public ChromatographProfile ReadFromFile(string fileName)
{
var result = new ChromatographProfile();
var root = XElement.Load(fileName);
result.Experimental = root.GetAttributeValue("Experimental", string.Empty);
result.Sequence = root.GetAttributeValue("Sequence", string.Empty);
result.Charge = root.GetAttributeValue("Charge", 0);
result.IdentifiedScan = root.GetAttributeValue("IdentifiedScan", 0);
result.ObservedMz = root.GetAttributeValue("ObservedMz", 0.0);
result.TheoreticalMz = root.GetAttributeValue("TheoreticalMz", 0.0);
List <IsotopicIon> ions = new List <IsotopicIon>();
foreach (var ionEle in root.Element("IsotopicIons").Elements("Ion"))
{
var ion = new IsotopicIon();
ion.Mz = ionEle.GetAttributeValue("Mz", 0.0);
ion.Intensity = ionEle.GetAttributeValue("Intensity", 0.0);
ions.Add(ion);
}
result.IsotopicIons = ions.ToArray();
foreach (var proEle in root.Element("ProfileScans").Elements("ProfileScan"))
{
var pscan = new ChromatographProfileScan();
result.Profiles.Add(pscan);
pscan.Identified = proEle.GetAttributeValue("Identified", false);
pscan.RetentionTime = proEle.GetAttributeValue("RetentionTime", 0.0);
pscan.Scan = proEle.GetAttributeValue("Scan", 0);
foreach (var scanEle in proEle.Elements("Peak"))
{
var peak = new ChromatographProfileScanPeak();
pscan.Add(peak);
peak.Isotopic = scanEle.GetAttributeValue("Isotopic", 0);
peak.Mz = scanEle.GetAttributeValue("Mz", 0.0);
peak.Intensity = scanEle.GetAttributeValue("Intensity", 0.0);
peak.Noise = scanEle.GetAttributeValue("Noise", 0.0);
peak.PPMDistance = scanEle.GetAttributeValue("PPMDistance", 0.0);
}
pscan.RawPeaks = new List <Peak>();
var rawPeaksELe = proEle.Element("RawPeaks");
foreach (var rawPeakEle in rawPeaksELe.Elements("RawPeak"))
{
var peak = new Peak();
pscan.RawPeaks.Add(peak);
peak.Mz = rawPeakEle.GetAttributeValue("Mz", 0.0);
peak.Intensity = rawPeakEle.GetAttributeValue("Intensity", 0.0);
peak.Noise = rawPeakEle.GetAttributeValue("Noise", 0.0);
}
}
return(result);
}
private ChromatographProfileScan FindEnvelope(PeakList <Peak> curPeaks, IsotopicIon[] isotopicIons, double mzTolerancePPM)
{
var result = new ChromatographProfileScan();
result.Scan = curPeaks.FirstScan;
result.RetentionTime = curPeaks.ScanTimes[0].RetentionTime;
int peakIndex = 0;
foreach (var peak in isotopicIons)
{
Peak findPeak = null;
while (peakIndex < curPeaks.Count)
{
var curPeak = curPeaks[peakIndex];
if (curPeak.Mz < peak.MinimumMzWithinTolerance)
{
peakIndex++;
continue;
}
if (curPeak.Mz > peak.MaximumMzWithinTolerance)
{
break;
}
if (findPeak == null || findPeak.Intensity < curPeak.Intensity)
{
findPeak = curPeak;
}
peakIndex++;
}
if (findPeak == null)
{
break;
}
else
{
result.Add(new ChromatographProfileScanPeak()
{
Mz = findPeak.Mz,
Intensity = findPeak.Intensity,
Charge = findPeak.Charge,
Noise = findPeak.Noise,
PPMDistance = PrecursorUtils.mz2ppm(findPeak.Mz, findPeak.Mz - peak.Mz)
});
}
}
return(result);
}
private bool AddEnvelope(ChromatographProfile chro, PeakList <Peak> curPeaks)
{
ChromatographProfileScan envelope = FindEnvelope(curPeaks, chro.IsotopicIons, options.MzTolerancePPM);
if (envelope.Count < options.ProfileLength)
{
return(false);
}
