public static IReaction GetReaction(IScanEvent scanEvent, int scanNumber)
{
IReaction reaction = null;
try
{
var order = (int)scanEvent.MSOrder;
reaction = scanEvent.GetReaction(order - 2);
}
catch (ArgumentOutOfRangeException)
{
Log.Warn("No reaction found for scan " + scanNumber);
}
return(reaction);
}
public static (ScanIndex, PrecursorScanCollection, ScanDependentsCollections) ScanIndicesPrecursorsDependents(IRawFileThreadManager rawFileAccessor)
{
Log.Information("Extracting scan indices");
ConcurrentDictionary <int, ScanData> allScans;
allScans = new ConcurrentDictionary <int, ScanData>();
Dictionary <int, ScanData> orphanScans = new Dictionary <int, ScanData>();
MSOrderType AnalysisOrder;
ConcurrentBag <int> ms1 = new ConcurrentBag <int>();
ConcurrentBag <int> ms2 = new ConcurrentBag <int>();
ConcurrentBag <int> ms3 = new ConcurrentBag <int>();
ConcurrentBag <int> msAny = new ConcurrentBag <int>();
ConcurrentDictionary <int, PrecursorScanData> precursorScans = new ConcurrentDictionary <int, PrecursorScanData>();
ConcurrentDictionary <int, IScanDependents> dependents = new ConcurrentDictionary <int, IScanDependents>();
var staticRawFile = rawFileAccessor.CreateThreadAccessor();
staticRawFile.SelectMsData();
// populate the scan indices
IEnumerable <int> scans = staticRawFile.GetFilteredScanEnumerator(staticRawFile.GetFilterFromString("")); // get all scans
// get ms order of experiment
Console.Write("Determing MS analysis order... ");
AnalysisOrder = (from x in scans select staticRawFile.GetScanEventForScanNumber(x).MSOrder).Max();
Console.WriteLine("Done!");
object lockTarget = new object();
ProgressIndicator P = new ProgressIndicator(scans.Count(), "Extracting scan indices");
int chunkSize = Constants.MultiThreading.ChunkSize(scans.Count());
var batches = scans.Chunk(chunkSize);
Parallel.ForEach(batches, batch =>
{
ScanData ms1ScanData;
ScanData ms2ScanData;
ScanData ms3ScanData;
foreach (int scan in batch)
{
//var rawFile = rawFileAccessor.CreateThreadAccessor();
using (var rawFile = rawFileAccessor.CreateThreadAccessor())
{
rawFile.SelectMsData();
IScanEvent scanEvent = rawFile.GetScanEventForScanNumber(scan);
ms1ScanData = new ScanData();
ms2ScanData = new ScanData();
ms3ScanData = new ScanData();
ms1ScanData.MassAnalyzer = scanEvent.MassAnalyzer;
ms1ScanData.MSOrder = scanEvent.MSOrder;
if (ms1ScanData.MSOrder == MSOrderType.Ms)
{
ms1.Add(scan);
msAny.Add(scan);
var scanDependents = rawFile.GetScanDependents(scan, 4);
dependents.TryAdd(scan, scanDependents);
// check if the ms1 scan has dependent scans
if (scanDependents == null)
{
// there are no scan dependents
ms1ScanData.HasDependents = false;
allScans.TryAdd(scan, ms1ScanData);
return;
}
else
{
ms1ScanData.HasDependents = true;
allScans.TryAdd(scan, ms1ScanData);
}
for (int i = 0; i < scanDependents.ScanDependentDetailArray.Length; i++)
{
int ms2Scan = scanDependents.ScanDependentDetailArray[i].ScanIndex;
ms2.Add(ms2Scan);
msAny.Add(ms2Scan);
if (AnalysisOrder == MSOrderType.Ms2) // it is ms2
{
ms2ScanData = new ScanData();
scanEvent = rawFile.GetScanEventForScanNumber(ms2Scan);
ms2ScanData.MassAnalyzer = scanEvent.MassAnalyzer;
ms2ScanData.MSOrder = scanEvent.MSOrder;
ms2ScanData.HasDependents = false;
ms2ScanData.HasPrecursors = true;
allScans.TryAdd(ms2Scan, ms2ScanData);
precursorScans.TryAdd(ms2Scan, new PrecursorScanData(ms2scan: ms2Scan, masterScan: scan));
}
else // it is ms3
{
var ms2Dependents = rawFile.GetScanDependents(ms2Scan, 4).ScanDependentDetailArray;
ms2ScanData = new ScanData();
scanEvent = rawFile.GetScanEventForScanNumber(ms2Scan);
ms2ScanData.MassAnalyzer = scanEvent.MassAnalyzer;
ms2ScanData.MSOrder = scanEvent.MSOrder;
ms2ScanData.HasPrecursors = true;
if (ms2Dependents.Length != 0) // make sure there is ms3 data
{
int ms3Scan = ms2Dependents[0].ScanIndex;
ms3.Add(ms3Scan);
