38 #include <OpenMS/VISUAL/OpenMS_GUIConfig.h> 56 #include <QtWidgets/QMainWindow> 57 #include <QtWidgets/QButtonGroup> 58 #include <QtWidgets/QActionGroup> 59 #include <QtCore/QStringList> 60 #include <QtCore/QProcess> 67 class QListWidgetItem;
69 class QTreeWidgetItem;
81 class EnhancedWorkspace;
83 class Spectrum1DWidget;
84 class Spectrum2DWidget;
85 class Spectrum3DWidget;
87 class MultiGradientSelector;
130 friend class TestTOPPView;
172 void addDataFile(
const String& filename,
bool show_options,
bool add_to_recent,
String caption =
"",
UInt window_id = 0,
Size spectrum_id = 0);
192 std::vector<PeptideIdentification>& peptides,
198 bool as_new_window =
true,
199 const String& filename =
"",
200 const String& caption =
"",
202 Size spectrum_id = 0);
205 void loadFiles(
const StringList& list, QSplashScreen* splash_screen);
212 void loadPreferences(
String filename =
"");
215 void savePreferences();
221 const LayerData* getCurrentLayer()
const;
253 void updateCurrentPath();
257 void openFileDialog();
259 void openExampleDialog();
261 void showGoToDialog();
263 void preferencesDialog();
265 void layerStatistics();
269 void layerActivated();
271 void layerZoomChanged();
275 void layerDeactivated();
279 void updateToolBar();
281 void updateLayerBar();
283 void updateViewBar();
285 void viewChanged(
int);
287 void viewTabwidgetDoubleClicked(
int);
289 void updateFilterBar();
293 void updateTabBar(QMdiSubWindow* w);
297 void tileHorizontal();
304 void showStatusMessage(std::string msg,
OpenMS::UInt time);
306 void showCursorStatus(
double mz,
double rt);
308 void showCursorStatusInvert(
double mz,
double rt);
310 void showTOPPDialog();
312 void annotateWithID();
314 void showSpectrumGenerationDialog();
316 void showSpectrumAlignmentDialog();
318 void showSpectrumAs1D(
int index);
319 void showSpectrumAs1D(std::vector<
int, std::allocator<int> > indices);
321 void showCurrentPeaksAs2D();
323 void showCurrentPeaksAs3D();
325 void showCurrentPeaksAsIonMobility();
327 void showCurrentPeaksAsDIA();
329 void showAboutDialog();
333 void saveLayerVisible();
335 void toggleGridLines();
337 void toggleAxisLegends();
339 void toggleInterestingMZs();
341 void showPreferences();
343 void metadataFileDialog();
348 void setDrawMode1D(
int);
349 void setIntensityMode(
int);
350 void changeLayerFlag(
bool);
351 void changeLabel(QAction*);
352 void changeUnassigned(QAction*);
354 void toggleProjections();
358 void loadFile(QString);
364 void layerSelectionChange(
int);
367 void layerFilterVisibilityChange(
bool);
369 void layerContextMenu(
const QPoint& pos);
371 void logContextMenu(
const QPoint& pos);
373 void layerVisibilityChange(QListWidgetItem* item);
375 void filterContextMenu(
const QPoint& pos);
377 void filterEdit(QListWidgetItem* item);
379 void layerEdit(QListWidgetItem* );
383 void finishTOPPToolExecution(
int exitCode, QProcess::ExitStatus exitStatus);
385 void abortTOPPTool();
387 void rerunTOPPTool();
389 void showSpectrumBrowser();
391 void showSpectrumMetaData(
int spectrum_index);
396 void closeByTab(
int id);
399 void enhancedWorkspaceWindowChanged(
int id);
401 void openRecentFile();
403 void copyLayer(
const QMimeData* data,
QWidget* source,
int id = -1);
407 void updateProcessLog();
410 void fileChanged_(
const String&);
413 void initializeDefaultParameters_();
417 bool annotateMS1FromMassFingerprinting_(
const FeatureMap& identifications);
420 std::set<String> getFilenamesOfOpenFiles_();
425 QStringList getFileList_(
const String& path_overwrite =
"");
504 QLabel* message_label_;
514 void addRecentFile_(
const String& filename);
517 void updateRecentMenu_();
547 void checkPreferences_();
550 void closeEvent(QCloseEvent* event)
override;
561 void showLogMessage_(LogState state,
const String& heading,
const String& body);
567 void showTOPPDialog_(
bool visible);
587 static bool containsIMData(
const MSSpectrum& s);
A more convenient string class.
