ptm island ods report OK

src/grouping/ptm/ptmgroupingexperiment.cpp

@@ -29,6 +29,7 @@
 
 #include "ptmgroupingexperiment.h"
 #include "../../grouping/ptm/ptmgroupingexperiment.h"
+#include "QDebug"
 
 PtmGroupingExperiment::PtmGroupingExperiment()
 {
@@ -74,6 +75,7 @@ PtmGroupingExperiment::~PtmGroupingExperiment()
 }
 
 const std::vector<PtmIslandSp> & PtmGroupingExperiment::getPtmIslandList() const {
+    qDebug() << "PtmGroupingExperiment::getPtmIslandList begin" << _ptm_island_list.size();
     return _ptm_island_list;
 }
 

src/output/ods/odsexport.cpp

@@ -38,6 +38,7 @@
 #include "infosheet.h"
 #include "samplesheet.h"
 #include "groupingsheet.h"
+#include "ptmislandsheet.h"
 #include <QSettings>
 
 OdsExport::OdsExport(const Project * project):_p_project(project) {
@@ -114,4 +115,11 @@ void OdsExport::write(CalcWriterInterface * p_writer, WorkMonitorInterface * p_m
         p_monitor->message(QObject::tr("writing samples"));
         SampleSheet(this, p_writer, _p_project);
     }
+
+    if (_p_project->hasPtmExperiment()) {
+        if (settings.value("export_ods/ptmislands", "true").toBool()) {
+            p_monitor->message(QObject::tr("writing PTM islands"));
+            PtmIslandSheet(this, p_writer, _p_project);
+        }
+    }
 }

src/output/ods/proteinsheet.cpp

@@ -145,7 +145,14 @@ void ProteinSheet::writeOneProtein(const GroupingGroup * p_group, const ProteinM
         _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());
+
+        const std::list<DbXref> & dbxref_list = p_protein->getDbxrefList();
+        if (dbxref_list.size() == 0) {
+            _p_writer->writeCell(p_protein->getAccession());
+        }
+        else {
+            _p_writer->writeCell(dbxref_list.front().getUrl(), p_protein->getAccession());
+        }
         _p_writer->writeCell(p_protein->getDescription());
         _p_writer->writeCell(p_protein_match->getLogEvalue());
         // _p_writer->writeCell("Coverage");

src/output/ods/ptmislandsheet.cpp

@@ -34,6 +34,7 @@
 #include <pappsomspp/pappsoexception.h>
 
 PtmIslandSheet::PtmIslandSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project): _p_project(p_project) {
+    qDebug() << "PtmIslandSheet::PtmIslandSheet begin" ;
     _p_writer = p_writer;
     _p_ods_export = p_ods_export;
     p_writer->writeSheet("PTM islands");
@@ -43,6 +44,7 @@ PtmIslandSheet::PtmIslandSheet (OdsExport * p_ods_export, CalcWriterInterface *
         //writeHeaders(p_ident);
         writeIdentificationGroup(p_ident);
     }
+    qDebug() << "PtmIslandSheet::PtmIslandSheet end" ;
 }
 void PtmIslandSheet::writeCellHeader(PtmIslandListColumn column) {
     qDebug() << "PtmIslandSheet::writeCellHeader begin " << (std::int8_t) column;
@@ -54,7 +56,7 @@ void PtmIslandSheet::writeCellHeader(PtmIslandListColumn column) {
 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
-
+    qDebug() << "PtmIslandSheet::writeHeaders begin" ;
     const std::vector<MsRunSp> msrun_list = p_ident->getMsRunSpList();
     if (msrun_list.size() == 1) {
         _p_writer->writeCell("sample");
@@ -86,31 +88,40 @@ void PtmIslandSheet::writeHeaders(IdentificationGroup * p_ident)  {
     _p_writer->setCellAnnotation("Number of proteins sharing this PTM island");
     _p_writer->writeCell("Number of proteins");
 
+    qDebug() << "PtmIslandSheet::writeHeaders end" ;
 
 }
 
 void PtmIslandSheet::writeIdentificationGroup(IdentificationGroup * p_ident) {
 
+    qDebug() << "PtmIslandSheet::writeIdentificationGroup begin" ;
     _p_ptm_grouping_experiment = p_ident->getPtmGroupingExperiment();
-    if (_p_ptm_grouping_experiment = nullptr) {
+    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();
-        });
+    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);
+    }
 
-        for (auto & ptm_island:ptm_island_list) {
-            writeOnePtmIsland(ptm_island);
-        }
 
-    
     _p_writer->writeLine();
+    qDebug() << "PtmIslandSheet::writeIdentificationGroup end" ;
 }
 
 
@@ -129,7 +140,7 @@ void PtmIslandSheet::writeOnePtmIsland(PtmIslandSp & sp_ptm_island) {
         const PtmIslandGroup * p_ptm_island_group = p_ptm_island_subgroup->getPtmIslandGroup();
         unsigned int group_number = p_ptm_island_group->getGroupNumber();
         unsigned int subgroup_number = p_ptm_island_subgroup->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);
@@ -139,16 +150,17 @@ void PtmIslandSheet::writeOnePtmIsland(PtmIslandSp & sp_ptm_island) {
         _p_writer->writeCell(p_protein->getAccession());
         _p_writer->writeCell(p_protein->getDescription());
         _p_writer->writeCell(p_protein->getMass());
-        
+
         QStringList position_list;
-            for (unsigned int position : sp_ptm_island.get()->getPositionList()) {
-                position_list << QString("%1").arg(position+1);
-            }
-            _p_writer->writeCell(position_list.join(" "));
+        for (unsigned int position : sp_ptm_island.get()->getPositionList()) {
+            position_list << QString("%1").arg(position+1);
+        }
+        _p_writer->writeCell(position_list.join(" "));
         // _p_writer->writeCell("Spectra");
         _p_writer->writeCell((unsigned int) sp_ptm_island.get()->getPtmIslandSubroup()->countSampleScan());
         // _p_writer->writeCell("Uniques");
         _p_writer->writeCell((unsigned int) sp_ptm_island.get()->countSequence());
+        _p_writer->writeCell((unsigned int) sp_ptm_island.get()->getPtmIslandSubroup()->getPtmIslandList().size());
 
 
         qDebug() << "ProteinSheet::writeOneProtein end" ;