better assign pointer first...

src/core/identification_sources/identificationdatasource.cpp

@@ -26,7 +26,6 @@
 #include <QFileInfo>
 #include "../../utils/readspectrum.h"
 
-FastaFileStore IdentificationDataSource::_fasta_file_store;
 
 IdentificationDataSource::IdentificationDataSource(const QString resource_name)
 {
@@ -83,8 +82,8 @@ pappso::SpectrumSp IdentificationDataSource::getSpectrumSp(unsigned int scan_num
     return spectrum_sp;
 }
 
-void IdentificationDataSource::addFastaFile (FastaFile file) {
-    _fastafile_list.push_back(IdentificationDataSource::_fasta_file_store.getInstance(file));
+void IdentificationDataSource::addFastaFile (FastaFileSp file) {
+    _fastafile_list.push_back(file);
 }
 const std::vector<FastaFileSp> & IdentificationDataSource::getFastaFileList() const {
     qDebug()<<  "IdentificationDataSource::getFastaFileList begin" << _fastafile_list.size();

src/core/identification_sources/identificationdatasource.h

@@ -73,7 +73,7 @@ public:
     
     /** \brief add Fastafile used by the identification engine
      */
-    void addFastaFile (FastaFile file);
+    void addFastaFile (FastaFileSp file);
     
     const std::vector<FastaFileSp> & getFastaFileList() const;
 
@@ -82,7 +82,6 @@ protected :
     IdentificationEngine _engine = IdentificationEngine::unknown;
 private :
     //static std::map<QString, pappso::MsRunIdSp> _map_msrunidsp;
-    static FastaFileStore _fasta_file_store;
     QString _version;
     MsRunSp _ms_run_sp = nullptr;
     std::map<IdentificationEngineParam, QString> _params;

src/core/project.cpp

@@ -65,6 +65,9 @@ const GroupingType Project::getGroupingType() const {
     return _grouping_type;
 }
 
+FastaFileStore & Project::getFastaFileStore() {
+    return _fasta_file_store;
+}
 MsRunStore & Project::getMsRunStore() {
     return _msrun_store;
 }

src/core/project.h

@@ -48,6 +48,7 @@ public:
     ProteinStore & getProteinStore();
     PeptideStore & getPeptideStore();
     MsRunStore & getMsRunStore();
+    FastaFileStore & getFastaFileStore();
     IdentificationDataSourceStore & getIdentificationDataSourceStore();
     void readXpipFile(QFileInfo xpip_source);
     IdentificationGroup* newIdentificationGroup();
@@ -83,6 +84,7 @@ private :
     PeptideStore _peptide_store;
     IdentificationDataSourceStore _identification_data_source_store;
     MsRunStore _msrun_store;
+    FastaFileStore _fasta_file_store;
     
 };
 

src/core/proteinmatch.cpp

@@ -62,7 +62,7 @@ bool ProteinMatch::contains(PeptideMatch * peptide_match) const {
 }
 
 void ProteinMatch::updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters) {
-    qDebug() <<"ProteinMatch::updateAutomaticFilters begin " ;
+    //qDebug() <<"ProteinMatch::updateAutomaticFilters begin " ;
     _proxy_valid = false;
     unsigned int number_of_valid_peptides =0;
     bool cross_sample = automatic_filter_parameters.getFilterCrossSamplePeptideNumber();
@@ -102,7 +102,7 @@ void ProteinMatch::updateAutomaticFilters(const AutomaticFilterParameters & auto
             }
         }
     }
-    qDebug() <<"ProteinMatch::updateAutomaticFilters end " << number_of_valid_peptides ;
+    //qDebug() <<"ProteinMatch::updateAutomaticFilters end " << number_of_valid_peptides ;
 }
 
 const ProteinXtpSp & ProteinMatch::getProteinXtpSp() const {
@@ -213,7 +213,7 @@ unsigned int ProteinMatch::countSequenceLi(ValidationState state, const MsRun *
             }
         }
     }
-    qDebug() <<"ProteinMatch::countValidAndCheckedPeptide end " << sequence_list.size();
+    //qDebug() <<"ProteinMatch::countValidAndCheckedPeptide end " << sequence_list.size();
     return sequence_list.size();
 }
 

src/files/fastafile.cpp

@@ -27,7 +27,7 @@ FastaFile::FastaFile(const QString & fasta_source) : _fasta_source(fasta_source)
 {
 
 }
-FastaFile::FastaFile(const QFileInfo & fasta_source): _fasta_source(fasta_source.absoluteFilePath())
+FastaFile::FastaFile(const QFileInfo & fasta_source): _fasta_source(fasta_source)
 {
 }
 FastaFile::FastaFile(const FastaFile & other) : _fasta_source(other._fasta_source)
@@ -39,15 +39,10 @@ FastaFile::~FastaFile()
 
