The msrun object now handles locally any specific statistics computation on any msrun file format

src/core/msrun.cpp

@@ -290,55 +290,62 @@ MsRun::findMsRunFile()
 void
 MsRun::checkMsRunStatistics()
 {
-  QVariant msrun_var = getMsRunStatistics(MsRunStatistics::total_spectra);
-  if(msrun_var.isNull())
-    {
-      try
-        {
 
-          MsRunStatisticsHandler stats;
-          _msrun_reader_sp = getMsRunReaderSPtr();
-          _msrun_reader_sp.get()->readSpectrumCollection(stats);
-
-          setMsRunStatistics(MsRunStatistics::total_spectra,
-                             (unsigned int)stats.getTotalCount());
-          setMsRunStatistics(MsRunStatistics::total_spectra_ms1,
-                             (unsigned int)stats.getMsLevelCount(1));
-          setMsRunStatistics(MsRunStatistics::total_spectra_ms2,
-                             (unsigned int)stats.getMsLevelCount(2));
-          setMsRunStatistics(MsRunStatistics::total_spectra_ms3,
-                             (unsigned int)stats.getMsLevelCount(3));
-          setMsRunStatistics(MsRunStatistics::tic_spectra_ms1,
-                             stats.getMsLevelTic(1));
-          setMsRunStatistics(MsRunStatistics::tic_spectra_ms2,
-                             stats.getMsLevelTic(2));
-          setMsRunStatistics(MsRunStatistics::tic_spectra_ms3,
-                             stats.getMsLevelTic(3));
-        }
-      catch(pappso::ExceptionNotFound &error)
-        {
-          // no file found, no statistics
-        }
-    }
-  freeMsRunReaderSp();
+  MsRunStatisticsHandler stats;
+  checkMsRunStatistics(&stats);
 }
 
 void
 MsRun::checkMsRunStatistics(MsRunStatisticsHandler *currentHandler)
 {
+
   QVariant msrun_var = getMsRunStatistics(MsRunStatistics::total_spectra);
   if(msrun_var.isNull())
     {
       try
         {
+
           _msrun_reader_sp = getMsRunReaderSPtr();
-          _msrun_reader_sp.get()->readSpectrumCollection(*currentHandler);
-          if(currentHandler->shouldStop())
-            { // statistics handler was stopped : don't use collected statistics
-              // because it is only partial
+          if(this->getMzFormat() == pappso::MzFormat::brukerTims)
+            {
+              pappso::TimsMsRunReaderMs2 *tims2_reader =
+                dynamic_cast<pappso::TimsMsRunReaderMs2 *>(
+                  _msrun_reader_sp.get());
+              if(tims2_reader != nullptr)
+                {
+                  pappso::TimsDataSp tims_data =
+                    tims2_reader->getTimsDataSPtr();
+                  if(currentHandler->shouldStop())
+                    { // statistics handler was stopped : don't use collected
+                      // statistics because it is only partial
+                    }
+                  else
+                    {
+                      setMsRunStatistics(MsRunStatistics::total_spectra, "NA");
+                      // not the number of MS1 or MS2 but the number of scans
+                      // and
+                      // precursors.
+                      // Compute from th mobillity results
+                      setMsRunStatistics(
+                        MsRunStatistics::total_spectra_ms1,
+                        (unsigned int)tims_data->getTotalNumberOfPrecursors());
+                      setMsRunStatistics(
+                        MsRunStatistics::total_spectra_ms2,
+                        (unsigned int)tims_data->getTotalNumberOfScans());
+                      setMsRunStatistics(MsRunStatistics::total_spectra_ms3, 0);
+                      setMsRunStatistics(MsRunStatistics::tic_spectra_ms1,
+                                         "NA");
+                      setMsRunStatistics(MsRunStatistics::tic_spectra_ms2,
+                                         "NA");
+                      setMsRunStatistics(MsRunStatistics::tic_spectra_ms3,
+                                         "NA");
+                    }
+                }
             }
           else
             {
+              _msrun_reader_sp.get()->readSpectrumCollection(*currentHandler);
+
               setMsRunStatistics(MsRunStatistics::total_spectra,
                                  (unsigned int)currentHandler->getTotalCount());
               setMsRunStatistics(
@@ -366,46 +373,6 @@ MsRun::checkMsRunStatistics(MsRunStatisticsHandler *currentHandler)
   freeMsRunReaderSp();
 }
 
-void
-MsRun::checkMsRunStatisticsForTdf(MsRunStatisticsHandler *currentHandler)
-{
-  QVariant msrun_var = getMsRunStatistics(MsRunStatistics::total_spectra);
-  if(msrun_var.isNull())
-    {
-      try
-        {
-          QString directory =
-            QFileInfo(getFileName()).absoluteDir().absolutePath();
-          pappso::TimsData *tims_data = new pappso::TimsData(directory);
-          if(currentHandler->shouldStop())
-            { // statistics handler was stopped : don't use collected statistics
-              // because it is only partial
-            }
-          else
-            {
-              setMsRunStatistics(MsRunStatistics::total_spectra, "NA");
-              // not the number of MS1 or MS2 but the number of scans and
-              // precursors.
-              // Compute from th mobillity results
-              setMsRunStatistics(
-                MsRunStatistics::total_spectra_ms1,
-                (unsigned int)tims_data->getTotalNumberOfPrecursors());
-              setMsRunStatistics(
-                MsRunStatistics::total_spectra_ms2,
-                (unsigned int)tims_data->getTotalNumberOfScans());
-              setMsRunStatistics(MsRunStatistics::total_spectra_ms3, 0);
-              setMsRunStatistics(MsRunStatistics::tic_spectra_ms1, "NA");
-              setMsRunStatistics(MsRunStatistics::tic_spectra_ms2, "NA");
-              setMsRunStatistics(MsRunStatistics::tic_spectra_ms3, "NA");
-            }
-        }
-      catch(pappso::ExceptionNotFound &error)
-        {
-          // no file found, no statistics
-        }
-    }
-}
-
 pappso::MsRunXicExtractorInterfaceSp
 MsRun::getMsRunXicExtractorInterfaceSp()
 {

