Merge branch 'master' of forgemia.inra.fr:pappso/xtpcpp into master

debian/copyright

@@ -79,11 +79,12 @@ Files: src/resources/icons/mit/jamicons/*
 Copyright: 2017-2020 Michael Amprimo <https://github.com/michaelampr/jam>
 License: MIT
 
+Files: */src/resources/html_doc
+Copyright: The Global Proteome Machine Organization <https://www.thegpm.org/TANDEM/>
+License: Artistic
 
 Files: debian/*
 Copyright: 2015-2020 Olivier Langella <olivier.langella@universite-paris-saclay.fr>
  2020 Filippo Rusconi <filippo.rusconi@universite-paris-saclay.fr>
 License: GPL-3+
 
-
-

src/core/automaticfilterparameters.cpp

@@ -30,6 +30,16 @@ AutomaticFilterParameters::AutomaticFilterParameters()
 
 AutomaticFilterParameters::AutomaticFilterParameters(
   const AutomaticFilterParameters &other)
+{
+  this->operator=(other);
+}
+
+AutomaticFilterParameters::~AutomaticFilterParameters()
+{
+}
+
+AutomaticFilterParameters &
+AutomaticFilterParameters::operator=(const AutomaticFilterParameters &other)
 {
   _filter_minimum_peptide_evalue    = other._filter_minimum_peptide_evalue;
   _filter_minimum_protein_evalue    = other._filter_minimum_protein_evalue;
@@ -39,12 +49,11 @@ AutomaticFilterParameters::AutomaticFilterParameters(
   m_filter_peptide_observed_in_less_samples_than =
     other.m_filter_peptide_observed_in_less_samples_than;
   m_filterFDR = other.m_filterFDR;
-}
 
-AutomaticFilterParameters::~AutomaticFilterParameters()
-{
+  return *this;
 }
 
+
 void
 AutomaticFilterParameters::setFilterPeptideFDR(double fdr)
 {

src/core/automaticfilterparameters.h

@@ -32,6 +32,8 @@ class AutomaticFilterParameters
   AutomaticFilterParameters(const AutomaticFilterParameters &other);
   ~AutomaticFilterParameters();
 
+  AutomaticFilterParameters &operator=(const AutomaticFilterParameters &);
+
 
   void setFilterPeptideEvalue(pappso::pappso_double evalue);
   void setFilterPeptideFDR(double fdr);

src/core/identificationgroup.cpp

@@ -385,6 +385,36 @@ IdentificationGroup::collectMhDelta(
         }
     }
 }
+
+
+void
+IdentificationGroup::collectTargetDecoyMhDelta(
+  std::vector<pappso::pappso_double> &delta_list,
+  pappso::PrecisionUnit unit,
+  ValidationState state) const
+{
+  std::set<const PeptideEvidence *> peptide_evidence_list;
+  for(auto &p_protein_match : _protein_match_list)
+    {
+      if(p_protein_match->getValidationState() == state)
+        {
+          p_protein_match->collectPeptideEvidences(peptide_evidence_list,
+                                                   state);
+        }
+    }
+  for(const PeptideEvidence *p_peptide_evidence : peptide_evidence_list)
+    {
+      if(unit == pappso::PrecisionUnit::ppm)
+        {
+          delta_list.push_back(p_peptide_evidence->getPpmDeltaMass());
+        }
+      else
+        {
+          delta_list.push_back(p_peptide_evidence->getDeltaMass());
+        }
+    }
+}
+
 void
 IdentificationGroup::startGrouping(
   ContaminantRemovalMode contaminantRemovalMode,

src/core/identificationgroup.h

@@ -157,14 +157,33 @@ class IdentificationGroup
   bool containSample(const QString &sample) const;
 
 
-  /** @brief collect mass delta between theoretical mass and observed mass
-   * each peptide evidence is only counted once
+  /** @brief collect mass delta between theoretical mass and observed mass for
+   * target sequences
+   *
+   * each peptide evidence is only counted once it counts only
+   * peptide evidence for target Sequences
+   * @param delta_list list of mass delta
+   * @param unit precision unit, ppm or dalton
+   * @param state validation state of the peptides to collect
    */
   void collectMhDelta(std::vector<pappso::pappso_double> &delta_list,
                       pappso::PrecisionUnit unit,
                       ValidationState state) const;
 
