protected PeakList <T> FindEnvelope(PeakList <T> t, T peak, double mzTolerance)
{
IsotopicType itype = IsotopicType.NONE;
var env = t.FindEnvelope(peak, mzTolerance, true);
if (env.Count <= 2)
{
return(env);
}
for (int i = 1; i < env.Count; i++)
{
if (env[i].Intensity >= env[i - 1].Intensity) //递增
{
if (itype == IsotopicType.DECREASING) //如果前面是递减，则这次递增无效。
{
env.RemoveRange(i, env.Count - i);
break;
}
}
else//递减
{
itype = IsotopicType.DECREASING;
}
}
return(env);
}
public static double GetPrecursorPercentage(this PeakList <Peak> isolationPeaks, double ppmTolerance)
{
var defaultValue = 0.0;
if (isolationPeaks.Count == 0)
{
return(defaultValue);
}
//parentPkl.ForEach(m => Console.WriteLine("new Peak({0:0.0000},{1:0.0},{2}),",m.Mz, m.Intensity,m.Charge));
var totalIntensity = isolationPeaks.Sum(m => m.Intensity);
if (0.0 == totalIntensity)
{
throw new ArgumentException("There is no intensity information in argument isolationPeaks");
}
var precursorPeak = isolationPeaks.Precursor;
var mzTolerance = PrecursorUtils.ppm2mz(precursorPeak.MonoIsotopicMass, ppmTolerance);
if (precursorPeak.Charge == 0)
{
var pPeak = isolationPeaks.FindAll(m => Math.Abs(m.Mz - precursorPeak.MonoIsotopicMass) < mzTolerance);
if (0 == pPeak.Count)
{
return(defaultValue);
}
var maxIntensity = pPeak.Max(m => m.Intensity);
pPeak.Find(m => m.Intensity == maxIntensity).Tag = 1;
return(maxIntensity / totalIntensity);
}
else
{
var pPeak = isolationPeaks.FindEnvelope(precursorPeak.MonoIsotopicMass, precursorPeak.Charge, mzTolerance, true);
if (0 == pPeak.Count)
{
return(defaultValue);
}
for (int i = 0; i < pPeak.Count; i++)
{
pPeak[i].Tag = i + 1;
}
return(pPeak.GetTotalIntensity() / totalIntensity);
}
}
public static List <PeakList <T> > GetEnvelopes <T>(PeakList <T> pkl, double ppmTolerance) where T : IPeak
{
var tmp = new PeakList <T>(pkl);
var result = new List <PeakList <T> >();
while (tmp.Count > 0)
{
double mzTolerance = 2 * PrecursorUtils.ppm2mz(tmp[0].Mz, ppmTolerance);
PeakList <T> envelope = tmp.FindEnvelope(tmp[0], mzTolerance, true);
result.Add(envelope);
foreach (T peak in envelope)
{
//Remove all peaks around current peak
PeakList <T> findPeaks = tmp.FindPeak(peak.Mz, peak.Charge, mzTolerance);
foreach (T findPeak in findPeaks)
{
tmp.Remove(findPeak);
}
}
}
/*
* Console.Out.WriteLine("---before merge");
* foreach (PeakList<T> pkl in result)
* {
* Console.Out.WriteLine("---");
* foreach (Peak p in pkl)
* {
* Console.Out.WriteLine(p);
* }
* }
*
* result.Sort(new PeakListMzAscendingComparer<T>());
*
* int current = 0;
*
* while (current < result.Count - 1)
* {
* PeakList<T> currentPkl = result[current];
* if (currentPkl[0].Charge > 0)
* {
* double expectMz = currentPkl[currentPkl.Count - 1].Mz + ChargeDeconvolution.C_GAP / currentPkl[0].Charge;
* double mzTolerance = 4 * Precursor.ppm2mz(currentPkl[0].Mz, ppmTolerance);
* int next = current + 1;
* while (next < result.Count)
* {
* double gap = result[next][0].Mz - expectMz;
* if (gap >= 2.0)
* {
* break;
* }
*
* if (Math.Abs(gap) > mzTolerance)
* {
* next++;
* continue;
* }
*
* if (result[next][0].Charge != currentPkl[0].Charge)
* {
* next++;
* continue;
* }
*
* Console.Out.WriteLine("Current----");
* foreach (T p in currentPkl)
* {
* Console.Out.WriteLine(p);
* }
* Console.Out.WriteLine("Add----");
* foreach (T p in result[next])
* {
* Console.Out.WriteLine(p);
* }
*
* currentPkl.AddRange(result[next]);
*
* Console.Out.WriteLine("To----");
* foreach (T p in currentPkl)
* {
* Console.Out.WriteLine(p);
* }
*
* result.RemoveAt(next);
* }
* }
*
* current++;
* }
*
* Console.Out.WriteLine("---after merge");
* foreach (PeakList<T> pkl in result)
* {
* Console.Out.WriteLine("---");
* foreach (Peak p in pkl)
* {
* Console.Out.WriteLine(p);
* }
* }
*/
return(result);
}
