public static Ms2Scan Create(MsScan scan)
{
var ms2 = new Ms2Scan(
scan.ScanNumber, scan.MsLevel, scan.PeaksCount, scan.Polarity, scan.ScanType, scan.FilterLine, scan.RetentionTime, scan.LowMz,
scan.HighMz, scan.BasePeakMz, scan.BasePeakIntensity, scan.TotIonCurrent, scan.PeakData);
return(ms2);
}
public static Ms1Scan Create(MsScan scan)
{
var ms1 = new Ms1Scan(
scan.ScanNumber, scan.MsLevel, scan.PeaksCount,
scan.Polarity, scan.ScanType, scan.FilterLine,
scan.RetentionTime, scan.LowMz, scan.HighMz,
scan.BasePeakMz, scan.BasePeakIntensity,
scan.TotIonCurrent, scan.PeakData)
{
// Initialize list to hold references to Ms2Scans
Ms2s = new List <Ms2Scan>()
};
return(ms1);
}
private bool ProcessFile(string filePath, string outputDirectoryPath)
{
try
{
OnStatusEvent(string.Format("Processing {0}", filePath));
// Compute the SHA-1 hash of the .Raw file
var fileSha1 = HashRawFile(filePath);
// Disable loading the method
// Method loading doesn't work on Linux and this program doesn't need that information
var readerOptions = new ThermoReaderOptions
{
LoadMSMethodInfo = false
};
// Open up the raw file connection
var reader = new XRawFileIO(filePath, readerOptions);
// Get all unique CV values from scans
var cvValues = GetUniqueCvValues(reader);
var totalScanCount = reader.GetNumScans();
var scansProcessed = 0;
var lastProgress = DateTime.UtcNow;
// Reset tracking variables
ByteTracking.Reset(true);
// Now work for each unique CV value (# files we're going to need to split into)
// get all scans that have the CV that we're currently targeting
foreach (var cvValue in cvValues)
{
var baseName = Path.GetFileNameWithoutExtension(filePath);
var mzXmlPath = Path.Combine(outputDirectoryPath, baseName + "_" + cvValue + ".mzXML");
OnDebugEvent(string.Format("Creating file {0}", mzXmlPath));
var targetScans = FindAllTargetScans(cvValue, reader);
var parentScanToMS2Map = new Dictionary <int, List <int> >();
using (var writer = new StreamWriter(new FileStream(mzXmlPath, FileMode.Create, FileAccess.Write, FileShare.Read)))
{
WriteHeader(writer, filePath, reader, fileSha1, targetScans);
Ms1Scan currentMS1Scan = null;
// Write out our target scans
foreach (var scanNumber in targetScans)
{
if (DateTime.UtcNow.Subtract(lastProgress).TotalSeconds >= 3)
{
var percentComplete = scansProcessed / (double)totalScanCount * 100;
OnDebugEvent(string.Format("... processing: {0:F0}% complete", percentComplete));
lastProgress = DateTime.UtcNow;
}
var scan = new MsScan(scanNumber, reader);
if (scan.MsLevel == 1)
{
parentScanToMS2Map.Add(scan.ScanNumber, new List <int>());
if (currentMS1Scan == null)
{
// Start condition
currentMS1Scan = Ms1Scan.Create(scan);
}
else
{
// Write currentMS1Scan to file
var outString = currentMS1Scan.ToXML(this);
writer.WriteLine(outString);
currentMS1Scan = Ms1Scan.Create(scan);
}
}
else if (scan.MsLevel == 2)
{
if (currentMS1Scan != null)
{
parentScanToMS2Map[currentMS1Scan.ScanNumber].Add(scan.ScanNumber);
}
var ms2Scan = Ms2Scan.Create(scan);
ms2Scan.AddMs2ScanParameters(reader);
currentMS1Scan?.AddMs2Scan(ms2Scan);
}
scansProcessed++;
}
if (currentMS1Scan != null)
{
// Once we're out, we need to write out our last currentMS1Scan
writer.WriteLine(currentMS1Scan.ToXML(this));
}
// Finish off msRun
writer.WriteLine(" </msRun>");
writer.WriteLine(" <index name=\"scan\">");
// Add special entry to our indexOffset list for where the offsets start
var index = new Index(0, ByteTracking.ByteDepth + ByteTracking.Encoder.GetByteCount(" </msRun>") + 3);
ByteTracking.ScanOffsets.Add(index);
// Write all index offsets
for (var i = 0; i < ByteTracking.ScanOffsets.Count - 1; i++)
{
var offset = ByteTracking.ScanOffsets[i];
writer.WriteLine(" <offset id=\"" + offset.ScanNumber + "\">" + offset.ByteDepth + "</offset>");
}
writer.WriteLine(" </index>");
writer.WriteLine(" <indexOffset>" + ByteTracking.ScanOffsets.Last().ByteDepth + "</indexOffset>");
writer.Write(" <sha1>");
}
// Compute the SHA-1 hash of the file up to this point
var mzXmlHash = HashMzXML(mzXmlPath);
// Append the hash
using (var writer = new StreamWriter(mzXmlPath, true))
{
writer.Write(mzXmlHash);
writer.WriteLine("</sha1>");
writer.WriteLine("</mzXML>");
}
// Reset tracking variables, but do not restart scan numbering
ByteTracking.Reset(false);
}
OnDebugEvent(string.Format("... processing: {0:F0}% complete", 100));
return(true);
}
catch (Exception ex)
{
OnErrorEvent("Error in ProcessFile", ex);
return(false);
}
}