diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 963b3c0762f1d429f9004921af7a83e5b6cd5532..be9ef9b05802f364d47e6f4b1310b493a56a8292 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -200,6 +200,7 @@ SET(XTPCPP_SRCS
./gui/widgets/automatic_filter_widget/automaticfilterwidget.cpp
./gui/widgets/contaminant_widget/contaminantwidget.cpp
./gui/widgets/decoy_widget/decoywidget.cpp
+ ./gui/widgets/xic_extraction_method_widget/xicextractionmethodwidget.cpp
./gui/widgets/massitemdelegate.cpp
./gui/xic_view/xic_box/xicbox.cpp
./gui/xic_view/xic_widgets/zivydialog.cpp
diff --git a/src/gui/export/export_masschroq_dialog/export_masschroq_dialog.ui b/src/gui/export/export_masschroq_dialog/export_masschroq_dialog.ui
index e2cd178ab2951b2e2da9e5b5c32775e6743f8e4f..b128ffc4cd3c9d2515f643c02ee459b8acc6f129 100644
--- a/src/gui/export/export_masschroq_dialog/export_masschroq_dialog.ui
+++ b/src/gui/export/export_masschroq_dialog/export_masschroq_dialog.ui
@@ -309,18 +309,7 @@
</widget>
</item>
<item>
- <widget class="QComboBox" name="sumMaxComboBox">
- <item>
- <property name="text">
- <string>max</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>sum</string>
- </property>
- </item>
- </widget>
+ <widget class="XicExtractionMethodWidget" name="xic_extraction_method_widget" native="true"/>
</item>
</layout>
</item>
@@ -402,6 +391,12 @@
<header>pappsomspp/widget/precisionwidget/precisionwidget.h</header>
<container>1</container>
</customwidget>
+ <customwidget>
+ <class>XicExtractionMethodWidget</class>
+ <extends>QWidget</extends>
+ <header>gui/widgets/xic_extraction_method_widget/xicextractionmethodwidget.h</header>
+ <container>1</container>
+ </customwidget>
</customwidgets>
<resources/>
<connections>
diff --git a/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp b/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp
index d45c1b9b80623b096aec0969b4b219dd694b806b..173012735187f985464a248b718edbd9546ace32 100644
--- a/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp
+++ b/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp
@@ -104,8 +104,6 @@ ExportMasschroqDialog::setMasschroqFileParameters(
ui->ms1SmoothingSpinBox->setValue(params.ms1_smoothing_half_window);
ui->xicRangeWidget->setPrecision(params.xic_extraction_range);
-
- ui->sumMaxComboBox->setCurrentText(params.xic_extraction_method);
}
@@ -139,7 +137,7 @@ ExportMasschroqDialog::getMasschroqFileParameters() const
params.xic_extraction_range = ui->xicRangeWidget->getPrecision();
- params.xic_extraction_method = ui->sumMaxComboBox->currentText();
+ params.xic_extraction_method = ui->xic_extraction_method_widget->getXicExtractionMethod();
return params;
}
diff --git a/src/gui/export/export_masschroq_dialog/masschroqfileparameters.cpp b/src/gui/export/export_masschroq_dialog/masschroqfileparameters.cpp
index e8e28f2f061ff031d49c6e469e9b2573cfd84532..44d8380c8c50f511cc446e3f207542e8e47a4dfc 100644
--- a/src/gui/export/export_masschroq_dialog/masschroqfileparameters.cpp
+++ b/src/gui/export/export_masschroq_dialog/masschroqfileparameters.cpp
@@ -67,7 +67,7 @@ MasschroqFileParameters::save() const
xic_extraction_range->toString());
settings.setValue("export_masschroqml/xic_extraction_method",
- xic_extraction_method);
+ QString("%1").arg((std::uint8_t)xic_extraction_method));
}
void
MasschroqFileParameters::load()
@@ -124,7 +124,9 @@ MasschroqFileParameters::load()
settings.value("export_masschroqml/xic_extraction_range", "10 ppm")
.toString());
+ /*
xic_extraction_method =
settings.value("export_masschroqml/xic_extraction_method", "max")
.toString();
+ */