msAny.Add(ms3Scan);
scanEvent = rawFile.GetScanEventForScanNumber(ms3Scan);
precursorScans.TryAdd(ms2Scan, new PrecursorScanData(ms2scan: ms2Scan, masterScan: scan));
precursorScans.TryAdd(ms3Scan, new PrecursorScanData(ms3scan: ms3Scan, ms2Scan: ms2Scan, masterScan: scan));
ms2ScanData.HasDependents = true;
ms3ScanData = new ScanData();
ms3ScanData.HasPrecursors = true;
ms3ScanData.MassAnalyzer = scanEvent.MassAnalyzer;
ms3ScanData.MSOrder = scanEvent.MSOrder;
allScans.TryAdd(ms3Scan, ms3ScanData);
}
else
{
// there is no ms3 scan, so we only add the ms2 scan
precursorScans.TryAdd(ms2Scan, new PrecursorScanData(ms2scan: ms2Scan, masterScan: scan));
ms2ScanData.HasDependents = false;
}
allScans.TryAdd(ms2Scan, ms2ScanData);
}
}
}
lock (lockTarget)
{
P.Update();
}
}
}
});
P.Done();
HashSet <int> allKeys = new HashSet <int>(allScans.Keys);
P = new ProgressIndicator(scans.Count(), "Checking for orphaned scans");
foreach (int scan in scans)
{
if (allKeys.Contains(scan))
{
continue;
}
else
{
ScanData scanData = new ScanData();
var scanEvent = staticRawFile.GetScanEventForScanNumber(scan);
scanData.MassAnalyzer = scanEvent.MassAnalyzer;
scanData.MSOrder = scanEvent.MSOrder;
orphanScans.Add(scan, scanData);
}
P.Update();
}
P.Done();
Console.WriteLine();
Console.WriteLine("================ Scan indexing report ================");
Console.WriteLine($"Total scans in file: {staticRawFile.RunHeaderEx.SpectraCount}");
Console.WriteLine($"Scans linked: {allScans.Count()}");
Console.WriteLine();
Console.WriteLine("Orphan scans:");
if (orphanScans.Count() > 0)
{
foreach (var scan in orphanScans)
{
Console.WriteLine($"\tScan: {scan.Key}, MSOrder: {scan.Value.MSOrder}");
}
Console.WriteLine("\nThe above scans will not be present in the output data. You should");
Console.WriteLine("manually check them to ensure they are not critical to you analysis.");
}
else
{
Console.WriteLine("None!");
}
Console.WriteLine();
if (staticRawFile.RunHeaderEx.SpectraCount == allScans.Count() + orphanScans.Count())
{
Console.WriteLine("All scans accounted for!");
}
else
{
Console.WriteLine($"Number of scans unaccounted for: {staticRawFile.RunHeaderEx.SpectraCount - (allScans.Count() + orphanScans.Count())}");
Console.WriteLine("If this number is alarming, please contact the RawTools authors\n" +
"by posting an issue at:\n" +
"https://github.com/kevinkovalchik/RawTools/issues");
}
Console.WriteLine("======================================================");
Console.WriteLine();
// we need to order the scan enumerators before sending them out
var orderedMs1 = ms1.ToList();
var orderedMs2 = ms2.ToList();
var orderedMs3 = ms3.ToList();
var orderedMsAny = msAny.ToList();
orderedMs1.Sort();
orderedMs2.Sort();
orderedMs3.Sort();
orderedMsAny.Sort();
ScanIndex scanIndex = new ScanIndex();
scanIndex.allScans = allScans.ConvertToDictionary();
scanIndex.AnalysisOrder = AnalysisOrder;
scanIndex.ScanEnumerators.Add(MSOrderType.Any, orderedMsAny.ToArray());
scanIndex.ScanEnumerators.Add(MSOrderType.Ms, orderedMs1.ToArray());
scanIndex.ScanEnumerators.Add(MSOrderType.Ms2, orderedMs2.ToArray());
scanIndex.ScanEnumerators.Add(MSOrderType.Ms3, orderedMs3.ToArray());
scanIndex.TotalScans = staticRawFile.RunHeaderEx.SpectraCount;
return(scanIndex, new PrecursorScanCollection(precursorScans), new ScanDependentsCollections(dependents));
}
public static ScanIndex ScanIndices(IRawDataPlus rawFile)
{
rawFile.SelectInstrument(Device.MS, 1);
Log.Information("Extracting scan indices");
Dictionary <int, ScanData> allScans;
allScans = new Dictionary <int, ScanData>();
MSOrderType AnalysisOrder;
List <int> ms1 = new List <int>();
List <int> ms2 = new List <int>();
List <int> ms3 = new List <int>();
List <int> msAny = new List <int>();
// populate the scan indices
IEnumerable <int> scans = rawFile.GetFilteredScanEnumerator(rawFile.GetFilterFromString("")); // get all scans
