WIP:handling labeled samples in compar ODS output

src/output/ods/comparbasesheet.cpp

@@ -42,6 +42,10 @@ ComparBaseSheet::ComparBaseSheet(OdsExport *p_ods_export,
 {
   _p_ods_export = p_ods_export;
   _p_writer     = p_writer;
+
+  _sp_labelling_method = p_project->getLabelingMethodSp();
+
+  _label_list = _sp_labelling_method.get()->getLabelList();
 }
 
 void
@@ -94,9 +98,22 @@ ComparBaseSheet::writeHeaders(IdentificationGroup *p_ident)
   _p_writer->writeCell("description");
   _p_writer->writeCell("Number of proteins");
 
+
   for(MsRunSp &msrun_sp : _msrun_list)
     {
-      _p_writer->writeCell(msrun_sp.get()->getSampleName());
+      if(_sp_labelling_method == nullptr)
+        {
+          _p_writer->writeCell(msrun_sp.get()->getSampleName());
+        }
+      else
+        {
+          for(const Label *p_label : _label_list)
+            {
+              _p_writer->writeCell(QString("%1-%2")
+                                     .arg(msrun_sp.get()->getSampleName())
+                                     .arg(p_label->getXmlId()));
+            }
+        }
     }
 }
 
@@ -142,11 +159,27 @@ ComparBaseSheet::writeProteinMatch(const ProteinMatch *p_protein_match)
 
   for(MsRunSp &msrun_sp : _msrun_list)
     {
-      writeComparValue(p_protein_match, ValidationState::validAndChecked,
-                       msrun_sp.get());
-      if(_first_cell_coordinate.isEmpty())
+      if(_label_list.size() == 0)
+        {
+          writeComparValue(
+            p_protein_match, ValidationState::validAndChecked, msrun_sp.get());
+          if(_first_cell_coordinate.isEmpty())
+            {
+              _first_cell_coordinate = _p_writer->getOdsCellCoordinate();
+            }
+        }
+      else
         {
-          _first_cell_coordinate = _p_writer->getOdsCellCoordinate();
+          for(const Label *p_label : _label_list)
+            {
+              writeComparValue(p_protein_match,
+                               ValidationState::validAndChecked,
+                               msrun_sp.get(),p_label);
+              if(_first_cell_coordinate.isEmpty())
+                {
+                  _first_cell_coordinate = _p_writer->getOdsCellCoordinate();
+                }
+            }
         }
     }
 
@@ -175,7 +208,8 @@ ComparBaseSheet::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();

src/output/ods/comparbasesheet.h

@@ -39,7 +39,8 @@
 class ComparBaseSheet
 {
   public:
-  ComparBaseSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+  ComparBaseSheet(OdsExport *p_ods_export,
+                  CalcWriterInterface *p_writer,
                   const Project *p_project);
 
   private:
@@ -52,7 +53,8 @@ class ComparBaseSheet
   protected:
   virtual void writeComparValue(const ProteinMatch *p_protein_match,
                                 ValidationState state,
-                                const MsRun *p_msrun) = 0;
+                                const MsRun *p_msrun,
+                                const Label *p_label = nullptr) = 0;
   void writeProteinMatch(const ProteinMatch *p_protein_match);
 
 
@@ -66,6 +68,9 @@ class ComparBaseSheet
   QString _first_cell_coordinate;
 
   IdentificationGroup *_p_current_identification_group;
+
+  LabelingMethodSp _sp_labelling_method;
+  std::vector<Label *> _label_list;
 };
 
