public LocalizationEngine(IEnumerable <PeptideSpectralMatch> allResultingIdentifications, List <ProductType> lp, MsDataFile myMsDataFile, CommonParameters commonParameters, List <string> nestedIds) : base(commonParameters, nestedIds)
{
AllResultingIdentifications = allResultingIdentifications;
ProductTypes = lp;
MyMsDataFile = myMsDataFile;
DissociationTypes = DetermineDissociationType(lp);
}
public SpectrumForm(MsDataFile msDataFile)
: base(msDataFile.Workspace)
{
InitializeComponent();
MsDataFile = msDataFile;
tbxScanIndex.Leave += (o, e) => ScanIndex = int.Parse(tbxScanIndex.Text);
}
private void resetFilesButton_Click(object sender, RoutedEventArgs e)
{
// clear spectra file path
if ((sender as Button).Name.Equals(resetSpectraFileButton.Name))
{
spectraFilePath = null;
spectraFileNameLabel.Text = "None Selected";
spectraFileNameLabel.ToolTip = null;
resetSpectraFileButton.IsEnabled = false;
}
// clear psm file path, psm data, and stat plot
else
{
tsvResultsFilePath = null;
psmFileNameLabel.Text = "None Selected";
psmFileNameLabel.ToolTip = null;
psmFileNameLabelStat.Text = "None Selected";
psmFileNameLabelStat.ToolTip = null;
resetPsmFileButton.IsEnabled = false;
resetPsmFileButtonStat.IsEnabled = false;
allPsms.Clear();
filteredListOfPsms.Clear();
psmsBySourceFile.Clear();
sourceFilesList.Clear();
plotViewStat.DataContext = null;
}
// clear main plot, base sequence, and properties table
mainViewModel.Model = null;
BaseDraw.clearCanvas(canvas);
propertyView.Clear();
MsDataFile = null;
}
public DataPointAcquisitionEngine(
List <PeptideSpectralMatch> goodIdentifications,
MsDataFile myMsDataFile,
Tolerance mzToleranceForMs1Search,
int minMS1isotopicPeaksNeededForConfirmedIdentification,
CommonParameters commonParameters,
List <(string FileName, CommonParameters Parameters)> fileSpecificParameters,
public static void TestFilterKeepsPeaksWithHighestIntensity()
{
double[] mzArray = new double[200];
double[] intArray = new double[200];
Random r = new Random();
for (int i = 0; i < 200; i++)
{
mzArray[i] = (double)(i + 1);
intArray[i] = (i * Math.Abs(r.Next(1, 100)) + 1d);
}
List <double> l = intArray.ToList();
l.Sort((x, y) => y.CompareTo(x));
l = l.Take(100).ToList();
FilteringParams f = new FilteringParams(100, null, null, null, false, false, false);
MsDataFile.WindowModeHelper(ref intArray, ref mzArray, f, mzArray.Min(), mzArray.Max());
List <double> myOut = intArray.ToList();
myOut.Sort((x, y) => y.CompareTo(x));
Assert.IsTrue(l.SequenceEqual(myOut));
}
public static void TestFilteringPeaksTopN_MultipleWindows(int peaksToKeep, int?nominalWindowWidthDaltons, int peakCount, bool normalize)
{
double[] mzArray = new double[100];
double[] intArray = new double[100];
for (int i = 0; i < 100; i++)
{
mzArray[i] = 100d + ((double)i / 100d) * 1900;
intArray[i] = i;
}
FilteringParams f = new FilteringParams(peaksToKeep, null, nominalWindowWidthDaltons, null, normalize, false, false);
MsDataFile.WindowModeHelper(ref intArray, ref mzArray, f, 100, 2000, false);
if (nominalWindowWidthDaltons.HasValue)
{
Assert.LessOrEqual((decimal)mzArray.Count(), (decimal)peaksToKeep * (decimal)nominalWindowWidthDaltons);
}
else
{
Assert.LessOrEqual((decimal)mzArray.Count(), (decimal)peaksToKeep * (decimal)1.0);
}
if (normalize)
{
Assert.That(50, Is.EqualTo(intArray.Max()).Within(0.1));
}
}
public bool Run_TdMzCal(InputFile raw_file, List <TopDownHit> topdown_hits)
{
all_topdown_hits = topdown_hits.Where(h => h.score > 0).ToList();
//need to reset m/z in case same td hits used for multiple calibration raw files...
Parallel.ForEach(all_topdown_hits, h => h.mz = h.reported_mass.ToMz(h.charge));
high_scoring_topdown_hits = all_topdown_hits.Where(h => h.score >= 40).ToList();
this.raw_file = raw_file;
if (high_scoring_topdown_hits.Count < 5)
{
return(false);
}
myMsDataFile = Path.GetExtension(raw_file.complete_path) == ".raw" ?
