fix problem getting peptide traces on labeled peptides

src/lib/peptides/peptide.h

@@ -166,6 +166,12 @@ public:
     getCharges(const msRunHashGroup & group) const;
 
     const QString getSequence() const;
+    
+    
+    
+    virtual const Peptide * getOriginalPeptidePointer() const {
+        return this;
+    };
 
 
 protected:

src/lib/peptides/peptide_isotope.h

@@ -76,6 +76,10 @@ public:
 
     virtual const PeptideRtSp & getPeptideRtSp() const override;
 
+    virtual const Peptide * getOriginalPeptidePointer() const {
+        return _p_peptide_original;
+    };
+
 private:
 
     const Peptide * _p_peptide_original;

src/lib/quanti_items/quantiItemPeptide.cpp

@@ -156,11 +156,19 @@ CalcWriterInterface * QuantiItemPeptide::newCalcWriterInterface(const Quantifica
     QDir trace_dir(QString("%1/%2/%3").arg(quantificator->getTracesDirectory().absolutePath()).arg(this->getPeptide()->getXmlId()).arg(p_msrun->getXmlId()));
     trace_dir.mkpath(trace_dir.absolutePath());
     CalcWriterInterface * _p_writer=nullptr;
+    const IsotopeLabel * p_label = this->getPeptide()->getIsotopeLabel();
+    QString begin_path;
+    if (p_label == nullptr) {
+        begin_path = QString("%1/%2_%3-%4-z%5").arg(trace_dir.absolutePath()).arg(prefix).arg(quantificator->getXmlId()).arg(this->getPeptide()->getXmlId()).arg(this->_z);
+    }
+    else {
+        begin_path = QString("%1/%2_%3-%4-%5-z%6").arg(trace_dir.absolutePath()).arg(prefix).arg(quantificator->getXmlId()).arg(this->getPeptide()->getXmlId()).arg(p_label->getXmlId()).arg(this->_z);
+    }
     if (quantificator->getTracesFormat() == McqTsvFormat::tsv) {
-        _p_writer = new TsvDirectoryWriter(QString("%1/%2_%3-%4-z%5.d").arg(trace_dir.absolutePath()).arg(prefix).arg(quantificator->getXmlId()).arg(this->getPeptide()->getXmlId()).arg(this->_z));
+        _p_writer = new TsvDirectoryWriter(begin_path.append(".d"));
     }
     else {
-        _p_writer = new OdsDocWriter(QString("%1/%2_%3-%4-z%5.ods").arg(trace_dir.absolutePath()).arg(prefix).arg(quantificator->getXmlId()).arg(this->getPeptide()->getXmlId()).arg(this->_z));
+        _p_writer = new OdsDocWriter(begin_path.append(".ods"));
     }
     return _p_writer;
 

src/lib/quanti_items/quantiitempeptidenaturalisotope.cpp

@@ -120,11 +120,20 @@ CalcWriterInterface * QuantiItemPeptideNaturalIsotope::newCalcWriterInterface(co
     QDir trace_dir(QString("%1/%2/%3").arg(quantificator->getTracesDirectory().absolutePath()).arg(this->getPeptide()->getXmlId()).arg(p_msrun->getXmlId()));
     trace_dir.mkpath(trace_dir.absolutePath());
     CalcWriterInterface * _p_writer=nullptr;
+
+    const IsotopeLabel * p_label = this->getPeptide()->getIsotopeLabel();
+    QString begin_path;
+    if (p_label == nullptr) {
+        begin_path = QString("%1/%2_%3-%4-z%5-%6-%7").arg(trace_dir.absolutePath()).arg(prefix).arg(quantificator->getXmlId()).arg(this->getPeptide()->getXmlId()).arg(this->_z).arg(this->getPeptideNaturalIsotopeAverageSp()->getIsotopeNumber()).arg(this->getPeptideNaturalIsotopeAverageSp()->getIsotopeRank());
+    }
+    else {
+        begin_path = QString("%1/%2_%3-%4-%5-z%6-%7-%8").arg(trace_dir.absolutePath()).arg(prefix).arg(quantificator->getXmlId()).arg(this->getPeptide()->getXmlId()).arg(p_label->getXmlId()).arg(this->_z).arg(this->getPeptideNaturalIsotopeAverageSp()->getIsotopeNumber()).arg(this->getPeptideNaturalIsotopeAverageSp()->getIsotopeRank());
+    }
     if (quantificator->getTracesFormat() == McqTsvFormat::tsv) {
-        _p_writer = new TsvDirectoryWriter(QString("%1/%2_%3-%4-z%5-%6-%7.d").arg(trace_dir.absolutePath()).arg(prefix).arg(quantificator->getXmlId()).arg(this->getPeptide()->getXmlId()).arg(this->_z).arg(this->getPeptideNaturalIsotopeAverageSp()->getIsotopeNumber()).arg(this->getPeptideNaturalIsotopeAverageSp()->getIsotopeRank()));
+        _p_writer = new TsvDirectoryWriter(begin_path.append(".d"));
     }
     else {
-        _p_writer = new OdsDocWriter(QString("%1/%2_%3-%4-z%5-%6-%7.ods").arg(trace_dir.absolutePath()).arg(prefix).arg(quantificator->getXmlId()).arg(this->getPeptide()->getXmlId()).arg(this->_z).arg(this->getPeptideNaturalIsotopeAverageSp()->getIsotopeNumber()).arg(this->getPeptideNaturalIsotopeAverageSp()->getIsotopeRank()));
+        _p_writer = new OdsDocWriter(begin_path.append(".ods"));
     }
     return _p_writer;
 

src/lib/quantificator.cpp

@@ -162,7 +162,8 @@ void Quantificator::add_peptide_quanti_items(
             ++itpep, debug_i++) {
         mcqout() << "Quantificator::add_peptide_quanti_items for " << debug_i << " " << isotope_peptides.size() << endl;
         bool trace_peptide = false;
-        if (std::find(trace_peptide_list.begin(), trace_peptide_list.end(), *itpep) != trace_peptide_list.end()) {
+	const Peptide * original_peptide_p = (*itpep)->getOriginalPeptidePointer();
+        if (std::find(trace_peptide_list.begin(), trace_peptide_list.end(), original_peptide_p) != trace_peptide_list.end()) {
             trace_peptide = true;
         }