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TOPPViewBase.h
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1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
6 //
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29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg$
32 // $Authors: Marc Sturm, Timo Sachsenberg $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 // OpenMS_GUI config
38 #include <OpenMS/VISUAL/OpenMS_GUIConfig.h>
39
40 //OpenMS
41 #include <OpenMS/KERNEL/StandardTypes.h>
42 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
43 #include <OpenMS/VISUAL/SpectrumCanvas.h>
44 #include <OpenMS/VISUAL/SpectrumWidget.h>
45 #include <OpenMS/SYSTEM/FileWatcher.h>
46 #include <OpenMS/VISUAL/SpectraViewWidget.h>
47 #include <OpenMS/VISUAL/SpectraIdentificationViewWidget.h>
48
49 #include <OpenMS/VISUAL/TOPPViewSpectraViewBehavior.h>
50 #include <OpenMS/VISUAL/TOPPViewIdentificationViewBehavior.h>
51
52 //STL
53 #include <map>
54
55 //QT
56 #include <QtWidgets/QMainWindow>
57 #include <QtWidgets/QButtonGroup>
58 #include <QtWidgets/QActionGroup>
59 #include <QtCore/QStringList>
60 #include <QtCore/QProcess>
61
62 class QAction;
63 class QComboBox;
64 class QLabel;
65 class QLineEdit;
66 class QListWidget;
67 class QListWidgetItem;
68 class QTreeWidget;
69 class QTreeWidgetItem;
70 class QDockWidget;
71 class QToolButton;
72 class QCloseEvent;
73 class QTextEdit;
74 class QCheckBox;
75 class QSplashScreen;
76 class QToolButton;
77 class QWorkspace;
78
79 namespace OpenMS
80 {
81 class EnhancedWorkspace;
82 class EnhancedTabBar;
83 class Spectrum1DWidget;
84 class Spectrum2DWidget;
85 class Spectrum3DWidget;
86 class ToolsDialog;
87 class MultiGradientSelector;
88 class FileWatcher;
89
124 class OPENMS_GUI_DLLAPI TOPPViewBase :
125 public QMainWindow,
126 public DefaultParamHandler
127 {
128 Q_OBJECT
129
130 friend class TestTOPPView;
131
132 public:
134
135 //Feature map type
136 typedef LayerData::FeatureMapType FeatureMapType;
137 //Feature map managed type
138 typedef LayerData::FeatureMapSharedPtrType FeatureMapSharedPtrType;
139
140 //Consensus feature map type
141 typedef LayerData::ConsensusMapType ConsensusMapType;
142 //Consensus map managed type
143 typedef LayerData::ConsensusMapSharedPtrType ConsensusMapSharedPtrType;
144
145 //Peak map type
146 typedef LayerData::ExperimentType ExperimentType;
147 //Main managed data type (experiment)
148 typedef LayerData::ExperimentSharedPtrType ExperimentSharedPtrType;
149 //Main on-disc managed data type (experiment)
150 typedef LayerData::ODExperimentSharedPtrType ODExperimentSharedPtrType;
152 typedef ExperimentType::SpectrumType SpectrumType;
154
156 TOPPViewBase(QWidget* parent = nullptr);
158 ~TOPPViewBase() override;
159
172 void addDataFile(const String& filename, bool show_options, bool add_to_recent, String caption = "", UInt window_id = 0, Size spectrum_id = 0);
173
190 void addData(FeatureMapSharedPtrType feature_map,
191 ConsensusMapSharedPtrType consensus_map,
192 std::vector<PeptideIdentification>& peptides,
193 ExperimentSharedPtrType peak_map,
194 ODExperimentSharedPtrType on_disc_peak_map,
195 LayerData::DataType data_type,
196 bool show_as_1d,
197 bool show_options,
198 bool as_new_window = true,
199 const String& filename = "",
200 const String& caption = "",
201 UInt window_id = 0,
202 Size spectrum_id = 0);
203
205 void loadFiles(const StringList& list, QSplashScreen* splash_screen);
206
212 void loadPreferences(String filename = "");
213
215 void savePreferences();
216
218 Param getSpectrumParameters(UInt dim);
219
221 const LayerData* getCurrentLayer() const;
222
223 //@name Accessors for the main gui components.
224 //@brief The top level enhanced workspace and the EnhancedTabWidgets resing in the EnhancedTabBar.
