preparing PTM spectra sheet

src/output/ods/ptm/ptmspectrasheet.cpp

@@ -28,32 +28,156 @@
 ******************************************************************************/
 
 #include "ptmspectrasheet.h"
+#include <tuple>
+#include <pappsomspp/utils.h>
+
+PtmSpectraSheet::PtmSpectraSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project, const QString & sheet_name): _p_project(p_project) {
+    _p_ods_export = p_ods_export;
+    _p_writer = p_writer;
+    p_writer->writeSheet(sheet_name);
+
+    std::vector<IdentificationGroup *> identification_list = p_project->getIdentificationGroupList();
+    for (IdentificationGroup * p_ident:identification_list) {
+        //writeHeaders(p_ident);
+        writeIdentificationGroup(p_ident);
+    }
+}
+
+PtmSpectraSheet::PtmSpectraSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project): PtmSpectraSheet(p_ods_export, p_writer, p_project, QString("PTM spectra")) {
+}
+
+
+void PtmSpectraSheet::writeCellHeader(PeptideListColumn column) {
+    qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
+    _p_writer->setCellAnnotation(PeptideTableModel::getDescription(column));
+    _p_writer->writeCell(PeptideTableModel::getTitle(column));
+    qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
+}
+
+
+void PtmSpectraSheet::writeHeaders(IdentificationGroup * p_ident)  {
+    // Group ID	Peptide ID	Sample	Scan	Rt (minutes)	Sequence (top)	Modifs (top)	Number of subgroups	Sub-groups Ids	Best E-value	Best hyperscore	m/z Obs	Charge	MH+ Obs	MH+ theo	DeltaMH+	Delta-ppm
+
+    //MS Sample :	20120906_balliau_extract_1_A01_urnb-1
+    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->writeLine();
+    _p_writer->writeCell("Group ID");
+    _p_writer->writeCell("Peptide ID");
+    _p_writer->setCellAnnotation("MS sample name (MS run)");
+    _p_writer->writeCell("Sample");
+    _p_writer->writeCell("Scan");
+    _p_writer->setCellAnnotation("retention time in seconds");
+    _p_writer->writeCell("Rt (seconds)");
+    _p_writer->setCellAnnotation("experimental precursor m/z");
+    _p_writer->writeCell("Precursor m/z");
+    _p_writer->setCellAnnotation("peptide sequence (best match)");
+    _p_writer->writeCell("Sequence (top)");
+    _p_writer->setCellAnnotation("peptide charge (best match)");
+    _p_writer->writeCell("Charge (top)");
+    _p_writer->setCellAnnotation("peptide modifications (best match)");
+    _p_writer->writeCell("Modifs (top)");
+    if (_p_project->getLabelingMethodSp().get() != nullptr) {
+        _p_writer->setCellAnnotation("peptide label (best match)");
+        _p_writer->writeCell("Label (top)");
+    }
+    _p_writer->writeCell("Best E-value");
+    _p_writer->writeCell("Best hyperscore");
+    writeCellHeader(PeptideListColumn::delta_mhplus);
+
+
+}
+
+void PtmSpectraSheet::writeBestPeptideEvidence(const GroupingGroup * p_group,const PeptideEvidence * p_peptide_evidence) {
+
+    _p_writer->writeLine();
+
+    unsigned int group_number = p_peptide_evidence->getGrpPeptideSp().get()->getGroupNumber();
+    unsigned int rank_number = p_peptide_evidence->getGrpPeptideSp().get()->getRank();
+
+    _p_ods_export->setEvenOrOddStyle(group_number, _p_writer);
+    _p_writer->writeCell(pappso::Utils::getLexicalOrderedString(group_number));
+    _p_ods_export->setEvenOrOddStyle(rank_number, _p_writer);
+    _p_writer->writeCell(p_peptide_evidence->getGrpPeptideSp().get()->getGroupingId());
+    _p_writer->clearTableCellStyleRef();
+    _p_writer->writeCell(p_peptide_evidence->getMsRunP()->getSampleName());
+    _p_writer->writeCell(p_peptide_evidence->getScan());
+    _p_writer->writeCell(p_peptide_evidence->getRetentionTime());
+    _p_writer->writeCell(p_peptide_evidence->getExperimentalMz());
+    _p_writer->writeCell(p_peptide_evidence->getPeptideXtpSp().get()->getSequence());
+    _p_writer->writeCell(p_peptide_evidence->getCharge());
+    _p_writer->writeCell(p_peptide_evidence->getPeptideXtpSp().get()->getModifString());
+    if (_p_project->getLabelingMethodSp().get() != nullptr) {
+        const Label * p_label = p_peptide_evidence->getPeptideXtpSp().get()->getLabel();
+        if (p_label != nullptr) {
+            _p_writer->writeCell(p_label->getXmlId());
+        }
+        else {
+            _p_writer->writeEmptyCell();
+        }
+    }
+    _p_writer->writeCell(p_peptide_evidence->getEvalue());
+    _p_writer->writeCell(p_peptide_evidence->getParam(PeptideEvidenceParam::tandem_hyperscore).toDouble());
+    _p_writer->writeCell(p_peptide_evidence->getDeltaMass());
 
