WIP: new peptide match store object

src/CMakeLists.txt

@@ -106,6 +106,7 @@ SET(CPP_FILES
   utils/identificationdatasourcestore.cpp
   utils/groupstore.cpp
   utils/msrunstore.cpp
+  utils/peptidematchstore.cpp
   utils/peptidestore.cpp
   utils/proteinstore.cpp
   utils/readspectrum.cpp

src/core/identification_sources/identificationdatasource.cpp

@@ -27,7 +27,6 @@
 #include <QFileInfo>
 #include "../../utils/readspectrum.h"
 
-
 IdentificationDataSource::IdentificationDataSource(const QString resource_name)
 {
     _resource_name = resource_name;
@@ -45,6 +44,10 @@ IdentificationDataSource::~IdentificationDataSource()
 
 }
 
+PeptideMatchStore & IdentificationDataSource::getPeptideMatchStore() {
+    return _peptide_match_store;
+}
+
 void IdentificationDataSource::setXmlId(const QString xmlid) {
     _xml_id = xmlid;
 }

src/core/identification_sources/identificationdatasource.h

@@ -29,12 +29,14 @@
 #include <QVariant>
 #include "../msrun.h"
 #include "../../utils/fastafilestore.h"
+#include "../../utils/peptidematchstore.h"
 
 class Project;
 
 class IdentificationDataSource;
 typedef std::shared_ptr<IdentificationDataSource> IdentificationDataSourceSp;
 
+
 class IdentificationDataSource
 {
 public:
@@ -44,6 +46,7 @@ public:
     ~IdentificationDataSource();
     bool operator==(const IdentificationDataSource& other) const;
     
+    PeptideMatchStore & getPeptideMatchStore();
     
     void setXmlId(const QString xmlid);
     const QString & getXmlId() const;
@@ -118,6 +121,8 @@ private :
     std::map<IdentificationEngineParam, QVariant> _params;
     std::map<IdentificationEngineStatistics, QVariant> _param_stats;
     std::vector<FastaFileSp> _fastafile_list;
+    
+    PeptideMatchStore _peptide_match_store;
 };
 
 #endif // IDENTIFICATIONDATASOURCE_H

src/core/peptidematch.cpp

@@ -49,6 +49,10 @@ PeptideMatch::PeptideMatch(const PeptideMatch & other): PeptideMatch(other._msru
     
 }
 
+PeptideMatchSp PeptideMatch::makePeptideMatchSp() const {
+    return std::make_shared<PeptideMatch>(*this);
+}
+
 void PeptideMatch::updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters) {
     _proxy_valid = false;
 

src/core/peptidematch.h

@@ -45,6 +45,8 @@ public :
     std::size_t getHashSampleScan() const;
     std::size_t getHashPeptideMassSample() const;
 
+    PeptideMatchSp makePeptideMatchSp() const;
+
     void setRetentionTime(pappso::pappso_double rt);
     void setEvalue(pappso::pappso_double evalue);
 
@@ -72,7 +74,7 @@ public :
     /** \brief get specific parameter value
      */
     virtual const QVariant getParam(PeptideMatchParam param) const;
-    
+
     const std::map<PeptideMatchParam, QVariant> & getParamList() const;
 
 
@@ -118,7 +120,7 @@ public :
     pappso::mz getDeltaMass() const;
 
     ValidationState getValidationState() const;
-    
+
     /** @brief tells if this peptide contains a protein position
      * the position is the amino acid position on the protein sequence (starts from 0)
      * */

src/core/proteinmatch.cpp

@@ -39,12 +39,8 @@ ProteinMatch::ProteinMatch()
 
 ProteinMatch::~ProteinMatch()
 {
-    auto it = _peptide_match_list.begin();
-    while (it != _peptide_match_list.end()) {
-        delete (*it);
-        it++;
-    }
 }
+
 ValidationState ProteinMatch::getValidationState() const {
     if (isGrouped()) {
         return ValidationState::grouped;
@@ -141,8 +137,8 @@ bool ProteinMatch::isGrouped() const {
 void ProteinMatch::setChecked(bool arg1) {
     _checked = arg1;
 }
-void ProteinMatch::addPeptideMatch(PeptideMatch * peptide_match) {
-    _peptide_match_list.push_back(peptide_match);
+void ProteinMatch::addPeptideMatchSp(PeptideMatchSp peptide_match) {
+    _peptide_match_list.push_back(peptide_match.get());
 }
 
