public bool Find(PeakList <Peak> ms1, ChromatographProfile chro, double mzTolerancePPM, int minimumProfileLength, ref ChromatographProfileScan result)
{
var rawPeaks = ms1.GetRange(chro.IsotopicIons[0].MinimumMzWithinTolerance, chro.IsotopicIons[chro.IsotopicIons.Length - 1].MaximumMzWithinTolerance);
if (rawPeaks.Count < minimumProfileLength)
{
return(false);
}
List <List <Peak> > envelope = new List <List <Peak> >();
int peakIndex = 0;
foreach (var peak in chro.IsotopicIons)
{
List <Peak> findPeaks = new List <Peak>();
while (peakIndex < rawPeaks.Count)
{
var curPeak = rawPeaks[peakIndex];
if (curPeak.Mz < peak.MinimumMzWithinTolerance)
{
peakIndex++;
continue;
}
if (curPeak.Mz > peak.MaximumMzWithinTolerance)
{
break;
}
findPeaks.Add(curPeak);
peakIndex++;
}
if (findPeaks.Count == 0)
{
break;
}
else
{
envelope.Add(findPeaks);
}
}
if (envelope.Count < minimumProfileLength)
{
return(false);
}
result = new ChromatographProfileScan();
result.Scan = ms1.FirstScan;
result.RetentionTime = ms1.ScanTimes[0].RetentionTime;
result.RawPeaks = new List <Peak>();
List <Peak> resolved = Resolve(chro, envelope);
foreach (var findPeak in rawPeaks)
{
var isotopicIndex = resolved.IndexOf(findPeak);
if (isotopicIndex == -1)
{
result.RawPeaks.Add(findPeak);
}
else
{
var ion = chro.IsotopicIons[isotopicIndex];
result.Add(new ChromatographProfileScanPeak()
{
Isotopic = isotopicIndex + 1,
Mz = findPeak.Mz,
Intensity = findPeak.Intensity,
Noise = findPeak.Noise,
PPMDistance = PrecursorUtils.mz2ppm(findPeak.Mz, findPeak.Mz - ion.Mz)
});
}
}
return(true);
}
