nter and cter flanking region in ODS export

src/core/proteinmatch.cpp

@@ -812,7 +812,7 @@ ProteinMatch::collectPeptideEvidences(
 
 QString
 ProteinMatch::getFlankingNterRegion(const PeptideMatch &peptide_match,
-                                    int orig_length)
+                                    int orig_length) const
 {
   int length = orig_length;
   int start  = peptide_match.getStart() - length;
@@ -836,7 +836,7 @@ ProteinMatch::getFlankingNterRegion(const PeptideMatch &peptide_match,
 
 QString
 ProteinMatch::getFlankingCterRegion(const PeptideMatch &peptide_match,
-                                    int orig_length)
+                                    int orig_length) const
 {
   int start = peptide_match.getStop();
   int max   = getProteinXtpSp().get()->getSequence().size();

src/core/proteinmatch.h

@@ -188,13 +188,15 @@ class ProteinMatch
    * @param peptide_match the peptide from which we want flanking region
    * @param length size of the protein flanking region
    */
-  QString getFlankingNterRegion(const PeptideMatch &peptide_match, int length);
+  QString getFlankingNterRegion(const PeptideMatch &peptide_match,
+                                int length) const;
 
   /** @brief get the flanking protein sequence at the Cter side of the peptide
    * @param peptide_match the peptide from which we want flanking region
    * @param length size of the protein flanking region
    */
-  QString getFlankingCterRegion(const PeptideMatch &peptide_match, int length);
+  QString getFlankingCterRegion(const PeptideMatch &peptide_match,
+                                int length) const;
 
   protected:
   void setGroupingExperiment(GroupingExperiment *p_grp_experiment);

src/output/ods/peptidepossheet.cpp

@@ -82,12 +82,14 @@ PeptidePosSheet::writeHeaders(IdentificationGroup *p_ident)
   _p_writer->writeCell("Protein ID");
   _p_writer->writeCell("accession");
   _p_writer->writeCell("description");
-  _p_writer->writeCell("Peptide ID");
-  _p_writer->writeCell("Sequence");
-  _p_writer->writeCell("Modifs");
-  _p_writer->writeCell("Start");
+  writeCellHeader(PeptideListColumn::peptide_grouping_id);
+  writeCellHeader(PeptideListColumn::sequence_nter);
+  writeCellHeader(PeptideListColumn::sequence);
+  writeCellHeader(PeptideListColumn::sequence_cter);
+  writeCellHeader(PeptideListColumn::modifs);
+  writeCellHeader(PeptideListColumn::start);
   _p_writer->writeCell("Stop");
-  _p_writer->writeCell("MH+ theo");
+  writeCellHeader(PeptideListColumn::theoretical_mhplus);
 }
 
 void
@@ -121,8 +123,12 @@ PeptidePosSheet::writeBestPeptideMatch(const ProteinMatch *p_protein_match,
     p_protein_match->getProteinXtpSp().get()->getDescription());
   _p_writer->writeCell(
     p_peptide_evidence->getGrpPeptideSp().get()->getGroupingId());
+  _p_writer->writeCell(
+    p_protein_match->getFlankingNterRegion(peptide_match, 1));
   _p_writer->writeCell(
     p_peptide_evidence->getPeptideXtpSp().get()->getSequence());
+  _p_writer->writeCell(
+    p_protein_match->getFlankingCterRegion(peptide_match, 1));
   _p_writer->writeCell(
     p_peptide_evidence->getPeptideXtpSp().get()->getModifString());
   _p_writer->writeCell(peptide_match.getStart() + 1);
@@ -149,7 +155,8 @@ PeptidePosSheet::writeIdentificationGroup(IdentificationGroup *p_ident)
     }
 
   std::sort(
-    protein_match_list.begin(), protein_match_list.end(),
+    protein_match_list.begin(),
+    protein_match_list.end(),
     [](const ProteinMatch *a, const ProteinMatch *b) {
       unsigned int agroup    = a->getGrpProteinSp().get()->getGroupNumber();
       unsigned int asubgroup = a->getGrpProteinSp().get()->getSubGroupNumber();
@@ -174,7 +181,8 @@ PeptidePosSheet::writeIdentificationGroup(IdentificationGroup *p_ident)
             continue;
           peptide_match_list.push_back(peptide_match);
         }
-      std::sort(peptide_match_list.begin(), peptide_match_list.end(),
+      std::sort(peptide_match_list.begin(),
+                peptide_match_list.end(),
                 [](const PeptideMatch &a, const PeptideMatch &b) {
                   unsigned int arank =
                     a.getPeptideEvidence()->getGrpPeptideSp().get()->getRank();
@@ -231,3 +239,14 @@ PeptidePosSheet::writeIdentificationGroup(IdentificationGroup *p_ident)
   _p_writer->writeLine();
   qDebug() << "PeptidePosSheet::writeIdentificationGroup end";
 }
+
+
+void
+PeptidePosSheet::writeCellHeader(PeptideListColumn column)
+{
+  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
+           << (std::int8_t)column;
+  _p_writer->setCellAnnotation(PeptideTableModel::getDescription(column));
+  _p_writer->writeCell(PeptideTableModel::getTitle(column));
+  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+}

src/output/ods/peptidepossheet.h

@@ -37,11 +37,13 @@
 #include <odsstream/calcwriterinterface.h>
 #include "../../core/proteinmatch.h"
 #include "odsexport.h"
+#include "../../gui/peptide_list_view/peptidetablemodel.h"
 
 class PeptidePosSheet
 {
   public:
-  PeptidePosSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+  PeptidePosSheet(OdsExport *p_ods_export,
+                  CalcWriterInterface *p_writer,
                   const Project *p_project);
 
   private:
@@ -50,6 +52,8 @@ class PeptidePosSheet
   void writeBestPeptideMatch(const ProteinMatch *p_protein_match,
                              const PeptideMatch &peptide_match);
 
+  void writeCellHeader(PeptideListColumn column);
+
   private:
   OdsExport *_p_ods_export;
   const Project *_p_project;

src/output/ods/proteinsheet.cpp

@@ -58,10 +58,11 @@ ProteinSheet::ProteinSheet(OdsExport *p_ods_export,
 void
 ProteinSheet::writeCellHeader(ProteinListColumn column)
 {
-  qDebug() << "ProteinSheet::writeCellHeader begin " << (std::int8_t)column;
+  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
+           << (std::int8_t)column;
   _p_writer->setCellAnnotation(ProteinTableModel::getDescription(column));
   _p_writer->writeCell(ProteinTableModel::getTitle(column));
-  qDebug() << "ProteinSheet::writeCellHeader end";
+  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
 }
 
 void
@@ -141,7 +142,8 @@ ProteinSheet::writeIdentificationGroup(IdentificationGroup *p_ident)
       std::vector<const ProteinMatch *> protein_match_list =
         group_pair.second.get()->getProteinMatchList();
 
-      std::sort(protein_match_list.begin(), protein_match_list.end(),
+      std::sort(protein_match_list.begin(),
+                protein_match_list.end(),
                 [](const ProteinMatch *a, const ProteinMatch *b) {
                   return a->getGrpProteinSp().get()->getGroupingId() <
                          b->getGrpProteinSp().get()->getGroupingId();