OpenMS  3.0.0
TOPPViewBase.h
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31 // $Maintainer: Timo Sachsenberg$
32 // $Authors: Marc Sturm, Timo Sachsenberg $
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34 
35 #pragma once
36 
37 // OpenMS_GUI config
38 #include <OpenMS/VISUAL/OpenMS_GUIConfig.h>
39 
40 //OpenMS
53 
54 //STL
55 #include <map>
56 
57 //QT
58 #include <QtWidgets/QMainWindow>
59 #include <QtWidgets/QButtonGroup>
60 #include <QtWidgets/QActionGroup>
61 #include <QtCore/QStringList>
62 #include <QtCore/QProcess>
63 #include <QElapsedTimer>
64 
65 class QAction;
66 class QComboBox;
67 class QLabel;
68 class QLineEdit;
69 class QListWidget;
70 class QListWidgetItem;
71 class QTreeWidget;
72 class QTreeWidgetItem;
73 class QDockWidget;
74 class QToolButton;
75 class QCloseEvent;
76 class QCheckBox;
77 class QSplashScreen;
78 class QToolButton;
79 
80 namespace OpenMS
81 {
82  class DataSelectionTabs;
83  class FileWatcher;
84  class LogWindow;
85  class LayerListView;
86  class MultiGradientSelector;
87  class Plot1DWidget;
88  class Plot2DWidget;
89  class Plot3DWidget;
90  class ToolsDialog;
91 
126  class OPENMS_GUI_DLLAPI TOPPViewBase :
127  public QMainWindow,
128  public DefaultParamHandler
129  {
130  Q_OBJECT
131 
132  friend class TestTOPPView;
133 
134 public:
136 
137  //Feature map type
139  //Feature map managed type
141 
142  //Consensus feature map type
144  //Consensus map managed type
146 
147  //Peak map type
149  //Main managed data type (experiment)
151  //Main on-disc managed data type (experiment)
156 
158  enum class TOOL_SCAN
159  {
164  SKIP_SCAN,
166  SCAN_IF_NEWER_VERSION,
168  FORCE_SCAN
169  };
170 
172  explicit TOPPViewBase(TOOL_SCAN scan_mode = TOOL_SCAN::SCAN_IF_NEWER_VERSION, QWidget* parent = nullptr);
174  ~TOPPViewBase() override;
175 
176  enum class LOAD_RESULT
177  {
178  OK,
179  FILE_NOT_FOUND,
180  FILETYPE_UNKNOWN,
181  FILETYPE_UNSUPPORTED,
182  LOAD_ERROR
183  };
184 
197  LOAD_RESULT addDataFile(const String& filename, bool show_options, bool add_to_recent, String caption = "", UInt window_id = 0, Size spectrum_id = 0);
198 
215  void addData(FeatureMapSharedPtrType feature_map,
216  ConsensusMapSharedPtrType consensus_map,
217  std::vector<PeptideIdentification>& peptides,
218  ExperimentSharedPtrType peak_map,
219  ODExperimentSharedPtrType on_disc_peak_map,
220  LayerDataBase::DataType data_type,
221  bool show_as_1d,
222  bool show_options,
223  bool as_new_window = true,
224  const String& filename = "",
225  const String& caption = "",
226  UInt window_id = 0,
227  Size spectrum_id = 0);
228 
230  void loadFiles(const StringList& list, QSplashScreen* splash_screen);
231 
237  void loadPreferences(String filename = "");
238 
240  void savePreferences();
241 
243  Param getCanvasParameters(UInt dim) const;
244 
246  const LayerDataBase* getCurrentLayer() const;
247 
249  LayerDataBase* getCurrentLayer();
250 
251  //@name Accessors for the main gui components.
252  //@brief The top level enhanced workspace and the EnhancedTabWidgets resing in the EnhancedTabBar.
254  EnhancedWorkspace* getWorkspace();
256 
258  PlotWidget* getActivePlotWidget() const;
259 
261  Plot1DWidget* getActive1DWidget() const;
262 
264  Plot2DWidget* getActive2DWidget() const;
265 
267  Plot3DWidget* getActive3DWidget() const;
269 
271  PlotCanvas* getActiveCanvas() const;
272 
274  void showPlotWidgetInWindow(PlotWidget* sw, const String& caption);
275 
276 public slots:
278  void updateCurrentPath();
280  void openFilesByDialog(const String& initial_directory = "");
282  void showGoToDialog() const;
284  void preferencesDialog();
286  void layerStatistics() const;
288  void editMetadata();
290  void layerActivated();
292  void layerZoomChanged() const;
294  void linkZoom();
296  void layerDeactivated();
298  void closeTab();
299 
301  void rerunTOPPTool();
302 
304  void updateBarsAndMenus();
306  void updateToolBar();
308  void updateLayerBar();
310  void updateViewBar();
312  void updateMenu();
314  void updateFilterBar();
321  void showStatusMessage(std::string msg, OpenMS::UInt time);
323  void showCursorStatus(double mz, double rt);
325  void showCursorStatusInvert(double mz, double rt);
327  void showTOPPDialog();
329  void annotateWithAMS();
331  void annotateWithID();
333  void annotateWithOSW();
335  void showSpectrumGenerationDialog();
337  void showSpectrumAlignmentDialog();
339  void showCurrentPeaksAs2D();
341  void showCurrentPeaksAs3D();
343  void showCurrentPeaksAsIonMobility();
345  void showCurrentPeaksAsDIA();
347  void saveLayerAll() const;
349  void saveLayerVisible() const;
351  void toggleGridLines() const;
353  void toggleAxisLegends() const;
355  void toggleInterestingMZs() const;
357  void showPreferences() const;
359  void metadataFileDialog();
360 
364  void setDrawMode1D(int) const;
365  void setIntensityMode(int);
366  void changeLayerFlag(bool);
