colors in ODS outout files

src/output/ods/odsexport.cpp

@@ -35,16 +35,33 @@
 
 OdsExport::OdsExport(const Project * project):_p_project(project) {
 }
+void OdsExport::setEvenOrOddStyle(unsigned int number, CalcWriterInterface * p_writer) {
+
+    if (number % 2) { /* x is odd */
+        p_writer->setTableCellStyleRef(_odd_style);
+
+    } else {
+        p_writer->setTableCellStyleRef(_even_style);
+    }
+
+}
 
 void OdsExport::write(CalcWriterInterface * p_writer) {
     QSettings settings;
+
+    OdsTableCellStyle style;
+    style.setBackgroundColor(QColor("red"));
+    _odd_style = p_writer->getTableCellStyleRef(style);
+    style.setBackgroundColor(QColor("orange"));
+    _even_style = p_writer->getTableCellStyleRef(style);
+
     if (settings.value("export_ods/simple", "false").toBool()) {
         SimpleSheet(p_writer, _p_project);
     }
     if (settings.value("export_ods/proteins", "true").toBool()) {
-        ProteinSheet(p_writer, _p_project);
+        ProteinSheet(this, p_writer, _p_project);
     }
     if (settings.value("export_ods/peptides", "true").toBool()) {
-        PeptideSheet(p_writer, _p_project);
+        PeptideSheet(this, p_writer, _p_project);
     }
 }

src/output/ods/odsexport.h

@@ -40,8 +40,12 @@ public:
     
     void write(CalcWriterInterface * p_writer);
     
+    void setEvenOrOddStyle(unsigned int number, CalcWriterInterface * p_writer);
+    
 private:
     const Project * _p_project;
+    OdsTableCellStyleRef _even_style;
+    OdsTableCellStyleRef _odd_style;
 };
 
 #endif // ODSEXPORT_H

src/output/ods/peptidesheet.cpp

@@ -28,9 +28,11 @@
 ******************************************************************************/
 
 #include "peptidesheet.h"
+#include <pappsomspp/utils.h>
 
 
-PeptideSheet::PeptideSheet (CalcWriterInterface * p_writer, const Project * p_project): _p_project(p_project) {
+PeptideSheet::PeptideSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project): _p_project(p_project) {
+    _p_ods_export = p_ods_export;
     _p_writer = p_writer;
     p_writer->writeSheet("peptides");
 
@@ -65,6 +67,7 @@ void PeptideSheet::writeHeaders(IdentificationGroup * p_ident)  {
     _p_writer->setCellAnnotation("theoretical mh");
     _p_writer->writeCell("MH+ theo");
     _p_writer->writeCell("Number of subgroups");
+    _p_writer->writeCell("Subgroup ids");
     _p_writer->setCellAnnotation("number of scans associated to this peptide");
     _p_writer->writeCell("Number of spectra");
 
@@ -116,11 +119,16 @@ void PeptideSheet::writeBestPeptideMatch(const GroupingGroup * p_group,const Pep
 
     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()); 
+    _sample_scan_list.erase(last, _sample_scan_list.end());
 
     _p_writer->writeLine();
 
-    _p_writer->writeCell(p_peptide_match->getGrpPeptideSp().get()->getGroupNumber());
+
+    unsigned int group_number = p_peptide_match->getGrpPeptideSp().get()->getGroupNumber();
+
+    _p_ods_export->setEvenOrOddStyle(group_number, _p_writer);
+    _p_writer->writeCell(pappso::Utils::getLexicalOrderedString(group_number));
+    _p_writer->clearTableCellStyleRef();
     _p_writer->writeCell(p_peptide_match->getGrpPeptideSp().get()->getGroupingId());
     _p_writer->writeCell(p_peptide_match->getGrpPeptideSp().get()->getSequence());
     _p_writer->writeCell(p_peptide_match->getPeptideXtpSp().get()->getModifString());
@@ -128,7 +136,8 @@ void PeptideSheet::writeBestPeptideMatch(const GroupingGroup * p_group,const Pep
     _p_writer->writeCell(p_peptide_match->getPeptideXtpSp().get()->getNativePeptideP()->getMz(1));
     QStringList sg_list = p_group->getSubgroupIdList(p_peptide_match);
     _p_writer->writeCell((unsigned int) sg_list.size());
+    _p_writer->writeCell(sg_list.join(" "));
     _p_writer->writeCell((unsigned int) _sample_scan_list.size());
-    
+
     _sample_scan_list.clear();
 }

src/output/ods/peptidesheet.h

@@ -33,17 +33,19 @@
 #include "../../core/project.h"
 #include <odsstream/calcwriterinterface.h>
 #include "../../core/proteinmatch.h"
+#include "odsexport.h"
 
 class PeptideSheet
 {
 public :
-    PeptideSheet (CalcWriterInterface * p_writer, const Project * p_project);
+    PeptideSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project);
 private :
     void writeIdentificationGroup(IdentificationGroup * p_ident);
     void writeHeaders(IdentificationGroup * p_ident);
     void writeBestPeptideMatch(const GroupingGroup * p_group, const PeptideMatch * p_peptide_match);
 
 private :
+    OdsExport * _p_ods_export;
     const Project * _p_project;
     CalcWriterInterface * _p_writer;
     std::vector<size_t> _sample_scan_list;

src/output/ods/proteinsheet.cpp

@@ -31,13 +31,13 @@
 #include "../../core/identificationgroup.h"
 #include <pappsomspp/utils.h>
 
