indentation with clang format v6.0

src/core/automaticfilterparameters.cpp

 
 /*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-*     XTPcpp 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.
-*
-*     XTPcpp 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 XTPcpp.  If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-*     Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ *     XTPcpp 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.
+ *
+ *     XTPcpp 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 XTPcpp.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ *     Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
 
 #include "automaticfilterparameters.h"
 
 AutomaticFilterParameters::AutomaticFilterParameters()
 {
-
 }
 
-AutomaticFilterParameters::AutomaticFilterParameters(const AutomaticFilterParameters& other)
+AutomaticFilterParameters::AutomaticFilterParameters(
+  const AutomaticFilterParameters &other)
 {
-    _filter_minimum_peptide_evalue=other._filter_minimum_peptide_evalue;
-    _filter_minimum_protein_evalue=other._filter_minimum_protein_evalue;
-    _filter_minimum_peptide_per_match=other._filter_minimum_peptide_per_match;
-    _filter_is_cross_sample_peptide_number=other._filter_is_cross_sample_peptide_number;
+  _filter_minimum_peptide_evalue    = other._filter_minimum_peptide_evalue;
+  _filter_minimum_protein_evalue    = other._filter_minimum_protein_evalue;
+  _filter_minimum_peptide_per_match = other._filter_minimum_peptide_per_match;
+  _filter_is_cross_sample_peptide_number =
+    other._filter_is_cross_sample_peptide_number;
 }
 
 AutomaticFilterParameters::~AutomaticFilterParameters()
 {
-
 }
 
-void AutomaticFilterParameters::setFilterPeptideEvalue( pappso::pappso_double evalue) {
-    _filter_minimum_peptide_evalue = evalue;
+void
+AutomaticFilterParameters::setFilterPeptideEvalue(pappso::pappso_double evalue)
+{
+  _filter_minimum_peptide_evalue = evalue;
 }
 
-void AutomaticFilterParameters::setFilterProteinEvalue( pappso::pappso_double evalue) {
-    _filter_minimum_protein_evalue = evalue;
+void
+AutomaticFilterParameters::setFilterProteinEvalue(pappso::pappso_double evalue)
+{
+  _filter_minimum_protein_evalue = evalue;
 }
-void AutomaticFilterParameters::setFilterMinimumPeptidePerMatch(unsigned int number) {
-    _filter_minimum_peptide_per_match = number;
+void
+AutomaticFilterParameters::setFilterMinimumPeptidePerMatch(unsigned int number)
+{
+  _filter_minimum_peptide_per_match = number;
 }
-void AutomaticFilterParameters::setFilterCrossSamplePeptideNumber(bool cross) {
-    _filter_is_cross_sample_peptide_number = cross;
+void
+AutomaticFilterParameters::setFilterCrossSamplePeptideNumber(bool cross)
+{
+  _filter_is_cross_sample_peptide_number = cross;
 }
-pappso::pappso_double AutomaticFilterParameters::getFilterPeptideEvalue() const {
-    return (_filter_minimum_peptide_evalue );
+pappso::pappso_double
+AutomaticFilterParameters::getFilterPeptideEvalue() const
+{
+  return (_filter_minimum_peptide_evalue);
 }
-pappso::pappso_double AutomaticFilterParameters::getFilterProteinEvalue() const {
-    return ( _filter_minimum_protein_evalue );
+pappso::pappso_double
+AutomaticFilterParameters::getFilterProteinEvalue() const
+{
+  return (_filter_minimum_protein_evalue);
 }
-unsigned int AutomaticFilterParameters::getFilterMinimumPeptidePerMatch()const {
-    return (_filter_minimum_peptide_per_match );
+unsigned int
+AutomaticFilterParameters::getFilterMinimumPeptidePerMatch() const
+{
+  return (_filter_minimum_peptide_per_match);
 }
-bool AutomaticFilterParameters::getFilterCrossSamplePeptideNumber()const {
-    return _filter_is_cross_sample_peptide_number ;
+bool
+AutomaticFilterParameters::getFilterCrossSamplePeptideNumber() const
+{
+  return _filter_is_cross_sample_peptide_number;
 }

src/core/automaticfilterparameters.h

 
 /*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-*     XTPcpp 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.
-*
-*     XTPcpp 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 XTPcpp.  If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-*     Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ *     XTPcpp 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.
+ *
+ *     XTPcpp 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 XTPcpp.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ *     Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
 