 #endif // COMPARBASESHEET_H

src/output/ods/comparspecificspectrasheet.cpp

@@ -32,7 +32,8 @@
 
 
 ComparSpecificSpectraSheet::ComparSpecificSpectraSheet(
-  OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+  OdsExport *p_ods_export,
+  CalcWriterInterface *p_writer,
   const Project *p_project)
   : ComparBaseSheet(p_ods_export, p_writer, p_project)
 {
@@ -42,8 +43,10 @@ ComparSpecificSpectraSheet::ComparSpecificSpectraSheet(
 
 void
 ComparSpecificSpectraSheet::writeComparValue(
-  const ProteinMatch *p_protein_match, ValidationState state,
-  const MsRun *p_msrun)
+  const ProteinMatch *p_protein_match,
+  ValidationState state,
+  const MsRun *p_msrun,
+  const Label *p_label)
 {
   qDebug() << "ComparSpecificSpectraSheet::writeComparValue begin";
   _p_writer->writeCell(
@@ -55,7 +58,8 @@ ComparSpecificSpectraSheet::writeComparValue(
 
 
 ComparSpecificSequenceSheet::ComparSpecificSequenceSheet(
-  OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+  OdsExport *p_ods_export,
+  CalcWriterInterface *p_writer,
   const Project *p_project)
   : ComparBaseSheet(p_ods_export, p_writer, p_project)
 {
@@ -64,8 +68,10 @@ ComparSpecificSequenceSheet::ComparSpecificSequenceSheet(
 
 void
 ComparSpecificSequenceSheet::writeComparValue(
-  const ProteinMatch *p_protein_match, ValidationState state,
-  const MsRun *p_msrun)
+  const ProteinMatch *p_protein_match,
+  ValidationState state,
+  const MsRun *p_msrun,
+  const Label *p_label)
 {
   qDebug() << "ComparSpecificSequenceSheet::writeComparValue begin";
   _p_writer->writeCell(

src/output/ods/comparspecificspectrasheet.h

@@ -42,7 +42,8 @@ class ComparSpecificSpectraSheet : public ComparBaseSheet
   protected:
   virtual void writeComparValue(const ProteinMatch *p_protein_match,
                                 ValidationState state,
-                                const MsRun *p_msrun) override;
+                                const MsRun *p_msrun,
+                                const Label *p_label = nullptr) override;
 };
 
 class ComparSpecificSequenceSheet : public ComparBaseSheet
@@ -55,7 +56,8 @@ class ComparSpecificSequenceSheet : public ComparBaseSheet
   protected:
   virtual void writeComparValue(const ProteinMatch *p_protein_match,
                                 ValidationState state,
-                                const MsRun *p_msrun) override;
+                                const MsRun *p_msrun,
+                                const Label *p_label = nullptr) override;
 };
 
 #endif // COMPARSPECIFICSPECTRASHEET_H

src/output/ods/comparspectrasheet.cpp

@@ -46,7 +46,8 @@ ComparSpectraSheet::ComparSpectraSheet(OdsExport *p_ods_export,
 void
 ComparSpectraSheet::writeComparValue(const ProteinMatch *p_protein_match,
                                      ValidationState state,
-                                     const MsRun *p_msrun)
+                                     const MsRun *p_msrun,
+                                     const Label *p_label)
 {
   qDebug() << "ComparSpectraSheet::writeComparValue begin";
   _p_writer->writeCell(p_protein_match->countSampleScan(state, p_msrun));
@@ -65,7 +66,8 @@ ComparSequenceSheet::ComparSequenceSheet(OdsExport *p_ods_export,
 void
 ComparSequenceSheet::writeComparValue(const ProteinMatch *p_protein_match,
                                       ValidationState state,
-                                      const MsRun *p_msrun)
+                                      const MsRun *p_msrun,
+                                      const Label *p_label)
 {
   qDebug() << "ComparSequenceSheet::writeComparValue begin";
   _p_writer->writeCell(
@@ -83,7 +85,9 @@ ComparPaiSheet::ComparPaiSheet(OdsExport *p_ods_export,
 
 void
 ComparPaiSheet::writeComparValue(const ProteinMatch *p_protein_match,
-                                 ValidationState state, const MsRun *p_msrun)
+                                 ValidationState state,
+                                 const MsRun *p_msrun,
+                                 const Label *p_label)
 {
   qDebug() << "ComparPaiSheet::writeComparValue begin";
   _p_writer->writeCell(p_protein_match->getPAI(p_msrun));
@@ -100,7 +104,9 @@ ComparEmpaiSheet::ComparEmpaiSheet(OdsExport *p_ods_export,
 
