public QuantificationChromotograph Build(IIdentifiedSpectrum mphit, IRawFile reader)
{
QuantificationChromotograph result = new QuantificationChromotograph();
var envelopes = builder.Build(mphit);
int startScan = mphit.Query.FileScan.FirstScan;
double mzTolerance = PrecursorUtils.ppm2mz(envelopes[0][0], ppmTolerance);
bool bFirst = true;
int firstScanNumber = reader.GetFirstSpectrumNumber();
int lastScanNumber = reader.GetLastSpectrumNumber();
//backward
for (int scan = startScan; scan >= firstScanNumber; scan--)
{
if (1 == reader.GetMsLevel(scan))
{
QuantificationScan qscan = reader.GetPeakList(scan).GetQuantificationScan(envelopes, mzTolerance);
if (!validate(qscan))
{
break;
}
if (bFirst)
{
qscan.IsIdentified = true;
bFirst = false;
}
result.Insert(0, qscan);
}
}
//forward
for (int scan = startScan + 1; scan <= lastScanNumber; scan++)
{
if (1 == reader.GetMsLevel(scan))
{
QuantificationScan qscan = reader.GetPeakList(scan).GetQuantificationScan(envelopes, mzTolerance);
if (!validate(qscan))
{
break;
}
result.Add(qscan);
}
}
if (result.Count > 0)
{
result.IdentifiedSpectra.Add(mphit);
}
return(result);
}
private O18QuanEnvelope GetCorrespondingEnvelope(IRawFile rawFile, double theoreticalMz, int charge, double mzTolerance, int scan)
{
PeakList <Peak> pkl = rawFile.GetPeakList(scan);
if (pkl.ScanTimes.Count == 0)
{
pkl.ScanTimes.Add(new ScanTime(scan, rawFile.ScanToRetentionTime(scan)));
}
PeakList <Peak> O16 = pkl.FindEnvelopeDirectly(theoreticalMz, charge, mzTolerance, 4, () => new Peak());
PeakList <Peak> O181 = pkl.FindEnvelopeDirectly(theoreticalMz + chargeGapMap1[charge], charge, mzTolerance, 2, () => new Peak());
for (int i = 2; i < 4; i++)
{
if (O16[i].Intensity < O181[i - 2].Intensity)
{
O16[i].Mz = O181[i - 2].Mz;
O16[i].Intensity = O181[i - 2].Intensity;
}
}
PeakList <Peak> O182 = pkl.FindEnvelopeDirectly(theoreticalMz + chargeGapMap2[charge], charge, mzTolerance, 2, () => new Peak());
O16.AddRange(O182);
return(new O18QuanEnvelope(O16));
}
public void TestGetPeakList()
{
PeakList <Peak> pkl = reader.GetPeakList(1);
Assert.AreEqual(397, pkl.Count);
Assert.AreEqual(301.1257, pkl[0].Mz, 0.0001);
}
private Spectrum.PeakList <Spectrum.Peak> GetPeakList(int scan)
{
var s1 = reader.GetPeakList(scan);
var s1max = s1.Max(l => l.Intensity);
s1.ForEach(m => m.Intensity = m.Intensity * 100.0 / s1max);
return(s1);
}
private PeakList <Peak> ReadScan(int scan)
{
if (pklMap.ContainsKey(scan))
{
return(pklMap[scan]);
}
PeakList <Peak> pkl = reader.GetPeakList(scan);
pkl.ScanTimes.Clear();
pkl.ScanTimes.Add(new ScanTime(scan, reader.ScanToRetentionTime(scan)));
pklMap[scan] = pkl;
return(pkl);
}
public static List <PeakList <Peak> > GetMS1List(this IRawFile reader)
{
var result = new List <PeakList <Peak> >();
var first = reader.GetFirstSpectrumNumber();
var last = reader.GetLastSpectrumNumber();
for (int i = first; i <= last; i++)
{
var mslevel = reader.GetMsLevel(i);
if (mslevel == 1)
{
var pkl = reader.GetPeakList(i);
result.Add(pkl);
}
}
return(result);
}
protected void DoGetOffsets(List <OffsetEntry> result, IRawFile reader, string msg)
{
var firstScan = reader.GetFirstSpectrumNumber();
