public static void WriteSpectrumAsRcode0(this IRawDataPlus rawFile, string filename)
{
int idxCharge = rawFile.GetIndexOfPattern();
int firstScanNumber = rawFile.RunHeaderEx.FirstSpectrum;
int lastScanNumber = rawFile.RunHeaderEx.LastSpectrum;
int charge = -1;
double pc = -1;
using (System.IO.StreamWriter file =
new System.IO.StreamWriter(filename))
{
for (int scanNumber = firstScanNumber; scanNumber < lastScanNumber; scanNumber++)
{
var scanTrailer = rawFile.GetTrailerExtraInformation(scanNumber);
var scanStatistics = rawFile.GetScanStatsForScanNumber(scanNumber);
var scanEvent = rawFile.GetScanEventForScanNumber(scanNumber);
var scanFilter = rawFile.GetFilterForScanNumber(scanNumber);
try{
var reaction0 = scanEvent.GetReaction(0);
pc = reaction0.PrecursorMass;
}
catch {
pc = -1;
}
try{
charge = int.Parse(scanTrailer.Values.ToArray()[idxCharge]);
}
catch {
charge = -1;
}
file.WriteLine("e$Spectrum[[{0}]] <- list(", scanNumber);
file.WriteLine("\tscan = {0};", scanNumber);
file.WriteLine("\tscanType = \"{0}\";", scanStatistics.ScanType.ToString());
file.WriteLine("\trtinseconds = {0};", Math.Round(scanStatistics.StartTime * 60 * 1000) / 1000);
file.WriteLine("\tprecursorMass = {0};", pc);
file.WriteLine("\tMSOrder = '{0}';", scanFilter.MSOrder.ToString());
file.WriteLine("\tcharge = {0}", charge);
file.WriteLine(")");
}
}
}
public static void GetIndex(this IRawDataPlus rawFile)
{
int firstScanNumber = rawFile.RunHeaderEx.FirstSpectrum;
int lastScanNumber = rawFile.RunHeaderEx.LastSpectrum;
int idx_CHARGE = rawFile.GetChargeIdx();
double charge, precursorMass;
Console.WriteLine("scan;scanType;rtinseconds;precursorMass;MSOrder;charge");
for (int scanNumber = firstScanNumber; scanNumber < lastScanNumber; scanNumber++)
{
var scanTrailer = rawFile.GetTrailerExtraInformation(scanNumber);
var scanStatistics = rawFile.GetScanStatsForScanNumber(scanNumber);
var scanEvent = rawFile.GetScanEventForScanNumber(scanNumber);
var scanFilter = rawFile.GetFilterForScanNumber(scanNumber);
try{
var reaction0 = scanEvent.GetReaction(0);
precursorMass = reaction0.PrecursorMass;
} catch {
precursorMass = -1;
}
try{
charge = int.Parse(scanTrailer.Values.ToArray()[idx_CHARGE]);
} catch {
charge = -1;
}
Console.WriteLine("{0};{1};{2};{3};{4};{5}", scanNumber,
scanStatistics.ScanType.ToString(),
Math.Round(scanStatistics.StartTime * 60 * 1000) / 1000,
precursorMass,
scanFilter.MSOrder.ToString(),
charge);
}
}
/// <summary>
/// Write the RAW file metadata to file.
/// <param name="rawFile">the RAW file object</param>
/// <param name="firstScanNumber">the first scan number</param>
/// <param name="lastScanNumber">the last scan number</param>
/// </summary>
public void WriteJsonMetada(IRawDataPlus rawFile, int firstScanNumber, int lastScanNumber)
{
// Get the start and end time from the RAW file
var startTime = rawFile.RunHeaderEx.StartTime;
var endTime = rawFile.RunHeaderEx.EndTime;
var metadata = new Metadata();
// File Properties
metadata.addFileProperty(new CVTerm("NCIT:C47922", "NCIT", "Pathname", rawFile.FileName));
metadata.addFileProperty(new CVTerm("NCIT:C25714", "NCIT", "Version",
rawFile.FileHeader.Revision.ToString()));
metadata.addFileProperty(new CVTerm("NCIT:C69199", "NCIT", "Content Creation Date",
rawFile.FileHeader.CreationDate.ToString()));
metadata.addFileProperty(new CVTerm("NCIT:C25365", "NCIT", "Description",
rawFile.FileHeader.FileDescription));
metadata.addScanSetting(new CVTerm("MS:1000016", "MS", "scan start time", startTime.ToString()));
metadata.addScanSetting(new CVTerm("MS:1000011", "MS", "mass resolution",
rawFile.RunHeaderEx.MassResolution.ToString()));
metadata.addScanSetting(new CVTerm("UO:0000002", "MS", "mass unit",
rawFile.GetInstrumentData().Units.ToString()));
metadata.addScanSetting(new CVTerm("PRIDE:0000478", "PRIDE", "Number of scans",
rawFile.RunHeaderEx.SpectraCount.ToString()));
metadata.addScanSetting(new CVTerm("PRIDE:0000479", "PRIDE", "MS scan range",
firstScanNumber + ":" + lastScanNumber));
metadata.addScanSetting(new CVTerm("PRIDE:0000484", "PRIDE", "Retention time range",
startTime + ":" + endTime));
metadata.addScanSetting(new CVTerm("PRIDE:0000485", "PRIDE", "Mz range",
rawFile.RunHeaderEx.LowMass + ":" + rawFile.RunHeaderEx.HighMass));
metadata.addInstrumentProperty(new CVTerm("MS:1000494", "MS", "Thermo Scientific instrument model",
rawFile.GetInstrumentData().Model));
metadata.addInstrumentProperty(new CVTerm("MS:1000496", "MS", "instrument attribute",
rawFile.GetInstrumentData().Name));
metadata.addInstrumentProperty(new CVTerm("MS:1000529", "MS", "instrument serial number",
rawFile.GetInstrumentData().SerialNumber));
var msTypes = new Dictionary <string, int>();
double minTime = 1000000000000000;
double maxTime = 0;
double minMz = 1000000000000000000;
double maxMz = 0;
double minCharge = 100000000000000;
double maxCharge = 0;
ICollection <CVTerm> fragmentationType = new HashSet <CVTerm>(CVTerm.CvTermComparer);
for (var scanNumber = firstScanNumber; scanNumber <= lastScanNumber; scanNumber++)
{
var time = rawFile.RetentionTimeFromScanNumber(scanNumber);
// Get the scan filter for this scan number
var scanFilter = rawFile.GetFilterForScanNumber(scanNumber);
// Get the scan event for this scan number
var scanEvent = rawFile.GetScanEventForScanNumber(scanNumber);
// Only consider MS2 spectra
if (msTypes.ContainsKey(scanFilter.MSOrder.ToString()))
{
var value = msTypes[scanFilter.MSOrder.ToString()];
value = value + 1;
msTypes[scanFilter.MSOrder.ToString()] = value;
}
else
{
msTypes.Add(scanFilter.MSOrder.ToString(), 1);
}
if (time > maxTime)
{
maxTime = time;
}
if (time < minTime)
{
minTime = time;
}
if (scanFilter.MSOrder == MSOrderType.Ms2)
{
fragmentationType.Add(ParseActivationType(scanFilter.GetActivation(0)));
if (scanEvent.ScanData == ScanDataType.Centroid || (scanEvent.ScanData == ScanDataType.Profile))
{
try
{
var reaction = scanEvent.GetReaction(0);
var precursorMass = reaction.PrecursorMass;
if (precursorMass > maxMz)
{
maxMz = precursorMass;
}
if (precursorMass < minMz)
{
minMz = precursorMass;
}
}
catch (ArgumentOutOfRangeException)
{
Log.Warn("No reaction found for scan " + scanNumber);
}
// trailer extra data list
var trailerData = rawFile.GetTrailerExtraInformation(scanNumber);
for (var i = 0; i < trailerData.Length; i++)
{
