private Dictionary <MSDeconvNode, List <MSDeconvNode> > GetEdges(List <MSDeconvNode> nodeList, Tolerance tol, double elutionInterval)
{
var edgeDict = new Dictionary <MSDeconvNode, List <MSDeconvNode> >();
var currentNode = nodeList[0];
var currentIndex = GetIndexRange(nodeList, elutionInterval, currentNode);
foreach (var n1 in nodeList)
{
if (n1.ScanNumber != currentNode.ScanNumber)
{
currentNode = n1;
currentIndex = GetIndexRange(nodeList, elutionInterval, currentNode);
if (currentIndex.Item2 == -1)
{
break;
}
}
edgeDict.Add(n1, new List <MSDeconvNode>());
for (var i = currentIndex.Item1; i < currentIndex.Item2; i++)
{
var deltaMass = Math.Abs(nodeList[i].RealMonoMass - n1.RealMonoMass);
if (deltaMass <= tol.GetValue())
{
edgeDict[n1].Add(nodeList[i]);
}
}
}
return(edgeDict);
}
public FeatureSet GetFeatures(double mz, Tolerance tolerance, DataReader.FrameType frameType)
{
var intensityBlock = _uimfUtil.GetXic(mz, tolerance.GetValue(), frameType,
tolerance.GetUnit() == ToleranceUnit.Ppm ? DataReader.ToleranceType.PPM : DataReader.ToleranceType.Thomson);
var features = new FeatureSet(intensityBlock);
return(features);
}
public LcMsPeakMatrixLowResolution(LcMsRun run, int maxFeaturesPerSpec = 100, double tolerancePpm = 64, int minScanCharge = 20, int maxScanCharge = 100, double minScanMass = 20000, double maxScanMass = 60000)
{
Run = run;
_tolerance = new Tolerance(Math.Max(tolerancePpm, 32));
_minCharge = minScanCharge;
_maxCharge = maxScanCharge;
_minMass = minScanMass;
_maxMass = maxScanMass;
_ms1Features = new NodeSet <Ms1Feature>();
var nBits = (int)Math.Round(27 - Math.Log(_tolerance.GetValue() / 16, 2));
_comparer = new MzComparerWithBinning(nBits);
_maxFeaturesPerSpec = maxFeaturesPerSpec;
}
public void TestPpmErrorCalculation(string seqText, string rawFilePath, int scanNum)
{
var methodName = MethodBase.GetCurrentMethod().Name;
ShowStarting(methodName, rawFilePath);
var tolerance = new Tolerance(10, ToleranceUnit.Ppm);
const int maxCharge = 15;
const double relIntThres = 0.1;
if (!File.Exists(rawFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rawFilePath);
}
// init
var sequence = Sequence.GetSequenceFromMsGfPlusPeptideStr(seqText);
var lcms = PbfLcMsRun.GetLcMsRun(rawFilePath);
var spectrum = lcms.GetSpectrum(scanNum);
var ionTypeFactory = new IonTypeFactory(maxCharge);
var iontypes = ionTypeFactory.GetAllKnownIonTypes();
foreach (var iontype in iontypes)
{
var ion = iontype.GetIon(sequence.Composition);
var obsPeaks = spectrum.GetAllIsotopePeaks(ion, tolerance, relIntThres);
if (obsPeaks == null)
{
continue;
}
var isotopes = ion.GetIsotopes(relIntThres).ToArray();
for (int i = 0; i < isotopes.Length; i++)
{
if (obsPeaks[i] == null)
{
continue;
}
var obsMz = obsPeaks[i].Mz;
var theoMz = ion.GetIsotopeMz(isotopes[i].Index);
var ppmError = (obsMz - theoMz) / theoMz * 1e6;
Assert.True(ppmError <= tolerance.GetValue());
}
}
}
public void TestIsotopePeakAlignment(string rawFilePath, string idFilePath)
{
var idFileReader = IdFileReaderFactory.CreateReader(idFilePath);
var lcms = PbfLcMsRun.GetLcMsRun(rawFilePath);
var ids = idFileReader.Read();
var idList = ids.ToList();
var rawFileName = Path.GetFileNameWithoutExtension(rawFilePath);
foreach (var id in idList)
{
id.LcMs = lcms;
id.RawFileName = rawFileName;
}
var prsms = idList.Where(prsm => prsm.Sequence.Count > 0);
const double relIntThres = 0.1;
var tolerance = new Tolerance(10, ToleranceUnit.Ppm);
var toleranceValue = tolerance.GetValue();
const int maxCharge = 15;
var ionTypeFactory = new IonTypeFactory(maxCharge);
var ionTypes = ionTypeFactory.GetAllKnownIonTypes().ToArray();
var psmsValidated = 0;
var ionsValidated = 0;
var validationErrors = new List <string>();
foreach (var prsm in prsms)
{
foreach (var ionType in ionTypes)
{
var composition = prsm.Sequence.Aggregate(Composition.Zero, (current, aa) => current + aa.Composition);
var ion = ionType.GetIon(composition);
var observedPeaks = prsm.Ms2Spectrum.GetAllIsotopePeaks(ion, tolerance, relIntThres);
if (observedPeaks == null)
{
continue;
}
var errors = IonUtils.GetIsotopePpmError(observedPeaks, ion, relIntThres);
foreach (var error in errors)
{
if (error == null)
{
continue;
}
if (error > toleranceValue)
{
validationErrors.Add(string.Format("In scan {0}, PSM {1} has error {2:F1} for ion at {3} m/z",
prsm.Scan, prsm.SequenceText, error, ion.GetIsotopeMz(0)));
}
ionsValidated++;
}
}
psmsValidated++;
}
Console.WriteLine("Validated {0:N0} ions for {1:N0} PSMs", ionsValidated, psmsValidated);
if (validationErrors.Count <= 0)
{
return;
}
var validationMsg = string.Format("{0} ions had errors greater than {1} ppm", validationErrors.Count, tolerance);
Console.WriteLine(validationMsg);
foreach (var item in validationErrors.Take(10))
{
Console.WriteLine(item);
}
Assert.Fail(validationMsg);
}
public Dictionary <int, FeatureSet> GetFeaturesMultiThreading(int minTargetBin, int maxTargetBin, Tolerance tolerance, DataReader.FrameType frameType)
{
var featureDictionary = new Dictionary <int, FeatureSet>();
var targetMzList = Enumerable.Range(minTargetBin, maxTargetBin - minTargetBin + 1).Select(targetBin => _uimfUtil.GetMzFromBin(targetBin)).ToList();
var featureStatisticsDictionary = _featureDetectionUtil.GetFeatureStatistics(targetMzList, tolerance.GetValue(), frameType,
tolerance.GetUnit() == ToleranceUnit.Ppm ? DataReader.ToleranceType.PPM : DataReader.ToleranceType.Thomson);
foreach (var entry in featureStatisticsDictionary)
{
var targetBin = _uimfUtil.GetBinFromMz(entry.Key);
var featureStats = entry.Value;
featureDictionary.Add(targetBin, new FeatureSet(featureStats));
}
return(featureDictionary);
}
