PeptideMatchParam renamed to PeptideEvidenceParam

src/core/peptideevidence.cpp

@@ -75,10 +75,10 @@ void PeptideEvidence::setEvalue(pappso::pappso_double evalue) {
 
 /** \brief set specific parameter value
  */
-void PeptideEvidence::setParam(PeptideMatchParam param, const QVariant& value) {
-    _params.insert(std::pair<PeptideMatchParam, QVariant>(param, value));
+void PeptideEvidence::setParam(PeptideEvidenceParam param, const QVariant& value) {
+    _params.insert(std::pair<PeptideEvidenceParam, QVariant>(param, value));
 }
-const QVariant PeptideEvidence::getParam(PeptideMatchParam param) const {
+const QVariant PeptideEvidence::getParam(PeptideEvidenceParam param) const {
     try {
         return _params.at(param);
     }
@@ -86,7 +86,7 @@ const QVariant PeptideEvidence::getParam(PeptideMatchParam param) const {
         return QVariant();
     }
 }
-const std::map<PeptideMatchParam, QVariant> & PeptideEvidence::getParamList() const {
+const std::map<PeptideEvidenceParam, QVariant> & PeptideEvidence::getParamList() const {
     return _params;
 }
 

src/core/peptideevidence.h

@@ -77,12 +77,12 @@ public :
 
     /** \brief set specific parameter value
      */
-    virtual void setParam(PeptideMatchParam param, const QVariant& value);
+    virtual void setParam(PeptideEvidenceParam param, const QVariant& value);
     /** \brief get specific parameter value
      */
-    virtual const QVariant getParam(PeptideMatchParam param) const;
+    virtual const QVariant getParam(PeptideEvidenceParam param) const;
 
-    const std::map<PeptideMatchParam, QVariant> & getParamList() const;
+    const std::map<PeptideEvidenceParam, QVariant> & getParamList() const;
 
 
     void setCharge(unsigned int charge);
@@ -133,7 +133,7 @@ private :
     pappso::pappso_double _exp_mass;
     unsigned int _charge;
     IdentificationDataSource* _p_identification_source = nullptr;
-    std::map<PeptideMatchParam, QVariant> _params;
+    std::map<PeptideEvidenceParam, QVariant> _params;
 
     /** @brief manually checked by user (true by default)
      */

src/gui/peptide_detail_view/peptidewindow.cpp

@@ -138,7 +138,7 @@ void PeptideWindow::updateDisplay() {
         ui->scan_label->setText(QString("%1").arg(_p_peptide_evidence->getScan()));
         ui->sample_label->setText(_p_peptide_evidence->getMsRunP()->getSampleName());
         ui->modification_label->setText(_p_peptide_evidence->getPeptideXtpSp().get()->getModifString());
-        ui->hyperscore_label->setText(_p_peptide_evidence->getParam(PeptideMatchParam::tandem_hyperscore).toString());
+        ui->hyperscore_label->setText(_p_peptide_evidence->getParam(PeptideEvidenceParam::tandem_hyperscore).toString());
         ui->evalue_label->setText(QString::number(_p_peptide_evidence->getEvalue(), 'g', 4));
         ui->mh_label->setText(QString::number(_p_peptide_evidence->getPeptideXtpSp().get()->getMz(1), 'f', 4));
         ui->mz_label->setText(QString::number(_p_peptide_evidence->getPeptideXtpSp().get()->getMz(_p_peptide_evidence->getCharge()), 'f', 4));

src/gui/peptide_list_view/peptidetablemodel.cpp

@@ -186,7 +186,7 @@ QVariant PeptideTableModel::data(const QModelIndex &index, int role ) const {
                 return QVariant((qreal) _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getDeltaMass());
                 break;
             case (std::int8_t)PeptideListColumn::hyperscore:
-                return _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getParam(PeptideMatchParam::tandem_hyperscore);
+                return _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getParam(PeptideEvidenceParam::tandem_hyperscore);
                 break;
             }
         }

src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.cpp

@@ -228,7 +228,7 @@ QVariant PtmPeptideTableModel::data(const QModelIndex &index, int role ) const {
                 return QVariant((qreal) _ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch().getPeptideEvidence()->getDeltaMass());
                 break;
             case (std::int8_t)PtmPeptideListColumn::besthyperscore:
-                return _ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch().getPeptideEvidence()->getParam(PeptideMatchParam::tandem_hyperscore);
+                return _ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch().getPeptideEvidence()->getParam(PeptideEvidenceParam::tandem_hyperscore);
                 break;
             case (std::int8_t)PtmPeptideListColumn::bestposition:
                 for (unsigned int position :_ptm_sample_scan_list.at(row).get()->getBestPtmPositionList(_p_ptm_grouping_experiment)) {

