/// <summary>
/// Extract ScanInfo from this RawFile for each scan and add it to the posLayer or negLayer RawFileLayer of this RawFile.
///
/// Only called from InitFromRawFile, which is called only from Init, which is only called from CreateRawFile.
/// </summary>
private void InitFromRawFileImpl()
{
InfoLists posInfoList = new InfoLists();
InfoLists negInfoList = new InfoLists();
for (int scanNum = FirstScanNumber; scanNum <= LastScanNumber; scanNum++)
{
if (FirstScanNumber > LastScanNumber)
{
break;
}
ScanInfo scanInfo = GetInfoForScanNumber(scanNum);
if (scanInfo == null)
{
continue;
}
if (scanInfo.positiveIonMode)
{
posInfoList.Add(scanInfo, scanNum);
}
else
{
negInfoList.Add(scanInfo, scanNum);
}
}
posLayer.SetData(posInfoList, MaximumIntensity);
negLayer.SetData(negInfoList, MaximumIntensity);
}
/// <summary>
/// Take the ScanInfo object and add its contents to the field simLists, ms1Lists, or ms2Lists,
/// depending on the values of the msLevel and isSim fields of the ScanInfo.
/// </summary>
/// <param name="scanInfo">an object containing details about this scan</param>
/// <param name="scanNum">the unique number of this scan</param>
public void Add(ScanInfo scanInfo, int scanNum)
{
switch (scanInfo.msLevel)
{
case MsLevel.Ms1:
//if (!scanInfo.isSim){
currentMs2Inds.Clear();
if (scanInfo.min < ms1Lists.massMin)
{
ms1Lists.massMin = scanInfo.min;
}
if (scanInfo.max > ms1Lists.massMax)
{
ms1Lists.massMax = scanInfo.max;
}
if (scanInfo.nImsScans > ms1Lists.maxNumIms)
{
ms1Lists.maxNumIms = scanInfo.nImsScans;
}
ms1Lists.scans.Add(scanNum);
ms1Lists.rts.Add(scanInfo.rt);
ms1Lists.ionInjectionTimes.Add(scanInfo.ionInjectionTime);
ms1Lists.basepeakIntensities.Add(scanInfo.basepeakIntensity);
ms1Lists.elapsedTimes.Add(scanInfo.elapsedTime);
if (scanInfo.hasProfile && !allMassRanges.ContainsKey(scanInfo.min))
{
allMassRanges.Add(scanInfo.min, null);
}
else if (!scanInfo.hasProfile && !allMassRanges.ContainsKey(0))
{
allMassRanges.Add(0, null);
}
ms1Lists.tics.Add(scanInfo.tic);
ms1Lists.hasCentroids.Add(scanInfo.hasCentroid);
ms1Lists.hasProfiles.Add(scanInfo.hasProfile);
ms1Lists.massAnalyzer.Add(scanInfo.analyzer);
ms1Lists.minMasses.Add(scanInfo.min);
ms1Lists.maxMasses.Add(scanInfo.max);
ms1Lists.resolutions.Add(scanInfo.resolution);
ms1Lists.intenseCompFactors.Add(scanInfo.intenseCompFactor);
ms1Lists.emIntenseComp.Add(scanInfo.emIntenseComp);
ms1Lists.rawOvFtT.Add(scanInfo.rawOvFtT);
ms1Lists.agcFillList.Add(scanInfo.agcFill);
ms1Lists.nImsScans.Add(scanInfo.nImsScans);
ms1Lists.isSim.Add(scanInfo.isSim);
//}
break;
case MsLevel.Ms2:
if (scanInfo.min < ms2Lists.massMin)
{
ms2Lists.massMin = scanInfo.min;
}
if (scanInfo.max > ms2Lists.massMax)
{
ms2Lists.massMax = scanInfo.max;
}
if (scanInfo.nImsScans > ms2Lists.maxNumIms)
{
ms2Lists.maxNumIms = scanInfo.nImsScans;
}
currentMs2Inds.Add(ms2Lists.scansList.Count);
ms2Lists.scansList.Add(scanNum);