if (trailerData.Labels[i] == "Charge State:")
{
if (int.Parse(trailerData.Values[i]) > maxCharge)
{
maxCharge = int.Parse(trailerData.Values[i]);
}
if (int.Parse(trailerData.Values[i]) < minCharge)
{
minCharge = int.Parse(trailerData.Values[i]);
}
}
}
}
}
}
if (minCharge == 100000000000000)
{
minCharge = 0;
}
foreach (KeyValuePair <string, int> entry in msTypes)
{
if (entry.Key.Equals(MSOrderType.Ms.ToString()))
{
metadata.addMSData(new CVTerm("PRIDE:0000481", "PRIDE", "Number of MS1 spectra",
entry.Value.ToString()));
}
if (entry.Key.Equals(MSOrderType.Ms2.ToString()))
{
metadata.addMSData(new CVTerm("PRIDE:0000482", "PRIDE", "Number of MS2 spectra",
entry.Value.ToString()));
}
if (entry.Key.Equals(MSOrderType.Ms3.ToString()))
{
metadata.addMSData(new CVTerm("PRIDE:0000483", "PRIDE", "Number of MS3 spectra",
entry.Value.ToString()));
}
}
metadata.addScanSetting(fragmentationType);
metadata.addMSData(new CVTerm("PRIDE:0000472", "PRIDE", "MS min charge", minCharge.ToString()));
metadata.addMSData(new CVTerm("PRIDE:0000473", "PRIDE", "MS max charge", maxCharge.ToString()));
metadata.addMSData(new CVTerm("PRIDE:0000474", "PRIDE", "MS min RT", minTime.ToString()));
metadata.addMSData(new CVTerm("PRIDE:0000475", "PRIDE", "MS max RT", maxTime.ToString()));
metadata.addMSData(new CVTerm("PRIDE:0000476", "PRIDE", "MS min MZ", minMz.ToString()));
metadata.addMSData(new CVTerm("PRIDE:0000477", "PRIDE", "MS max MZ", maxMz.ToString()));
// Write the meta data to file
var json = JsonConvert.SerializeObject(metadata);
json.Replace("\r\n", "\n");
string metadataOutputPath;
if (_outputDirectory == null)
{
metadataOutputPath = _metadataFileName;
}
else
{
metadataOutputPath = _outputDirectory + "/" + _metadataFileName + "-metadata.json";
}
File.WriteAllText(metadataOutputPath, json);
}
/// <inheritdoc />
public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastScanNumber)
{
ConfigureWriter(".mgf");
using (Writer)
{
for (var scanNumber = firstScanNumber; scanNumber <= lastScanNumber; scanNumber++)
{
// Get each scan from the RAW file
var scan = Scan.FromFile(rawFile, scanNumber);
// Check to see if the RAW file contains label (high-res) data and if it is present
// then look for any data that is out of order
var time = rawFile.RetentionTimeFromScanNumber(scanNumber);
// Get the scan filter for this scan number
var scanFilter = rawFile.GetFilterForScanNumber(scanNumber);
// Get the scan event for this scan number
var scanEvent = rawFile.GetScanEventForScanNumber(scanNumber);
// Only consider MS2 spectra
if (scanFilter.MSOrder == MSOrderType.Ms2)
{
if (scanEvent.ScanData == ScanDataType.Centroid ||
(scanEvent.ScanData == ScanDataType.Profile && !ParseInput.ExcludeProfileData))
{
Writer.WriteLine("BEGIN IONS");
Writer.WriteLine($"TITLE={ConstructSpectrumTitle(scanNumber)}");
Writer.WriteLine($"SCAN={scanNumber}");
Writer.WriteLine($"RTINSECONDS={time * 60}");
// Get the reaction information for the first precursor
try
{
var reaction = scanEvent.GetReaction(0);
var precursorMass = reaction.PrecursorMass;
Writer.WriteLine($"PEPMASS={precursorMass:F7}");
}
catch (ArgumentOutOfRangeException exception)
{
Log.Warn("No reaction found for scan " + scanNumber);
}
// trailer extra data list
var trailerData = rawFile.GetTrailerExtraInformation(scanNumber);
for (var i = 0; i < trailerData.Length; i++)
{
if (trailerData.Labels[i] == "Charge State:")
{
if (Convert.ToInt32(trailerData.Values[i]) > 0)
{
Writer.WriteLine($"CHARGE={trailerData.Values[i]}+");
}
}
}
// Check if the scan has a centroid stream
if (scan.HasCentroidStream)
{
var centroidStream = rawFile.GetCentroidStream(scanNumber, false);
if (scan.CentroidScan.Length > 0)
{
for (var i = 0; i < centroidStream.Length; i++)
{
Writer.WriteLine(
$"{centroidStream.Masses[i]:F7} {centroidStream.Intensities[i]:F10}");
}
}
}
// Otherwise take the profile data
else
{
// Get the scan statistics from the RAW file for this scan number
var scanStatistics = rawFile.GetScanStatsForScanNumber(scanNumber);
// Get the segmented (low res and profile) scan data
var segmentedScan = rawFile.GetSegmentedScanFromScanNumber(scanNumber, scanStatistics);
for (var i = 0; i < segmentedScan.Positions.Length; i++)
{
Writer.WriteLine(
$"{segmentedScan.Positions[i]:F7} {segmentedScan.Intensities[i]:F10}");
}
}
Writer.WriteLine("END IONS");
}
}
}
}
}
/// <summary>
/// Write the RAW file metadata to file.
/// <param name="rawFile">the RAW file object</param>
/// <param name="firstScanNumber">the first scan number</param>
/// <param name="lastScanNumber">the last scan number</param>
/// </summary>
public void WriteJsonMetada(IRawDataPlus rawFile, int firstScanNumber, int lastScanNumber)
{
// Get the start and end time from the RAW file
var startTime = rawFile.RunHeaderEx.StartTime;
var endTime = rawFile.RunHeaderEx.EndTime;
var metadata = new Metadata();
/** File Properties **/
metadata.addFileProperty("path", rawFile.FileName);
metadata.addFileProperty("version", rawFile.FileHeader.Revision.ToString());
metadata.addFileProperty("creation-date", rawFile.FileHeader.CreationDate.ToString());
metadata.addFileProperty("number-instruments", rawFile.InstrumentCount.ToString());
metadata.addFileProperty("description", rawFile.FileHeader.FileDescription);
/** Sample Properties **/
metadata.addSampleProperty("name", rawFile.SampleInformation.SampleName);
metadata.addSampleProperty("id", rawFile.SampleInformation.SampleId);
metadata.addSampleProperty("type", rawFile.SampleInformation.SampleType.ToString());
metadata.addSampleProperty("comment", rawFile.SampleInformation.Comment);
metadata.addSampleProperty("vial", rawFile.SampleInformation.Vial);
metadata.addSampleProperty("volume", rawFile.SampleInformation.SampleVolume.ToString());
metadata.addSampleProperty("injection-volume", rawFile.SampleInformation.InjectionVolume.ToString());
metadata.addSampleProperty("row-number", rawFile.SampleInformation.RowNumber.ToString());
metadata.addSampleProperty("dilution-factor", rawFile.SampleInformation.DilutionFactor.ToString());
metadata.addScanSetting("start-time", new CVTerm("MS:1000016", "MS", "scan start time", startTime.ToString()));
metadata.addScanSetting("resolution", new CVTerm("MS:1000011", "MS", "mass resolution", rawFile.RunHeaderEx.MassResolution.ToString()));
