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 List <Tuple <double, PointPairList> > GetMS3Spectra(int scan)
{
var result = new List <Tuple <double, PointPairList> >();
for (int i = scan + 1; i <= lastScan; i++)
{
var mslevel = reader.GetMsLevel(i);
if (mslevel != 3)
{
break;
}
var pplms3 = new PointPairList();
var ms3spectra = GetPeakList(i);
var ms3precursor = reader.GetPrecursorPeak(i);
foreach (var m in ms3spectra)
{
pplms3.Add(new PointPair(m.Mz, m.Intensity));
}
result.Add(new Tuple <double, PointPairList>(ms3precursor.Mz, pplms3));
}
result.Sort((m1, m2) => m1.Item1.CompareTo(m2.Item1));
return(result);
}
public int Find(IRawFile reader, int scan)
{
int level = reader.GetMsLevel(scan);
var masterLevel = level - 1;
scan--;
int firstScan = reader.GetFirstSpectrumNumber();
while (scan >= firstScan)
{
var curlevel = reader.GetMsLevel(scan);
if (curlevel == masterLevel)
{
return(scan);
}
scan--;
}
return(0);
}
public static int FindNextFullScan(this IRawFile rawFile, int fromScan, int lastScan)
{
for (int scan = fromScan; scan <= lastScan; scan++)
{
if (1 == rawFile.GetMsLevel(scan))
{
return(scan);
}
}
return(-1);
}
public static int FindParentScan(this IRawFile rawFile, int fromScan, int firstScan, int msParentLevel)
{
for (int scan = fromScan; scan >= firstScan; scan--)
{
if (msParentLevel == rawFile.GetMsLevel(scan))
{
return(scan);
}
}
return(-1);
}
public static void FillScanLevels(List <ScanLevel> levels, IRawFile rawFile)
{
var firstScan = rawFile.GetFirstSpectrumNumber();
var lastScan = rawFile.GetLastSpectrumNumber();
for (var scan = firstScan; scan <= lastScan; scan++)
{
var mslevel = rawFile.GetMsLevel(scan);
levels.Add(new ScanLevel()
{
Scan = scan,
Level = mslevel
});
}
}
protected List <ScanLevel> GetRawScanLevels(IRawFile rawFile)
{
var result = new List <ScanLevel>();
var firstScan = rawFile.GetFirstSpectrumNumber();
var lastScan = rawFile.GetLastSpectrumNumber();
for (var scan = firstScan; scan <= lastScan; scan++)
{
var mslevel = rawFile.GetMsLevel(scan);
result.Add(new ScanLevel()
{
Scan = scan,
Level = mslevel
});
}
return(result);
}
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 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 fileName)
{
var result = new List <string>();
QueryItemListFormat format = new QueryItemListFormat();
FileInfo rawFile = new FileInfo(rawFileName);
Progress.SetMessage("Reading query product ion from " + fileName);
var queryItems = format.ReadFromFile(fileName);
using (IRawFile reader = RawFileFactory.GetRawFileReader(rawFileName))
{
reader.Open(rawFileName);
int firstSpectrumNumber = reader.GetFirstSpectrumNumber();
LipidPrecursorQuery queryFunc = new LipidPrecursorQuery(reader);
queryFunc.Progress = this.Progress;
char[] chars = new char[] { '\t' };
int curIndex = 0;
foreach (var query in queryItems)
{
Progress.SetMessage(MyConvert.Format("{0}/{1} - Querying precursor ions for product ion {2} ...", ++curIndex, queryItems.Count, query.ProductIonMz));
string savedQueryFile = GetQueryFileName(rawFileName, query.ProductIonMz, productIonPPM, precursorPPM);
PrecursorItemListXmlFormat pilFormat = new PrecursorItemListXmlFormat();
