2.5.0-shortNms/html/a04088_source.html

// --------------------------------------------------------------------------

//                   OpenMS -- Open-Source Mass Spectrometry

// --------------------------------------------------------------------------

// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,

// ETH Zurich, and Freie Universitaet Berlin 2002-2020.

//

// 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.

// --------------------------------------------------------------------------

// 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

// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING

// 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

// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF

// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

//

// --------------------------------------------------------------------------

// $Maintainer: Mathias Walzer $

// $Authors: Mathias Walzer $

// --------------------------------------------------------------------------


#pragma once


#include <OpenMS/CONCEPT/ProgressLogger.h>

#include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>

#include <OpenMS/FORMAT/XMLFile.h>


#include <vector>

#include <map>

#include <set>

#include <algorithm>


namespace OpenMS

{

  class OPENMS_DLLAPI QcMLFile :

    public Internal::XMLHandler,

    public Internal::XMLFile,

    public ProgressLogger

  {

public:


    struct OPENMS_DLLAPI QualityParameter

    {

      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;

    };


    struct OPENMS_DLLAPI Attachment

    {

      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 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