ProgressIndicator P = new ProgressIndicator(scans.Count(), "Extracting scan indices");
foreach (int scan in scans)
{
IScanEvent scanEvent = rawFile.GetScanEventForScanNumber(scan);
ScanData scanData = new ScanData();
scanData.MassAnalyzer = scanEvent.MassAnalyzer;
scanData.MSOrder = scanEvent.MSOrder;
allScans.Add(scan, scanData);
msAny.Add(scan);
if (allScans[scan].MSOrder == MSOrderType.Ms)
{
ms1.Add(scan);
}
if (allScans[scan].MSOrder == MSOrderType.Ms2)
{
ms2.Add(scan);
}
if (allScans[scan].MSOrder == MSOrderType.Ms3)
{
ms3.Add(scan);
}
P.Update();
}
P.Done();
// determine the msorder of the experiment
if ((ms1.Count > 0) & (ms2.Count == 0) & (ms3.Count == 0))
{
AnalysisOrder = MSOrderType.Ms;
}
else
{
if ((ms1.Count > 0) & (ms2.Count > 0) & (ms3.Count == 0))
{
AnalysisOrder = MSOrderType.Ms2;
}
else
{
AnalysisOrder = MSOrderType.Ms3;
}
}
ScanIndex scanIndex = new ScanIndex();
scanIndex.allScans = allScans;
scanIndex.AnalysisOrder = AnalysisOrder;
scanIndex.ScanEnumerators.Add(MSOrderType.Any, msAny.ToArray());
scanIndex.ScanEnumerators.Add(MSOrderType.Ms, ms1.ToArray());
scanIndex.ScanEnumerators.Add(MSOrderType.Ms2, ms2.ToArray());
scanIndex.ScanEnumerators.Add(MSOrderType.Ms3, ms3.ToArray());
return(scanIndex);
}
/// <summary>
/// Populate the scan list element
/// </summary>
/// <param name="scanNumber">the scan number</param>
/// <param name="scan">the scan object</param>
/// <param name="scanFilter">the scan filter</param>
/// <param name="scanEvent">the scan event</param>
/// <param name="monoisotopicMass">the monoisotopic mass</param>
/// <returns></returns>
private ScanListType ConstructScanList(int scanNumber, Scan scan, IScanFilter scanFilter, IScanEvent scanEvent,
double?monoisotopicMass)
{
// Scan list
var scanList = new ScanListType
{
count = "1",
scan = new ScanType[1],
cvParam = new CVParamType[1]
};
scanList.cvParam[0] = new CVParamType
{
accession = "MS:1000795",
cvRef = "MS",
name = "no combination",
value = ""
};
// Reference the right instrument configuration
if (!_massAnalyzers.TryGetValue(scanFilter.MassAnalyzer, out var instrumentConfigurationRef))
{
instrumentConfigurationRef = "IC1";
}
var scanType = new ScanType
{
instrumentConfigurationRef = instrumentConfigurationRef,
cvParam = new CVParamType[2]
};
scanType.cvParam[0] = new CVParamType
{
name = "scan start time",
accession = "MS:1000016",
value = _rawFile.RetentionTimeFromScanNumber(scanNumber).ToString(CultureInfo.InvariantCulture),
unitCvRef = "UO",
unitAccession = "UO:0000031",
unitName = "minute",
cvRef = "MS"
};
scanType.cvParam[1] = new CVParamType
{
name = "filter string",
accession = "MS:1000512",
value = scanEvent.ToString(),
cvRef = "MS"
};
if (monoisotopicMass.HasValue)
{
scanType.userParam = new UserParamType[1];
scanType.userParam[0] = new UserParamType
{
name = "[Thermo Trailer Extra]Monoisotopic M/Z:",
value = monoisotopicMass.ToString(),
type = "xsd:float"
};
}
// Scan window list
scanType.scanWindowList = new ScanWindowListType
{
count = 1,
scanWindow = new ParamGroupType[1]
};
var scanWindow = new ParamGroupType
{
cvParam = new CVParamType[2]
};
scanWindow.cvParam[0] = new CVParamType
{
name = "scan window lower limit",
accession = "MS:1000501",
value = scan.ScanStatistics.LowMass.ToString(CultureInfo.InvariantCulture),
cvRef = "MS",
unitAccession = "MS:1000040",
unitCvRef = "MS",
unitName = "m/z"
};
scanWindow.cvParam[1] = new CVParamType
{
name = "scan window upper limit",
accession = "MS:1000500",
value = scan.ScanStatistics.HighMass.ToString(CultureInfo.InvariantCulture),
cvRef = "MS",
unitAccession = "MS:1000040",
unitCvRef = "MS",
unitName = "m/z"
};
scanType.scanWindowList.scanWindow[0] = scanWindow;
scanList.scan[0] = scanType;
return(scanList);
}
/// <summary>
/// Open the given file and import scans into the reader.
