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Maintenance - Mise à jour mensuelle Lundi 6 Février entre 7h00 et 9h00
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PAPPSO
xtpcpp
Commits
d4954213
Commit
d4954213
authored
Nov 05, 2019
by
Renne Thomas
Browse files
Complete xtandem view and add no engine view
parent
c497f4d6
Changes
10
Expand all
Hide whitespace changes
Inline
Side-by-side
src/CMakeLists.txt
View file @
d4954213
...
...
@@ -207,6 +207,7 @@ SET(XTPCPP_SRCS
./gui/waiting_message_dialog/waitingmessagedialog.cpp
./gui/widgets/automatic_filter_widget/automaticfilterwidget.cpp
./gui/widgets/engines_view/xtandemparamwidget.cpp
./gui/widgets/engines_view/noengineparamwidget.cpp
./gui/widgets/contaminant_widget/contaminantwidget.cpp
./gui/widgets/decoy_widget/decoywidget.cpp
./gui/widgets/xic_extraction_method_widget/xicextractionmethodwidget.cpp
...
...
@@ -245,6 +246,7 @@ SET (GUI_UIS
./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/engines_view/no_engine_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 @
d4954213
...
...
@@ -20,63 +20,56 @@
<property
name=
"contextMenuPolicy"
>
<enum>
Qt::CustomContextMenu
</enum>
</property>
<layout
class=
"Q
V
BoxLayout"
name=
"
vertic
alLayout"
>
<layout
class=
"Q
H
BoxLayout"
name=
"
horizont
alLayout
_3
"
>
<item>
<layout
class=
"Q
H
BoxLayout"
name=
"
horizont
alLayout
_2
"
>
<layout
class=
"Q
V
BoxLayout"
name=
"
vertic
alLayout"
>
<item>
<widget
class=
"QLabel"
name=
"labelEngineName"
>
<property
name=
"text"
>
<string>
Engine name
</string>
</property>
</widget>
<layout
class=
"QHBoxLayout"
name=
"horizontalLayout_2"
>
<item>
<widget
class=
"QLabel"
name=
"labelEngineName"
>
<property
name=
"text"
>
<string>
Engine name
</string>
</property>
</widget>
</item>
<item>
<widget
class=
"QLabel"
name=
"labelEngineVersion"
>
<property
name=
"text"
>
<string>
Engine Version
</string>
</property>
</widget>
</item>
</layout>
</item>
<item>
<widget
class=
"QLabel"
name=
"labelEngineVersion"
>
<property
name=
"text"
>
<string>
Engine Version
</string>
</property>
</widget>
</item>
</layout>
</item>
<item>
<widget
class=
"XtandemParamWidget"
name=
"xtandem_view_widget"
native=
"true"
/>
</item>
<item>
<layout
class=
"QHBoxLayout"
name=
"horizontalLayout"
>
<item>
<spacer
name=
"horizontalSpacer"
>
<property
name=
"orientation"
>
<enum>
Qt::Horizontal
</enum>
</property>
<property
name=
"sizeHint"
stdset=
"0"
>
<size>
<width>
40
</width>
<height>
20
</height>
</size>
</property>
</spacer>
</item>
<item>
<widget
class=
"QPushButton"
name=
"closeButton"
>
<property
name=
"text"
>
<string>
Close
</string>
</property>
</widget>
<layout
class=
"QHBoxLayout"
name=
"horizontalLayout"
>
<item>
<spacer
name=
"horizontalSpacer"
>
<property
name=
"orientation"
>
<enum>
Qt::Horizontal
</enum>
</property>
<property
name=
"sizeHint"
stdset=
"0"
>
<size>
<width>
40
</width>
<height>
20
</height>
</size>
</property>
</spacer>
</item>
<item>
<widget
class=
"QPushButton"
name=
"closeButton"
>
<property
name=
"text"
>
<string>
Close
</string>
</property>
</widget>
</item>
</layout>
</item>
</layout>
</item>
</layout>
</widget>
</widget>
<customwidgets>
<customwidget>
<class>
XtandemParamWidget
</class>
<extends>
QWidget
</extends>
<header>
gui/widgets/engines_view/xtandemparamwidget.h
</header>
<container>
1
</container>
</customwidget>
</customwidgets>
<resources/>
<connections>
<connection>
...