 void
 ComparEmpaiSheet::writeComparValue(const ProteinMatch *p_protein_match,
-                                   ValidationState state, const MsRun *p_msrun)
+                                   ValidationState state,
+                                   const MsRun *p_msrun,
+                                   const Label *p_label)
 {
   qDebug() << "ComparEmpaiSheet::writeComparValue begin";
   _p_writer->writeCell(p_protein_match->getEmPAI(p_msrun));
@@ -117,7 +123,9 @@ ComparNsafSheet::ComparNsafSheet(OdsExport *p_ods_export,
 
 void
 ComparNsafSheet::writeComparValue(const ProteinMatch *p_protein_match,
-                                  ValidationState state, const MsRun *p_msrun)
+                                  ValidationState state,
+                                  const MsRun *p_msrun,
+                                  const Label *p_label)
 {
   qDebug() << "ComparNsafSheet::writeComparValue begin";
   pappso::pappso_double proto_nsaf_sum = 0;

src/output/ods/comparspectrasheet.h

@@ -36,62 +36,72 @@
 class ComparSpectraSheet : public ComparBaseSheet
 {
   public:
-  ComparSpectraSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+  ComparSpectraSheet(OdsExport *p_ods_export,
+                     CalcWriterInterface *p_writer,
                      const Project *p_project);
 
   protected:
   virtual void writeComparValue(const ProteinMatch *p_protein_match,
                                 ValidationState state,
-                                const MsRun *p_msrun) override;
+                                const MsRun *p_msrun,
+                                const Label *p_label = nullptr) override;
 };
 
 
 class ComparSequenceSheet : public ComparBaseSheet
 {
   public:
-  ComparSequenceSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+  ComparSequenceSheet(OdsExport *p_ods_export,
+                      CalcWriterInterface *p_writer,
                       const Project *p_project);
 
   protected:
   virtual void writeComparValue(const ProteinMatch *p_protein_match,
                                 ValidationState state,
-                                const MsRun *p_msrun) override;
+                                const MsRun *p_msrun,
+                                const Label *p_label = nullptr) override;
 };
 
 class ComparPaiSheet : public ComparBaseSheet
 {
   public:
-  ComparPaiSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+  ComparPaiSheet(OdsExport *p_ods_export,
+                 CalcWriterInterface *p_writer,
                  const Project *p_project);
 
   protected:
   virtual void writeComparValue(const ProteinMatch *p_protein_match,
                                 ValidationState state,
-                                const MsRun *p_msrun) override;
+                                const MsRun *p_msrun,
+                                const Label *p_label = nullptr) override;
 };
 
 class ComparEmpaiSheet : public ComparBaseSheet
 {
   public:
-  ComparEmpaiSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+  ComparEmpaiSheet(OdsExport *p_ods_export,
+                   CalcWriterInterface *p_writer,
                    const Project *p_project);
 
   protected:
   virtual void writeComparValue(const ProteinMatch *p_protein_match,
                                 ValidationState state,
-                                const MsRun *p_msrun) override;
+                                const MsRun *p_msrun,
+                                const Label *p_label = nullptr) override;
 };
 
 class ComparNsafSheet : public ComparBaseSheet
 {
   public:
-  ComparNsafSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+  ComparNsafSheet(OdsExport *p_ods_export,
+                  CalcWriterInterface *p_writer,
                   const Project *p_project);
 
   protected:
   virtual void writeComparValue(const ProteinMatch *p_protein_match,
                                 ValidationState state,
-                                const MsRun *p_msrun) override;
+                                const MsRun *p_msrun,
+                                const Label *p_label = nullptr) override;
 
   private:
   std::map<const MsRun *, pappso::pappso_double> _map_proto_nsaf_sum_by_msrun;