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 2002-2023.
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// This software is released under a three-clause BSD license:
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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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);
 
private:
    QuantitativeExperimentalDesign(const QuantitativeExperimentalDesign &);
 
    QuantitativeExperimentalDesign & operator=(const QuantitativeExperimentalDesign &);
 
    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