/// </summary>
/// <returns></returns>
public System.Collections.IEnumerator GetEnumerator()
{
rawFile.SelectInstrument(ThermoBiz.Device.MS, 1);
// Get the first and last scan from the RAW file
int FirstScan = rawFile.RunHeaderEx.FirstSpectrum;
int LastScan = rawFile.RunHeaderEx.LastSpectrum;
for (int iScanNumber = FirstScan; iScanNumber <= LastScan; iScanNumber++)
{
ThermoBiz.Scan thermoScan = ThermoBiz.Scan.FromFile(rawFile, iScanNumber);
IScanFilter scanFilter = rawFile.GetFilterForScanNumber(iScanNumber);
IScanEvent scanEvent = rawFile.GetScanEventForScanNumber(iScanNumber);
if ((int)scanFilter.MSOrder == 1)
{
LastMS1 = iScanNumber;
}
Data.Scan scan = new Data.Scan()
{
ScanNumber = iScanNumber,
ScanEvent = (iScanNumber - LastMS1) + 1,
BasePeakIntensity = thermoScan.ScanStatistics.BasePeakIntensity,
BasePeakMz = thermoScan.ScanStatistics.BasePeakMass,
TotalIonCurrent = thermoScan.ScanStatistics.TIC,
LowestMz = thermoScan.ScanStatistics.LowMass,
HighestMz = thermoScan.ScanStatistics.HighMass,
StartMz = scanFilter.GetMassRange(0).Low,
EndMz = scanFilter.GetMassRange(0).High,
ScanType = ReadScanType(scanFilter.ToString()),
MsOrder = (int)scanFilter.MSOrder,
Polarity = (scanFilter.Polarity == PolarityType.Positive) ? Data.Polarity.Positive : Data.Polarity.Negative,
FilterLine = scanFilter.ToString(),
DetectorType = readDetectorType(scanFilter.MassAnalyzer),
RetentionTime = rawFile.RetentionTimeFromScanNumber(iScanNumber)
};
if (scan.MsOrder > 1)
{
// Get the current scan's activation method while ignoring upstream activation
scan.PrecursorActivationMethod = ConvertActivationType(scanFilter.GetActivation(scan.MsOrder - 2));
// handle dependent scans and not SPS (processed below)
scan.Precursors.Clear();
for (int i = 0; i < scanEvent.MassCount; ++i)
{
var reaction = scanEvent.GetReaction(i);
scan.CollisionEnergy = reaction.CollisionEnergy;
var precursor = new Data.Precursor
{
IsolationWidth = reaction.IsolationWidth,
IsolationMz = reaction.PrecursorMass,
Mz = reaction.PrecursorMass,
OriginalMz = reaction.PrecursorMass
};
scan.Precursors.Add(precursor);
}
}
ThermoBiz.RunHeader runHeader = rawFile.RunHeader;
ThermoBiz.LogEntry trailer = rawFile.GetTrailerExtraInformation(iScanNumber);
for (int i = 0; i < trailer.Length; i++)
{
var value = trailer.Values[i];
if (value == null)
{
continue;
}
switch (trailer.Labels[i])
{
case "Access ID":
int access_id = Convert.ToInt32(value);
if (access_id > 0)
{
scan.PrecursorMasterScanNumber = access_id;
}
break;
case "Scan Description:":
scan.Description = value.Trim();
break;
case "Ion Injection Time (ms):":
scan.IonInjectionTime = double.Parse(value);
break;
case "Elapsed Scan Time (sec):":
scan.ElapsedScanTime = double.Parse(value);
break;
case "Charge State:":
int charge = int.Parse(value);
foreach (var precursor in scan.Precursors)
{
precursor.Charge = charge;
precursor.OriginalCharge = precursor.Charge;
}
break;
case "Master Scan Number:":
scan.PrecursorMasterScanNumber = int.Parse(value);
break;
case "Master Index:":
scan.MasterIndex = int.Parse(value);
break;
case "Monoisotopic M/Z:":
if (Options.RawMonoMz && scan.Precursors.Count > 0)
{
double mz = double.Parse(value);
if (mz > 0)
{
scan.Precursors[0].Mz = mz;
}
}
break;
case "FAIMS CV:":
scan.FaimsCV = (int)double.Parse(value);
break;
case "FAIMS Voltage On:":
scan.FaimsState = (value == "No") ? Data.TriState.Off : Data.TriState.On;
break;
case "SPS Masses:":
string[] spsIonStringArray = value.TrimEnd(',').Split(',');
if (!string.IsNullOrWhiteSpace(spsIonStringArray[0]) && spsIonStringArray.Length > 0)
{
scan.Precursors.Clear();
for (int spsIndex = 0; spsIndex < spsIonStringArray.Length; spsIndex++)
{
if (double.TryParse(spsIonStringArray[spsIndex], out double spsIon))
{
scan.Precursors.Add(new Data.Precursor(spsIon, 0, 1));
}
}
}
break;
}
}
if (scan.PrecursorMasterScanNumber <= 0 && scan.MsOrder > 1)
{
// Try again to set the precursor scan.
