diff --git a/src/core/mcqr/mcqrexperiment.cpp b/src/core/mcqr/mcqrexperiment.cpp
index 4443aa516bf4df9a41c32618c4a37e1c8989bb95..479825014e542c54ac4e864bc2fe25a1d8b583b6 100644
--- a/src/core/mcqr/mcqrexperiment.cpp
+++ b/src/core/mcqr/mcqrexperiment.cpp
@@ -152,3 +152,27 @@ McqrExperiment::getMetadataOdsFilePath() const
{
return m_metadataOdsFilePath;
}
+
+void
+McqrExperiment::setMcqrWorkingDirectory(const QString &wd)
+{
+ m_mcqrWorkingDirectoryPath = wd;
+}
+
+const QString &
+McqrExperiment::getMcqrWorkingDirectory() const
+{
+ return m_mcqrWorkingDirectoryPath;
+}
+
+McqrExperimentType
+McqrExperiment::getMcqrExperimentType() const
+{
+ return m_mcqrExperimentType;
+}
+
+void
+McqrExperiment::setMcqrExperimentType(McqrExperimentType exp_type)
+{
+ m_mcqrExperimentType = exp_type;
+}
diff --git a/src/core/mcqr/mcqrexperiment.h b/src/core/mcqr/mcqrexperiment.h
index 39ffb1fb8bf9c4381466655298289296082d47f0..111cf3bdf3c38ae5914787b5802bfa165cf8a012 100644
--- a/src/core/mcqr/mcqrexperiment.h
+++ b/src/core/mcqr/mcqrexperiment.h
@@ -60,6 +60,8 @@ class McqrExperiment
McqrLoadDataMode getMcqrLoadDataMode() const;
+ void setMcqrWorkingDirectory(const QString &wd);
+ const QString &getMcqrWorkingDirectory() const;
void setRdataFilePath(const QString &rdata_file);
const QString &getRdataFilePath() const;
@@ -69,6 +71,10 @@ class McqrExperiment
QString getMassChroqMlFilePath() const;
+
+ McqrExperimentType getMcqrExperimentType() const;
+ void setMcqrExperimentType(McqrExperimentType exp_type);
+
private:
std::vector<McqrMetadata *> m_metadataList;
std::vector<QString> m_metadataColumns;
@@ -77,4 +83,6 @@ class McqrExperiment
QString m_rdata_absolute_path;
QString m_metadataOdsFilePath;
+ QString m_mcqrWorkingDirectoryPath;
+ McqrExperimentType m_mcqrExperimentType;
};
diff --git a/src/gui/mainwindow.cpp b/src/gui/mainwindow.cpp
index 7430a35c203214b147e4cbdf4a1b393800812f98..026fcf853fb35675c1316459773f95b7bb6db07e 100644
--- a/src/gui/mainwindow.cpp
+++ b/src/gui/mainwindow.cpp
@@ -884,21 +884,26 @@ MainWindow::doAcceptedMcqrParamAllQuantiDialog()
try
{
QSettings settings;
+ McqrExperimentSp mcqr_experiment =
+ _project_sp.get()->getMcqrExperimentSp();
+ mcqr_experiment.get()->setMcqrExperimentType(
+ McqrExperimentType::spectralCount);
if(mp_mcqrParamAllQuantiDialog->getMassChroqResultsUsed())
{ // XIC
+
+ mcqr_experiment.get()->setMcqrExperimentType(McqrExperimentType::xic);
if(mp_mcqrParamAllQuantiDialog->getMcqrRunStatus())
{
- _project_sp.get()
- ->getMcqrExperimentSp()
- .get()
- ->setMetadataOdsFilePath(
- mp_mcqrParamAllQuantiDialog->getMetadataOdsFileInfo()
- .absoluteFilePath());
+ mcqr_experiment.get()->setMetadataOdsFilePath(
+ mp_mcqrParamAllQuantiDialog->getMetadataOdsFileInfo()
+ .absoluteFilePath());
+ mcqr_experiment.get()->setMcqrWorkingDirectory(
+ mp_mcqrParamAllQuantiDialog->getMetadataOdsFileInfo()
+ .absolutePath());
- mp_mcqrRunView = new McqrRunView(
- this, _project_sp.get()->getMcqrExperimentSp(), true);
+ mp_mcqrRunView = new McqrRunView(this, mcqr_experiment);