var lastScan = reader.GetLastSpectrumNumber();
SetMessage(msg);
SetRange(firstScan, lastScan);
for (int scan = firstScan; scan <= lastScan; scan++)
{
if (reader.GetMsLevel(scan) == 1)
{
SetPosition(scan);
if (IsLoopStopped)
{
return;
}
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
var pkl = reader.GetPeakList(scan);
var rt = reader.ScanToRetentionTime(scan);
var offsetValues = GetOffsetsFromPeakList(pkl);
if (offsetValues.Count > 0)
{
var weightedPPM = GetWeightedPPM(offsetValues);
result.Add(new OffsetEntry(scan, rt, weightedPPM, offsetValues.Count));
}
else
{
result.Add(new OffsetEntry(scan, rt, 0, 0));
}
}
}
CalculateOffset(result, m => m.InitValue);
}
private bool AddPeaks(IRawFile rawReader, int scan, SimplePeakChro chro, bool bIdentified)
{
var pkl = rawReader.GetPeakList(scan, chro.Mz - chro.MzTolerance, chro.Mz + chro.MzTolerance);
if (pkl.Count == 0)
{
return(false);
}
var p = (from o in pkl
where (o.Charge == chro.Charge) || (o.Charge == 0)
orderby o.Intensity descending
select o).FirstOrDefault();
if (null == p)
{
return(false);
}
var iit = rawReader.GetIonInjectionTime(scan);
if (iit <= 0)
{
iit = 1.0;
}
chro.Peaks.Add(new ScanPeak()
{
Mz = p.Mz,
Intensity = p.Intensity,
Charge = p.Charge,
Scan = scan,
RetentionTime = rawReader.ScanToRetentionTime(scan),
IonInjectionTime = iit,
Identified = bIdentified
});
return(true);
}
private SilacPeakListPair GetLightHeavyPeakList(IRawFile rawFile, SilacCompoundInfo sci, int maxIndex, double mzTolerance, int scan, bool force = false)
{
PeakList <Peak> pkl = rawFile.GetPeakList(scan);
if (pkl.Count == 0)
{
return(null);
}
var scantime = new ScanTime(scan, rawFile.ScanToRetentionTime(scan));
PeakList <Peak> light = pkl.FindEnvelopeDirectly(sci.Light.Profile, option.ProfileLength, mzTolerance, () => new Peak());
//如果电荷不对，则认为该scan无效。
if (!CheckPeakListCharge(light, maxIndex, sci.Light.Charge) && !force)
{
return(null);
}
PeakList <Peak> heavy = pkl.FindEnvelopeDirectly(sci.Heavy.Profile, option.ProfileLength, mzTolerance, () => new Peak());
//如果电荷不对，则认为该scan无效。
if (!CheckPeakListCharge(heavy, maxIndex, sci.Heavy.Charge) && !force)
{
return(null);
}
//如果轻或者重的总强度为0，则认为该scan无效。
if ((0 == light.Sum(m => m.Intensity) || 0 == heavy.Sum(m => m.Intensity)) && !force)
{
return(null);
}
light.ScanTimes.Add(scantime);
heavy.ScanTimes.Add(scantime);
return(new SilacPeakListPair(light, heavy));
}
public FileData3 ReadFromFile(string fileName)
{
FileData3 result = new FileData3();
result.FileName = new FileInfo(fileName).Name;
rawFile.Open(fileName);
try
{
for (int scan = rawFile.GetFirstSpectrumNumber(); scan <= rawFile.GetLastSpectrumNumber(); scan++)
{
PeakList <Peak> pkl = rawFile.GetPeakList(scan, minPeakMz - 1, maxPeakMz + 1);
result.AddPeaks(minPeakMz, maxPeakMz, scan, pkl);
}
}
finally
{
rawFile.Close();
}
return(result);
}
public override IEnumerable <string> Process(string fileName)
{
string resultFile = new FileInfo(targetDir + "\\" + FileUtils.ChangeExtension(new FileInfo(fileName).Name, ".txt")).FullName;
reader.Open(fileName);
try
{
using (StreamWriter sw = new StreamWriter(resultFile))
{