metadata.addScanSetting("tolerance-unit", new CVTerm("UO:0000002", "MS", "mass unit", rawFile.GetInstrumentData().Units.ToString()));
metadata.addScanSetting("number-scans", rawFile.RunHeaderEx.SpectraCount.ToString());
metadata.addScanSetting("scan-range", firstScanNumber + ":" + lastScanNumber);
metadata.addScanSetting("time-range", startTime + ":" + endTime);
metadata.addScanSetting("mass-range", rawFile.RunHeaderEx.LowMass + ":" + rawFile.RunHeaderEx.HighMass);
metadata.addInstrumentProperty("model", new CVTerm("MS:1000494", "MS", "Thermo Scientific instrument model", rawFile.GetInstrumentData().Model));
metadata.addInstrumentProperty("name", new CVTerm("MS:1000496", "MS", "instrument attribute", rawFile.GetInstrumentData().Name));
metadata.addInstrumentProperty("serial", new CVTerm("MS:1000529", "MS", "instrument serial number", rawFile.GetInstrumentData().SerialNumber));
var msTypes = new Dictionary <string, int>();
double minTime = 1000000000000000;
double maxTime = 0;
double minMz = 1000000000000000000;
double maxMz = 0;
double minCharge = 100000000000000;
double maxCharge = 0;
HashSet <CVTerm> fragmentationType = new HashSet <CVTerm>(CVTerm.CvTermComparer);
for (var scanNumber = firstScanNumber; scanNumber <= lastScanNumber; scanNumber++)
{
var time = rawFile.RetentionTimeFromScanNumber(scanNumber);
// Get the scan filter for this scan number
var scanFilter = rawFile.GetFilterForScanNumber(scanNumber);
// Get the scan event for this scan number
var scanEvent = rawFile.GetScanEventForScanNumber(scanNumber);
// Only consider MS2 spectra
if (msTypes.ContainsKey(scanFilter.MSOrder.ToString()))
{
var value = msTypes[scanFilter.MSOrder.ToString()];
value = value + 1;
msTypes[scanFilter.MSOrder.ToString()] = value;
}
else
{
msTypes.Add(scanFilter.MSOrder.ToString(), 1);
}
if (time > maxTime)
{
maxTime = time;
}
if (time < minTime)
{
minTime = time;
}
if (scanFilter.MSOrder == MSOrderType.Ms2)
{
fragmentationType.Add(parseActivationType(scanFilter.GetActivation(0)));
if (scanEvent.ScanData == ScanDataType.Centroid || (scanEvent.ScanData == ScanDataType.Profile))
{
try
{
var reaction = scanEvent.GetReaction(0);
var precursorMass = reaction.PrecursorMass;
if (precursorMass > maxMz)
{
maxMz = precursorMass;
}
if (precursorMass < minMz)
{
minMz = precursorMass;
}
}
catch (ArgumentOutOfRangeException exception)
{
Log.Warn("No reaction found for scan " + scanNumber);
}
// trailer extra data list
var trailerData = rawFile.GetTrailerExtraInformation(scanNumber);
for (var i = 0; i < trailerData.Length; i++)
{
if (trailerData.Labels[i] == "Charge State:")
{
if (Int32.Parse(trailerData.Values[i]) > maxCharge)
{
maxCharge = Int32.Parse(trailerData.Values[i]);
}
if (Int32.Parse(trailerData.Values[i]) < minCharge)
{
maxCharge = Int32.Parse(trailerData.Values[i]);
}
}
}
}
}
}
if (minCharge == 100000000000000)
{
minCharge = 0;
}
metadata.addMSData("ms-number", msTypes);
metadata.addMSData("activation-ypes", fragmentationType);
metadata.addMSData("min-charge", minCharge);
metadata.addMSData("max-charge", maxCharge);
metadata.addMSData("min-Time", minTime);
metadata.addMSData("max-Time", maxTime);
metadata.addMSData("min-Mz", minMz);
metadata.addMSData("max-Mz", maxMz);
// Write the meta data to file
var json = JsonConvert.SerializeObject(metadata);
json.Replace("\r\n", "\n");
File.WriteAllText(_outputDirectory + "/" + _rawFileNameWithoutExtension + "-metadata.json", json);
}
/// <inheritdoc />
public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastScanNumber)
{
ConfigureWriter(".mgf");
using (Writer)
{
for (var scanNumber = firstScanNumber; scanNumber <= lastScanNumber; scanNumber++)
{
// Get each scan from the RAW file
var scan = Scan.FromFile(rawFile, scanNumber);
// Check to see if the RAW file contains label (high-res) data and if it is present
// then look for any data that is out of order
var time = rawFile.RetentionTimeFromScanNumber(scanNumber);
// Get the scan filter for this scan number
var scanFilter = rawFile.GetFilterForScanNumber(scanNumber);
// Get the scan event for this scan number
var scanEvent = rawFile.GetScanEventForScanNumber(scanNumber);
switch (scanFilter.MSOrder)
{
case MSOrderType.Ms:
// Keep track of scan number for precursor reference
_precursorScanNumber = scanNumber;
break;
case MSOrderType.Ms2:
{
if (scanEvent.ScanData == ScanDataType.Centroid ||
(scanEvent.ScanData == ScanDataType.Profile &&
(scan.HasCentroidStream || ParseInput.OutputFormat != OutputFormat.MGFNoProfileData)))
{
Writer.WriteLine("BEGIN IONS");
Writer.WriteLine($"TITLE={ConstructSpectrumTitle(scanNumber)}");
Writer.WriteLine($"SCANS={scanNumber}");
Writer.WriteLine($"RTINSECONDS={(time * 60).ToString(CultureInfo.InvariantCulture)}");
// Get the reaction information for the first precursor
try
{
var reaction = scanEvent.GetReaction(0);
var precursorMass = reaction.PrecursorMass;
Writer.WriteLine("PEPMASS=" +
precursorMass.ToString("0.0000000", CultureInfo.InvariantCulture));
//var precursorIntensity = 0.0;
//GetPrecursorIntensity(rawFile, _precursorScanNumber, precursorMass);
//Writer.WriteLine(precursorIntensity != null
// ? $"PEPMASS={precursorMass:F7} {precursorIntensity}"
// : $"PEPMASS={precursorMass:F7}");
}
catch (ArgumentOutOfRangeException exception)
{
Log.Warn("No reaction found for scan " + scanNumber);
}
// trailer extra data list
var trailerData = rawFile.GetTrailerExtraInformation(scanNumber);
for (var i = 0; i < trailerData.Length; i++)
{
if (trailerData.Labels[i] == "Charge State:")
{
if (Convert.ToInt32(trailerData.Values[i]) > 0)
{
Writer.WriteLine($"CHARGE={trailerData.Values[i]}+");
}
}
}
// write the filter string
//Writer.WriteLine($"SCANEVENT={scanEvent.ToString()}");
// Check if the scan has a centroid stream
if (scan.HasCentroidStream)
{
var centroidStream = rawFile.GetCentroidStream(scanNumber, false);
if (scan.CentroidScan.Length > 0)
{
for (var i = 0; i < centroidStream.Length; i++)
{
Writer.WriteLine(
centroidStream.Masses[i].ToString("0.0000000",
CultureInfo.InvariantCulture)
+ " "
+ centroidStream.Intensities[i].ToString("0.0000000",
CultureInfo.InvariantCulture));
}
}
}
// Otherwise take the profile data
else
{
// Get the scan statistics from the RAW file for this scan number
var scanStatistics = rawFile.GetScanStatsForScanNumber(scanNumber);
// Get the segmented (low res and profile) scan data