mp_mcqrRunView->show();
mp_mcqrRunView->raise();
mp_mcqrRunView->activateWindow();
@@ -907,8 +912,6 @@ MainWindow::doAcceptedMcqrParamAllQuantiDialog()
}
else
{ // spectral count
- McqrExperimentSp mcqr_experiment =
- _project_sp.get()->getMcqrExperimentSp();
QString default_location =
settings.value("mcqr/rdata_path").toString();
QString rdata_path =
@@ -925,6 +928,9 @@ MainWindow::doAcceptedMcqrParamAllQuantiDialog()
mcqr_experiment.get()->setRdataFilePath(
QFileInfo(rdata_path).absoluteFilePath());
+
+ mcqr_experiment.get()->setMcqrWorkingDirectory(
+ QFileInfo(rdata_path).absolutePath());
showWaitingMessage(tr("Writing %1 RData file").arg(rdata_path));
settings.setValue("mcqr/rdata_path",
mcqr_experiment.get()->getRdataFilePath());
@@ -949,7 +955,7 @@ MainWindow::doWritingMcqrSpectralCountRdataFinished(
hideWaitingMessage();
if(mp_mcqrParamAllQuantiDialog->getMcqrRunStatus())
{
- mp_mcqrRunView = new McqrRunView(this, p_mcqr_experiment, false);
+ mp_mcqrRunView = new McqrRunView(this, p_mcqr_experiment);
mp_mcqrRunView->show();
mp_mcqrRunView->raise();
mp_mcqrRunView->activateWindow();
diff --git a/src/gui/mcqr_run_view/mcqr_sds_xic_widget/mcqrsdsxicwidget.cpp b/src/gui/mcqr_run_view/mcqr_sds_xic_widget/mcqrsdsxicwidget.cpp
index 6bf7c06b6a4c59cf3df0b3e9281179f0308a22d6..2bee59034a2850e07004fcb9a19d143df33b3cba 100644
--- a/src/gui/mcqr_run_view/mcqr_sds_xic_widget/mcqrsdsxicwidget.cpp
+++ b/src/gui/mcqr_run_view/mcqr_sds_xic_widget/mcqrsdsxicwidget.cpp
@@ -336,9 +336,8 @@ McqrSdsXicWidget::runQualityCheckingXic()
Grantlee::Context grantlee_context;
grantlee_context.insert("mcqr_step", (std::int8_t)m_ongoingMcqrStep);
grantlee_context.insert(
- "rdata_folder",
- QFileInfo(getMcqrExperimentSpLoaded().get()->getMetadataOdsFilePath())
- .absoluteDir()
+ "mcqr_working_directory",
+ QDir(getMcqrExperimentSpLoaded().get()->getMcqrWorkingDirectory())
.path());
grantlee_context.insert(
"metadata_ods_path",
diff --git a/src/gui/mcqr_run_view/mcqrrunview.cpp b/src/gui/mcqr_run_view/mcqrrunview.cpp
index d1104987783186e8da05f117e3c79ae409c08679..4afc0d433eef40203d2a7f2c26bdd707e3dd8249 100644
--- a/src/gui/mcqr_run_view/mcqrrunview.cpp
+++ b/src/gui/mcqr_run_view/mcqrrunview.cpp
@@ -48,18 +48,17 @@
McqrRunView::McqrRunView(MainWindow *parent,
- const McqrExperimentSp &p_mcqr_experiment,
- bool use_masschroq_results)
+ const McqrExperimentSp &p_mcqr_experiment)
: QWidget(), ui(new Ui::McqrRunView)
{
ui->setupUi(this);
+ msp_mcqrExperiment = p_mcqr_experiment;
setWindowTitle("MCQR run window");
mp_main = parent;
// Create the output page
mp_documentText = new QTextDocument();
ui->mcqr_result_browser->setDocument(mp_documentText);
- m_useMassChroqResults = use_masschroq_results;
- loadSpecificMcqrParameterWidget(p_mcqr_experiment);
+ loadSpecificMcqrParameterWidget();
// Set the Loading icon
mp_loadingIcon = new QMovie(":icons/resources/icons/icon_wait.gif");
@@ -164,16 +163,16 @@ McqrRunView::endRProcess()
}
void
-McqrRunView::loadSpecificMcqrParameterWidget(