226 EnhancedWorkspace* getWorkspace() const;
228
230 SpectrumWidget* getActiveSpectrumWidget() const;
231
233 Spectrum1DWidget* getActive1DWidget() const;
234
236 Spectrum2DWidget* getActive2DWidget() const;
237
239 Spectrum3DWidget* getActive3DWidget() const;
241
243 SpectrumCanvas* getActiveCanvas() const;
244
246 SpectraIdentificationViewWidget* getSpectraIdentificationViewWidget();
247
249 void showSpectrumWidgetInWindow(SpectrumWidget* sw, const String& caption);
250
251 public slots:
253 void updateCurrentPath();
255 void showURL();
257 void openFileDialog();
259 void openExampleDialog();
261 void showGoToDialog();
263 void preferencesDialog();
265 void layerStatistics();
267 void editMetadata();
269 void layerActivated();
271 void layerZoomChanged();
273 void linkZoom();
275 void layerDeactivated();
277 void closeFile();
279 void updateToolBar();
281 void updateLayerBar();
283 void updateViewBar();
285 void viewChanged(int);
287 void viewTabwidgetDoubleClicked(int);
289 void updateFilterBar();
291 void updateMenu();
293 void updateTabBar(QMdiSubWindow* w);
295 void tileVertical();
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();
331 void saveLayerAll();
333 void saveLayerVisible();
335 void toggleGridLines();
337 void toggleAxisLegends();
339 void toggleInterestingMZs();
341 void showPreferences();
343 void metadataFileDialog();
344
348 void setDrawMode1D(int);
349 void setIntensityMode(int);
350 void changeLayerFlag(bool);
351 void changeLabel(QAction*);
352 void changeUnassigned(QAction*);
353 void resetZoom();
354 void toggleProjections();
356
358 void loadFile(QString);
359
360 protected slots:
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* /*item*/);
381
383 void finishTOPPToolExecution(int exitCode, QProcess::ExitStatus exitStatus);
385 void abortTOPPTool();
387 void rerunTOPPTool();
389 void showSpectrumBrowser();
391 void showSpectrumMetaData(int spectrum_index);
392
396 void closeByTab(int id);
399 void enhancedWorkspaceWindowChanged(int id);
401 void openRecentFile();
403 void copyLayer(const QMimeData* data, QWidget* source, int id = -1);
405
407 void updateProcessLog();
408
410 void fileChanged_(const String&);
411 protected:
413 void initializeDefaultParameters_();
414
417 bool annotateMS1FromMassFingerprinting_(const FeatureMap& identifications);
418
420 std::set<String> getFilenamesOfOpenFiles_();
421
425 QStringList getFileList_(const String& path_overwrite = "");
426
428 EnhancedTabBarWidgetInterface* window_(int id) const;
429
431
432 QDockWidget* layer_dock_widget_;
433 QDockWidget* views_dockwidget_;
434 QDockWidget* filter_dock_widget_;
436
438
439 SpectraViewWidget* spectra_view_widget_;
440 SpectraIdentificationViewWidget* spectra_identification_view_widget_;
442
444 QListWidget* layers_view_;
445
447
448 QListWidget* filters_;
449 QCheckBox* filters_check_box_;
451
453 FileWatcher* watcher_;
454
456 bool watcher_msgbox_;
457
459 bool zoom_together_;
460
461 QAction* linkZoom_action_;
462
464 QTextEdit* log_;
465
469 QToolBar* tool_bar_;
470
471 // common intensity modes
472 QButtonGroup* intensity_button_group_;
473
474 // 1D specific stuff
475 QToolBar* tool_bar_1d_;
476 QButtonGroup* draw_group_1d_;
477
478 // 2D specific stuff
479 QToolBar* tool_bar_2d_peak_;
480 QToolBar* tool_bar_2d_feat_;
481 QToolBar* tool_bar_2d_cons_;
482 QToolBar* tool_bar_2d_ident_;
483 QAction* dm_precursors_2d_;
484 QAction* dm_hull_2d_;
485 QAction* dm_hulls_2d_;
486 QToolButton* dm_label_2d_;
487 QActionGroup* group_label_2d_;
488 QToolButton* dm_unassigned_2d_;
489 QActionGroup* group_unassigned_2d_;
490 QAction* dm_elements_2d_;
491 QAction* projections_2d_;
492 QAction* dm_ident_2d_;
494
496 EnhancedWorkspace* ws_;
