diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index b28de307f81a8394c5e12d429c1c8ecf10d4f689..76b83adf50be9ec63c244513e6eda552724d2113 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -193,6 +193,7 @@ SET(XTPCPP_SRCS
./gui/widgets/contaminant_widget/contaminantwidget.cpp
./gui/widgets/massitemdelegate.cpp
./gui/xic_view/xic_box/xicbox.cpp
+ ./gui/xic_view/xic_widgets/zivydialog.cpp
./gui/xic_view/xic_widgets/zivywidget.cpp
./gui/xic_view/xicwindow.cpp
./gui/xic_view/xicworkerthread.cpp
diff --git a/src/gui/xic_view/xic_box/xicbox.h b/src/gui/xic_view/xic_box/xicbox.h
index 62a83aec4cd60900f7a0f9f28a5188cf9943936d..32bb2093333b4e052936521fa8de9c5e4ffa70b1 100644
--- a/src/gui/xic_view/xic_box/xicbox.h
+++ b/src/gui/xic_view/xic_box/xicbox.h
@@ -60,7 +60,7 @@ class XicBox: public QWidget
public:
explicit XicBox(XicWindow * parent = 0);
- ~XicBox();
+ virtual ~XicBox();
void setPeptideEvidence(const PeptideEvidence * p_peptide_evidence) ;
void setPeptideEvidenceInMsRun(const PeptideEvidence * p_peptide_evidence, MsRunSp msrun_sp);
diff --git a/src/gui/xic_view/xic_widgets/zivy_widget.ui b/src/gui/xic_view/xic_widgets/zivy_widget.ui
index 34d312fbc2c79ed1777a16bdfd5057e5e7efb63d..df084748404a7230d30b1cf2c388b9aabd4bfd45 100644
--- a/src/gui/xic_view/xic_widgets/zivy_widget.ui
+++ b/src/gui/xic_view/xic_widgets/zivy_widget.ui
@@ -27,9 +27,6 @@
</property>
</widget>
</item>
- <item row="0" column="1">
- <widget class="QSpinBox" name="smoothing_spinbox"/>
- </item>
<item row="1" column="0">
<widget class="QLabel" name="label_2">
<property name="text">
@@ -57,9 +54,6 @@
</property>
</widget>
</item>
- <item row="3" column="1">
- <widget class="QSpinBox" name="minmax_threshold_spinbox"/>
- </item>
<item row="4" column="0">
<widget class="QLabel" name="label_5">
<property name="text">
@@ -67,29 +61,39 @@
</property>
</widget>
</item>
+ <item row="3" column="1">
+ <widget class="QDoubleSpinBox" name="minmax_threshold_spinbox">
+ <property name="decimals">
+ <number>0</number>
+ </property>
+ <property name="maximum">
+ <double>1000000.000000000000000</double>
+ </property>
+ <property name="singleStep">
+ <double>10000.000000000000000</double>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="1">
+ <widget class="QSpinBox" name="smoothing_spinbox"/>
+ </item>
<item row="4" column="1">
- <widget class="QSpinBox" name="maxmin_threshold_spinbox"/>
+ <widget class="QDoubleSpinBox" name="maxmin_threshold_spinbox">
+ <property name="decimals">
+ <number>0</number>
+ </property>
+ <property name="maximum">
+ <double>1000000.000000000000000</double>
+ </property>
+ <property name="singleStep">
+ <double>10000.000000000000000</double>
+ </property>
+ </widget>
</item>
</layout>
</widget>
<resources/>
<connections>
- <connection>
- <sender>smoothing_spinbox</sender>
- <signal>valueChanged(int)</signal>
- <receiver>ZivyWidget</receiver>
- <slot>doSpinboxChanged(int)</slot>
- <hints>
- <hint type="sourcelabel">
- <x>339</x>
- <y>31</y>
- </hint>
- <hint type="destinationlabel">
- <x>615</x>
- <y>47</y>
- </hint>
- </hints>
- </connection>
<connection>
<sender>minmax_spinbox</sender>
<signal>valueChanged(int)</signal>
@@ -123,34 +127,18 @@
