QcMLFile.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: 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 <OpenMS/METADATA/PeptideIdentificationList.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:
      std::string name; 
      std::string id; 
      std::string value; 
      std::string cvRef; 
      std::string cvAcc; 
      std::string unitRef; 
      std::string unitAcc; 
      std::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;
 
      std::string toXMLString(UInt indentation_level) const;
    };
 
    class OPENMS_DLLAPI Attachment
    {
    public:
      std::string name; 
      std::string id; 
      std::string value; 
      std::string cvRef; 
      std::string cvAcc; 
      std::string unitRef; 
      std::string unitAcc; 
      std::string binary; 
      std::string qualityRef; 
      std::vector<std::string> colTypes; 
      std::vector< std::vector<std::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;
 
      std::string toXMLString(UInt indentation_level) const;
      std::string toCSVString(const std::string& separator) const;
    };
 
    QcMLFile();
    ~QcMLFile() override;
 
    std::string map2csv(const std::map< std::string, std::map<std::string, std::string> >& cvs_table, const std::string& separator) const;
    std::string exportIDstats(const std::string& filename) const;
    
    void registerRun(const std::string& id, const std::string& name);
    void registerSet(const std::string& id, const std::string& name, const std::set<std::string>& names);
    void addRunQualityParameter(const std::string& r, const QualityParameter& qp);
    void addRunAttachment(const std::string& r, const Attachment& at);
    void addSetQualityParameter(const std::string& r, const QualityParameter& qp);
    void addSetAttachment(const std::string& r, const Attachment& at);
    void removeAttachment(const std::string& r, std::vector<std::string>& ids, const std::string& at = "");
    void removeAttachment(const std::string& r, const std::string& at);
    void removeAllAttachments(const std::string& at);
    void removeQualityParameter(const std::string& r, std::vector<std::string>& ids);
    void merge(const QcMLFile & addendum, const std::string& setname = "");
    void/* std::vector<std::string>& */ collectSetParameter(const std::string& setname, const std::string& qp, std::vector<std::string>& ret);
    std::string exportAttachment(const std::string& filename, const std::string& qpname) const; 
    std::string exportQP(const std::string& filename, const std::string& qpname) const;
    std::string exportQPs(const std::string& filename, const StringList& qpnames) const;
    void getRunIDs (std::vector<std::string>& ids) const;
    void getRunNames (std::vector<std::string>& ids) const;
    bool existsRun(const std::string& filename, bool checkname = false) const;
    bool existsSet(const std::string& filename, bool checkname = false) const;
    void existsRunQualityParameter(const std::string& filename, const std::string& qpname, std::vector<std::string>& ids) const;
    void existsSetQualityParameter(const std::string& filename, const std::string& qpname, std::vector<std::string>& ids) const;
 
    void collectQCData(std::vector<ProteinIdentification>& prot_ids,
                       PeptideIdentificationList& pep_ids,
                       const FeatureMap& feature_map,
                       const ConsensusMap& consensus_map,
                       const std::string& inputfile_raw,
                       const bool remove_duplicate_features,
                       const MSExperiment& exp);
 
    void store(const std::string& filename) const;
 
    void load(const std::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<std::string, std::vector< QualityParameter > > runQualityQPs_; //TODO run name attribute to schema of RunQuality
    std::map<std::string, std::vector< Attachment > > runQualityAts_;
    std::map<std::string, std::vector< QualityParameter > > setQualityQPs_;
    std::map<std::string, std::vector< Attachment > > setQualityAts_;
    std::map<std::string, std::set< std::string > > setQualityQPs_members_;
    std::map<std::string, std::string > run_Name_ID_map_;
    std::map<std::string, std::string > set_Name_ID_map_;
 
    std::string tag_;
    UInt progress_;
    QualityParameter qp_;
    Attachment at_;
    std::vector<std::string> row_;
    std::vector<std::string> header_;
    std::string name_;
    std::string run_id_;
    std::set<std::string> names_;
    std::vector<QualityParameter> qps_;
    std::vector<Attachment> ats_;
  };
 
} // namespace OpenMS