 
+  /** @brief collect mass delta between theoretical mass and observed mass
+   *
+   * each peptide evidence is only counted once it counts target or decoy
+   * peptide evidence
+   * @param delta_list list of mass delta
+   * @param unit precision unit, ppm or dalton
+   * @param state validation state of the peptides to collect
+   */
+  void collectTargetDecoyMhDelta(std::vector<pappso::pappso_double> &delta_list,
+                                 pappso::PrecisionUnit unit,
+                                 ValidationState state) const;
+
+
   /** @brief look for a peptide in the same XIC
    * @param peptide_evidence_list the peptide evidence list to build
    * @param p_msrun MSrun to look for

src/core/peptidematch.cpp

@@ -32,8 +32,7 @@ PeptideMatch::PeptideMatch()
 
 PeptideMatch::PeptideMatch(const PeptideMatch &other)
 {
-  _start              = other._start;
-  _p_peptide_evidence = other._p_peptide_evidence;
+  this->operator=(other);
 }
 bool
 PeptideMatch::operator==(const PeptideMatch &other) const
@@ -45,6 +44,17 @@ PeptideMatch::operator==(const PeptideMatch &other) const
     }
   return false;
 }
+
+PeptideMatch &
+PeptideMatch::operator=(const PeptideMatch &other)
+{
+
+  _start              = other._start;
+  _p_peptide_evidence = other._p_peptide_evidence;
+  return *this;
+}
+
+
 void
 PeptideMatch::setPeptideEvidenceSp(PeptideEvidenceSp sp_peptide_evidence)
 {

src/core/peptidematch.h

@@ -22,8 +22,7 @@
  *implementation
  ******************************************************************************/
 
-#ifndef PEPTIDEMATCH_H
-#define PEPTIDEMATCH_H
+#pragma once
 #include "peptideevidence.h"
 
 
@@ -35,6 +34,8 @@ class PeptideMatch
 
   bool operator==(const PeptideMatch &other) const;
 
+  PeptideMatch &operator=(const PeptideMatch &);
+
 
   /** @brief set start position of this peptide inside the protein sequence
    * @param start position in the protein amino acid sequence (starts at 0)
@@ -66,5 +67,3 @@ class PeptideMatch
   unsigned int _start                  = 0;
   PeptideEvidence *_p_peptide_evidence = nullptr;
 };
-
-#endif // PEPTIDEMATCH_H

src/main.cpp

 
 /*******************************************************************************
- * Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
+ * Copyright (c) 2015 Olivier Langella <olivier.langella@u-psud.fr>.
  *
- * This file is part of PAPPSOms-tools.
+ * This file is part of XTPcpp.
  *
- *     PAPPSOms-tools is free software: you can redistribute it and/or modify
+ *     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.
  *
- *     PAPPSOms-tools is distributed in the hope that it will be useful,
+ *     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 PAPPSOms-tools.  If not, see <http://www.gnu.org/licenses/>.
+ *     along with XTPcpp.  If not, see <http://www.gnu.org/licenses/>.
  *
- * Contributors:
- *     Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
- *implementation
  ******************************************************************************/
 
 #include "config.h"

src/output/proticdbml.cpp

@@ -832,7 +832,7 @@ ProticdbMl::writeMatch(std::vector<const ProteinMatch *> &protein_match_sg_list)
           sample_name_list
             << peptide_match.getPeptideEvidence()->getMsRunP()->getSampleName();
         }
-      sample_name_list = sample_name_list.toSet().toList();
+      sample_name_list = sample_name_list.toSet().values();
       for(QString sample_name : sample_name_list)
         {
           _output_stream->writeStartElement("matchSample");

src/output/proticdbml.h

@@ -28,13 +28,12 @@
  *implementation
  ******************************************************************************/
 
-#ifndef PROTICDBML_H
-#define PROTICDBML_H
+#pragma once
 
 #include <QXmlStreamWriter>
 #include <QFile>
 #include <QString>
-#include <QTime>
+#include <QElapsedTimer>
 #include <pappsomspp/amino_acid/aamodification.h>
 #include "../core/project.h"
 #include "../grouping/groupinggroup.h"
@@ -76,10 +75,8 @@ class ProticdbMl
   QXmlStreamWriter *_output_stream;
   ProjectSp _sp_project;
   IdentificationGroup *_p_identification_group;
-  QTime _duracel;
+  QElapsedTimer _duracel;
   std::map<QString, QString> _map_accession2xmlid;
   std::map<QString, QString> _sample_to_id;
   std::map<QString, QString> _peptidekey_to_id;
 };
-
-#endif // PROTICDBML_H

src/utils/utils.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/>.
+ *
+ ******************************************************************************/
+
 #include "utils.h"
 #include <pappsomspp/exception/exceptionnotfound.h>
 #include <pappsomspp/mzrange.h>