ThermoStaticData.LoadAllStaticData(raw_file.complete_path) :
null;
if (myMsDataFile == null)
{
myMsDataFile = Mzml.LoadAllStaticData(raw_file.complete_path);
}
if (myMsDataFile == null)
{
return(false);
}
DataPointAquisitionResults dataPointAcquisitionResult = GetDataPoints();
if (dataPointAcquisitionResult.Ms1List.Count < 10)
{
return(false);
}
var myMs1DataPoints = new List <(double[] xValues, double yValue)>();
for (int i = 0; i < dataPointAcquisitionResult.Ms1List.Count; i++)
{
//x values
var explanatoryVariables = new double[4];
explanatoryVariables[0] = dataPointAcquisitionResult.Ms1List[i].mz;
explanatoryVariables[1] = dataPointAcquisitionResult.Ms1List[i].retentionTime;
explanatoryVariables[2] = dataPointAcquisitionResult.Ms1List[i].logTotalIonCurrent;
explanatoryVariables[3] = dataPointAcquisitionResult.Ms1List[i].logInjectionTime;
//yvalue
double mzError = dataPointAcquisitionResult.Ms1List[i].massError;
myMs1DataPoints.Add((explanatoryVariables, mzError));
}
var ms1Model = GetRandomForestModel(myMs1DataPoints);
CalibrateHitsAndComponents(ms1Model);
if (Sweet.lollipop.calibrate_raw_files)
{
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(myMsDataFile, raw_file.directory + "\\" + raw_file.filename + "_calibrated.mzML", false);
}
return(true);
}
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 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, 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);
}
/// <summary>
/// Uses the boxcar algorithm to merge the boxcar scans in a file, writes a new mzml file to the directory.
/// </summary>
/// <param name="file"></param>
/// <param name="boxcarRanges"></param>
/// <param name="finalFilePath"></param>
/// <returns></returns> mergedScans, a list of final merged boxcar scans.
public static List <MsDataScan> MergeBoxCarScans(MsDataFile file, SetOfBoxcarRanges[] boxcarRanges, string finalFilePath)
{
SetOfBoxcarRanges[] bcRanges = RemoveOverlap(boxcarRanges);
List <SetOfScans> scans = SeparateScans(file);
List <MsDataScan> mergedScans = MergeScans(scans, bcRanges);
// WriteMzmlFile(mergedScans, file, finalFilePath);
return(mergedScans);
}
public DataPointAcquisitionEngine(
List <PeptideSpectralMatch> goodIdentifications,
List <Ms2ScanWithSpecificMass> goodScans,
MsDataFile myMsDataFile,
Tolerance precursorMassTolerance,
Tolerance productMassTolerance,
int minMS1isotopicPeaksNeededForConfirmedIdentification,
CommonParameters commonParameters,
List <(string FileName, CommonParameters Parameters)> fileSpecificParameters,
public DataRow(MsDataFile dataFile, RegressionWithOutliers unrefined, IList <string> regressedPeptides)
{
MsDataFile = dataFile;
Unrefined = unrefined;
RegressedPeptides = regressedPeptides;
if (Unrefined != null)
{
Refined = Unrefined.Refine();
}
}
public bool EnsureMsDataFile(MsDataFile msDataFile, bool alwaysPrompt)
{
String errorMessage;
if (!alwaysPrompt && msDataFile.Workspace.IsRejected(msDataFile))
{
return(false);
}
if (TryInitMsDataFile(this, msDataFile, out errorMessage))
{
return(true);
}
if (null == errorMessage)
{
return(false);
}
DialogResult dialogResult = MessageBox.Show(
"Unable to open the data file for " + msDataFile.Name + ". " + errorMessage +
" Do you want to look for this file?",
Program.AppName, MessageBoxButtons.OKCancel);
while (dialogResult == DialogResult.OK)
{
using (OpenFileDialog fileDialog = new OpenFileDialog
{
Filter = msDataFile.Name + ".*|" + msDataFile.Name + ".*"
+ "|All Files|*.*",
Title = "Browser for " + msDataFile.Name,
InitialDirectory = Settings.Default.RawFilesDirectory
})
{
fileDialog.ShowDialog(this);
if (String.IsNullOrEmpty(fileDialog.FileName))
{
break;
}
Workspace.SetDataDirectory(Path.GetDirectoryName(fileDialog.FileName));
}
if (TryInitMsDataFile(this, msDataFile, out errorMessage))
{
return(true);
}
if (null == errorMessage)
{
return(false);
}
dialogResult =
MessageBox.Show(errorMessage + " Do you want to keep looking for a different file?", Program.AppName,
MessageBoxButtons.OKCancel);
}
Workspace.RejectMsDataFile(msDataFile);
return(false);
}
public static void Test_ChargeDeconv()
{
string FilepathMZML = Path.Combine(TestContext.CurrentContext.TestDirectory, @"Data/2076.mzML");
MsDataFile file = Mzml.LoadAllStaticData(FilepathMZML, null);
var scans = file.GetAllScansList();
DeconvolutionParameter deconvolutionParameter = new DeconvolutionParameter();
Stopwatch stopwatch0 = new Stopwatch();
stopwatch0.Start();
var spectrum = new MzSpectrumXY(scans.First().MassSpectrum.XArray, scans.First().MassSpectrum.YArray, true);
stopwatch0.Stop();
Stopwatch stopwatch_iso = new Stopwatch();
stopwatch_iso.Start();
var iso = IsoDecon.MsDeconv_Deconvolute(spectrum, spectrum.Range, deconvolutionParameter);
stopwatch_iso.Stop();
