(allPsmsArray[0] != null);
Assert.That(allPsmsArray2[0] != null);
Assert.IsTrue(allPsmsArray2[0].Score > 1);
Assert.AreEqual(allPsmsArray[0].ScanNumber, allPsmsArray2[0].ScanNumber);
Assert.IsTrue(allPsmsArray2[0].Score <= allPsmsArray[0].Score * 2 && allPsmsArray2[0].Score > allPsmsArray[0].Score + 3);
}
private readonly string OutputFolder; // used for storing PEP training models
public FdrAnalysisEngine(List <PeptideSpectralMatch> psms, int massDiffAcceptorNumNotches, CommonParameters commonParameters,
List <(string fileName, CommonParameters fileSpecificParameters)> fileSpecificParameters, List <string> nestedIds, string analysisType = "PSM", string outputFolder = null) : base(commonParameters, fileSpecificParameters, nestedIds)
public HomeParameters(CommonParameters param) : base(param)
{
}
public CrosslinkSearchEngine(List <CrosslinkSpectralMatch>[] globalCsms, Ms2ScanWithSpecificMass[] listOfSortedms2Scans, List <PeptideWithSetModifications> peptideIndex,
List <int>[] fragmentIndex, List <int>[] secondFragmentIndex, int currentPartition, CommonParameters commonParameters, Crosslinker crosslinker, bool CrosslinkSearchTop, int CrosslinkSearchTopNum,
bool quench_H2O, bool quench_NH2, bool quench_Tris, List <string> nestedIds)
: base(null, listOfSortedms2Scans, peptideIndex, fragmentIndex, currentPartition, commonParameters, new OpenSearchMode(), 0, nestedIds)
{
this.GlobalCsms = globalCsms;
this.Crosslinker = crosslinker;
this.CrosslinkSearchTopN = CrosslinkSearchTop;
this.TopN = CrosslinkSearchTopNum;
this.QuenchH2O = quench_H2O;
this.QuenchNH2 = quench_NH2;
this.QuenchTris = quench_Tris;
SecondFragmentIndex = secondFragmentIndex;
if (CommonParameters.ChildScanDissociationType != DissociationType.Unknown && DissociationTypeGenerateSameTypeOfIons(CommonParameters.DissociationType, CommonParameters.ChildScanDissociationType))
{
SecondFragmentIndex = FragmentIndex;
}
GenerateCrosslinkModifications(crosslinker);
AllCrosslinkerSites = Crosslinker.CrosslinkerModSites.ToCharArray().Concat(Crosslinker.CrosslinkerModSites2.ToCharArray()).Distinct().ToArray();
if (commonParameters.PrecursorMassTolerance is PpmTolerance)
{
XLPrecusorSearchMode = new SinglePpmAroundZeroSearchMode(commonParameters.PrecursorMassTolerance.Value);
}
else
{
XLPrecusorSearchMode = new SingleAbsoluteAroundZeroSearchMode(commonParameters.PrecursorMassTolerance.Value);
}
}
/// <summary>
/// Sets claims in the query. Use when the AAD admin has enabled conditional access. Acquiring the token normally will result in a
/// <see cref="MsalServiceException"/> with the <see cref="MsalServiceException.Claims"/> property set. Retry the
/// token acquisition, and use this value in the <see cref="WithClaims(string)"/> method. See https://aka.ms/msal-exceptions for details
/// </summary>
/// <param name="claims">A string with one or multiple claims.</param>
/// <returns>The builder to chain .With methods</returns>
public T WithClaims(string claims)
{
CommonParameters.AddApiTelemetryFeature(ApiTelemetryFeature.WithClaims);
CommonParameters.Claims = claims;
return((T)this);
}
/// <summary>
/// Localizes the deadend mod to a residue
/// </summary>
private CrosslinkSpectralMatch LocalizeDeadEndSite(PeptideWithSetModifications originalPeptide, Ms2ScanWithSpecificMass theScan, CommonParameters commonParameters,
List <int> possiblePositions, Modification deadEndMod, int notch, int scanIndex, int peptideIndex)
{
double bestScore = 0;
List <MatchedFragmentIon> bestMatchingFragments = new List <MatchedFragmentIon>();
PeptideWithSetModifications bestLocalizedPeptide = null;
int bestPosition = 0;
foreach (int location in possiblePositions)
{
Dictionary <int, Modification> mods = originalPeptide.AllModsOneIsNterminus.ToDictionary(p => p.Key, p => p.Value);
if (mods.ContainsKey(location + 1))
{
var alreadyAnnotatedMod = mods[location + 1];