- const McqrExperimentSp &p_mcqr_experiment)
+McqrRunView::loadSpecificMcqrParameterWidget()
{
- if(m_useMassChroqResults)
+ if(msp_mcqrExperiment.get()->getMcqrExperimentType() ==
+ McqrExperimentType::xic)
{
- mp_mcqrParam = new McqrSdsXicWidget(this, p_mcqr_experiment);
+ mp_mcqrParam = new McqrSdsXicWidget(this, msp_mcqrExperiment);
}
else
{
- mp_mcqrParam = new McqrSdsWidget(this, p_mcqr_experiment);
+ mp_mcqrParam = new McqrSdsWidget(this, msp_mcqrExperiment);
}
ui->mcqr_param_layout->addWidget(mp_mcqrParam);
}
diff --git a/src/gui/mcqr_run_view/mcqrrunview.h b/src/gui/mcqr_run_view/mcqrrunview.h
index 0aac4a8729d7addb5a8fbb0e2979c82b8507b33d..6513b9905fffc1072c4a6174a1fcb93dc473ab2d 100644
--- a/src/gui/mcqr_run_view/mcqrrunview.h
+++ b/src/gui/mcqr_run_view/mcqrrunview.h
@@ -54,8 +54,7 @@ class McqrRunView : public QWidget
public:
explicit McqrRunView(MainWindow *parent,
- const McqrExperimentSp &p_mcqr_experiment,
- bool use_masschroq_results);
+ const McqrExperimentSp &p_mcqr_experiment);
~McqrRunView();
McqrQProcess *getRProcessRunning();
@@ -77,16 +76,15 @@ class McqrRunView : public QWidget
void startRProcess();
void endRProcess();
void checkLibrariesInstalled();
- void
- loadSpecificMcqrParameterWidget(const McqrExperimentSp &p_mcqr_experiment);
+ void loadSpecificMcqrParameterWidget();
void handleMcqrErrors(QString error_message);
private:
Ui::McqrRunView *ui;
MainWindow *mp_main = nullptr;
- bool m_useMassChroqResults = false;
McqrParamWidget *mp_mcqrParam = nullptr;
QMovie *mp_loadingIcon = nullptr;
McqrQProcess *mp_rProcess = nullptr;
QTextDocument *mp_documentText = nullptr;
+ McqrExperimentSp msp_mcqrExperiment;
};
diff --git a/src/resources/templates/mcqr_scripts/mcqr_basic_xic_analysis.R b/src/resources/templates/mcqr_scripts/mcqr_basic_xic_analysis.R
index c6f40eadd995b2a5170f8ec79cd35fc6e56a3fe8..c33b34e3ad02f94f57190cfd5c3a8e0f60a78b3a 100644
--- a/src/resources/templates/mcqr_scripts/mcqr_basic_xic_analysis.R
+++ b/src/resources/templates/mcqr_scripts/mcqr_basic_xic_analysis.R
@@ -2,7 +2,7 @@
message("MCQRBegin: quality_xic")
cat("<h1>MCQR basic XIC Analysis</h1>")
- setwd("{{ rdata_folder }}")
+ setwd("{{ mcqr_working_directory }}")
cat(paste("working directory: ", getwd()))
capture.output(library("MCQR", verbose=FALSE), file=stderr())
message(paste("MCQRInfo: MCQR version :", packageVersion("MCQR")))
diff --git a/src/utils/types.h b/src/utils/types.h
index 7bbb7e35d561ba2fd34d0817129670dd505df853..9430f08a0efc400782e4e5c285dd06f5270c8823 100644
--- a/src/utils/types.h
+++ b/src/utils/types.h
@@ -232,8 +232,18 @@ enum class PtmMode : std::int8_t
*/
enum class McqrLoadDataMode : std::int8_t
{
- basic = 0, ///< mcq.read.masschroq
+ basic = 0, ///< mcq.read.masschroq
fraction = 1, ///< mcq.read.masschroq.fraction
label = 2, ///< mcq.read.masschroq.label
both = 3, ///<
};
+
+
+/** \def McqrExperimentType spectral count, xic
+ *
+ */
+enum class McqrExperimentType : std::int8_t
+{
+ spectralCount = 0, ///< use xtpcpp data
+ xic = 1, ///< use masschroq results
+};