}
diff --git a/src/gui/export/export_masschroq_dialog/masschroqfileparameters.h b/src/gui/export/export_masschroq_dialog/masschroqfileparameters.h
index a4dda270b07ef9f8b5842a889fbc64e86a3cc2d6..4badb5b79650e60c2fdbecb594a0c8139d37fae8 100644
--- a/src/gui/export/export_masschroq_dialog/masschroqfileparameters.h
+++ b/src/gui/export/export_masschroq_dialog/masschroqfileparameters.h
@@ -58,5 +58,5 @@ struct MasschroqFileParameters
pappso::PrecisionPtr xic_extraction_range;
- QString xic_extraction_method; // sum or max
+ pappso::XicExtractMethod xic_extraction_method; // sum or max
};
diff --git a/src/gui/widgets/xic_extraction_method_widget/xicextractionmethodwidget.cpp b/src/gui/widgets/xic_extraction_method_widget/xicextractionmethodwidget.cpp
index d5d38d803680ca454f3269e68646aa8849f1b4f0..dde03a391c127b4fa190a5d7358fb228dba56284 100644
--- a/src/gui/widgets/xic_extraction_method_widget/xicextractionmethodwidget.cpp
+++ b/src/gui/widgets/xic_extraction_method_widget/xicextractionmethodwidget.cpp
@@ -31,6 +31,7 @@
#include "xicextractionmethodwidget.h"
#include <QDebug>
#include <QHBoxLayout>
+#include <QSettings>
XicExtractionMethodWidget::XicExtractionMethodWidget(QWidget *parent)
: QWidget(parent)
@@ -47,6 +48,16 @@ XicExtractionMethodWidget::XicExtractionMethodWidget(QWidget *parent)
mp_methodComboBox->addItem("max", QString("max"));
mp_methodComboBox->addItem("sum", QString("sum"));
+ QSettings settings;
+
+ m_oldMethod =
+ (pappso::XicExtractMethod)settings
+ .value("xic/xic_extraction_method",
+ QString("%1").arg((std::uint8_t)pappso::XicExtractMethod::max))
+ .toUInt();
+
+ mp_methodComboBox->setCurrentIndex((std::uint8_t)m_oldMethod);
+
connect(mp_methodComboBox,
SIGNAL(currentIndexChanged(int)),
this,
@@ -64,18 +75,21 @@ void
XicExtractionMethodWidget::setCurrentIndex(int index)
{
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ pappso::XicExtractMethod new_method = (pappso::XicExtractMethod)index;
- if(m_oldIndex != index)
+ if(m_oldMethod != new_method)
{
- m_oldIndex = index;
-
- if(mp_methodComboBox->itemData(index) == "sum")
- {
- emit xicExtractionMethodChanged(pappso::XicExtractMethod::sum);
- }
- else
- {
- emit xicExtractionMethodChanged(pappso::XicExtractMethod::max);
- }
+ m_oldMethod = new_method;
+ QSettings settings;
+ settings.setValue("xic/xic_extraction_method",
+ QString("%1").arg((std::uint8_t)new_method));
+ emit xicExtractionMethodChanged(new_method);
}
}
+
+
+pappso::XicExtractMethod
+XicExtractionMethodWidget::getXicExtractionMethod() const
+{
+ return m_oldMethod;
+}
diff --git a/src/gui/widgets/xic_extraction_method_widget/xicextractionmethodwidget.h b/src/gui/widgets/xic_extraction_method_widget/xicextractionmethodwidget.h
index 3deb3496a55b5b5ccf0e2f7abdfe735b737a56e2..962543d9c2a4291d02e5ded2689c37a97640b9b7 100644
--- a/src/gui/widgets/xic_extraction_method_widget/xicextractionmethodwidget.h
+++ b/src/gui/widgets/xic_extraction_method_widget/xicextractionmethodwidget.h
@@ -40,7 +40,7 @@ class XicExtractionMethodWidget : public QWidget
private:
QComboBox *mp_methodComboBox;
- int m_oldIndex = 0;
+ pappso::XicExtractMethod m_oldMethod = pappso::XicExtractMethod::max;
private:
Q_SLOT void setCurrentIndex(int);
@@ -48,6 +48,8 @@ class XicExtractionMethodWidget : public QWidget
public:
XicExtractionMethodWidget(QWidget *parent = 0);
~XicExtractionMethodWidget();
+ pappso::XicExtractMethod getXicExtractionMethod() const;
+
signals:
void xicExtractionMethodChanged(pappso::XicExtractMethod method) const;
};
diff --git a/src/gui/xic_view/xic_box/xicbox.cpp b/src/gui/xic_view/xic_box/xicbox.cpp