SetPrecursorScanNumber(scan);
}
if (scan.MsOrder > 1 && scan.PrecursorMasterScanNumber > rawFile.RunHeader.FirstSpectrum && scan.PrecursorMasterScanNumber < rawFile.RunHeader.LastSpectrum)
{
// Fill precursor information
var parentScan = ThermoBiz.Scan.FromFile(rawFile, scan.PrecursorMasterScanNumber);
if (parentScan != null)
{
foreach (var precursor in scan.Precursors)
{
precursor.Intensity = GetMaxIntensity(parentScan, precursor.IsolationMz, precursor.IsolationWidth);
}
}
}
if (thermoScan.HasCentroidStream)
{
// High res data
CentroidsFromArrays(scan, thermoScan.CentroidScan.Masses, thermoScan.CentroidScan.Intensities, thermoScan.CentroidScan.Baselines, thermoScan.CentroidScan.Noises);
}
else
{
// Low res data
CentroidsFromArrays(scan, thermoScan.PreferredMasses, thermoScan.PreferredIntensities);
}
if (scan.PeakCount > 0)
{
scan.LowestMz = scan.Centroids[0].Mz;
scan.HighestMz = scan.Centroids[scan.PeakCount - 1].Mz;
}
yield return(scan);
}
}
public static void ExtractScanIndex(this RawDataCollection rawData, IRawDataPlus rawFile)
{
Log.Information("Extracting scan indices");
Dictionary <int, (MSOrderType MSOrder, MassAnalyzerType MassAnalyzer)> allScans;
allScans = new Dictionary <int, (MSOrderType MSOrder, MassAnalyzerType MassAnalyzer)>();
MSOrderType AnalysisOrder;
List <int> ms1 = new List <int>();
List <int> ms2 = new List <int>();
List <int> ms3 = new List <int>();
List <int> msAny = new List <int>();
// populate the scan indices
IEnumerable <int> scans = rawFile.GetFilteredScanEnumerator(rawFile.GetFilterFromString("")); // get all scans
foreach (int scan in scans)
{
IScanEvent scanEvent = rawFile.GetScanEventForScanNumber(scan);
allScans.Add(scan, (scanEvent.MSOrder, scanEvent.MassAnalyzer));
msAny.Add(scan);
if (allScans[scan].MSOrder == MSOrderType.Ms)
{
ms1.Add(scan);
}
if (allScans[scan].MSOrder == MSOrderType.Ms2)
{
ms2.Add(scan);
}
if (allScans[scan].MSOrder == MSOrderType.Ms3)
{
ms3.Add(scan);
}
}
// determine the msorder of the experiment
if ((ms1.Count > 0) & (ms2.Count == 0) & (ms3.Count == 0))
{
AnalysisOrder = MSOrderType.Ms;
}
else
{
if ((ms1.Count > 0) & (ms2.Count > 0) & (ms3.Count == 0))
{
AnalysisOrder = MSOrderType.Ms2;
}
else
{
AnalysisOrder = MSOrderType.Ms3;
}
}
rawData.scanIndex = new ScanIndex();
rawData.scanIndex.allScans = allScans;
rawData.scanIndex.AnalysisOrder = AnalysisOrder;
rawData.scanIndex.ScanEnumerators.Add(MSOrderType.Any, msAny.ToArray());
rawData.scanIndex.ScanEnumerators.Add(MSOrderType.Ms, ms1.ToArray());
rawData.scanIndex.ScanEnumerators.Add(MSOrderType.Ms2, ms2.ToArray());
rawData.scanIndex.ScanEnumerators.Add(MSOrderType.Ms3, ms3.ToArray());
// we need to check if it is a boxcar file because those have some scan index issues
bool isBoxCar = rawFile.GetScanEventForScanNumber(1).MassRangeCount > 1;
rawData.Performed.Add(Operations.ScanIndex);
if (isBoxCar)
{
Log.Information("Raw file looks like a boxcar run. Scan indices being adjusted to account for missing scan dependents.");
rawData.ExtractPrecursorScans(rawFile);
rawData.scanIndex.ScanEnumerators[rawData.scanIndex.AnalysisOrder] = rawData.precursorScans.Keys.ToArray();
}
}
//Console.ReadKey();
}
public static void getentityData(string resFilePath, string rawFile, string headerInfo, string paraIndex)
{
IRawDataPlus plus = RawFileReaderAdapter.FileFactory(rawFile);
plus.SelectInstrument(Device.MS, 1);
ArrayList indexOfpara = new ArrayList();
string[] selectIndex = paraIndex.Split(',');
foreach (string ele in selectIndex)
{
int index = Int32.Parse(ele);
indexOfpara.Add(index);
}
//string fileName = DateTime.Now.ToLocalTime().ToString().Replace("/", "").Replace(":", "").Replace(" ", "_") + ".csv";
FileStream stream = new FileStream(resFilePath, FileMode.Create, FileAccess.Write);
StreamWriter writer = new StreamWriter(stream, Encoding.UTF8);
headerInfo = "RT," + headerInfo;
headerInfo = "#," + headerInfo;
writer.WriteLine(headerInfo);
int offset = 0;
int maxoffset = plus.GetStatusLogEntriesCount();
while (offset < maxoffset)
{
string temp = "";
IStatusLogEntry statusLogEntry = plus.GetStatusLogEntry(offset);
temp += offset.ToString() + ",";
temp += statusLogEntry.Time.ToString() + ",";
foreach (int ele in indexOfpara)
{
temp += Convert.ToString(statusLogEntry.Values[ele]) + ",";
}
writer.WriteLine(temp.Substring(0, temp.Length - 1));
offset += 1;
}
writer.Close();
