more information in masschroq spreadsheet output for issue #6

src/lib/monitors/monitorodsoutput.cpp

@@ -25,8 +25,10 @@
 #include "monitorodsoutput.h"
 #include "../peptides/peptide.h"
 #include "../quantificator.h"
+#include "../share/utilities.h"
 #include <QDir>
 #include <odsstream/writer/options/odstablesettings.h>
+#include <pappsomspp/processing/detection/tracedetectionzivy.h>
 
 MonitorTsvOutput::MonitorTsvOutput(const QString &output_directory)
 {
@@ -100,9 +102,83 @@ MonitorOdsInterfaceOutput::writeQuantifyBegin(
       _p_writer->writeSheet(
         QString("MassChroQ informations - %1").arg(_current_quantification_id));
 
-      _p_writer->writeCell("MassChroQ version :");
-      _p_writer->writeLine();
+      _p_writer->writeCell("MassChroQ version");
       _p_writer->writeCell(QString("%1").arg(MASSCHROQ_VERSION));
+      _p_writer->writeLine();
+
+      // alignment parameters
+      // ms2_tendency_halfwindow \t 10
+      // ms2_smoothing_halfwindow \t 15
+      // ms1_smoothing_halfwindow \t 0
+
+      // extraction parameters
+      _p_writer->writeCell("extraction range lower limit");
+      _p_writer->writeCell(p_quantificator->getQuantificationMethod()
+                             ->getLowerPrecision()
+                             ->toString());
+      _p_writer->writeLine();
+      _p_writer->writeCell("extraction range upper limit");
+      _p_writer->writeCell(p_quantificator->getQuantificationMethod()
+                             ->getUpperPrecision()
+                             ->toString());
+      _p_writer->writeLine();
+      _p_writer->writeCell("natural isotope minimum abundance");
+      _p_writer->writeCell(p_quantificator->getNiMinimumAbundance());
+      _p_writer->writeLine();
+      _p_writer->writeCell("matching mode");
+      _p_writer->writeCell(
+        Utilities::toString(p_quantificator->getMatchingMode()));
+      _p_writer->writeLine();
+
+      const pappso::FilterSuite &filters =
+        p_quantificator->getQuantificationMethod()->getXicFilters();
+
+      for(auto &&one_filter : filters)
+        {
+          const pappso::FilterNameInterface *p_filter =
+            dynamic_cast<const pappso::FilterNameInterface *>(one_filter.get());
+          if(p_filter != nullptr)
+            {
+              _p_writer->writeCell(p_filter->toString());
+              _p_writer->writeLine();
+            }
+        }
+
+
+      const pappso::TraceDetectionInterface *p_detection =
+        p_quantificator->getQuantificationMethod()->getDetectionMethod().get();
+      if(p_detection != nullptr)
+        {
+          const pappso::TraceDetectionZivy *p_detectionZivy =
+            dynamic_cast<const pappso::TraceDetectionZivy *>(p_detection);
+          if(p_detectionZivy != nullptr)
+            {
+              _p_writer->writeCell("detection Zivy");
+              _p_writer->writeLine();
+              _p_writer->writeCell("smoothing half edge window");
+              _p_writer->writeCell(
+                (std::size_t)p_detectionZivy->getSmoothingHalfEdgeWindows());
+              _p_writer->writeLine();
+              _p_writer->writeCell("maxmin half edge window");
+              _p_writer->writeCell(
+                (std::size_t)p_detectionZivy->getMaxMinHalfEdgeWindows());
+              _p_writer->writeLine();
+              _p_writer->writeCell("minmax half edge window");
+              _p_writer->writeCell(
+                (std::size_t)p_detectionZivy->getMinMaxHalfEdgeWindows());
+              _p_writer->writeLine();
+              _p_writer->writeCell("detection threshold on maxmin");
+              _p_writer->writeCell(
+                (std::size_t)p_detectionZivy->getDetectionThresholdOnMaxmin());
+              _p_writer->writeLine();
+              _p_writer->writeCell("detection threshold on minmax");
+              _p_writer->writeCell(
+                (std::size_t)p_detectionZivy->getDetectionThresholdOnMinmax());
+              _p_writer->writeLine();
+            }
+        }
+
+
       _p_writer->writeLine();
       _p_writer->writeLine();
 

src/lib/quantifications/quantificationMethod.h

@@ -29,6 +29,7 @@
 #include <pappsomspp/types.h>
 #include <pappsomspp/processing/detection/tracedetectioninterface.h>
 #include <pappsomspp/processing/filters/filtersuite.h>
+#include <odsstream/calcwriterinterface.h>
 
 /**
    \class QuantificationMethod