...
src/gui/lists/ms_identification_run_list_view/engine_detail_view/enginedetailwindow.cpp
View file @
d4954213
...
...
@@ -24,7 +24,8 @@
#include
"ui_engine_detail_view.h"
#include
"enginedetailwindow.h"
#include
"gui/widgets/engines_view/xtandemparamwidget.h"
#include
"gui/widgets/engines_view/noengineparamwidget.h"
#include
"../../../mainwindow.h"
#include
<QSettings>
...
...
@@ -53,11 +54,33 @@ EngineDetailWindow::setIdentificationEngineParam(
void
EngineDetailWindow
::
updateDisplay
()
{
QString
params_file
=
m_identificationEngine
->
get
()
->
getResourceName
();
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
);
TandemParametersFile
param_file
(
params_file
);
if
(
param_file
.
exists
())
{
TandemParameters
xtandem_parameters
=
param_file
.
getTandemParameters
();
if
(
m_identificationEngine
->
get
()
->
getIdentificationEngineName
()
==
"X!Tandem"
)
{
XtandemParamWidget
*
xtandem_view_widget
;
xtandem_view_widget
=
new
XtandemParamWidget
(
this
);
ui
->
verticalLayout
->
insertWidget
(
1
,
xtandem_view_widget
);
xtandem_view_widget
->
setAutomaticXTandemParameters
(
xtandem_parameters
);
}
}
else
{
NoEngineParamWidget
*
no_engine_view_widget
;
no_engine_view_widget
=
new
NoEngineParamWidget
(
this
,
params_file
);
ui
->
verticalLayout
->
insertWidget
(
1
,
no_engine_view_widget
);
}
}
src/gui/lists/ms_identification_run_list_view/engine_detail_view/enginedetailwindow.h
View file @
d4954213
...
...
@@ -55,6 +55,5 @@ class EngineDetailWindow : public QMainWindow
private:
Ui
::
EngineDetailView
*
ui
;
ProjectWindow
*
m_project_window
;
QString
m_params_file
;
IdentificationDataSourceSp
*
m_identificationEngine
=
nullptr
;
};
src/gui/widgets/engines_view/no_engine_view_widget.ui
0 → 100644
View file @
d4954213
<?xml version="1.0" encoding="UTF-8"?>
<ui
version=
"4.0"
>
<class>
NoEngineParamWidget
</class>
<widget
class=
"QWidget"
name=
"NoEngineParamWidget"
>
<property
name=
"geometry"
>
<rect>
<x>
0
</x>
<y>
0
</y>
<width>
605
</width>
<height>
740
</height>
</rect>
</property>
<property
name=
"font"
>
<font>
<pointsize>
16
</pointsize>
</font>
</property>
<property
name=
"windowTitle"
>
<string>
Form
</string>
</property>
<layout
class=
"QGridLayout"
name=
"gridLayout_7"
>
<item
row=
"0"
column=
"0"
>
<layout
class=
"QVBoxLayout"
name=
"verticalLayout"
>
<item>
<spacer
name=
"verticalSpacer_2"
>
<property
name=
"orientation"
>
<enum>
Qt::Vertical
</enum>
</property>
<property
name=
"sizeHint"
stdset=
"0"
>
<size>
<width>
20
</width>
<height>
40
</height>
</size>
</property>
</spacer>
</item>
<item>
<widget
class=
"QLabel"
name=
"label"
>
<property
name=
"text"
>
<string>
label
</string>
</property>
<property
name=
"alignment"
>
<set>
Qt::AlignCenter
</set>
</property>
</widget>
</item>
<item>
<spacer
name=
"verticalSpacer"
>
<property
name=
"orientation"
>
<enum>
Qt::Vertical
</enum>
</property>
<property
name=
"sizeHint"
stdset=
"0"
>
<size>
<width>
20
</width>
<height>
40
</height>
</size>
</property>
</spacer>
</item>
</layout>
</item>
</layout>
</widget>
<resources/>
<connections/>
</ui>
src/gui/widgets/engines_view/noengineparamwidget.cpp
0 → 100644
View file @
d4954213
/*******************************************************************************
* 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
"noengineparamwidget.h"
#include
"../../project_view/projectwindow.h"
#include
"ui_no_engine_view_widget.h"
#include
<QDebug>
NoEngineParamWidget
::
NoEngineParamWidget
(
QWidget
*
parent
,
QString
file_name
)
:
QWidget
(
parent
),
ui
(
new
Ui
::
NoEngineParamWidget
)
{
qDebug
()
<<
"begin"
;
ui
->
setupUi
(
this
);
QString
message
=
file_name
+
"
\n
wasn't found !!