List <PrecursorItem> precursors;
if (!File.Exists(savedQueryFile))
{
precursors = queryFunc.QueryPrecursorFromProductIon(query, productIonPPM, precursorPPM);
pilFormat.WriteToFile(savedQueryFile, precursors);
}
else
{
precursors = pilFormat.ReadFromFile(savedQueryFile);
}
result.Add(savedQueryFile);
var precursorMzs = (from item in precursors
group item by item.PrecursorMZ into mzGroup
let count = mzGroup.Where(m => m.PrecursorIntensity > 0).Count()
orderby count descending
select new PrecursorArea {
PrecursorMz = mzGroup.Key, ScanCount = count, Area = 0.0
}).ToList();
//去掉冗余的precursor
for (int i = precursorMzs.Count - 1; i >= 0; i--)
{
if (precursorMzs[i].ScanCount >= 5)
{
break;
}
for (int j = 0; j < i; j++)
{
if (precursorMzs[j].ScanCount < 5)
{
break;
}
double ppm = PrecursorUtils.mz2ppm(precursorMzs[i].PrecursorMz, Math.Abs(precursorMzs[i].PrecursorMz - precursorMzs[j].PrecursorMz));
if (ppm < precursorPPM)
{
precursorMzs.RemoveAt(i);
break;
}
}
}
string savedDetailDir = FileUtils.ChangeExtension(savedQueryFile, "");
if (!Directory.Exists(savedDetailDir))
{
Directory.CreateDirectory(savedDetailDir);
}
for (int i = 0; i < precursorMzs.Count; i++)
{
Progress.SetMessage(MyConvert.Format("{0}/{1} {2} - {3}/{4} Get chromotograph for precursor {5} ...", curIndex, queryItems.Count, query.ProductIonMz, i + 1, precursorMzs.Count, precursorMzs[i].PrecursorMz));
string targetFile = savedDetailDir + "\\" + GetDetailFileName(rawFileName, precursorMzs[i].PrecursorMz);
var itemFormat = new LabelFreeSummaryItemXmlFormat();
LabelFreeSummaryItem item;
if (File.Exists(targetFile))
{
item = itemFormat.ReadFromFile(targetFile);
}
else
{
var ions = queryFunc.QueryChromotograph(precursorMzs[i].PrecursorMz, precursorPPM);
int continueCount = 0;
int firstIndex = -1;
for (int j = 0; j < ions.Count; j++)
{
if (ions[j].Intensity > 0)
{
if (firstIndex == -1)
{
firstIndex = j;
continueCount = 1;
}
else
{
continueCount++;
if (continueCount >= 5)
{
break;
}
}
}
else
{
firstIndex = -1;
continueCount = 0;
}
}
if (continueCount >= 5)
{
ions.RemoveRange(0, firstIndex);
}
continueCount = 0;
int lastIndex = -1;
for (int j = ions.Count - 1; j >= 0; j--)
{
if (ions[j].Intensity > 0)
{
if (lastIndex == -1)
{
lastIndex = j;
continueCount = 1;
}
else
{
continueCount++;
if (continueCount >= 5)
{
break;
}
}
}
else
{
lastIndex = -1;
continueCount = 0;
}
}
if (continueCount >= 5)
{
ions.RemoveRange(lastIndex + 1, ions.Count - lastIndex - 1);
}
//get full ms corresponding to identified ms/ms
var identified = new HashSet <int>();
foreach (var p in precursors)
{
if (p.PrecursorMZ == precursorMzs[i].PrecursorMz)
{
for (int j = p.Scan - 1; j >= firstSpectrumNumber; j--)
{
if (reader.GetMsLevel(j) == 1)
{
identified.Add(j);
break;
}
}
}
}
ions.ForEach(m =>
{
m.Identified = identified.Contains(m.Scan);
m.Enabled = true;
});
Debug.Assert(ions.FindAll(m => m.Identified == true).Count == identified.Count);
item = new LabelFreeSummaryItem()
{
RawFilename = rawFileName,
Sequence = MyConvert.Format("{0:0.0000}; {1:0.00}", query.ProductIonMz, query.MinRelativeIntensity)
};
item.AddRange(ions);
item.CalculatePPM(precursorMzs[i].PrecursorMz);