497
499 EnhancedTabBar* tab_bar_;
500
504 QLabel* message_label_;
507 QLabel* mz_label_;
509 QLabel* rt_label_;
511
513
514 void addRecentFile_(const String& filename);
517 void updateRecentMenu_();
519 QStringList recent_files_;
521 std::vector<QAction*> recent_actions_;
523
524
526
527 void runTOPPTool_();
530 struct
531 {
532 Param param;
533 String tool;
534 String in;
535 String out;
536 String file_name;
537 String layer_name;
538 UInt window_id;
539 Size spectrum_id;
540 QProcess* process;
541 QTime timer;
542 bool visible;
543 } topp_;
545
547 void checkPreferences_();
549
550 void closeEvent(QCloseEvent* event) override;
552
554 enum LogState
555 {
556 LS_NOTICE,
557 LS_WARNING,
558 LS_ERROR
559 };
561 void showLogMessage_(LogState state, const String& heading, const String& body);
562
564 QMenu* add_2d_context_;
565
567 void showTOPPDialog_(bool visible);
568
571 String current_path_;
572
574 QTabWidget* views_tabwidget_;
575
577 TOPPViewIdentificationViewBehavior* identificationview_behavior_;
579 TOPPViewSpectraViewBehavior* spectraview_behavior_;
580
581 // static helper functions
582 public:
584 static bool containsMS1Scans(const ExperimentType& exp);
585
587 static bool containsIMData(const MSSpectrum& s);
588
590 float estimateNoiseFromRandomMS1Scans(const ExperimentType& exp, UInt n_scans = 10);
591
593 static bool hasMS1Zeros(const ExperimentType& exp);
594
596 static bool hasPeptideIdentifications(const ExperimentType& map);
597
598 private:
600 static const String CAPTION_3D_SUFFIX_;
601 }; //class
602
603 } //namespace
604
FileWatcher.h
QLineEdit
QListWidget
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::TOPPViewBase::FeatureMapType
LayerData::FeatureMapType FeatureMapType
Definition: TOPPViewBase.h:136
OpenMS::TOPPViewBase::CAPTION_3D_SUFFIX_
static const String CAPTION_3D_SUFFIX_
Suffix appended to caption of tabs when layer is shown in 3D.
Definition: TOPPViewBase.h:600
OpenMS::TOPPViewBase::ConsensusMapSharedPtrType
LayerData::ConsensusMapSharedPtrType ConsensusMapSharedPtrType
Definition: TOPPViewBase.h:143
QWidget
OpenMS::LayerData
Class that stores the data for one layer.
Definition: LayerData.h:85
OpenMS::TOPPViewBase::views_dockwidget_
QDockWidget * views_dockwidget_
Definition: TOPPViewBase.h:433
OpenMS::TOPPViewBase::views_tabwidget_
QTabWidget * views_tabwidget_
Tabwidget that hold the different views on the loaded data.
Definition: TOPPViewBase.h:574
QTreeWidget
OpenMS::TOPPViewBase
Main window of TOPPView tool.
Definition: TOPPViewBase.h:124
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS::TOPPViewIdentificationViewBehavior
Behavior of TOPPView in identification mode.
Definition: TOPPViewIdentificationViewBehavior.h:49
OpenMS::TOPPViewBase::draw_group_1d_
QButtonGroup * draw_group_1d_
Definition: TOPPViewBase.h:476
OpenMS::Spectrum2DWidget
Widget for 2D-visualization of peak map and feature map data.
Definition: Spectrum2DWidget.h:63
OpenMS::TOPPViewBase::ConsensusMapType
LayerData::ConsensusMapType ConsensusMapType
Definition: TOPPViewBase.h:141
OpenMS::TOPPViewBase::spectra_view_widget_
SpectraViewWidget * spectra_view_widget_
Definition: TOPPViewBase.h:439
OpenMS::TOPPViewBase::filters_
QListWidget * filters_
Definition: TOPPViewBase.h:448
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::TOPPViewBase::filter_dock_widget_
QDockWidget * filter_dock_widget_
Definition: TOPPViewBase.h:434
OpenMS::FileWatcher
Watcher that monitors file changes.
Definition: FileWatcher.h:65
OpenMS::TOPPViewBase::ODExperimentSharedPtrType
LayerData::ODExperimentSharedPtrType ODExperimentSharedPtrType
Definition: TOPPViewBase.h:150
OpenMS::SpectrumWidget
Base class for spectrum widgets.
