new identification data source store OK

src/CMakeLists.txt

@@ -29,8 +29,8 @@ SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${Qt5Xml_EXECUTABLE_COMPILE_FLAGS} ${Qt5
 
 #sudo apt-get install libpappsomspp-dev
 #FIND_PACKAGE( Pappsomspp REQUIRED )
- SET (PAPPSOMSPP_DIR  "/home/olivier/eclipse/git/pappsomspp")
-# SET (PAPPSOMSPP_DIR  "/home/langella/developpement/git/pappsomspp")
+# SET (PAPPSOMSPP_DIR  "/home/olivier/eclipse/git/pappsomspp")
+ SET (PAPPSOMSPP_DIR  "/home/langella/developpement/git/pappsomspp")
  SET (PAPPSOMSPP_INCLUDE_DIR "${PAPPSOMSPP_DIR}/src")
  SET (PAPPSOMSPP_QT4_LIBRARY "${PAPPSOMSPP_DIR}/cbuild/src/libpappsomspp-qt4.so")
 
@@ -69,6 +69,7 @@ SET(CPP_FILES
   grouping/groupingpeptidemass.cpp
   gui/peptide_detail_view/spectrum_widget/spectrumpainter.cpp
   input/xpipsaxhandler.cpp
+  utils/identificationdatasourcestore.cpp
   utils/groupstore.cpp
   utils/peptidestore.cpp
   utils/proteinstore.cpp

src/core/identification_sources/identificationdatasource.cpp

@@ -26,14 +26,6 @@
 #include <QFileInfo>
 #include "../../utils/readspectrum.h"
 
-
-IdentificationDataSource::MapIdentificationDataSources IdentificationDataSource::_map_identification_data_sources = []
-{
-    MapIdentificationDataSources ret;
-
-    return ret;
-}();
-
 IdentificationDataSource::IdentificationDataSource(const QString resource_name)
 {
     _resource_name = resource_name;
@@ -55,31 +47,6 @@ bool IdentificationDataSource::operator==(const IdentificationDataSource& other)
 
 }
 
-void IdentificationDataSource::clear() {
-    _map_identification_data_sources.clear();
-}
-
-IdentificationDataSource * IdentificationDataSource::getInstance(const QString & location) {
-
-    std::map< QString, IdentificationDataSource* >::iterator it = IdentificationDataSource::_map_identification_data_sources.find(location);
-    if (it != IdentificationDataSource::_map_identification_data_sources.end()) {
-        return it->second;
-    }
-    else {
-        QFileInfo location_file(location);
-        QString ext = location_file.suffix();
-        //QString sample_name = location_file.baseName();
-        if (ext.toLower() == "xml") {
-            //X!Tandem result file
-            IdentificationXtandemFile * p_xtfile = new IdentificationXtandemFile(location_file);
-            _map_identification_data_sources.insert(std::pair< QString, IdentificationDataSource* >(location, p_xtfile));
-            _map_identification_data_sources.insert(std::pair< QString, IdentificationDataSource* >(location_file.absoluteFilePath(), p_xtfile));
-            return p_xtfile;
-        }
-    }
-    throw pappso::PappsoException(QObject::tr("Identification resource %1 not recognized").arg(location));
-}
-
 const QString & IdentificationDataSource::getResourceName () const {
     return _resource_name;
 }

src/core/identification_sources/identificationdatasource.h

@@ -26,17 +26,16 @@
 
 #include <pappsomspp/msrun/msrunid.h>
 #include <pappsomspp/spectrum/spectrum.h>
-#include <map>
+#include <memory>
 
 
+class IdentificationDataSource;
+typedef std::shared_ptr<IdentificationDataSource> IdentificationDataSourceSp;
+
 class IdentificationDataSource
 {
 public:
 
-    using MapIdentificationDataSources = std::map<QString, IdentificationDataSource *>;
-    static void clear();
-    static IdentificationDataSource * getInstance(const QString & location);
-
     IdentificationDataSource(const QString resource_name);
     IdentificationDataSource(const IdentificationDataSource& other);
     ~IdentificationDataSource();
@@ -53,7 +52,6 @@ public:
 protected :
     QString _resource_name;
 private :
-    static MapIdentificationDataSources _map_identification_data_sources;
     //static std::map<QString, pappso::MsRunIdSp> _map_msrunidsp;
     pappso::MsRunIdSp _ms_run_sp = nullptr;
 };

src/core/project.cpp

@@ -42,7 +42,7 @@ std::vector<IdentificationGroup *> Project::getIdentificationGroupList() {
     return _identification_goup_list;
 }
 const GroupingType Project::getGroupingType() const {
-  return _grouping_type;
+    return _grouping_type;
 }
 PeptideStore & Project::getPeptideStore() {
     return _peptide_store;
@@ -51,6 +51,10 @@ PeptideStore & Project::getPeptideStore() {
 ProteinStore & Project::getProteinStore() {
     return _protein_store;
 }
+
+IdentificationDataSourceStore & Project::getIdentificationDataSourceStore() {
+    return _identification_data_source_store;
+}
 const AutomaticFilterParameters & Project::getAutomaticFilterParameters() const {
     return _automatic_filter_parameters;
 }
@@ -101,7 +105,7 @@ void Project::readXpipFile(QFileInfo xpip_fileinfo) {
 }
 