var segmentedScan =
rawFile.GetSegmentedScanFromScanNumber(scanNumber, scanStatistics);
for (var i = 0; i < segmentedScan.Positions.Length; i++)
{
Writer.WriteLine(
segmentedScan.Positions[i].ToString("0.0000000",
CultureInfo.InvariantCulture)
+ " "
+ segmentedScan.Intensities[i].ToString("0.0000000000",
CultureInfo.InvariantCulture));
}
}
Writer.WriteLine("END IONS");
}
break;
}
}
}
}
}
/// <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);
}
}
//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);
//var masses = segmentedScan.Positions;
//var intensitis = segmentedScan.Intensities;
//Console.WriteLine(masses.Length);
//Console.WriteLine(intensitis.Length);
//Console.WriteLine(filterObj.MSOrder);
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},{7}", startNum.ToString(), rt.ToString(),
msval.ToString(), resolution.ToString(), intensity.ToString(), noise.ToString(),
scanFilter.ToString(), levelInfo);
}
cnt += 1;
}
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());
}
cnt += 1;
}
startNum += 1;
}
writer.Close();
}
/// <inheritdoc />
public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastScanNumber)
{
ConfigureWriter(".mgf");
using (Writer)
{
Log.Info("Processing " + (lastScanNumber - firstScanNumber + 1) + " scans");
var lastScanProgress = 0;
for (var scanNumber = firstScanNumber; scanNumber <= lastScanNumber; scanNumber++)
{
if (ParseInput.LogFormat == LogFormat.DEFAULT)
{
var scanProgress = (int)((double)scanNumber / (lastScanNumber - firstScanNumber + 1) * 100);
if (scanProgress % ProgressPercentageStep == 0)
{
if (scanProgress != lastScanProgress)
{
Console.Write("" + scanProgress + "% ");
lastScanProgress = scanProgress;
}
}
}
// Get each scan from the RAW file
var scan = Scan.FromFile(rawFile, scanNumber);
// Check to see if the RAW file contains label (high-res) data and if it is present
// then look for any data that is out of order
var time = rawFile.RetentionTimeFromScanNumber(scanNumber);
// Get the scan filter for this scan number
var scanFilter = rawFile.GetFilterForScanNumber(scanNumber);
// Get the scan event for this scan number
var scanEvent = rawFile.GetScanEventForScanNumber(scanNumber);
// precursor reference
var spectrumRef = "";
//keeping track of precursor scan
switch (scanFilter.MSOrder)
{
case MSOrderType.Ms:
// Keep track of scan number for precursor reference
_precursorMs1ScanNumber = scanNumber;
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, scanNumber);
}
spectrumRef = ConstructSpectrumTitle((int)Device.MS, 1, _precursorMs1ScanNumber);
break;
case MSOrderType.Ms3:
var precursorMs2ScanNumber = _precursorMs2ScanNumbers.Keys.FirstOrDefault(
isolationMz => scanEvent.ToString().Contains(isolationMz));
if (!precursorMs2ScanNumber.IsNullOrEmpty())
{
spectrumRef = ConstructSpectrumTitle((int)Device.MS, 1, _precursorMs2ScanNumbers[precursorMs2ScanNumber]);
}
else
{
throw new InvalidOperationException("Couldn't find a MS2 precursor scan for MS3 scan " + scanEvent);
}
break;
default:
break;
}
// don't include MS1 spectra
if (ParseInput.MsLevel.Contains((int)scanFilter.MSOrder))
{
IReaction reaction = GetReaction(scanEvent, scanNumber);
Writer.WriteLine("BEGIN IONS");
if
(ParseInput.MGFPrecursor)
{
Writer.WriteLine($"TITLE={ConstructSpectrumTitle((int)Device.MS, 1, scanNumber)} [PRECURSOR={spectrumRef}]");
}
else
{
Writer.WriteLine($"TITLE={ConstructSpectrumTitle((int)Device.MS, 1, scanNumber)}");
}
Writer.WriteLine($"SCANS={scanNumber}");
Writer.WriteLine(
$"RTINSECONDS={(time * 60).ToString(CultureInfo.InvariantCulture)}");
// trailer extra data list
var trailerData = rawFile.GetTrailerExtraInformation(scanNumber);
int? charge = null;
double?monoisotopicMz = null;
double?isolationWidth = null;
for (var i = 0; i < trailerData.Length; i++)
{
if (trailerData.Labels[i] == "Charge State:")
{
if (Convert.ToInt32(trailerData.Values[i]) > 0)
{
charge = Convert.ToInt32(trailerData.Values[i]);
}
}
if (trailerData.Labels[i] == "Monoisotopic M/Z:")
{
monoisotopicMz = double.Parse(trailerData.Values[i], NumberStyles.Any,
CultureInfo.CurrentCulture);
}
if (trailerData.Labels[i] == "MS" + (int)scanFilter.MSOrder + " Isolation Width:")
{
isolationWidth = double.Parse(trailerData.Values[i], NumberStyles.Any,
CultureInfo.CurrentCulture);
}
}
if (reaction != null)
{
var selectedIonMz =
CalculateSelectedIonMz(reaction, monoisotopicMz, isolationWidth);
Writer.WriteLine("PEPMASS=" +
selectedIonMz.ToString(CultureInfo.InvariantCulture));
}
// charge
if (charge != null)
{
// Scan polarity
var polarity = PositivePolarity;
if (scanFilter.Polarity == PolarityType.Negative)
{
polarity = NegativePolarity;
}
Writer.WriteLine($"CHARGE={charge}{polarity}");
}
// write the filter string
//Writer.WriteLine($"SCANEVENT={scanEvent.ToString()}");
if (!ParseInput.NoPeakPicking)
{
// check if the scan has a centroid stream
if (scan.HasCentroidStream)
{
if (scan.CentroidScan.Length > 0)
{
for (var i = 0; i < scan.CentroidScan.Length; i++)
{
Writer.WriteLine(
scan.CentroidScan.Masses[i].ToString("0.0000000",
CultureInfo.InvariantCulture)
+ " "
+ scan.CentroidScan.Intensities[i].ToString("0.0000000000",
CultureInfo.InvariantCulture));
}
}
}
else // otherwise take segmented (low res) scan data
{
// if the spectrum is profile perform centroiding
var segmentedScan = scanEvent.ScanData == ScanDataType.Profile
? Scan.ToCentroid(scan).SegmentedScan
: scan.SegmentedScan;
for (var i = 0; i < segmentedScan.Positions.Length; i++)
{
Writer.WriteLine(
segmentedScan.Positions[i].ToString("0.0000000",
CultureInfo.InvariantCulture)
+ " "
+ segmentedScan.Intensities[i].ToString("0.0000000000",
CultureInfo.InvariantCulture));
}
}
}
else // use the segmented data as is
{
for (var i = 0; i < scan.SegmentedScan.Positions.Length; i++)
{
Writer.WriteLine(
scan.SegmentedScan.Positions[i].ToString("0.0000000",
CultureInfo.InvariantCulture)
+ " "
+ scan.SegmentedScan.Intensities[i].ToString("0.0000000000",
CultureInfo.InvariantCulture));
}
}
Writer.WriteLine("END IONS");
Log.Debug("Spectrum written to file -- SCAN " + scanNumber);
}
}
if (ParseInput.LogFormat == LogFormat.DEFAULT)
{
Console.WriteLine();
}
}
}
//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();
}
}
}
}
}
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)
/// <summary>
/// Write the RAW files' spectra to a MGF file.