Stopwatch stopwatch1 = new Stopwatch();
stopwatch1.Start();
var x = ChargeDecon.FindChargesForScan(spectrum, deconvolutionParameter);
stopwatch1.Stop();
//Stopwatch stopwatch2 = new Stopwatch();
//stopwatch2.Start();
var stopwatch2 = Stopwatch.StartNew();
var x2 = ChargeDecon.QuickFindChargesForScan(spectrum, deconvolutionParameter);
stopwatch2.Stop();
// Stopwatch stopwatch3 = new Stopwatch();
// stopwatch3.Start();
// int indUp = spectrum.ExtractIndicesByY().First();
// double mass_up = spectrum.XArray[indUp];
// var highest = ChargeDecon.FindChargesForPeak(spectrum, indUp, new DeconvolutionParameter());
// stopwatch3.Stop();
// var Parameters = Program.AddParametersFromFile("");
// List<double> masses = highest.Select(p => p.Value.Mz).ToList();
// string dynamicTargets;
// string dynamicMaxITs;
// Stopwatch stopwatch4 = new Stopwatch();
// stopwatch4.Start();
// var test = BoxCarScan.BuildDynamicBoxString(Parameters, masses, out dynamicTargets, out dynamicMaxITs);
// stopwatch4.Stop();
// Assert.That(test == "[(400.0,522.8),(524.8,542.2),(544.2,563.1),(565.1,585.6),(587.6,610.0),(612.0,636.5),(638.5,665.4),(667.4,697.1),(699.1,732.0),(734.0,770.5),(772.5,813.3),(815.3,861.1),(863.1,915.0),(917.0,976.0),(978.0,1045.7),(1047.7,1126.1),(1128.1,1200.0)]");
}
public static void Test_RealDataDeconv()
{
string FilepathMZML = Path.Combine(TestContext.CurrentContext.TestDirectory, @"Data/20170802_QEp1_FlMe_SA_BOX0_SILAC_BoxCar_SLICED.mzML");
MsDataFile file = Mzml.LoadAllStaticData(FilepathMZML, null);
var scans = file.GetAllScansList();
var test = new MzSpectrumXY(scans.First().MassSpectrum.XArray, scans.First().MassSpectrum.YArray, true);
var ms1scans = scans.Where(p => p.MsnOrder == 1).ToList();
DeconvolutionParameter deconvolutionParameter = new DeconvolutionParameter();
}
private async void loadFilesButton_Click(object sender, RoutedEventArgs e)
{
// check for validity
propertyView.Clear();
if (spectraFilePath == null)
{
MessageBox.Show("Please add a spectra file.");
return;
}
if (tsvResultsFilePath == null)
{
MessageBox.Show("Please add a search result file.");
return;
}
// load the spectra file
(sender as Button).IsEnabled = false;
selectSpectraFileButton.IsEnabled = false;
selectPsmFileButton.IsEnabled = false;
resetSpectraFileButton.IsEnabled = false;
resetPsmFileButton.IsEnabled = false;
prgsFeed.IsOpen = true;
prgsText.Content = "Loading spectra file...";
// Add EventHandlers for popup click-in/click-out behaviour
Deactivated += new EventHandler(prgsFeed_Deactivator);
Activated += new EventHandler(prgsFeed_Reactivator);
var slowProcess = Task <MsDataFile> .Factory.StartNew(() => spectraFileManager.LoadFile(spectraFilePath, new CommonParameters(trimMsMsPeaks: false)));
await slowProcess;
MsDataFile = slowProcess.Result;
// load the PSMs
this.prgsText.Content = "Loading PSMs...";
LoadPsms(tsvResultsFilePath, false);
DisplayLoadedAndFilteredPsms();
// done loading - restore controls
this.prgsFeed.IsOpen = false;
// Remove added EventHandlers
Deactivated -= new EventHandler(prgsFeed_Deactivator);
Activated -= new EventHandler(prgsFeed_Reactivator);
(sender as Button).IsEnabled = true;
selectSpectraFileButton.IsEnabled = true;
selectPsmFileButton.IsEnabled = true;
resetSpectraFileButton.IsEnabled = true;
resetPsmFileButton.IsEnabled = true;
}
// Grouping the scans in the file
/// <summary>
/// Given a file, reads through the scans and groups them into SetOfScans objects, each containing one or more full ms1 scans and the corresponding boxcar scans.
/// Discards all ms2 scans (although the SetOfScans object also has a list to hold these, if you wanted to include them).
/// This method includes many comments which can be uncommented for debugging to write information to the console.
/// </summary>
/// <param name="file"></param>
/// <returns></returns> list of SetOfScans objects, each SetOfScans contains one full ms1 scan and its corresponding boxcar scans.
public static List <SetOfScans> SeparateScans(MsDataFile file)
{
List <SetOfScans> sorted = new List <SetOfScans>();
// Get only the ms1 and boxcar scans (discard ms2):
var ms1scans = file.GetMS1Scans().ToList();
//Console.WriteLine("Number of ms1scans (full ms and boxcar method): " + ms1scans.Count);
// Initialize variables:
MsDataScan current = ms1scans.ElementAt(0);
string currentFilter = current.ScanFilter;
//Console.WriteLine("first scan filter: " + currentFilter);
MsDataScan next = ms1scans.ElementAt(1);
string nextFilter = next.ScanFilter;
//Console.WriteLine("next scan filter: " + nextFilter);
SetOfScans set = new SetOfScans();
// Loop through to group the scans. This should create as many SetOfScans objects as there are boxes (specified in the setup of the scan).