}
public static void showheaderInfo(string filePath)
{
IRawDataPlus plus = RawFileReaderAdapter.FileFactory(filePath);
plus.SelectInstrument(Device.MS, 1);
HeaderItem[] statuslogheaderinformation = plus.GetStatusLogHeaderInformation();
int index = 0;
Console.OutputEncoding = Encoding.UTF8;
while (index < statuslogheaderinformation.Length)
{
Console.WriteLine(statuslogheaderinformation[index].Label);
//headerInfo[index] = statuslogheaderinformation[index].Label;
//writer.WriteLine(statuslogheaderinformation[index].Label);
index += 1;
}
//writer.Close();
//while (true)
//{
//if (index >= statuslogheaderinformation.Length)
//{
// Console.WriteLine(plus.RunHeaderEx.FirstSpectrum.ToString());
// Console.WriteLine(plus.RunHeaderEx.LastSpectrum.ToString());
// Console.WriteLine(plus.RunHeaderEx.StartTime.ToString("F2"));
// Console.WriteLine(plus.RunHeaderEx.EndTime.ToString("F2"));
// Console.WriteLine(plus.RunHeaderEx.LowMass.ToString());
// Console.WriteLine(plus.RunHeaderEx.HighMass.ToString());
// break;
//}
// Console.WriteLine(statuslogheaderinformation[index].Label);
// writer.WriteLine(statuslogheaderinformation[index].Label);
// index++;
//}
//writer.Close();
}
public static void getTuneInfo(string filePath)
{
IRawDataPlus plus = RawFileReaderAdapter.FileFactory(filePath);
plus.SelectInstrument(Device.MS, 1);
string fileName = DateTime.Now.ToLocalTime().ToString().Replace("/", "").Replace(":", "").Replace(" ", "_") + ".txt";
FileStream stream = new FileStream(fileName, FileMode.Create, FileAccess.Write);
StreamWriter writer = new StreamWriter(stream, Encoding.UTF8);
writer.WriteLine("*********************InstrumentMethod(0)***************************");
writer.WriteLine(plus.GetInstrumentMethod(0));
writer.WriteLine("*********************InstrumentMethod(1)****************************");
writer.WriteLine(plus.GetInstrumentMethod(1));
HeaderItem[] tuneDataHeaderInfo = plus.GetTuneDataHeaderInformation();
writer.WriteLine("*********************Tune DATA ****************************");
int tuneCnt = plus.GetTuneDataCount();
for (int i = 0; i < tuneDataHeaderInfo.Length; ++i)
{
writer.WriteLine(tuneDataHeaderInfo[i].Label);
}
writer.Close();
}
public static void getMSdataFromScanNum(int startNum, int endNum, string filePath, double lowMS = 0.00, double highMS = 0.00)
{
IRawDataPlus plus = RawFileReaderAdapter.FileFactory(filePath);
//////////////////////////////////
plus.SelectInstrument(Device.MS, 1);
/////////////////////////////////
const string FilterStringIsolationMzPattern = @"ms2 (.*?)@";
int precursorMs1ScanNumber = 0;
double precursorMS= 0.00;
IReaction reaction = null;
var value = "";
var firstScanNumber = plus.RunHeaderEx.FirstSpectrum;
var lastScanNumber = plus.RunHeaderEx.LastSpectrum;
startNum = firstScanNumber;
endNum = lastScanNumber;
//int maxNum = plus.RunHeaderEx.LastSpectrum > endNum ? endNum : plus.RunHeaderEx.LastSpectrum;
LimitedSizeDictionary<string, int> precursorMs2ScanNumbers = new LimitedSizeDictionary<string, int>(40);
plus.SelectInstrument(Device.MS, 1);
if(highMS - 0.00 <= 0.01)
{
highMS = plus.RunHeaderEx.HighMass;
}
double maxMs = plus.RunHeaderEx.HighMass;
double minMs = plus.RunHeaderEx.LowMass;
lowMS = minMs;
highMS = maxMs;
string fileName = DateTime.Now.ToLocalTime().ToString().Replace("/", "").Replace(":", "").Replace(" ", "_") + ".csv";
FileStream stream = new FileStream(fileName, FileMode.Create, FileAccess.Write);
StreamWriter writer = new StreamWriter(stream, Encoding.UTF8);
writer.WriteLine("ScanNumber, RT, Mass, Resolution, Intensity, Noise, Filter,MSLevel,collisionEnergy, precursorNum,precursorMS");
while (startNum <= endNum)
{
var levelInfo = "";
var spectrumRef = "";
Scan scan = Scan.FromFile(plus, startNum);
IScanFilter scanFilter = plus.GetFilterForScanNumber(startNum);
IScanEvent scanEvent = plus.GetScanEventForScanNumber(startNum);
switch (scanFilter.MSOrder)
{
case MSOrderType.Ms:
// Keep track of scan number for precursor reference
precursorMs1ScanNumber = startNum;
reaction = scanEvent.GetReaction(0);
value = reaction.CollisionEnergy.ToString(CultureInfo.InvariantCulture).ToString();
levelInfo = scanFilter.MSOrder.ToString() + "," + "" + "," + "" + "," + "";
break;
case MSOrderType.Ms2:
// Keep track of scan number and isolation m/z for precursor reference
var result = Regex.Match(scanEvent.ToString(), FilterStringIsolationMzPattern);