 #ifndef AUTOMATICFILTERPARAMETERS_H
 #define AUTOMATICFILTERPARAMETERS_H
@@ -27,29 +28,28 @@
 
 class AutomaticFilterParameters
 {
-public:
-    AutomaticFilterParameters();
-    AutomaticFilterParameters(const AutomaticFilterParameters& other);
-    ~AutomaticFilterParameters();
+  public:
+  AutomaticFilterParameters();
+  AutomaticFilterParameters(const AutomaticFilterParameters &other);
+  ~AutomaticFilterParameters();
 
 
-    void setFilterPeptideEvalue( pappso::pappso_double evalue);
-    void setFilterProteinEvalue( pappso::pappso_double evalue);
-    void setFilterMinimumPeptidePerMatch(unsigned int number);
-    void setFilterCrossSamplePeptideNumber(bool cross);
+  void setFilterPeptideEvalue(pappso::pappso_double evalue);
+  void setFilterProteinEvalue(pappso::pappso_double evalue);
+  void setFilterMinimumPeptidePerMatch(unsigned int number);
+  void setFilterCrossSamplePeptideNumber(bool cross);
 
-    pappso::pappso_double getFilterPeptideEvalue() const;
-    pappso::pappso_double getFilterProteinEvalue()const;
-    unsigned int getFilterMinimumPeptidePerMatch()const;
-    bool getFilterCrossSamplePeptideNumber()const;
+  pappso::pappso_double getFilterPeptideEvalue() const;
+  pappso::pappso_double getFilterProteinEvalue() const;
+  unsigned int getFilterMinimumPeptidePerMatch() const;
+  bool getFilterCrossSamplePeptideNumber() const;
 
 
-private :
-
-    pappso::pappso_double _filter_minimum_peptide_evalue=1;
-    pappso::pappso_double _filter_minimum_protein_evalue=1;
-    unsigned int _filter_minimum_peptide_per_match=1;
-    bool _filter_is_cross_sample_peptide_number=false;
+  private:
+  pappso::pappso_double _filter_minimum_peptide_evalue = 1;
+  pappso::pappso_double _filter_minimum_protein_evalue = 1;
+  unsigned int _filter_minimum_peptide_per_match       = 1;
+  bool _filter_is_cross_sample_peptide_number          = false;
 };
 
 #endif // AUTOMATICFILTERPARAMETERS_H

src/core/identification_sources/identificationdatasource.h

 
 /*******************************************************************************
-* Copyright (c) 2016 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
-*
-* This file is part of XTPcpp.
-*
-*     XTPcpp 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.
-*
-*     XTPcpp 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 XTPcpp.  If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-*     Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2016 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ *     XTPcpp 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.
+ *
+ *     XTPcpp 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 XTPcpp.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ *     Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
+ *implementation
+ ******************************************************************************/
 #ifndef IDENTIFICATIONDATASOURCE_H
 #define IDENTIFICATIONDATASOURCE_H
 
@@ -39,106 +40,116 @@ typedef std::shared_ptr<IdentificationDataSource> IdentificationDataSourceSp;
 
