private static DataTypes.ICompound getCompound(Agilent.MassSpectrometry.DataAnalysis.ICompound curCompound, KeyValuePair <int, ProfinderLogic.Strcuctplots> element)
{
DataTypes.ICompound compound = new DataTypes.Compound();
compound.RT = curCompound.RetentionTime;
compound.Mass = curCompound.Mass;
compound.ZCount = curCompound.ZCount;
//Area is not implemented by Agilent.MassSpectrometry.DataAnalysis.ICompound
compound.Ions = curCompound.IonCount;
compound.Volume = curCompound.Volume;
compound.FileName = curCompound.DataFileName;
compound.Saturated = curCompound.SaturationWarning;
compound.FileName = curCompound.DataFileName;
compound.Width = curCompound.Width;
int key = element.Key;
ProfinderLogic.Strcuctplots plots = element.Value;
List <IFXData> plotData = plots.ifxdata;
foreach (IFXData data in plotData)
{
var xyStore = data.XYStore;
if (data.Description is MSChromDescription)
{
var chromatogram = getChromatogram(xyStore, data, curCompound.RetentionTime);
compound.Chromatogram = chromatogram;
}
if (data.Description is MassSpecDescription)
{
var spectrum = getSpectrum(xyStore, data);
compound.Spectrum = spectrum;
}
}
return(compound);
}
private DataTypes.CompoundGroup getICompoundGroup(Agilent.MassSpectrometry.DataAnalysis.ICompoundGroup cpdGroup, List <string> analysisFiles)
{
DataTypes.CompoundGroup compoundGroup = new DataTypes.CompoundGroup();
if (cpdGroup == null)
{
return(null);
}
compoundGroup.Group = cpdGroup.CompoundGroupName;
compoundGroup.RTTgt = cpdGroup.TargetRetentionTime;
compoundGroup.RTMed = cpdGroup.RetentionTimeMedian;
compoundGroup.Found = cpdGroup.FrequencyFound;
compoundGroup.Missed = cpdGroup.FrequencyMissed;
//compoundGroup.ScoreTgtMax = cpdGroup.TgtScoreMax;
//compoundGroup.TgtScorePctRSD = cpdGroup.TgtScorePctRSD;
compoundGroup.ScoreMFEMax = cpdGroup.QScoreMax;
compoundGroup.HeightMed = cpdGroup.HeightMedian;
compoundGroup.MassAvg = cpdGroup.MassAverage;
compoundGroup.RTAvg = cpdGroup.RetentionTimeAverage;
compoundGroup.TargetMass = cpdGroup.TargetMass;
compoundGroup.MassMedian = cpdGroup.MassMedian;
compoundGroup.MassPpmRSD = cpdGroup.MassPpmRSD;
compoundGroup.Saturated = cpdGroup.SaturationWarning;
compoundGroup.RetentionTimeSpan = cpdGroup.RetentionTimeSpan;
compoundGroup.SingleIonFeatures = cpdGroup.SingleIonFeatures;
compoundGroup.RetentionTimeWidthAtBase = cpdGroup.RetentionTimeWidthAtBase;
compoundGroup.AreaAvg = cpdGroup.AreaAverage;
compoundGroup.HeightAvg = cpdGroup.HeightAverage;
compoundGroup.VolumeAvg = cpdGroup.VolumeAverage;
compoundGroup.RetentionTimeDifference = cpdGroup.RetentionTimeDifference;
//TODO dnt know about sigma(A^2)
compoundGroup.TimeSegment = cpdGroup.TimeSegment;
var vals = cpdGroup.Values;
IDictionary <string, DataTypes.ICompound> sampleWiseDict = new Dictionary <string, DataTypes.ICompound>();
ConcurrentDictionary <int, ProfinderLogic.Strcuctplots> plotDict = getPlots(cpdGroup, analysisFiles);
int ind = 0;
foreach (var element in plotDict)
{
Agilent.MassSpectrometry.DataAnalysis.ICompound curCompound = vals.ElementAt(ind);
DataTypes.ICompound compound = getCompound(curCompound, element);
sampleWiseDict.Add(curCompound.DataFileName, compound);
ind++;
}
compoundGroup.SampleWiseDataDictionary = sampleWiseDict;
return(compoundGroup);
}
private ConcurrentDictionary <int, ProfinderLogic.Strcuctplots> getPlots(Agilent.MassSpectrometry.DataAnalysis.ICompoundGroup cpdGroup, List <string> analysisFiles)
{
var plotDict = new ConcurrentDictionary <int, ProfinderLogic.Strcuctplots>();
var dictAnalysisID = qualAppLogic.DataHeirarchy.AnalysisStore.Cast <DictionaryEntry>()
.ToDictionary(kvp => kvp.Value as Analysis, kvp => (int)kvp.Key);
if (!dictAnalysisID.Any())
{
return(plotDict);
}
Agilent.MassSpectrometry.DataAnalysis.ICompound c = cpdGroup.First().Value;
CpdDataObjectType plotTypes = CpdDataObjectType.MFECpdChromatogram | CpdDataObjectType.MFESpectrum;
ConcurrentDictionary <int, StrcuctFindCpdItem> concurrentDict = new ConcurrentDictionary <int, StrcuctFindCpdItem>();
List <string> sItems = new List <string> {
};
foreach (string analsisFilePath in analysisFiles)
{
StrcuctFindCpdItem strcItems;
IFindCompounds findCpds = null;
IParameterSet resultOptions = null;
Agilent.MassSpectrometry.DataAnalysis.ICompound cpd;
if (dictAnalysisID.FirstOrDefault(p => p.Key.FilePath == analsisFilePath).Key == null)
{
continue;
}