/// </summary>
/// <param name="rawFile">the RAW file interface</param>
/// <param name="firstScanNumber">the first scan number</param>
/// <param name="lastScanNumber">the last scan number</param>
private void WriteSpectraToMgf(IRawDataPlus rawFile, int firstScanNumber, int lastScanNumber)
{
// Test centroid (high resolution/label) data
using (var mgfFile =
File.CreateText(outputDirectory + "//" + rawFileNameWithoutExtension + ".mgf"))
{
for (int scanNumber = firstScanNumber; scanNumber <= lastScanNumber; scanNumber++)
{
// Get each scan from the RAW file
var scan = Scan.FromFile(rawFile, scanNumber);
if (scan.HasCentroidStream)
{
// Check to see if the RAW file contains label (high-res) data and if it is present
// then look for any data that is out of order
double time = rawFile.RetentionTimeFromScanNumber(scanNumber);
// Get the scan filter for this scan number
var scanFilter = rawFile.GetFilterForScanNumber(scanNumber);
// Get the scan event for this scan number
var scanEvent = rawFile.GetScanEventForScanNumber(scanNumber);
// Get the ionizationMode, MS2 precursor mass, collision energy, and isolation width for each scan
if (scanFilter.MSOrder == ThermoFisher.CommonCore.Data.FilterEnums.MSOrderType.Ms2)
{
mgfFile.WriteLine("BEGIN IONS");
mgfFile.WriteLine($"TITLE={ConstructSpectrumTitle(scanNumber)}");
mgfFile.WriteLine($"SCAN={scanNumber}");
mgfFile.WriteLine($"RTINSECONDS={time * 60}");
// trailer extra data list
var trailerData = rawFile.GetTrailerExtraInformation(scanNumber);
for (int i = 0; i < trailerData.Length; i++)
{
if ((trailerData.Labels[i] == "Charge State:"))
{
if (Convert.ToInt32(trailerData.Values[i]) > 0)
{
mgfFile.WriteLine($"CHARGE={trailerData.Values[i]}+");
}
}
}
// Get the reaction information for the first precursor
var reaction = scanEvent.GetReaction(0);
double precursorMass = reaction.PrecursorMass;
mgfFile.WriteLine(
$"PEPMASS={precursorMass:F4}");
//$"PEPMASS={precursorMass:F2} {GetPrecursorIntensity(rawFile, scanNumber)}");
double collisionEnergy = reaction.CollisionEnergy;
mgfFile.WriteLine($"COLLISIONENERGY={collisionEnergy}");
var ionizationMode = scanFilter.IonizationMode;
mgfFile.WriteLine($"IONMODE={ionizationMode}");
var centroidStream = rawFile.GetCentroidStream(scanNumber, false);
if (scan.CentroidScan.Length > 0)
{
for (int i = 0; i < centroidStream.Length; i++)
{
mgfFile.WriteLine(
$"{centroidStream.Masses[i]:F7} {centroidStream.Intensities[i]:F10}");
}
}
mgfFile.WriteLine("END IONS");
}
}
}
}
}
/// <summary>
/// Construct a spectrum element for the given scan
/// </summary>
/// <param name="scanNumber">the scan number</param>
/// <returns>The SpectrumType object</returns>
private SpectrumType ConstructSpectrum(int scanNumber)
{
// Get each scan from the RAW file
var scan = Scan.FromFile(_rawFile, scanNumber);
// Get the scan filter for this scan number
var scanFilter = _rawFile.GetFilterForScanNumber(scanNumber);
// Get the scan event for this scan number
var scanEvent = _rawFile.GetScanEventForScanNumber(scanNumber);
var spectrum = new SpectrumType
{
id = ConstructSpectrumTitle(scanNumber),
defaultArrayLength = 0
};
// Add the ionization type if necessary
if (!_ionizationTypes.ContainsKey(scanFilter.IonizationMode))
{
_ionizationTypes.Add(scanFilter.IonizationMode,
OntologyMapping.IonizationTypes[scanFilter.IonizationMode]);
}
// Add the mass analyzer if necessary
if (!_massAnalyzers.ContainsKey(scanFilter.MassAnalyzer) &&
OntologyMapping.MassAnalyzerTypes.ContainsKey(scanFilter.MassAnalyzer))
{
_massAnalyzers.Add(scanFilter.MassAnalyzer, "IC" + (_massAnalyzers.Count + 1));
}
// Keep the CV params in a list and convert to array afterwards
var spectrumCvParams = new List <CVParamType>
{
new CVParamType
{
name = "ms level",
accession = "MS:1000511",
value = ((int)scanFilter.MSOrder).ToString(CultureInfo.InvariantCulture),
cvRef = "MS"
}
};
// Trailer extra data list
var trailerData = _rawFile.GetTrailerExtraInformation(scanNumber);
int? charge = null;
double?monoisotopicMass = null;
for (var i = 0; i < trailerData.Length; i++)
{
if (trailerData.Labels[i] == "Charge State:")
{
if (Convert.ToInt32(trailerData.Values[i]) > 0)
{
charge = Convert.ToInt32(trailerData.Values[i]);
}
}
if (trailerData.Labels[i] == "Monoisotopic M/Z:")
{
monoisotopicMass = double.Parse(trailerData.Values[i]);
}
}
// Construct and set the scan list element of the spectrum
var scanListType = ConstructScanList(scanNumber, scan, scanFilter, scanEvent, monoisotopicMass);
spectrum.scanList = scanListType;
switch (scanFilter.MSOrder)
{
case MSOrderType.Ms:
spectrumCvParams.Add(new CVParamType
{
accession = "MS:1000579",
cvRef = "MS",
name = "MS1 spectrum",
value = ""
});
// Keep track of scan number for precursor reference
_precursorScanNumber = scanNumber;
break;
case MSOrderType.Ms2:
spectrumCvParams.Add(new CVParamType
{
accession = "MS:1000580",
cvRef = "MS",
name = "MSn spectrum",
value = ""
});
// Construct and set the precursor list element of the spectrum
var precursorListType = ConstructPrecursorList(scanEvent, charge);
spectrum.precursorList = precursorListType;
break;
case MSOrderType.Ng:
break;
case MSOrderType.Nl:
break;
case MSOrderType.Par:
break;
case MSOrderType.Any:
break;
case MSOrderType.Ms3:
break;
case MSOrderType.Ms4:
break;
case MSOrderType.Ms5:
break;
case MSOrderType.Ms6:
break;
case MSOrderType.Ms7:
break;
case MSOrderType.Ms8:
break;
case MSOrderType.Ms9:
break;
case MSOrderType.Ms10:
break;
default:
throw new ArgumentOutOfRangeException();
}
// Scan polarity
var polarityType = scanFilter.Polarity;
switch (polarityType)
{
case PolarityType.Positive:
spectrumCvParams.Add(new CVParamType
{
accession = "MS:1000130",
cvRef = "MS",
name = "positive scan",
value = ""
});
break;
case PolarityType.Negative:
spectrumCvParams.Add(new CVParamType
{
accession = "MS:1000129",
cvRef = "MS",
name = "negative scan",
value = ""
});
break;
case PolarityType.Any:
break;
default:
throw new ArgumentOutOfRangeException();
}
// Total ion current
spectrumCvParams.Add(new CVParamType
{
name = "total ion current",
accession = "MS:1000285",
value = scan.ScanStatistics.TIC.ToString(CultureInfo.InvariantCulture),
cvRef = "MS"
});
double?basePeakMass = null;
double?basePeakIntensity = null;
double?lowestObservedMz = null;
double?highestObservedMz = null;
double[] masses = null;
double[] intensities = null;
if (scan.HasCentroidStream)
{
var centroidStream = _rawFile.GetCentroidStream(scanNumber, false);
if (scan.CentroidScan.Length > 0)
{
basePeakMass = centroidStream.BasePeakMass;
basePeakIntensity = centroidStream.BasePeakIntensity;
lowestObservedMz = centroidStream.Masses[0];
highestObservedMz = centroidStream.Masses[centroidStream.Masses.Length - 1];
masses = centroidStream.Masses;
intensities = centroidStream.Intensities;