for (int i = 0; i < ms1scans.Count; i++)
{
if (current.ScanFilter.Contains("Full ms ")) // the space is important! Otherwise this will be recorded as a boxcar scan instead of an ms1
{
set.AddToMs1Scans(current);
// Console.WriteLine("Found full ms, added to set");
}
// if this boxcar scan has boxcar scans after it
else if (current.ScanFilter.Contains("Full msx ms") && next.ScanFilter.Contains("Full msx ms"))
{
set.AddToBoxcarScans(current);
//Console.WriteLine("Found msx ms, added to set");
}
// if this boxcar scan is the last boxcar scan in the set, start a new set
else if (current.ScanFilter.Contains("Full msx ms") && !next.ScanFilter.Contains("Full msx ms"))
{
set.AddToBoxcarScans(current);
//Console.WriteLine("Found last msx ms in set, added to set");
sorted.Add(set);
//Console.WriteLine("Added set to Sorted");
set = new SetOfScans();
}
current = next;
currentFilter = current.ScanFilter;
if ((i + 1) < ms1scans.Count) // if there is a next MsDataScan in the file
{
next = ms1scans.ElementAt(i + 1);
nextFilter = next.ScanFilter;
}
}
return(sorted);
}
public DataPointAcquisitionEngine(
List <PeptideSpectralMatch> goodIdentifications,
MsDataFile myMsDataFile,
Tolerance mzToleranceForMs1Search,
int minMS1isotopicPeaksNeededForConfirmedIdentification,
CommonParameters commonParameters,
List <string> nestedIds) : base(commonParameters, nestedIds)
{
GoodIdentifications = goodIdentifications;
MyMsDataFile = myMsDataFile;
MzToleranceForMs1Search = mzToleranceForMs1Search;
MinMS1isotopicPeaksNeededForConfirmedIdentification = minMS1isotopicPeaksNeededForConfirmedIdentification;
}
private async void loadFilesButton_Click(object sender, RoutedEventArgs e)
{
// check for validity
propertyView.Clear();
if (spectraFilePath == null)
{
MessageBox.Show("Please add a spectra file.");
return;
}
if (psmFilePath == null)
{
MessageBox.Show("Please add a search result file.");
return;
}
if (proteinFilePath == null)
{
MessageBox.Show("Please add a protein search result file."); //fixme
return;
}
// load the spectra file
(sender as Button).IsEnabled = false;
selectSpectraFileButton.IsEnabled = false;
selectPsmFileButton.IsEnabled = false;
selectProteinGroupFileButton.IsEnabled = false;
prgsFeed.IsOpen = true;
prgsText.Content = "Loading spectra file...";
var slowProcess = Task <MsDataFile> .Factory.StartNew(() => spectraFileManager.LoadFile(spectraFilePath, new CommonParameters(trimMsMsPeaks: false)));
await slowProcess;
MsDataFile = slowProcess.Result;
// load protein groups
this.prgsText.Content = "Loading protein groups...";
LoadProteinGroups(proteinFilePath);
// load the PSMs
this.prgsText.Content = "Loading PSMs...";
LoadAndDisplayPsms(psmFilePath);
// done loading - restore controls
prgsFeed.IsOpen = false;
(sender as Button).IsEnabled = true;
selectSpectraFileButton.IsEnabled = true;
selectPsmFileButton.IsEnabled = true;
selectProteinGroupFileButton.IsEnabled = true;
}
private DataPointAquisitionResults GetDataAcquisitionResults(MsDataFile myMsDataFile, string currentDataFile, List <Modification> variableModifications, List <Modification> fixedModifications, List <Protein> proteinList, string taskId, CommonParameters combinedParameters, Tolerance initPrecTol, Tolerance initProdTol)
{
var fileNameWithoutExtension = Path.GetFileNameWithoutExtension(currentDataFile);
MassDiffAcceptor searchMode = initPrecTol is PpmTolerance ?
