diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 577012f0fa3e870a32a0b58e58a27e9290701396..6e3c1b18b089ed3a262af140452a0351ab4ed78d 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -73,6 +73,7 @@ set(CPP_FILES
core/labeling/labelingmethod.cpp
core/masschroq_run/masschroqbatchprocess.cpp
core/masschroq_run/masschroqcondorprocess.cpp
+ core/masschroq_run/masschroqfileparameters.cpp
core/mcqr/mcqrexperiment.cpp
core/qvalue/computeqvalues.cpp
core/tandem_run/tandembatchprocess.cpp
@@ -177,7 +178,6 @@ set(XTPCPP_SRCS
./gui/lists/ms_identification_run_list_view/ms_identification_worker/msidlistworkerstatus.cpp
./gui/lists/ms_identification_run_list_view/engine_detail_view/enginedetailwindow.cpp
./gui/masschroq_run_dialog/masschroqrundialog.cpp
- ./gui/masschroq_run_dialog/masschroqfileparameters.cpp
./gui/mcqr_param_dialog/mcqrparamallquantidialog.cpp
./gui/mcqr_run_view/mcqrparamwidget.cpp
./gui/mcqr_run_view/mcqrrunview.cpp
diff --git a/src/core/alignmentgroup.cpp b/src/core/alignmentgroup.cpp
index 45a8b9319d446aedf53325e9c1970c186db466c6..175d2b34b49ba421b4a4af3c1ec4cef7235b61e4 100644
--- a/src/core/alignmentgroup.cpp
+++ b/src/core/alignmentgroup.cpp
@@ -175,14 +175,9 @@ MsRunAlignmentGroup::prepareMsrunRetentionTimesForAlignment() const
}
void
-MsRunAlignmentGroup::savePostMassChroqmlParameters(
- MasschroqFileParameters file_parameters,
- ZivyParams zivy_params,
- QString masschroqml_file)
+MsRunAlignmentGroup::savePostMassChroqmlParameters(QString masschroqml_file)
{
- m_masschroqFileParameters = file_parameters;
- m_zivyParams = zivy_params;
- m_masschroqmlPath = masschroqml_file;
+ m_masschroqmlPath = masschroqml_file;
}
void
@@ -203,11 +198,6 @@ MsRunAlignmentGroup::getGroupStatus()
return m_status;
}
-MasschroqFileParameters
-MsRunAlignmentGroup::getMassChroQFileParams()
-{
- return m_masschroqFileParameters;
-}
QString
MsRunAlignmentGroup::getMassChroqmlPath()
@@ -215,17 +205,6 @@ MsRunAlignmentGroup::getMassChroqmlPath()
return m_masschroqmlPath;
}
-ZivyParams
-MsRunAlignmentGroup::getZivyParams()
-{
- return m_zivyParams;
-}
-
-void
-MsRunAlignmentGroup::setMassChroQFileParams(MasschroqFileParameters mcq_params)
-{
- m_masschroqFileParameters = mcq_params;
-}
void
MsRunAlignmentGroup::setMassChroqmlPath(QString masschroqml_path)
@@ -233,11 +212,6 @@ MsRunAlignmentGroup::setMassChroqmlPath(QString masschroqml_path)
m_masschroqmlPath = masschroqml_path;
}
-void
-MsRunAlignmentGroup::setZivyParams(ZivyParams zivy_params)
-{
- m_zivyParams = zivy_params;
-}
QString
MsRunAlignmentGroup::getMassChroqmlRdataPath() const
diff --git a/src/core/alignmentgroup.h b/src/core/alignmentgroup.h
index a7b7fa11097e1497743856c9bb9fb652a510a455..c1dec0ab6c3c0053177622d7b11a0b836cf085a9 100644
--- a/src/core/alignmentgroup.h
+++ b/src/core/alignmentgroup.h
@@ -25,9 +25,8 @@
#include <QDebug>
#include <memory>
#include "msrun.h"
-// #include "project.h"
-#include "../gui/masschroq_run_dialog/masschroqfileparameters.h"
#include "../gui/xic_view/xic_widgets/zivywidget.h"
+#include "masschroq_run/masschroqfileparameters.h"
