public static int[][] FindChargePairs(int nsilac, SilacType silacType, double matchPpm,
double silacTimeCorrelationThreshold, SilacCluster[] silacClusters,
IsotopeCluster[] isotopeClusters, IPeakList peakList, float[] intensities,
double[] centerMz)
{
double[] m = new double[nsilac];
for (int i = 0; i < m.Length; i++)
{
SilacCluster si = silacClusters[i];
m[i] = GetUncalibratedSilacMass(si, silacType, isotopeClusters, centerMz, intensities);
}
int[] o = ArrayUtil.Order(m);
m = ArrayUtil.SubArray(m, o);
List <int[]> pairs = new List <int[]>();
for (int i = 0; i < m.Length; i++)
{
SilacCluster si = silacClusters[o[i]];
int chargei = isotopeClusters[si.IsotopeClusterindex1].Charge;
double m1 = m[i];
int ind1 = ArrayUtil.CeilIndex(m, m1 - matchPpm * 1e-6 * m1);
for (int j = ind1; j < i; j++)
{
SilacCluster sj = silacClusters[o[j]];
int chargej = isotopeClusters[sj.IsotopeClusterindex1].Charge;
if (chargei == chargej)
{
continue;
}
int mini;
double[] pi = CalcSilacClusterProfile(si, out mini, silacType, isotopeClusters, peakList,
intensities);
int minj;
double[] pj = CalcSilacClusterProfile(sj, out minj, silacType, isotopeClusters, peakList,
intensities);
if (T03SilacAssembly.Correlate(pi, mini, pj, minj) > silacTimeCorrelationThreshold)
{
pairs.Add(new int[] { o[i], o[j] });
}
}
}
return(pairs.ToArray());
}
//** cluster the peaks **
public static List <int[]> CalcClusterIndices(int minCharge, int maxCharge, double correlationThreshold, int peakCount,
double[] centerMz, float[] centerMzErrors, float[] minTimes,
float[] maxTimes,
Peak[] peaks, IPeakList peakList)
{
NeighbourList neighbourList = new NeighbourList();
//** iterate through all peaks **
for (int j = 0; j < peakCount; j++)
{
//** current peak's mz and RT range **
double massJ = centerMz[j];
float massErrorJ = centerMzErrors[j];
float timeMinJ = minTimes[j];
float timeMaxJ = maxTimes[j];
//** get index of nearest peak at or above current mass -1.1 **
int start = ArrayUtil.CeilIndex(centerMz, massJ - 1.1);
//** get index of nearest peak at or below current mass -1.2
int w = ArrayUtil.FloorIndex(centerMz, massJ - 1.2);
//** remove any peaks outside of massj - 1.2 **
//** so there's a removal to the left of this peak outside 1.2 away... **
//** what is this all about?? **
for (int i = 0; i < w; i++)
{
if (peaks != null && peaks[i] != null)
{
peaks[i].Dispose();
peaks[i] = null;
}
}
//** iterate from current peak at mass - 1.1 to current peak **
//** iterates through left "adjacent" traces, neihbors with current trace (j) if valid **
for (int i = start; i < j; i++)
{
//** comparing peak mz and RT range **
double massI = centerMz[i];
double massErrorI = centerMzErrors[i];
double timeMinI = minTimes[i];
double timeMaxI = maxTimes[i];
//** difference in mass and synthesized mass error
double massDiff = Math.Abs(massI - massJ);
double massError = 5 * Math.Sqrt(massErrorI * massErrorI + massErrorJ * massErrorJ);
//** invalidating conditions: **
//** 1) mass difference is greater than minimum **
if (massDiff > MolUtil.C13C12Diff + massError)
{
continue;
}
//** 2) no RT overlap
if (timeMinI >= timeMaxJ)
{
continue;
}
//** 2) no RT overlap
if (timeMinJ >= timeMaxI)
{
continue;
}
//** 3) mass difference doesn't match any charge states **
if (!FitsMassDifference(massDiff, massError, minCharge, maxCharge))
{
continue;
}
//** 4) The intensity profile correlation (cosine similarity) fails the threshold **
if (CalcCorrelation(peakList.GetPeakKeep(i), peakList.GetPeakKeep(j)) < correlationThreshold)
{
continue;
}
//** create an edge between peak I and peak J if valid: **
//** 1) mass difference exceeds minimum
//** 2) RT has overlap
//** 3) mass difference fits a charge state
//** 4) intensity profiles have strong correlation
neighbourList.Add(i, j);
}
}
//** convert edge list to clusters! **
List <int[]> clusterList = new List <int[]>();
//** iterate through all peaks **
for (int i = 0; i < peakCount; i++)
{
//** if the peak has neighbors... **
if (!neighbourList.IsEmptyAt(i))
{
HashSet <int> currentCluster = new HashSet <int>();
AddNeighbors(i, currentCluster, neighbourList);
int[] c = SortByMass(currentCluster.ToArray(), centerMz);
clusterList.Add(c);
}
}
return(clusterList);
}