sw.NewLine = "\n";
sw.WriteLine();
sw.WriteLine("FUNCTION 1");
int firstScan = reader.GetFirstSpectrumNumber();
int lastScan = reader.GetLastSpectrumNumber();
for (int i = firstScan; i <= lastScan; i++)
{
var pkl = reader.GetPeakList(i);
sw.WriteLine("");
sw.WriteLine("Scan\t\t{0}", i);
sw.WriteLine("Retention Time\t{0:0.000}", reader.ScanToRetentionTime(i));
sw.WriteLine("");
foreach (var peak in pkl)
{
sw.WriteLine("{0:0.0000}\t{1:0}", peak.Mz, peak.Intensity);
}
}
}
}
finally
{
reader.Close();
}
return(new string[] { resultFile });
}
public void Update(object sender, UpdateQuantificationItemEventArgs e)
{
var summary = e.Item as SilacQuantificationSummaryItem;
if (summary == null)
{
throw new ArgumentNullException("UpdateQuantificationItemEventArgs.Item cannot be null");
}
ZedGraphicExtension.ClearData(zgcGraph, false);
try
{
var envelope = summary.ObservedEnvelopes.Find(m => m.IsSelected);
if (envelope == null)
{
return;
}
double minMz = envelope.Light[0].Mz - 1.0;
double maxMz = envelope.Heavy[envelope.Heavy.Count - 1].Mz + 1.0;
zgcGraph.GraphPane.XAxis.Scale.Min = minMz;
zgcGraph.GraphPane.XAxis.Scale.Max = maxMz;
var pplLight = new PointPairList();
envelope.Light.ForEach(p => pplLight.Add(p.Mz, p.Intensity));
var pplHeavy = new PointPairList();
envelope.Heavy.ForEach(p => pplHeavy.Add(p.Mz, p.Intensity));
if (summary.SampleIsLight)
{
ZedGraphicExtension.AddIndividualLine(zgcGraph, "Sample", pplLight, SilacQuantificationConstants.SAMPLE_COLOR, false);
ZedGraphicExtension.AddIndividualLine(zgcGraph, "Reference", pplHeavy, SilacQuantificationConstants.REFERENCE_COLOR, false);
}
else
{
ZedGraphicExtension.AddIndividualLine(zgcGraph, "Sample", pplHeavy, SilacQuantificationConstants.SAMPLE_COLOR, false);
ZedGraphicExtension.AddIndividualLine(zgcGraph, "Reference", pplLight, SilacQuantificationConstants.REFERENCE_COLOR, false);
}
// Shift the text items up by 5 user scale units above the bars
const float shift = 5;
var ppl = new PointPairList();
ppl.AddRange(pplLight);
ppl.AddRange(pplHeavy);
for (int i = 0; i < ppl.Count; i++)
{
// format the label string to have 1 decimal place
string lab = ppl[i].X.ToString("0.00");
// create the text item (assumes the x axis is ordinal or text)
// for negative bars, the label appears just above the zero value
var text = new TextObj(lab, ppl[i].X, ppl[i].Y + shift);
// tell Zedgraph to use user scale units for locating the TextItem
text.Location.CoordinateFrame = CoordType.AxisXYScale;
// AlignH the left-center of the text to the specified point
text.Location.AlignH = AlignH.Left;
text.Location.AlignV = AlignV.Center;
text.FontSpec.Border.IsVisible = false;
text.FontSpec.Fill.IsVisible = false;
// rotate the text 90 degrees
text.FontSpec.Angle = 90;
// add the TextItem to the list
zgcGraph.GraphPane.GraphObjList.Add(text);
}
if (File.Exists(summary.RawFilename))
{
if (rawFile == null)
{
rawFile = new RawFileImpl(summary.RawFilename);
}
else if (!rawFile.FileName.Equals(summary.RawFilename))
{
rawFile.Open(summary.RawFilename);
}
PeakList <Peak> pkl = rawFile.GetPeakList(envelope.Light.ScanTimes[0].Scan);
var pplRaw = new PointPairList();