\n
Please check if the file exist"
;
ui
->
label
->
setText
(
message
);
qDebug
()
<<
"end"
;
}
NoEngineParamWidget
::~
NoEngineParamWidget
()
{
qDebug
()
<<
"NoEngineParamWidget::~NoEngineParamWidget"
;
delete
ui
;
qDebug
()
<<
"end"
;
}
src/gui/widgets/engines_view/noengineparamwidget.h
0 → 100644
View file @
d4954213
/*******************************************************************************
* 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>
namespace
Ui
{
class
NoEngineParamWidget
;
}
class
NoEngineParamWidget
:
public
QWidget
{
Q_OBJECT
public:
explicit
NoEngineParamWidget
(
QWidget
*
parent
,
QString
file_name
);
~
NoEngineParamWidget
();
Ui
::
NoEngineParamWidget
*
ui
;
};
src/gui/widgets/engines_view/xtandem_view_widget.ui
View file @
d4954213
This diff is collapsed.
Click to expand it.
src/gui/widgets/engines_view/xtandemparamwidget.cpp
View file @
d4954213
...
...
@@ -47,13 +47,10 @@ XtandemParamWidget::~XtandemParamWidget()
}
void
XtandemParamWidget
::
setAutomaticXTandemParameters
(
QString
params_file
)
XtandemParamWidget
::
setAutomaticXTandemParameters
(
TandemParameters
xtandem_parameters
)
{
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
);
...
...
@@ -67,11 +64,77 @@ XtandemParamWidget::setAutomaticXTandemParameters(QString params_file)
void
XtandemParamWidget
::
setSpectrumParameters
(
TandemParameters
xtandem_parameters
)
{
ui
->
parenttIonMHMassToleranceWindowUnitLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"spectrum, parent monoisotopic mass error units"
));
ui
->
parentIonMHMassToleranceLowerWindowLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"spectrum, parent monoisotopic mass error minus"
));
ui
->
parentIonMHMassToleranceUpperWindowLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"spectrum, parent monoisotopic mass error plus"
));
ui
->
anticipateCarbonIsotopeParentIonAssignmentsErrorsLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"spectrum, parent monoisotopic mass isotope error"
));
ui
->
setTheMaximumPrecursorChargeToBeScoredLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"spectrum, maximum parent charge"
));
ui
->
useChemicalAverageOrMonoisotopicMassForFragmentIonsLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"spectrum, fragment mass type"
));
ui
->
unitsForFragmentIonMassToleranceMonoisotopicLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"spectrum, fragment monoisotopic mass error units"
));
ui
->
fragmentIonMassToleranceMonoisotopicLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"spectrum, parent monoisotopic mass error minus"
));
ui
->
controlTheUseOfTheNeutralLossWindowLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"spectrum, use neutral loss window"
));
ui
->
neutralLossMassLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"spectrum, neutral loss mass"
));
ui
->
neutralLossWindowDaltonsLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"spectrum, neutral loss window"
));
ui
->
setTheDynamicRangeToScoreSpectraLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"spectrum, dynamic range"
));
ui
->
maximumNumberOfPeaksToUseInASpectrumLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"spectrum, total peaks"
));
ui
->
minimumNumberOfPeaksForASpectrumToBeConsideredLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"spectrum, minimum peaks"
));
ui
->
minimumMZFragmentToBeConsideredLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"spectrum, minimum fragment mz"
));
ui
->
minimumParentMHToBeConsideredLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"spectrum, minimum parent m+h"
));
ui
->
alterHowProteinSequencesAreRetrievedFromFASTAFilesLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"spectrum, sequence batch size"
));
ui
->
useContrastAngleLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"spectrum, use contrast angle"
));
ui
->
setNumberOfThreadsLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"spectrum, threads"
));
}
void
XtandemParamWidget
::
setProteinParameters
(
TandemParameters
xtandem_parameters
)
{
ui
->
defineProteinCleavageSiteLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"protein, cleavage site"
));
ui
->
useSemiEnzymaticCleavageRulesLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"protein, cleavage semi"
));
ui
->
moietyAddedToPeptideCTerminusByCleavageLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"protein, cleavage C-terminal mass change"