enum class AlignmentGroupStatus : std::int8_t
{
@@ -61,17 +60,11 @@ class MsRunAlignmentGroup
void removeMsRunFromMsRunAlignmentGroupList(MsRunSp removed_msrun);
void prepareMsrunRetentionTimesForAlignment() const;
- void savePostMassChroqmlParameters(MasschroqFileParameters file_parameters,
- ZivyParams zivy_params,
- QString masschroqml_file);
+ void savePostMassChroqmlParameters(QString masschroqml_file);
void setMassChroQRunStatus(AlignmentGroupStatus status);
void setMassChroQRunStatusFromInt(int status);
AlignmentGroupStatus getGroupStatus();
- MasschroqFileParameters getMassChroQFileParams();
- ZivyParams getZivyParams();
QString getMassChroqmlPath();
- void setMassChroQFileParams(MasschroqFileParameters mcq_params);
- void setZivyParams(ZivyParams zivy_params);
void setMassChroqmlPath(QString masschroqml_path);
QString getMassChroqmlRdataPath() const;
@@ -85,7 +78,6 @@ class MsRunAlignmentGroup
// Post MassChroQ run params
AlignmentGroupStatus m_status;
- MasschroqFileParameters m_masschroqFileParameters;
- ZivyParams m_zivyParams;
+ MasschroqFileParametersSp msp_masschroqFileParametersSp;
QString m_masschroqmlPath;
};
diff --git a/src/gui/masschroq_run_dialog/masschroqfileparameters.cpp b/src/core/masschroq_run/masschroqfileparameters.cpp
similarity index 98%
rename from src/gui/masschroq_run_dialog/masschroqfileparameters.cpp
rename to src/core/masschroq_run/masschroqfileparameters.cpp
index 28e674212f007d6c1e7ba8f95b98bce09a413e23..b7549ecea45d4dacfda334621775b5c444c39609 100644
--- a/src/gui/masschroq_run_dialog/masschroqfileparameters.cpp
+++ b/src/core/masschroq_run/masschroqfileparameters.cpp
@@ -1,5 +1,5 @@
/**
- * \file gui/export/export_masschroq_dialog/masschroqfileparameters.cpp
+ * \file src/core/masschroq_run/masschroqfileparameters.cpp
* \date 25/01/2019
* \author Olivier Langella
* \brief all needed information to write a MassChroqML file
diff --git a/src/gui/masschroq_run_dialog/masschroqfileparameters.h b/src/core/masschroq_run/masschroqfileparameters.h
similarity index 80%
rename from src/gui/masschroq_run_dialog/masschroqfileparameters.h
rename to src/core/masschroq_run/masschroqfileparameters.h
index 9443f30a03235d80c1aa7920df76b243e1f83534..8be09382892459bcd20a6f5fdd0fe72f051fe3d8 100644
--- a/src/gui/masschroq_run_dialog/masschroqfileparameters.h
+++ b/src/core/masschroq_run/masschroqfileparameters.h
@@ -1,5 +1,5 @@
/**
- * \file gui/export/export_masschroq_dialog/masschroqfileparameters.h
+ * \file src/core/masschroq_run/masschroqfileparameters.h
* \date 25/01/2019
* \author Olivier Langella
* \brief all needed information to write a MassChroqML file
@@ -23,9 +23,6 @@
* 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
******************************************************************************/
#pragma once
@@ -34,11 +31,28 @@
#include <QString>
#include <pappsomspp/mzrange.h>
#include <pappsomspp/processing/filters/filtersuitestring.h>
+#include <pappsomspp/processing/detection/tracedetectionzivy.h>
#include "../../core/msrun.h"
class MasschroqFileParameters;
