first working prototype of the peptidomic compar spectra ODS sheet

src/CMakeLists.txt

@@ -135,6 +135,7 @@ SET(CPP_FILES
   output/ods/ptm/ptmspectrasheet.cpp
   output/ods/comparbasesheet.cpp
   output/ods/comparspecificspectrasheet.cpp
+  output/ods/comparspectrabypeptide.cpp
   output/ods/comparspectrasheet.cpp
   output/ods/groupingsheet.cpp
   output/ods/infosheet.cpp

src/output/ods/comparspectrabypeptide.cpp

@@ -140,7 +140,7 @@ ComparSpectraByPeptide::writeIdentificationGroup(IdentificationGroup *p_ident)
                 });
 
       const PeptideEvidence *p_best_peptide_evidence = nullptr;
-      std::vector<size_t> sample_scan_list;
+      std::map<QString, std::vector<size_t>> sample_scan_list;
 
       for(auto &peptide_evidence : peptide_evidence_list)
         {
@@ -155,6 +155,7 @@ ComparSpectraByPeptide::writeIdentificationGroup(IdentificationGroup *p_ident)
               writeBestPeptideEvidence(group_pair.second.get(),
                                        p_best_peptide_evidence,
                                        sample_scan_list);
+              sample_scan_list.clear();
               p_best_peptide_evidence = peptide_evidence;
             }
           else
@@ -165,16 +166,54 @@ ComparSpectraByPeptide::writeIdentificationGroup(IdentificationGroup *p_ident)
                   p_best_peptide_evidence = peptide_evidence;
                 }
             }
-          sample_scan_list.push_back(peptide_evidence->getHashSampleScan());
+
+          QString key_sample;
+          const Label *p_label =
+            peptide_evidence->getPeptideXtpSp().get()->getLabel();
+          if(p_label == nullptr)
+            {
+              key_sample = peptide_evidence->getMsRunP()->getXmlId();
+            }
+          else
+            {
+              key_sample = QString("%1-%2")
+                             .arg(peptide_evidence->getMsRunP()->getXmlId())
+                             .arg(p_label->getXmlId());
+            }
+
+          auto it = sample_scan_list.find(key_sample);
+          if(it != sample_scan_list.end())
+            {
+              it->second.push_back(peptide_evidence->getHashSampleScan());
+            }
+          else
+            {
+              std::vector<size_t> one_element;
+              one_element.push_back(peptide_evidence->getHashSampleScan());
+              sample_scan_list.insert(std::pair<QString, std::vector<size_t>>(
+                key_sample, one_element));
+            }
+          //_p_writer->writeCell(msrun_sp.get()->getSampleName());
+          // sample_scan_list.push_back(peptide_evidence->getHashSampleScan());
         }
 
       if(p_best_peptide_evidence != nullptr)
         {
           writeBestPeptideEvidence(
             group_pair.second.get(), p_best_peptide_evidence, sample_scan_list);
+          sample_scan_list.clear();
         }
     }
 
+  if(!_first_cell_coordinate.isEmpty())
+    {
+      QString last_cell_coordinate = _p_writer->getOdsCellCoordinate();
+      qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
+               << _first_cell_coordinate << " " << last_cell_coordinate;
+      OdsColorScale color_scale(_first_cell_coordinate, last_cell_coordinate);
+      _p_writer->addColorScale(color_scale);
+      _first_cell_coordinate = "";
+    }
   _p_writer->writeLine();
   _p_writer->writeLine();
   qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " end";
@@ -185,13 +224,9 @@ void
 ComparSpectraByPeptide::writeBestPeptideEvidence(
   const GroupingGroup *p_group,
   const PeptideEvidence *p_peptide_evidence,
-  std::vector<size_t> &sample_scan_list)
+  const std::map<QString, std::vector<size_t>> &sample_scan_list)
 {
 
-  std::sort(sample_scan_list.begin(), sample_scan_list.end());
-  auto last = std::unique(sample_scan_list.begin(), sample_scan_list.end());
-  sample_scan_list.erase(last, sample_scan_list.end());
-
   _p_writer->writeLine();
 
 
@@ -213,17 +248,17 @@ ComparSpectraByPeptide::writeBestPeptideEvidence(
   QStringList sg_list = p_group->getSubgroupIdList(p_peptide_evidence);
   _p_writer->writeCell((unsigned int)sg_list.size());
   _p_writer->writeCell(sg_list.join(" "));
-  
-  
-  _p_writer->writeCell((unsigned int)sample_scan_list.size());
 