Definition: String.h:58
LayerData::FeatureMapType FeatureMapType
Definition: TOPPViewBase.h:136
static const String CAPTION_3D_SUFFIX_
Suffix appended to caption of tabs when layer is shown in 3D.
Definition: TOPPViewBase.h:600
LayerData::ConsensusMapSharedPtrType ConsensusMapSharedPtrType
Definition: TOPPViewBase.h:143
Class that stores the data for one layer.
Definition: LayerData.h:85
QDockWidget * views_dockwidget_
Definition: TOPPViewBase.h:433
QTabWidget * views_tabwidget_
Tabwidget that hold the different views on the loaded data.
Definition: TOPPViewBase.h:574
Main window of TOPPView tool.
Definition: TOPPViewBase.h:124
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
Behavior of TOPPView in identification mode.
Definition: TOPPViewIdentificationViewBehavior.h:49
QButtonGroup * draw_group_1d_
Definition: TOPPViewBase.h:476
Widget for 2D-visualization of peak map and feature map data.
Definition: Spectrum2DWidget.h:63
LayerData::ConsensusMapType ConsensusMapType
Definition: TOPPViewBase.h:141
SpectraViewWidget * spectra_view_widget_
Definition: TOPPViewBase.h:439
QListWidget * filters_
Definition: TOPPViewBase.h:448
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
QDockWidget * filter_dock_widget_
Definition: TOPPViewBase.h:434
Watcher that monitors file changes.
Definition: FileWatcher.h:65
LayerData::ODExperimentSharedPtrType ODExperimentSharedPtrType
Definition: TOPPViewBase.h:150
Base class for spectrum widgets.
Definition: SpectrumWidget.h:80
Definition: EnhancedWorkspace.h:49
QToolBar * tool_bar_2d_ident_
Definition: TOPPViewBase.h:482
A container for features.
Definition: FeatureMap.h:95
QToolBar * tool_bar_2d_peak_
Definition: TOPPViewBase.h:479
LogState
Log message states.
Definition: TOPPViewBase.h:554
QLabel * mz_label_
m/z label for messages in the status bar
Definition: TOPPViewBase.h:507
QToolBar * tool_bar_2d_feat_
Definition: TOPPViewBase.h:480
EnhancedWorkspace * ws_
Main workspace.
Definition: TOPPViewBase.h:496
QAction * dm_ident_2d_
Definition: TOPPViewBase.h:492
QActionGroup * group_unassigned_2d_
Definition: TOPPViewBase.h:489
SpectraIdentificationViewWidget * spectra_identification_view_widget_
Definition: TOPPViewBase.h:440
LayerData::ExperimentSharedPtrType ExperimentSharedPtrType
Definition: TOPPViewBase.h:148
LayerData::ExperimentType ExperimentType
Definition: TOPPViewBase.h:146
Base class for visualization canvas classes.
Definition: SpectrumCanvas.h:98
Widgets that are placed into an EnhancedTabBar must implement this interface.
Definition: EnhancedTabBarWidgetInterface.h:51
TOPPViewIdentificationViewBehavior * identificationview_behavior_
TOPPView behavior for the identification view.
Definition: TOPPViewBase.h:577
Behavior of TOPPView in spectra view mode.
Definition: TOPPViewSpectraViewBehavior.h:48
QToolBar * tool_bar_2d_cons_
Definition: TOPPViewBase.h:481
boost::shared_ptr< OnDiscMSExperiment > ODExperimentSharedPtrType
SharedPtr on On-Disc MSExperiment.