367  void changeLabel(QAction*);
368  void changeUnassigned(QAction*);
369  void resetZoom() const;
370  void toggleProjections();
372 
375  void openFile(const String& filename);
376 
378  void layerFilterVisibilityChange(bool) const;
379 
381  void showSpectrumMetaData(int spectrum_index) const;
382 
383 protected slots:
385  void finishTOPPToolExecution(int exitCode, QProcess::ExitStatus exitStatus);
387  void abortTOPPTool();
389  void showSpectrumBrowser();
390 
394  void closeByTab(int id);
397  void showWindow(int id);
399  void copyLayer(const QMimeData* data, QWidget* source, int id = -1);
401 
403  void updateProcessLog();
404 
406  void fileChanged_(const String&);
407 protected:
409  void initializeDefaultParameters_();
410 
414  QStringList chooseFilesDialog_(const String& path_overwrite = "");
415 
417 
418  QDockWidget* layer_dock_widget_;
419  QDockWidget* views_dockwidget_;
420  QDockWidget* filter_dock_widget_;
422 
425 
427 
429 
432 
434  FileWatcher* watcher_ = nullptr;
435 
437  bool watcher_msgbox_ = false;
438 
440  bool zoom_together_ = false;
441 
444 
449 
453  QToolBar* tool_bar_;
454 
455  // common intensity modes
456  QButtonGroup* intensity_button_group_;
457 
458  // 1D specific stuff
459  QToolBar* tool_bar_1d_;
460  QButtonGroup* draw_group_1d_;
461 
462  // 2D specific stuff
463  QToolBar* tool_bar_2d_peak_;
464  QToolBar* tool_bar_2d_feat_;
465  QToolBar* tool_bar_2d_cons_;
468  QAction* dm_hull_2d_;
469  QAction* dm_hulls_2d_;
470  QToolButton* dm_label_2d_;
471  QActionGroup* group_label_2d_;
472  QToolButton* dm_unassigned_2d_;
473  QActionGroup* group_unassigned_2d_;
474  QAction* dm_elements_2d_;
475  QAction* projections_2d_;
476  QAction* dm_ident_2d_;
478 
480  EnhancedWorkspace ws_; // not a pointer, but an actual object, so it gets destroyed before the DefaultParamhandler (on which it depends)
484  QMdiSubWindow* lastActiveSubwindow_ = nullptr; // due to Qt bugs or confusing features we need to save the current Window id in the children of the workspace;
488  RecentFilesMenu recent_files_; // needs to be declared before 'menu_', because its needed there
491 
495  QLabel* message_label_;
498  QLabel* mz_label_;
500  QLabel* rt_label_;
502 
504 
505  void addRecentFile_(const String& filename);
507 
509 
510 
512 
513  void runTOPPTool_();
516  struct
517  {
518  Param param;
519  String tool;
520  String in;
521  String out;
522  String file_name;
523  String layer_name;
524  UInt window_id;
525  Size spectrum_id;
526  QProcess* process = nullptr;
527  QElapsedTimer timer;
528  bool visible_area_only;
529  } topp_;
531 
533  void checkPreferences_();
535 
536  void closeEvent(QCloseEvent* event) override;
538 
541 
543  void showTOPPDialog_(bool visible);
544 
548 
549 private:
552 
555  }; //class
556 
557 } //namespace
558 
OpenMS::TOPPViewBase::group_label_2d_
QActionGroup * group_label_2d_
Definition: TOPPViewBase.h:471
LogStream.h
IMDataConverter.h
DefaultParamHandler.h
tool_name
const char * tool_name
Definition: TOPPView.cpp:79
OpenMS::PlotCanvas::setLayerName
void setLayerName(Size i, const String &name)
Sets the name of layer i.
OpenMS::TOPPViewBase::openFile
void openFile(const String &filename)
Definition: TOPPViewBase.cpp:1013
OpenMS::LayerDataBase::F_HULL
Features: Overall convex hull.
Definition: LayerDataBase.h:117
OpenMS::TOPPViewBase::showStatusMessage
void showStatusMessage(std::string msg, OpenMS::UInt time)
Shows a status message in the status bar.
Definition: TOPPViewBase.cpp:1059
OpenMS::TOPPViewBase::layers_view_
LayerListView * layers_view_
Layer management widget.
Definition: TOPPViewBase.h:424
OpenMS::FileTypes::IDXML
OpenMS identification format (.idXML)
Definition: FileTypes.h:64
OpenMS::TOPPViewBase::showWindow
void showWindow(int id)
Raises the window corresponding to the data of the tab with identifier id.
Definition: TOPPViewBase.cpp:1028
SpectrumAlignmentDialog.h
LayerListView.h
ConsensusXMLFile.h
TOPPViewBase.h
OpenMS::EnhancedWorkspace
Definition: EnhancedWorkspace.h:51
PlotWidget.h
OpenMS::StringUtils::hasSubstring
static bool hasSubstring(const String &this_s, const String &string)
Definition: StringUtilsSimple.h:137
OpenMS::DataSelectionTabs::showSpectrumAsNew1D
void showSpectrumAsNew1D(int index)
forwards to the TOPPView*Behaviour classes, to show a certain spectrum in 1D
OpenMS::TheoreticalSpectrumGenerationDialog::getSpectrum
const MSSpectrum & getSpectrum() const
returns the calculated spectrum
OpenMS::Plot2DWidget::getHorizontalProjection
const Plot1DWidget * getHorizontalProjection() const
const reference to the horizontal projection
FileHandler.h
OpenMS::TOPPViewOpenDialog::isDataDIA
bool isDataDIA() const
Returns if the data is DIA / SWATH-MS data.
FileTypes.h
TextFile.h
OpenMS::LayerDataBase::getChromatogramData
const ExperimentSharedPtrType & getChromatogramData() const
Returns a mutable reference to the current chromatogram data.
