convenient functions to get a spectrum index even if we have only a scan number

src/core/msrun.cpp

@@ -674,3 +674,47 @@ MsRun::getQualifiedMassSpectrumBySpectrumIndex(std::size_t spectrum_index,
            << " index=" << spectrum_index;
   return msrun_reader_sp.get()->qualifiedMassSpectrum(spectrum_index, data);
 }
+
+
+std::size_t
+MsRun::scanNumber2SpectrumIndex(std::size_t scan_number)
+{
+
+  qDebug() << "scan=" << scan_number;
+  if(getMzFormat() == pappso::MzFormat::MGF)
+    {
+      scan_number = scan_number - 1;
+      qDebug() << "MGF format";
+    }
+  pappso::MsRunReaderSPtr msrun_reader_sp = getMsRunReaderSPtr();
+
+  if(msrun_reader_sp == nullptr)
+    {
+      msrun_reader_sp = findMsRunFile();
+      if(msrun_reader_sp == nullptr)
+        {
+          throw pappso::ExceptionNotFound(
+            QObject::tr("mz data \"%1\" file not found").arg(getFileName()));
+        }
+    }
+  qDebug();
+  msrun_reader_sp = getMsRunReaderSPtr();
+  if(msrun_reader_sp == nullptr)
+    {
+      throw pappso::ExceptionNotFound(
+        QObject::tr("mz data \"%1\" file not found").arg(getFileName()));
+    }
+
+
+  if(msrun_reader_sp.get()->hasScanNumbers())
+    {
+      qDebug() << "HAS SCAN NUMBERS";
+      return msrun_reader_sp.get()->scanNumber2SpectrumIndex(scan_number);
+    }
+  else
+    {
+      throw pappso::ExceptionNotFound(
+        QObject::tr("mz data \"%1\" file does not contain scan numbers")
+          .arg(getFileName()));
+    }
+}

src/core/msrun.h

@@ -144,6 +144,14 @@ class MsRun : public pappso::MsRunId
   pappso::QualifiedMassSpectrum
   getQualifiedMassSpectrumByScanNumber(std::size_t scan_number, bool data);
 
+
+  /** @brief finds the spectrum index corresponding to a scan number
+   *
+   * @param scan_number the scan number to convert
+   * @return spectrum index or an exception
+   */
+  std::size_t scanNumber2SpectrumIndex(std::size_t scan_number);
+
   private:
   void buildMsRunReaderSp();
 

src/core/peptideevidence.cpp

@@ -446,11 +446,33 @@ PeptideEvidence::getSpectrumIndex() const
     }
   throw pappso::ExceptionNotFound(
     QObject::tr(
-      "this peptide evidence has no spectrum index, only a scan number : ")
+      "this peptide evidence has no spectrum index, only a scan number : %1")
       .arg(m_scan_number));
 }
 
 
+std::size_t
+PeptideEvidence::getSpectrumIndexByScanNumber() const
+{
+  if(m_isSpectrumIndex)
+    {
+      return m_scan_number;
+    }
+  else
+    {
+      if(_msrunid_sp != nullptr)
+        {
+          return _msrunid_sp->scanNumber2SpectrumIndex(m_scan_number);
+        }
+      else
+        {
+          throw pappso::PappsoException(
+            QObject::tr("_msrunid_sp == nullptr"));
+        }
+    }
+}
+
+
 QString
 PeptideEvidence::getHtmlSequence() const
 {

src/core/peptideevidence.h

@@ -200,6 +200,16 @@ class PeptideEvidence
    * @return spectrum index or not found exception
    */
   std::size_t getSpectrumIndex() const;
+  
+  
+  /** @brief get the spectrum index from the scan number
+   * 
+   * finds a spectrum index using a scan number if necessary
+   * 
+   * @return spectrum_index or not found exception
+   * 
+   */ 
+  std::size_t getSpectrumIndexByScanNumber() const;
 
 
   /** @brief get HTML sequence of the peptide

src/gui/xic_view/xic_box/xicbox.cpp

@@ -636,7 +636,7 @@ XicBox::setIsotopeMassList(
       ->getMsRunReaderSPtr()
       .get()
       ->newXicCoordSPtrFromSpectrumIndex(
-        _p_peptide_evidence->getSpectrumIndex(),
+        _p_peptide_evidence->getSpectrumIndexByScanNumber(),
         _p_xic_window->getXicExtractPrecision());
 
   std::vector<pappso::XicCoordSPtr> mass_list;