pplRaw.Add(minMz, 0.0);
for (int i = 0; i < pkl.Count; i++)
{
if (pkl[i].Mz < minMz)
{
continue;
}
else if (pkl[i].Mz > maxMz)
{
break;
}
pplRaw.Add(pkl[i].Mz, -pkl[i].Intensity);
}
pplRaw.Add(maxMz, 0.0);
ZedGraphicExtension.AddIndividualLine(zgcGraph, "PeakList From RawFile", pplRaw, SilacQuantificationConstants.IDENTIFIED_COLOR, true);
}
}
finally
{
ZedGraphicExtension.UpdateGraph(zgcGraph);
}
}
private List <SrmScan> GetMRMScans(string directory)
{
var fileName = GetPeakFileName(directory);
if (File.Exists(fileName))
{
SetProgressMessage("Reading scan from " + fileName + " ...");
return(new SrmScanFileFormat().ReadFromFile(fileName));
}
else
{
List <PeakList <Peak> > pkls = new List <PeakList <Peak> >();
SetProgressMessage("Reading scan from " + directory + " ...");
IRawFile reader = RawFileFactory.GetRawFileReader(directory);
try
{
var firstCount = reader.GetFirstSpectrumNumber();
var lastCount = reader.GetLastSpectrumNumber();
Progress.SetRange(firstCount, lastCount);
Progress.SetPosition(firstCount);
for (int i = firstCount; i <= lastCount; i++)
{
if (reader.GetMsLevel(i) != 2)
{
continue;
}
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
Progress.Increment(1);
var pkl = reader.GetPeakList(i);
var precursor = reader.GetPrecursorPeak(i);
if (precursor != null)
{
pkl.PrecursorMZ = precursor.Mz;
pkl.PrecursorCharge = precursor.Charge;
}
pkl.ScanTimes.Add(new ScanTime(i, reader.ScanToRetentionTime(i)));
pkls.Add(pkl);
}
List <SrmScan> result = new List <SrmScan>();
pkls.ForEach(m => m.ForEach(n => result.Add(new SrmScan(m.PrecursorMZ, n.Mz, m.ScanTimes[0].RetentionTime, n.Intensity, true))));
new SrmScanFileFormat().WriteToFile(fileName, result);
SetProgressMessage("finished.");
return(result);
}
finally
{
reader.Close();
}
}
}
public override IEnumerable <string> Process(string targetDir)
{
foreach (var raw in rawFiles)
{
List <RetentionTimePeak> waitingPeaks = new List <RetentionTimePeak>();
foreach (var peak in targetPeaks)
{
string file = GetTargetFile(targetDir, raw, peak);
if (force || !File.Exists(file))
{
waitingPeaks.Add(peak);
}
}
if (waitingPeaks.Count == 0)
{
continue;
}
rawReader.Open(raw);
try
{
int firstScan = rawReader.GetFirstSpectrumNumber();
int lastScan = rawReader.GetLastSpectrumNumber();
waitingPeaks.ForEach(m => m.Chromotographs.Clear());
for (int scan = firstScan; scan <= lastScan; scan++)
{
if (rawReader.GetMsLevel(scan) != 1)
{
continue;
}
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
PeakList <Peak> pkl = rawReader.GetPeakList(scan);
double rt = rawReader.ScanToRetentionTime(scan);
var st = new ScanTime(scan, rt);
foreach (var peak in waitingPeaks)
{
var env = pkl.FindEnvelopeDirectly(peak.PeakEnvelope, peak.MzTolerance, () => new Peak());
env.ScanTimes.Add(st);
peak.Chromotographs.Add(env);
}
}
waitingPeaks.ForEach(m => m.TrimPeaks());
}
finally
{
rawReader.Close();
}
foreach (var peak in waitingPeaks)
{
string file = GetTargetFile(targetDir, raw, peak);
new RetentionTimePeakXmlFormat().WriteToFile(file, peak);
}
}
return(new string[] { targetDir });
}
public override IEnumerable <string> Process(string rawFilename)
{