Definition: LayerDataBase.h:262
OpenMS::TOPPViewBase::setIntensityMode
void setIntensityMode(int)
Definition: TOPPViewBase.cpp:1118
OpenMS::PlotCanvas::setCurrentLayerParameters
void setCurrentLayerParameters(const Param &param)
Sets the parameters of the current layer.
Definition: PlotCanvas.h:465
OpenMS::TOPPViewBase::showPlotWidgetInWindow
void showPlotWidgetInWindow(PlotWidget *sw, const String &caption)
Opens the provided spectrum widget in a new window.
Definition: TOPPViewBase.cpp:1436
OpenMS::PlotCanvas::IntensityModes
IntensityModes
Display modes of intensity.
Definition: PlotCanvas.h:184
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:486
OpenMS::LayerDataBase::L_INDEX
The element number is used.
Definition: LayerDataBase.h:135
AxisWidget.h
TheoreticalSpectrumGenerationDialog.h
OpenMS::LayerDataBase::DT_UNKNOWN
Undefined data type indicating an error.
Definition: LayerDataBase.h:111
OpenMS::LayerListView::update
void update(PlotWidget *active_widget)
rebuild list of layers and remember current widget (for context menu etc)
OpenMS::FileWatcher::removeFile
void removeFile(const String &path)
removes a file from the watcher
Definition: FileWatcher.h:90
OpenMS::Plot1DCanvas
Canvas for visualization of one or several spectra.
Definition: Plot1DCanvas.h:70
OpenMS::PeakFileOptions::setMetadataOnly
void setMetadataOnly(bool only)
sets whether or not to load only meta data
OpenMS::user_section
const std::string user_section
Definition: TOPPViewBase.cpp:110
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:551
OpenMS::Internal::IndexedMzMLHandler::openFile
void openFile(const String &filename)
Open a file.
OpenMS::PlotCanvas::getLayerCount
Size getLayerCount() const
Returns the number of layers.
Definition: PlotCanvas.h:368
OpenMS::LayerDataBase::I_PEPTIDEMZ
Identifications: m/z source.
Definition: LayerDataBase.h:123
OpenMS::EnhancedTabBarWidgetInterface
Widgets that are placed into an EnhancedTabBar must implement this interface.
Definition: EnhancedTabBarWidgetInterface.h:84
OpenMS::PlotWidget
Base class for spectrum widgets.
Definition: PlotWidget.h:80
VersionInfo.h
OpenMS::TOPPViewBase::ExperimentSharedPtrType
LayerDataBase::ExperimentSharedPtrType ExperimentSharedPtrType
Definition: TOPPViewBase.h:150
OpenMS::PlotCanvas::setVisibleArea
void setVisibleArea(const AreaType &area)
Sets the visible area.
OpenMS::ConsensusXMLFile::store
void store(const String &filename, const ConsensusMap &consensus_map)
Stores a consensus map to file.
OpenMS::LayerListView::layerDataChanged
void layerDataChanged()
emitted whenever a change to a layer happened, e.g. its name was changed, it was removed,...
OpenMS::TOPPViewBase::addRecentFile_
void addRecentFile_(const String &filename)
adds a Filename to the recent files
Definition: TOPPViewBase.cpp:1008
OpenMS::LogWindow
A log window (QTextEdit) with convenience functions.
Definition: LogWindow.h:53
SpectraTreeTab.h
OpenMS::Plot1DCanvas::activateSpectrum
void activateSpectrum(Size index, bool repaint=true)
Sets current spectrum index of current layer to index.
OpenMS::Param::setValue
void setValue(const std::string &key, const ParamValue &value, const std::string &description="", const std::vector< std::string > &tags=std::vector< std::string >())
Sets a value.
OpenMS::TOPPViewBase::mz_label_
QLabel * mz_label_
m/z label for messages in the status bar
Definition: TOPPViewBase.h:498
OpenMS::Internal::IndexedMzMLHandler::getParsingSuccess
bool getParsingSuccess() const
Returns whether parsing was successful.
OpenMS::Plot3DWidget::showCurrentPeaksAs2D
void showCurrentPeaksAs2D()
Requests to display all spectra in 2D plot.
Plot3DWidget.h
QListWidget
OpenMS::Plot2DWidget::showCurrentPeaksAs3D
void showCurrentPeaksAs3D()
Requests to display all spectra as 1D.
OpenMS::DataSelectionTabs::IDENT_IDX
second tab
Definition: DataSelectionTabs.h:84
OpenMS::TOPPViewBase::annotateWithOSW
void annotateWithOSW()
Annotates current chromatogram layer with ID data.
Definition: TOPPViewBase.cpp:2015
OpenMS::TOPPViewBase::TOOL_SCAN
TOOL_SCAN
Used for deciding whether new tool/util params should be generated or reused from TOPPView's ini file...
Definition: TOPPViewBase.h:158
OpenMS::LayerDataBase::filename
String filename
file name of the file the data comes from (if available)
Definition: LayerDataBase.h:464
OpenMS::LayerDataBase::C_ELEMENTS
Consensus features: Show elements.
Definition: LayerDataBase.h:122
OpenMS::TheoreticalSpectrumGenerationDialog::getSequence
const String getSequence() const
returns the input sequence (is public for TOPPView)
CONNECTCAST
#define CONNECTCAST(class, func, args)
Definition: CommonDefs.h:46
OpenMS::Plot3DOpenGLCanvas::setYLabel
void setYLabel(const QString &l)
Definition: Plot3DOpenGLCanvas.h:102
OpenMS::TV_STATUS::HAS_LAYER
OpenMS::TOPPViewBase::runTOPPTool_
void runTOPPTool_()
Runs the TOPP tool according to the information in topp_.
Definition: TOPPViewBase.cpp:1755
OpenMS::Param::insert
void insert(const std::string &prefix, const Param &param)
OpenMS::LayerDataBase::type
DataType type
data type (peak or feature data)
Definition: LayerDataBase.h:447
OpenMS::SpectraTreeTab
Hierarchical visualization and selection of spectra.