typedef std::shared_ptr<MasschroqFileParameters> MasschroqFileParametersSp;
+
+struct ZivyParams
+{
+ std::shared_ptr<pappso::TraceDetectionInterface>
+ newTraceDetectionZivySPtr() const;
+ void saveSettings() const;
+ void loadSettings();
+
+ unsigned int _maxmin_half_window = 3;
+ unsigned int _minmax_half_window = 2;
+ double _maxmin_threshold = 3000;
+ double _minmax_threshold = 5000;
+ unsigned int _smoothing_half_window = 1;
+};
+
+
struct MasschroqFileParameters
{
void save() const;
@@ -69,4 +83,6 @@ struct MasschroqFileParameters
pappso::FilterSuiteStringSPtr msp_xicFilterSuiteString;
std::vector<MsRunAlignmentGroupSp> alignment_groups;
+
+ ZivyParams m_zivyParams;
};
diff --git a/src/core/project.cpp b/src/core/project.cpp
index da3f3f59a96cd2e509ce8bcbdc372a48ab188e63..a3474556814256e3d3d2aab2ee4f1e4483a1a448 100644
--- a/src/core/project.cpp
+++ b/src/core/project.cpp
@@ -30,6 +30,8 @@
Project::Project()
{
msp_masschroqFileParametersSp = std::make_shared<MasschroqFileParameters>();
+ msp_masschroqFileParametersSp.get()->load();
+ msp_masschroqFileParametersSp.get()->m_zivyParams.loadSettings();
}
Project::~Project()
@@ -273,8 +275,8 @@ Project::startGrouping(WorkMonitorInterface *p_work_monitor)
qDebug();
for(IdentificationGroup *p_id_group : _identification_goup_list)
{
- p_id_group->startGrouping(m_contaminantRemovalMode, m_groupingType,
- p_work_monitor);
+ p_id_group->startGrouping(
+ m_contaminantRemovalMode, m_groupingType, p_work_monitor);
}
qDebug();
}
@@ -302,12 +304,14 @@ Project::hasPtmExperiment() const
void
Project::getSameXicPeptideEvidenceList(
std::vector<const PeptideEvidence *> &peptide_evidence_list,
- const MsRun *p_msrun, const PeptideXtp *p_peptide, unsigned int charge) const
+ const MsRun *p_msrun,
+ const PeptideXtp *p_peptide,
+ unsigned int charge) const
{
for(const IdentificationGroup *p_ident_group : _identification_goup_list)
{
- p_ident_group->getSameXicPeptideEvidenceList(peptide_evidence_list,
- p_msrun, p_peptide, charge);
+ p_ident_group->getSameXicPeptideEvidenceList(
+ peptide_evidence_list, p_msrun, p_peptide, charge);
}
}
diff --git a/src/core/project.h b/src/core/project.h
index 64b9299a99c10f14d681d8642a8734b7cd436b0a..f0fd181e469cea89861e2e6af1ca80d8258d6269 100644
--- a/src/core/project.h
+++ b/src/core/project.h
@@ -38,6 +38,7 @@
#include "labeling/labelingmethod.h"
#include "alignmentgroup.h"
#include "mcqr/mcqrexperiment.h"
+#include "masschroq_run/masschroqfileparameters.h"
class Project;
typedef std::shared_ptr<Project> ProjectSp;
@@ -208,7 +209,8 @@ class Project
*/
void getSameXicPeptideEvidenceList(
std::vector<const PeptideEvidence *> &peptide_evidence_list,
- const MsRun *p_msrun, const PeptideXtp *p_peptide,
+ const MsRun *p_msrun,
+ const PeptideXtp *p_peptide,
unsigned int charge) const;
diff --git a/src/gui/mainwindow.cpp b/src/gui/mainwindow.cpp
index 026fcf853fb35675c1316459773f95b7bb6db07e..32bbacd5263d04e29d3960626bd57c109fe0c599 100644
--- a/src/gui/mainwindow.cpp
+++ b/src/gui/mainwindow.cpp
@@ -34,7 +34,6 @@
#include <pappsomspp/pappsoexception.h>
