WIP: writing PTM islands

src/output/ods/ptmislandsheet.cpp

@@ -29,5 +29,157 @@
 
 #include "ptmislandsheet.h"
 
+#include "../../core/identificationgroup.h"
+#include <pappsomspp/utils.h>
+#include <pappsomspp/pappsoexception.h>
+
+PtmIslandSheet::PtmIslandSheet (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("PTM islands");
+
+    std::vector<IdentificationGroup *> identification_list = p_project->getIdentificationGroupList();
+    for (IdentificationGroup * p_ident:identification_list) {
+        //writeHeaders(p_ident);
+        writeIdentificationGroup(p_ident);
+    }
+}
+void PtmIslandSheet::writeCellHeader(PtmIslandListColumn column) {
+    qDebug() << "PtmIslandSheet::writeCellHeader begin " << (std::int8_t) column;
+    _p_writer->setCellAnnotation(PtmIslandTableModel::getDescription(column));
+    _p_writer->writeCell(PtmIslandTableModel::getTitle(column));
+    qDebug() << "PtmIslandSheet::writeCellHeader end" ;
+}
+
+void PtmIslandSheet::writeHeaders(IdentificationGroup * p_ident)  {
 //Group ID	Sub-group ID	PhosphoIsland ID	Description	MW	Phosphosites positions	Spectra	Uniques	number of proteins sharing these phosphosites
 //a1	a1.a1	a1.a1.a1	AT1G01100.1 | Symbols:  | 60S acidic ribosomal protein family | chr1:50284-50954 REVERSE LENGTH=112	11,1000003814697	102	435	3	6
+
+    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->setCellAnnotation("PTM group number");
+    _p_writer->writeCell("PTM group ID");
+    _p_writer->setCellAnnotation("PTM subgroup number");
+    _p_writer->writeCell("PTM sub-group ID");
+    writeCellHeader(PtmIslandListColumn::ptm_island_id);
+    //_p_writer->PtmIslandListColumn("unique protein identifier within this grouping experiment");
+    //_p_writer->writeCell("Protein ID");
+
+    writeCellHeader(PtmIslandTableModel::accession);
+    writeCellHeader(PtmIslandTableModel::description);
+    _p_writer->setCellAnnotation("computed molecular weight for this protein (sum of amino acid masses)");
+    _p_writer->writeCell("MW");
+    writeCellHeader(PtmIslandListColumn::ptm_position_list);
+
+    writeCellHeader(PtmIslandListColumn::spectrum);
+    //_p_writer->setCellAnnotation("number of scans (spectra) attributed to this protein");
+    // _p_writer->writeCell("Spectra");
+    writeCellHeader(PtmIslandListColumn::sequence);
+
+    _p_writer->setCellAnnotation("Number of proteins sharing this PTM island");
+    _p_writer->writeCell("Number of proteins");
+
+
+}
+
+void PtmIslandSheet::writeIdentificationGroup(IdentificationGroup * p_ident) {
+
+    _p_ptm_grouping_experiment = p_ident->getPtmGroupingExperiment();
+    if (_p_ptm_grouping_experiment = nullptr) {
+        throw pappso::PappsoException(QObject::tr("Error writing PTM island :\n_p_ptm_grouping_experiment = nullptr"));
+    }
+    writeHeaders(p_ident);
+
+        std::vector<PtmIslandSp> ptm_island_list = _p_ptm_grouping_experiment->getPtmIslandList();
+
+        std::sort(ptm_island_list.begin(), ptm_island_list.end(),
+                  [](PtmIslandSp & a, PtmIslandSp & b)
+        {
+            return a.get()->getGroupingId() < b.get()->getGroupingId();
+        });
+
+        for (auto & ptm_island:ptm_island_list) {
+            writeOnePtmIsland(ptm_island);
+        }
+
+    
+    _p_writer->writeLine();
+}
+
+
+void PtmIslandSheet::writeOnePtmIsland(PtmIslandSp & sp_ptm_island) {
+    try {
+        _p_writer->writeLine();
+
+        qDebug() << "PtmIslandSheet::writeOnePtmIsland begin" ;