Definition: SpectraTreeTab.h:56
OpenMS::TOPPViewBase::TOOL_SCAN::SKIP_SCAN
OpenMS::TVToolDiscovery::waitForToolParams
void waitForToolParams()
Wait for all future params to finish evaluating.
StopWatch.h
OpenMS::LogWindow::appendNewHeader
void appendNewHeader(const LogState state, const String &heading, const String &body)
appends a new block with heading and a body
OpenMS::TOPPViewOpenDialog::getMergeLayer
Int getMergeLayer() const
Returns the index of the selected merge layer. If the option is not selected -1 is returned.
OpenMS::Param::hasSection
bool hasSection(const std::string &key) const
Checks whether a section is present.
OpenMS::PlotWidget::showStatistics
void showStatistics()
Shows statistics about the data (count, min, max, avg of intensity, charge, quality and meta data)
OpenMS::Plot1DCanvas::getDrawMode
DrawModes getDrawMode() const
Returns the draw mode of the current layer.
OpenMS::LayerAnnotatorAMS
Definition: LayerDataBase.h:591
OpenMS::TOPPViewBase::intensity_button_group_
QButtonGroup * intensity_button_group_
Definition: TOPPViewBase.h:456
OpenMS::TOPPViewBase::menu_
TOPPViewMenu menu_
manages the menu items (active/inactive) and recent files etc
Definition: TOPPViewBase.h:490
OpenMS::File::basename
static String basename(const String &file)
OpenMS::Exception::InvalidValue
Invalid value exception.
Definition: Exception.h:327
OpenMS::PlotWidget::xAxis
virtual AxisWidget * xAxis()
Returns a pointer to the x-axis axis widget.
Definition: PlotWidget.h:126
OpenMS::LayerDataBase::isIonMobilityData
bool isIonMobilityData() const
Check whether the current layer should be represented as ion mobility.
Definition: LayerDataBase.h:357
OpenMS::StringUtils::toQString
static QString toQString(const String &this_s)
Definition: StringUtils.h:201
OpenMS::Plot3DCanvas
Canvas for 3D-visualization of peak map data.
Definition: Plot3DCanvas.h:66
OpenMS::MzMLFile::store
void store(const String &filename, const PeakMap &map) const
Stores a map in an MzML file.
OpenMS::TOPPViewOpenDialog::disableDimension
void disableDimension(bool as_2d)
Disables view dimension section and sets the selected option.
OpenMS::EnhancedTabBar::addTab
int addTab(const String &text, int id)
Adds a new tab with the name text and the identifier id.
OpenMS::Constants::k
const double k
Definition: Constants.h:153
OpenMS::FileTypes::MZML
MzML file (.mzML)
Definition: FileTypes.h:70
OpenMS::Plot2DWidget
Widget for 2D-visualization of peak map and feature map data.
Definition: Plot2DWidget.h:63
OpenMS::LayerDataBase::getName
const String & getName() const
Definition: LayerDataBase.h:454
OpenMS::LayerDataBase::param
Param param
Layer parameters.
Definition: LayerDataBase.h:467
OpenMS::FileWatcher::addFile
void addFile(const String &path)
Adds a file to the watcher.
Definition: FileWatcher.h:84
OpenMS::TOPPViewOpenDialog
Dataset opening options for TOPPView.
Definition: TOPPViewOpenDialog.h:61
OpenMS::TOPPViewBase::layerZoomChanged
void layerZoomChanged() const
gets called when a layer changes in zoom
Definition: TOPPViewBase.cpp:1403
OpenMS::TOPPViewBase::getWorkspace
EnhancedWorkspace * getWorkspace()
returns a pointer to the EnhancedWorkspace containing PlotWidgets
Definition: TOPPViewBase.cpp:1498
OpenMS::MzMLFile
File adapter for MzML files.
Definition: MzMLFile.h:57
OpenMS::TVToolDiscovery
Scans for tools/utils and generates a param for each asynchronously.
Definition: TVToolDiscovery.h:62
OpenMS::String
A more convenient string class.
Definition: String.h:58
Annotation1DDistanceItem.h
OpenMS::Plot1DWidget::showCurrentPeaksAs2D
void showCurrentPeaksAs2D()
Requests to display the whole spectrum in 2D view.
OpenMS::PlotCanvas::IM_PERCENTAGE
Shows intensities normalized by layer maximum: f(x)=x/max(x)*100.
Definition: PlotCanvas.h:187
ParamXMLFile.h
OpenMS::DataFilters::DataFilter
Representation of a peak/feature filter combining FilterType, FilterOperation and a value (either dou...
Definition: DataFilters.h:75
OpenMS::DRange< 2 >
OpenMS::Exception::FileNotFound
File not found exception.
Definition: Exception.h:509
OpenMS::QApplicationTOPP::fileOpen
void fileOpen(QString file)
MzMLFile.h
OpenMS::TOPPViewBase::spec_gen_dialog_
TheoreticalSpectrumGenerationDialog spec_gen_dialog_
This dialog is a member so that its settings can be perserved upon closing.
Definition: TOPPViewBase.h:554
Plot3DOpenGLCanvas.h
RAIICleanup.h
OpenMS::TOPPViewBase::current_path_
String current_path_
Definition: TOPPViewBase.h:547
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS::SpectrumSettings::getPrecursors
const std::vector< Precursor > & getPrecursors() const
returns a const reference to the precursors
OpenMS::FileTypes::CONSENSUSXML
OpenMS consensus map format (.consensusXML)
Definition: FileTypes.h:65
OpenMS::TOPPViewBase::abortTOPPTool
void abortTOPPTool()
aborts the execution of a TOPP tool
Definition: TOPPViewBase.cpp:2325
OpenMS::TOPPViewBase
Main window of TOPPView tool.
