using zivy detection parameters

src/gui/xic_view/xic_widgets/zivywidget.cpp

@@ -29,6 +29,7 @@
 #include "zivywidget.h"
 #include "ui_zivy_widget.h"
 #include <QDebug>
+#include <QSettings>
 
 void ZivyParams::setDetectionParameters(pappso::XicDetectionZivy * detect_zivy) const {
     detect_zivy->setSmoothingHalfEdgeWindows(_smoothing_half_window);
@@ -38,6 +39,23 @@ void ZivyParams::setDetectionParameters(pappso::XicDetectionZivy * detect_zivy)
     detect_zivy->setDetectionThresholdOnMaxmin(_maxmin_threshold);
 }
 
+void ZivyParams::saveSettings() const {
+    QSettings settings;
+    settings.setValue("xic/zivy_maxmin_threshold", QString("%1").arg(_maxmin_threshold));
+    settings.setValue("xic/zivy_minmax_threshold", QString("%1").arg(_minmax_threshold));
+    settings.setValue("xic/zivy_maxmin_half_window", QString("%1").arg(_maxmin_half_window));
+    settings.setValue("xic/zivy_minmax_half_window", QString("%1").arg(_minmax_half_window));
+    settings.setValue("xic/zivy_smoothing", QString("%1").arg(_smoothing_half_window));
+}
+void ZivyParams::loadSettings() {
+    QSettings settings;
+    _maxmin_threshold  = settings.value("xic/zivy_maxmin_threshold", QString("%1").arg(_maxmin_threshold)).toDouble();
+    _minmax_threshold = settings.value("xic/zivy_minmax_threshold", QString("%1").arg(_minmax_threshold)).toDouble();
+    _maxmin_half_window = settings.value("xic/zivy_maxmin_half_window", QString("%1").arg(_maxmin_half_window)).toInt();
+    _minmax_half_window = settings.value("xic/zivy_minmax_half_window", QString("%1").arg(_minmax_half_window)).toInt();
+    _smoothing_half_window = settings.value("xic/zivy_smoothing", QString("%1").arg(_smoothing_half_window)).toInt();
+}
+
 ZivyWidget::ZivyWidget(QWidget *parent):
     QWidget(parent),
     ui(new Ui::ZivyWidget)

src/gui/xic_view/xic_widgets/zivywidget.h

@@ -39,6 +39,8 @@ class ZivyWidget;
 
 struct ZivyParams {
     void setDetectionParameters(pappso::XicDetectionZivy * detect_zivy) const;
+    void saveSettings() const;
+    void loadSettings();
     
     unsigned int _maxmin_half_window = 3;
     unsigned int _minmax_half_window = 2;

src/gui/xic_view/xicwindow.cpp

@@ -47,11 +47,7 @@ XicWindow::XicWindow(ProjectWindow *parent):
 
 
     ZivyParams zivy_params;
-    zivy_params._maxmin_threshold  = settings.value("xic/zivy_maxmin_threshold", "30000").toDouble();
-    zivy_params._minmax_threshold = settings.value("xic/zivy_minmax_threshold", "50000").toDouble();
-    zivy_params._maxmin_half_window = settings.value("xic/zivy_maxmin_half_window", "2").toInt();
-    zivy_params._minmax_half_window = settings.value("xic/zivy_minmax_half_window", "4").toInt();
-    zivy_params._smoothing_half_window = settings.value("xic/zivy_smoothing", "1").toInt();
+    zivy_params.loadSettings();
 
 
     zivy_params.setDetectionParameters(&_detect_zivy);
@@ -143,6 +139,7 @@ bool XicWindow::isRetentionTimeSeconds() const {
 
 void XicWindow::doAcceptedZivyDialog() {
     _p_zivy_dialog->getZivyParams().setDetectionParameters(&_detect_zivy);
+    _p_zivy_dialog->getZivyParams().saveSettings();
     emit reExtractXicNeeded();
     
 }

src/output/masschroqml.cpp

@@ -35,7 +35,6 @@
 #include <QStringList>
 #include <QSettings>
 
-
 struct McqObserved {
     bool operator ==(const McqObserved &other) const {
         return (msrun==other.msrun && scan==other.scan && charge==other.charge);
@@ -80,12 +79,7 @@ MassChroQml::MassChroQml(const QString & out_filename)
     _output_stream->setAutoFormatting(true);
     _output_stream->writeStartDocument("1.0");
 