-  
+
+  //_p_writer->writeCell((unsigned int)sample_scan_list.size());
+
+
   for(MsRunSp &msrun_sp : _msrun_list)
     {
       if(_label_list.size() == 0)
         {
           writeComparValue(
-            p_protein_match, ValidationState::validAndChecked, msrun_sp.get());
+            sample_scan_list, ValidationState::validAndChecked, msrun_sp.get());
           if(_first_cell_coordinate.isEmpty())
             {
               _first_cell_coordinate = _p_writer->getOdsCellCoordinate();
@@ -233,7 +268,7 @@ ComparSpectraByPeptide::writeBestPeptideEvidence(
         {
           for(const Label *p_label : _label_list)
             {
-              writeComparValue(p_protein_match,
+              writeComparValue(sample_scan_list,
                                ValidationState::validAndChecked,
                                msrun_sp.get(),
                                p_label);
@@ -245,3 +280,43 @@ ComparSpectraByPeptide::writeBestPeptideEvidence(
         }
     }
 }
+
+
+void
+ComparSpectraByPeptide::writeComparValue(
+  const std::map<QString, std::vector<size_t>> &sample_scan_list,
+  ValidationState state,
+  const MsRun *p_msrun,
+  const Label *p_label)
+{
+  /*
+  std::sort(sample_scan_list.begin(), sample_scan_list.end());
+  auto last = std::unique(sample_scan_list.begin(), sample_scan_list.end());
+  sample_scan_list.erase(last, sample_scan_list.end());
+*/
+
+  QString key_sample;
+  if(p_label == nullptr)
+    {
+      key_sample = p_msrun->getXmlId();
+    }
+  else
+    {
+      key_sample =
+        QString("%1-%2").arg(p_msrun->getXmlId()).arg(p_label->getXmlId());
+    }
+
+  auto it = sample_scan_list.find(key_sample);
+  if(it == sample_scan_list.end())
+    {
+      _p_writer->writeCell((unsigned int)0);
+    }
+  else
+    {
+      std::vector<size_t> new_list = it->second;
+      std::sort(new_list.begin(), new_list.end());
+      auto last = std::unique(new_list.begin(), new_list.end());
+      new_list.erase(last, new_list.end());
+      _p_writer->writeCell((unsigned int)new_list.size());
+    }
+}

src/output/ods/comparspectrabypeptide.h

@@ -49,9 +49,15 @@ class ComparSpectraByPeptide
   private:
   void writeIdentificationGroup(IdentificationGroup *p_ident);
   void writeHeaders(IdentificationGroup *p_ident);
-  void writeBestPeptideEvidence(const GroupingGroup *p_group,
-                                const PeptideEvidence *p_peptide_evidence,
-                                std::vector<size_t> &sample_scan_list);
+  void writeBestPeptideEvidence(
+    const GroupingGroup *p_group,
+    const PeptideEvidence *p_peptide_evidence,
+    const std::map<QString, std::vector<size_t>> &sample_scan_list);
+  void writeComparValue(
+    const std::map<QString, std::vector<size_t>> &sample_scan_list,
+    ValidationState state,
+    const MsRun *p_msrun,
+    const Label *p_label = nullptr);
 
   public:
   ComparSpectraByPeptide(OdsExport *p_ods_export,

src/output/ods/odsexport.cpp

@@ -36,6 +36,7 @@
 #include "peptidepossheet.h"
 #include "comparspectrasheet.h"
 #include "comparspecificspectrasheet.h"
+#include "comparspectrabypeptide.h"
 #include "infosheet.h"
 #include "samplesheet.h"
 #include "groupingsheet.h"
@@ -110,11 +111,11 @@ OdsExport::write(CalcWriterInterface *p_writer, WorkMonitorInterface *p_monitor)
         {
           // export compar sheets not possible in individual mode
             
-          if(settings.value("export_ods/peptidomiccomparspectra", "true").toBool())
-            {
+          //if(settings.value("export_ods/peptidomiccomparspectra", "true").toBool())
+          //  {
               p_monitor->message(QObject::tr("writing spectra comparisons for peptidomic"));
-              ComparSpectraSheet(this, p_writer, _p_project).writeSheet();
-            }
+              ComparSpectraByPeptide(this, p_writer, _p_project).writeSheet();
+          //  }
           if(settings.value("export_ods/comparspectra", "true").toBool())
             {
               p_monitor->message(QObject::tr("writing spectra comparisons"));