Definition: TOPPViewBase.h:126
LogWindow.h
OpenMS::TOPPViewBase::fileChanged_
void fileChanged_(const String &)
Called if a data file has been externally changed.
Definition: TOPPViewBase.cpp:2586
OpenMS::TOPPViewOpenDialog::disableCutoff
void disableCutoff(bool cutoff_on)
Disables cutoff section and sets the selected option.
OpenMS::QApplicationTOPP
Extension to the QApplication for running TOPPs GUI tools.
Definition: QApplicationTOPP.h:50
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::TOPPViewBase::group_unassigned_2d_
QActionGroup * group_unassigned_2d_
Definition: TOPPViewBase.h:473
IdXMLFile.h
OpenMS::EnhancedWorkspace::dropReceived
void dropReceived(const QMimeData *data, QWidget *source, int id)
Signal that is emitted, when a drag-and-drop action ends on this widget.
FeatureXMLFile.h
OpenMS::TOPPViewBase::selection_view_
DataSelectionTabs * selection_view_
Definition: TOPPViewBase.h:426
OpenMS::LayerDataBase::NamesOfLabelType
static const std::string NamesOfLabelType[SIZE_OF_LABEL_TYPE]
Label names.
Definition: LayerDataBase.h:143
OpenMS::FileHandler::loadFeatures
bool loadFeatures(const String &filename, FeatureMap &map, FileTypes::Type force_type=FileTypes::UNKNOWN)
Loads a file into a FeatureMap.
OpenMS::LayerDataBase::getCurrentSpectrum
const ExperimentType::SpectrumType & getCurrentSpectrum() const
Returns a const reference to the current spectrum (1D view)
OpenMS::DataFilters::add
void add(const DataFilter &filter)
Adds a filter.
OpenMS::TVToolDiscovery::setPluginPath
bool setPluginPath(const String &path, bool create=false)
Sets the path that will be searched for Plugins.
OpenMS::TOPPViewBase::closeEvent
void closeEvent(QCloseEvent *event) override
Definition: TOPPViewBase.cpp:514
OpenMS::ParamXMLFile
The file pendant of the Param class used to load and store the param datastructure as paramXML.
Definition: ParamXMLFile.h:49
OpenMS::EnhancedTabBar::closeRequested
void closeRequested(int id)
Signal that indicates that the tab with identifier id is requested to be removed (double click or con...
OpenMS::TOPPViewBase::showPreferences
void showPreferences() const
Shows current layer preferences.
Definition: TOPPViewBase.cpp:2453
OpenMS::TOPPViewBase::annotateWithAMS
void annotateWithAMS()
Annotates current layer with ID data from AccurateMassSearch.
Definition: TOPPViewBase.cpp:1991
OpenMS::PlotWidget::canvas
PlotCanvas * canvas()
Returns a pointer to canvas object.
Definition: PlotWidget.h:115
EnumHelpers.h
OpenMS::TOPPViewBase::lastActiveSubwindow_
QMdiSubWindow * lastActiveSubwindow_
Definition: TOPPViewBase.h:484
OpenMS::TOPPViewBase::updateViewBar
void updateViewBar()
adapts view bar to the active window
Definition: TOPPViewBase.cpp:1337
OpenMS::TOPPViewOpenDialog::isCutoffEnabled
bool isCutoffEnabled() const
Returns if the low intensity peaks should be hidden.
OpenMS::TOPPViewBase::updateMenu
void updateMenu()
activates/deactivates menu entries
Definition: TOPPViewBase.cpp:1342
OpenMS::Plot1DWidget::showCurrentPeaksAsDIA
void showCurrentPeaksAsDIA()
Requests to display a full DIA window.
OpenMS::String::prefix
String prefix(SizeType length) const
returns the prefix of length length
OpenMS::LayerDataBase::P_PRECURSORS
Peaks: Mark precursor peaks of MS/MS scans.
Definition: LayerDataBase.h:120
OpenMS::TOPPViewBase::toggleProjections
void toggleProjections()
Definition: TOPPViewBase.cpp:1973
OpenMS::EnhancedTabBar::currentIdChanged
void currentIdChanged(int id)
Signal that indicates that the current tab changed, giving the id of the Tab.
OpenMS::PlotCanvas::getIntensityMode
IntensityModes getIntensityMode() const
Returns the intensity mode.
Definition: PlotCanvas.h:241
OpenMS::PlotCanvas::showMetaData
virtual void showMetaData(bool modifiable=false, Int index=-1)
Shows a dialog with the meta data.
OpenMS::SpectrumAlignmentDialog::get1stLayerIndex
Int get1stLayerIndex()
Returns the index of the selected non-flipped layer.
OpenMS::PlotCanvas::getVisiblePeakData
void getVisiblePeakData(ExperimentType &map) const
Fills the handed over map with the visible peaks of the current layer.
OpenMS::FileTypes::MZIDENTML
mzIdentML (HUPO PSI AnalysisXML followup format) (.mzid)
Definition: FileTypes.h:75
OpenMS::TOPPViewBase::tool_bar_
QToolBar * tool_bar_
Definition: TOPPViewBase.h:453
OpenMS::TOPPViewBase::resetZoom
void resetZoom() const
Definition: TOPPViewBase.cpp:1109
OpenMS::TOPPViewBase::ws_
EnhancedWorkspace ws_
Main workspace.
Definition: TOPPViewBase.h:480
Plot1DWidget.h
RecentFilesMenu.h
OpenMS::File::remove
static bool remove(const String &file)
Removes a file (if it exists).
OpenMS::TVToolDiscovery::getPluginPath
const std::string getPluginPath()
Returns the current set path to search plugins in.
OpenMS::File::getUniqueName
static String getUniqueName(bool include_hostname=true)
Returns a string, consisting of date, time, hostname, process id, and a incrementing number....
OpenMS::LayerDataBase::DT_CONSENSUS
Consensus feature data.