#include "../utils/utils.h"
#include "output/xpip.h"
-#include "masschroq_run_dialog/masschroqfileparameters.h"
MainWindow::MainWindow(QWidget *parent) : QMainWindow(parent), ui(new Ui::Main)
{
diff --git a/src/gui/masschroq_run_dialog/masschroqrundialog.cpp b/src/gui/masschroq_run_dialog/masschroqrundialog.cpp
index b85191bba1b089ad5d07e2e86b94fdb2c23a9997..58276dd6603e2e15ec3a0f395f96eec6eda63e9e 100644
--- a/src/gui/masschroq_run_dialog/masschroqrundialog.cpp
+++ b/src/gui/masschroq_run_dialog/masschroqrundialog.cpp
@@ -61,6 +61,10 @@ MassChroqRunDialog::MassChroqRunDialog(MainWindow *parent,
ui->ht_condor_memory_spin->setValue(
settings.value("masschroq/condor_request_memory", "5000").toInt());
+
+ msp_masschroqFileParametersSp =
+ parent->getProjectSp().get()->getMasschroqFileParametersSp();
+
setMassChroQRunParamTab();
mp_poModel = new QStandardItemModel(ui->group_listView);
@@ -568,10 +572,7 @@ MassChroqRunDialog::updateAlignmentGroupsStatus(QString masschroqml_file)
{
group = msp_alignmentGroups.at(i - 1);
}
- ZivyParams zivy_params;
- zivy_params.loadSettings();
- group->savePostMassChroqmlParameters(
- getMasschroqFileParameters(), zivy_params, masschroqml_file);
+ group->savePostMassChroqmlParameters(masschroqml_file);
if(getMassChroqRunStatus() == true)
{
group->setMassChroQRunStatus(AlignmentGroupStatus::masschroq_run);
diff --git a/src/gui/masschroq_run_dialog/masschroqrundialog.h b/src/gui/masschroq_run_dialog/masschroqrundialog.h
index a35c9ede152be41a6fd11e02a43916615ba55be9..5786a8ac737f13fb7b6a5ed70301060b4853b221 100644
--- a/src/gui/masschroq_run_dialog/masschroqrundialog.h
+++ b/src/gui/masschroq_run_dialog/masschroqrundialog.h
@@ -30,8 +30,6 @@
#pragma once
-#include "masschroqfileparameters.h"
-
#include <QDialog>
#include <QStandardItemModel>
@@ -108,4 +106,5 @@ class MassChroqRunDialog : public QDialog
MsRunAlignmentGroupSp msp_allMsrunAlignmentGroup;
QStandardItemModel *mp_poModel;
MsRunAlignmentGroupSp msp_selected_group;
+ MasschroqFileParametersSp msp_masschroqFileParametersSp;
};
diff --git a/src/gui/workerthread.h b/src/gui/workerthread.h
index 524073e4864b2eb691a4a4dd7bfb93a31af45fd7..b35caa30e87673b7f32e3fdaad82119ba850587c 100644
--- a/src/gui/workerthread.h
+++ b/src/gui/workerthread.h
@@ -37,7 +37,6 @@
#include "../utils/workmonitor.h"
#include "../core/tandem_run/tandemrunbatch.h"
#include "../core/masschroq_run/masschroqrunbatch.h"
-#include "../gui/masschroq_run_dialog/masschroqfileparameters.h"
#include "../gui/xic_view/xic_box/xicbox.h"
class MainWindow;
diff --git a/src/gui/xic_view/xic_widgets/zivywidget.h b/src/gui/xic_view/xic_widgets/zivywidget.h
index 02022f19d7fe6ba06e547efd605bf718b035d633..174d5d007355bb9c0904f1214d919ca918a9b4ae 100644
--- a/src/gui/xic_view/xic_widgets/zivywidget.h
+++ b/src/gui/xic_view/xic_widgets/zivywidget.h
@@ -30,7 +30,7 @@
#pragma once
#include <QWidget>
-#include <pappsomspp/processing/detection/tracedetectionzivy.h>
+#include "../../../core/masschroq_run/masschroqfileparameters.h"
namespace Ui
{
@@ -38,20 +38,6 @@ class ZivyWidget;
}
