private void RunScript(ProfinderLogic qualAppLogic, List <string> analysisFiles)
{
List <Analysis> Analyses = new List <Analysis>();
foreach (string analysisPath in analysisFiles)
{
Analysis anlysis = qualAppLogic.DataHeirarchy.AnalysisStore.Values.Cast <Analysis>().First(a => a.FilePath == analysisPath);
Analyses.Add(anlysis);
}
CmdFindByMFE cmdMFE1 = new CmdFindByMFE(qualAppLogic, MFEMode.RECURSIVE_STAGE_1, Analyses);
ExecuteCommand(qualAppLogic, cmdMFE1);
Console.WriteLine(" Find by MFE of " + MFEMode.RECURSIVE_STAGE_1 + " has completed");
CmdRecursiveMFE rmfe = new CmdRecursiveMFE(qualAppLogic, Analyses);
ExecuteCommand(qualAppLogic, rmfe);
Console.WriteLine(" recursive mfe is done ");
CmdFilterCompoundGroupsMFE cgMfe = new CmdFilterCompoundGroupsMFE(qualAppLogic, analysisFiles);
ExecuteCommand(qualAppLogic, cgMfe);
CmdFindByMFE cmdMFE2 = new CmdFindByMFE(qualAppLogic, MFEMode.RECURSIVE_STAGE_2, Analyses);
ExecuteCommand(qualAppLogic, cmdMFE2);
Console.WriteLine(" Find by MFE of " + MFEMode.RECURSIVE_STAGE_2 + " has completed");
CmdFilterCompoundGroupsMFEPost cgpMfePost = new CmdFilterCompoundGroupsMFEPost(qualAppLogic, analysisFiles);
ExecuteCommand(qualAppLogic, cgpMfePost);
Console.WriteLine(" Filtering Done ");
Console.WriteLine(" Compound Groups of datastore updated");
}
public static void SavePSet(ProfinderLogic AppLogic, IParameterSet pset, string usageKey)
{
pset.UsageKey = usageKey;
IParameterSet[] Pset = { pset as ParameterSet };
var cmdSetParam = new CmdSetParameters(AppLogic, Pset);
cmdSetParam.Execute();
}
private void InitiaizeApplication()
{
qualAppLogic = new ProfinderLogic();
qualAppLogic.AppExecutionMode = AppExecutionMode.WorkListAutomation;
Console.WriteLine("Initializing ..");
CmdInitializeApplication cmdInit = new CmdInitializeApplication(qualAppLogic);
ExecuteCommand(qualAppLogic, cmdInit);
}
/// <summary>
/// c'tor
/// </summary>
/// <param name="appManager"></param>
/// <param name="filePaths"></param>
public CmdFilterCompoundGroupsMFE(ProfinderLogic appManager) : base(appManager)
{
m_psetFilters = m_AppManager[QualDAMethod.ParamKeyCpdGroupFilters] as IPSetCpdGroupFilters;
var psetFileList = m_PFLogic[QualInMemoryMethod.ParamDataFileList] as PSetDataFileList;
m_sampleGroupDict = psetFileList.SelectedFileName.ToDictionary(
fs => fs.FileName,
fs => string.Join(":", fs.SampleGroups));
}
/// <summary>
/// c'tor
/// </summary>
/// <param name="appManager"></param>
/// <param name="mfeMode"></param>
/// <param name="analysis"></param>
public CmdFindByMFE(ProfinderLogic appManager, MFEMode mfeMode, List <Analysis> analysis)
: base(appManager)
{
// if the user passes a reference to a List<ICompoundGroup>
// use that as the data store
m_cpdGroupList = new List <ICompoundGroup>();
m_MFEMode = mfeMode;
m_analyses = analysis;
m_cpdGroupList = new List <ICompoundGroup>();
m_cpdResults = new SortedDictionary <string, IFindCpdResults>();
}
/// <summary>
/// constructor
/// </summary>
/// <param name="appManager"></param>
/// <param name="analysis"></param>
public CmdRecursiveMFE(ProfinderLogic appManager, List <Analysis> analysis) : base(appManager)
{
m_analyses = analysis;
}
public static PSetCpdGroupFilters GetFilterParameters(ProfinderLogic AppLogic)
{
PSetCpdGroupFilters filterInfo = AppLogic[QualDAMethod.ParamKeyCpdGroupFilters] as PSetCpdGroupFilters;
return(filterInfo);
}
public static IPSetChargeStateAssignment GetChargeStateParameters(ProfinderLogic AppLogic)
{
IPSetChargeStateAssignment chargeStateInfo = AppLogic[QualDAMethod.GetUsageKey(QualFunctionality.ChargeStateAssignment, QualDataType.MS)] as IPSetChargeStateAssignment;
return(chargeStateInfo);
}
public static IPSetMassHunterProcessing GetMFEProcessingParameters(ProfinderLogic AppLogic)
{
IPSetMassHunterProcessing extractionInfo = AppLogic[QualDAMethod.ParamKeyMFEProcessing] as IPSetMassHunterProcessing;
return(extractionInfo);
}
public static IPSetAlignmentInfo GetAlignmentParameters(ProfinderLogic AppLogic)
{
IPSetAlignmentInfo alignmentInfo = AppLogic[QualDAMethod.ParamKeyAlignmentInformation] as IPSetAlignmentInfo;
return(alignmentInfo);
}
public MFE()
{
qualAppLogic = new ProfinderLogic();
}
/// <summary>
/// c'tor
/// </summary>
/// <param name="appManager"></param>
public PFCmdCommandBase(ProfinderLogic appManager)
: base(appManager)
{
m_PFLogic = appManager;
}