Definition: LayerDataBase.h:109
OpenMS::PlotWidget::showLegend
virtual void showLegend(bool show)
Shows/hides axis labels.
OpenMS::Helpers::indexOf
Size indexOf(const ContainerType &cont, const typename ContainerType::value_type &val)
Definition: EnumHelpers.h:45
OpenMS::Plot1DCanvas::DM_CONNECTEDLINES
draw as connected lines
Definition: Plot1DCanvas.h:116
OpenMS::Plot2DWidget::projectionsVisible
bool projectionsVisible() const
Returns if one of the projections is visible (or both are visible)
OpenMS::LayerDataBase::label
LabelType label
Label type.
Definition: LayerDataBase.h:488
OpenMS::Internal::TOPPViewPrefDialog::setParam
void setParam(const Param &param)
initialize GUI values with these parameters
OpenMS::FileHandler::getOptions
PeakFileOptions & getOptions()
Mutable access to the options for loading/storing.
OpenMS::FileTypes::UNKNOWN
Unknown file extension.
Definition: FileTypes.h:58
QWidget
OpenMS::TOPPViewBase::linkZoom
void linkZoom()
link the zoom of individual windows
Definition: TOPPViewBase.cpp:1398
OpenMS::TOPPViewBase::getCurrentLayer
const LayerDataBase * getCurrentLayer() const
Returns the active Layer data (0 if no layer is active)
Definition: TOPPViewBase.cpp:1953
OpenMS::PlotWidget::sendCursorStatus
void sendCursorStatus(double mz=-1.0, double rt=-1.0)
Emitted when the cursor position changes (for displaying e.g. in status bar)
Plot3DCanvas.h
OpenMS::TOPPViewBase::showGoToDialog
void showGoToDialog() const
shows the DB dialog for opening files
Definition: TOPPViewBase.cpp:1489
OpenMS::LayerListView
Pimped QListView for Layers of a Canvas.
Definition: LayerListView.h:52
OpenMS::TOPPViewBase::getActivePlotWidget
PlotWidget * getActivePlotWidget() const
returns a pointer to the active PlotWidget (0 if none is active)
Definition: TOPPViewBase.cpp:1503
OpenMS::LayerDataBase::L_NONE
No label is displayed.
Definition: LayerDataBase.h:134
OpenMS::LayerDataBase::DT_CHROMATOGRAM
Chromatogram data.
Definition: LayerDataBase.h:107
OpenMS::TOPPViewBase::showSpectrumMetaData
void showSpectrumMetaData(int spectrum_index) const
shows a spectrum's metadata with index spectrum_index from the currently active canvas
Definition: TOPPViewBase.cpp:2486
OpenMS::PlotCanvas::layerActivated
void layerActivated(QWidget *w)
Signal emitted whenever a new layer is activated within the current window.
OpenMS::LayerDataBase::DataType
DataType
Definition: LayerDataBase.h:104
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
OpenMS::TOPPViewBase::dm_unassigned_2d_
QToolButton * dm_unassigned_2d_
Definition: TOPPViewBase.h:472
PlotCanvas.h
OpenMS::Plot1DWidget::showCurrentPeaksAs3D
void showCurrentPeaksAs3D()
Requests to display the whole spectrum in 3D view.
OpenMS::File::writable
static bool writable(const String &file)
Return true if the file is writable.
OpenMS::IdXMLFile::load
void load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)
Loads the identifications of an idXML file without identifier.
OpenMS::Exception::InvalidParameter
Exception indicating that an invalid parameter was handed over to an algorithm.
Definition: Exception.h:339
OpenMS::TOPPViewBase::filter_list_
FilterList * filter_list_
Definition: TOPPViewBase.h:430
OpenMS::TOPPViewBase::closeByTab
void closeByTab(int id)
Closes the window corresponding to the data of the tab with identifier id.
Definition: TOPPViewBase.cpp:1018
OpenMS::RAIICleanup
Exception-safe way of executing arbitrary code at the end of a scope.
Definition: RAIICleanup.h:48
OpenMS::SpectraIDViewTab
Tabular visualization / selection of identified spectra.
Definition: SpectraIDViewTab.h:59
OpenMS::RecentFilesMenu::setFromParam
unsigned setFromParam(const Param &filenames)
Extracts all values from all elements in the param object and tries to interpret them as filenames If...
OpenMS::Plot1DCanvas::DrawModes
DrawModes
Enumerate all available paint styles.
Definition: Plot1DCanvas.h:113
OpenMS::RecentFilesMenu::add
void add(const String &filename)
put a new recent file at the top (removing any duplicates in other positions); will update the QMenu
print_usage
void print_usage()
Definition: TOPPView.cpp:85
OpenMS::PlotWidget::showGoToDialog
virtual void showGoToDialog()=0
Shows a goto dialog.
OpenMS::TOPPViewBase::metadataFileDialog
void metadataFileDialog()
dialog for inspecting database meta data
Definition: TOPPViewBase.cpp:2458
OpenMS::MzIdentMLFile
File adapter for MzIdentML files.
Definition: MzIdentMLFile.h:67
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS::TOPPViewBase::LOAD_RESULT::FILE_NOT_FOUND
file did not exist
OpenMS::TV_STATUS::IS_1D_VIEW
OpenMS::File::exists
static bool exists(const String &file)
Method used to test if a file exists.
OpenMS::TOPPViewBase::addData
void addData(FeatureMapSharedPtrType feature_map, ConsensusMapSharedPtrType consensus_map, std::vector< PeptideIdentification > &peptides, ExperimentSharedPtrType peak_map, ODExperimentSharedPtrType on_disc_peak_map, LayerDataBase::DataType data_type, bool show_as_1d, bool show_options, bool as_new_window=true, const String &filename="", const String &caption="", UInt window_id=0, Size spectrum_id=0)
Adds a peak or feature map to the viewer.
