/// <summary>
/// Constructor
/// </summary>
/// <param name="tolerance"></param>
public MzComparerWithTolerance(Tolerance tolerance)
{
if (tolerance.GetUnit() == ToleranceUnit.Ppm)
{
_equalityComparer = new MzComparerWithPpmTolerance(tolerance.GetValue());
}
else if (tolerance.GetUnit() == ToleranceUnit.Mz)
{
_equalityComparer = new MzComparerWithToleranceMz(tolerance.GetValue());
}
else
{
throw new NotSupportedException("The tolerance unite must be ppm or Th.");
}
}
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 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;
}
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());
}
}
}
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;
}