</hints>
</connection>
<connection>
- <sender>minmax_threshold_spinbox</sender>
- <signal>valueChanged(int)</signal>
- <receiver>ZivyWidget</receiver>
- <slot>doSpinboxChanged(int)</slot>
- <hints>
- <hint type="sourcelabel">
- <x>254</x>
- <y>129</y>
- </hint>
- <hint type="destinationlabel">
- <x>683</x>
- <y>194</y>
- </hint>
- </hints>
- </connection>
- <connection>
- <sender>maxmin_threshold_spinbox</sender>
+ <sender>smoothing_spinbox</sender>
<signal>valueChanged(int)</signal>
<receiver>ZivyWidget</receiver>
<slot>doSpinboxChanged(int)</slot>
<hints>
<hint type="sourcelabel">
- <x>215</x>
- <y>160</y>
+ <x>339</x>
+ <y>31</y>
</hint>
<hint type="destinationlabel">
- <x>574</x>
- <y>220</y>
+ <x>615</x>
+ <y>47</y>
</hint>
</hints>
</connection>
diff --git a/src/gui/xic_view/xic_widgets/zivydialog.cpp b/src/gui/xic_view/xic_widgets/zivydialog.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..5f4244c55cbb2bf2de6c34487af4ca8edc6ef788
--- /dev/null
+++ b/src/gui/xic_view/xic_widgets/zivydialog.cpp
@@ -0,0 +1,61 @@
+/**
+ * \file src/gui/xic_view/xic_widgets/zivydialog.h
+ * \date 30/5/2018
+ * \author Olivier Langella
+ * \brief dialog window to edit Zivy quantification method
+ */
+/*******************************************************************************
+* Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
+*
+* This file is part of XTPcpp.
+*
+* XTPcpp is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* XTPcpp is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+*
+* Contributors:
+* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
+******************************************************************************/
+
+#include "zivydialog.h"
+#include <QVBoxLayout>
+#include <QDebug>
+
+ZivyDialog::ZivyDialog(QWidget *parent) {
+ _p_zivy_widget = new ZivyWidget(this);
+ _p_button_box = new QDialogButtonBox(QDialogButtonBox::Ok
+ | QDialogButtonBox::Cancel);
+
+ connect(_p_button_box, &QDialogButtonBox::accepted, this, &QDialog::accept);
+ connect(_p_button_box, &QDialogButtonBox::rejected, this, &QDialog::reject);
+
+ QVBoxLayout *mainLayout = new QVBoxLayout;
+ mainLayout->addWidget(_p_zivy_widget);
+ mainLayout->addWidget(_p_button_box);
+ setLayout(mainLayout);
+
+ setWindowTitle(tr("Edit parameters"));
+}
+
+
+ZivyDialog::~ZivyDialog()
+{
+ qDebug() << "ZivyDialog::~ZivyDialog";
+}
+
+void ZivyDialog::setZivyParams(const ZivyParams & params) {
+ _p_zivy_widget->setZivyParams(params);
+}
+
+const ZivyParams ZivyDialog::getZivyParams() const {
+ return _p_zivy_widget->getZivyParams();
+}
diff --git a/src/gui/xic_view/xic_widgets/zivydialog.h b/src/gui/xic_view/xic_widgets/zivydialog.h
new file mode 100644
index 0000000000000000000000000000000000000000..25c1625b46d9d1bd77d8a707e0133113ce4f5ac6
--- /dev/null
+++ b/src/gui/xic_view/xic_widgets/zivydialog.h
@@ -0,0 +1,53 @@
+/**
+ * \file src/gui/xic_view/xic_widgets/zivydialog.h
+ * \date 30/5/2018
+ * \author Olivier Langella
+ * \brief dialog window to edit Zivy quantification method
+ */
+/*******************************************************************************
+* Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
+*
+* This file is part of XTPcpp.