double combinedMass = mods[location + 1].MonoisotopicMass.Value + deadEndMod.MonoisotopicMass.Value;
Modification combinedMod = new Modification(_originalId: alreadyAnnotatedMod.OriginalId + "+" + deadEndMod.OriginalId, _modificationType: "Crosslink", _target: alreadyAnnotatedMod.Target, _locationRestriction: "Anywhere.", _monoisotopicMass: combinedMass);
mods[location + 1] = combinedMod;
}
else
{
mods.Add(location + 1, deadEndMod);
}
var localizedPeptide = new PeptideWithSetModifications(originalPeptide.Protein, originalPeptide.DigestionParams, originalPeptide.OneBasedStartResidueInProtein,
originalPeptide.OneBasedEndResidueInProtein, originalPeptide.CleavageSpecificityForFdrCategory, originalPeptide.PeptideDescription, originalPeptide.MissedCleavages, mods, originalPeptide.NumFixedMods);
var products = localizedPeptide.Fragment(commonParameters.DissociationType, FragmentationTerminus.Both).ToList();
var matchedFragmentIons = MatchFragmentIons(theScan, products, commonParameters);
double score = CalculatePeptideScore(theScan.TheScan, matchedFragmentIons);
if (score > bestScore)
{
bestMatchingFragments = matchedFragmentIons;
bestScore = score;
bestLocalizedPeptide = localizedPeptide;
bestPosition = location;
}
}
if (bestScore < commonParameters.ScoreCutoff)
{
return(null);
}
var csm = new CrosslinkSpectralMatch(bestLocalizedPeptide, notch, bestScore, scanIndex, theScan, originalPeptide.DigestionParams, bestMatchingFragments);
if (deadEndMod == TrisDeadEnd)
{
csm.CrossType = PsmCrossType.DeadEndTris;
}
else if (deadEndMod == H2ODeadEnd)
{
csm.CrossType = PsmCrossType.DeadEndH2O;
}
else if (deadEndMod == NH2DeadEnd)
{
csm.CrossType = PsmCrossType.DeadEndNH2;
}
csm.LinkPositions = new List <int> {
bestPosition
};
csm.XlRank = new List <int> {
peptideIndex
};
return(csm);
}
public LocalizationEngine(IEnumerable <PeptideSpectralMatch> allResultingIdentifications, MsDataFile myMsDataFile, CommonParameters commonParameters, List <string> nestedIds) : base(commonParameters, nestedIds)
{
AllResultingIdentifications = allResultingIdentifications;
MyMsDataFile = myMsDataFile;
}
/// <summary>
/// Localizes the loop to a begin and end residue
/// </summary>
private CrosslinkSpectralMatch LocalizeLoopSites(PeptideWithSetModifications originalPeptide, Ms2ScanWithSpecificMass theScan, CommonParameters commonParameters,
List <int> possiblePositions, Modification loopMod, int notch, int scanIndex, int peptideIndex)
{
var possibleFragmentSets = CrosslinkedPeptide.XlLoopGetTheoreticalFragments(commonParameters.DissociationType, Loop, possiblePositions, originalPeptide);
double bestScore = 0;
Tuple <int, int> bestModPositionSites = null;
List <MatchedFragmentIon> bestMatchingFragments = new List <MatchedFragmentIon>();
foreach (var setOfPositions in possibleFragmentSets)
{
var matchedFragmentIons = MatchFragmentIons(theScan, setOfPositions.Value, commonParameters);
double score = CalculatePeptideScore(theScan.TheScan, matchedFragmentIons);
if (score > bestScore)
{
bestMatchingFragments = matchedFragmentIons;
bestScore = score;
bestModPositionSites = setOfPositions.Key;
}
}
if (bestScore < commonParameters.ScoreCutoff)
{
return(null);
}
var csm = new CrosslinkSpectralMatch(originalPeptide, notch, bestScore, scanIndex, theScan, originalPeptide.DigestionParams, bestMatchingFragments)
{
CrossType = PsmCrossType.Loop,
XlRank = new List <int> {
peptideIndex
},
LinkPositions = new List <int> {
bestModPositionSites.Item1, bestModPositionSites.Item2
}
};
return(csm);
}
private void SaveButton_Click(object sender, RoutedEventArgs e)
{
CommonParameters CommonParamsToSave = new CommonParameters();
DigestionParams digestionParamsToSave = new DigestionParams();
digestionParamsToSave.MaxMissedCleavages = int.Parse(missedCleavagesTextBox.Text, CultureInfo.InvariantCulture);
digestionParamsToSave.MinPeptideLength = int.TryParse(txtMinPeptideLength.Text, NumberStyles.Any, CultureInfo.InvariantCulture, out int temp) ? (int?)temp : null;
