public override IsobaricResult ReadFromFile(string fileName)
{
IsobaricResult result = new IsobaricResult()
{
Mode = ITraqResultXmlFormatReader.GetMode(fileName)
};
var reader = new ITraqResultXmlFormatReader()
{
Progress = this.Progress,
Accept = this.Accept,
ReadPeaks = this.ReadPeaks
};
reader.OpenFile(fileName);
try
{
IsobaricItem item;
while (null != (item = reader.Next()))
{
result.Add(item);
}
}
finally
{
reader.Close();
}
return(result);
}
public override IsobaricResult ReadFromFile(string fileName)
{
XElement root = XElement.Load(fileName);
IsobaricResult result = new IsobaricResult();
foreach (var ele in root.Elements("ITraqScan"))
{
var item = new IsobaricItem();
item.PlexType = EnumUtils.StringToEnum(ele.Element("PlexType").Value, IsobaricType.PLEX4);
item.Experimental = ele.Element("Experimental").Value;
item.ScanMode = ele.Element("ScanMode").Value;
item.Scan = new ScanTime(Convert.ToInt32(ele.Element("Scan").Value),
MyConvert.ToDouble(ele.Element("RetentionTime").Value));
item.Scan.IonInjectionTime = MyConvert.ToDouble(ele.Element("IonInjectionTime").Value);
var ppEle = ele.Element("PrecursorPercentage");
if (null != ppEle)
{
item.PrecursorPercentage = MyConvert.ToDouble(ppEle.Value);
}
if (!Accept(item))
{
continue;
}
var ions = ele.Element("Ions");
var defs = item.Definition.Items;
foreach (var def in defs)
{
item[def.Index] = MyConvert.ToDouble(ions.Element(def.Name).Value);
}
if (ReadPeaks)
{
item.RawPeaks = ElementToPeakList(ele, "RawPeaks", false);
item.PeakInIsolationWindow = ElementToPeakList(ele, "PeakInIsolationWindow", true);
}
result.Add(item);
}
return(result);
}
public virtual IsobaricResult GetITraqResult(List <IsobaricItem> pkls, List <MeanStandardDeviation> accs, double peakFolderTolerance, int minPeakCount)
{
IsobaricResult result = new IsobaricResult();
double[] ions = GetIons();
List <double> means = new List <double>();
List <double> peakTolerances = new List <double>();
for (int i = 0; i < ions.Length; i++)
{
var ion = ions[i];
means.Add(ion + accs[i].Mean);
peakTolerances.Add(accs[i].StdDev * peakFolderTolerance);
}
List <Peak> peaks = new List <Peak>();
foreach (var pkl in pkls)
{
peaks.Clear();
int nullCount = 0;
for (int i = 0; i < means.Count; i++)
{
Peak peak = pkl.RawPeaks.FindPeak(means[i], peakTolerances[i]).FindMaxIntensityPeak();
CheckPeakNull(ref peak, ref nullCount);
peaks.Add(peak);
}
if (nullCount > ions.Length - minPeakCount)
{
continue;
}
AssignItraqItem(pkl, peaks);
result.Add(pkl);
}
return(result);
}
public void Setup()
{
t1 = new IsobaricItem()
{
Experimental = "S1",
ScanMode = "HCD",
PlexType = IsobaricType.PLEX4,
PrecursorPercentage = 0.85,
Scan = new ScanTime(255, 3.4),
RawPeaks = new PeakList <Peak>(new Peak[] { new Peak(114.1, 114.1), new Peak(115.1, 115.1), new Peak(116.1, 116.1), new Peak(117.1, 117.1) }.ToList()),
PeakInIsolationWindow = new PeakList <Peak>(new Peak[] { new Peak(214.1, 114.1), new Peak(215.1, 115.1), new Peak(216.1, 116.1), new Peak(217.1, 117.1) }.ToList())
{
Precursor = new PrecursorPeak()
{
MasterScan = 1,
Charge = 2,
Intensity = 3.0,
IsolationMass = 1800.1,
IsolationWidth = 2.0,
MonoIsotopicMass = 1879.1
}
}
};
t1[114] = 4.5;
t1[115] = 5.5;
t1[116] = 6.5;
t1[117] = 7.5;
t2 = new IsobaricItem()
{
Experimental = "S2",
ScanMode = "ETD",
PlexType = IsobaricType.PLEX8,
PrecursorPercentage = 0.33,
Scan = new ScanTime(355, 4.4),
RawPeaks = new PeakList <Peak>(new Peak[] { new Peak(114.1, 1114.1), new Peak(115.1, 1115.1), new Peak(116.1, 1116.1), new Peak(117.1, 1117.1) }.ToList()),
PeakInIsolationWindow = new PeakList <Peak>(new Peak[] { new Peak(1214.1, 114.1), new Peak(1215.1, 115.1), new Peak(1216.1, 116.1), new Peak(1217.1, 117.1) }.ToList())
{
Precursor = new PrecursorPeak()
{
MasterScan = 3,
Charge = 3,
Intensity = 4.0,
IsolationMass = 2800.1,
IsolationWidth = 3.0,
MonoIsotopicMass = 2879.1
}
}
};
t2[113] = 3.5;
t2[114] = 4.5;
t2[115] = 5.5;
t2[116] = 6.5;
t2[117] = 7.5;
t2[118] = 8.5;
t2[119] = 9.5;
t2[121] = 11.5;
tr = new IsobaricResult();
tr.Mode = "PQD";
tr.Add(t1);
tr.Add(t2);
}