Export PTm spectra of checked ptm island

src/grouping/ptm/ptmisland.cpp

@@ -62,7 +62,7 @@ PtmIsland::size() const
   return _protein_stop - _protein_start;
 }
 
-bool PtmIsland::isChecked()
+bool PtmIsland::isChecked() const
 {
   return m_checked;
 }

src/grouping/ptm/ptmisland.h

@@ -77,7 +77,7 @@ class PtmIsland
   unsigned int getStart() const;
   unsigned int size() const;
   void setChecked(bool check_status);
-  bool isChecked();
+  bool isChecked() const;
 
   std::vector<PtmSampleScanSp> getPtmSampleScanSpList() const;
 

src/output/ods/ptm/ptmspectrasheet.cpp

@@ -237,7 +237,10 @@ PtmSpectraSheet::writeBestPeptideEvidence(
   // return _ptm_sample_scan_list.at(row).get()->getObservedPtmPositionList();
   for(const PtmIsland *ptm_island : ptmisland_occurence_list)
     {
-      position_list << ptm_island->getGroupingId();
+      if(ptm_island->isChecked())
+        {
+          position_list << ptm_island->getGroupingId();
+        }
     }
   _p_writer->writeCell(position_list.join(" "));
 
@@ -286,41 +289,48 @@ PtmSpectraSheet::writePtmIslandSubgroupSp(
   for(PtmIslandSp ptm_island_sp :
       ptm_island_subgroup_sp.get()->getPtmIslandList())
     {
-
-      qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
-      for(PeptideMatch peptide_match :
-          ptm_island_sp.get()->getPeptideMatchList())
+      if(ptm_island_sp->isChecked())
         {
-
           qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
-          std::vector<PtmSampleScanOccurence>::iterator it_ptm =
-            ptm_sample_scan_occurence_list.begin();
-          std::vector<PtmSampleScanOccurence>::iterator it_ptm_end =
-            ptm_sample_scan_occurence_list.end();
-          while((it_ptm != it_ptm_end) &&
-                (it_ptm->ptm_sample_scan.add(peptide_match) == false))
-            {
-              // peptide added
-              it_ptm++;
-            }
-          if(it_ptm == it_ptm_end)
+          for(PeptideMatch peptide_match :
+              ptm_island_sp.get()->getPeptideMatchList())
             {
-              qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
-              // peptide NOT added
-              PtmSampleScanOccurence new_occurence = {
-                PtmSampleScan(peptide_match), std::set<const PtmIsland *>()};
-              new_occurence.ptmisland_occurence_list.insert(
-                ptm_island_sp.get());
-              ptm_sample_scan_occurence_list.push_back(new_occurence);
-              qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
-            }
-          else
-            {
-              // peptide added
-              qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
-              it_ptm->ptmisland_occurence_list.insert(ptm_island_sp.get());
 
               qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+              std::vector<PtmSampleScanOccurence>::iterator it_ptm =
+                ptm_sample_scan_occurence_list.begin();
+              std::vector<PtmSampleScanOccurence>::iterator it_ptm_end =
+                ptm_sample_scan_occurence_list.end();
+              while((it_ptm != it_ptm_end) &&
+                    (it_ptm->ptm_sample_scan.add(peptide_match) == false))
+                {
+                  // peptide added
+                  it_ptm++;
+                }
+              if(it_ptm == it_ptm_end)
+                {
+                  qDebug() << __FILE__ << " " << __FUNCTION__ << " "
+                           << __LINE__;
+                  // peptide NOT added
+                  PtmSampleScanOccurence new_occurence = {
+                    PtmSampleScan(peptide_match),
+                    std::set<const PtmIsland *>()};
+                  new_occurence.ptmisland_occurence_list.insert(
+                    ptm_island_sp.get());
+                  ptm_sample_scan_occurence_list.push_back(new_occurence);
+                  qDebug() << __FILE__ << " " << __FUNCTION__ << " "
+                           << __LINE__;
+                }
+              else
+                {
+                  // peptide added
+                  qDebug() << __FILE__ << " " << __FUNCTION__ << " "
+                           << __LINE__;
+                  it_ptm->ptmisland_occurence_list.insert(ptm_island_sp.get());
+
+                  qDebug() << __FILE__ << " " << __FUNCTION__ << " "
+                           << __LINE__;
+                }
             }
         }
     }