Change PseudoCentroid filter to deconvolution filter

src/core/msrun.cpp

@@ -133,19 +133,12 @@ MsRun::setMsRunReaderSp(QString ms_run_file)
                 {
                   QStringList option_list = m_centroidOptions.split(" ");
 
-                  std::shared_ptr<pappso::FilterSuite> ms2filter = std::make_shared<pappso::FilterSuite>();
-//                   ms2filter.get()->push_back(
-//                     std::make_shared<pappso::FilterPseudoCentroid>(
-//                       option_list.at(0).toDouble(),
-//                       option_list.at(1).toDouble(),
-//                       option_list.at(2).toDouble(),
-//                       option_list.at(3).toDouble()));
-                  std::shared_ptr<pappso::FilterTriangle> triangle = std::make_shared<pappso::FilterTriangle>();
-                  triangle.get()->setTriangleSlope(50,0.02);
-                  
-                  ms2filter.get()->push_back(triangle);
+                  std::shared_ptr<pappso::FilterSuite> ms2filter =
+                    std::make_shared<pappso::FilterSuite>();
+
                   ms2filter.get()->push_back(
-                    std::make_shared<pappso::FilterCorrectTdfPeaks>(pappso::PrecisionFactory::getDaltonInstance(0.02)));
+                    std::make_shared<pappso::FilterCorrectTdfPeaks>(
+                      pappso::PrecisionFactory::getDaltonInstance(0.02)));
 
                   tims2_reader->setMs2FilterCstSPtr(ms2filter);
                   qDebug() << m_centroidOptions;

src/core/tandem_run/tandembatchprocess.cpp

@@ -34,6 +34,7 @@
 #include <QTemporaryDir>
 #include "../../files/tandemparametersfile.h"
 #include <pappsomspp/processing/tandemwrapper/tandemwrapperrun.h>
+#include <pappsomspp/processing/filters/filtertdfcorrectpeak.h>
 
 TandemBatchProcess::TandemBatchProcess(MainWindow *p_main_window,
                                        WorkMonitorInterface *p_monitor,
@@ -409,10 +410,16 @@ TandemBatchProcess::runOne(const QString &mz_file)
             }
 
           pappso::TandemWrapperRun tandem_run(
-            _tandem_run_batch._tandem_bin_path,
-            tmpDirOption,
-            m_centroid_timstof_option);
+            _tandem_run_batch._tandem_bin_path, tmpDirOption);
 
+          std::shared_ptr<pappso::FilterSuite> ms2_filter_suite =
+            std::make_shared<pappso::FilterSuite>();
+
+          ms2_filter_suite.get()->push_back(
+            std::make_shared<pappso::FilterCorrectTdfPeaks>(
+              pappso::PrecisionFactory::getDaltonInstance(0.01)));
+
+          tandem_run.setMs2FilterSuite(ms2_filter_suite);
 
           tandem_run.run(xml_input_file.fileName(), outputStream, errorStream);