Commit 0a4569f6 authored by Langella Olivier's avatar Langella Olivier
Browse files

more information in masschroq spreadsheet output for issue #6

parent e48fa24b
...@@ -25,8 +25,10 @@ ...@@ -25,8 +25,10 @@
#include "monitorodsoutput.h" #include "monitorodsoutput.h"
#include "../peptides/peptide.h" #include "../peptides/peptide.h"
#include "../quantificator.h" #include "../quantificator.h"
#include "../share/utilities.h"
#include <QDir> #include <QDir>
#include <odsstream/writer/options/odstablesettings.h> #include <odsstream/writer/options/odstablesettings.h>
#include <pappsomspp/processing/detection/tracedetectionzivy.h>
MonitorTsvOutput::MonitorTsvOutput(const QString &output_directory) MonitorTsvOutput::MonitorTsvOutput(const QString &output_directory)
{ {
...@@ -100,9 +102,83 @@ MonitorOdsInterfaceOutput::writeQuantifyBegin( ...@@ -100,9 +102,83 @@ MonitorOdsInterfaceOutput::writeQuantifyBegin(
_p_writer->writeSheet( _p_writer->writeSheet(
QString("MassChroQ informations - %1").arg(_current_quantification_id)); QString("MassChroQ informations - %1").arg(_current_quantification_id));
_p_writer->writeCell("MassChroQ version :"); _p_writer->writeCell("MassChroQ version");
_p_writer->writeLine();
_p_writer->writeCell(QString("%1").arg(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();
_p_writer->writeLine(); _p_writer->writeLine();
......
...@@ -29,6 +29,7 @@ ...@@ -29,6 +29,7 @@
#include <pappsomspp/types.h> #include <pappsomspp/types.h>
#include <pappsomspp/processing/detection/tracedetectioninterface.h> #include <pappsomspp/processing/detection/tracedetectioninterface.h>
#include <pappsomspp/processing/filters/filtersuite.h> #include <pappsomspp/processing/filters/filtersuite.h>
#include <odsstream/calcwriterinterface.h>
/** /**
\class QuantificationMethod \class QuantificationMethod
......
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