/// <summary>
/// Extract peaks that may be isotopes of the peak indicated by targetMz
/// </summary>
/// <param name="scans">Peaks will be extracted from this list of scans</param>
/// <param name="targetMz">The m/z to start extraction</param>
/// <param name="charge">The charge used to find neighboring isotopes</param>
/// <param name="left">A negative or zero number to indicate the number of isotopes to extract to the left of targetMz</param>
/// <param name="numIsotopes">The total number of isotopes to extract including the number indicated by "left"</param>
/// <returns></returns>
public static PeptideEnvelope Extract(List <Scan> scans, double targetMz, int charge, int left, int numIsotopes)
{
PeptideEnvelope output = new PeptideEnvelope(numIsotopes, scans.Count);
foreach (Scan scan in scans)
{
for (int i = 0; i < numIsotopes; ++i)
{
double matchMz = targetMz + (((i + left) * Mass.AVERAGINE_DIFF) / charge);
int index = PeakMatcher.Match(scan, matchMz, 3, PeakMatcher.PPM);
if (index >= 0)
{
double mz = scan.Centroids[index].Mz;
double intensity = scan.Centroids[index].Intensity;
output.mzs[i].Add(mz);
output.intensities[i].Add(intensity);
}
}
}
int max = 0;
foreach (var intensities in output.intensities)
{
if (intensities.Count > max)
{
max = intensities.Count;
}
output.averageIntensity.Add(Vector.Average(intensities));
}
output.MaxPeakCount = max;
return(output);
}
/// <summary>
/// Scale based on how many peaks were observed at a given m/z
/// </summary>
/// <param name="x"></param>
/// <param name="envelope"></param>
/// <param name="i"></param>
public static void ScaleByPeakCount(List <double> x, PeptideEnvelope envelope, int i)
{
if (envelope.MaxPeakCount > 0)
{
for (int j = i; j < i + x.Count; ++j)
{
x[j - i] *= envelope.mzs[j].Count / (double)envelope.MaxPeakCount;
}
}
}