digestionParamsToSave.MaxPeptideLength = int.TryParse(txtMaxPeptideLength.Text, NumberStyles.Any, CultureInfo.InvariantCulture, out temp) ? (int?)temp : null;
digestionParamsToSave.Protease = (Protease)proteaseComboBox.SelectedItem;
digestionParamsToSave.MaxModificationIsoforms = int.Parse(maxModificationIsoformsTextBox.Text, CultureInfo.InvariantCulture);
CommonParamsToSave.DigestionParams = digestionParamsToSave;
CommonParamsToSave.BIons = bCheckBox.IsChecked.Value;
CommonParamsToSave.YIons = yCheckBox.IsChecked.Value;
CommonParamsToSave.CIons = cCheckBox.IsChecked.Value;
CommonParamsToSave.ZdotIons = zdotCheckBox.IsChecked.Value;
//CommonParamsToSave.ConserveMemory = conserveMemoryCheckBox.IsChecked.Value;
CommonParamsToSave.ScoreCutoff = double.Parse(minScoreAllowed.Text, CultureInfo.InvariantCulture);
//TheTask.CalibrationParameters.WriteIntermediateFiles = writeIntermediateFilesCheckBox.IsChecked.Value;
if (OutputFileNameTextBox.Text != "")
{
CommonParamsToSave.TaskDescriptor = OutputFileNameTextBox.Text;
}
else
{
CommonParamsToSave.TaskDescriptor = "CalibrateTask";
}
var listOfModsVariable = new List <(string, string)>();
foreach (var heh in variableModTypeForTreeViewObservableCollection)
{
listOfModsVariable.AddRange(heh.Children.Where(b => b.Use).Select(b => (b.Parent.DisplayName, b.DisplayName)));
}
CommonParamsToSave.ListOfModsVariable = listOfModsVariable;
var listOfModsFixed = new List <(string, string)>();
foreach (var heh in fixedModTypeForTreeViewObservableCollection)
{
listOfModsFixed.AddRange(heh.Children.Where(b => b.Use).Select(b => (b.Parent.DisplayName, b.DisplayName)));
}
CommonParamsToSave.ListOfModsFixed = listOfModsFixed;
//if (localizeAllCheckBox.IsChecked.Value)
{
CommonParamsToSave.ListOfModTypesLocalize = null;
CommonParamsToSave.LocalizeAll = true;
}
//else
//{
// CommonParamsToSave.LocalizeAll = false;
// CommonParamsToSave.ListOfModTypesLocalize = localizeModTypeForTreeViewObservableCollection.Where(b => b.Use.HasValue && b.Use.Value).Select(b => b.DisplayName).ToList();
//}
if (productMassToleranceComboBox.SelectedIndex == 0)
{
CommonParamsToSave.ProductMassTolerance = new AbsoluteTolerance(double.Parse(productMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
else
{
CommonParamsToSave.ProductMassTolerance = new PpmTolerance(double.Parse(productMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
if (precursorMassToleranceComboBox.SelectedIndex == 0)
{
CommonParamsToSave.PrecursorMassTolerance = new AbsoluteTolerance(double.Parse(precursorMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
else
{
CommonParamsToSave.PrecursorMassTolerance = new PpmTolerance(double.Parse(precursorMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
//if (int.TryParse(maxDegreesOfParallelism.Text, out int jsakdf))
// CommonParamsToSave.MaxParallelFilesToAnalyze = jsakdf;
TheTask.CommonParameters = CommonParamsToSave;
DialogResult = true;
}
public static List <PeptideSpectralMatch> ResolveFdrCategorySpecificPsms(List <PeptideSpectralMatch>[] AllPsms, int numNotches, string taskId, CommonParameters commonParameters)
{
//update all psms with peptide info
AllPsms.ToList()
.Where(psmArray => psmArray != null).ToList()
.ForEach(psmArray => psmArray.Where(psm => psm != null).ToList()
.ForEach(psm => psm.ResolveAllAmbiguities()));
foreach (List <PeptideSpectralMatch> psmsArray in AllPsms)
{
if (psmsArray != null)
{
List <PeptideSpectralMatch> cleanedPsmsArray = psmsArray.Where(b => b != null).OrderByDescending(b => b.Score)
.ThenBy(b => b.PeptideMonisotopicMass.HasValue ? Math.Abs(b.ScanPrecursorMass - b.PeptideMonisotopicMass.Value) : double.MaxValue)
.GroupBy(b => (b.FullFilePath, b.ScanNumber, b.PeptideMonisotopicMass)).Select(b => b.First()).ToList();
new FdrAnalysisEngine(cleanedPsmsArray, numNotches, commonParameters, new List <string> {
taskId
