/// <summary>
/// Returns the index of the most intense peak in the window.
/// Returns -1 if none is found.
/// </summary>
/// <param name="scan">The scan that will be searched</param>
/// <param name="targetMz">The center of the window where peaks will be considered</param>
/// <param name="tolerance">window will be +/- this value</param>
/// <param name="tolUnits">Units can be DALTON or PPM</param>
/// <returns></returns>
public static int MostIntenseIndex(Scan scan, double targetMz, double tolerance, int tolUnits)
{
double lowMz = targetMz - tolerance;
double highMz = targetMz + tolerance;
if (tolUnits == PPM)
{
double delta = tolerance * targetMz / 1000000;
lowMz = targetMz - delta;
highMz = targetMz + delta;
}
var peaks = scan.Centroids;
int i = PeakMatcher.NearestIndex(peaks, lowMz);
if (peaks[i].Mz < lowMz)
{
++i;
}
double maxIntensity = 0;
int bestIndex = -1;
for ( ; i < peaks.Count && peaks[i].Mz < highMz; ++i)
{
if (peaks[i].Intensity > maxIntensity)
{
maxIntensity = peaks[i].Intensity;
bestIndex = i;
}
}
return(bestIndex);
}
/// <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);
}
public static double calculate(List <Centroid> peaks, double isolationMz, double precursorMz, int charge, double isolationWindow)
{
if (peaks.Count == 0)
{
return(0);
}
double precursorIntensity = 0;
double totalIntensity = 0;
double lowMz = isolationMz - (isolationWindow / 2.0);
double highMz = isolationMz + (isolationWindow / 2.0);
int i = PeakMatcher.NearestIndex(peaks, lowMz);
if (peaks[i].Mz < lowMz)
{
++i;
}
for ( ; i < peaks.Count && peaks[i].Mz < highMz; ++i)
{
var peak = peaks[i];
// if the peak is within 20 ppm of any isotope
bool isPrecursor = false;
for (int j = -6; j < 7; ++j)
{
double theoreticalMass = precursorMz + (j * (Mass.AVERAGINE_DIFF / charge));
if (System.Math.Abs(PeakMatcher.getPpm(theoreticalMass, peak.Mz)) < 20)
{
isPrecursor = true;
break;
}
}
if (isPrecursor)
{
precursorIntensity += peak.Intensity;
}
totalIntensity += peak.Intensity;
}
if (totalIntensity < 1)
{
return(0);
}
return(precursorIntensity / totalIntensity);
}