Definition: SpectrumWidget.h:80
OpenMS::EnhancedWorkspace
Definition: EnhancedWorkspace.h:49
OpenMS::TOPPViewBase::tool_bar_2d_ident_
QToolBar * tool_bar_2d_ident_
Definition: TOPPViewBase.h:482
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:95
OpenMS::TOPPViewBase::tool_bar_2d_peak_
QToolBar * tool_bar_2d_peak_
Definition: TOPPViewBase.h:479
OpenMS::TOPPViewBase::LogState
LogState
Log message states.
Definition: TOPPViewBase.h:554
OpenMS::TOPPViewBase::mz_label_
QLabel * mz_label_
m/z label for messages in the status bar
Definition: TOPPViewBase.h:507
OpenMS::TOPPViewBase::tool_bar_2d_feat_
QToolBar * tool_bar_2d_feat_
Definition: TOPPViewBase.h:480
StandardTypes.h
OpenMS::TOPPViewBase::ws_
EnhancedWorkspace * ws_
Main workspace.
Definition: TOPPViewBase.h:496
OpenMS::TOPPViewBase::dm_ident_2d_
QAction * dm_ident_2d_
Definition: TOPPViewBase.h:492
OpenMS::TOPPViewBase::group_unassigned_2d_
QActionGroup * group_unassigned_2d_
Definition: TOPPViewBase.h:489
OpenMS::TOPPViewBase::spectra_identification_view_widget_
SpectraIdentificationViewWidget * spectra_identification_view_widget_
Definition: TOPPViewBase.h:440
OpenMS::TOPPViewBase::ExperimentSharedPtrType
LayerData::ExperimentSharedPtrType ExperimentSharedPtrType
Definition: TOPPViewBase.h:148
OpenMS::TOPPViewBase::ExperimentType
LayerData::ExperimentType ExperimentType
Definition: TOPPViewBase.h:146
OpenMS::SpectrumCanvas
Base class for visualization canvas classes.
Definition: SpectrumCanvas.h:98
TOPPViewIdentificationViewBehavior.h
OpenMS::EnhancedTabBarWidgetInterface
Widgets that are placed into an EnhancedTabBar must implement this interface.
Definition: EnhancedTabBarWidgetInterface.h:51
OpenMS::TOPPViewBase::identificationview_behavior_
TOPPViewIdentificationViewBehavior * identificationview_behavior_
TOPPView behavior for the identification view.
Definition: TOPPViewBase.h:577
OpenMS::TOPPViewSpectraViewBehavior
Behavior of TOPPView in spectra view mode.
Definition: TOPPViewSpectraViewBehavior.h:48
OpenMS::TOPPViewBase::tool_bar_2d_cons_
QToolBar * tool_bar_2d_cons_
Definition: TOPPViewBase.h:481
OpenMS::LayerData::ODExperimentSharedPtrType
boost::shared_ptr< OnDiscMSExperiment > ODExperimentSharedPtrType
SharedPtr on On-Disc MSExperiment.
Definition: LayerData.h:154
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS::TOPPViewBase::LS_NOTICE
Notice.
Definition: TOPPViewBase.h:556
OpenMS::LayerData::ExperimentSharedPtrType
boost::shared_ptr< ExperimentType > ExperimentSharedPtrType
SharedPtr on MSExperiment.
Definition: LayerData.h:149
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::SpectraIdentificationViewWidget
Tabular visualization / selection of identified spectra.
Definition: SpectraIdentificationViewWidget.h:53
SpectrumCanvas.h
OpenMS::TOPPViewBase::dm_elements_2d_
QAction * dm_elements_2d_
Definition: TOPPViewBase.h:490
OpenMS::TOPPViewBase::linkZoom_action_
QAction * linkZoom_action_
Definition: TOPPViewBase.h:461
OpenMS::TOPPViewBase::dm_precursors_2d_
QAction * dm_precursors_2d_
Definition: TOPPViewBase.h:483
OpenMS::TOPPViewBase::tool_bar_
QToolBar * tool_bar_
Definition: TOPPViewBase.h:469
SpectraViewWidget.h
OpenMS::TOPPViewBase::current_path_
String current_path_
Definition: TOPPViewBase.h:571
TOPPViewSpectraViewBehavior.h
SpectrumWidget.h
DefaultParamHandler.h
OpenMS::TOPPViewBase::layer_dock_widget_
QDockWidget * layer_dock_widget_
Definition: TOPPViewBase.h:432
OpenMS::TOPPViewBase::tool_bar_1d_
QToolBar * tool_bar_1d_
Definition: TOPPViewBase.h:475
OpenMS::TOPPViewBase::FeatureMapSharedPtrType
LayerData::FeatureMapSharedPtrType FeatureMapSharedPtrType
Definition: TOPPViewBase.h:138
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::TOPPViewBase::intensity_button_group_
QButtonGroup * intensity_button_group_
Definition: TOPPViewBase.h:472
QMainWindow
OpenMS::LayerData::ConsensusMapSharedPtrType
boost::shared_ptr< ConsensusMap > ConsensusMapSharedPtrType
SharedPtr on consensus features.
