/// <summary>
/// source和当前对象将共享rawpeaks和peakinisolationwindow
/// </summary>
/// <param name="source"></param>
public IsobaricScan(IsobaricScan source)
{
this.ScanMode = source.ScanMode;
this.RawPeaks = source.RawPeaks;
this.PeakInIsolationWindow = source.PeakInIsolationWindow;
this.Valid = source.Valid;
this.ValidProbability = source.ValidProbability;
this.PrecursorPercentage = source.PrecursorPercentage;
}
public void WriteChannels(XmlWriter xw, List <UsedChannel> used, IsobaricScan item)
{
xw.WriteStartElement("Reporters");
for (int i = 0; i < used.Count; i++)
{
xw.WriteStartElement("Reporter");
xw.WriteAttribute("name", used[i].Name);
xw.WriteAttributeFormat("mz", "{0:0.#####}", item[i].Mz);
xw.WriteAttributeFormat("intensity", "{0:0.0}", item[i].Intensity);
xw.WriteEndElement();
}
xw.WriteEndElement();
}
protected void AppendScan(IRawFile2 rawReader, List <IsobaricScan> result, int scan, string mode, double isolationWidth)
{
IsobaricScan item = new IsobaricScan();
PeakList <Peak> pkl = rawReader.GetPeakList(scan, MinMz, MaxMz);
if (pkl.Count < MinPeakCount)
{
return;
}
var recordScan = GetIdentificationScan(scan);
item.ScanMode = mode;
item.RawPeaks = pkl;
item.PeakInIsolationWindow = rawReader.GetPeakInIsolationWindow(scan, isolationWidth);
item.Scan = rawReader.GetScanTime(recordScan);
result.Add(item);
}
public void WriteIsobaricItem(XmlTextWriter w, IsobaricResult ir, IsobaricScan item)
{
w.WriteStartElement("IsobaricScan");
w.WriteElement("Experimental", item.Experimental);
w.WriteElement("ScanMode", item.ScanMode);
w.WriteElement("Scan", item.Scan.Scan);
w.WriteElementFormat("RetentionTime", "{0:0.0}", item.Scan.RetentionTime);
w.WriteElementFormat("IonInjectionTime", "{0:0.000}", item.Scan.IonInjectionTime);
w.WriteElementFormat("PrecursorPercentage", "{0:0.000}", item.PrecursorPercentage);
if (HasReporters)
{
WriteChannels(w, ir.UsedChannels, item);
}
WriteElementPeakList(w, item.RawPeaks, "RawPeaks", false);
WriteElementPeakList(w, item.PeakInIsolationWindow, "PeakInIsolationWindow", true);
w.WriteEndElement();
w.Flush();
}
public double GetReference(IsobaricScan item)
{
return((from f in References
select f.GetValue(item)).Average());
}
public double GetValue(IsobaricScan item)
{
return(item[Index].Intensity);
}
public override List <IsobaricScan> ReadFromFile(string fileName)
{
var result = new List <IsobaricScan>();
using (var rawReader = RawFileFactory.GetRawFileReader(fileName))
{
int startScan = rawReader.GetFirstSpectrumNumber();
int endScan = rawReader.GetLastSpectrumNumber();
Progress.SetRange(startScan, endScan);
for (int scan = startScan; scan <= endScan; scan++)
{
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
Progress.SetPosition(scan);
if (2 == rawReader.GetMsLevel(scan))
{
string scanMode = rawReader.GetScanMode(scan);
if (string.IsNullOrEmpty(scanMode))
{
AppendScan(rawReader, result, scan, "UNKNOWN");
continue;
}
scanMode = scanMode.ToLower();
if (scanMode.Equals("pqd"))
{
AppendScan(rawReader, result, scan, "PQD");
}
else if (scanMode.Equals("cid"))
{
//如果上一个scan是pqd，那么，现在这个cid的结果从该pqd读取。
if (result.Count > 0 && result[result.Count - 1].RawPeaks.ScanTimes[0].Scan == scan - 1 && result[result.Count - 1].RawPeaks.ScanMode == "PQD")
{
var lastItem = result[result.Count - 1];
var item = new IsobaricScan(lastItem);
item.Scan = rawReader.GetScanTime(scan);
item.ScanMode = "CID";
result.Add(item);
}
else//否则，从自己的peaklist中读取。
{
AppendScan(rawReader, result, scan, "CID");
}
}
else
{
Console.WriteLine("Scan {0} is skipped with mode {1}", scan, scanMode);
}
}
}
}
return(result);
}
/// <summary>
/// 从XmlReader中读取IsobaricItem信息。
/// </summary>
/// <param name="reader">XmlReader</param>
/// <param name="used">Used channels</param>
/// <param name="readReporters">是否读取Reporter信息</param>
/// <param name="readPeaks">是否读取Peak信息</param>
/// <param name="accept">在读取Peak前，对IsobaricItem进行筛选</param>
/// <param name="untilSucceed">如果筛选失败，是否进行读取下一个IsobaricItem</param>
/// <returns></returns>
public static IsobaricScan Parse(XmlReader reader, List <UsedChannel> used, bool readReporters, bool readPeaks, Predicate <IsobaricScan> accept, bool untilSucceed = false)
{
IsobaricScan result = null;
while (reader.MoveToElement("IsobaricScan"))
{
XElement el = XNode.ReadFrom(reader) as XElement;
var dic = el.ToDictionary();
result = new IsobaricScan();
result.Experimental = dic["Experimental"].Value;
result.ScanMode = dic["ScanMode"].Value;
result.Scan = new ScanTime(int.Parse(dic["Scan"].Value), double.Parse(dic["RetentionTime"].Value));
result.Scan.IonInjectionTime = double.Parse(dic["IonInjectionTime"].Value);
result.PrecursorPercentage = double.Parse(dic["PrecursorPercentage"].Value);
if (null != accept && !accept(result))
{
result = null;
if (untilSucceed)
{
continue;
}
else
{
break;
}
}
if (readReporters)
{
result.Reporters = new Peak[used.Count];
XElement ions;
if (dic.TryGetValue("Reporters", out ions))
{
var ionsElement = ions.FindElements("Reporter");
if (ionsElement.Count != used.Count)
{
throw new Exception(string.Format("Reporter element number {0} is not equals to used channel number {1} in scan {2}",
ionsElement.Count,
used.Count,
result.Scan));
}
for (int i = 0; i < used.Count; i++)
{
var ionEle = ionsElement[i];
result[i] = new Peak(double.Parse(ionEle.FindAttribute("mz").Value), double.Parse(ionEle.FindAttribute("intensity").Value));
}
}
}
if (readPeaks)
{
result.RawPeaks = ReadElementPeakList(dic["RawPeaks"], false);
result.RawPeaks.ScanTimes.Add(result.Scan);
result.PeakInIsolationWindow = ReadElementPeakList(dic["PeakInIsolationWindow"], true);
}
break;
}
return(result);
}
//public static IsobaricScan FindOrCreateIsobaricItem(this IAnnotation ann, IsobaricType plexType)
//{
// if (ann.Annotations.ContainsKey(IsobaricConsts.TYPE))
// {
// return ann.Annotations[IsobaricConsts.TYPE] as IsobaricScan;
// }
// else
// {
// var result = new IsobaricScan();
// ann.Annotations[IsobaricConsts.TYPE] = result;
// return result;
// }
//}
public static void SetIsobaricItem(this IAnnotation ann, IsobaricScan item)
{
ann.Annotations[IsobaricConsts.TYPE] = item;
}