private void DisplayScan()
{
if (this.reader == null)
{
return;
}
try
{
this.scan.ValidateComponent();
this.minPeakIntensity.ValidateComponent();
double rt = retentionTimes[this.scan.Value - 1];
PeakList <Peak> pkl = reader.GetPeakList(rt, this.minPeakIntensity.Value, topPeak.Value);
try
{
ZedGraphicExtension.ClearData(this.zgcScan, false);
var pplLight = new PointPairList();
pkl.ForEach(p => pplLight.Add(p.Mz, p.Intensity));
ZedGraphicExtension.AddIndividualLine(this.zgcScan, MyConvert.Format("Scan {0}", this.scan.Value), pplLight, Color.Blue, false);
if (reader.GetMsLevel(rt) == 2)
{
this.zgcScan.GraphPane.Title.Text = MyConvert.Format("Precursor MZ = {0:0.0000}", pkl.PrecursorMZ);
}
else
{
this.zgcScan.GraphPane.Title.Text = string.Empty;
}
}
finally
{
ZedGraphicExtension.UpdateGraph(this.zgcScan);
}
StringBuilder sb = new StringBuilder();
pkl.ForEach(m => sb.AppendLine(MyConvert.Format("{0:0.0000}\t{1:0.00}", m.Mz, m.Intensity)));
txtPeaks.Text = sb.ToString();
}
catch (Exception ex)
{
MessageBox.Show(ex.Message);
}
}
protected override void DoRealGo()
{
PeakList <MatchedPeak> pkl = GetAnnotatedPeakList();
var points = new PointPairList();
pkl.ForEach(p => {
if (p.PeakType == IonType.UNKNOWN)
{
points.Add(new PointPair(p.Mz, p.Intensity));
}
else
{
points.Add(new PointPair(p.Mz, p.Intensity, p.PeakType.ToString()));
}
});
zgcPeaks.InitGraph(new FileInfo(dtaFile.FullName).Name, "MZ", "Intensity", false, 1.0);
zgcPeaks.AddIndividualLine("", points, Color.Black, true);
}
public override IEnumerable <string> Process(string rootDirectory)
{
DirectoryInfo[] dirs = new DirectoryInfo(rootDirectory).GetDirectories("*.d");
Regex reg = new Regex(@"([\d-_]*)");
Progress.SetRange(1, dirs.Length);
int count = 0;
foreach (var dir in dirs)
{
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
count++;
Progress.SetPosition(count);
Progress.SetMessage("Processing " + dir.FullName + "...");
Match match = reg.Match(dir.Name);
string name = match.Groups[1].Value;
if (name.StartsWith("_"))
{
name = name.Substring(1);
}
string fileName = GetFileName(dir);
if (File.Exists(fileName))
{
continue;
}
double[] intensities = new double[maxPeakMz + 1];
using (StreamWriter sw = new StreamWriter(fileName))
{
rawFile.Open(dir.FullName);
sw.Write("{0:0}", rawFile.GetTotalIntensity());
for (int peak = minPeakMz; peak <= maxPeakMz; peak++)
{
sw.Write("\t{0}", peak);
}
sw.WriteLine();
for (int scan = rawFile.GetFirstSpectrumNumber(); scan <= rawFile.GetLastSpectrumNumber(); scan++)
{
if (Progress.IsCancellationPending())
{
sw.Close();
File.Delete(fileName);
throw new UserTerminatedException();
}
PeakList <Peak> pkl = rawFile.GetPeakList(scan, minPeakMz, maxPeakMz);
for (int peak = minPeakMz; peak <= maxPeakMz; peak++)
{
intensities[peak] = 0.0;
}
pkl.ForEach(m =>
{
int mz = (int)Math.Abs(m.Mz);
if (m.Intensity > intensities[mz])
{
intensities[mz] = m.Intensity;
}
});
sw.Write(scan);
for (int peak = minPeakMz; peak <= maxPeakMz; peak++)
{
sw.Write("\t{0:0.0}", intensities[peak]);
}
sw.WriteLine();
}
}
}
return(new string[] { rootDirectory });
}
