/*
 Copyright (C) 2003 Ronald C Beavis, all rights reserved
 X! tandem
 This software is a component of the X! proteomics software
 development project

Use of this software governed by the Artistic license, as reproduced here:

The Artistic License for all X! software, binaries and documentation

Preamble
The intent of this document is to state the conditions under which a
Package may be copied, such that the Copyright Holder maintains some
semblance of artistic control over the development of the package,
while giving the users of the package the right to use and distribute
the Package in a more-or-less customary fashion, plus the right to
make reasonable modifications.

Definitions
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  Holder, and derivatives of that collection of files created through
  textual modification.

"Standard Version" refers to such a Package if it has not been modified,
  or has been modified in accordance with the wishes of the Copyright
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  for the package.

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  media cost, duplication charges, time of people involved, and so on.
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"Freely Available" means that no fee is charged for the item itself,
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1. You may make and give away verbatim copies of the source form of the
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  document the differences in manual pages (or equivalent), together
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d.	make other distribution arrangements with the Copyright Holder.

5. You may charge a reasonable copying fee for any distribution of
this Package. You may charge any fee you choose for support of
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However, you may distribute this Package in aggregate with other
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6. The scripts and library files supplied as input to or produced as
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do not represent such an executable image as a Standard Version of
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7. C subroutines (or comparably compiled subroutines in other languages)
supplied by you and linked into this Package in order to emulate
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products derived from this software without specific prior written permission.

10. THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
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The End
*/

#pragma once

// File version: 2003-07-01

/*
 * the mreport object provides the functionality to export all of the
 * information collected in mprocess to an XML file. The file path was defined
 * in the original XML input parameter file. The file produced by mreport can be
 * used as an input parameter file to repeat a protein modeling session at a
 * later time.
 */

#include <QFile>
#include <QXmlStreamWriter>
#include <map>
#include <set>

class mscore;
class msequtilities;

class mreport
{
  public:
  mreport(mscore &score);
  virtual ~mreport(void);
  bool end(void);
  bool endProteinGroup() const;
  bool startProteinGroup(const mspectrum &_s) const;
  bool histogram(mspectrum &_s);
  bool info(XmlParameter &_x);
  bool masses(msequtilities &_p);
  bool performance(XmlParameter &_x);
  bool sequence(mspectrum &_s, vector<string> &_p, map<string, string> &_ann);
  bool spectrum(mspectrum &_s, string &_f);
  bool start(XmlParameter &_x);
  bool set_columns(const long _v);
  bool set_compression(const bool _b);


  static QString massStr(double mass);
  static QString scoreStr(float score);
  static QString evalueStr(double score);

  private:
  void writeStartGamlTrace(std::size_t xml_id,
                           const QString &label,
                           const QString &type) const;
  void writeGamlValues(const QString &data_str,
                       std::size_t xml_id,
                       const QString &label,
                       const QString &units,
                       const std::vector<double> &list_values) const;
  QString label80Str(const QString &label) const;


  private:
  long m_lHistogramColumns;
  set<size_t> m_setProteins;
  bool check_proteins(const size_t _t);
  map<size_t, bool> m_maptUids;
  bool m_bCompress;

  static const QString m_xmlnsGaml;
  static const QString m_processFlavor;
  QFile *m_outputFile;
  QXmlStreamWriter *m_outputStream;

  // ofstream m_ofOut; // the output file stream
  mscore &m_Score; // mscore used to generate scores in report
};
