protected List <PeakList <Peak> > ReadTandemMassFromRaw(FileInfo rawFilename, List <int> ignoreScans)
{
string experimental = FileUtils.ChangeExtension(rawFilename.Name, "");
var result = new List <PeakList <Peak> >();
bool bReadAgain = false;
rawReader.Open(rawFilename.FullName);
try
{
int firstSpectrumNumber = rawReader.GetFirstSpectrumNumber();
int lastSpectrumNumber = rawReader.GetLastSpectrumNumber();
Progress.SetRange(firstSpectrumNumber, lastSpectrumNumber);
Progress.Begin();
try
{
for (int scan = firstSpectrumNumber; scan <= lastSpectrumNumber; scan++)
{
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
if (ignoreScans.Contains(scan))
{
continue;
}
Progress.SetPosition(scan);
int msLevel = rawReader.GetMsLevel(scan);
if (msLevel > 1)
{
PeakList <Peak> pkl;
try
{
pkl = rawReader.GetPeakList(scan);
}
catch (RawReadException ex)
{
ignoreScans.Add(ex.Scan);
File.WriteAllLines(GetIgnoreScanFile(rawFilename), (from i in ignoreScans
let s = i.ToString()
select s).ToArray());
bReadAgain = true;
break;
}
pkl.Precursor = rawReader.GetPrecursorPeakWithMasterScan(scan);
pkl.MsLevel = msLevel;
pkl.Experimental = experimental;
pkl.ScanTimes.Add(new ScanTime(scan, rawReader.ScanToRetentionTime(scan)));
pkl.ScanMode = rawReader.GetScanMode(scan);
if (pkl.PrecursorCharge == 0)
{
pkl.PrecursorCharge = PrecursorUtils.GuessPrecursorCharge(pkl, pkl.PrecursorMZ);
}
PeakList <Peak> pklProcessed = this.pklProcessor.Process(pkl);
if (null != pklProcessed && pklProcessed.Count > 0)
{
result.Add(pklProcessed);
}
}
}
}
finally
{
Progress.End();
}
}
finally
{
rawReader.Close();
}
if (bReadAgain)
{
return(ReadTandemMassFromRaw(rawFilename, ignoreScans));
}
else
{
return(result);
}
}
private int DoWritePeakList(IRawFile2 rawReader, int scan, string fileName, List <string> returnFiles, string experimental, int lastSpectrumNumber, List <int> ignoreScans, ref bool bReadAgain)
{
var result = scan + 1;
if (ignoreScans.Contains(scan))
{
return(result);
}
SetPosition(scan);
int msLevel = rawReader.GetMsLevel(scan);
if (!DoAcceptMsLevel(msLevel))
{
return(result);
}
//Console.WriteLine("Reading scan {0}", scan);
PeakList <Peak> pkl;
try
{
pkl = rawReader.GetPeakList(scan);
}
catch (RawReadException ex)
{
ignoreScans.Add(ex.Scan);
File.WriteAllLines(GetIgnoreScanFile(fileName), (from i in ignoreScans
let s = i.ToString()
select s).ToArray());
bReadAgain = true;
return(result);
}
pkl.MsLevel = msLevel;
pkl.Experimental = experimental;
pkl.ScanTimes.Add(new ScanTime(scan, rawReader.ScanToRetentionTime(scan)));
pkl.ScanMode = rawReader.GetScanMode(scan);
PeakList <Peak> pklProcessed;
if (msLevel > 1)
{
pkl.Precursor = new PrecursorPeak(rawReader.GetPrecursorPeak(scan));
if (pkl.PrecursorCharge == 0)
{
pkl.PrecursorCharge = PrecursorUtils.GuessPrecursorCharge(pkl, pkl.PrecursorMZ);
}
if (options.ExtractRawMS3 && pkl.MsLevel == 3)
{
pklProcessed = pkl;
}
else
{
pklProcessed = this.PeakListProcessor.Process(pkl);
}
}
else
{
pklProcessed = pkl;
}
if (null != pklProcessed && pklProcessed.Count > 0)
{
DoWritePeakList(rawReader, pklProcessed, fileName, returnFiles);
if (!options.MzXmlNestedScan)
{
var intent = GetScanIntent(pkl.MsLevel);
sw.WriteLine(intent + "</scan>");
}
while (result < lastSpectrumNumber && rawReader.GetMsLevel(result) > msLevel)
{
result = DoWritePeakList(rawReader, result, fileName, returnFiles, experimental, lastSpectrumNumber, ignoreScans, ref bReadAgain);
