public MS3Item Build(List <MS3Item> g)
{
var result = new MS3Item();
result.PrecursorMZ = g.Sum(m => m.PrecursorMZ * m.Sum(p => p.Intensity)) / g.Sum(m => m.Sum(p => p.Intensity));
List <MS3Peak> peaks = new List <MS3Peak>();
for (int i = 0; i < g.Count; i++)
{
peaks.AddRange(from peak in g[i]
select new MS3Peak()
{
Mz = peak.Mz, Intensity = peak.Intensity, Tag = i, CombinedCount = peak.CombinedCount
});
}
peaks.Sort((m1, m2) => m1.Mz.CompareTo(m2.Mz));
//group peak by m/z
var pgroups = new List <List <MS3Peak> >();
var currentPkl = new List <MS3Peak>();
currentPkl.Add(peaks.First());
for (int i = 1; i < peaks.Count; i++)
{
foreach (var peak in currentPkl)
{
var diff = Math.Abs(peaks[i].Mz - peak.Mz);
var ppmdiff = PrecursorUtils.mz2ppm(peak.Mz, diff);
if (ppmdiff <= fragmentPPMTolerance)
{
currentPkl.Add(peaks[i]);
break;
}
}
if (peaks[i] != currentPkl.Last())
{
pgroups.Add(currentPkl);
currentPkl = new List <MS3Peak>();
currentPkl.Add(peaks[i]);
}
}
pgroups.Add(currentPkl);
result.Clear();
foreach (var pg in pgroups)
{
if (pg.Count == 1)
{
result.Add(pg.First());
}
else
{
//for each spectrum, only the peak with most intensity will be used for merge
var waiting = (from t in pg.GroupBy(m => m.Tag)
select(from tt in t
orderby tt.Intensity descending
select tt).First()).ToArray();
var combinedpeak = new MS3Peak()
{
Mz = waiting.Sum(m => m.Mz * m.Intensity) / waiting.Sum(m => m.Intensity),
Intensity = waiting.Sum(m => m.Intensity),
CombinedCount = waiting.Sum(m => m.CombinedCount)
};
result.Add(combinedpeak);
}
}
result.CombinedCount = g.Count;
if (result.Count > maxPeakCount)
{
result.Sort((m1, m2) =>
{
var res = m2.CombinedCount.CompareTo(m1.CombinedCount);
if (res == 0)
{
res = m2.Intensity.CompareTo(m1.Intensity);
}
return(res);
});
for (int i = result.Count - 1; i >= maxPeakCount; i--)
{
result.RemoveAt(i);
}
result.SortByMz();
}
return(result);
}
public List <MS2Item> ReadFromFile(string fileName)
{
if (!File.Exists(fileName))
{
throw new FileNotFoundException(fileName);
}
XElement root = XElement.Load(fileName);
List <MS2Item> result = new List <MS2Item>();
foreach (var ms2ele in root.Elements("MS2"))
{
var item = new MS2Item();
result.Add(item);
item.CombinedCount = int.Parse(ms2ele.Attribute("PKL").Value);
item.Precursor = double.Parse(ms2ele.Attribute("MZ").Value);
item.Charge = int.Parse(ms2ele.Attribute("Z").Value);
item.FileScans = (from ele in ms2ele.Elements("FileScan")
let exp = ele.Attribute("F").Value
let firstscan = int.Parse(ele.Attribute("S").Value)
select new SequestFilename(exp, firstscan, firstscan, item.Charge, string.Empty)).ToList();
item.Score = double.Parse(ms2ele.Attribute("Score").Value);
item.ExpectValue = double.Parse(ms2ele.Attribute("ExpectValue").Value);
if (ms2ele.Attribute("Seq") != null)
{
item.Peptide = ms2ele.Attribute("Seq").Value;
}
if (ms2ele.Attribute("Mod") != null)
{
item.Modification = ms2ele.Attribute("Mod").Value;
}
if (ms2ele.Attribute("Proteins") != null)
{
item.Proteins = ms2ele.Attribute("Proteins").Value;
}
foreach (var ele in ms2ele.Elements("TerminalLoss"))
{
item.TerminalLoss.Add(new TerminalLossItem(bool.Parse(ele.Attribute("IsNterminal").Value), ele.Attribute("Seq").Value, double.Parse(ele.Attribute("MZ").Value)));
}
foreach (var ms3ele in ms2ele.Elements("MS3"))
{
var ms3 = new MS3Item();
item.MS3Spectra.Add(ms3);
if (item.CombinedCount > 1)
{
ms3.CombinedCount = int.Parse(ms3ele.Attribute("PKL").Value);
}
else
{
ms3.CombinedCount = 1;
}
ms3.PrecursorMZ = double.Parse(ms3ele.Attribute("MZ").Value);
foreach (var pEle in ms3ele.Elements("P"))
{
var peak = new MS3Peak();
ms3.Add(peak);
peak.Mz = double.Parse(pEle.Attribute("MZ").Value);
peak.Intensity = double.Parse(pEle.Attribute("I").Value);
if (ms3.CombinedCount > 1)
{
peak.CombinedCount = int.Parse(pEle.Attribute("PKL").Value);
}
else
{
peak.CombinedCount = 1;
}
}
}
}
return(result);
}