src/core/msrun.h

@@ -85,7 +85,6 @@ class MsRun : public pappso::MsRunId
 
   void checkMsRunStatistics();
   void checkMsRunStatistics(MsRunStatisticsHandler *currentHandler);
-  void checkMsRunStatisticsForTdf(MsRunStatisticsHandler *currentHandler);
 
   pappso::MsRunXicExtractorInterfaceSp getMsRunXicExtractorInterfaceSp();
 

src/gui/lists/ms_identification_run_list_view/ms_identification_worker/msidlistworkerstatus.cpp

@@ -153,68 +153,6 @@ MsIdListWorkerStatus::getStatus(
 void
 MsIdListWorkerStatus::doComputeMsNumber(
   IdentificationDataSourceSp identificationDataSource)
-{
-  if(QFileInfo(identificationDataSource.get()->getMsRunSp()->getFileName())
-       .completeSuffix() == "tdf")
-    {
-      doComputeMsNumberForTDF(identificationDataSource);
-    }
-  else
-    {
-      doComputeMsNumberForMzXML(identificationDataSource);
-    }
-}
-
-void
-MsIdListWorkerStatus::changeWaitingQueue(int row [[maybe_unused]])
-{
-  m_waitingComputing.clear();
-  qDebug() << m_waitingComputing.size();
-}
-
-void
-MsIdListWorkerStatus::doComputeMsNumberForTDF(
-  IdentificationDataSourceSp identificationDataSource)
-{
-  if(identificationDataSource->getMsRunSp()->findMsRunFile())
-    {
-      try
-        {
-          if(mpa_currentHandler == nullptr)
-            {
-              mpa_currentHandler =
-                new MsIdentificationTableMsRunStatisticsHandler;
-              identificationDataSource->getMsRunSp()
-                ->checkMsRunStatisticsForTdf(mpa_currentHandler);
-              if(!mpa_currentHandler->shouldStop())
-                {
-                  // if statistics computing is interrupted : don't take
-                  // into account results because it is partial
-                  m_identificationReady.push_back(
-                    identificationDataSource.get());
-                }
-
-              delete mpa_currentHandler;
-              mpa_currentHandler = nullptr;
-            }
-        }
-      catch(pappso::PappsoException &error)
-        {
-          // error while computing
-          qDebug() << error.qwhat();
-          m_identificationError.push_back(identificationDataSource.get());
-        }
-    }
-  else
-    {
-      // file not found
-      m_identificationFileNotFound.push_back(identificationDataSource.get());
-    }
-}
-
-void
-MsIdListWorkerStatus::doComputeMsNumberForMzXML(
-  IdentificationDataSourceSp identificationDataSource)
 {
   qDebug() << "AAAAAAAAAAAAAAAAAAAAAAAA";
   pappso::MsRunReaderSPtr msrun_reader_sp =
@@ -272,3 +210,10 @@ MsIdListWorkerStatus::doComputeMsNumberForMzXML(
       m_identificationFileNotFound.push_back(identificationDataSource.get());
     }
 }
+
+void
+MsIdListWorkerStatus::changeWaitingQueue(int row [[maybe_unused]])
+{
+  m_waitingComputing.clear();
+  qDebug() << m_waitingComputing.size();
+}

src/gui/lists/ms_identification_run_list_view/ms_identification_worker/msidlistworkerstatus.h

@@ -77,10 +77,6 @@ class MsIdListWorkerStatus
    */
   WorkerStatus getStatus(IdentificationDataSourceSp identificationDataSource);
   void doComputeMsNumber(IdentificationDataSourceSp identificationDataSource);
-  void
-  doComputeMsNumberForTDF(IdentificationDataSourceSp identificationDataSource);
-  void doComputeMsNumberForMzXML(
-    IdentificationDataSourceSp identificationDataSource);
   void changeWaitingQueue(int row);
 
 

src/output/ods/samplesheet.cpp

@@ -153,15 +153,7 @@ SampleSheet::writeIdentificationDataSource(
     {
       if(msrun_sp->findMsRunFile())
         {
-          if(QFileInfo(msrun_sp->getFileName()).completeSuffix() == "tdf")
-            {
-              msrun_sp->checkMsRunStatisticsForTdf(
-                new MsRunStatisticsHandler());
-            }
-          else
-            {
-              msrun_sp->checkMsRunStatistics();
-            }
+          msrun_sp->checkMsRunStatistics();
         }
       msrun_sp->freeMsRunReaderSp();
     }