if (envelope.CalculateProfileCorrelation(chro.IsotopicIons) < options.MinimumCorrelation)
{
return(false);
}
chro.Profiles.Add(envelope);
return(true);
}
private bool AddEnvelope(ChromatographProfile chro, CacheRawFile rawReader, List <FullMS> fullMSList, int scanIndex)
{
PeakList <Peak> ms1 = ReadFullMS(rawReader, fullMSList, scanIndex);
ChromatographProfileScan envelope = null;
if (!profileFinder.Find(ms1, chro, options.MzTolerancePPM, options.MinimumProfileLength, ref envelope))
{
return(false);
}
if (options.MinimumProfileCorrelation > 0 && envelope.CalculateProfileCorrelation(chro.IsotopicIntensities) < options.MinimumProfileCorrelation)
{
return(false);
}
chro.Profiles.Add(envelope);
return(true);
}
public ChromatographProfile ReadFromFile(string fileName)
{
var result = new ChromatographProfile();
using (var sr = new StreamReader(fileName))
{
var line = sr.ReadLine();
while ((line = sr.ReadLine()) != null)
{
var parts = line.Split('\t');
var scan = int.Parse(parts[0]);
ChromatographProfileScan profilescan;
if (result.Profiles.Count > 0 && result.Profiles.Last().Scan == scan)
{
profilescan = result.Profiles.Last();
}
else
{
profilescan = new ChromatographProfileScan();
result.Profiles.Add(profilescan);
profilescan.Scan = scan;
profilescan.RetentionTime = double.Parse(parts[1]);
profilescan.Identified = bool.Parse(parts[9]);
}
var peak = new ChromatographProfileScanPeak();
profilescan.Add(peak);
peak.Isotopic = int.Parse(parts[2]);
peak.Mz = double.Parse(parts[3]);
peak.Intensity = double.Parse(parts[4]);
peak.PPMDistance = double.Parse(parts[5]);
peak.Noise = peak.Intensity / double.Parse(parts[6]);
}
}
return(result);
}
public bool Find(PeakList <Peak> ms1, ChromatographProfile chro, double mzTolerancePPM, int minimumProfileLength, ref ChromatographProfileScan result)
{
var rawPeaks = ms1.GetRange(chro.IsotopicIons[0].MinimumMzWithinTolerance, chro.IsotopicIons[chro.IsotopicIons.Length - 1].MaximumMzWithinTolerance);
if (rawPeaks.Count < minimumProfileLength)
{
return(false);
}
List <List <Peak> > envelope = new List <List <Peak> >();
int peakIndex = 0;
foreach (var peak in chro.IsotopicIons)
{
List <Peak> findPeaks = new List <Peak>();
while (peakIndex < rawPeaks.Count)
{
var curPeak = rawPeaks[peakIndex];
if (curPeak.Mz < peak.MinimumMzWithinTolerance)
{
peakIndex++;
continue;
}
if (curPeak.Mz > peak.MaximumMzWithinTolerance)
{
break;
}
findPeaks.Add(curPeak);
peakIndex++;
}
if (findPeaks.Count == 0)
{
break;
}
else
{
envelope.Add(findPeaks);
}
}
if (envelope.Count < minimumProfileLength)
{
return(false);
}
result = new ChromatographProfileScan();
result.Scan = ms1.FirstScan;
result.RetentionTime = ms1.ScanTimes[0].RetentionTime;
result.RawPeaks = new List <Peak>();
List <Peak> resolved = Resolve(chro, envelope);
foreach (var findPeak in rawPeaks)
{
var isotopicIndex = resolved.IndexOf(findPeak);
if (isotopicIndex == -1)
{
result.RawPeaks.Add(findPeak);
}
else
{
var ion = chro.IsotopicIons[isotopicIndex];
result.Add(new ChromatographProfileScanPeak()
{
Isotopic = isotopicIndex + 1,
Mz = findPeak.Mz,
Intensity = findPeak.Intensity,
Noise = findPeak.Noise,
PPMDistance = PrecursorUtils.mz2ppm(findPeak.Mz, findPeak.Mz - ion.Mz)
});
}
}
return(true);
}