 class IdentificationDataSource
 {
-public:
-
-    IdentificationDataSource(const QString resource_name);
-    IdentificationDataSource(const IdentificationDataSource& other);
-    ~IdentificationDataSource();
-    bool operator==(const IdentificationDataSource& other) const;
-    
-    PeptideEvidenceStore & getPeptideEvidenceStore();
-    const PeptideEvidenceStore & getPeptideEvidenceStore() const;
-    
-    void setXmlId(const QString xmlid);
-    const QString & getXmlId() const;
-
-    /** @brief URL or filename containing identification data
-     * */
-    const QString & getResourceName () const;
-    
-    /** @brief get biological sample name
-     * */
-    const QString getSampleName () const;
-    void setMsRunSp (MsRunSp ms_run_sp);
-    MsRunSp getMsRunSp () const;
-    /** @brief get the spectrum with scan number
-     * */
-    virtual pappso::SpectrumSp getSpectrumSp(unsigned int scan_number) const;
-    
-    
-    /** \brief read source content to store it in project
-     */
-    virtual void parseTo(Project* p_project)=0;
-    
-    /** \brief set identification engine
-     */
-    virtual void setIdentificationEngine(IdentificationEngine engine);
-
-    /** \brief identification engine
-     */
-    virtual IdentificationEngine getIdentificationEngine() const;
-
-    /** \brief identification engine name
-     */
-    const QString getIdentificationEngineName() const;
-    
-    /** \brief identification engine version
-     */
-    virtual const QString& getIdentificationEngineVersion() const;
-    /** \brief set identification engine version
-     */
-    virtual void setIdentificationEngineVersion(const QString& version);
-    
-    /** \brief set identification engine parameter value
-     */
-    virtual void setIdentificationEngineParam(IdentificationEngineParam param, const QVariant& value);
-    
-    
-    /** \brief get specific identification engine parameter value
-     */
-    virtual const QVariant getIdentificationEngineParam(IdentificationEngineParam param) const;
-
-       
-    /** \brief set identification engine statistics
-     * any statistics on this identification run that can be told by the identification engine
-     */
-    virtual void setIdentificationEngineStatistics(IdentificationEngineStatistics param, const QVariant& value);
-    
-    
-    /** \brief get specific identification engine statistics value
-     */
-    virtual const QVariant getIdentificationEngineStatistics(IdentificationEngineStatistics param) const;
-
-    /** \brief add Fastafile used by the identification engine
-     */
-    void addFastaFile (FastaFileSp file);
-    
-    const std::vector<FastaFileSp> & getFastaFileList() const;
-    
-        
-    /** \brief get identification engine statistics map
-     */
-    virtual const std::map<IdentificationEngineStatistics, QVariant> & getIdentificationEngineStatisticsMap() const;
-    
-    /** \brief get identification engine param map
-     */
-    virtual const std::map<IdentificationEngineParam, QVariant> & getIdentificationEngineParamMap() const;
-
-    virtual const bool isValid(const PeptideEvidence * p_peptide_evidence, const AutomaticFilterParameters & automatic_filter_parameters) const;
-
-protected :
-    QString _resource_name;
-    IdentificationEngine _engine = IdentificationEngine::unknown;
-private :
-    //static std::map<QString, pappso::MsRunIdSp> _map_msrunidsp;
-    QString _xml_id;
-    QString _version;
-    MsRunSp _ms_run_sp = nullptr;
-    std::map<IdentificationEngineParam, QVariant> _params;
-    std::map<IdentificationEngineStatistics, QVariant> _param_stats;
-    std::vector<FastaFileSp> _fastafile_list;
-    
-    PeptideEvidenceStore _peptide_evidence_store;
+  public:
+  IdentificationDataSource(const QString resource_name);
+  IdentificationDataSource(const IdentificationDataSource &other);
+  ~IdentificationDataSource();
+  bool operator==(const IdentificationDataSource &other) const;
+
+  PeptideEvidenceStore &getPeptideEvidenceStore();
+  const PeptideEvidenceStore &getPeptideEvidenceStore() const;
+
+  void setXmlId(const QString xmlid);
+  const QString &getXmlId() const;
+
+  /** @brief URL or filename containing identification data
+   * */
+  const QString &getResourceName() const;
+
+  /** @brief get biological sample name
+   * */
+  const QString getSampleName() const;
+  void setMsRunSp(MsRunSp ms_run_sp);
+  MsRunSp getMsRunSp() const;
+  /** @brief get the spectrum with scan number
+   * */
+  virtual pappso::SpectrumSp getSpectrumSp(unsigned int scan_number) const;
+
+
+  /** \brief read source content to store it in project
+   */
+  virtual void parseTo(Project *p_project) = 0;
+
+  /** \brief set identification engine
+   */
+  virtual void setIdentificationEngine(IdentificationEngine engine);
+
+  /** \brief identification engine
+   */
+  virtual IdentificationEngine getIdentificationEngine() const;
+
+  /** \brief identification engine name
+   */
+  const QString getIdentificationEngineName() const;
+
+  /** \brief identification engine version
+   */
+  virtual const QString &getIdentificationEngineVersion() const;
+  /** \brief set identification engine version
+   */
+  virtual void setIdentificationEngineVersion(const QString &version);
+
+  /** \brief set identification engine parameter value
+   */
+  virtual void setIdentificationEngineParam(IdentificationEngineParam param,
+                                            const QVariant &value);
+
+
+  /** \brief get specific identification engine parameter value
+   */
+  virtual const QVariant
+  getIdentificationEngineParam(IdentificationEngineParam param) const;
+
+
+  /** \brief set identification engine statistics
+   * any statistics on this identification run that can be told by the
+   * identification engine
+   */
+  virtual void
+  setIdentificationEngineStatistics(IdentificationEngineStatistics param,
+                                    const QVariant &value);
+
+
+  /** \brief get specific identification engine statistics value
+   */
+  virtual const QVariant
+  getIdentificationEngineStatistics(IdentificationEngineStatistics param) const;
+
+  /** \brief add Fastafile used by the identification engine
+   */
+  void addFastaFile(FastaFileSp file);
+
+  const std::vector<FastaFileSp> &getFastaFileList() const;
+
+
+  /** \brief get identification engine statistics map
+   */
+  virtual const std::map<IdentificationEngineStatistics, QVariant> &
+  getIdentificationEngineStatisticsMap() const;
+
+  /** \brief get identification engine param map
+   */
+  virtual const std::map<IdentificationEngineParam, QVariant> &
+  getIdentificationEngineParamMap() const;
+
+  virtual const bool
+  isValid(const PeptideEvidence *p_peptide_evidence,
+          const AutomaticFilterParameters &automatic_filter_parameters) const;
+
+  protected:
+  QString _resource_name;
+  IdentificationEngine _engine = IdentificationEngine::unknown;
+
+  private:
+  // static std::map<QString, pappso::MsRunIdSp> _map_msrunidsp;
+  QString _xml_id;
+  QString _version;
+  MsRunSp _ms_run_sp = nullptr;
+  std::map<IdentificationEngineParam, QVariant> _params;
+  std::map<IdentificationEngineStatistics, QVariant> _param_stats;
+  std::vector<FastaFileSp> _fastafile_list;
+
+  PeptideEvidenceStore _peptide_evidence_store;
 };
 
