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Maintenance - Mise à jour mensuelle Lundi 6 Février entre 7h00 et 9h00
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PAPPSO
xtpcpp
Commits
c497f4d6
Commit
c497f4d6
authored
Nov 04, 2019
by
Renne Thomas
Browse files
add xtandem parameters to engine detail
parent
8017164b
Changes
10
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Side-by-side
src/CMakeLists.txt
View file @
c497f4d6
...
...
@@ -206,6 +206,7 @@ SET(XTPCPP_SRCS
./gui/tandem_run_dialog/tandemrundialog.cpp
./gui/waiting_message_dialog/waitingmessagedialog.cpp
./gui/widgets/automatic_filter_widget/automaticfilterwidget.cpp
./gui/widgets/engines_view/xtandemparamwidget.cpp
./gui/widgets/contaminant_widget/contaminantwidget.cpp
./gui/widgets/decoy_widget/decoywidget.cpp
./gui/widgets/xic_extraction_method_widget/xicextractionmethodwidget.cpp
...
...
@@ -243,6 +244,7 @@ SET (GUI_UIS
./gui/tandem_run_dialog/tandem_run_dialog.ui
./gui/waiting_message_dialog/waiting_message_dialog.ui
./gui/widgets/automatic_filter_widget/automatic_filter_widget.ui
./gui/widgets/engines_view/xtandem_view_widget.ui
./gui/widgets/contaminant_widget/contaminant_widget.ui
./gui/widgets/decoy_widget/decoy_widget.ui
./gui/xic_view/xic_box/xic_box.ui
...
...
src/gui/lists/ms_identification_run_list_view/engine_detail_view/engine_detail_view.ui
View file @
c497f4d6
This diff is collapsed.
Click to expand it.
src/gui/lists/ms_identification_run_list_view/engine_detail_view/enginedetailwindow.cpp
View file @
c497f4d6
...
...
@@ -27,8 +27,7 @@
#include
"../../../mainwindow.h"
#include
<QSettings>
#include
<odsstream/odsdocwriter.h>
#include
<odsstream/qtablewriter.h>
EngineDetailWindow
::
EngineDetailWindow
(
ProjectWindow
*
parent
)
:
QMainWindow
(
parent
),
ui
(
new
Ui
::
EngineDetailView
)
...
...
@@ -36,7 +35,6 @@ EngineDetailWindow::EngineDetailWindow(ProjectWindow *parent)
m_project_window
=
parent
;
ui
->
setupUi
(
this
);
setWindowIcon
(
QIcon
(
":/xtpcpp_icon/resources/xtandempipeline_icon.svg"
));
}
...
...
@@ -45,15 +43,21 @@ EngineDetailWindow::~EngineDetailWindow()
}
void
EngineDetailWindow
::
setIdentificationEngineParam
(
IdentificationDataSourceSp
*
identificationEngine
)
EngineDetailWindow
::
setIdentificationEngineParam
(
IdentificationDataSourceSp
*
identificationEngine
)
{
m_identificationEngine
=
identificationEngine
;
updateDisplay
();
}
void
EngineDetailWindow
::
updateDisplay
()
void
EngineDetailWindow
::
updateDisplay
()
{
ui
->
labelEngineName
->
setText
(
m_identificationEngine
->
get
()
->
getIdentificationEngineName
());
ui
->
labelEngineVersion
->
setText
(
m_identificationEngine
->
get
()
->
getIdentificationEngineVersion
());
//ui->alterFixedModifications1Label->setText(m_identificationEngine->get()->getIdentificationEngine));
ui
->
labelEngineName
->
setText
(
m_identificationEngine
->
get
()
->
getIdentificationEngineName
());
ui
->
labelEngineVersion
->
setText
(
m_identificationEngine
->
get
()
->
getIdentificationEngineVersion
());
m_params_file
=
m_identificationEngine
->
get
()
->
getResourceName
();
ui
->
xtandem_view_widget
->
setAutomaticXTandemParameters
(
m_params_file
);
}
src/gui/lists/ms_identification_run_list_view/engine_detail_view/enginedetailwindow.h
View file @
c497f4d6
...
...