-struct ZivyParams
-{
- std::shared_ptr<pappso::TraceDetectionInterface>
- newTraceDetectionZivySPtr() const;
- void saveSettings() const;
- void loadSettings();
-
- unsigned int _maxmin_half_window = 3;
- unsigned int _minmax_half_window = 2;
- double _maxmin_threshold = 3000;
- double _minmax_threshold = 5000;
- unsigned int _smoothing_half_window = 1;
-};
-
class ZivyWidget : public QWidget
{
Q_OBJECT
diff --git a/src/input/xtpxpipsaxhandler.cpp b/src/input/xtpxpipsaxhandler.cpp
index 8449ec86ac9f4ac08f3a8736e520abed3f145614..bbc3601e8257997061140cbaeb1b230f742fa322 100644
--- a/src/input/xtpxpipsaxhandler.cpp
+++ b/src/input/xtpxpipsaxhandler.cpp
@@ -654,21 +654,23 @@ XtpXpipSaxHandler::startElement_msrunInAlignmentGroup(QXmlAttributes attributes)
bool
XtpXpipSaxHandler::startElement_alignment_param(QXmlAttributes attributes)
{
- m_massChroQFileParams.ms2_tendency_half_window =
+ MasschroqFileParameters *p_masschroq_file_params =
+ _p_project->getMasschroqFileParametersSp().get();
+ p_masschroq_file_params->ms2_tendency_half_window =
attributes.value("ms2_tendency").toInt();
- m_massChroQFileParams.ms2_smoothing_half_window =
+ p_masschroq_file_params->ms2_smoothing_half_window =
attributes.value("ms2_smoothing").toInt();
- m_massChroQFileParams.ms1_smoothing_half_window =
+ p_masschroq_file_params->ms1_smoothing_half_window =
attributes.value("ms1_smoothing").toInt();
if(!attributes.value("time_corrections").simplified().isEmpty())
{
- m_massChroQFileParams.write_alignment_times = true;
- m_massChroQFileParams.alignment_times_directory =
+ p_masschroq_file_params->write_alignment_times = true;
+ p_masschroq_file_params->alignment_times_directory =
attributes.value("time_corrections").simplified();
}
else
{
- m_massChroQFileParams.write_alignment_times = false;
+ p_masschroq_file_params->write_alignment_times = false;
}
return true;
}
@@ -676,19 +678,22 @@ XtpXpipSaxHandler::startElement_alignment_param(QXmlAttributes attributes)
bool
XtpXpipSaxHandler::startElement_masschroq_param(QXmlAttributes attributes)
{
+
+ MasschroqFileParameters *p_masschroq_file_params =
+ _p_project->getMasschroqFileParametersSp().get();
msp_alignment_group->setMassChroqmlPath(attributes.value("masschroqml"));
if(QFileInfo(attributes.value("result")).suffix() == "ods")
{
- m_massChroQFileParams.result_file_format = TableFileFormat::ods;
+ p_masschroq_file_params->result_file_format = TableFileFormat::ods;
}
else
{
- m_massChroQFileParams.result_file_format = TableFileFormat::tsv;
+ p_masschroq_file_params->result_file_format = TableFileFormat::tsv;
}
if(!attributes.value("compar").isEmpty())
{
- m_massChroQFileParams.export_compar_file = true;
+ p_masschroq_file_params->export_compar_file = true;
}
return true;
}
@@ -696,26 +701,31 @@ XtpXpipSaxHandler::startElement_masschroq_param(QXmlAttributes attributes)
bool
XtpXpipSaxHandler::startElement_quantification_param(QXmlAttributes attributes)
{
- m_massChroQFileParams.xic_extraction_range =
+ MasschroqFileParameters *p_masschroq_file_params =
+ _p_project->getMasschroqFileParametersSp().get();