));
ui
->
moietyAddedToPeptideNTerminusByCleavageLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"protein, cleavage N-terminal mass change"
));
ui
->
moietyAddedToProteinCTerminusLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"protein, C-terminal residue modification mass"
));
ui
->
moietyAddedToProteinNTerminusLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"protein, N-terminal residue modification mass"
));
ui
->
proteinNTerminusCommonModificationsLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"protein, quick acetyl"
));
ui
->
proteinNTerminusCyclisationLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"protein, quick pyrolidone"
));
ui
->
interpretationOfPeptidePhosphorylationModelLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"protein, stP bias"
));
ui
->
modifyTheResidueMassesOfOneAllAminoAcidsLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"protein, modified residue mass file"
));
}
void
...
...
@@ -93,6 +156,20 @@ XtandemParamWidget::setResidueParameters(TandemParameters xtandem_parameters)
void
XtandemParamWidget
::
setScoringParameters
(
TandemParameters
xtandem_parameters
)
{
ui
->
minimumNumberOfIonsToScoreAPeptideLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"scoring, minimum ion count"
));
ui
->
maximumMissedCleavageSitesLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"scoring, maximum missed cleavage sites"
));
ui
->
compensateForVerySmallSequenceListFileLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"scoring, cyclic permutation"
));
ui
->
automaticallyPerformReverseDatabaseSearchLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"scoring, include reverse"
));
ui
->
useYIonsLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"scoring, y ions"
));
ui
->
useBIonsLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"scoring, b ions"
));
ui
->
useCIonsLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"scoring, c ions"
));
ui
->
useZIonsLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"scoring, z ions"
));
ui
->
useAIonsLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"scoring, a ions"
));
ui
->
useXIonsLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"scoring, x ions"
));
}
void
...
...
@@ -145,4 +222,31 @@ XtandemParamWidget::setRefineParameters(TandemParameters xtandem_parameters)
void
XtandemParamWidget
::
setOutputParameters
(
TandemParameters
xtandem_parameters
)
{
ui
->
highestEValueToRecordPeptidesLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"output, maximum valid expectation value"
));
ui
->
highestEValueToRecordProteinsLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"output, maximum valid protein expectation value"
));
ui
->
resultsTypeLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"output, results"
));
ui
->
sortResultsByLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"output, sort results by"
));
ui
->
writeProteinsLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"output, proteins"
));
ui
->
writeProteinSequencesLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"output, sequences"
));
ui
->
writeOnlyFirstProteinSequenceLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"output, one sequence copy"
));
ui
->
writeSpectrumInformationsLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"output, spectra"
));
ui
->
writeParametersLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"output, parameters"
));
ui
->
writeHistogramsLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"output, histograms"
));
ui
->
histogramColumnWidthLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"output, histogram column width"
));
ui
->
hashFilenameWithDateAndTimeStampLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"output, path hashing"
));
ui
->
xSLTStyleSheetPathToViewXMLResultsLineEdit
->
setText
(
xtandem_parameters
.
getValue
(
"output, xsl path"
));
}
src/gui/widgets/engines_view/xtandemparamwidget.h
View file @
d4954213
...
...
@@ -41,7 +41,7 @@ class XtandemParamWidget : public QWidget
explicit
XtandemParamWidget
(
QWidget
*
parent
);
~
XtandemParamWidget
();
void
setAutomaticXTandemParameters
(
QString
params_file
);
void
setAutomaticXTandemParameters
(
TandemParameters
xtandem_parameters
);
private
slots
:
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