QCBase.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Chris Bielow $
// $Authors: Chris Bielow, Tom Waschischeck $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/DATASTRUCTURES/FlagSet.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <algorithm>
#include <map>
 
namespace OpenMS
{
  class MSExperiment;
  class ConsensusMap;
 
  class OPENMS_DLLAPI QCBase
  {
  public:
    enum class Requires : UInt64 // 64 bit unsigned type for bitwise and/or operations (see below)
    {
      NOTHING,      //< default, does not require anything
      RAWMZML,      //< mzML file is required
      POSTFDRFEAT,  //< Features with FDR-filtered pepIDs
      PREFDRFEAT,   //< Features with unfiltered pepIDs
      CONTAMINANTS, //< Contaminant Database
      TRAFOALIGN,   //< transformationXMLs for RT-alignment
      ID,           //< idXML with protein IDs
      SIZE_OF_REQUIRES
    };
    static const std::string names_of_requires[];
 
    enum class ToleranceUnit
    {
      AUTO,
      PPM,
      DA,
      SIZE_OF_TOLERANCEUNIT
    };
    static const std::string names_of_toleranceUnit[];
 
 
    class OPENMS_DLLAPI SpectraMap
    {
    public:
      SpectraMap() = default;
 
      explicit SpectraMap(const MSExperiment& exp);
 
      ~SpectraMap() = default;
 
      void calculateMap(const MSExperiment& exp);
 
      UInt64 at(const String& identifier) const;
 
      void clear();
 
      bool empty() const;
 
      Size size() const;
 
    private:
      std::map<String, UInt64> nativeid_to_index_; //< nativeID to index
    };
 
    using Status = FlagSet<Requires>;
 
 
    virtual const String& getName() const = 0;
 
    virtual Status requirements() const = 0;
 
 
    bool isRunnable(const Status& s) const;
 
    static bool isLabeledExperiment(const ConsensusMap& cm);
 
    template<typename MAP>
    static bool hasPepID(const MAP& fmap)
    {
      if (!fmap.getUnassignedPeptideIdentifications().empty())
        return true;
 
      return std::any_of(fmap.cbegin(), fmap.cend(), [](const auto& f) { return !f.getPeptideIdentifications().empty(); });
    }
  };
} // namespace OpenMS