}).Run();
for (int i = 0; i < psmsArray.Count; i++)
{
if (psmsArray[i] != null)
{
if (psmsArray[i].FdrInfo == null) //if it was grouped in the cleanedPsmsArray
{
psmsArray[i] = null;
}
}
}
}
}
int[] ranking = new int[AllPsms.Length]; //high int is good ranking
List <int> indexesOfInterest = new List <int>();
for (int i = 0; i < ranking.Length; i++)
{
if (AllPsms[i] != null)
{
ranking[i] = AllPsms[i].Where(x => x != null).Count(x => x.FdrInfo.QValue <= 0.01); //set ranking as number of psms above 1% FDR
indexesOfInterest.Add(i);
}
}
//get the index of the category with the highest ranking
int majorCategoryIndex = indexesOfInterest[0];
for (int i = 1; i < indexesOfInterest.Count; i++)
{
int currentCategoryIndex = indexesOfInterest[i];
if (ranking[currentCategoryIndex] > ranking[majorCategoryIndex])
{
majorCategoryIndex = currentCategoryIndex;
}
}
//update other category q-values
//There's a chance of weird categories getting a random decoy before a random target, but we don't want to give that target a q value of zero.
//We can't just take the q of the first decoy, because if the target wasn't random (score = 40), but there are no other targets before the decoy (score = 5), then we're incorrectly dinging the target
//The current solution is such that if a minor category has a lower q value than it's corresponding score in the major category, then its q-value is changed to what it would be in the major category
List <PeptideSpectralMatch> majorCategoryPsms = AllPsms[majorCategoryIndex].Where(x => x != null).OrderByDescending(x => x.Score).ToList(); //get sorted major category
for (int i = 0; i < indexesOfInterest.Count; i++)
{
int minorCategoryIndex = indexesOfInterest[i];
if (minorCategoryIndex != majorCategoryIndex)
{
List <PeptideSpectralMatch> minorCategoryPsms = AllPsms[minorCategoryIndex].Where(x => x != null).OrderByDescending(x => x.Score).ToList(); //get sorted minor category
int minorPsmIndex = 0;
int majorPsmIndex = 0;
while (minorPsmIndex < minorCategoryPsms.Count && majorPsmIndex < majorCategoryPsms.Count) //while in the lists
{
PeptideSpectralMatch majorPsm = majorCategoryPsms[majorPsmIndex];
PeptideSpectralMatch minorPsm = minorCategoryPsms[minorPsmIndex];
//major needs to be a lower score than the minor
if (majorPsm.Score > minorPsm.Score)
{
majorPsmIndex++;
}
else
{
if (majorPsm.FdrInfo.QValue > minorPsm.FdrInfo.QValue)
{
minorPsm.FdrInfo.QValue = majorPsm.FdrInfo.QValue;
}
minorPsmIndex++;
}
}
//wrap up if we hit the end of the major category
while (minorPsmIndex < minorCategoryPsms.Count)
{
PeptideSpectralMatch majorPsm = majorCategoryPsms[majorPsmIndex - 1]; //-1 because it's out of index right now
PeptideSpectralMatch minorPsm = minorCategoryPsms[minorPsmIndex];
if (majorPsm.FdrInfo.QValue > minorPsm.FdrInfo.QValue)
{
minorPsm.FdrInfo.QValue = majorPsm.FdrInfo.QValue;
}
minorPsmIndex++;
}
}
}
int numTotalSpectraWithPrecursors = AllPsms[indexesOfInterest[0]].Count;
List <PeptideSpectralMatch> bestPsmsList = new List <PeptideSpectralMatch>();
for (int i = 0; i < numTotalSpectraWithPrecursors; i++)
{
PeptideSpectralMatch bestPsm = null;
double lowestQ = double.MaxValue;
int bestIndex = -1;
foreach (int index in indexesOfInterest) //foreach category
{
PeptideSpectralMatch currentPsm = AllPsms[index][i];
if (currentPsm != null)
{
double currentQValue = currentPsm.FdrInfo.QValue;
if (currentQValue < lowestQ || //if the new one is better
(currentQValue == lowestQ && currentPsm.Score > bestPsm.Score))
{
if (bestIndex != -1)
{
//remove the old one so we don't use it for fdr later
AllPsms[bestIndex][i] = null;
}
bestPsm = currentPsm;
lowestQ = currentQValue;
bestIndex = index;
}
else //remove the old one so we don't use it for fdr later
{
AllPsms[index][i] = null;
}
}
}
if (bestPsm != null)
{
bestPsmsList.Add(bestPsm);
}
}
//It's probable that psms from some categories were removed by psms from other categories.