@@ -46,13 +46,15 @@ class EngineDetailWindow : public QMainWindow
public:
explicit
EngineDetailWindow
(
ProjectWindow
*
parent
=
0
);
~
EngineDetailWindow
();
void
setIdentificationEngineParam
(
IdentificationDataSourceSp
*
identificationEngine
);
void
setIdentificationEngineParam
(
IdentificationDataSourceSp
*
identificationEngine
);
protected:
void
updateDisplay
();
private:
Ui
::
EngineDetailView
*
ui
;
ProjectWindow
*
m_project_window
;
QString
m_params_file
;
IdentificationDataSourceSp
*
m_identificationEngine
=
nullptr
;
};
src/gui/lists/ms_identification_run_list_view/msidentificationlistwindow.cpp
View file @
c497f4d6
...
...
@@ -146,7 +146,8 @@ MsIdentificationListWindow::doExportAsOdsFile()
}
void
MsIdentificationListWindow
::
askEngineDetailView
(
IdentificationDataSourceSp
*
identificationEngine
)
MsIdentificationListWindow
::
askEngineDetailView
(
IdentificationDataSourceSp
*
identificationEngine
)
{
qDebug
()
<<
"begin"
;
m_project_window
->
doViewEngineDetail
(
identificationEngine
);
...
...
src/gui/lists/ms_identification_run_list_view/msidentificationlistwindow.h
View file @
c497f4d6
...
...
@@ -67,7 +67,7 @@ class MsIdentificationListWindow : public QMainWindow
protected:
void
askEngineDetailView
(
IdentificationDataSourceSp
*
identificationEngine
);
private:
Ui
::
MsIdentificationView
*
ui
;
MsIdentificationTableModel
*
m_msid_table_model_p
=
nullptr
;
...
...
src/gui/lists/ms_identification_run_list_view/msidentificationtableproxymodel.cpp
View file @
c497f4d6
...
...
@@ -192,9 +192,10 @@ MsIdentificationTableProxyModel::onTableClicked(const QModelIndex &index)
QModelIndex
source_index
(
this
->
mapToSource
(
index
));
int
row
=
source_index
.
row
();
m_identificationEngine
=
m_msid_table_model_p
->
getIdentificationDataSourceSpList
().
at
(
row
);
m_identificationEngine
=
m_msid_table_model_p
->
getIdentificationDataSourceSpList
().
at
(
row
);
msIdentificationListColumn
col
=
(
msIdentificationListColumn
)
source_index
.
column
();
if
(
col
==
msIdentificationListColumn
::
engine_name
)
...
...
src/gui/widgets/engines_view/xtandem_view_widget.ui
0 → 100644
View file @
c497f4d6
This diff is collapsed.
Click to expand it.
src/gui/widgets/engines_view/xtandemparamwidget.cpp
0 → 100644
View file @
c497f4d6
/*******************************************************************************
* Copyright (c) 2017 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
"xtandemparamwidget.h"
#include
"../../project_view/projectwindow.h"
#include
"ui_xtandem_view_widget.h"
#include
<QDebug>
#include
<files/tandemparametersfile.h>
XtandemParamWidget
::
XtandemParamWidget
(
QWidget
*
parent
)
:
QWidget
(
parent
),
ui
(
new
Ui
::
XtandemParamWidget
)
{
qDebug
()
<<
"begin"
;
ui
->
setupUi
(
this
);
qDebug
()
<<
"end"
;
}
XtandemParamWidget
::~
XtandemParamWidget
()
{
qDebug
()
<<
"XtandemParamWidget::~XtandemParamWidget"
;
delete
ui
;
qDebug
()
<<
"end"
;
}
void
XtandemParamWidget
::
setAutomaticXTandemParameters
(
QString
params_file
)
{
qDebug
()
<<
"begin "
;
// TandemParametersFile param_file(params_file);
TandemParametersFile
param_file
(
"/home/trenne/test_tandem.xml"
);
TandemParameters
xtandem_parameters
=
param_file
.
