public static void WriteNDPResultForSytoscape(List <SpectrumData> allSpecList, string outputPath) //output NDP for Sytoscape input
{
using (StreamWriter sw = new StreamWriter(outputPath)) {
for (int i = 0; i < allSpecList.Count - 1; i++)
{
for (int j = i + 1; j < allSpecList.Count; j++)
{
double ndp = Cal_Cosine_Product.CalCosineProduct(allSpecList[i], allSpecList[j]);
if (ndp >= 0.01)
{
List <double> commonNeutralLostList = new List <double>();
for (int m = 0; m < allSpecList[i].neutralLossList.Count; m++)
{
for (int n = 0; n < allSpecList[j].neutralLossList.Count; n++)
{
if (Cal_Cosine_Product.IsEqualMZ(allSpecList[i].neutralLossList[m], allSpecList[j].neutralLossList[n])) // judge whether 2 mz values <=0.01
{
commonNeutralLostList.Add(Math.Round(allSpecList[i].neutralLossList[m], 2));
}
}
}
commonNeutralLostList = commonNeutralLostList.Distinct().ToList();
commonNeutralLostList = commonNeutralLostList.OrderBy(x => x).ToList();
sw.Write(allSpecList[i].group.Replace(" ", "") + "," + ndp + "," + allSpecList[j].group.Replace(" ", "") + ",");
for (int k = 0; k < commonNeutralLostList.Count; k++)
{
sw.Write(commonNeutralLostList[k] + ",");
}
sw.WriteLine();
}
}
}
}
}
/**
* Merge multiple idMSMS (if mz difference less than 0.01, pick the higher intensity one)
* This function is used in two cases：1, merge 20-50ev idMSMSs， 2, merge idMSMSs in the same pcgroup with NDP>threshold
*/
private static SpectrumData MergeSpectraToOne(List <SpectrumData> spectraWithSamePcgrp)
{
SpectrumData maxSpectrum = new SpectrumData();
maxSpectrum.peakList = new List <PeakData>();
maxSpectrum.group = spectraWithSamePcgrp.OrderByDescending(x => double.Parse(x.group.Split('_')[0])).ToList()[0].group; //choose the highest mz as precursor(if this is 20-50ev, group is the same, then no influnce)
List <PeakData> allPeaksInOneGroup = new List <PeakData>();
for (int i = 0; i < spectraWithSamePcgrp.Count; i++)
{
allPeaksInOneGroup.AddRange(spectraWithSamePcgrp[i].peakList);
}
var allpeaks = from peaks in allPeaksInOneGroup
group peaks by peaks.mz;
foreach (var peaks in allpeaks)
{
PeakData maxPeak = peaks.OrderByDescending(x => x.intensity).ToList()[0]; //choose the highest intensity peak in one mz
maxSpectrum.peakList.Add(maxPeak);
}
for (int m = 0; m < maxSpectrum.peakList.Count; m++) //remove redundancy(two mz <0.01)
{
for (int n = m + 1; n < maxSpectrum.peakList.Count; n++)
{
if (Cal_Cosine_Product.IsEqualMZ(maxSpectrum.peakList[m].mz, maxSpectrum.peakList[n].mz))
{
if (maxSpectrum.peakList[m].intensity >= maxSpectrum.peakList[n].intensity)
{
maxSpectrum.peakList.RemoveAt(n);
n = n - 1;
}
else
{
maxSpectrum.peakList[m] = maxSpectrum.peakList[n];
n = n - 1;
}
}
}
}
for (int i = 0; i < maxSpectrum.peakList.Count; i++) //assign max precursor to all peaks
{
maxSpectrum.peakList[i].precursor = maxSpectrum.group;
}
maxSpectrum.peakList = maxSpectrum.peakList.OrderBy(x => x.mz).ToList();
return(maxSpectrum);
}