if (result.Success)
{
if (precursorMs2ScanNumbers.ContainsKey(result.Groups[1].Value))
{
precursorMs2ScanNumbers.Remove(result.Groups[1].Value);
}
precursorMs2ScanNumbers.Add(result.Groups[1].Value, startNum);
}
spectrumRef = precursorMs1ScanNumber.ToString();
reaction = scanEvent.GetReaction(0);
value = reaction.CollisionEnergy.ToString(CultureInfo.InvariantCulture).ToString();
precursorMS = reaction.PrecursorMass;
levelInfo = scanFilter.MSOrder.ToString() + "," + value + "," + spectrumRef.ToString() + "," + precursorMS.ToString() ;
break;
case MSOrderType.Ms3:
var precursorMs2ScanNumber = precursorMs2ScanNumbers.Keys.FirstOrDefault(isolationMz => scanEvent.ToString().Contains(isolationMz));
spectrumRef = precursorMs2ScanNumbers[precursorMs2ScanNumber].ToString();
if (!precursorMs2ScanNumber.IsNullOrEmpty())
{
reaction = scanEvent.GetReaction(1);
}
else
{
throw new InvalidOperationException("Couldn't find a MS2 precursor scan for MS3 scan " + scanEvent);
}
precursorMS = reaction.PrecursorMass;
value = reaction.CollisionEnergy.ToString(CultureInfo.InvariantCulture).ToString();
levelInfo = scanFilter.MSOrder.ToString() + "," + value + "," + spectrumRef.ToString() + "," + precursorMS.ToString();
break;
default:
throw new ArgumentOutOfRangeException();
}
//var scanStatistics = plus.GetScanStatsForScanNumber(startNum);
//// Get the segmented (low res and profile) scan data
//var segmentedScan = plus.GetSegmentedScanFromScanNumber(startNum, scanStatistics);
//double[] masses = segmentedScan.Positions;
//double[] intensitis = segmentedScan.Intensities;
//Console.WriteLine(masses.Length);
//Console.WriteLine(intensitis.Length);
int cnt = 0;
if (scanFilter.MSOrder == MSOrderType.Ms)
{
while (cnt < scan.PreferredMasses.Length)
{
if (lowMS < scan.PreferredMasses[cnt] && scan.PreferredMasses[cnt] < highMS)
{
double rt = plus.RetentionTimeFromScanNumber(startNum);
double msval = scan.PreferredMasses[cnt];
double resolution = (scan.PreferredResolutions.Length == 0) ? 0.0 : scan.PreferredResolutions[cnt];
double intensity = (scan.PreferredIntensities.Length == 0) ? 0.0 : scan.PreferredIntensities[cnt];
double noise = (scan.PreferredNoises.Length == 0) ? 0.0 : scan.PreferredNoises[cnt];
//msval.ToString("f4");Return a number to a given precision,carry bit
//msval.ToString("n4");Return a number to a given precision,not carry bit
//writer.WriteLine("{0},{1},{2},{3},{4},{5},{6},{7}", startNum.ToString(), rt.ToString(),
// msval.ToString("n4"), resolution.ToString(), intensity.ToString(), noise.ToString(),
// scanFilter.ToString(), levelInfo);
writer.WriteLine("{0},{1},{2},{3}", startNum.ToString(), rt.ToString(), msval.ToString(), intensity.ToString());
}
cnt += 1;
}
}
writer.Flush();
startNum += 1;
}
writer.Close();
}
public static void getMSdataFromRT(double startRT, int endRT, string filePath, double lowMS = 0.00, double highMS = 0.00)
{
IRawDataPlus plus = RawFileReaderAdapter.FileFactory(filePath);
plus.SelectInstrument(Device.MS, 1);
if (highMS - 0.00 <= 0.01)
{
highMS = plus.RunHeaderEx.HighMass;
}
int startNum = plus.ScanNumberFromRetentionTime(startRT);
int endNum = plus.ScanNumberFromRetentionTime(endRT);
int maxNum = plus.RunHeaderEx.LastSpectrum > endNum ? endNum : plus.RunHeaderEx.LastSpectrum;
string fileName = DateTime.Now.ToLocalTime().ToString().Replace("/", "").Replace(":", "").Replace(" ", "_") + ".csv";
FileStream stream = new FileStream(fileName, FileMode.Create, FileAccess.Write);
StreamWriter writer = new StreamWriter(stream, Encoding.UTF8);
writer.WriteLine("ScanNumber, RT, Mass, Resolution, Intensity, Noise, Filter");
while (startNum <= endNum)
{
Scan scan = Scan.FromFile(plus, startNum);
string filter = plus.GetFilterForScanNumber(startNum).ToString();
int cnt = 0;
while (cnt < scan.PreferredMasses.Length)
{
if (lowMS < scan.PreferredMasses[cnt] && scan.PreferredMasses[cnt] < highMS)
{
double rt = plus.RetentionTimeFromScanNumber(startNum);
double msval = scan.PreferredMasses[cnt];
double resolution = (scan.PreferredResolutions.Length == 0) ? 0.0 : scan.PreferredResolutions[cnt];
double intensity = (scan.PreferredIntensities.Length == 0) ? 0.0 : scan.PreferredIntensities[cnt];
double noise = (scan.PreferredNoises.Length == 0) ? 0.0 : scan.PreferredNoises[cnt];