index efd25ee93eb1659e0e898b0c66b6364e28693592..72086bc3f492b6cd7ed4a4d85503968ccbad9d7a 100644
--- a/src/gui/xic_view/xic_box/xicbox.cpp
+++ b/src/gui/xic_view/xic_box/xicbox.cpp
@@ -571,7 +571,7 @@ XicBox::reExtractXic()
xic_isotope.peptide_natural_isotope_sp.get()->getMz());
}
emit loadXic(_msrun_sp, mass_list, _p_xic_window->getXicExtractPrecision(),
- pappso::XicExtractMethod::max);
+ _p_xic_window->getXicExtractionMethod());
qDebug() << "XicBox::reExtractXic end";
}
diff --git a/src/gui/xic_view/xic_window.ui b/src/gui/xic_view/xic_window.ui
index b1ae1e260294942ba1fa90f624408b2fc643d2bf..f1ffb29e6adc084ff8539d5298411424889f0434 100644
--- a/src/gui/xic_view/xic_window.ui
+++ b/src/gui/xic_view/xic_window.ui
@@ -43,6 +43,9 @@
<item>
<widget class="pappso::PrecisionWidget" name="xic_precision" native="true"/>
</item>
+ <item>
+ <widget class="XicExtractionMethodWidget" name="xic_extraction_method_widget" native="true"/>
+ </item>
<item>
<widget class="QRadioButton" name="rt_sec_radiobutton">
<property name="text">
@@ -131,6 +134,15 @@
<signal>precisionChanged(pappso::PrecisionPtr)</signal>
</slots>
</customwidget>
+ <customwidget>
+ <class>XicExtractionMethodWidget</class>
+ <extends>QWidget</extends>
+ <header>gui/widgets/xic_extraction_method_widget/xicextractionmethodwidget.h</header>
+ <container>1</container>
+ <slots>
+ <signal>xicExtractionMethodChanged(pappso::XicExtractMethod)</signal>
+ </slots>
+ </customwidget>
</customwidgets>
<resources/>
<connections>
@@ -173,8 +185,8 @@
<slot>doEditZivyParams()</slot>
<hints>
<hint type="sourcelabel">
- <x>351</x>
- <y>38</y>
+ <x>408</x>
+ <y>61</y>
</hint>
<hint type="destinationlabel">
<x>918</x>
@@ -182,11 +194,28 @@
</hint>
</hints>
</connection>
+ <connection>
+ <sender>xic_extraction_method_widget</sender>
+ <signal>xicExtractionMethodChanged(pappso::XicExtractMethod)</signal>
+ <receiver>XicWindow</receiver>
+ <slot>doXicExtractionMethodChanged(pappso::XicExtractMethod)</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>100</x>
+ <y>44</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>210</x>
+ <y>-25</y>
+ </hint>
+ </hints>
+ </connection>
</connections>
<slots>
<slot>xicPrecisionChanged(pappso::PrecisionPtr)</slot>
<slot>rtUnitChanged(QAbstractButton*)</slot>
<slot>doEditZivyParams()</slot>
+ <slot>doXicExtractionMethodChanged(pappso::XicExtractMethod)</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 51cf71c93d8eac0263b6f46f10410aee5c677d24..165ae9fcc03b10de6d9b72a3fa4193c21896ec58 100644
--- a/src/gui/xic_view/xicwindow.cpp
+++ b/src/gui/xic_view/xicwindow.cpp
@@ -46,7 +46,6 @@ XicWindow::XicWindow(ProjectWindow *parent)
ui->xic_precision->setPrecision(
pappso::PrecisionFactory::fromString(precision_str));
-
ZivyParams zivy_params;
zivy_params.loadSettings();
@@ -57,7 +56,9 @@ XicWindow::XicWindow(ProjectWindow *parent)
_p_zivy_dialog->setZivyParams(zivy_params);
- connect(_p_zivy_dialog, &ZivyDialog::accepted, this,
+ connect(_p_zivy_dialog,
+ &ZivyDialog::accepted,
+ this,
&XicWindow::doAcceptedZivyDialog);
#if QT_VERSION >= 0x050000
@@ -128,6 +129,14 @@ XicWindow::getXicExtractPrecision() const
return (ui->xic_precision->getPrecision());
}
+
+pappso::XicExtractMethod
+XicWindow::getXicExtractionMethod() const
+{
+ return (ui->xic_extraction_method_widget->getXicExtractionMethod());
+}
+
+
void
XicWindow::xicPrecisionChanged(pappso::PrecisionPtr precision)
{
@@ -169,3 +178,10 @@ XicWindow::doAcceptedZivyDialog()
_p_zivy_dialog->getZivyParams().saveSettings();
emit reExtractXicNeeded();
}
+
+
+void