-ProteinSheet::ProteinSheet (CalcWriterInterface * p_writer, const Project * p_project): _p_project(p_project) {
+ProteinSheet::ProteinSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project): _p_project(p_project) {
     _p_writer = p_writer;
+    _p_ods_export = p_ods_export;
     p_writer->writeSheet("proteins");
 
     std::vector<IdentificationGroup *> identification_list = p_project->getIdentificationGroupList();
     for (IdentificationGroup * p_ident:identification_list) {
-
         //writeHeaders(p_ident);
         writeIdentificationGroup(p_ident);
     }
@@ -47,12 +47,12 @@ void ProteinSheet::writeHeaders(IdentificationGroup * p_ident)  {
     // Group ID Sub-group ID Protein ID Description log(E value)
     // Coverage MW Spectra Specific uniques Uniques PAI Redundancy
 
-const std::vector<MsRunSp> msrun_list = p_ident->getMsRunSpList();
+    const std::vector<MsRunSp> msrun_list = p_ident->getMsRunSpList();
     if (msrun_list.size() == 1) {
-    _p_writer->writeCell("sample");
-    _p_writer->writeLine();
-    _p_writer->writeCell(msrun_list[0].get()->getSampleName());
-    _p_writer->writeLine();
+        _p_writer->writeCell("sample");
+        _p_writer->writeLine();
+        _p_writer->writeCell(msrun_list[0].get()->getSampleName());
+        _p_writer->writeLine();
     }
     _p_writer->writeLine();
     _p_writer->writeCell("Group ID");
@@ -95,8 +95,7 @@ void ProteinSheet::writeIdentificationGroup(IdentificationGroup * p_ident) {
         for (auto & protein_match:protein_match_list) {
             writeOneProtein(group_pair.second.get(), protein_match);
         }
-        
-    _p_writer->writeLine();
+
     }
     _p_writer->writeLine();
 }
@@ -104,15 +103,20 @@ void ProteinSheet::writeIdentificationGroup(IdentificationGroup * p_ident) {
 
 void ProteinSheet::writeOneProtein(const GroupingGroup * p_group, const ProteinMatch * p_protein_match) {
     _p_writer->writeLine();
-    
+
     ValidationState validation_state = ValidationState::validAndChecked;
 
     pappso::GrpProtein * p_grp_protein = p_protein_match->getGrpProteinSp().get();
 
     ProteinXtp * p_protein = p_protein_match->getProteinXtpSp().get();
 
-    _p_writer->writeCell(pappso::Utils::getLexicalOrderedString(p_grp_protein->getGroupNumber()));
-    _p_writer->writeCell(QString("%1.%2").arg(pappso::Utils::getLexicalOrderedString(p_grp_protein->getGroupNumber())).arg(pappso::Utils::getLexicalOrderedString(p_grp_protein->getSubGroupNumber())));
+    unsigned int group_number = p_grp_protein->getGroupNumber();
+    unsigned int subgroup_number = p_grp_protein->getSubGroupNumber();
+    _p_ods_export->setEvenOrOddStyle(group_number, _p_writer);
+    _p_writer->writeCell(pappso::Utils::getLexicalOrderedString(group_number));
+    _p_ods_export->setEvenOrOddStyle(subgroup_number, _p_writer);
+    _p_writer->writeCell(QString("%1.%2").arg(pappso::Utils::getLexicalOrderedString(group_number)).arg(pappso::Utils::getLexicalOrderedString(subgroup_number)));
+    _p_writer->clearTableCellStyleRef();
     _p_writer->writeCell(p_grp_protein->getGroupingId());
     _p_writer->writeCell(p_protein->getAccession());
     _p_writer->writeCell(p_protein->getDescription());
@@ -126,14 +130,14 @@ void ProteinSheet::writeOneProtein(const GroupingGroup * p_group, const ProteinM
     _p_writer->writeCell(p_protein_match->countSampleScan(validation_state));
 
     // _p_writer->writeCell("Specific");
-     _p_writer->writeCell((unsigned int) p_group->countSpecificSampleScan(p_protein_match, validation_state));
+    _p_writer->writeCell((unsigned int) p_group->countSpecificSampleScan(p_protein_match, validation_state));
 
     // _p_writer->writeCell("Uniques");
     _p_writer->writeCell((unsigned int) p_protein_match->countUniqueSequenceLi(validation_state));
 
     // _p_writer->writeCell("Specific uniques");
-     _p_writer->writeCell((unsigned int) p_group->countSpecificSequenceLi(p_protein_match, validation_state));
-     
+    _p_writer->writeCell((unsigned int) p_group->countSpecificSequenceLi(p_protein_match, validation_state));
+
 
     _p_writer->writeCell(p_protein_match->countPeptideMassCharge(validation_state));
     _p_writer->writeCell(p_protein->countTrypticPeptidesForPAI());

src/output/ods/proteinsheet.h

@@ -33,17 +33,19 @@
 #include "../../core/project.h"
 #include <odsstream/calcwriterinterface.h>
 #include "../../core/proteinmatch.h"
+#include "odsexport.h"
 
 class ProteinSheet
 {
 public :
-    ProteinSheet (CalcWriterInterface * p_writer, const Project * p_project);
+    ProteinSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project);
 private :
     void writeIdentificationGroup(IdentificationGroup * p_ident);
     void writeHeaders(IdentificationGroup * p_ident);
     void writeOneProtein(const GroupingGroup * p_group, const ProteinMatch * p_protein_match);
 
 private :
+  OdsExport * _p_ods_export;
     const Project * _p_project;
     CalcWriterInterface * _p_writer;
 };