(MassDiffAcceptor) new SinglePpmAroundZeroSearchMode(initPrecTol.Value) :
new SingleAbsoluteAroundZeroSearchMode(initPrecTol.Value);
var listOfSortedms2Scans = GetMs2Scans(myMsDataFile, currentDataFile, combinedParameters).OrderBy(b => b.PrecursorMass).ToArray();
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
Log("Searching with searchMode: " + searchMode, new List <string> {
taskId, "Individual Spectra Files", fileNameWithoutExtension
});
Log("Searching with productMassTolerance: " + initProdTol, new List <string> {
taskId, "Individual Spectra Files", fileNameWithoutExtension
});
new ClassicSearchEngine(allPsmsArray, listOfSortedms2Scans, variableModifications, fixedModifications, null, null, null, proteinList, searchMode, combinedParameters, this.FileSpecificParameters, new List <string> {
taskId, "Individual Spectra Files", fileNameWithoutExtension
}).Run();
List <PeptideSpectralMatch> allPsms = allPsmsArray.Where(b => b != null).ToList();
allPsms = allPsms.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(allPsms, searchMode.NumNotches, CommonParameters, this.FileSpecificParameters, new List <string> {
taskId, "Individual Spectra Files", fileNameWithoutExtension
}).Run();
List <PeptideSpectralMatch> goodIdentifications = allPsms.Where(b => b.FdrInfo.QValueNotch < 0.001 && !b.IsDecoy && b.FullSequence != null).ToList();
if (!goodIdentifications.Any())
{
return(new DataPointAquisitionResults(null, new List <PeptideSpectralMatch>(), new List <LabeledDataPoint>(), new List <LabeledDataPoint>(), 0, 0, 0, 0));
}
DataPointAquisitionResults currentResult = (DataPointAquisitionResults) new DataPointAcquisitionEngine(
goodIdentifications,
myMsDataFile,
initPrecTol,
CalibrationParameters.MinMS1IsotopicPeaksNeededForConfirmedIdentification,
CommonParameters,
this.FileSpecificParameters,
new List <string> {
taskId, "Individual Spectra Files", fileNameWithoutExtension
}).Run();
return(currentResult);
}
public static void Test_FragmentMesh()
{
string FilepathMZML = Path.Combine(TestContext.CurrentContext.TestDirectory, @"Data/2076.mzML");
MsDataFile file = Mzml.LoadAllStaticData(FilepathMZML, null);
var scans = file.GetAllScansList();
DeconvolutionParameter deconvolutionParameter = new DeconvolutionParameter();
var spectrum = new MzSpectrumXY(scans.First().MassSpectrum.XArray, scans.First().MassSpectrum.YArray, true);
var CEs = ChargeDecon.FindChargesForScan(spectrum, deconvolutionParameter);
var mesh = CEs.First().mzs_box;
Assert.That(mesh.Count() == 3);
}
public CalibrationEngine(MsDataFile myMSDataFile, DataPointAquisitionResults datapoints, CommonParameters commonParameters, List <string> nestedIds) : base(commonParameters, nestedIds)
{
MyMsDataFile = myMSDataFile;
Datapoints = datapoints;
// set the random seed based on raw file properties
if (MyMsDataFile.SourceFile != null && !string.IsNullOrEmpty(MyMsDataFile.SourceFile.CheckSum))
{
RandomSeed = MyMsDataFile.SourceFile.CheckSum.GetHashCode();
}
else
{
RandomSeed = MyMsDataFile.NumSpectra;
}
}
public static bool TryInitMsDataFile(IWin32Window parent, MsDataFile msDataFile, out string errorMessage)
{
bool success = false;
string message = null;
using (var longWaitDialog = new LongWaitDialog(parent, Program.AppName))
{
new LongOperationBroker(broker =>
{
broker.UpdateStatusMessage(string.Format("Reading retention times for {0}", msDataFile.Name));
success = MsDataFileUtil.TryInitMsDataFile(msDataFile.Workspace, msDataFile, broker.CancellationToken, out message);
}, longWaitDialog).LaunchJob();
}
errorMessage = message;
return(success);
}
public static void BU_dynamicBoxCarRange()
{
string FilepathMZML = Path.Combine(TestContext.CurrentContext.TestDirectory, @"Data/20170802_QEp1_FlMe_SA_BOX0_SILAC_BoxCar_SLICED.mzML");
MsDataFile file = Mzml.LoadAllStaticData(FilepathMZML, null);
var scans = file.GetAllScansList();
var spectrum = new MzSpectrumXY(scans.First().MassSpectrum.XArray, scans.First().MassSpectrum.YArray, true);
Parameters parameters = Program.AddParametersFromFile("");
var isos = IsoDecon.MsDeconv_Deconvolute(spectrum, spectrum.Range, parameters.DeconvolutionParameter);
List <List <Tuple <double, double, double> > > Boxes = new List <List <Tuple <double, double, double> > >();
BoxCarScan.GenerateDynamicBoxes_BU(isos, parameters, Boxes);
Assert.That(Boxes.Count == 2);
}
private void SaveChromatograms(ICollection <AnalysisChromatograms> analyses, MsDataFile msDataFile)
{
using (ISession session = workspace.OpenWriteSession())
{
ITransaction transaction = session.BeginTransaction();
foreach (AnalysisChromatograms analysis in analyses)
{
var dbPeptideAnalysis = session.Get <DbPeptideFileAnalysis>(analysis.PeptideFileAnalysis.Id);
if (dbPeptideAnalysis == null)
{
continue;
}
dbPeptideAnalysis.Times = analysis.Times.ToArray();
dbPeptideAnalysis.ScanIndexes = analysis.ScanIndexes.ToArray();
dbPeptideAnalysis.HasChromatograms = true;
session.Update(dbPeptideAnalysis);
var dbChromatogramDict = dbPeptideAnalysis.GetChromatogramDict();
foreach (Chromatogram chromatogram in analysis.Chromatograms)
{
DbChromatogram dbChromatogram;
if (!dbChromatogramDict.TryGetValue(chromatogram.MzKey, out dbChromatogram))
{
dbChromatogram = new DbChromatogram
{
PeptideFileAnalysis = dbPeptideAnalysis,
MzKey = chromatogram.MzKey,
};
}
dbChromatogram.IntensitiesBytes = ArrayConverter.ToBytes(chromatogram.Intensities.ToArray());
dbChromatogram.PeakMzsBytes = ArrayConverter.ToBytes(chromatogram.PeakMzs.ToArray());
dbChromatogram.Mz = chromatogram.Mz;
session.SaveOrUpdate(dbChromatogram);
}
}
if (msDataFile != null)
{
msDataFile.MsDataFileData.Save(session);
}
transaction.Commit();
}
foreach (var analysis in analyses)
{
Debug.Assert(_activePeptideFileAnalysisIds.Contains(analysis.PeptideFileAnalysis.Id.Value));
analysis.PeptideFileAnalysis.HasChromatograms = true;
}
}
public static string GetCohort(MsDataFile msDataFile, bool bySample)
{
var result = new StringBuilder();
if (msDataFile.Cohort != null)
{
result.Append(msDataFile.Cohort);
}
if (bySample && !string.IsNullOrEmpty(msDataFile.Sample))
{
if (result.Length > 0)
{
result.Append(" ");
}
result.Append(msDataFile.Sample);
}
return(result.ToString());
}
public static void TestFilterLowIntensity()
{
double[] mzArray = new double[100];
double[] intArray = new double[100];
for (int i = 0; i < 100; i++)
{
mzArray[i] = (double)i;
intArray[i] = (double)i;
}
FilteringParams f = new FilteringParams(null, 0.05, null, null, false, false, false);
MsDataFile.WindowModeHelper(ref intArray, ref mzArray, f, mzArray.Min(), mzArray.Max());
//The first five intensities are below 5% and therefore removed.