+XicWindow::doXicExtractionMethodChanged(pappso::XicExtractMethod xic_method)
+{
+ emit reExtractXicNeeded();
+}
diff --git a/src/gui/xic_view/xicwindow.h b/src/gui/xic_view/xicwindow.h
index 22d49a1c2ca3cedb4b2e1d27c651d5326cb5500f..362d3913148fa9025b1beba183132c0b034854a6 100644
--- a/src/gui/xic_view/xicwindow.h
+++ b/src/gui/xic_view/xicwindow.h
@@ -43,7 +43,7 @@ class ProjectWindow;
namespace Ui
{
- class XicWindow;
+class XicWindow;
}
class XicBox;
@@ -62,6 +62,7 @@ class XicWindow : public QMainWindow
MsRunSp msrun_sp);
pappso::PrecisionPtr getXicExtractPrecision() const;
+ pappso::XicExtractMethod getXicExtractionMethod() const;
bool isRetentionTimeSeconds() const;
@@ -73,6 +74,7 @@ class XicWindow : public QMainWindow
protected slots:
void doEditZivyParams();
void doAcceptedZivyDialog();
+ void doXicExtractionMethodChanged(pappso::XicExtractMethod xic_method);
signals:
void reExtractXicNeeded();
diff --git a/src/output/masschroqml.cpp b/src/output/masschroqml.cpp
index 1b0a9e404e1abd58b35c42d2977e8c293d6a0f4c..bf89e8d2ddac0f75605e12d0c196a31d8efe02fc 100644
--- a/src/output/masschroqml.cpp
+++ b/src/output/masschroqml.cpp
@@ -231,8 +231,9 @@ MassChroQml::writeQuantificationTraces()
_output_stream->writeStartElement("quantification_traces");
//<peptide_traces peptide_ids="pep0 pep1" output_dir="pep_traces"
// format="tsv" />
- _output_stream->writeComment("<peptide_traces peptide_ids=\"pep0 pep1\" "
- "output_dir=\"pep_traces\" format=\"tsv\" />");
+ _output_stream->writeComment(
+ "<peptide_traces peptide_ids=\"pep0 pep1\" "
+ "output_dir=\"pep_traces\" format=\"tsv\" />");
/*
<all_xics_traces output_dir="all_xics_traces" format="tsv" />
<mz_traces mz_values="634.635 449.754 552.234" output_dir="mz_traces"
@@ -277,8 +278,9 @@ MassChroQml::writeQuantify()
}
_output_stream->writeEndElement();
- _output_stream->writeComment("<mz_list>732.317 449.754 552.234 464.251 "
- "381.577 569.771 575.256</mz_list>");
+ _output_stream->writeComment(
+ "<mz_list>732.317 449.754 552.234 464.251 "
+ "381.577 569.771 575.256</mz_list>");
_output_stream->writeComment(
"<mzrt_list>\n <mzrt mz=\"732.317\" rt=\"230.712\" />\n <mzrt "
"mz=\"575.256\" rt=\"254.788\" />\n </mzrt_list>");
@@ -297,7 +299,14 @@ MassChroQml::writeQuantificationMethods()
_output_stream->writeAttribute("id", "quant1");
//<xic_extraction xic_type="sum">
_output_stream->writeStartElement("xic_extraction");
- _output_stream->writeAttribute("xic_type", m_params.xic_extraction_method);
+ if(m_params.xic_extraction_method == pappso::XicExtractMethod::max)
+ {
+ _output_stream->writeAttribute("xic_type", "max");
+ }
+ else
+ {
+ _output_stream->writeAttribute("xic_type", "sum");
+ }
_output_stream->writeComment("max : XIC on BasePeak; sum : XIC on TIC");
//<ppm_range min="10" max="10"/><!--For XIC extraction on Da use: mz_range-->
@@ -503,7 +512,8 @@ MassChroQml::writePeptideListInGroup(const GroupingGroup *p_group)
}
// sort list
- std::sort(mcq_peptide_list.begin(), mcq_peptide_list.end(),
+ std::sort(mcq_peptide_list.begin(),
+ mcq_peptide_list.end(),
[](const McqPeptide &first, const McqPeptide &second) {
return (first.id < second.id);
});
@@ -589,7 +599,8 @@ MassChroQml::writePeptideListInGroup(const GroupingGroup *p_group)
}
//<observed_in data="samp0" scan="655" z="2" />
- std::sort(mcq_peptide.observed_in.begin(), mcq_peptide.observed_in.end(),
+ std::sort(mcq_peptide.observed_in.begin(),
+ mcq_peptide.observed_in.end(),
[](const McqObserved &first, const McqObserved &second) {
return std::tie(first.charge, first.scan, first.msrun) <
std::tie(second.charge, second.scan, second.msrun);