string ms1Filename = GetResultFilename(rawFilename);
string ms1IndexFilename = ms1Filename + ".index";
rawFile.Open(rawFilename);
try
{
int firstScan = rawFile.GetFirstSpectrumNumber();
int lastScan = rawFile.GetLastSpectrumNumber();
int firstFullScan = 0;
for (firstFullScan = firstScan; firstFullScan < lastScan; firstFullScan++)
{
if (rawFile.GetMsLevel(firstFullScan) == 1)
{
break;
}
}
if (firstFullScan >= lastScan)
{
return(new List <string>());
}
Progress.SetRange(firstScan, lastScan);
using (var sw = new StreamWriter(ms1Filename))
{
//write header
sw.Write("H\tCreationDate\t{0:m/dd/yyyy HH:mm:ss}\n", DateTime.Now);
sw.Write("H\tExtractor\t{0}\n", GetProgramName());
sw.Write("H\tExtractorVersion\t{0}\n", GetProgramVersion());
sw.Write("H\tComments\t{0} written by Quanhu Sheng, 2008-2009\n", GetProgramName());
sw.Write("H\tExtractorOptions\tMS1\n");
sw.Write("H\tAcquisitionMethod\tData-Dependent\n");
sw.Write("H\tDataType\tCentriod\n");
sw.Write("H\tScanType\tMS1\n");
sw.Write("H\tFirstScan\t{0}\n", firstScan);
sw.Write("H\tLastScan\t{0}\n", lastScan);
using (var swIndex = new StreamWriter(ms1IndexFilename))
{
for (int scan = firstScan; scan <= lastScan; scan++)
{
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
Progress.SetPosition(scan);
if (rawFile.GetMsLevel(scan) == 1)
{
sw.Flush();
swIndex.Write("{0}\t{1}\n", scan, sw.BaseStream.Position);
sw.Write("S\t{0}\t{0}\n", scan);
sw.Write("I\tRetTime\t{0:0.####}\n", rawFile.ScanToRetentionTime(scan));
PeakList <Peak> pkl = rawFile.GetPeakList(scan);
foreach (Peak p in pkl)
{
sw.Write("{0:0.0000} {1:0.0} {2}\n", p.Mz, p.Intensity, p.Charge);
}
}
}
}
}
}
finally
{
rawFile.Close();
}
Progress.End();
return(new[] { ms1Filename });
}
public override IEnumerable <string> Process(string targetDir)
{
foreach (var raw in rawFiles)
{
List <SimplePeakChro> waitingPeaks = new List <SimplePeakChro>();
foreach (var peak in targetPeaks)
{
string file = GetTargetFile(targetDir, raw, peak);
if (force || !File.Exists(file))
{
waitingPeaks.Add(peak);
}
else
{
var p = new SimplePeakChroXmlFormat().ReadFromFile(file);
peak.MaxRetentionTime = p.MaxRetentionTime;
peak.Peaks = p.Peaks;
}
}
if (waitingPeaks.Count == 0)
{
continue;
}
rawReader.Open(raw);
try
{
int firstScan = rawReader.GetFirstSpectrumNumber();
int lastScan = rawReader.GetLastSpectrumNumber();
var lastRt = rawReader.ScanToRetentionTime(lastScan);
waitingPeaks.ForEach(m =>
{
m.Peaks.Clear();
m.MaxRetentionTime = lastRt;
});
Progress.SetMessage("Processing chromotograph extracting...");
Progress.SetRange(firstScan, lastScan);
for (int scan = firstScan; scan <= lastScan; scan++)
{
if (rawReader.GetMsLevel(scan) != 1)
{
continue;
}
Progress.SetPosition(scan);
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
PeakList <Peak> pkl = rawReader.GetPeakList(scan);
double rt = rawReader.ScanToRetentionTime(scan);
foreach (var peak in waitingPeaks)
{
var env = pkl.FindPeak(peak.Mz, peak.MzTolerance);
Peak findPeak = new Peak(peak.Mz, 0.0, 0);
if (env.Count > 0)
{
if (env.Count == 1)
{
findPeak = env[0];
}
else
{
var charge = env.FindCharge(peak.Charge);
if (charge.Count > 0)
{