src/input/identificationpwizreader.cpp

@@ -255,7 +255,7 @@ void IdentificationPwizReader::read(
                     QVariant hyperscore = getQVariantDoubleParam(spid_item.get(), pwiz::cv::MS_X_Tandem_hyperscore);
                     if (!hyperscore.isNull())
                     {
-                        p_peptide_evidence->setParam(PeptideMatchParam::tandem_hyperscore, hyperscore);
+                        p_peptide_evidence->setParam(PeptideEvidenceParam::tandem_hyperscore, hyperscore);
                     }
 
 

src/input/xpipsaxhandler.cpp

@@ -263,7 +263,7 @@ bool XpipSaxHandler::startElement_peptide(QXmlAttributes attributes) {
     _p_peptide_evidence->setExperimentalMass(exp_mass);
     _current_peptide_match.setStart(attributes.value("start").simplified().toUInt()-1);
     _p_peptide_evidence->setCharge(attributes.value("charge").simplified().toUInt());
-    _p_peptide_evidence->setParam(PeptideMatchParam::tandem_hyperscore,  QVariant( attributes.value("hypercorr").toDouble()));
+    _p_peptide_evidence->setParam(PeptideEvidenceParam::tandem_hyperscore,  QVariant( attributes.value("hypercorr").toDouble()));
 
     IdentificationDataSource* p_identification_data_source = _p_project->getIdentificationDataSourceStore().getInstance(attributes.value("sample_file").simplified()).get();
     _p_peptide_evidence->setIdentificationDataSource( p_identification_data_source);

src/input/xtandemsaxhandler.cpp

@@ -299,7 +299,7 @@ bool XtandemSaxHandler::startElement_domain(QXmlAttributes attributes) {
     _current_peptide_match.setStart(attributes.value("start").simplified().toUInt()-1);
     _p_peptide_evidence->setCharge(_charge);
 
-    _p_peptide_evidence->setParam(PeptideMatchParam::tandem_hyperscore,  QVariant( attributes.value("hyperscore").toDouble()));
+    _p_peptide_evidence->setParam(PeptideEvidenceParam::tandem_hyperscore,  QVariant( attributes.value("hyperscore").toDouble()));
 
     _p_peptide_evidence->setIdentificationDataSource( _p_identification_data_source);
     _p_peptide_evidence->setChecked(true);

src/input/xtpxpipsaxhandler.cpp

@@ -74,6 +74,8 @@ bool XtpXpipSaxHandler::startElement(const QString & namespaceURI, const QString
             is_ok = startElement_protein(attributes);
         } else if (qName == "identification_source") {
             is_ok = startElement_identification_source(attributes);
+        } else if (qName == "param") {
+            is_ok = startElement_param(attributes);
         }
         //<sample value="P6_08_10"/>
         else if (qName == "sample") {
@@ -180,6 +182,23 @@ bool XtpXpipSaxHandler::startElement_description(QXmlAttributes attributes) {
     return true;
 }
 
+        
+bool XtpXpipSaxHandler::startElement_param(QXmlAttributes attributes) {
+
+    /*
+    <param key="0" value="48.5"/>
+    */
+    qDebug() << "startElement_param ";
+
+    if (_sp_current_peptide_evidence.get() != nullptr) {
+        PeptideEvidenceParam type = static_cast<PeptideEvidenceParam>(attributes.value("key").toUInt());
+        _sp_current_peptide_evidence.get()->setParam(type, QVariant( attributes.value("value").toDouble()));
+    }
+
+    qDebug() << "startElement_param end" ;
+    return true;
+}
+
 bool XtpXpipSaxHandler::startElement_modification(QXmlAttributes attributes) {
 
     /*
@@ -249,8 +268,8 @@ bool XtpXpipSaxHandler::startElement_peptide_evidence(QXmlAttributes attributes)
     _p_peptide_evidence->setExperimentalMass(attributes.value("exp_mass").toDouble());
     _p_peptide_evidence->setPeptideXtpSp(_map_peptides.at( attributes.value("peptide_id").simplified()));
     