+*
+* XTPcpp is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* XTPcpp is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+*
+* Contributors:
+* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
+******************************************************************************/
+
+#ifndef ZIVYDIALOG_H
+#define ZIVYDIALOG_H
+
+#include <QDialogButtonBox>
+#include <QDialog>
+#include "zivywidget.h"
+
+class ZivyDialog : public QDialog
+{
+ Q_OBJECT
+
+public:
+ explicit ZivyDialog(QWidget *parent = 0);
+ virtual ~ZivyDialog();
+
+
+ void setZivyParams(const ZivyParams & params);
+ const ZivyParams getZivyParams() const;
+
+private:
+ ZivyWidget * _p_zivy_widget;
+ QDialogButtonBox * _p_button_box;
+};
+
+#endif // ZIVYDIALOG_H
diff --git a/src/gui/xic_view/xic_widgets/zivywidget.cpp b/src/gui/xic_view/xic_widgets/zivywidget.cpp
index 55d21c5ea8d7346338437ee4324d51782b77bbad..9755c10baae126491383c63061d593ad61c2af1a 100644
--- a/src/gui/xic_view/xic_widgets/zivywidget.cpp
+++ b/src/gui/xic_view/xic_widgets/zivywidget.cpp
@@ -30,7 +30,13 @@
#include "ui_zivy_widget.h"
#include <QDebug>
-
+void ZivyParams::setDetectionParameters(pappso::XicDetectionZivy * detect_zivy) const {
+ detect_zivy->setSmoothingHalfEdgeWindows(_smoothing_half_window);
+ detect_zivy->setMinMaxHalfEdgeWindows(_minmax_half_window);
+ detect_zivy->setMaxMinHalfEdgeWindows(_maxmin_half_window);
+ detect_zivy->setDetectionThresholdOnMinmax(_minmax_threshold);
+ detect_zivy->setDetectionThresholdOnMaxmin(_maxmin_threshold);
+}
ZivyWidget::ZivyWidget(QWidget *parent):
QWidget(parent),
diff --git a/src/gui/xic_view/xic_widgets/zivywidget.h b/src/gui/xic_view/xic_widgets/zivywidget.h
index 77c32ba07d19e93df003815c39f6ff411468563e..c6bc0ca934e09823ab53bc33d5a8ad00c727383b 100644
--- a/src/gui/xic_view/xic_widgets/zivywidget.h
+++ b/src/gui/xic_view/xic_widgets/zivywidget.h
@@ -30,6 +30,7 @@
#define ZIVYWIDGET_H
#include <QWidget>
+#include <pappsomspp/xic/detection/xicdetectionzivy.h>
namespace Ui {
class ZivyWidget;
@@ -37,10 +38,12 @@ class ZivyWidget;
struct ZivyParams {
+ void setDetectionParameters(pappso::XicDetectionZivy * detect_zivy) const;
+
unsigned int _maxmin_half_window = 3;
unsigned int _minmax_half_window = 2;
- unsigned int _maxmin_threshold = 3000;
- unsigned int _minmax_threshold = 5000;
+ double _maxmin_threshold = 3000;
+ double _minmax_threshold = 5000;
unsigned int _smoothing_half_window = 1;
};
@@ -50,7 +53,7 @@ class ZivyWidget: public QWidget
public:
explicit ZivyWidget(QWidget * parent = 0);
- ~ZivyWidget();
+ virtual ~ZivyWidget();
void setZivyParams(const ZivyParams & params);
diff --git a/src/gui/xic_view/xic_window.ui b/src/gui/xic_view/xic_window.ui
index 6f01750e3f92edfae081c50177fc7b7bc4c1e018..725bbd06d255a1723c6458f0b3b4ca0dfe7d92ad 100644
--- a/src/gui/xic_view/xic_window.ui
+++ b/src/gui/xic_view/xic_window.ui
@@ -66,6 +66,13 @@
</attribute>
</widget>
</item>
+ <item>
+ <widget class="QPushButton" name="edit_zivy_params_pushbutton">
+ <property name="text">
+ <string>Edit</string>
+ </property>
+ </widget>
+ </item>
<item>
<spacer name="horizontalSpacer">
<property name="orientation">
@@ -93,7 +100,7 @@
<x>0</x>
<y>0</y>
<width>780</width>
- <height>498</height>
