QcMLFile.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2022.
//
// This software is released under a three-clause BSD license:
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//  * Redistributions in binary form must reproduce the above copyright
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//    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"
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// $Maintainer: Mathias Walzer, Axel Walter $
// $Authors: Mathias Walzer $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
#include <OpenMS/FORMAT/XMLFile.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <vector>

namespace OpenMS
{
  class ConsensusMap;
  class FeatureMap;

  class OPENMS_DLLAPI QcMLFile :
    public Internal::XMLHandler,
    public Internal::XMLFile,
    public ProgressLogger
  {
public:
    class OPENMS_DLLAPI QualityParameter
    {
    public:
      String name; 
      String id; 
      String value; 
      String cvRef; 
      String cvAcc; 
      String unitRef; 
      String unitAcc; 
      String flag; 

      QualityParameter();

      QualityParameter(const QualityParameter& rhs);

      QualityParameter& operator=(const QualityParameter& rhs);
      bool operator==(const QualityParameter& rhs) const;
      bool operator<(const QualityParameter& rhs) const;
      bool operator>(const QualityParameter& rhs) const;

      String toXMLString(UInt indentation_level) const;
    };

    class OPENMS_DLLAPI Attachment
    {
    public:
      String name; 
      String id; 
      String value; 
      String cvRef; 
      String cvAcc; 
      String unitRef; 
      String unitAcc; 
      String binary; 
      String qualityRef; 
      std::vector<String> colTypes; 
      std::vector< std::vector<String> > tableRows; 
      //~ TODO -schema- coltypes with full definition (uintRef, unitAcc)

      Attachment();

      Attachment(const Attachment& rhs);

      Attachment& operator=(const Attachment& rhs);
      bool operator==(const Attachment& rhs) const;
      bool operator<(const Attachment& rhs) const;
      bool operator>(const Attachment& rhs) const;

      String toXMLString(UInt indentation_level) const;
      String toCSVString(const String& separator) const;
    };

    QcMLFile();
    ~QcMLFile() override;

    String map2csv(const std::map< String, std::map<String, String> >& cvs_table, const String& separator) const;
    String exportIDstats(const String& filename) const;
    
    void registerRun(const String& id, const String& name);
    void registerSet(const String& id, const String& name, const std::set<String>& names);
    void addRunQualityParameter(const String& r, const QualityParameter& qp);
    void addRunAttachment(const String& r, const Attachment& at);
    void addSetQualityParameter(const String& r, const QualityParameter& qp);
    void addSetAttachment(const String& r, const Attachment& at);
    void removeAttachment(const String& r, std::vector<String>& ids, const String& at = "");
    void removeAttachment(const String& r, const String& at);
    void removeAllAttachments(const String& at);
    void removeQualityParameter(const String& r, std::vector<String>& ids);
    void merge(const QcMLFile & addendum, const String& setname = "");
    void/* std::vector<String>& */ collectSetParameter(const String& setname, const String& qp, std::vector<String>& ret);
    String exportAttachment(const String& filename, const String& qpname) const; 
    String exportQP(const String& filename, const String& qpname) const;
    String exportQPs(const String& filename, const StringList& qpnames) const;
    void getRunIDs (std::vector<String>& ids) const;
    void getRunNames (std::vector<String>& ids) const;
    bool existsRun(const String& filename, bool checkname = false) const;
    bool existsSet(const String& filename, bool checkname = false) const;
    void existsRunQualityParameter(const String& filename, const String& qpname, std::vector<String>& ids) const;
    void existsSetQualityParameter(const String& filename, const String& qpname, std::vector<String>& ids) const;

    void collectQCData(std::vector<ProteinIdentification>& prot_ids,
                       std::vector<PeptideIdentification>& pep_ids,
                       const FeatureMap& feature_map,
                       const ConsensusMap& consensus_map,
                       const String& inputfile_raw,
                       const bool remove_duplicate_features,
                       const MSExperiment& exp);

    void store(const String& filename) const;

    void load(const String & filename);

    //~ int siz; //debug

protected:
    // Docu in base class
    void endElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname) override;

    // Docu in base class
    void startElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname, const xercesc::Attributes & attributes) override;

    // Docu in base class
    void characters(const XMLCh * const chars, const XMLSize_t length) override;

    std::map<String, std::vector< QualityParameter > > runQualityQPs_; //TODO run name attribute to schema of RunQuality
    std::map<String, std::vector< Attachment > > runQualityAts_;
    std::map<String, std::vector< QualityParameter > > setQualityQPs_;
    std::map<String, std::vector< Attachment > > setQualityAts_;
    std::map<String, std::set< String > > setQualityQPs_members_;
    std::map<String, String > run_Name_ID_map_;
    std::map<String, String > set_Name_ID_map_;

    String tag_;
    UInt progress_;
    QualityParameter qp_;
    Attachment at_;
    std::vector<String> row_;
    std::vector<String> header_;
    String name_;
    String run_id_;
    std::set<String> names_;
    std::vector<QualityParameter> qps_;
    std::vector<Attachment> ats_;
  };

} // namespace OpenMS