identification data source read and write fixed

src/core/identification_sources/identificationdatasource.cpp

@@ -37,6 +37,12 @@ IdentificationDataSource::IdentificationDataSource(const IdentificationDataSourc
     _ms_run_sp = other._ms_run_sp;
     _resource_name = other._resource_name;
     _xml_id = other._xml_id;
+    _version = other._version;
+    _params = other._params;
+    _param_stats = other._param_stats;
+    _fastafile_list = other._fastafile_list;
+    
+    //PeptideEvidenceStore _peptide_evidence_store;
 }
 
 IdentificationDataSource::~IdentificationDataSource()

src/core/msrun.cpp

@@ -43,6 +43,8 @@ MsRun::MsRun(const MsRun& other) {
     _xml_id = other._xml_id;
     _location = other._location;
     _name = other._name;
+    _mz_format=other._mz_format;
+    _param_stats = other._param_stats;
 }
 
 MsRun::~MsRun() {

src/input/xtpxpipsaxhandler.cpp

@@ -167,7 +167,9 @@ bool XtpXpipSaxHandler::endElement(const QString & namespaceURI, const QString &
         else if (qName == "identification_group") {
             is_ok = endElement_identification_group();
         }
-
+        else if (qName == "identification_source") {
+            is_ok = endElement_identification_source();
+        }
 
         // end of detection_moulon
         // else if ((_tag_stack.size() > 1) &&
@@ -307,17 +309,17 @@ bool XtpXpipSaxHandler::startElement_identification_source(QXmlAttributes attrib
     qDebug() << "startElement_identification_source ";
 
     IdentificationEngine engine = static_cast<IdentificationEngine>(attributes.value("engine").toUInt());
-    IdentificationDataSourceSp sp_ident_source =  _p_project->getIdentificationDataSourceStore().getInstance(attributes.value("path").simplified(), engine);
-    sp_ident_source.get()->setXmlId(attributes.value("id").simplified());
-    _map_ident_sources.insert(std::pair<QString, IdentificationDataSourceSp>(sp_ident_source.get()->getXmlId(), sp_ident_source));
+    _sp_current_identification_source =  _p_project->getIdentificationDataSourceStore().getInstance(attributes.value("path").simplified(), engine);
+    _sp_current_identification_source.get()->setXmlId(attributes.value("id").simplified());
+    _map_ident_sources.insert(std::pair<QString, IdentificationDataSourceSp>(_sp_current_identification_source.get()->getXmlId(), _sp_current_identification_source));
 
     qDebug() << "startElement_identification_source setMsRunSp";
-    sp_ident_source->setMsRunSp(_map_msruns.at(attributes.value("msrun_id").simplified()));
+    _sp_current_identification_source->setMsRunSp(_map_msruns.at(attributes.value("msrun_id").simplified()));
     qDebug() << "startElement_identification_source setIdentificationEngineVersion";
-    sp_ident_source->setIdentificationEngineVersion(attributes.value("version"));
+    _sp_current_identification_source->setIdentificationEngineVersion(attributes.value("version"));
     
     for (const QString & fasta_id : attributes.value("fasta_ids").split(" ")) {
-        sp_ident_source.get()->addFastaFile(_map_fasta_files.at(fasta_id));
+        _sp_current_identification_source.get()->addFastaFile(_map_fasta_files.at(fasta_id));
     }
 
     //_current_identification_group_p->addMsRunSp(ms_run);
@@ -482,6 +484,11 @@ bool XtpXpipSaxHandler::endElement_identification_group() {
     _current_identification_group_p = nullptr;
     return true;
 }
+bool XtpXpipSaxHandler::endElement_identification_source() {
+    qDebug() << "endElement_identification_source ";
+    _sp_current_identification_source = nullptr;
+    return true;
+}
 
 bool XtpXpipSaxHandler::endElement_peptide_evidence_list() {
     qDebug() << "endElement_peptide_evidence_list ";

src/input/xtpxpipsaxhandler.h

@@ -94,6 +94,7 @@ private:
     bool endElement_peptide_evidence();
     bool endElement_peptide_evidence_list();
     bool endElement_identification_group();
+    bool endElement_identification_source();
 
 private:
     WorkMonitorInterface * _p_monitor;