getTandemParameters
();
setSpectrumParameters
(
xtandem_parameters
);
setProteinParameters
(
xtandem_parameters
);
setResidueParameters
(
xtandem_parameters
);
setScoringParameters
(
xtandem_parameters
);
setRefineParameters
(
xtandem_parameters
);
setOutputParameters
(
xtandem_parameters
);
qDebug
()
<<
"end "
;
}
void
XtandemParamWidget
::
setSpectrumParameters
(
TandemParameters
xtandem_parameters
)
{
}
void
XtandemParamWidget
::
setProteinParameters
(
TandemParameters
xtandem_parameters
)
{
}
void
XtandemParamWidget
::
setResidueParameters
(
TandemParameters
xtandem_parameters
)
{
ui
->
fixedModificationsLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"residue, modification mass"
));
ui
->
fixedModifications1LineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"residue, modification mass 1"
));
ui
->
fixedModifications2LineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"residue, modification mass 2"
));
ui
->
potentialModificationsLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"residue, potential modification mass"
));
ui
->
potentialModificationsMotifLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"residue, potential modification motif"
));
}
void
XtandemParamWidget
::
setScoringParameters
(
TandemParameters
xtandem_parameters
)
{
}
void
XtandemParamWidget
::
setRefineParameters
(
TandemParameters
xtandem_parameters
)
{
ui
->
useOfTheRefinementModuleLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"refine"
));
ui
->
maximumEValueToAcceptPeptideLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"refine, maximum valid expectation value"
));
ui
->
peptideNTerPotentialModificationsLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"refine, potential N-terminus modifications"
));
ui
->
peptideCTerPotentialModificationsLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"refine, potential C-terminus modifications"
));
ui
->
alterFixedModificationsLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"refine, modification mass"
));
ui
->
alterFixedModifications1LineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"refine, modification mass 1"
));
ui
->
alterFixedModifications2LineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"refine, modification mass 2"
));
ui
->
alterFixedModificationsLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"refine, potential modification mass"
));
ui
->
alterFixedModifications1LineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"refine, potential modification mass 1"
));
ui
->
alterFixedModifications2LineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"refine, potential modification mass 2"
));
ui
->
potentialModificationsMotifLineEdit_2
->
setText
(
xtandem_parameters
.
getValue
(
"refine, potential modification motif"
));
ui
->
potentialModificationsMotif1LineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"refine, potential modification motif 1"
));
ui
->
potentialModificationsMotif2LineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"refine, potential modification motif 2"
));
ui
->
usePotentialModificationsInRefinementModuleLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"refine, use potential modifications for full refinement"
));
ui
->
useSemiEnzymaticCleavageRulesLineEdit_2
->
setText
(
xtandem_parameters
.
getValue
(
"refine, cleavage semi"
));
ui
->
cleavageAtEachResiduesLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"refine, unanticipated cleavage"
));
ui
->
spectrumIntensityModelSynthesisLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"refine, spectrum synthesis"
));
ui
->
pointMutationsLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"refine, point mutations"
));
}
void
XtandemParamWidget
::
setOutputParameters
(
TandemParameters
xtandem_parameters
)
{
}
src/gui/widgets/engines_view/xtandemparamwidget.h
0 → 100644
View file @
c497f4d6
/*******************************************************************************
* Copyright (c) 2017 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
******************************************************************************/
#pragma once
#include
<QWidget>
#include
<core/tandem_run/tandemparameters.h>
namespace
Ui
{
class
XtandemParamWidget
;
}
class
XtandemParamWidget
:
public
QWidget
{
Q_OBJECT
public:
explicit
XtandemParamWidget
(
QWidget
*
parent
);
~
XtandemParamWidget
();
void
setAutomaticXTandemParameters
(
QString
params_file
);
private
slots
:
private:
void
setSpectrumParameters
(
TandemParameters
xtandem_parameters
);
void
setProteinParameters
(
TandemParameters
xtandem_parameters
);
void
setResidueParameters
(
TandemParameters
xtandem_parameters
);
void
setScoringParameters
(
TandemParameters
xtandem_parameters
);
void
setRefineParameters
(
TandemParameters
xtandem_parameters
);
void
setOutputParameters
(
TandemParameters
xtandem_parameters
);
Ui
::
XtandemParamWidget
*
ui
;
};
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