 }
 
-bool FastaFile::operator<( const FastaFile& other ) const
-{
-    return (_fasta_source.absoluteFilePath() < other._fasta_source.absoluteFilePath());
-}
-bool FastaFile::operator==( const FastaFile& other ) const
-{
-    return (_fasta_source == other._fasta_source);
-}
-
 const QString FastaFile::getFilename() const {
     return _fasta_source.fileName();
 }
+
+const QString FastaFile::getAbsoluteFilePath() const {
+    return _fasta_source.absoluteFilePath();
+}

src/files/fastafile.h

@@ -38,10 +38,10 @@ public:
     FastaFile(const FastaFile & other);
     ~FastaFile();
 
-    bool operator<( const FastaFile& other ) const;
-    bool operator==( const FastaFile& other ) const;
     
     const QString getFilename() const;
+    const QString getAbsoluteFilePath() const;
+
 private :
     const QFileInfo _fasta_source;
 

src/gui/mainwindow.cpp

@@ -219,7 +219,10 @@ void MainWindow::doProjectReady(ProjectSp project_sp) {
 
     qDebug() << "MainWindow::doProjectReady begin";
     try {
+    qDebug() << "MainWindow::doProjectReady begin a " << project_sp.get()->getFastaFileStore().getFastaFileList().size() ;
         _project_sp = project_sp;
+        
+    qDebug() << "MainWindow::doProjectReady begin b " << _project_sp.get()->getFastaFileStore().getFastaFileList().size() ;
         doDisplayLoadingMessage(tr("grouping proteins"));
         project_sp.get()->startGrouping();
         doDisplayLoadingMessage(tr("grouping proteins finished"));

src/gui/project_view/projectwindow.cpp

@@ -346,8 +346,12 @@ void ProjectWindow::doViewProteinList(IdentificationGroup* p_identification_grou
 }
 
 void ProjectWindow::setProjectSp(ProjectSp project_sp) {
+    qDebug() << "ProjectWindow::setProjectSp begin" ;
     
-    _fastafile_list = _project_sp.get()->getIdentificationDataSourceStore().getFastaFileList();
+    _project_sp = project_sp;
+
+    qDebug() << "ProjectWindow::setProjectSp begin " << _project_sp.get()->getFastaFileStore().getFastaFileList().size() ;
+    _fastafile_list = _project_sp.get()->getFastaFileStore().getFastaFileList();
     
     
     for (FastaFileSp fasta_file : _fastafile_list ) {
@@ -384,8 +388,6 @@ void ProjectWindow::setProjectSp(ProjectSp project_sp) {
     _peptide_detail_window_collection.clear();
     _p_current_peptide_detail_window = nullptr;
 
-    _project_sp = project_sp;
-
     if (_p_identification_widget != nullptr) {
         delete _p_identification_widget;
     }

src/gui/project_view/projectwindow.h

@@ -105,7 +105,7 @@ private:
     ProjectSp _project_sp;
     
     QStandardItemModel * _p_fasta_str_li;
-    std::set<FastaFileSp> _fastafile_list;
+    std::vector<FastaFileSp> _fastafile_list;
 
 
 };

src/input/xpipsaxhandler.cpp

@@ -215,6 +215,7 @@ bool XpipSaxHandler::startElement_protein(QXmlAttributes attributes) {
               </protein>
               */
     _current_protein.setCompleteDescription(attributes.value("description"));
+    _current_fasta_file_sp = _p_project->getFastaFileStore().getInstance(FastaFile(attributes.value("URL")));
     qDebug() << "startElement_protein end" ;
     return true;
 }
@@ -247,6 +248,7 @@ bool XpipSaxHandler::startElement_peptide(QXmlAttributes attributes) {
     if (p_identification_data_source->getMsRunSp().get() != ms_run_id.get()) {
         throw pappso::PappsoException(QObject::tr("p_identification_data_source->getMsRunSp().get() != ms_run_id.get()"));
     }
+    p_identification_data_source->addFastaFile(_current_fasta_file_sp);
     _p_peptide_match->setChecked(false);
     if (attributes.value("validate").simplified().toLower() == "true") {
         _p_peptide_match->setChecked(true);

src/input/xpipsaxhandler.h

@@ -85,6 +85,7 @@ private:
     ProteinXtp _current_protein;
     PeptideXtpSp _current_peptide_sp;
     IdentificationGroup * _current_identification_group_p;
+    FastaFileSp _current_fasta_file_sp;
     
     QMap<QString, pappso::AaModificationP> _map_massstr_aamod;
 };

src/input/xtandemsaxhandler.cpp

@@ -449,8 +449,8 @@ bool XtandemSaxHandler::endElement_note() {
 
         //<note label="list path, sequence source #1">/gorgone/pappso/formation/TD/Database/Genome_Z_mays_5a.fasta</note>
         //<note label="list path, sequence source #2">/gorgone/pappso/formation/TD/Database/contaminants_standarts.fasta</note>
-        if (_current_note_label.startsWith("list path, sequence source")) {
-            _p_identification_data_source->addFastaFile(FastaFile(_current_text));
+        if (_current_note_label.startsWith("list path, sequence source #")) {
+            _p_identification_data_source->addFastaFile(_p_project->getFastaFileStore().getInstance( FastaFile(_current_text)));
         }
 
