disable centroid option for timstof, set mz data format in msrun

src/core/identification_sources/identificationxtandemfile.cpp

@@ -158,6 +158,6 @@ IdentificationXtandemFile::setTimstofMs2CentroidParameters(
 
   if(_ms_run_sp.get() != nullptr)
     {
-      _ms_run_sp.get()->setTimstofMs2CentroidParameters(m_centroidOptions);
+      //_ms_run_sp.get()->setTimstofMs2CentroidParameters(m_centroidOptions);
     }
 }

src/core/msrun.cpp

@@ -55,8 +55,8 @@ MsRun::MsRun(const QString &location) : pappso::MsRunId(location)
 
 MsRun::MsRun(const MsRun &other) : pappso::MsRunId(other)
 {
-  _param_stats      = other._param_stats;
-  m_centroidOptions = other.m_centroidOptions;
+  _param_stats = other._param_stats;
+  // m_centroidOptions = other.m_centroidOptions;
 }
 
 MsRun::~MsRun()
@@ -123,28 +123,23 @@ MsRun::setMsRunReaderSp(QString ms_run_file)
           delete p_accessor;
           p_accessor = nullptr;
 
-          qDebug() << m_centroidOptions;
-          if(!m_centroidOptions.isEmpty())
+          pappso::TimsMsRunReaderMs2 *tims2_reader =
+            dynamic_cast<pappso::TimsMsRunReaderMs2 *>(_msrun_reader_sp.get());
+          if(tims2_reader != nullptr)
             {
-              pappso::TimsMsRunReaderMs2 *tims2_reader =
-                dynamic_cast<pappso::TimsMsRunReaderMs2 *>(
-                  _msrun_reader_sp.get());
-              if(tims2_reader != nullptr)
-                {
-                  QStringList option_list = m_centroidOptions.split(" ");
 
-                  std::shared_ptr<pappso::FilterSuite> ms2filter =
-                    std::make_shared<pappso::FilterSuite>();
+              std::shared_ptr<pappso::FilterSuite> ms2filter =
+                std::make_shared<pappso::FilterSuite>();
 
-                  ms2filter.get()->push_back(
-                    std::make_shared<pappso::FilterChargeDeconvolution
-                    >(
-                      pappso::PrecisionFactory::getDaltonInstance(0.02)));
+              ms2filter.get()->push_back(
+                std::make_shared<pappso::FilterChargeDeconvolution>(
+                  pappso::PrecisionFactory::getDaltonInstance(0.02)));
 
-                  tims2_reader->setMs2FilterCstSPtr(ms2filter);
-                  qDebug() << m_centroidOptions;
-                }
+              tims2_reader->setMs2FilterCstSPtr(ms2filter);
             }
+
+          this->setMzFormat(
+            _msrun_reader_sp.get()->getMsRunId().get()->getMzFormat());
         }
 
       catch(pappso::PappsoException &error2)
@@ -251,6 +246,11 @@ MsRun::findMsRunFile()
                       msrun_reader_sp = accessor.getMsRunReaderSPtrByRunId(
                         getRunId(), getXmlId());
 
+                      this->setMzFormat(msrun_reader_sp.get()
+                                          ->getMsRunId()
+                                          .get()
+                                          ->getMzFormat());
+
                       freeMsRunReaderSp();
                       return msrun_reader_sp;
                     }
@@ -280,6 +280,10 @@ MsRun::findMsRunFile()
                       msrun_reader_sp = accessor.getMsRunReaderSPtrByRunId(
                         getRunId(), getXmlId());
 
+                      this->setMzFormat(msrun_reader_sp.get()
+                                          ->getMsRunId()
+                                          .get()
+                                          ->getMzFormat());
                       freeMsRunReaderSp();
                       return msrun_reader_sp;
                     }
@@ -538,13 +542,6 @@ MsRun::getMsRunRetentionTimePtr()
 }
 
 
-void
-MsRun::setTimstofMs2CentroidParameters(const QString &centroid_parameters)
-{
-  // qDebug() << centroid_parameters;
-  m_centroidOptions = centroid_parameters;
-}
-
 MsRunAlignmentGroupSp
 MsRun::getAlignmentGroup()
 {

src/core/msrun.h

@@ -111,7 +111,6 @@ class MsRun : public pappso::MsRunId
   pappso::MsRunRetentionTime<const pappso::Peptide *> *mpa_msrunRetentionTime =
     nullptr;
 
-  QString m_centroidOptions;
   MsRunAlignmentGroupSp msp_alignmentGroup;
 };