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);
}
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);
}