         /*

src/utils/fastafilestore.cpp

@@ -29,6 +29,7 @@
 ******************************************************************************/
 
 #include "fastafilestore.h"
+#include <QDebug>
 FastaFileStore::FastaFileStore()
 {
 
@@ -40,24 +41,27 @@ FastaFileStore::~FastaFileStore()
 }
 
 FastaFileSp FastaFileStore::getInstance(const FastaFile & location) {
-
-    std::map< FastaFile, FastaFileSp >::iterator it = _map_fastafile.find(location);
-    if (it != _map_fastafile.end()) {
-        return it->second;
-    }
-    else {
-        FastaFileSp p_xtfile = std::make_shared<FastaFile>(location);
-        _map_fastafile.insert(std::pair< FastaFile, FastaFileSp >(location, p_xtfile));
-        return p_xtfile;
-
+qDebug() << "FastaFileStore::getInstance() begin ";
+qDebug() << "FastaFileStore::getInstance() begin "<< location.getAbsoluteFilePath();
+    std::vector<FastaFileSp>::iterator it = _map_fastafile.begin();
+    std::vector<FastaFileSp>::iterator itend = _map_fastafile.end();
+    while (it != itend) {
+        if (it->get()->getAbsoluteFilePath() == location.getAbsoluteFilePath()) {
+            
+qDebug() << "FastaFileStore::getInstance() end b "<< it->get()->getAbsoluteFilePath();
+            return *it;
+        }
+        it++;
     }
+    FastaFileSp fastafile_sp = std::make_shared<FastaFile>(location);
+    _map_fastafile.push_back(fastafile_sp);
+    qDebug() << "FastaFileStore::getFastaFileList() end a "  << _map_fastafile.size();
+    return fastafile_sp;
 }
 
 
-std::vector<FastaFileSp> FastaFileStore::getFastaFileList() const {
-    std::vector<FastaFileSp> msrun_list;
-    for (auto & msrun_pair :_map_fastafile) {
-        msrun_list.push_back(msrun_pair.second);
-    }
-    return msrun_list;
+const std::vector<FastaFileSp> & FastaFileStore::getFastaFileList() const {
+    qDebug() << "FastaFileStore::getFastaFileList() begin" ;
+    qDebug() << "FastaFileStore::getFastaFileList() begin" <<  _map_fastafile.size();
+    return _map_fastafile;
 }

src/utils/fastafilestore.h

@@ -31,7 +31,6 @@
 #ifndef FASTAFILESTORE_H
 #define FASTAFILESTORE_H
 
-#include <map>
 #include <vector>
 #include "../files/fastafile.h"
 
@@ -43,9 +42,9 @@ public:
 
     FastaFileSp getInstance(const FastaFile & fastafile);
     
-    std::vector<FastaFileSp> getFastaFileList() const;
+    const std::vector<FastaFileSp> & getFastaFileList() const;
 private:
-    std::map<FastaFile, FastaFileSp> _map_fastafile;
+    std::vector<FastaFileSp> _map_fastafile;
 };
 
 

src/utils/identificationdatasourcestore.cpp

@@ -63,17 +63,3 @@ qDebug() << " " << _map_identification_data_sources.size();
     }
     throw pappso::PappsoException(QObject::tr("Identification resource %1 not recognized").arg(location));
 }
-
-std::set<FastaFileSp> IdentificationDataSourceStore::getFastaFileList() const {
-    qDebug()<<  "IdentificationDataSourceStore::getFastaFileList begin ";
-    std::set<FastaFileSp> list_fasta_set;
-    /*
-    for (auto pair_ident:_map_identification_data_sources) {
-        qDebug()<<  "IdentificationDataSourceStore::getFastaFileList 1";
-        std::vector<FastaFileSp> idfastalist = pair_ident.second.get()->getFastaFileList();
-        list_fasta_set.insert(idfastalist.begin(), idfastalist.end()); 
-    }
-    */
-    qDebug()<<  "IdentificationDataSourceStore::getFastaFileList end";
-    return list_fasta_set;
-}

src/utils/identificationdatasourcestore.h

@@ -42,8 +42,6 @@ public:
     IdentificationDataSourceStore();
     ~IdentificationDataSourceStore();
     IdentificationDataSourceSp getInstance(const QString & location);
-    
-    std::set<FastaFileSp> getFastaFileList() const;
 private :
     std::map<QString, IdentificationDataSourceSp> _map_identification_data_sources;
 };