Assert.AreEqual(95, intArray.Count());
Assert.AreEqual(95, mzArray.Count());
}
public static void AnotherSpectralLibrarySearchTestDecoy()
{
var testDir = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\SpectralLibrarySearch");
string myFile = Path.Combine(testDir, @"slicedMouse.raw");
MyFileManager myFileManager = new MyFileManager(true);
CommonParameters commonParameters = new CommonParameters(maxThreadsToUsePerFile: 1, scoreCutoff: 1);
MsDataFile myMsDataFile = myFileManager.LoadFile(myFile, commonParameters);
var variableModifications = new List <Modification>();
var fixedModifications = new List <Modification>();
var proteinList = new List <Protein> {
new Protein("QTATIAHVTTMLGEVIGFNDHIVK", "P16858")
};
string targetSpectralLibrary = Path.Combine(testDir, @"P16858_target.msp");
string decoySpectralLibrary = Path.Combine(testDir, @"P16858_decoy.msp");
List <string> specLibs = new List <string> {
targetSpectralLibrary, decoySpectralLibrary
};
SpectralLibrary sl = new SpectralLibrary(specLibs);
var searchModes = new SinglePpmAroundZeroSearchMode(5);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, new CommonParameters()).OrderBy(b => b.PrecursorMass).ToArray();
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
bool writeSpectralLibrary = false;
new ClassicSearchEngine(allPsmsArray, listOfSortedms2Scans, variableModifications, fixedModifications, null, null, null,
proteinList, searchModes, commonParameters, null, sl, new List <string>(), writeSpectralLibrary).Run();
// Single search mode
Assert.AreEqual(7, allPsmsArray.Length);
Assert.IsTrue(allPsmsArray[5].Score > 38);
Assert.AreEqual("VIHDNFGIVEGLMTTVHAITATQK", allPsmsArray[5].BaseSequence);
Assert.IsTrue(allPsmsArray[5].IsDecoy);
SpectralLibrarySearchFunction.CalculateSpectralAngles(sl, allPsmsArray, listOfSortedms2Scans, commonParameters);
Assert.That(allPsmsArray[5].SpectralAngle, Is.EqualTo(0.69).Within(0.01));
}
public static bool TryInitMsDataFile(Workspace workspace, MsDataFile msDataFile, CancellationToken cancellationToken, out String message)
{
if (string.IsNullOrEmpty(workspace.GetDataDirectory()))
{
message = "Workspace data directory has not been specified";
return(false);
}
var path = workspace.GetDataFilePath(msDataFile.Name);
if (path == null)
{
message = "File could not be found";
return(false);
}
if (msDataFile.HasTimes())
{
message = "File exists and has been read before.";
return(true);
}
try
{
using (var cMsDataFile = new MsDataFileImpl(path))
{
msDataFile.Init(cancellationToken, cMsDataFile);
using (var session = workspace.OpenWriteSession())
{
session.BeginTransaction();
msDataFile.SaveBinary(session);
session.Transaction.Commit();
message = "Success";
return(true);
}
}
}
catch (Exception exception)
{
ErrorHandler.LogException("MsDataFiles", "Exception trying to open " + path, exception);
message =
"An exception occurred while trying to open the file. Either the file is corrupted, or the necessary libraries to read this file type have not been installed.";
return(false);
}
}
public static bool TryInitMsDataFile(Workspace workspace, MsDataFile msDataFile, String path, out String message)
{
if (path == null)
{
message = "Location of data file has never been specified.";
return(false);
}
if (!File.Exists(path))
{
message = "File does not exist.";
return(false);
}
if (msDataFile.HasTimes())
{
message = "File exists and has been read before.";
return(true);
}
try
{
using (var cMsDataFile = new MsDataFileImpl(path))
{
msDataFile.Init(path, cMsDataFile);
using (var session = workspace.OpenWriteSession())
{
session.BeginTransaction();
msDataFile.Save(session);
session.Transaction.Commit();
message = "Success";
return(true);
}
}
}
catch (Exception exception)
{
Console.Out.Write(exception);
message =
"An exception occurred while trying to open the file. Either the file is corrupted, or the necessary libraries to read this file type have not been installed.";
return(false);
}
}
public static void TestFilterNumberPeaksPerWindowTenWindows()
{
double[] mzArray = new double[200];
double[] intArray = new double[200];
for (int i = 0; i < 200; i++)
{
mzArray[i] = (double)(i + 1);
intArray[i] = (double)(i + 1);
}
FilteringParams f = new FilteringParams(10, null, 20, 10, false, false, false);
MsDataFile.WindowModeHelper(ref intArray, ref mzArray, f, mzArray.Min(), mzArray.Max());