+ p_masschroq_file_params->xic_extraction_range =
pappso::PrecisionFactory::fromString(attributes.value("xic_range"));
if(attributes.value("xic_method").toInt() == 0)
{
- m_massChroQFileParams.xic_extraction_method =
+ p_masschroq_file_params->xic_extraction_method =
pappso::XicExtractMethod::max;
}
else
{
- m_massChroQFileParams.xic_extraction_method =
+ p_masschroq_file_params->xic_extraction_method =
pappso::XicExtractMethod::sum;
}
- ZivyParams zivy;
- zivy._smoothing_half_window = attributes.value("smoothing").toInt();
- zivy._minmax_half_window = attributes.value("minmax_half").toInt();
- zivy._maxmin_half_window = attributes.value("maxmin_half").toInt();
- zivy._minmax_threshold = attributes.value("minmax_thre").toDouble();
- zivy._maxmin_threshold = attributes.value("maxmin_thre").toDouble();
- msp_alignment_group->setZivyParams(zivy);
+ p_masschroq_file_params->m_zivyParams._smoothing_half_window =
+ attributes.value("smoothing").toInt();
+ p_masschroq_file_params->m_zivyParams._minmax_half_window =
+ attributes.value("minmax_half").toInt();
+ p_masschroq_file_params->m_zivyParams._maxmin_half_window =
+ attributes.value("maxmin_half").toInt();
+ p_masschroq_file_params->m_zivyParams._minmax_threshold =
+ attributes.value("minmax_thre").toDouble();
+ p_masschroq_file_params->m_zivyParams._maxmin_threshold =
+ attributes.value("maxmin_thre").toDouble();
return true;
}
@@ -1008,7 +1018,6 @@ XtpXpipSaxHandler::endElement_msrun()
bool
XtpXpipSaxHandler::endElement_alignmentGroup()
{
- msp_alignment_group->setMassChroQFileParams(m_massChroQFileParams);
msp_alignment_group = nullptr;
return true;
}
diff --git a/src/input/xtpxpipsaxhandler.h b/src/input/xtpxpipsaxhandler.h
index fd4aa5e4585ae805e1e5a9a9c9e139ee4c9dccf1..65df3d3f1b0b221aec235470be615e24e9a787b2 100644
--- a/src/input/xtpxpipsaxhandler.h
+++ b/src/input/xtpxpipsaxhandler.h
@@ -130,7 +130,6 @@ class XtpXpipSaxHandler : public QXmlDefaultHandler
LabelingMethodSp _sp_labeling_method;
MsRunSp _sp_msrun;
MsRunAlignmentGroupSp msp_alignment_group;
- MasschroqFileParameters m_massChroQFileParams;
std::map<QString, PeptideXtpSp> _map_peptides;
bool _is_xtpcpp_xpip = false;
QString _current_id;
diff --git a/src/output/masschroqml.cpp b/src/output/masschroqml.cpp
index 4d334defc20f8d4debbcbaf1d79aec022b2a8763..5624b2b3bcd398b83a91ed2931ab002c2537206e 100644
--- a/src/output/masschroqml.cpp
+++ b/src/output/masschroqml.cpp
@@ -91,8 +91,6 @@ MassChroQml::MassChroQml(const QString &out_filename,
_output_stream->setAutoFormatting(true);
_output_stream->writeStartDocument("1.0");
-
- _detect_zivy.loadSettings();
}
MassChroQml::~MassChroQml()
@@ -376,27 +374,27 @@ MassChroQml::writeQuantificationMethods()
//<mean_filter_half_edge>1</mean_filter_half_edge>
_output_stream->writeStartElement("mean_filter_half_edge");
_output_stream->writeCharacters(
- QString("%1").arg(_detect_zivy._smoothing_half_window));
+ QString("%1").arg(m_params.m_zivyParams._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._minmax_half_window));