//writer.WriteLine("{0},{1},{2},{3},{4},{5},{6}", startNum.ToString(), rt.ToString(), msval.ToString(), resolution.ToString(), intensity.ToString(), noise.ToString(), filter.ToString());
}
}
writer.Flush();
startNum += 1;
}
writer.Close();
}
public static void getMSdataFromRT(double startRT, int endRT, string filePath, double lowMS = 0.00, double highMS = 0.00)
{
IRawDataPlus plus = RawFileReaderAdapter.FileFactory(filePath);
plus.SelectInstrument(Device.MS, 1);
if (highMS - 0.00 <= 0.01)
{
highMS = plus.RunHeaderEx.HighMass;
}
int startNum = plus.ScanNumberFromRetentionTime(startRT);
int endNum = plus.ScanNumberFromRetentionTime(endRT);
int maxNum = plus.RunHeaderEx.LastSpectrum > endNum ? endNum : plus.RunHeaderEx.LastSpectrum;
string fileName = DateTime.Now.ToLocalTime().ToString().Replace("/", "").Replace(":", "").Replace(" ", "_") + ".csv";
FileStream stream = new FileStream(fileName, FileMode.Create, FileAccess.Write);
StreamWriter writer = new StreamWriter(stream, Encoding.UTF8);
writer.WriteLine("ScanNumber, RT, Mass, Resolution, Intensity, Noise, Filter");
while (startNum <= endNum)
{
Scan scan = Scan.FromFile(plus, startNum);
string filter = plus.GetFilterForScanNumber(startNum).ToString();
int cnt = 0;
while (cnt < scan.PreferredMasses.Length)
{
if (lowMS < scan.PreferredMasses[cnt] && scan.PreferredMasses[cnt] < highMS)
{
double rt = plus.RetentionTimeFromScanNumber(startNum);
double msval = scan.PreferredMasses[cnt];
double resolution = (scan.PreferredResolutions.Length == 0) ? 0.0 : scan.PreferredResolutions[cnt];
double intensity = (scan.PreferredIntensities.Length == 0) ? 0.0 : scan.PreferredIntensities[cnt];
double noise = (scan.PreferredNoises.Length == 0) ? 0.0 : scan.PreferredNoises[cnt];
//writer.WriteLine("{0},{1},{2},{3},{4},{5},{6}", startNum.ToString(), rt.ToString(), msval.ToString(), resolution.ToString(), intensity.ToString(), noise.ToString(), filter.ToString());
writer.WriteLine("{0},{1},{2},{3}", startNum.ToString(), rt.ToString(), msval.ToString(), intensity.ToString());
}
cnt += 1;
}
startNum += 1;
}
writer.Close();
}
public static void getSRMIacdMZ(string filePath, double valMS,int recVal)
{
IRawDataPlus plus = RawFileReaderAdapter.FileFactory(filePath);
//////////////////////////////////
plus.SelectInstrument(Device.MS, 1);
/////////////////////////////////
var startNum = plus.RunHeaderEx.FirstSpectrum;
var endNum = plus.RunHeaderEx.LastSpectrum;
string fileName = DateTime.Now.ToLocalTime().ToString().Replace("/", "").Replace(":", "").Replace(" ", "_") + ".csv";
FileStream stream = new FileStream(fileName, FileMode.Create, FileAccess.Write);
StreamWriter writer = new StreamWriter(stream, Encoding.UTF8);
double[] masses = null;
double[] intensities = null;
writer.WriteLine("ScanNumber, RT, Mass, Intensity");
while (startNum <= endNum)
{
double rt = plus.RetentionTimeFromScanNumber(startNum);
IScanFilter scanFilter = plus.GetFilterForScanNumber(startNum);
if (scanFilter.MSOrder == MSOrderType.Ms)
{
Scan scan = Scan.FromFile(plus, startNum);
IScanEvent scanEvent = plus.GetScanEventForScanNumber(startNum);
if (scan.HasCentroidStream && (scanEvent.ScanData == ScanDataType.Centroid || scanEvent.ScanData == ScanDataType.Profile))
{
var centroidStream = plus.GetCentroidStream(startNum, false);
if (scan.CentroidScan.Length > 0)
{
masses = centroidStream.Masses;
intensities = centroidStream.Intensities;
}
}
else
{
// Get the scan statistics from the RAW file for this scan number
var scanStatistics = plus.GetScanStatsForScanNumber(startNum);
// Get the segmented (low res and profile) scan data
var segmentedScan = plus.GetSegmentedScanFromScanNumber(startNum, scanStatistics);
if (segmentedScan.Positions.Length > 0)
{
masses = segmentedScan.Positions;
intensities = segmentedScan.Intensities;
}
}
for(int i = 0; i < masses.Length; ++ i)
{
masses[i] = Double.Parse(masses[i].ToString("n4"));
}
int front = 0;
int rear = masses.Length - 1;
int mid = front + ((rear - front) >> 1);
bool findVal = false;
while(front <= rear)
{
if (Double.Equals(masses[mid],valMS))
{
findVal = true;
break;
}
else if(masses[mid] < valMS)
{
front = mid + 1;
}
else
{
rear = mid - 1;
}
mid = front + ((rear - front) >> 1);
}
if(findVal && intensities[mid] >= recVal)
{
writer.WriteLine("{0},{1},{2},{3}",startNum.ToString(), rt.ToString(), masses[mid].ToString(), intensities[mid].ToString());
}
}
writer.Flush();
startNum += 1;
}
writer.Close();
}
}
}