solved modification string

src/core/peptidextp.cpp

@@ -23,6 +23,7 @@
 
 
 #include "peptidextp.h"
+#include <QStringList>
 
 PeptideXtp::PeptideXtp(const QString & pepstr):pappso::Peptide(pepstr)
 {
@@ -39,11 +40,35 @@ PeptideXtp::~PeptideXtp()
 
 }
 
+const QString PeptideXtp::getModifString() const {
+    QStringList modif_list;
+    unsigned int i=1;
+    for (const pappso::Aa & amino_acid:_aa_vec) {
+        std::list<pappso::AaModificationP> aa_modif_list = amino_acid.getModificationList();
+        QStringList aamodif;
+        for (auto && aa_modif : aa_modif_list) {
+            if (!aa_modif->isInternal()) {
+                aamodif << QString::number(aa_modif->getMass(), 'f', 2);
+            }
+        }
+        QString mod_str(aamodif.join("|"));
+        if (!mod_str.isEmpty()) {
+            modif_list << QString("%1%2:%3").arg(i).arg(amino_acid.getLetter()).arg(mod_str);
+        }
+        i++;
+    }
+    //return QString ("%1 %2").arg(modif_list.join(" ")).arg(this->toAbsoluteString());
+    return modif_list.join(" ");
+}
+
 PeptideXtpSp PeptideXtp::makePeptideXtpSp() const {
     return std::make_shared<PeptideXtp>(*this);
 }
 
 
 pappso::mz PeptideXtp::getGroupingMass() const {
-    return getMass();
+    if (_sp_native_peptide.get() == nullptr) {
+        return getMass();
+    }
+    return _sp_native_peptide.get()->getMass();
 }

src/core/peptidextp.h

@@ -45,6 +45,16 @@ public:
      * peptide with taget modification is a light, inter or heavy version of the same peptide
  */
     pappso::mz getGroupingMass() const;
+    
+    /** \brief human readable string that contains modifications
+     * */
+    const QString getModifString() const;
+    
+private:
+    /** \brief if the peptide is tagged, this is the native peptide without tags
+     */
+    pappso::PeptideSp _sp_native_peptide = nullptr;
+    
 
 };
 

src/gui/peptide_list_view/peptidetablemodel.cpp

@@ -98,7 +98,7 @@ int PeptideTableModel::rowCount(const QModelIndex &parent ) const {
     return 0;
 }
 int PeptideTableModel::columnCount(const QModelIndex &parent ) const {
-    return 7;
+    return 8;
 }
 QVariant PeptideTableModel::headerData(int section, Qt::Orientation orientation, int role) const
 {
@@ -121,6 +121,8 @@ QVariant PeptideTableModel::headerData(int section, Qt::Orientation orientation,
                 return QString("charge");
             case 6:
                 return QString("sequence");
+            case 7:
+                return QString("modifs");
             }
         }
     }
@@ -179,6 +181,9 @@ QVariant PeptideTableModel::data(const QModelIndex &index, int role ) const {
             if (col ==6) {
                 return _p_protein_match->getPeptideMatchList().at(row)->getPeptideXtpSp().get()->getSequence();
             }
+            if (col ==7) {
+                return _p_protein_match->getPeptideMatchList().at(row)->getPeptideXtpSp().get()->getModifString();
+            }
         }
         return QString("Row%1, Column%2")
                .arg(index.row() + 1)

src/input/xpipsaxhandler.cpp

@@ -270,8 +270,8 @@ bool XpipSaxHandler::startElement_modif(QXmlAttributes attributes) {
     //<modifs><modif aa="M" modvalue="15.99491" posi="17" posi_in_prot="49"/>
     qDebug() << "startElement_modif ";
     pappso::AaModificationP modif = _map_massstr_aamod[attributes.value("modvalue").simplified()];
-    unsigned int position = attributes.value("modvalue").simplified().toUInt();
-    _current_peptide_sp.get()->addAaModification(modif, position);
+    unsigned int position = attributes.value("posi").simplified().toUInt();
+    _current_peptide_sp.get()->addAaModification(modif, position-1);
     qDebug() << "startElement_modif end" ;
     return true;
 }