new function to get retention time from mz data if needed

src/core/peptideevidence.cpp

@@ -315,6 +315,33 @@ PeptideEvidence::getRetentionTime() const
 {
   return _rt;
 }
+
+pappso::pappso_double
+PeptideEvidence::getHardenedRetentionTime() const
+{
+  if(_rt == 0)
+    {
+      // try to look at mz data file
+      if(_p_identification_source != nullptr)
+        {
+          MsRunSp msrunsp = _p_identification_source->getMsRunSp();
+          if(msrunsp != nullptr)
+            {
+              pappso::MsRunReaderSPtr reader =
+                msrunsp.get()->getMsRunReaderSPtr();
+              if(reader != nullptr)
+                {
+                  pappso::QualifiedMassSpectrum qmassspec =
+                    reader.get()->qualifiedMassSpectrum(m_scan_number, false);
+
+                  return qmassspec.getRtInSeconds();
+                }
+            }
+        }
+    }
+  return _rt;
+}
+
 unsigned int
 PeptideEvidence::getCharge() const
 {

src/core/peptideevidence.h

@@ -119,7 +119,22 @@ class PeptideEvidence
   MsRun *getMsRunPtr();
   IdentificationDataSource *getIdentificationDataSource() const;
   unsigned int getScanNumber() const;
+
+  /** @brief get retention time of this PSM in seconds
+   * the retention time must have been present when reading MS identification
+   * results. If no retention time was set, this returns O
+   * @return retention time in seconds or zero if data is missing
+   */
   pappso::pappso_double getRetentionTime() const;
+
+  /** @brief get retention time of this PSM in seconds by all means
+   *
+   * if retention time is missing, this tries to guess it by all means. It will
+   * try to look at mz data file.
+   * This could be time consuming.
+   * @return retention time in seconds or zero if data is missing
+   */
+  pappso::pappso_double getHardenedRetentionTime() const;
   unsigned int getCharge() const;
   const PeptideXtpSp &getPeptideXtpSp() const;
   pappso::pappso_double getEvalue() const;

src/gui/xic_view/xic_box/xicbox.cpp

@@ -63,7 +63,7 @@ class XicDetectionList : public pappso::TraceDetectionSinkInterface
   {
     for(const PeptideEvidence *p_evidence : peptide_evidence_list)
       {
-        _rt_list.push_back(p_evidence->getRetentionTime());
+        _rt_list.push_back(p_evidence->getHardenedRetentionTime());
       }
   }
   void
@@ -363,9 +363,10 @@ XicBox::setXic(std::vector<pappso::XicCstSPtr> xic_sp_list)
           for(const PeptideEvidence *peptide_evidence : _peptide_evidence_list)
             {
               qDebug() << "XicBox::setXic peptide_evidence "
-                       << peptide_evidence->getRetentionTime();
+                       << peptide_evidence->getHardenedRetentionTime();
               ui->xic_widget->addMsMsEvent(
-                xic_isotope.xic_sp.get(), peptide_evidence->getRetentionTime());
+                xic_isotope.xic_sp.get(),
+                peptide_evidence->getHardenedRetentionTime());
             }
         }
     }