// Note that although the scan data type is profile,
// centroid data might be available
spectrumCvParams.Add(new CVParamType
{
accession = "MS:1000127",
cvRef = "MS",
name = "centroid spectrum",
value = ""
});
}
}
else
{
// Get the scan statistics from the RAW file for this scan number
var scanStatistics = _rawFile.GetScanStatsForScanNumber(scanNumber);
basePeakMass = scanStatistics.BasePeakMass;
basePeakIntensity = scanStatistics.BasePeakIntensity;
// Get the segmented (low res and profile) scan data
var segmentedScan = _rawFile.GetSegmentedScanFromScanNumber(scanNumber, scanStatistics);
if (segmentedScan.Positions.Length > 0)
{
lowestObservedMz = segmentedScan.Positions[0];
highestObservedMz = segmentedScan.Positions[segmentedScan.Positions.Length - 1];
masses = segmentedScan.Positions;
intensities = segmentedScan.Intensities;
spectrumCvParams.Add(new CVParamType
{
accession = "MS:1000128",
cvRef = "MS",
name = "profile spectrum",
value = ""
});
}
}
// Base peak m/z
if (basePeakMass != null)
{
spectrumCvParams.Add(new CVParamType
{
name = "base peak m/z",
accession = "MS:1000504",
value = basePeakMass.ToString(),
unitCvRef = "MS",
unitName = "m/z",
unitAccession = "MS:1000040",
cvRef = "MS"
});
}
// Base peak intensity
if (basePeakMass != null)
{
spectrumCvParams.Add(new CVParamType
{
name = "base peak intensity",
accession = "MS:1000505",
value = basePeakIntensity.ToString(),
unitCvRef = "MS",
unitName = "number of detector counts",
unitAccession = "MS:1000131",
cvRef = "MS"
});
}
// Lowest observed mz
if (lowestObservedMz != null)
{
spectrumCvParams.Add(new CVParamType
{
name = "lowest observed m/z",
accession = "MS:1000528",
value = lowestObservedMz.ToString(),
unitCvRef = "MS",
unitAccession = "MS:1000040",
unitName = "m/z",
cvRef = "MS"
});
}
// Highest observed mz
if (highestObservedMz != null)
{
spectrumCvParams.Add(new CVParamType
{
name = "highest observed m/z",
accession = "MS:1000527",
value = highestObservedMz.ToString(),
unitAccession = "MS:1000040",
unitName = "m/z",
unitCvRef = "MS",
cvRef = "MS"
});
}
// Add the CV params to the spectrum
spectrum.cvParam = spectrumCvParams.ToArray();
// Binary data array list
var binaryData = new List <BinaryDataArrayType>();
// M/Z Data
if (!masses.IsNullOrEmpty())
{
// Set the spectrum default array length
spectrum.defaultArrayLength = masses.Length;
var massesBinaryData =
new BinaryDataArrayType
{
binary = GetZLib64BitArray(masses)
};
massesBinaryData.encodedLength =
(4 * Math.Ceiling((double)massesBinaryData
.binary.Length / 3)).ToString(CultureInfo.InvariantCulture);
massesBinaryData.cvParam =
new CVParamType[3];
massesBinaryData.cvParam[0] =
new CVParamType
{
accession = "MS:1000514",
name = "m/z array",
cvRef = "MS",
unitName = "m/z",
value = "",
unitCvRef = "MS",
unitAccession = "MS:1000040"
};
massesBinaryData.cvParam[1] =
new CVParamType
{
accession = "MS:1000523",
name = "64-bit float",
cvRef = "MS",
value = ""
};
massesBinaryData.cvParam[2] =
new CVParamType
{
accession = "MS:1000574",
name = "zlib compression",
cvRef = "MS",
value = ""
};
binaryData.Add(massesBinaryData);
}
// Intensity Data
if (!intensities.IsNullOrEmpty())
{
// Set the spectrum default array length if necessary
if (spectrum.defaultArrayLength == 0)
{
spectrum.defaultArrayLength = masses.Length;
}
var intensitiesBinaryData =
new BinaryDataArrayType
{
binary = GetZLib64BitArray(intensities)
};
intensitiesBinaryData.encodedLength =
(4 * Math.Ceiling((double)intensitiesBinaryData
.binary.Length / 3)).ToString(CultureInfo.InvariantCulture);
intensitiesBinaryData.cvParam =
new CVParamType[3];
intensitiesBinaryData.cvParam[0] =
new CVParamType
{
accession = "MS:1000515",
name = "intensity array",
cvRef = "MS",
unitCvRef = "MS",
unitAccession = "MS:1000131",
unitName = "number of counts",
value = ""
};
intensitiesBinaryData.cvParam[1] =
new CVParamType
{
accession = "MS:1000523",
name = "64-bit float",
cvRef = "MS",
value = ""
};
intensitiesBinaryData.cvParam[2] =
new CVParamType
{
accession = "MS:1000574",
name = "zlib compression",
cvRef = "MS",
value = ""
};
binaryData.Add(intensitiesBinaryData);
}
if (!binaryData.IsNullOrEmpty())
{
spectrum.binaryDataArrayList = new BinaryDataArrayListType
{
count = binaryData.Count.ToString(),
binaryDataArray = binaryData.ToArray()
};
}
return(spectrum);
}
/// <inheritdoc />
public override void Write(int firstScanNumber, int lastScanNumber)
{
ConfigureWriter(".mgf");
using (Writer)
{
//Log.Info("Processing " + (lastScanNumber - firstScanNumber + 1) + " scans");
var lastScanProgress = 0;
for (var scanNumber = firstScanNumber; scanNumber <= lastScanNumber; scanNumber++)
{
if (ParseInput.LogFormat == LogFormat.DEFAULT)
{
var scanProgress = (int)((double)scanNumber / (lastScanNumber - firstScanNumber + 1) * 100);
if (scanProgress % ProgressPercentageStep == 0)
{
if (scanProgress != lastScanProgress)
{
Console.Write("" + scanProgress + "% ");
lastScanProgress = scanProgress;
}
}
}
// Get each scan from the RAW file
var scan = Scan.FromFile(_rawFile, scanNumber);
// Check to see if the RAW file contains label (high-res) data and if it is present
// then look for any data that is out of order
var time = _rawFile.RetentionTimeFromScanNumber(scanNumber);
// Get the scan filter for this scan number
var scanFilter = _rawFile.GetFilterForScanNumber(scanNumber);
// Get the scan event for this scan number
var scanEvent = _rawFile.GetScanEventForScanNumber(scanNumber);
// don't include MS1 spectra
if (scanFilter.MSOrder != MSOrderType.Ms)
{
IReaction reaction = GetReaction(scanEvent, scanNumber);
Writer.WriteLine("BEGIN IONS");
Writer.WriteLine($"TITLE={ConstructSpectrumTitle(scanNumber)}");
Writer.WriteLine($"SCANS={scanNumber}");
Writer.WriteLine(
$"RTINSECONDS={(time * 60).ToString(CultureInfo.InvariantCulture)}");
// trailer extra data list
var trailerData = _rawFile.GetTrailerExtraInformation(scanNumber);
int? charge = null;
double?monoisotopicMz = null;
double?isolationWidth = null;
for (var i = 0; i < trailerData.Length; i++)
{
if (trailerData.Labels[i] == "Charge State:")
{
if (Convert.ToInt32(trailerData.Values[i]) > 0)
{
charge = Convert.ToInt32(trailerData.Values[i]);
}
}
if (trailerData.Labels[i] == "Monoisotopic M/Z:")
{
monoisotopicMz = double.Parse(trailerData.Values[i], NumberStyles.Any,
CultureInfo.CurrentCulture);
}
if (trailerData.Labels[i] == "MS" + (int)scanFilter.MSOrder + " Isolation Width:")
{
isolationWidth = double.Parse(trailerData.Values[i], NumberStyles.Any,
CultureInfo.CurrentCulture);
}
}
if (reaction != null)
{
var selectedIonMz =
CalculateSelectedIonMz(reaction, monoisotopicMz, isolationWidth);
Writer.WriteLine("PEPMASS=" +
selectedIonMz.ToString(CultureInfo.InvariantCulture));
}
// charge
if (charge != null)
{
// Scan polarity
