QCBase.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2021.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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// --------------------------------------------------------------------------
// $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 <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 requires() 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;
 
      for (const auto& features : fmap)
      {
        if (!features.getPeptideIdentifications().empty()) return true;
      }
      return false;
    }
  };
}