 IdentificationGroup* Project::getCurrentIdentificationGroupP() const {
-    
+
     qDebug() << "Project::getCurrentIdentificationGroupP begin " << _p_current_identification_group;
     return _p_current_identification_group;
 }

src/core/project.h

@@ -29,6 +29,7 @@
 #include "../utils/types.h"
 #include "../utils/peptidestore.h"
 #include "../utils/proteinstore.h"
+#include "../utils/identificationdatasourcestore.h"
 
 class Project;
 typedef std::shared_ptr<Project> ProjectSp;
@@ -45,6 +46,7 @@ public:
     ProjectSp makeProjectSp() const;
     ProteinStore & getProteinStore();
     PeptideStore & getPeptideStore();
+    IdentificationDataSourceStore & getIdentificationDataSourceStore();
     void readXpipFile(QFileInfo xpip_source);
     IdentificationGroup* newIdentificationGroup();
     IdentificationGroup* getCurrentIdentificationGroupP() const;
@@ -69,6 +71,7 @@ private :
     
     ProteinStore _protein_store;
     PeptideStore _peptide_store;
+    IdentificationDataSourceStore _identification_data_source_store;
 };
 
 #endif // PROJECT_H

src/input/xpipsaxhandler.cpp

@@ -248,7 +248,7 @@ bool XpipSaxHandler::startElement_peptide(QXmlAttributes attributes) {
 
     _p_peptide_match->setCharge(attributes.value("charge").simplified().toUInt());
 
-    IdentificationDataSource* p_identification_data_source = IdentificationDataSource::getInstance(attributes.value("sample_file").simplified());
+    IdentificationDataSource* p_identification_data_source = _p_project->getIdentificationDataSourceStore().getInstance(attributes.value("sample_file").simplified()).get();
     _p_peptide_match->setIdentificationDataSource( p_identification_data_source);
     if (p_identification_data_source->getMsRunSp().get() == nullptr) {
         p_identification_data_source->setMsRunSp(ms_run_id);
@@ -340,7 +340,6 @@ bool XpipSaxHandler::endDocument() {
 }
 
 bool XpipSaxHandler::startDocument() {
-    IdentificationDataSource::clear();
     return true;
 }
 

src/utils/identificationdatasourcestore.cpp

+/**
+ * \file utils/identificationdatasourcestore.cpp
+ * \date 5/4/2017
+ * \author Olivier Langella
+ * \brief store unique version of identification data sources (output files from identification engines)
+ */
+
+
+/*******************************************************************************
+* 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 "identificationdatasourcestore.h"
+#include "../core/identification_sources/identificationxtandemfile.h"
+#include <pappsomspp/pappsoexception.h>
+
+IdentificationDataSourceStore::IdentificationDataSourceStore()
+{
+
+}
+
+IdentificationDataSourceStore::~IdentificationDataSourceStore()
+{
+
+}
+
+IdentificationDataSourceSp IdentificationDataSourceStore::getInstance(const QString & location) {
+
+    std::map< QString, IdentificationDataSourceSp >::iterator it = _map_identification_data_sources.find(location);
+    if (it != _map_identification_data_sources.end()) {
+        return it->second;
+    }
+    else {
+        QFileInfo location_file(location);
+        QString ext = location_file.suffix();
+        //QString sample_name = location_file.baseName();
+        if (ext.toLower() == "xml") {
+            //X!Tandem result file
+            IdentificationDataSourceSp p_xtfile = std::make_shared<IdentificationXtandemFile>(location_file);
+            _map_identification_data_sources.insert(std::pair< QString, IdentificationDataSourceSp >(location, p_xtfile));
+            _map_identification_data_sources.insert(std::pair< QString, IdentificationDataSourceSp >(location_file.absoluteFilePath(), p_xtfile));
+            return p_xtfile;
+        }
+    }
+    throw pappso::PappsoException(QObject::tr("Identification resource %1 not recognized").arg(location));
+}

src/utils/identificationdatasourcestore.h

+/**
+ * \file utils/identificationdatasourcestore.h
+ * \date 5/4/2017
+ * \author Olivier Langella
+ * \brief store unique version of identification data sources (output files from identification engines)
+ */
+
+
+/*******************************************************************************
+* 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 IDENTIFICATIONDATASOURCESTORE_H
+#define IDENTIFICATIONDATASOURCESTORE_H
+
+#include <map>
+#include "../core/identification_sources/identificationdatasource.h"
+
+class IdentificationDataSourceStore
+{
+public:
+    IdentificationDataSourceStore();
+    ~IdentificationDataSourceStore();
+    IdentificationDataSourceSp getInstance(const QString & location);
+    void clear();
+private :
+    std::map<QString, IdentificationDataSourceSp> _map_identification_data_sources;
+};
+
+#endif // IDENTIFICATIONDATASOURCESTORE_H