if (charge.Count == 1)
{
findPeak = charge[0];
}
else
{
findPeak = charge.FindMaxIntensityPeak();
}
}
else
{
findPeak = env.FindMaxIntensityPeak();
}
}
}
peak.Peaks.Add(new ScanPeak()
{
Mz = findPeak.Mz,
Intensity = findPeak.Intensity,
Scan = scan,
RetentionTime = rt,
Charge = findPeak.Charge,
PPMDistance = PrecursorUtils.mz2ppm(peak.Mz, findPeak.Mz - peak.Mz)
});
}
}
waitingPeaks.ForEach(m => m.TrimPeaks(minRetentionTime));
}
finally
{
rawReader.Close();
}
Progress.SetMessage("Saving ... ");
foreach (var peak in waitingPeaks)
{
string file = GetTargetFile(targetDir, raw, peak);
new SimplePeakChroXmlFormat().WriteToFile(file, peak);
}
Progress.SetMessage("Finished.");
Progress.End();
}
return(new string[] { targetDir });
}
public override void Update(object sender, UpdateQuantificationItemEventArgs e)
{
var summary = e.Item as O18QuantificationSummaryItem;
if (summary == null)
{
throw new ArgumentNullException("UpdateQuantificationItemEventArgs.Item cannot be null");
}
panel.InitGraphPane(this.title, "m/z", "Intensity", true, 0.0);
ZedGraphicExtension.ClearData(zgcGraph, false);
try
{
var envelope = summary.ObservedEnvelopes.Find(m => m.IsSelected);
if (envelope == null)
{
return;
}
panel.InitGraphPane(this.title + ", Scan=" + envelope.Scan.ToString(), "m/z", "Intensity", true, 0.0);
double minMz = envelope[0].Mz - 1.0;
double maxMz = envelope[envelope.Count - 1].Mz + 1.0;
zgcGraph.GraphPane.XAxis.Scale.Min = minMz;
zgcGraph.GraphPane.XAxis.Scale.Max = maxMz;
var ppl = new PointPairList();
envelope.ForEach(p => { if (p.Intensity > 0)
{
ppl.Add(p.Mz, p.Intensity);
}
});
panel.AddIndividualLine("Isotopic Envelope", ppl, Color.Red);
panel.AddTextUp(ppl, 5, (m => m.X.ToString("0.0000")));
var halfMax = (from env in envelope
select env.Intensity).Max() / 2;
ppl.Clear();
envelope.ForEach(p => { if (p.Intensity == 0)
{
ppl.Add(p.Mz, halfMax);
}
});
panel.AddIndividualLine("", ppl, defaultColor: Color.Red, dStyle: DashStyle.Dash);
panel.AddTextUp(ppl, 5, (m => m.X.ToString("0.0000")));
if (File.Exists(summary.RawFilename))
{
if (rawFile == null)
{
rawFile = RawFileFactory.GetRawFileReader(summary.RawFilename);
}
else if (!rawFile.FileName.Equals(summary.RawFilename))
{
rawFile.Close();
rawFile = RawFileFactory.GetRawFileReader(summary.RawFilename);
}
PeakList <Peak> pkl = rawFile.GetPeakList(envelope.ScanTimes[0].Scan);
var pplRaw = new PointPairList();
for (int i = 0; i < pkl.Count; i++)
{
if (pkl[i].Mz < minMz)
{
continue;
}
else if (pkl[i].Mz > maxMz)
{
break;
}
pplRaw.Add(pkl[i].Mz, -pkl[i].Intensity);
}
panel.AddIndividualLine("PeakList From RawFile", pplRaw, Color.Blue);
panel.AddTextDown(pplRaw, 5, (m => m.X.ToString("0.0000")));
/*
* foreach (var p in ppl)
* {
* if (p.Y == 0)
* {
* double ppm = double.MaxValue;
* double ppmAbs = Math.Abs(ppm);
* foreach (var pp in pplRaw)
* {
* double ppmCur = PrecursorUtils.mz2ppm(pp.X, pp.X - p.X);
* double ppmCurAbs = Math.Abs(ppmCur);
* if (Math.Abs(ppmCur) < ppmAbs)
* {
* ppm = ppmCur;
* ppmAbs = ppmCurAbs;
* }
*
* if (pp.X > p.X)
* {
* break;
* }
* }
*
* p.Z = ppm;
* }
* }
*/
}
}
finally
{
ZedGraphicExtension.UpdateGraph(zgcGraph);
}
}