 
-PtmSpectraSheet::PtmSpectraSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project): SpectraSheet(p_ods_export, p_writer, p_project, QString("PTM spectra")) {
-    qDebug() << "PtmSpectraSheet::PtmSpectraSheet begin" ;
-    qDebug() << "PtmSpectraSheet::PtmSpectraSheet end" ;
 }
 
 void PtmSpectraSheet::writeIdentificationGroup(IdentificationGroup * p_ident) {
+    qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
     _p_ptm_grouping_experiment = p_ident->getPtmGroupingExperiment();
-    
-    
-    qDebug() << "PtmIslandSheet::writeIdentificationGroup getPtmIslandList" ;
-    std::vector<PtmIslandSp> ptm_island_list;
-    for (auto ptm_island_sp : _p_ptm_grouping_experiment->getPtmIslandList() ) {
-        qDebug() << "PtmIslandSheet::writeIdentificationGroup getPtmIslandList copy" ;
-        ptm_island_list.push_back(ptm_island_sp);
-    }
-    qDebug() << "PtmIslandSheet::writeIdentificationGroup sort" ;
-    std::sort(ptm_island_list.begin(), ptm_island_list.end(),
-              [](PtmIslandSp & a, PtmIslandSp & b)
-    {
-        return a.get()->getGroupingId() < b.get()->getGroupingId();
-    });
-
-    qDebug() << "PtmIslandSheet::writeIdentificationGroup 2" ;
-    for (auto & ptm_island:ptm_island_list) {
-        writeOnePtmIsland(ptm_island);
+
+    writeHeaders(p_ident);
+    for (const std::pair<unsigned int, GroupingGroupSp> & group_pair : p_ident->getGroupStore().getGroupMap()) {
+
+        std::vector<const PeptideEvidence *> peptide_evidence_list = group_pair.second.get()->getPeptideEvidenceList();
+
+        std::sort(peptide_evidence_list.begin(), peptide_evidence_list.end(),
+                  [](const PeptideEvidence * a, const PeptideEvidence * b)
+        {
+            unsigned int arank = a->getGrpPeptideSp().get()->getRank();
+            unsigned int ascan = a->getScan();
+            unsigned int brank = b->getGrpPeptideSp().get()->getRank();
+            unsigned int bscan = b->getScan();
+            return  std::tie(arank, a->getMsRunP()->getSampleName(), ascan) < std::tie(brank, b->getMsRunP()->getSampleName(), bscan);
+        });
+
+        const PeptideEvidence * p_best_peptide_evidence = nullptr;
+
+        for (auto & peptide_evidence:peptide_evidence_list) {
+            if (p_best_peptide_evidence == nullptr) {
+                p_best_peptide_evidence = peptide_evidence;
+            }
+            //change spectra :
+            unsigned int arank = p_best_peptide_evidence->getGrpPeptideSp().get()->getRank();
+            unsigned int ascan = p_best_peptide_evidence->getScan();
+            unsigned int brank = peptide_evidence->getGrpPeptideSp().get()->getRank();
+            unsigned int bscan = peptide_evidence->getScan();
+
+            if (std::tie(arank, p_best_peptide_evidence->getMsRunP()->getSampleName(), ascan) != std::tie(brank, peptide_evidence->getMsRunP()->getSampleName(), bscan)) {
+                //write p_best_peptide_match
+                writeBestPeptideEvidence(group_pair.second.get(), p_best_peptide_evidence);
+                p_best_peptide_evidence = peptide_evidence;
+            }
+            else {
+                if (p_best_peptide_evidence->getEvalue()> peptide_evidence->getEvalue()) {
+                    p_best_peptide_evidence = peptide_evidence;
+                }
+            }
+        }
+
+        if (p_best_peptide_evidence != nullptr) {
+            writeBestPeptideEvidence(group_pair.second.get(), p_best_peptide_evidence);
+        }
     }
+    _p_writer->writeLine();
+    _p_writer->writeLine();
+    qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
 }

src/output/ods/ptm/ptmspectrasheet.h

@@ -36,16 +36,23 @@
 #include "../odsexport.h"
 #include "../spectrasheet.h"
 
-class PtmSpectraSheet:public SpectraSheet
+class PtmSpectraSheet
 {
 public :
     PtmSpectraSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project);
+
 protected :
-    void writeIdentificationGroup(IdentificationGroup * p_ident);
+    PtmSpectraSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project, const QString & sheet_name);
+    virtual void writeIdentificationGroup(IdentificationGroup * p_ident);
+    void writeHeaders(IdentificationGroup * p_ident);
+    void writeBestPeptideEvidence(const GroupingGroup * p_group, const PeptideEvidence * p_peptide_evidence);
+    void writeCellHeader(PeptideListColumn column);
 
-protected:
+protected :
+    OdsExport * _p_ods_export;
     const PtmGroupingExperiment * _p_ptm_grouping_experiment;
-
+    const Project * _p_project;
+    CalcWriterInterface * _p_writer;
 };
 
 #endif // PTMSPECTRASHEET_H