+        ValidationState validation_state = ValidationState::validAndChecked;
+
+        //pappso::GrpProtein * p_grp_protein = p_protein_match->getGrpProteinSp().get();
+
+        ProteinXtp * p_protein = sp_ptm_island.get()->getProteinMatch()->getProteinXtpSp().get();
+
+        unsigned int group_number = sp_ptm_island.get()->->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());
+        _p_writer->writeCell(p_protein_match->getLogEvalue());
+        // _p_writer->writeCell("Coverage");
+        _p_writer->writeCellPercentage(p_protein_match->getCoverage());
+        // _p_writer->writeCell("MW");
+        _p_writer->writeCell(p_protein->getMass());
+        _p_writer->writeCell(p_protein->size());
+        // _p_writer->writeCell("Spectra");
+        _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("Uniques");
+        _p_writer->writeCell((unsigned int) p_protein_match->countSequenceLi(validation_state));
+
+        // _p_writer->writeCell("Specific uniques");
+        _p_writer->writeCell((unsigned int) p_group->countSpecificSequenceLi(p_protein_match, validation_state));
+
+
+        _p_writer->writeCell(p_protein_match->countPeptideMassCharge(validation_state));
+        qDebug() << "ProteinSheet::writeOneProtein tryptic" ;
+        _p_writer->writeCell(p_protein->countTrypticPeptidesForPAI());
+        // _p_writer->writeCell("PAI");
+        // _p_writer->writeCell(new Double((float) hashProt
+        // .getTotalHashSampleScan() / prot.get_PAI_count()));
+        _p_writer->writeCell(p_protein_match->getPAI());
+        // _p_writer->writeCell(match.getPAI());//this is the same
+        /*
+         * ancien PAI _p_writer->writeCell(new Double((float)
+         * top.get_spectra_numbers_to(sample) /
+         * top.get_protein_match().get_PAI_count()));
+         */
+        _p_writer->writeCell(p_protein_match->getEmPAI());
+
+        //_p_writer->writeCell(p_protein_match->getSpectralCountAI());
+
+        // _p_writer->writeCell("Redundancy");
+        _p_writer->writeCell(p_group->countProteinInSubgroup(p_grp_protein->getSubGroupNumber()));
+
+        //number of MS sample
+        _p_writer->writeCell(p_protein_match->countDistinctMsSamples(validation_state));
+
+        qDebug() << "ProteinSheet::writeOneProtein end" ;
+    }
+    catch (pappso::PappsoException error) {
+        throw pappso::PappsoException(QObject::tr("Error writing protein %1 :\n%2").arg(p_protein_match->getProteinXtpSp().get()->getAccession()).arg(error.qwhat()));
+    }
+}

src/output/ods/ptmislandsheet.h

@@ -30,8 +30,28 @@
 #ifndef PTMISLANDSHEET_H
 #define PTMISLANDSHEET_H
 
+#include "../../core/project.h"
+#include <odsstream/calcwriterinterface.h>
+#include "../../grouping/ptm/ptmisland.h"
+#include "odsexport.h"
+#include "../../gui/ptm_island_list_view/ptmislandtablemodel.h"
+
 class PtmIslandSheet
 {
+public :
+    PtmIslandSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project);
+private :
+    void writeIdentificationGroup(IdentificationGroup * p_ident);
+    void writeHeaders(IdentificationGroup * p_ident);
+    void writeOnePtmIsland(PtmIslandSp & sp_ptm_island);
+
+protected:
+    void writeCellHeader(PtmIslandListColumn column);
+private :
+    OdsExport * _p_ods_export;
+    const Project * _p_project;
+    CalcWriterInterface * _p_writer;
+    const PtmGroupingExperiment * _p_ptm_grouping_experiment;
 };
 
 #endif // PTMISLANDSHEET_H