public static void ExtractTrailerExtra(this RawDataCollection rawData, IRawDataPlus rawFile)
{
if (rawData.Performed.Contains(Operations.TrailerExtras))
{
return;
}
Log.Information("Extracting trailer extras");
rawData.trailerExtras = new Dictionary <int, TrailerExtraData>();
TrailerExtraIndices indices = new TrailerExtraIndices(rawFile);
Double[] spsMasses;
IEnumerable <int> scans = rawData.scanIndex.ScanEnumerators[MSOrderType.Any];
ProgressIndicator progress = new ProgressIndicator(scans.Count(), "Extracting trailer extra data");
foreach (int scan in scans)
{
try
{
rawData.trailerExtras.Add(scan, ExtractTrailerExtra(rawData, rawFile, scan, indices));
}
catch (Exception e)
{
Log.Error(e, "Failed during extraction of trailer extra {Scan}", scan);
throw e;
}
progress.Update();
}
progress.Done();
rawData.Performed.Add(Operations.TrailerExtras);
}
public static void ExtractAll(this RawDataCollection rawData, IRawDataPlus rawFile)
{
Log.Information("Beginning extraction of all possible data");
rawFile.SelectInstrument(Device.MS, 1);
rawData.ExtractPrecursorScans(rawFile);
ProgressIndicator P = new ProgressIndicator(rawData.scanIndex.allScans.Count(), "Extracting raw data");
TrailerExtraIndices indices = new TrailerExtraIndices(rawFile);
for (int i = 1; i <= rawData.scanIndex.allScans.Count(); i++)
{
try
{
// first get out the mass spectrum
if (rawData.scanIndex.allScans[i].MassAnalyzer == MassAnalyzerType.MassAnalyzerFTMS)
{
rawData.centroidStreams.Add(i, new CentroidStreamData(rawFile.GetCentroidStream(i, false)));
}
else
{
rawData.segmentedScans.Add(i, new SegmentedScanData(rawFile.GetSegmentedScanFromScanNumber(i, null)));
}
// add the trailer extra data
rawData.trailerExtras.Add(i, TrailerExtras.ExtractTrailerExtra(rawData, rawFile, i, indices));
rawData.Performed.Add(Operations.TrailerExtras);
// add the retention time
rawData.retentionTimes.Add(i, rawFile.RetentionTimeFromScanNumber(i));
rawData.Performed.Add(Operations.RetentionTimes);
// add the precursor mass
PrecursorMasses.ExtractPrecursorMasses(rawData, rawFile, i);
rawData.Performed.Add(Operations.PrecursorMasses);
P.Update();
}
catch (Exception e)
{
Log.Error("Extraction failed on scan {Scan}", i);
throw e;
}
}
if (rawData.methodData.AnalysisOrder == MSOrderType.Ms2 | rawData.methodData.AnalysisOrder == MSOrderType.Ms3)
{
rawData.Performed.Add(Operations.Ms1CentroidStreams);
if (rawData.methodData.MassAnalyzers[MSOrderType.Ms2] == MassAnalyzerType.MassAnalyzerFTMS)
{
rawData.Performed.Add(Operations.Ms2CentroidStreams);
}
else
{
rawData.Performed.Add(Operations.Ms2SegmentedScans);
}
}
if (rawData.methodData.AnalysisOrder == MSOrderType.Ms3)
{
if (rawData.methodData.MassAnalyzers[MSOrderType.Ms3] == MassAnalyzerType.MassAnalyzerFTMS)
{
rawData.Performed.Add(Operations.Ms3CentroidStreams);
}
else
{
rawData.Performed.Add(Operations.Ms3SegmentedScans);
}
}
P.Done();
}
public static TrailerExtraData ExtractTrailerExtra(RawDataCollection rawData, IRawDataPlus rawFile, int scan, TrailerExtraIndices indices)
{
TrailerExtraData trailerExtra = new TrailerExtraData();
Double[] spsMasses;
if (indices.InjectionTime != -1)
{
trailerExtra.InjectionTime = Convert.ToDouble(rawFile.GetTrailerExtraValue(scan, indices.InjectionTime));
}
if (indices.ChargeState != -1)
{
trailerExtra.ChargeState = Convert.ToInt32(rawFile.GetTrailerExtraValue(scan, indices.ChargeState));
}
if (indices.MonoisotopicMZ != -1)
{
trailerExtra.MonoisotopicMZ = Convert.ToDouble(rawFile.GetTrailerExtraValue(scan, indices.MonoisotopicMZ));
}
if (indices.MasterScan != -1)
{
try
{
trailerExtra.MasterScan = Convert.ToInt32(rawFile.GetTrailerExtraValue(scan, indices.MasterScan));
}
// if that doesn't work the master scan is (hopefully) not applicable, we can leave it at the defaule value of -1
catch (FormatException)
{
}
}
if (indices.HCDEnergy != -1)
{
try
{
trailerExtra.HCDEnergy = Convert.ToDouble(rawFile.GetTrailerExtraValue(scan, indices.HCDEnergy));
}
catch (FormatException)
{
}
}
if (indices.SPSMasses.Count > 2) // if so, this means with have all SPS masses listed individually
{
spsMasses = new double[indices.SPSMasses.Count];
for (int i = 0; i < indices.SPSMasses.Count; i++)
{
spsMasses[i] = Convert.ToDouble(rawFile.GetTrailerExtraValue(scan, indices.SPSMasses[i]));
}
}
if (indices.SPSMasses.Count == 0) // there are no SPS masses
{
spsMasses = new double[0];
}
else // they are broken into two lists of strings, comma delimited
{
char[] delimiter = { ' ', ',' };
string[] stringsps1 = rawFile.GetTrailerExtraValue(scan, indices.SPSMasses[0]).ToString().Split(delimiter, StringSplitOptions.RemoveEmptyEntries);
string[] stringsps2 = rawFile.GetTrailerExtraValue(scan, indices.SPSMasses[1]).ToString().Split(delimiter, StringSplitOptions.RemoveEmptyEntries);
double[] sps1 = Array.ConvertAll(stringsps1, Convert.ToDouble);
double[] sps2 = Array.ConvertAll(stringsps2, Convert.ToDouble);
spsMasses = new double[sps1.Length + sps2.Length];
sps1.CopyTo(spsMasses, 0);
sps2.CopyTo(spsMasses, sps1.Length);
}
trailerExtra.SPSMasses = spsMasses;
return(trailerExtra);
}