+ <height>496</height>
</rect>
</property>
<layout class="QVBoxLayout" name="verticalLayout"/>
@@ -159,10 +166,27 @@
</hint>
</hints>
</connection>
+ <connection>
+ <sender>edit_zivy_params_pushbutton</sender>
+ <signal>clicked()</signal>
+ <receiver>XicWindow</receiver>
+ <slot>doEditZivyParams()</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>351</x>
+ <y>38</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>918</x>
+ <y>77</y>
+ </hint>
+ </hints>
+ </connection>
</connections>
<slots>
<slot>xicPrecisionChanged(pappso::PrecisionP)</slot>
<slot>rtUnitChanged(QAbstractButton*)</slot>
+ <slot>doEditZivyParams()</slot>
</slots>
<buttongroups>
<buttongroup name="rt_unit_buttongroup"/>
diff --git a/src/gui/xic_view/xicwindow.cpp b/src/gui/xic_view/xicwindow.cpp
index 1a4046aaaf6686ae48573d555cc8b4da0abcc5b8..e19f78de5aeeda06d4ca81bae22f1acec5d82d09 100644
--- a/src/gui/xic_view/xicwindow.cpp
+++ b/src/gui/xic_view/xicwindow.cpp
@@ -45,12 +45,23 @@ XicWindow::XicWindow(ProjectWindow *parent):
ui->xic_precision->setPrecision(pappso::Precision::fromString(precision_str));
- _detect_zivy.setSmoothingHalfEdgeWindows(settings.value("xic/zivy_smoothing", "1").toInt());
- _detect_zivy.setMinMaxHalfEdgeWindows(settings.value("xic/zivy_minmax_half_window", "4").toInt());
- _detect_zivy.setMaxMinHalfEdgeWindows(settings.value("xic/zivy_maxmin_half_window", "2").toInt());
- _detect_zivy.setDetectionThresholdOnMinmax(settings.value("xic/zivy_minmax_threshold", "50000").toDouble());
- _detect_zivy.setDetectionThresholdOnMaxmin(settings.value("xic/zivy_maxmin_threshold", "30000").toDouble());
+ 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.setDetectionParameters(&_detect_zivy);
+
+ _p_zivy_dialog = new ZivyDialog(this);
+ _p_zivy_dialog->setZivyParams(zivy_params);
+
+
+
+ connect(_p_zivy_dialog, &ZivyDialog::accepted, this, &XicWindow::doAcceptedZivyDialog);
#if QT_VERSION >= 0x050000
// Qt5 code
@@ -65,6 +76,11 @@ XicWindow::XicWindow(ProjectWindow *parent):
XicWindow::~XicWindow()
{
qDebug() << "XicWindow::~XicWindow";
+ delete _p_zivy_dialog;
+}
+
+void XicWindow::doEditZivyParams() {
+ _p_zivy_dialog->show();
}
void XicWindow::clear() {
@@ -124,3 +140,9 @@ bool XicWindow::isRetentionTimeSeconds() const {
}
return false;
}
+
+void XicWindow::doAcceptedZivyDialog() {
+ _p_zivy_dialog->getZivyParams().setDetectionParameters(&_detect_zivy);
+ emit reExtractXicNeeded();
+
+}
diff --git a/src/gui/xic_view/xicwindow.h b/src/gui/xic_view/xicwindow.h
index 6d0bd3d76f9fab7867aba3bf7c1fb48c69619d62..47e30679690f753e5667c7f2ce043e60cab18a49 100644
--- a/src/gui/xic_view/xicwindow.h
+++ b/src/gui/xic_view/xicwindow.h
@@ -35,6 +35,7 @@
#include <pappsomspp/xic/detection/xicdetectionzivy.h>
#include "../../core/peptideevidence.h"
+#include "xic_widgets/zivydialog.h"
class ProjectWindow;
@@ -66,6 +67,10 @@ public slots:
void xicPrecisionChanged(pappso::PrecisionP precision);
void rtUnitChanged(QAbstractButton* button);
+ protected slots :
+ void doEditZivyParams();
+ void doAcceptedZivyDialog();
+
signals :
void reExtractXicNeeded();
void rtUnitChangeNeeded();
@@ -82,6 +87,9 @@ private:
Ui::XicWindow *ui;
pappso::XicDetectionZivy _detect_zivy;
+
+
+ ZivyDialog * _p_zivy_dialog;
};
#endif // XICWINDOW_H