 

src/core/proteinmatch.h

@@ -74,7 +74,7 @@ public:
     pappso::pappso_double getEmPAI(const MsRun * sp_msrun_id = nullptr) const;
 
     void setProteinXtpSp(ProteinXtpSp protein_sp);
-    void addPeptideMatch(PeptideMatch * peptide_match);
+    void addPeptideMatchSp(PeptideMatchSp peptide_match);
     std::vector<PeptideMatch *> & getPeptideMatchList();
     const std::vector<PeptideMatch *> & getPeptideMatchList() const;
     

src/input/identificationpwizreader.cpp

@@ -278,7 +278,10 @@ void IdentificationPwizReader::read(
                         }
                         ProteinMatch * protein_match_p = it->second;
 
-                        protein_match_p->addPeptideMatch(p_peptide_match_from_evidence);
+                        protein_match_p->addPeptideMatchSp(p_peptide_match_from_evidence->getIdentificationDataSource()->getPeptideMatchStore().getInstance(p_peptide_match_from_evidence));
+
+                        delete p_peptide_match_from_evidence;
+                        //protein_match_p->addPeptideMatch(p_peptide_match_from_evidence);
                     }
                     delete p_peptide_match;
                 }

src/input/xpipsaxhandler.cpp

@@ -279,7 +279,6 @@ bool XpipSaxHandler::startElement_peptide(QXmlAttributes attributes) {
     if (attributes.value("validate").simplified().toLower() == "true") {
         _p_peptide_match->setChecked(true);
     }
-    _p_protein_match->addPeptideMatch(_p_peptide_match);
     qDebug() << "startElement_peptide end" ;
     return true;
 }
@@ -296,10 +295,11 @@ bool XpipSaxHandler::startElement_modif(QXmlAttributes attributes) {
 }
 bool XpipSaxHandler::endElement_peptide() {
     qDebug() << "endElement_peptide ";
-
     PeptideXtpSp peptide_const = PeptideXtp(*(_current_peptide_sp.get())).makePeptideXtpSp();
     peptide_const = _p_project->getPeptideStore().getInstance(peptide_const);
     _p_peptide_match->setPeptideXtpSp(peptide_const);
+    _p_protein_match->addPeptideMatchSp(_p_peptide_match->getIdentificationDataSource()->getPeptideMatchStore().getInstance(_p_peptide_match));
+    delete _p_peptide_match;
     return true;
 }
 

src/input/xtandemsaxhandler.cpp

@@ -303,7 +303,6 @@ bool XtandemSaxHandler::startElement_domain(QXmlAttributes attributes) {
 
     _p_peptide_match->setIdentificationDataSource( _p_identification_data_source);
     _p_peptide_match->setChecked(true);
-    _p_protein_match->addPeptideMatch(_p_peptide_match);
 
 
 
@@ -331,6 +330,11 @@ bool XtandemSaxHandler::endElement_domain() {
     _current_peptide_sp = _p_project->getPeptideStore().getInstance(_current_peptide_sp);
 
     _p_peptide_match->setPeptideXtpSp(_current_peptide_sp);
+    
+    
+    _p_protein_match->addPeptideMatchSp(_p_peptide_match->getIdentificationDataSource()->getPeptideMatchStore().getInstance(_p_peptide_match));
+    
+    delete _p_peptide_match;
     return is_ok;
 }
 bool XtandemSaxHandler::endElement_note() {

src/utils/peptidematchstore.cpp

+/**
+ * \file utils/peptidematchstore.cpp
+ * \date 18/11/2017
+ * \author Olivier Langella
+ * \brief store unique instances of peptide match
+ */
+
+
+/*******************************************************************************
+* 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 "peptidematchstore.h"
+
+#include "../core/peptidematch.h"
+
+std::shared_ptr<PeptideMatch> & PeptideMatchStore::getInstance(const PeptideMatch * p_peptide_match) {
+}

src/utils/peptidematchstore.h

+/**
+ * \file utils/peptidematchstore.h
+ * \date 18/11/2017
+ * \author Olivier Langella
+ * \brief store unique instances of peptide match
+ */
+
+
+/*******************************************************************************
+* 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 PEPTIDEMATCHSTORE_H
+#define PEPTIDEMATCHSTORE_H
+
+#include <memory>
+
+class PeptideMatch;
+
+class PeptideMatchStore
+{
+public:
+    std::shared_ptr<PeptideMatch> & getInstance(const PeptideMatch * p_peptide_match);
+};
+
+#endif // PEPTIDEMATCHSTORE_H