Definition: LayerData.h:143
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:73
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::TOPPViewBase::zoom_together_
bool zoom_together_
Stores whether the individual windows should zoom together (be linked) or not.
Definition: TOPPViewBase.h:459
OpenMS::TOPPViewBase::layers_view_
QListWidget * layers_view_
Layer management widget.
Definition: TOPPViewBase.h:444
OpenMS::LayerData::FeatureMapSharedPtrType
boost::shared_ptr< FeatureMap > FeatureMapSharedPtrType
SharedPtr on feature map.
Definition: LayerData.h:137
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:79
QTextEdit
OpenMS::TOPPViewBase::group_label_2d_
QActionGroup * group_label_2d_
Definition: TOPPViewBase.h:487
OpenMS::LayerData::DataType
DataType
Definition: LayerData.h:92
OpenMS::TOPPViewBase::dm_hull_2d_
QAction * dm_hull_2d_
Definition: TOPPViewBase.h:484
OpenMS::SpectraViewWidget
Hierarchical visualization and selection of spectra.
Definition: SpectraViewWidget.h:51
OpenMS::TOPPViewBase::watcher_msgbox_
bool watcher_msgbox_
Holds the messageboxes for each layer that are currently popped up (to avoid popping them up again...
Definition: TOPPViewBase.h:456
OpenMS::TOPPViewBase::filters_check_box_
QCheckBox * filters_check_box_
Definition: TOPPViewBase.h:449
OpenMS::TOPPViewBase::dm_label_2d_
QToolButton * dm_label_2d_
Definition: TOPPViewBase.h:486
OpenMS::TOPPViewBase::tab_bar_
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
OpenMS::TOPPViewBase::recent_actions_
std::vector< QAction * > recent_actions_
list of the recently opened files actions (menu entries)
Definition: TOPPViewBase.h:521
OpenMS::TOPPViewBase::log_
QTextEdit * log_
Log output window.
Definition: TOPPViewBase.h:464
OpenMS::TOPPViewBase::watcher_
FileWatcher * watcher_
Watcher that tracks file changes (in order to update the data in the different views) ...
Definition: TOPPViewBase.h:453
OpenMS::TOPPViewBase::recent_files_
QStringList recent_files_
list of the recently opened files
Definition: TOPPViewBase.h:519
OpenMS::Spectrum1DWidget
Widget for visualization of several spectra.
Definition: Spectrum1DWidget.h:65
OpenMS::TOPPViewBase::spectraview_behavior_
TOPPViewSpectraViewBehavior * spectraview_behavior_
TOPPView behavior for the spectra view.
Definition: TOPPViewBase.h:579
OpenMS::TOPPViewBase::rt_label_
QLabel * rt_label_
RT label for messages in the status bar.
Definition: TOPPViewBase.h:509
OpenMS::TOPPViewBase::SpectrumType
ExperimentType::SpectrumType SpectrumType
Peak spectrum type.
Definition: TOPPViewBase.h:152
OpenMS::TOPPViewBase::projections_2d_
QAction * projections_2d_
Definition: TOPPViewBase.h:491
OpenMS::TOPPViewBase::dm_unassigned_2d_
QToolButton * dm_unassigned_2d_
Definition: TOPPViewBase.h:488
OpenMS::TOPPViewBase::LS_WARNING
Warning.
Definition: TOPPViewBase.h:557
OpenMS::TOPPViewBase::add_2d_context_
QMenu * add_2d_context_
Additional context menu for 2D layers.
Definition: TOPPViewBase.h:564
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
SpectraIdentificationViewWidget.h
QProcess
OpenMS::Spectrum3DWidget
Widget for 3D-visualization of map data.
Definition: Spectrum3DWidget.h:53
OpenMS::EnhancedTabBar
Convenience tab bar implementation.
Definition: EnhancedTabBar.h:60
OpenMS::TOPPViewBase::dm_hulls_2d_
QAction * dm_hulls_2d_
Definition: TOPPViewBase.h:485