var polarity = PositivePolarity;
if (scanFilter.Polarity == PolarityType.Negative)
{
polarity = NegativePolarity;
}
Writer.WriteLine($"CHARGE={charge}{polarity}");
}
// write the filter string
//Writer.WriteLine($"SCANEVENT={scanEvent.ToString()}");
if (!ParseInput.NoPeakPicking)
{
// check if the scan has a centroid stream
if (scan.HasCentroidStream)
{
if (scan.CentroidScan.Length > 0)
{
for (var i = 0; i < scan.CentroidScan.Length; i++)
{
Writer.WriteLine(
scan.CentroidScan.Masses[i].ToString("0.0000000",
CultureInfo.InvariantCulture)
+ " "
+ scan.CentroidScan.Intensities[i].ToString("0.0000000000",
CultureInfo.InvariantCulture));
}
}
}
else // otherwise take segmented (low res) scan data
{
// if the spectrum is profile perform centroiding
var segmentedScan = scanEvent.ScanData == ScanDataType.Profile
? Scan.ToCentroid(scan).SegmentedScan
: scan.SegmentedScan;
for (var i = 0; i < segmentedScan.Positions.Length; i++)
{
Writer.WriteLine(
segmentedScan.Positions[i].ToString("0.0000000",
CultureInfo.InvariantCulture)
+ " "
+ segmentedScan.Intensities[i].ToString("0.0000000000",
CultureInfo.InvariantCulture));
}
}
}
else // use the segmented data as is
{
for (var i = 0; i < scan.SegmentedScan.Positions.Length; i++)
{
Writer.WriteLine(
scan.SegmentedScan.Positions[i].ToString("0.0000000",
CultureInfo.InvariantCulture)
+ " "
+ scan.SegmentedScan.Intensities[i].ToString("0.0000000000",
CultureInfo.InvariantCulture));
}
}
Writer.WriteLine("END IONS");
//Log.Debug("Spectrum written to file -- SCAN " + scanNumber);
}
}
if (ParseInput.LogFormat == LogFormat.DEFAULT)
{
Console.WriteLine();
}
}
}
/// <inheritdoc />
public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastScanNumber)
{
ConfigureWriter(".mgf");
using (Writer)
{
Log.Info("Processing " + (lastScanNumber - firstScanNumber + 1) + " scans");
var lastScanProgress = 0;
for (var scanNumber = firstScanNumber; scanNumber <= lastScanNumber; scanNumber++)
{
if (!ParseInput.Verbose)
{
var scanProgress = (int)((double)scanNumber / (lastScanNumber - firstScanNumber + 1) * 100);
if (scanProgress % ProgressPercentageStep == 0)
{
if (scanProgress != lastScanProgress)
{
Console.Write("" + scanProgress + "% ");
lastScanProgress = scanProgress;
}
}
}
// Get each scan from the RAW file
var scan = Scan.FromFile(rawFile, scanNumber);
// Check to see if the RAW file contains label (high-res) data and if it is present
// then look for any data that is out of order
var time = rawFile.RetentionTimeFromScanNumber(scanNumber);
// Get the scan filter for this scan number
var scanFilter = rawFile.GetFilterForScanNumber(scanNumber);
// Get the scan event for this scan number
var scanEvent = rawFile.GetScanEventForScanNumber(scanNumber);
IReaction reaction = null;
switch (scanFilter.MSOrder)
{
case MSOrderType.Ms:
// Keep track of scan number for precursor reference
_precursorScanNumber = scanNumber;
break;
case MSOrderType.Ms2:
try
{
reaction = scanEvent.GetReaction(0);
}
catch (ArgumentOutOfRangeException exception)
{
Log.Warn("No reaction found for scan " + scanNumber);
}
goto default;
case MSOrderType.Ms3:
{
try
{
reaction = scanEvent.GetReaction(1);
}
catch (ArgumentOutOfRangeException)
{
Log.Warn("No reaction found for scan " + scanNumber);
}
goto default;
}
default:
Writer.WriteLine("BEGIN IONS");
Writer.WriteLine($"TITLE={ConstructSpectrumTitle(scanNumber)}");
Writer.WriteLine($"SCANS={scanNumber}");
Writer.WriteLine(
$"RTINSECONDS={(time * 60).ToString(CultureInfo.InvariantCulture)}");
// trailer extra data list
var trailerData = rawFile.GetTrailerExtraInformation(scanNumber);
int? charge = null;
double?monoisotopicMz = null;
double?isolationWidth = null;
for (var i = 0; i < trailerData.Length; i++)
{
if (trailerData.Labels[i] == "Charge State:")
{
if (Convert.ToInt32(trailerData.Values[i]) > 0)
{
charge = Convert.ToInt32(trailerData.Values[i]);
}
}
if (trailerData.Labels[i] == "Monoisotopic M/Z:")
{
monoisotopicMz = double.Parse(trailerData.Values[i], NumberStyles.Any,
CultureInfo.CurrentCulture);
}
if (trailerData.Labels[i] == "MS" + (int)scanFilter.MSOrder + " Isolation Width:")
{
isolationWidth = double.Parse(trailerData.Values[i], NumberStyles.Any,
CultureInfo.CurrentCulture);
}
}
if (reaction != null)
{
var selectedIonMz =
CalculateSelectedIonMz(reaction, monoisotopicMz, isolationWidth);
Writer.WriteLine("PEPMASS=" +
selectedIonMz.ToString(CultureInfo.InvariantCulture));
}
// charge
if (charge != null)
{
// Scan polarity
var polarity = PositivePolarity;
if (scanFilter.Polarity == PolarityType.Negative)
{
polarity = NegativePolarity;
}
Writer.WriteLine($"CHARGE={charge}{polarity}");
}
// write the filter string
//Writer.WriteLine($"SCANEVENT={scanEvent.ToString()}");
// Check if the scan has a centroid stream
if (scan.HasCentroidStream && (scanEvent.ScanData == ScanDataType.Centroid ||
(scanEvent.ScanData == ScanDataType.Profile &&
!ParseInput.NoPeakPicking)))
{
var centroidStream = rawFile.GetCentroidStream(scanNumber, false);
if (scan.CentroidScan.Length > 0)
{
for (var i = 0; i < centroidStream.Length; i++)
{
Writer.WriteLine(
centroidStream.Masses[i].ToString("0.0000000",
CultureInfo.InvariantCulture)
+ " "
+ centroidStream.Intensities[i].ToString("0.0000000000",
CultureInfo.InvariantCulture));
}
}
}
// Otherwise take the profile data
else
{
// Get the scan statistics from the RAW file for this scan number
var scanStatistics = rawFile.GetScanStatsForScanNumber(scanNumber);
// Get the segmented (low res and profile) scan data
var segmentedScan =
rawFile.GetSegmentedScanFromScanNumber(scanNumber, scanStatistics);
for (var i = 0; i < segmentedScan.Positions.Length; i++)
{
Writer.WriteLine(
segmentedScan.Positions[i].ToString("0.0000000",
CultureInfo.InvariantCulture)
+ " "
+ segmentedScan.Intensities[i].ToString("0.0000000000",
CultureInfo.InvariantCulture));
}
}
Writer.WriteLine("END IONS");
Log.Debug("Spectrum written to file -- SCAN " + scanNumber);
break;
}
}
if (!ParseInput.Verbose)
{
Console.WriteLine();
}
}
}
private static void WritePScans(string outputDirectory, string fileName,
IRawDataPlus raw,
List <PScan> scans)
{
var enumerator = raw.GetFilteredScanEnumerator(" ");
foreach (var scanNumber in enumerator
) // note in my tests serial is faster than Parallel.Foreach() (this involves disk access, so it makes sense)
{
//trailer information is extracted via index
var trailers = raw.GetTrailerExtraValues(scanNumber);
var trailerLabels = raw.GetTrailerExtraInformation(scanNumber);
object chargeState = 0;
for (int i = 0; i < trailerLabels.Labels.Length; i++)
{
if (trailerLabels.Labels[i] == "Charge State:")
{
chargeState = raw.GetTrailerExtraValue(scanNumber, i);
break;
}
}
var scanFilter = raw.GetFilterForScanNumber(scanNumber);
var scanStats = raw.GetScanStatsForScanNumber(scanNumber);