//however, the fdr is still affected by their presence, since it was calculated before their removal.
foreach (List <PeptideSpectralMatch> psmsArray in AllPsms)
{
if (psmsArray != null)
{
List <PeptideSpectralMatch> cleanedPsmsArray = psmsArray.Where(b => b != null).OrderByDescending(b => b.Score)
.ThenBy(b => b.PeptideMonisotopicMass.HasValue ? Math.Abs(b.ScanPrecursorMass - b.PeptideMonisotopicMass.Value) : double.MaxValue)
.ToList();
new FdrAnalysisEngine(cleanedPsmsArray, numNotches, commonParameters, new List <string> {
taskId
}).Run();
}
}
return(bestPsmsList.OrderBy(b => b.FdrInfo.QValue).ThenByDescending(b => b.Score).ToList());
}
public static void TestIndexEngine()
{
var proteinList = new List <Protein> {
new Protein("MNNNKQQQ", null)
};
var variableModifications = new List <Modification>();
var fixedModifications = new List <Modification>();
var localizeableModifications = new List <Modification>();
Dictionary <Modification, ushort> modsDictionary = new Dictionary <Modification, ushort>();
foreach (var mod in fixedModifications)
{
modsDictionary.Add(mod, 0);
}
int i = 1;
foreach (var mod in variableModifications)
{
modsDictionary.Add(mod, (ushort)i);
i++;
}
foreach (var mod in localizeableModifications)
{
modsDictionary.Add(mod, (ushort)i);
i++;
}
List <DigestionMotif> motifs = new List <DigestionMotif> {
new DigestionMotif("K", null, 1, null)
};
Protease p = new Protease("Custom Protease2", CleavageSpecificity.Full, null, null, motifs);
ProteaseDictionary.Dictionary.Add(p.Name, p);
CommonParameters CommonParameters = new CommonParameters(scoreCutoff: 1, digestionParams: new DigestionParams(protease: p.Name, minPeptideLength: 1));
var fsp = new List <(string fileName, CommonParameters fileSpecificParameters)>();
fsp.Add(("", CommonParameters));
var engine = new IndexingEngine(proteinList, variableModifications, fixedModifications, null, null, null, 1, DecoyType.None, CommonParameters,
fsp, 30000, false, new List <FileInfo>(), TargetContaminantAmbiguity.RemoveContaminant, new List <string>());
var results = (IndexingResults)engine.Run();
Assert.AreEqual(5, results.PeptideIndex.Count);
var digestedList = proteinList[0].Digest(CommonParameters.DigestionParams, new List <Modification>(), variableModifications).ToList();
Assert.AreEqual(5, digestedList.Count);
foreach (PeptideWithSetModifications peptide in digestedList)
{
Assert.Contains(peptide, results.PeptideIndex);
var fragments = new List <Product>();
peptide.Fragment(CommonParameters.DissociationType, FragmentationTerminus.Both, fragments);
int positionInPeptideIndex = results.PeptideIndex.IndexOf(peptide);
foreach (Product fragment in fragments)
{
// mass of the fragment
double fragmentMass = fragment.NeutralMass;
int integerMassRepresentation = (int)Math.Round(fragmentMass * 1000);
// look up the peptides that have fragments with this mass
// the result of the lookup is a list of peptide IDs that have this fragment mass
List <int> fragmentBin = results.FragmentIndex[integerMassRepresentation];
// this list should contain this peptide!