if (bReadAgain)
{
return(result);
}
}
if (options.MzXmlNestedScan)
{
var intent = GetScanIntent(pkl.MsLevel);
sw.WriteLine(intent + "</scan>");
}
}
return(result);
}
protected override void DoInitialize(IRawFile2 rawFile, string rawFileName)
{
var resultFile = GetResultFile(rawFile, rawFileName);
var scans = GetOutputScans(rawFile);
this.scanIndeies = new List <Pair <int, long> >();
var utf8WithoutBom = new System.Text.UTF8Encoding(false);
this.sw = new StreamWriter(resultFile, false, utf8WithoutBom);
this.sw.NewLine = "\n";
/*
* xml header and namespace info
*/
sw.WriteLine(@"<?xml version=""1.0"" encoding=""ISO-8859-1""?>");
sw.WriteLine(@"<mzXML xmlns=""http://sashimi.sourceforge.net/schema_revision/mzXML_3.1""");
sw.WriteLine(@" xmlns:xsi=""http://www.w3.org/2001/XMLSchema-instance""");
sw.WriteLine(@" xsi:schemaLocation=""http://sashimi.sourceforge.net/schema_revision/mzXML_3.1 http://sashimi.sourceforge.net/schema_revision/mzXML_3.1/mzXML_idx_3.1.xsd"" >");
int firstScan = rawFile.GetFirstSpectrumNumber();
int lastScan = rawFile.GetLastSpectrumNumber();
double startTime = rawFile.ScanToRetentionTime(firstScan) * 60;
double endTime = rawFile.ScanToRetentionTime(lastScan) * 60;
/*
* begin msRun
*/
sw.WriteLine(MyConvert.Format(@" <msRun scanCount=""{0}"" startTime=""PT{1:G6}S"" endTime=""PT{2:G6}S"" >", scans.Count, startTime, endTime));
string sha1;
try
{
sha1 = HashUtils.GetSHA1Hash(rawFileName).ToLower();
}
catch (Exception ex)
{
throw new Exception("Exception when calculating sha1 value of file " + rawFileName, ex);
}
/*
* parent (raw input) file
*/
//sw.WriteLine(@" <parentFile fileName=""file://DATA-PC/L/5168TP_mouse_phos_TMT/raw/6.raw"" fileType=""RAWData"" fileSha1=""f6db29dd3e26dec7eb16422138f0b2b06f02ba06"" />");
sw.WriteLine(@" <parentFile fileName=""file://{0}"" fileType=""RAWData"" fileSha1=""{1}""/>", rawFileName.Replace("\\", "/"), sha1);
if (rawFile is RawFileImpl)
{
var impl = rawFile as RawFileImpl;
/*
* mass spec instrument section
*/
// get the instrument model
string instModel = impl.GetInstModel();
// get acquisition software version
string instSoftVersion = impl.GetInstSoftwareVersion();
sw.WriteLine(@" <msInstrument>");
sw.WriteLine(@" <msManufacturer category=""msManufacturer"" value=""Thermo Finnigan"" />");
sw.WriteLine(@" <msModel category=""msModel"" value=""{0}"" />", instModel);
sw.WriteLine(@" <msIonisation category=""msIonisation"" value=""NSI"" />");
sw.WriteLine(@" <msMassAnalyzer category=""msMassAnalyzer"" value=""unknown"" />");
sw.WriteLine(@" <msDetector category=""msDetector"" value=""unknown"" />");
sw.WriteLine(@" <software type=""acquisition"" name=""Xcalibur"" version=""{0}"" />", instSoftVersion);
sw.WriteLine(@" </msInstrument>");
}
/*
* data processing info
*/
sw.WriteLine(@" <dataProcessing>");
sw.WriteLine(@" <software type=""conversion"" name=""{0}"" version=""{1}"" />", this.DataProcessingSoftware, this.DataProcessingSoftwareVersion);
foreach (string dataProcessingOperationName in this.dataProcessingOperations.Keys)
{
sw.WriteLine(MyConvert.Format(@" <processingOperation name=""{0}"" value=""{1}""/>", dataProcessingOperationName, this.dataProcessingOperations[dataProcessingOperationName]));
}
sw.WriteLine(" </dataProcessing>");
}
public double ScanToRetentionTime(int scan)
{
return(rawFile.ScanToRetentionTime(scan));
}