+ QString("%1").arg(m_params.m_zivyParams._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._maxmin_half_window));
+ QString("%1").arg(m_params.m_zivyParams._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._minmax_threshold));
+ QString("%1").arg(m_params.m_zivyParams._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._maxmin_threshold));
+ QString("%1").arg(m_params.m_zivyParams._maxmin_threshold));
_output_stream->writeEndElement();
//</detection_zivy>
_output_stream->writeEndElement();
diff --git a/src/output/masschroqml.h b/src/output/masschroqml.h
index e22486f8beb68aa571d3b487c4f5d5cfe57a266d..f7c368b253d5e6f3687620bc3689a72c64404fd9 100644
--- a/src/output/masschroqml.h
+++ b/src/output/masschroqml.h
@@ -37,7 +37,7 @@
#include "../core/project.h"
#include "../grouping/groupinggroup.h"
#include "../gui/xic_view/xic_widgets/zivywidget.h"
-#include "../gui/masschroq_run_dialog/masschroqfileparameters.h"
+#include "../core/masschroq_run/masschroqfileparameters.h"
class MassChroQml
{
@@ -68,5 +68,4 @@ class MassChroQml
QXmlStreamWriter *_output_stream;
ProjectSp _sp_project;
IdentificationGroup *_p_identification_group;
- ZivyParams _detect_zivy;
};
diff --git a/src/output/xpip.cpp b/src/output/xpip.cpp
index 7f641848ffdd5749c5709058bbfa197ea587c5d5..9e8385033ca82582027d6eb1120bcabc57522bcb 100644
--- a/src/output/xpip.cpp
+++ b/src/output/xpip.cpp
@@ -431,10 +431,9 @@ Xpip::writeMsrunAlignmentGroup(const MsRunAlignmentGroupSp alignment_group,
void
Xpip::writeAlignmentGroupParameters(const MsRunAlignmentGroupSp alignment_group)
{
- ZivyParams zivy_params = alignment_group->getZivyParams();
QString masschroqml_path = alignment_group->getMassChroqmlPath();
MasschroqFileParameters mcq_file_params =
- alignment_group->getMassChroQFileParams();
+ *(_sp_project.get()->getMasschroqFileParametersSp().get());
// Alignment parameters
_output_stream->writeStartElement("alignment_params");
@@ -465,15 +464,20 @@ Xpip::writeAlignmentGroupParameters(const MsRunAlignmentGroupSp alignment_group)
"xic_method",
QString::number((std::int8_t)mcq_file_params.xic_extraction_method));
_output_stream->writeAttribute(
- "smoothing", QString::number(zivy_params._smoothing_half_window));
+ "smoothing",
+ QString::number(mcq_file_params.m_zivyParams._smoothing_half_window));
_output_stream->writeAttribute(
- "minmax_half", QString::number(zivy_params._minmax_half_window));
+ "minmax_half",
+ QString::number(mcq_file_params.m_zivyParams._minmax_half_window));
_output_stream->writeAttribute(
- "maxmin_half", QString::number(zivy_params._maxmin_half_window));
+ "maxmin_half",
+ QString::number(mcq_file_params.m_zivyParams._maxmin_half_window));
_output_stream->writeAttribute(
- "minmax_thre", QString::number(zivy_params._minmax_threshold));
+ "minmax_thre",
+ QString::number(mcq_file_params.m_zivyParams._minmax_threshold));
_output_stream->writeAttribute(
- "maxmin_thre", QString::number(zivy_params._maxmin_threshold));
+ "maxmin_thre",
+ QString::number(mcq_file_params.m_zivyParams._maxmin_threshold));
_output_stream->writeEndElement();
// Masschroq parameters