CentroidStream centroidStream = new CentroidStream();
//check for FT mass analyzer data
if (scanFilter.MassAnalyzer == MassAnalyzerType.MassAnalyzerFTMS)
{
centroidStream = raw.GetCentroidStream(scanNumber, false);
}
//check for IT mass analyzer data
if (scanFilter.MassAnalyzer == MassAnalyzerType.MassAnalyzerITMS)
{
var scanData = raw.GetSimplifiedScan(scanNumber);
centroidStream.Masses = scanData.Masses;
centroidStream.Intensities = scanData.Intensities;
}
var msOrder = raw.GetScanEventForScanNumber(scanNumber).MSOrder;
if (msOrder == MSOrderType.Ms)
{
var pscan = GetPScan(scanStats, centroidStream, fileName, Convert.ToInt32(chargeState));
scans.Add(pscan);
}
if (msOrder == MSOrderType.Ms2)
{
var precursorMz = raw.GetScanEventForScanNumber(scanNumber).GetReaction(0).PrecursorMass;
var pscan = GetPScan(scanStats, centroidStream, fileName, precursorMz,
Convert.ToInt32(chargeState));
scans.Add(pscan);
}
var t = raw.GetTrailerExtraValues(scanNumber);
}
WriteScans(outputDirectory, scans, fileName);
}
public static MsDataScan GetOneBasedScan(IRawDataPlus rawFile, IFilteringParams filteringParams, int scanNumber)
{
var filter = rawFile.GetFilterForScanNumber(scanNumber);
string scanFilterString = filter.ToString();
int msOrder = (int)filter.MSOrder;
if (msOrder < 1 || msOrder > 10)
{
throw new MzLibException("Unknown MS Order (" + msOrder + ") for scan number " + scanNumber);
}
string nativeId = "controllerType=0 controllerNumber=1 scan=" + scanNumber;
MzSpectrum spectrum = GetSpectrum(rawFile, filteringParams, scanNumber, scanFilterString, msOrder);
var scanStats = rawFile.GetScanStatsForScanNumber(scanNumber);
double scanRangeHigh = scanStats.HighMass;
double scanRangeLow = scanStats.LowMass;
MzRange scanWindowRange = new MzRange(scanRangeLow, scanRangeHigh);
double? ionInjectionTime = null;
double? precursorSelectedMonoisotopicIonMz = null;
int? selectedIonChargeState = null;
double? ms2IsolationWidth = null;
int? precursorScanNumber = null;
double? isolationMz = null;
string HcdEnergy = null;
ActivationType activationType = ActivationType.Any; // thermo enum
DissociationType dissociationType = DissociationType.Unknown; // mzLib enum
var trailer = rawFile.GetTrailerExtraInformation(scanNumber);
string[] labels = trailer.Labels;
string[] values = trailer.Values;
for (int i = 0; i < trailer.Labels.Length; i++)
{
if (labels[i].StartsWith("Ion Injection Time (ms)", StringComparison.Ordinal))
{
ionInjectionTime = double.Parse(values[i], CultureInfo.InvariantCulture) == 0 ?
(double?)null :
double.Parse(values[i], CultureInfo.InvariantCulture);
}
if (msOrder < 2)
{
continue;
}
if (labels[i].StartsWith("MS" + msOrder + " Isolation Width", StringComparison.Ordinal))
{
ms2IsolationWidth = double.Parse(values[i], CultureInfo.InvariantCulture) == 0 ?
(double?)null :
double.Parse(values[i], CultureInfo.InvariantCulture);
}
if (labels[i].StartsWith("Monoisotopic M/Z", StringComparison.Ordinal))
{
precursorSelectedMonoisotopicIonMz = double.Parse(values[i], CultureInfo.InvariantCulture) == 0 ?
(double?)null :
double.Parse(values[i], CultureInfo.InvariantCulture);
}
if (labels[i].StartsWith("Charge State", StringComparison.Ordinal))
{
selectedIonChargeState = int.Parse(values[i], CultureInfo.InvariantCulture) == 0 ?
(int?)null :
int.Parse(values[i], CultureInfo.InvariantCulture);
}
if (labels[i].StartsWith("Master Scan Number", StringComparison.Ordinal) ||
labels[i].StartsWith("Master Index", StringComparison.Ordinal))
{
precursorScanNumber = int.Parse(values[i], CultureInfo.InvariantCulture) <= 1 ?
(int?)null :
int.Parse(values[i], CultureInfo.InvariantCulture);
}
if (labels[i].StartsWith("HCD Energy:", StringComparison.Ordinal))
{
HcdEnergy = values[i];
}
}
if (msOrder > 1)
{
var scanEvent = rawFile.GetScanEventForScanNumber(scanNumber);
var reaction = scanEvent.GetReaction(0);
isolationMz = reaction.PrecursorMass;
activationType = reaction.ActivationType;
dissociationType = GetDissociationType(activationType);
// thermo does not have an enum value for ETHcD, so this needs to be detected from the scan filter
if (scanFilterString.Contains("@etd", StringComparison.OrdinalIgnoreCase) &&
scanFilterString.Contains("@hcd", StringComparison.OrdinalIgnoreCase))
{
dissociationType = DissociationType.EThcD;
}
if (ms2IsolationWidth == null)
{
ms2IsolationWidth = reaction.IsolationWidth;
}
if (precursorScanNumber == null)
{
// we weren't able to get the precursor scan number, so we'll have to guess;
// loop back to find precursor scan
// (assumed to be the first scan before this scan with an MS order of this scan's MS order - 1)
// e.g., if this is an MS2 scan, find the first MS1 scan before this and assume that's the precursor scan
for (int i = scanNumber; i >= 1; i--)
{
var possiblePrecursorScanFilter = rawFile.GetFilterForScanNumber(i);
int order = (int)possiblePrecursorScanFilter.MSOrder;
if (order == msOrder - 1)
{
precursorScanNumber = i;
break;
}
}
if (precursorScanNumber == null)
{
throw new MzLibException("Could not get precursor for scan #" + scanNumber);
}
}
}
// at this point, we have the m/z value of the species that got fragmented, from the scan header
// this section of the code finds that peak in the spectrum (it's actual intensity and centroided m/z values)
// the intention is to remove any rounding issues caused by what is in the scan header and what is observable in the spectrum
double?selectedIonIntensity = null;
if (isolationMz.HasValue)
{
if (spectrum.Size != 0)
{
int closest = spectrum.GetClosestPeakIndex(isolationMz.Value);
double mz = spectrum.XArray[closest];
double intensity = spectrum.YArray[closest];
if (Math.Abs(mz - isolationMz.Value) < 0.1)
{
selectedIonIntensity = intensity;
isolationMz = mz;
}
}
}
return(new MsDataScan(
massSpectrum: spectrum,
oneBasedScanNumber: scanNumber,
msnOrder: msOrder,
isCentroid: true,
polarity: GetPolarity(filter.Polarity),
retentionTime: rawFile.RetentionTimeFromScanNumber(scanNumber),
scanWindowRange: scanWindowRange,
scanFilter: scanFilterString,
mzAnalyzer: GetMassAnalyzerType(filter.MassAnalyzer),
totalIonCurrent: spectrum.SumOfAllY,
injectionTime: ionInjectionTime,
noiseData: null, //TODO: implement reading noise data. it's unused right now, so it's just left as null
nativeId: nativeId,
selectedIonMz: isolationMz,
selectedIonChargeStateGuess: selectedIonChargeState,
selectedIonIntensity: selectedIonIntensity,
isolationMZ: isolationMz,
isolationWidth: ms2IsolationWidth,
dissociationType: dissociationType,
oneBasedPrecursorScanNumber: precursorScanNumber,
selectedIonMonoisotopicGuessMz: precursorSelectedMonoisotopicIonMz,
hcdEnergy: HcdEnergy));
}
public string GetScanFilter(int scanNumber)
{
var scanFilter = rawFile.GetFilterForScanNumber(scanNumber);
return(scanFilter.ToString());
}