Assert.AreEqual(100, intArray.Count());
Assert.AreEqual(100, mzArray.Count());
Assert.AreEqual(11, intArray.Min());
Assert.AreEqual(200, intArray.Max());
Assert.AreEqual(11, mzArray.Min());
Assert.AreEqual(200, mzArray.Max());
}
public IEnumerable <DeconvolutedEnvelope> Deconvolute(MsDataFile file, string fileName = null, int threads = -1)
{
var items = new List <DeconvolutedEnvelope>();
var scans = file.GetMS1Scans().ToList();
int scansComplete = 0;
Parallel.ForEach(Partitioner.Create(0, scans.Count),
new ParallelOptions {
MaxDegreeOfParallelism = threads
},
(range, loopState) =>
{
for (int i = range.Item1; i < range.Item2; i++)
{
var scan = scans[i];
var deconvolutedEnvs = Deconvolute(scan).ToList();
foreach (var env in deconvolutedEnvs)
{
env.SpectraFileName = fileName;
}
lock (items)
{
items.AddRange(deconvolutedEnvs);
scansComplete++;
}
}
});
foreach (var item in items.OrderByDescending(p => p.Score))
{
// TODO: feature finding
yield return(item);
}
}
public bool EnsureMsDataFile(MsDataFile msDataFile, bool alwaysPrompt)
{
String errorMessage;
if (!alwaysPrompt && msDataFile.Workspace.IsRejected(msDataFile))
{
return false;
}
if (TryInitMsDataFile(this, msDataFile, out errorMessage))
{
return true;
}
if (null == errorMessage)
{
return false;
}
DialogResult dialogResult = MessageBox.Show(
"Unable to open the data file for " + msDataFile.Name + ". " + errorMessage +
" Do you want to look for this file?",
Program.AppName, MessageBoxButtons.OKCancel);
while (dialogResult == DialogResult.OK)
{
using (OpenFileDialog fileDialog = new OpenFileDialog
{
Filter = msDataFile.Name + ".*|" + msDataFile.Name + ".*"
+ "|All Files|*.*",
Title = "Browser for " + msDataFile.Name,
InitialDirectory = Settings.Default.RawFilesDirectory
})
{
fileDialog.ShowDialog(this);
if (String.IsNullOrEmpty(fileDialog.FileName))
{
break;
}
Workspace.SetDataDirectory(Path.GetDirectoryName(fileDialog.FileName));
}
if (TryInitMsDataFile(this, msDataFile, out errorMessage))
{
return true;
}
if (null == errorMessage)
{
return false;
}
dialogResult =
MessageBox.Show(errorMessage + " Do you want to keep looking for a different file?", Program.AppName,
MessageBoxButtons.OKCancel);
}
Workspace.RejectMsDataFile(msDataFile);
return false;
}
public static bool TryInitMsDataFile(IWin32Window parent, MsDataFile msDataFile, out string errorMessage)
{
bool success = false;
string message = null;
using (var longWaitDialog = new LongWaitDialog(parent, Program.AppName))
{
new LongOperationBroker(broker=>
{
broker.UpdateStatusMessage(string.Format("Reading retention times for {0}", msDataFile.Name));
success = MsDataFileUtil.TryInitMsDataFile(msDataFile.Workspace, msDataFile, broker.CancellationToken, out message);
}, longWaitDialog).LaunchJob();
}
errorMessage = message;
return success;
}
public bool EnsureMsDataFile(MsDataFile msDataFile)
{
return EnsureMsDataFile(msDataFile, false);
}
public DataRow(MsDataFile dataFile, RegressionWithOutliers unrefined, IList<string> regressedPeptides)
{
MsDataFile = dataFile;
Unrefined = unrefined;
RegressedPeptides = regressedPeptides;
if (Unrefined != null)
{
Refined = Unrefined.Refine();
}
}
public static string GetCohort(MsDataFile msDataFile, bool bySample)
{
var result = new StringBuilder();
if (msDataFile.Cohort != null)
{
result.Append(msDataFile.Cohort);
}
if (bySample && !string.IsNullOrEmpty(msDataFile.Sample))
{
if (result.Length > 0)
{
result.Append(" ");
}
result.Append(msDataFile.Sample);
}
return result.ToString();
}
private void GenerateChromatograms(MsDataFile msDataFile, List<AnalysisChromatograms> analyses)
{
int totalAnalyses = analyses.Count;
if (totalAnalyses == 0)
{
return;
}
if (!UpdateProgress(0))
{
return;
}
analyses = new List<AnalysisChromatograms>(analyses);
using (var pwizMsDataFileImpl = new MsDataFileImpl(msDataFile.Path))
{
var completeAnalyses = new List<AnalysisChromatograms>();
int totalScanCount = pwizMsDataFileImpl.SpectrumCount;
double minTime = msDataFile.GetTime(msDataFile.GetSpectrumCount() - 1);
double maxTime = msDataFile.GetTime(0);
foreach (var analysis in analyses)
{
minTime = Math.Min(minTime, analysis.FirstTime);
maxTime = Math.Max(maxTime, analysis.LastTime);
}
int firstScan = msDataFile.FindScanIndex(minTime);