new LabelFreeSummaryItemXmlFormat().WriteToFile(targetFile, item);
}
precursorMzs[i].Area = item.GetArea();
string savedAreaFile = GetAreaFileName(rawFileName, query.ProductIonMz, productIonPPM, precursorPPM);
new PrecursorAreaListTextFormat().WriteToFile(savedAreaFile, precursorMzs);
}
}
return(result);
}
}
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 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 void TestGetMsLevel()
{
Assert.AreEqual(1, reader.GetMsLevel(1));
Assert.AreEqual(2, reader.GetMsLevel(3));
}
public List <PrecursorItem> QueryPrecursorFromProductIon(QueryItem productIon, double ppmProductTolerance, double ppmPrecursorTolerance)
{
List <PrecursorItem> result = new List <PrecursorItem>();
int firstScan = reader.GetFirstSpectrumNumber();
int lastScan = reader.GetLastSpectrumNumber();
double mzTolerance = PrecursorUtils.ppm2mz(productIon.ProductIonMz, ppmProductTolerance);
PeakList <Peak> lastFullScan = new PeakList <Peak>();
Progress.SetRange(firstScan, lastScan);
for (int scan = firstScan; scan <= lastScan; scan++)
{
Progress.SetPosition(scan);
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
//ignore ms 1
if (reader.GetMsLevel(scan) == 1)
{
lastFullScan = ReadScan(scan);
continue;
}
//read all peaks
PeakList <Peak> pkl = ReadScan(scan);
//find product ions
PeakList <Peak> productIons = pkl.FindPeak(productIon.ProductIonMz, mzTolerance);
if (productIons.Count == 0)
{
continue;
}
//get minimum product ion intensity
double maxIntensity = pkl.FindMaxIntensityPeak().Intensity;
double relativeIntensity = productIons.FindMaxIntensityPeak().Intensity / maxIntensity;
if (relativeIntensity < productIon.MinRelativeIntensity)
{
continue;
}
Peak peak = reader.GetPrecursorPeak(scan);
double precursorMzTolerance = PrecursorUtils.ppm2mz(peak.Mz, ppmPrecursorTolerance);
var precursorPkl = lastFullScan.FindPeak(peak.Mz, precursorMzTolerance);
bool isotopic = false;
if (precursorPkl.Count == 0)
{
isotopic = true;
precursorPkl = lastFullScan.FindPeak(peak.Mz - 1.0, precursorMzTolerance);
}
if (precursorPkl.Count == 0)
{
precursorPkl = lastFullScan.FindPeak(peak.Mz + 1.0, precursorMzTolerance);
}
var precursorInFullMs = precursorPkl.FindMaxIntensityPeak();
var precursor = new PrecursorItem()
{
Scan = scan,
ProductIonRelativeIntensity = relativeIntensity
};
if (isotopic && precursorInFullMs != null)
{
precursor.PrecursorMZ = precursorInFullMs.Mz;
precursor.IsIsotopic = true;
}
else
{
precursor.PrecursorMZ = peak.Mz;
precursor.IsIsotopic = false;
}
if (precursorInFullMs != null)
{
precursor.PrecursorIntensity = precursorInFullMs.Intensity;
}
result.Add(precursor);
}
var precursorMzs = from item in result
group item by item.PrecursorMZ into mzGroup
let mzcount = mzGroup.Where(m => m.PrecursorIntensity > 0).Count()
orderby mzcount descending
select mzGroup.Key;
foreach (var mz in precursorMzs)
{
double mzPrecursorTolerance = PrecursorUtils.ppm2mz(mz, ppmPrecursorTolerance);
foreach (var item in result)
{
if (!item.IsIsotopic)
{
continue;
}
if (Math.Abs(item.PrecursorMZ - mz) <= mzPrecursorTolerance)
{
item.PrecursorMZ = mz;
}
}
}
return(result);
}
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 });
}