var diAnalysis = dictAnalysisID.First(a => a.Key.FilePath == analsisFilePath);
var analysis = diAnalysis.Key;
var analysisID = diAnalysis.Value;
bool flag = cpdGroup.TryGetValue(analsisFilePath, out cpd);
if (!flag)
{
continue;
}
IList <ICpdDetails> cpdDetailsList = cpd.CpdDetailsList;
ICpdDetails cpdDetails = null;
if ((cpdDetailsList.Count > 0) && (cpdDetailsList[0] != null))
{
cpdDetails = cpd.CpdDetailsList.First();
}
if (cpdDetails == null && c.CpdMiningAlgorithm == CpdMiningAlgorithm.FindByMolecularFeature)
{
MGDBAccessor DBAccessor = MGDBAccessor.GetMGDBAccessor();
string sKey = cpd.DataFileName + cpd.TargetID.ToString();
try
{
byte[] cpdDetailObj = DBAccessor.GetCompoundDetailItem(analysis.FilePath, sKey);
using (MemoryStream ms = new MemoryStream(cpdDetailObj))
{
BinaryFormatter bf = new BinaryFormatter();
cpdDetails = (MFECpdDetails)bf.Deserialize(ms);
}
}
catch
{
continue; // not a saved item
}
List <IParameterSet> parameterSets = new List <IParameterSet>();
parameterSets.Add(qualAppLogic.ProcessingParameters);
parameterSets.Add(qualAppLogic.ResultFilters);
parameterSets.Add(qualAppLogic.ChargeStateAssignment);
parameterSets.Add(qualAppLogic.TofPeakFinderPset);
parameterSets.Add(qualAppLogic.MSMSPeakFilter);
((MFECpdDetails)cpdDetails).ChargeStateAssignmentPset = qualAppLogic.ChargeStateAssignment;
((MFECpdDetails)cpdDetails).TofPeakFinderPset = qualAppLogic.TofPeakFinderPset;
((MFECpdDetails)cpdDetails).MSMSPeakFilterPset = qualAppLogic.MSMSPeakFilter;
((MFECpdDetails)cpdDetails).ParameterSets = parameterSets;
}
List <Type> algoTypeList = cpd.GetFindCompoundAlgorithmTypes();
if (algoTypeList.Count > 0)
{
Type algoType = cpd.GetFindCompoundAlgorithmTypes().First();
try
{
findCpds = new FindCpdsMassHunter(QualCommandBase.CreatePeakFinderForMassSpectrum());
resultOptions = qualAppLogic[QualDAMethod.ParamKeyMFEProcessing] as PSetMassHunterProcessing;
}
catch (Exception ex)
{
if (findCpds != null && qualAppLogic.OpenProject) // no pset verification for open project
{
if (algoType == typeof(FindByIsotopologue))
{
resultOptions = qualAppLogic.GetParameterSetNoValidate(QualDAMethod.ParamKeyFindByIsotopologue);
}
else
{
resultOptions = qualAppLogic.GetParameterSetNoValidate(QualDAMethod.ParamKeyFindCompoundsFormula);
}
}
else
{
throw ex;
}
}
}
var psetFbF = resultOptions as IPSetFindCpdsFormula;
if (psetFbF != null)
{
psetFbF.PreferProfileRawSpectra = false;
}
var psetMFE = resultOptions as IPSetMassHunterProcessing;
if (psetMFE != null)
{
psetMFE.PreferProfileRawSpectra = false;
}
strcItems.icompound = cpd;
strcItems.idetails = cpdDetails;
strcItems.ifindcpd = findCpds;
strcItems.ipset = resultOptions;
strcItems.idataaccess = analysis.DataAccess;
strcItems.bheight = cpd.HasValue(ResultAttribute.Height);
concurrentDict.TryAdd(analysisID, strcItems);
}
try
{
Parallel.ForEach(concurrentDict, new ParallelOptions {
MaxDegreeOfParallelism = Environment.ProcessorCount
}, strctItem =>
{
StrcuctFindCpdItem myItems = (StrcuctFindCpdItem)strctItem.Value;
Agilent.MassSpectrometry.DataAnalysis.Qualitative.ProfinderLogic.Strcuctplots strcplots = new Agilent.MassSpectrometry.DataAnalysis.Qualitative.ProfinderLogic.Strcuctplots();
IFindCompounds findCpds = myItems.ifindcpd;
IParameterSet resultOptions = myItems.ipset;
if (myItems.idetails != null)
{
if (myItems.idetails is CpdDetailsFindByIsotopologue)
{
IPSetFindByIsotopologue psetFindIso = resultOptions as IPSetFindByIsotopologue;
if (psetFindIso != null && psetFindIso.PreferRawSpectrumDisplay)
{
plotTypes = CpdDataObjectType.MsChromatogram | CpdDataObjectType.MsSpectrum;
}
else
{
plotTypes = CpdDataObjectType.MsChromatogram | CpdDataObjectType.CleanedSpectrum;
}
}
var ifxData = findCpds.GetCpdDataObjects(myItems.icompound, myItems.idetails, plotTypes, myItems.idataaccess, resultOptions);
strcplots.ifxdata = ifxData;
List <IFXData> fxList = strcplots.ifxdata;
foreach (var chromItem in fxList)
{
//chromItem.RemoveCompoundInformation(); // label will use it
FXDataBase fxDatabase = chromItem as FXDataBase;
if ((fxDatabase != null) && (fxDatabase.AcquisitionMetaData != null))
{
fxDatabase.AcquisitionMetaData = null;
}
}
strcplots.bheight = myItems.icompound.HasValue(ResultAttribute.Height);
strcplots.cpdGroupNum = cpdGroup.CompoundGroupNumber;
plotDict[strctItem.Key] = strcplots;
}
});
}
catch (AggregateException e)
{
throw e.InnerException;
}
return(plotDict);
}