Definition: TOPPViewBase.cpp:810
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::Plot2DWidget::showSpectrumAsNew1D
void showSpectrumAsNew1D(int index)
Requests to display the spectrum with index index in 1D.
OpenMS::TOPPViewBase::draw_group_1d_
QButtonGroup * draw_group_1d_
Definition: TOPPViewBase.h:460
OpenMS::TOPPViewBase::toggleAxisLegends
void toggleAxisLegends() const
Toggles the axis legends.
Definition: TOPPViewBase.cpp:2441
OpenMS::PlotCanvas
Base class for visualization canvas classes.
Definition: PlotCanvas.h:135
OpenMS::String::number
static String number(double d, UInt n)
returns a string for d with exactly n decimal places
OpenMS::MSExperiment::addSpectrum
void addSpectrum(const MSSpectrum &spectrum)
adds a spectrum to the list
OpenMS::Plot1DCanvas::setDrawMode
void setDrawMode(DrawModes mode)
Sets draw mode of the current layer.
OpenMS::TOPPViewBase::filter_dock_widget_
QDockWidget * filter_dock_widget_
Definition: TOPPViewBase.h:420
OpenMS::TOPPViewBase::add_2d_context_
QMenu * add_2d_context_
Additional context menu for 2D layers.
Definition: TOPPViewBase.h:540
OpenMS::TOPPViewBase::setDrawMode1D
void setDrawMode1D(int) const
Definition: TOPPViewBase.cpp:1128
OpenMS::PlotCanvas::IM_LOG
Logarithmic mode.
Definition: PlotCanvas.h:189
OpenMS::TOPPViewBase::showCurrentPeaksAs2D
void showCurrentPeaksAs2D()
Shows the current peak data of the active layer in 2D.
Definition: TOPPViewBase.cpp:2086
OpenMS::FileTypes::FEATUREXML
OpenMS feature file (.featureXML)
Definition: FileTypes.h:63
OpenMS::TOPPViewBase::changeLabel
void changeLabel(QAction *)
Definition: TOPPViewBase.cpp:1137
OpenMS::PlotWidget::setIntensityMode
void setIntensityMode(PlotCanvas::IntensityModes mode)
Sets the intensity mode of the PlotCanvas.
TVToolDiscovery.h
OpenMS::LayerDataBase::F_UNASSIGNED
Features: Unassigned peptide hits.
Definition: LayerDataBase.h:119
MetaDataBrowser.h
OpenMS::TOPPViewBase::rt_label_
QLabel * rt_label_
RT label for messages in the status bar.
Definition: TOPPViewBase.h:500
OpenMS::TOPPViewBase::getActiveCanvas
PlotCanvas * getActiveCanvas() const
returns a pointer to the active PlotCanvas (0 if none is active)
Definition: TOPPViewBase.cpp:1522
OpenMS::TOPPViewOpenDialog::viewMapAs1D
bool viewMapAs1D() const
Returns true, if 1D mode is to be used for maps.
OpenMS::LayerDataBase::visible
bool visible
if this layer is visible
Definition: LayerDataBase.h:441
OpenMS::PlotCanvas::changeLayerFilterState
void changeLayerFilterState(Size i, bool b)
change if the defined data filters are used
OpenMS::TOPPViewBase::copyLayer
void copyLayer(const QMimeData *data, QWidget *source, int id=-1)
Slot for drag-and-drop of layer manager to tabbar.
Definition: TOPPViewBase.cpp:2491
OpenMS::TV_STATUS::HAS_CANVAS
OpenMS::TOPPViewBase::LOAD_RESULT::FILETYPE_UNSUPPORTED
filetype is known, but the format not supported as layer data
OpenMS::EnhancedWorkspace::getWidget
EnhancedTabBarWidgetInterface * getWidget(int id) const
OpenMS::TOPPViewBase::loadPreferences
void loadPreferences(String filename="")
Loads the preferences from the filename given.
Definition: TOPPViewBase.cpp:1547
OpenMS::RecentFilesMenu
Manages recent files opened by the user and provides a QMenu to go with it.
Definition: RecentFilesMenu.h:59
OpenMS::DataFilters::INTENSITY
Filter the intensity value.
Definition: DataFilters.h:59
OpenMS::TOPPViewBase::SpectrumType
ExperimentType::SpectrumType SpectrumType
Peak spectrum type.
Definition: TOPPViewBase.h:154
OpenMS::PlotWidget::dropReceived
void dropReceived(const QMimeData *data, QWidget *source, int id)
Signal that is emitted, when a drag-and-drop action ends on this widget.
OpenMS::RecentFilesMenu::recentFileClicked
void recentFileClicked(const String &filename)
when a recent file action item from the getMenu() was clicked
OpenMS::TOPPViewBase::initializeDefaultParameters_
void initializeDefaultParameters_()
Initializes the default parameters on TOPPView construction.
Definition: TOPPViewBase.cpp:464
OpenMS::StopWatch::getClockTime
double getClockTime() const
OpenMS::TOPPViewBase::getActive3DWidget
Plot3DWidget * getActive3DWidget() const
returns a pointer to the active Plot3DWidget (0 the active window is no Plot2DWidget or there is no a...
Definition: TOPPViewBase.cpp:1542
OpenMS::TOPPViewBase::views_dockwidget_
QDockWidget * views_dockwidget_
Definition: TOPPViewBase.h:419
OpenMS::TOPPViewBase::log_
LogWindow * log_
Log output window.
Definition: TOPPViewBase.h:443
OpenMS::LayerDataBase::DT_IDENT
Peptide identification data.
Definition: LayerDataBase.h:110
OpenMS::TOPPViewBase::FeatureMapSharedPtrType
LayerDataBase::FeatureMapSharedPtrType FeatureMapSharedPtrType
Definition: TOPPViewBase.h:140
OpenMS::TVToolDiscovery::getToolParams
const Param & getToolParams()
Returns a Param object containing the params for each tool/util.