-    PeptideEvidenceSp sp_peptide_evidence = sp_ident_source.get()->getPeptideEvidenceStore().getInstance(_p_peptide_evidence);
-    _map_peptide_evidences.insert(std::pair<QString, PeptideEvidenceSp>(attributes.value("id").simplified(), sp_peptide_evidence));
+    _sp_current_peptide_evidence = sp_ident_source.get()->getPeptideEvidenceStore().getInstance(_p_peptide_evidence);
+    _map_peptide_evidences.insert(std::pair<QString, PeptideEvidenceSp>(attributes.value("id").simplified(), _sp_current_peptide_evidence));
     qDebug() << "startElement_peptide_evidence end" ;
     return true;
 }

src/input/xtpxpipsaxhandler.h

@@ -78,6 +78,7 @@ private:
     bool startElement_identification_source(QXmlAttributes attributes);
     bool startElement_modification(QXmlAttributes attributes);
     bool startElement_mod(QXmlAttributes attributes);
+    bool startElement_param(QXmlAttributes attributes);
     //bool endElement_identification();
     bool endElement_sequence();
     bool endElement_protein();
@@ -103,6 +104,7 @@ private:
     std::map<QString, MsRunSp> _map_msruns;
     std::map<QString, IdentificationDataSourceSp> _map_ident_sources;
     std::map<QString, PeptideEvidenceSp> _map_peptide_evidences;
+    PeptideEvidenceSp _sp_current_peptide_evidence;
     ProteinXtp _current_protein;
     PeptideXtpSp _current_peptide_sp;
     std::map<QString, PeptideXtpSp> _map_peptides;

src/output/ods/spectrasheet.cpp

@@ -107,7 +107,7 @@ void SpectraSheet::writeBestPeptideEvidence(const GroupingGroup * p_group,const
         }
     }
     _p_writer->writeCell(p_peptide_evidence->getEvalue());
-    _p_writer->writeCell(p_peptide_evidence->getParam(PeptideMatchParam::tandem_hyperscore).toDouble());
+    _p_writer->writeCell(p_peptide_evidence->getParam(PeptideEvidenceParam::tandem_hyperscore).toDouble());
 
 
 }

src/output/proticdbml.cpp

@@ -487,7 +487,7 @@ void ProticdbMl::writePeptideHit(QString xml_id, ProticPeptideHit & protic_pepti
         writeCvParam("PROTICdbO:0000287", Utils::getXmlDouble(protic_peptide_hit.peptide_match->getPeptideEvidence()->getEvalue()),
                      "xtandem peptide evalue");
 
-        writeCvParam("PROTICdbO:0000288", Utils::getXmlDouble(protic_peptide_hit.peptide_match->getPeptideEvidence()->getParam(PeptideMatchParam::tandem_hyperscore).toDouble()),
+        writeCvParam("PROTICdbO:0000288", Utils::getXmlDouble(protic_peptide_hit.peptide_match->getPeptideEvidence()->getParam(PeptideEvidenceParam::tandem_hyperscore).toDouble()),
                      "xtandem peptide hyperscore");
     }
 

src/output/xpip.cpp

@@ -389,11 +389,11 @@ void Xpip::writePeptideEvidence(const PeptideEvidence * p_peptide_evidence) {
         _output_stream->writeAttribute("checked","false");
     }
 
-    const std::map<PeptideMatchParam, QVariant> & params = p_peptide_evidence->getParamList();
+    const std::map<PeptideEvidenceParam, QVariant> & params = p_peptide_evidence->getParamList();
 
     //if (params.size() > 0) {
     //   _output_stream->writeStartElement("stats");
-    for (const std::pair<PeptideMatchParam, QVariant> param_pair: params) {
+    for (const std::pair<PeptideEvidenceParam, QVariant> param_pair: params) {
         _output_stream->writeStartElement("param");
         _output_stream->writeAttribute("key",QString("%1").arg(static_cast<std::int8_t>(param_pair.first)));
         _output_stream->writeAttribute("value",param_pair.second.toString());

src/utils/types.h

@@ -50,18 +50,18 @@ enum class IdentificationEngine: std::int8_t {
     peptider=3 ///< peptider
 };
 
-/** \def PeptideMatchParam peptide match specific parameters
+/** \def PeptideEvidenceParam peptide evidence specific parameters
  *
  */
-enum class PeptideMatchParam: std::int8_t {
+enum class PeptideEvidenceParam: std::int8_t {
     tandem_hyperscore=0 ///< X!Tandem hyperscore
 };
 
 /** \def IdentificationEngineParam identification engine parameters
  *
  */
-enum class IdentificationEngineParam {
-    tandem_param ///< X!Tandem xml parameters file
+enum class IdentificationEngineParam: std::int8_t {
+    tandem_param=0 ///< X!Tandem xml parameters file
 };