for (int iScan = firstScan; analyses.Count > 0 && iScan < totalScanCount; iScan++)
{
double time = msDataFile.GetTime(iScan);
int progress = (int)(100 * (time - minTime) / (maxTime - minTime));
progress = Math.Min(progress, 100);
progress = Math.Max(progress, 0);
if (!UpdateProgress(progress))
{
return;
}
List<AnalysisChromatograms> activeAnalyses = new List<AnalysisChromatograms>();
double nextTime = Double.MaxValue;
if (msDataFile.GetMsLevel(iScan, pwizMsDataFileImpl) != 1)
{
continue;
}
foreach (var analysis in analyses)
{
nextTime = Math.Min(nextTime, analysis.FirstTime);
if (analysis.FirstTime <= time)
{
activeAnalyses.Add(analysis);
}
}
if (activeAnalyses.Count == 0)
{
int nextScan = msDataFile.FindScanIndex(nextTime);
iScan = Math.Max(iScan, nextScan - 1);
continue;
}
double[] mzArray, intensityArray;
pwizMsDataFileImpl.GetSpectrum(iScan, out mzArray, out intensityArray);
foreach (var analysis in activeAnalyses)
{
var points = new List<MsDataFileUtil.ChromatogramPoint>();
foreach (var chromatogram in analysis.Chromatograms)
{
points.Add(MsDataFileUtil.GetIntensity(chromatogram.Mz, mzArray, intensityArray));
}
analysis.AddPoints(iScan, time, points);
}
var incompleteAnalyses = new List<AnalysisChromatograms>();
foreach (var analysis in analyses)
{
if (analysis.LastTime <= time)
{
completeAnalyses.Add(analysis);
}
else
{
incompleteAnalyses.Add(analysis);
}
}
if (completeAnalyses.Count > 10)
{
SaveChromatograms(completeAnalyses, null);
completeAnalyses.Clear();
}
analyses = incompleteAnalyses;
}
completeAnalyses.AddRange(analyses);
SaveChromatograms(completeAnalyses, msDataFile);
lock(this)
{
_activePeptideFileAnalysisIds.Clear();
}
}
}
private void SaveChromatograms(ICollection<AnalysisChromatograms> analyses, MsDataFile msDataFile)
{
using (ISession session = workspace.OpenWriteSession())
{
ITransaction transaction = session.BeginTransaction();
foreach (AnalysisChromatograms analysis in analyses)
{
var dbPeptideAnalysis = session.Get<DbPeptideFileAnalysis>(analysis.PeptideFileAnalysis.Id);
if (dbPeptideAnalysis == null)
{
continue;
}
dbPeptideAnalysis.Times = analysis.Times.ToArray();
dbPeptideAnalysis.ScanIndexes = analysis.ScanIndexes.ToArray();
dbPeptideAnalysis.HasChromatograms = true;
session.Update(dbPeptideAnalysis);
var dbChromatogramDict = dbPeptideAnalysis.GetChromatogramDict();
foreach (Chromatogram chromatogram in analysis.Chromatograms)
{
DbChromatogram dbChromatogram;
if (!dbChromatogramDict.TryGetValue(chromatogram.MzKey, out dbChromatogram))
{
dbChromatogram = new DbChromatogram
{
PeptideFileAnalysis = dbPeptideAnalysis,
MzKey = chromatogram.MzKey,
};
}
dbChromatogram.IntensitiesBytes = ArrayConverter.ToBytes(chromatogram.Intensities.ToArray());
dbChromatogram.PeakMzsBytes = ArrayConverter.ToBytes(chromatogram.PeakMzs.ToArray());
dbChromatogram.Mz = chromatogram.Mz;
session.SaveOrUpdate(dbChromatogram);
}
}
if (msDataFile != null)
{
msDataFile.MsDataFileData.Save(session);
}
transaction.Commit();
}
foreach (var analysis in analyses)
{
Debug.Assert(_activePeptideFileAnalysisIds.Contains(analysis.PeptideFileAnalysis.Id.Value));
analysis.PeptideFileAnalysis.HasChromatograms = true;
}
}
public DataFileRow(DataFilesForm form, MsDataFile dataFile)
{
_form = form;
_dataFile = dataFile;
}
public static bool InitMsDataFile(Workspace workspace, MsDataFile msDataFile)
{
String error;
return TryInitMsDataFile(workspace, msDataFile, msDataFile.Path, out error);
}
public static bool TryInitMsDataFile(Workspace workspace, MsDataFile msDataFile, String path, out String message)
{
if (path == null)
{
message = "Location of data file has never been specified.";
return false;
}
if (!File.Exists(path))
{
message = "File does not exist.";
return false;
}
if (msDataFile.HasTimes())
{
message = "File exists and has been read before.";
return true;
}
try
{
using(var cMsDataFile = new MsDataFileImpl(path))
{
msDataFile.Init(path, cMsDataFile);
using (var session = workspace.OpenWriteSession())
{
session.BeginTransaction();
msDataFile.Save(session);
session.Transaction.Commit();
message = "Success";
return true;
}
}
}
catch (Exception exception)
{
Console.Out.Write(exception);
message =
"An exception occurred while trying to open the file. Either the file is corrupted, or the necessary libraries to read this file type have not been installed.";
return false;
}
}