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 2002-2021.
//
// 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
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// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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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(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(String r, QualityParameter qp);
    void addRunAttachment(String r, Attachment at);
    void addSetQualityParameter(String r, QualityParameter qp);
    void addSetAttachment(String r, Attachment at);
    void removeAttachment(String r, std::vector<String>& ids, String at = "");
    void removeAttachment(String r, String at);
    void removeAllAttachments(String at);
    void removeQualityParameter(String r, std::vector<String>& ids);
    void merge(const QcMLFile & addendum, 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