Definition: LayerData.h:154
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
Notice.
Definition: TOPPViewBase.h:556
boost::shared_ptr< ExperimentType > ExperimentSharedPtrType
SharedPtr on MSExperiment.
Definition: LayerData.h:149
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Tabular visualization / selection of identified spectra.
Definition: SpectraIdentificationViewWidget.h:53
QAction * dm_elements_2d_
Definition: TOPPViewBase.h:490
QAction * linkZoom_action_
Definition: TOPPViewBase.h:461
QAction * dm_precursors_2d_
Definition: TOPPViewBase.h:483
QToolBar * tool_bar_
Definition: TOPPViewBase.h:469
String current_path_
Definition: TOPPViewBase.h:571
QDockWidget * layer_dock_widget_
Definition: TOPPViewBase.h:432
QToolBar * tool_bar_1d_
Definition: TOPPViewBase.h:475
LayerData::FeatureMapSharedPtrType FeatureMapSharedPtrType
Definition: TOPPViewBase.h:138
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
QButtonGroup * intensity_button_group_
Definition: TOPPViewBase.h:472
boost::shared_ptr< ConsensusMap > ConsensusMapSharedPtrType
SharedPtr on consensus features.
Definition: LayerData.h:143
Management and storage of parameters / INI files.
Definition: Param.h:73
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
bool zoom_together_
Stores whether the individual windows should zoom together (be linked) or not.
Definition: TOPPViewBase.h:459
QListWidget * layers_view_
Layer management widget.
Definition: TOPPViewBase.h:444
boost::shared_ptr< FeatureMap > FeatureMapSharedPtrType
SharedPtr on feature map.
Definition: LayerData.h:137
A container for consensus elements.
Definition: ConsensusMap.h:79
QActionGroup * group_label_2d_
Definition: TOPPViewBase.h:487
DataType
Definition: LayerData.h:92
QAction * dm_hull_2d_
Definition: TOPPViewBase.h:484
Hierarchical visualization and selection of spectra.
Definition: SpectraViewWidget.h:51
bool watcher_msgbox_
Holds the messageboxes for each layer that are currently popped up (to avoid popping them up again...
Definition: TOPPViewBase.h:456
QCheckBox * filters_check_box_
Definition: TOPPViewBase.h:449
QToolButton * dm_label_2d_
Definition: TOPPViewBase.h:486
EnhancedTabBar * tab_bar_
Tab bar. The address of the corresponding window to a tab is stored as an int in tabData() ...
Definition: TOPPViewBase.h:499
std::vector< QAction * > recent_actions_
list of the recently opened files actions (menu entries)
Definition: TOPPViewBase.h:521
QTextEdit * log_
Log output window.
Definition: TOPPViewBase.h:464
FileWatcher * watcher_
Watcher that tracks file changes (in order to update the data in the different views) ...
Definition: TOPPViewBase.h:453
QStringList recent_files_
list of the recently opened files
Definition: TOPPViewBase.h:519
Widget for visualization of several spectra.
Definition: Spectrum1DWidget.h:65
TOPPViewSpectraViewBehavior * spectraview_behavior_
TOPPView behavior for the spectra view.
Definition: TOPPViewBase.h:579
QLabel * rt_label_
RT label for messages in the status bar.
Definition: TOPPViewBase.h:509
ExperimentType::SpectrumType SpectrumType
Peak spectrum type.
Definition: TOPPViewBase.h:152
QAction * projections_2d_
Definition: TOPPViewBase.h:491
QToolButton * dm_unassigned_2d_
Definition: TOPPViewBase.h:488
Warning.
Definition: TOPPViewBase.h:557
QMenu * add_2d_context_
Additional context menu for 2D layers.
Definition: TOPPViewBase.h:564
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Widget for 3D-visualization of map data.
Definition: Spectrum3DWidget.h:53
Convenience tab bar implementation.
Definition: EnhancedTabBar.h:60
QAction * dm_hulls_2d_
Definition: TOPPViewBase.h:485