Assert.Contains(positionInPeptideIndex, fragmentBin);
}
}
}
public RegisterViewModel(CommonParameters commonParameters)
: base(commonParameters)
{
NewUser = new User();
}
private AcquireTokenSilentParameterBuilder WithAccount(IAccount account)
{
CommonParameters.AddApiTelemetryFeature(ApiTelemetryFeature.WithAccount);
Parameters.Account = account;
return(this);
}
public static void AddCompIonsCommonParams()
{
CommonParameters cp = new CommonParameters(null, DissociationType.HCD, DissociationType.Unknown, DissociationType.Unknown, null, true, true, 3, 12, true, true, 1,
5, 200, 0.01, null, null, false, false, true, false, null, null, null, -1, null, null, null, 1, true, 4, 1);
var myMsDataFile = new TestDataFile();
var variableModifications = new List <Modification>();
var fixedModifications = new List <Modification>();
var localizeableModifications = new List <Modification>();
Dictionary <Modification, ushort> modsDictionary = new Dictionary <Modification, ushort>();
foreach (var mod in fixedModifications)
{
modsDictionary.Add(mod, 0);
}
int ii = 1;
foreach (var mod in variableModifications)
{
modsDictionary.Add(mod, (ushort)ii);
ii++;
}
foreach (var mod in localizeableModifications)
{
modsDictionary.Add(mod, (ushort)ii);
ii++;
}
var proteinList = new List <Protein> {
new Protein("MNNNKQQQ", null)
};
SearchParameters SearchParameters = new SearchParameters
{
MassDiffAcceptorType = MassDiffAcceptorType.Exact,
SearchTarget = true,
};
List <DigestionMotif> motifs = new List <DigestionMotif> {
new DigestionMotif("K", null, 1, null)
};
Protease protease = new Protease("Test", CleavageSpecificity.Full, null, null, motifs);
ProteaseDictionary.Dictionary.Add(protease.Name, protease);
var fsp = new List <(string fileName, CommonParameters fileSpecificParameters)>();
fsp.Add(("", cp));
var indexEngine = new IndexingEngine(proteinList, variableModifications, fixedModifications, new List <SilacLabel>(), null, null,
1, DecoyType.Reverse, cp, fsp, SearchParameters.MaxFragmentSize, false, new List <FileInfo>(), TargetContaminantAmbiguity.RemoveContaminant, new List <string>());
var indexResults = (IndexingResults)indexEngine.Run();
Tolerance DeconvolutionMassTolerance = new PpmTolerance(5);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, new CommonParameters()).OrderBy(b => b.PrecursorMass).ToArray();
MassDiffAcceptor massDiffAcceptor = SearchTask.GetMassDiffAcceptor(cp.PrecursorMassTolerance, SearchParameters.MassDiffAcceptorType, SearchParameters.CustomMdac);
// without complementary ions
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
var mse = new ModernSearchEngine(allPsmsArray, listOfSortedms2Scans, indexResults.PeptideIndex, indexResults.FragmentIndex, 0, cp, fsp, massDiffAcceptor, SearchParameters.MaximumMassThatFragmentIonScoreIsDoubled, new List <string>()).Run();
}
/// <summary>
/// Specifies if the client application should force refreshing the
/// token from the user token cache. By default the token is taken from the
/// the application token cache (forceRefresh=false)
/// </summary>
/// <param name="forceRefresh">If <c>true</c>, ignore any access token in the user token cache
/// and attempt to acquire new access token using the refresh token for the account
/// if one is available. This can be useful in the case when the application developer wants to make
/// sure that conditional access policies are applied immediately, rather than after the expiration of the access token.
/// The default is <c>false</c></param>
/// <returns>The builder to chain the .With methods</returns>
/// <remarks>Avoid un-necessarily setting <paramref name="forceRefresh"/> to <c>true</c> true in order to
/// avoid negatively affecting the performance of your application</remarks>
public AcquireTokenSilentParameterBuilder WithForceRefresh(bool forceRefresh)
{
CommonParameters.AddApiTelemetryFeature(ApiTelemetryFeature.WithForceRefresh, forceRefresh);
Parameters.ForceRefresh = forceRefresh;
return(this);
}
public CrosslinkSearchEngine(List <CrosslinkSpectralMatch>[] globalCsms, Ms2ScanWithSpecificMass[] listOfSortedms2Scans, List <PeptideWithSetModifications> peptideIndex,
List <int>[] fragmentIndex, List <int>[] secondFragmentIndex, int currentPartition, CommonParameters commonParameters, List <(string fileName, CommonParameters fileSpecificParameters)> fileSpecificParameters, Crosslinker crosslinker, int CrosslinkSearchTopNum,
