QuantitativeExperimentalDesign.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Immanuel Luhn$
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/FORMAT/TextFile.h>
#include <OpenMS/ANALYSIS/QUANTITATION/PeptideAndProteinQuant.h>
#include <OpenMS/ANALYSIS/QUANTITATION/ProteinResolver.h>

//#include <vector>

namespace OpenMS
{
  class OPENMS_DLLAPI QuantitativeExperimentalDesign :
    public DefaultParamHandler
  {
public:

    QuantitativeExperimentalDesign();

    //Destructor
    ~QuantitativeExperimentalDesign() override;

    void applyDesign2Resolver(ProteinResolver & resolver, TextFile & file, StringList & fileNames);

    void applyDesign2Quantifier(PeptideAndProteinQuant & quantifier, TextFile & file, StringList & fileNames);
    //std::vector< std::pair<PeptideAndProteinQuant::PeptideData,PeptideAndProteinQuant::ProteinQuant> >& result);

private:
    QuantitativeExperimentalDesign(const QuantitativeExperimentalDesign &);

    QuantitativeExperimentalDesign & operator=(const QuantitativeExperimentalDesign &);

    void mergeFeatureMaps_(FeatureMap & map, const String & experiment, StringList & file_paths);

    void mergeConsensusMaps_(ConsensusMap & map, const String & experiment, StringList & file_paths);

    void mergeIDFiles_(std::vector<ProteinIdentification> & proteins, std::vector<PeptideIdentification> & peptides, const String & experiment, StringList & file_paths);

    void findRelevantFilePaths_(std::map<String, StringList> & design2FileBaseName, std::map<String, StringList> & design2FilePath, StringList & filePaths);

    void analyzeHeader_(UInt & expCol, UInt & fileCol, StringList & header);

    void getSeparator_(String & separator);

    void mapFiles2Design_(std::map<String, StringList> & experiments, TextFile & file);


  };

} // namespace OpenMS