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);
}
public List <DataTypes.CompoundGroup> GetCompoundGroups(List <string> analysisFiles)
{
try
{
qualAppLogic.AppExecutionMode = AppExecutionMode.WorkListAutomation;
CmdInitializeApplication cmdInit = new CmdInitializeApplication(qualAppLogic);
ExecuteCommand(qualAppLogic, cmdInit);
QualFeatureConfig.InitRegistryFromAppConfig();
qualAppLogic.AppProgressEvent += new AppProgressEventHandler(OnAppProgressEvent);
IAppState appState = qualAppLogic as IAppState;
//appState.ThreadErrorReporter = m_messageReporter;
AnalysisMethodLoadOptions loadMethod = GetAnalysisMethodLoadOptions(null);
//if (analysisFiles.Count > 0)
//{
bool loadResults = false;
bool runLoadTimeScripts = false;
CmdOpenAnalysisFile cmdOpenAnalysis = new CmdOpenAnalysisFile
(qualAppLogic,
analysisFiles.ToArray(),
loadMethod,
loadResults,
runLoadTimeScripts);
ExecuteCommand(qualAppLogic, cmdOpenAnalysis);
RunScript(qualAppLogic, analysisFiles);
IEnumerable <Agilent.MassSpectrometry.DataAnalysis.ICompoundGroup> cpdGroups = qualAppLogic.DataStore.CompoundGroups;
List <DataTypes.CompoundGroup> compoundGroups = new List <DataTypes.CompoundGroup>();
foreach (Agilent.MassSpectrometry.DataAnalysis.ICompoundGroup cpdGroup in cpdGroups)
{
DataTypes.CompoundGroup compoundGroup = getICompoundGroup(cpdGroup, analysisFiles) as DataTypes.CompoundGroup;
compoundGroups.Add(compoundGroup);
}
Console.ReadKey();
}
catch (MSDAApplicationException msdaExep)
{
Console.WriteLine(msdaExep.Message);
}
catch (Exception e)
{
string analysisName = "";
for (int analysisInd = 0; analysisInd < analysisFiles.Count; analysisInd++)
{
if (analysisName == "")
{
analysisName = analysisFiles[analysisInd];
}
else
{
analysisName = analysisName + " , " + analysisFiles[analysisInd];
}
}
Console.WriteLine(e.StackTrace);
}
return(null);
}