ms2Lists.prevMs1IndexList.Add(ms1Lists.scans.Count - 1);
ms2Lists.mzList.Add(scanInfo.ms2ParentMz);
ms2Lists.fragmentTypeList.Add(scanInfo.ms2FragType);
ms2Lists.rtList.Add(scanInfo.rt);
ms2Lists.ionInjectionTimesList.Add(scanInfo.ionInjectionTime);
ms2Lists.basepeakIntensityList.Add(scanInfo.basepeakIntensity);
ms2Lists.elapsedTimesList.Add(scanInfo.elapsedTime);
ms2Lists.energiesList.Add(scanInfo.energy);
ms2Lists.summationsList.Add(scanInfo.summations);
ms2Lists.monoisotopicMzList.Add(scanInfo.ms2MonoMz);
ms2Lists.ticList.Add(scanInfo.tic);
ms2Lists.hasCentroidList.Add(scanInfo.hasCentroid);
ms2Lists.hasProfileList.Add(scanInfo.hasProfile);
ms2Lists.analyzerList.Add(scanInfo.analyzer);
ms2Lists.minMassList.Add(scanInfo.min);
ms2Lists.maxMassList.Add(scanInfo.max);
ms2Lists.isolationMzMinList.Add(scanInfo.ms2IsolationMin);
ms2Lists.isolationMzMaxList.Add(scanInfo.ms2IsolationMax);
ms2Lists.resolutionList.Add(scanInfo.resolution);
ms2Lists.intenseCompFactor.Add(scanInfo.intenseCompFactor);
ms2Lists.emIntenseComp.Add(scanInfo.emIntenseComp);
ms2Lists.rawOvFtT.Add(scanInfo.rawOvFtT);
ms2Lists.agcFillList.Add(scanInfo.agcFill);
ms2Lists.nImsScans.Add(scanInfo.nImsScans);
break;
case MsLevel.Ms3:
if (scanInfo.min < ms3Lists.massMin)
{
ms3Lists.massMin = scanInfo.min;
}
if (scanInfo.max > ms3Lists.massMax)
{
ms3Lists.massMax = scanInfo.max;
}
if (scanInfo.nImsScans > ms3Lists.maxNumIms)
{
ms3Lists.maxNumIms = scanInfo.nImsScans;
}
ms3Lists.scansList.Add(scanNum);
ms3Lists.prevMs2IndexList.Add(GetPrecursorMs2(currentMs2Inds, scanInfo.ms2ParentMz));
//ms3Lists.ms3PrevMs2IndexList.Add(ms2Lists.ms2ScansList.Count - 1);
ms3Lists.mz1List.Add(scanInfo.ms2ParentMz);
ms3Lists.mz2List.Add(scanInfo.ms3ParentMz);
ms3Lists.fragmentTypeList.Add(scanInfo.ms2FragType);
ms3Lists.rtList.Add(scanInfo.rt);
ms3Lists.ionInjectionTimesList.Add(scanInfo.ionInjectionTime);
ms3Lists.basepeakIntensityList.Add(scanInfo.basepeakIntensity);
ms3Lists.elapsedTimesList.Add(scanInfo.elapsedTime);
ms3Lists.energiesList.Add(scanInfo.energy);
ms3Lists.summationsList.Add(scanInfo.summations);
ms3Lists.monoisotopicMzList.Add(scanInfo.ms2MonoMz);
ms3Lists.ticList.Add(scanInfo.tic);
ms3Lists.hasCentroidList.Add(scanInfo.hasCentroid);
ms3Lists.hasProfileList.Add(scanInfo.hasProfile);
ms3Lists.analyzerList.Add(scanInfo.analyzer);
ms3Lists.minMassList.Add(scanInfo.min);
ms3Lists.maxMassList.Add(scanInfo.max);
ms3Lists.isolationMzMinList.Add(scanInfo.ms2IsolationMin);
ms3Lists.isolationMzMaxList.Add(scanInfo.ms2IsolationMax);
ms3Lists.resolutionList.Add(scanInfo.resolution);
ms3Lists.intenseCompFactor.Add(scanInfo.intenseCompFactor);
ms3Lists.emIntenseComp.Add(scanInfo.emIntenseComp);
ms3Lists.rawOvFtT.Add(scanInfo.rawOvFtT);
ms3Lists.agcFillList.Add(scanInfo.agcFill);
ms3Lists.nImsScans.Add(scanInfo.nImsScans);
break;
default:
throw new Exception("Invalid MS level.");
}
}
