mzintegrationparams.h

Go to the documentation of this file.

/* BEGIN software license
 *
 * msXpertSuite - mass spectrometry software suite
 * -----------------------------------------------
 * Copyright(C) 2009,...,2018 Filippo Rusconi
 *
 * http://www.msxpertsuite.org
 *
 * This file is part of the msXpertSuite project.
 *
 * The msXpertSuite project is the successor of the massXpert project. This
 * project now includes various independent modules:
 *
 * - massXpert, model polymer chemistries and simulate mass spectrometric data;
 * - mineXpert, a powerful TIC chromatogram/mass spectrum viewer/miner;
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program. If not, see <http://www.gnu.org/licenses/>.
 *
 * END software license
 */
 
 
#pragma once
 
 
#include <map>
 
#include "../../precision.h"
#include "../../massspectrum/massspectrum.h"
 
 
namespace pappso
{
 
//! Type of binning when performing integrations to a mass spectrum
enum class BinningType
{
  //! < no binning
  NONE = 0,
 
  //! binning based on mass spectral data
  DATA_BASED,
 
  //! binning based on arbitrary bin size value
  ARBITRARY,
 
  LAST,
};
 
extern std::map<BinningType, QString> binningTypeMap;
BinningType getBinningTypeFromString(const QString &text);
 
 
//! The MzIntegrationParams class provides the parameters definining how m/z !
// integrations must be performed.
/*!
 * Depending on the various mass spectrometer vendors, the mass spectrometry
 * data files are structured in different ways and the software for mass data
 * format conversion from raw files to mzML or mzXML produce mass data
 * characterized by different behaviours.
 *
 * The different characteristics of mass spectrometry data set are:
 *
 * The size of the various mass spectra in the file is constant or variable;
 *
 * The first m/z value of the various spectra is identical or not (that is,
 * the spectra are root in a constant or variable root m/z value);
 *
 * The m/z delta between two consecutive m/z values of a given spectrum are
 * constant or variable;
 *
 * The spectra contain or not 0-value m/z data points;
 
*/
class PMSPP_LIB_DECL MzIntegrationParams
{
  public:
 
  enum class InitializationResult
  {
    // The order is important.
    DEFAULT = 0,
    FROM_SETTINGS_BIN_SIZE_MODEL_PARTIAL = 1,
    FROM_SETTINGS_BIN_SIZE_MODEL_FULL = 2,
    FROM_SETTINGS_FULL = 3
  };
 
  Q_INVOKABLE MzIntegrationParams();
  Q_INVOKABLE MzIntegrationParams(const QString &text);
  Q_INVOKABLE MzIntegrationParams(pappso::pappso_double minMz,
                                  pappso::pappso_double maxMz,
                                  BinningType binningType,
                                  int decimalPlaces,
                                  pappso::PrecisionPtr precisionPtr,
                                  int binSizeDivisor,
                                  bool removeZeroValDataPoints);
 
  Q_INVOKABLE MzIntegrationParams(const MzIntegrationParams &other);
 
  virtual ~MzIntegrationParams();
 
  InitializationResult initialize(const QString &text);
 
  MzIntegrationParams &operator=(const MzIntegrationParams &other);
 
  Q_INVOKABLE void setSmallestMz(pappso::pappso_double value);
  Q_INVOKABLE void updateSmallestMz(pappso::pappso_double value);
  pappso::pappso_double getSmallestMz() const;
 
  Q_INVOKABLE void setGreatestMz(pappso::pappso_double value);
  Q_INVOKABLE void updateGreatestMz(pappso::pappso_double value);
  Q_INVOKABLE pappso::pappso_double getGreatestMz() const;
 
  Q_INVOKABLE void setBinningType(BinningType binningType);
  Q_INVOKABLE BinningType getBinningType() const;
 
  Q_INVOKABLE void setDecimalPlaces(int decimal_places);
  Q_INVOKABLE int getDecimalPlaces() const;
 
  Q_INVOKABLE void setBinSizeModel(pappso::PrecisionPtr bin_size_model);
  Q_INVOKABLE pappso::PrecisionPtr getBinSizeModel() const;
 
  void setBinSizeDivisor(int divisor);
  int getBinSizeDivisor() const;
 
  Q_INVOKABLE void setRemoveZeroValDataPoints(bool removeOrNot = true);
  Q_INVOKABLE bool isRemoveZeroValDataPoints() const;
 
  Q_INVOKABLE void reset();
 
  Q_INVOKABLE bool isValid() const;
 
  Q_INVOKABLE bool hasValidMzRange() const;
 
  Q_INVOKABLE std::vector<pappso::pappso_double> createBins();
  Q_INVOKABLE std::vector<pappso::pappso_double>
  createBins(pappso::MassSpectrumCstSPtr mass_spectrum_csp);
 
  Q_INVOKABLE QString toString(int offset, const QString &spacer = " ") const;
  // The string below is used to recreate the MzIntegrationParams from string
  Q_INVOKABLE QString toString() const;
 
  private:
  // That smallest value needs to be set to max, because it will be necessary
  // compare any new m/z valut to it.
  pappso::pappso_double m_smallestMz = std::numeric_limits<double>::max();
 
  // That greatest value needs to be set to min, because it will be necessary
  // compare any new m/z valut to it.
  pappso::pappso_double m_greatestMz = std::numeric_limits<double>::min();
 
  BinningType m_binningType = BinningType::ARBITRARY;
 
  // -1 means that there is no restriction on the number of digits after the
  // decimal point.
  int m_decimalPlaces = -1;
 
  // This should actually be called "bin size model" as it describes the width of
  // the bins on the basis of a unit (ppm, res, dalton) and of a nominal value (nominal).
  pappso::PrecisionPtr mp_binSizeModel =
    pappso::PrecisionFactory::getResInstance(40000);
 
  int m_binSizeDivisor = 1;
 
  bool m_removeZeroValDataPoints = true;
 
  std::vector<double> createArbitraryBins();
  std::vector<double>
  createDataBasedBins(pappso::MassSpectrumCstSPtr massSpectrum);
};
 
 
} // namespace pappso
 
Q_DECLARE_METATYPE(pappso::MzIntegrationParams);
Q_DECLARE_METATYPE(pappso::MzIntegrationParams *);
 
extern int mzIntegrationParamsMetaTypeId;
extern int mzIntegrationParamsPtrMetaTypeId;