-    QSettings settings;
-    _detect_zivy.setSmoothingHalfEdgeWindows(settings.value("xic/zivy_smoothing", "1").toInt());
-    _detect_zivy.setMinMaxHalfEdgeWindows(settings.value("xic/zivy_minmax_half_window", "3").toInt());
-    _detect_zivy.setMaxMinHalfEdgeWindows(settings.value("xic/zivy_maxmin_half_window", "2").toInt());
-    _detect_zivy.setDetectionThresholdOnMinmax(settings.value("xic/zivy_minmax_threshold", "5000").toDouble());
-    _detect_zivy.setDetectionThresholdOnMaxmin(settings.value("xic/zivy_maxmin_threshold", "3000").toDouble());
+    _detect_zivy.loadSettings();
 
 }
 
@@ -219,11 +213,11 @@ void MassChroQml::writeQuantify() {
     _output_stream->writeAttribute("mode","post_matching");
     _output_stream->writeAttribute("ni_min_abundance","0.8");
     if (_sp_project.get()->getLabelingMethodSp().get() != nullptr) {
-      QStringList isotope_label_ref;
-      for (const Label * p_label :_sp_project.get()->getLabelingMethodSp().get()->getLabelList()) {
-	isotope_label_ref << p_label->getXmlId();
-      }
-      _output_stream->writeAttribute("isotope_label_refs",isotope_label_ref.join(" "));
+        QStringList isotope_label_ref;
+        for (const Label * p_label :_sp_project.get()->getLabelingMethodSp().get()->getLabelList()) {
+            isotope_label_ref << p_label->getXmlId();
+        }
+        _output_stream->writeAttribute("isotope_label_refs",isotope_label_ref.join(" "));
     }
     _output_stream->writeEndElement();
 
@@ -271,23 +265,23 @@ void MassChroQml::writeQuantificationMethods() {
     _output_stream->writeStartElement("detection_zivy");
     //<mean_filter_half_edge>1</mean_filter_half_edge>
     _output_stream->writeStartElement("mean_filter_half_edge");
-    _output_stream->writeCharacters(QString("%1").arg(_detect_zivy.getSmoothingHalfEdgeWindows()));
+    _output_stream->writeCharacters(QString("%1").arg(_detect_zivy._smoothing_half_window));
     _output_stream->writeEndElement();
     //<minmax_half_edge>3</minmax_half_edge>
     _output_stream->writeStartElement("minmax_half_edge");
-    _output_stream->writeCharacters(QString("%1").arg(_detect_zivy.getMinMaxHalfEdgeWindows()));
+    _output_stream->writeCharacters(QString("%1").arg(_detect_zivy._minmax_half_window));
     _output_stream->writeEndElement();
     //<maxmin_half_edge>2</maxmin_half_edge>
     _output_stream->writeStartElement("maxmin_half_edge");
-    _output_stream->writeCharacters(QString("%1").arg(_detect_zivy.getMaxMinHalfEdgeWindows()));
+    _output_stream->writeCharacters(QString("%1").arg(_detect_zivy._maxmin_half_window));
     _output_stream->writeEndElement();
     //<detection_threshold_on_max>5000</detection_threshold_on_max>
     _output_stream->writeStartElement("detection_threshold_on_max");
-    _output_stream->writeCharacters(QString("%1").arg(_detect_zivy.getDetectionThresholdOnMinmax()));
+    _output_stream->writeCharacters(QString("%1").arg(_detect_zivy._minmax_threshold));
     _output_stream->writeEndElement();
     //<detection_threshold_on_min>3000</detection_threshold_on_min>
     _output_stream->writeStartElement("detection_threshold_on_min");
-    _output_stream->writeCharacters(QString("%1").arg(_detect_zivy.getDetectionThresholdOnMaxmin()));
+    _output_stream->writeCharacters(QString("%1").arg(_detect_zivy._maxmin_threshold));
     _output_stream->writeEndElement();
     //</detection_zivy>
     _output_stream->writeEndElement();

src/output/masschroqml.h

@@ -36,6 +36,7 @@
 #include <pappsomspp/xic/detection/xicdetectionzivy.h>
 #include "../core/project.h"
 #include "../grouping/groupinggroup.h"
+#include "../gui/xic_view/xic_widgets/zivywidget.h"
 
 class MassChroQml
 {
@@ -62,7 +63,7 @@ private :
     QXmlStreamWriter * _output_stream;
     ProjectSp _sp_project;
     IdentificationGroup * _p_identification_group;
-    pappso::XicDetectionZivy _detect_zivy;
+    ZivyParams _detect_zivy;
 };
 
 #endif // MASSCHROQML_H