 #endif // IDENTIFICATIONDATASOURCE_H

src/core/identification_sources/identificationmascotdatfile.cpp

@@ -6,26 +6,27 @@
  */
 
 /*******************************************************************************
-* Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-*     XTPcpp 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.
-*
-*     XTPcpp 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 XTPcpp.  If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-*     Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ *     XTPcpp 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.
+ *
+ *     XTPcpp 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 XTPcpp.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ *     Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
 
 #include "identificationmascotdatfile.h"
 
@@ -33,75 +34,98 @@
 #include "../project.h"
 #include "../../input/mascot/mascotdatparser.h"
 
-IdentificationMascotDatFile::IdentificationMascotDatFile(const QFileInfo & mascot_dat_file) : IdentificationDataSource(mascot_dat_file.absoluteFilePath()), _mascot_dat_file(mascot_dat_file)
+IdentificationMascotDatFile::IdentificationMascotDatFile(
+  const QFileInfo &mascot_dat_file)
+  : IdentificationDataSource(mascot_dat_file.absoluteFilePath())
+  , _mascot_dat_file(mascot_dat_file)
 {
-    _engine = IdentificationEngine::mascot;
+  _engine = IdentificationEngine::mascot;
 }
 
-IdentificationMascotDatFile::IdentificationMascotDatFile(const IdentificationMascotDatFile& other) : IdentificationDataSource(other),_mascot_dat_file (other._mascot_dat_file)
+IdentificationMascotDatFile::IdentificationMascotDatFile(
+  const IdentificationMascotDatFile &other)
+  : IdentificationDataSource(other), _mascot_dat_file(other._mascot_dat_file)
 {
-    _engine = IdentificationEngine::mascot;
+  _engine = IdentificationEngine::mascot;
 }
 
 IdentificationMascotDatFile::~IdentificationMascotDatFile()
 {
-
 }
 
-bool IdentificationMascotDatFile::operator==(const IdentificationMascotDatFile& other) const
+bool
+IdentificationMascotDatFile::
+operator==(const IdentificationMascotDatFile &other) const
 {
-
 }
 
-pappso::SpectrumSp IdentificationMascotDatFile::getSpectrumSp(unsigned int scan_number) const {
-    pappso::SpectrumSp spectrum_sp = IdentificationDataSource::getSpectrumSp(scan_number);
-    return spectrum_sp;
+pappso::SpectrumSp
+IdentificationMascotDatFile::getSpectrumSp(unsigned int scan_number) const
+{
+  pappso::SpectrumSp spectrum_sp =
+    IdentificationDataSource::getSpectrumSp(scan_number);
+  return spectrum_sp;
 }
 
 
-void IdentificationMascotDatFile::parseTo(Project* p_project) {
-    qDebug() << "IdentificationMascotDatFile::parseTo begin";
-
-    qDebug() << "Read Mascot dat result file '" << _mascot_dat_file.absoluteFilePath() << "'";
-
-    MsRunSp msrun_sp = p_project->getMsRunStore().getInstance(QFileInfo(_mascot_dat_file).baseName());
-    setMsRunSp(msrun_sp);
-    std::vector<IdentificationGroup *> identification_list = p_project->getIdentificationGroupList();
-    IdentificationGroup * identification_group_p = nullptr;
-    if (p_project->getProjectMode() == ProjectMode::combined) {
-        if (identification_list.size() == 0) {
-            identification_group_p = p_project->newIdentificationGroup();
+void
+IdentificationMascotDatFile::parseTo(Project *p_project)
+{
+  qDebug() << "IdentificationMascotDatFile::parseTo begin";
+
+  qDebug() << "Read Mascot dat result file '"
+           << _mascot_dat_file.absoluteFilePath() << "'";
+
+