OpenMS::FileHandler
Facilitates file handling by file type recognition.
Definition: FileHandler.h:66
Annotation1DTextItem.h
OpenMS::TOPPViewBase::dm_label_2d_
QToolButton * dm_label_2d_
Definition: TOPPViewBase.h:470
OpenMS::LayerAnnotatorBase::getAnnotatorWhichSupports
static std::unique_ptr< LayerAnnotatorBase > getAnnotatorWhichSupports(const FileTypes::Type &type)
OpenMS::MetaDataBrowser::add
void add(PeakMap &exp)
Adds a peak map.
Definition: MetaDataBrowser.h:115
QProcess
Plot1DCanvas.h
OpenMS::OnDiscMSExperiment
Representation of a mass spectrometry experiment on disk.
Definition: OnDiscMSExperiment.h:66
OpenMS::LayerDataBase::DT_PEAK
Spectrum profile or centroided data.
Definition: LayerDataBase.h:106
OpenMS::FileHandler::loadExperiment
bool loadExperiment(const String &filename, MSExperiment &exp, FileTypes::Type force_type=FileTypes::UNKNOWN, ProgressLogger::LogType log=ProgressLogger::NONE, const bool rewrite_source_file=true, const bool compute_hash=true)
Loads a file into an MSExperiment.
OpenMS::FeatureXMLFile::load
void load(const String &filename, FeatureMap &feature_map)
loads the file with name filename into map and calls updateRanges().
OpenMS::TOPPViewBase::TOOL_SCAN::FORCE_SCAN
Forces TVToolDiscovery to generate params and using them instead of the params in TOPPView's ini file...
Plot2DWidget.h
OpenMS::LayerDataBase::ExperimentSharedPtrType
boost::shared_ptr< ExperimentType > ExperimentSharedPtrType
SharedPtr on MSExperiment.
Definition: LayerDataBase.h:161
OpenMS::TV_STATUS::HAS_MIRROR_MODE
OpenMS::Internal::IndexedMzMLHandler::getNrChromatograms
size_t getNrChromatograms() const
Returns the number of chromatograms available.
OpenMS::TOPPViewBase::scan_mode_
TOOL_SCAN scan_mode_
Determines TVToolDiscovery scans for tool/utils and generates new params.
Definition: TOPPViewBase.h:446
OpenMS::TOPPViewMenu
The file menu items for TOPPView.
Definition: TOPPViewMenu.h:82
OpenMS::FileTypes::Type
Type
Actual file types enum.
Definition: FileTypes.h:56
OpenMS::Exception::UnableToCreateFile
Unable to create file exception.
Definition: Exception.h:636
OpenMS::PlotCanvas::setFilters
virtual void setFilters(const DataFilters &filters)
Sets the filters applied to the data before drawing (for the current layer)
OpenMS::TOPPViewOpenDialog::openAsNewWindow
bool openAsNewWindow() const
Returns true, if the data should be opened in a new window.
OpenMS::Param::parseCommandLine
void parseCommandLine(const int argc, const char **argv, const std::string &prefix="")
Parses command line arguments.
OpenMS::Param::setSectionDescription
void setSectionDescription(const std::string &key, const std::string &description)
Sets a description for an existing section.
OpenMS::TOPPViewBase::saveLayerAll
void saveLayerAll() const
Saves the whole current layer data.
Definition: TOPPViewBase.cpp:2426
OpenMS::Plot3DCanvas::openglwidget
Plot3DOpenGLCanvas * openglwidget() const
returns the Plot3DOpenGLcanvas
OpenMS::TOPPViewBase::dm_hulls_2d_
QAction * dm_hulls_2d_
Definition: TOPPViewBase.h:469
OpenMS::TOPPViewBase::tool_bar_1d_
QToolBar * tool_bar_1d_
Definition: TOPPViewBase.h:459
OpenMS::TOPPViewBase::message_label_
QLabel * message_label_
Label for messages in the status bar.
Definition: TOPPViewBase.h:496
OpenMS::TOPPViewBase::dm_precursors_2d_
QAction * dm_precursors_2d_
Definition: TOPPViewBase.h:467
OpenMS::LayerDataBase::DT_FEATURE
Feature data.
Definition: LayerDataBase.h:108
OpenMS::StopWatch::start
void start()
Start the stop watch.
OpenMS::PlotCanvas::setLabel
void setLabel(LayerDataBase::LabelType label)
Definition: PlotCanvas.h:328
OpenMS::GUIHelpers::GUILock::unlock
void unlock()
manually unlock the GUI (does nothing if already unlocked)
GUIHelpers.h
OpenMS::GUIHelpers::GUILock
RAII class to disable the GUI and set a busy cursor and go back to the original state when this class...
Definition: GUIHelpers.h:137
OpenMS::LayerAnnotatorOSW
Definition: LayerDataBase.h:608
OpenMS::FileHandler::getType
static FileTypes::Type getType(const String &filename)
Tries to determine the file type (by name or content)
OpenMS::Plot1DCanvas::getAlignmentSize
Size getAlignmentSize()
Returns the number of aligned pairs of peaks.
OpenMS::TOPPViewBase::tool_bar_2d_cons_
QToolBar * tool_bar_2d_cons_
Definition: TOPPViewBase.h:465
OpenMS::Exception::BaseException
Exception base class.
Definition: Exception.h:89
OpenMS::TOPPViewBase::LOAD_RESULT
LOAD_RESULT
Definition: TOPPViewBase.h:176
OpenMS::LayerDataBase::getFeatureMap
const FeatureMapSharedPtrType & getFeatureMap() const
Returns a const reference to the current feature data.
Definition: LayerDataBase.h:192
OpenMS::Param::exists
bool exists(const std::string &key) const
Tests if a parameter is set (expecting its fully qualified name, e.g., TextExporter:1:proteins_only)
OpenMS::StopWatch::stop
void stop()
Stop the stop watch (can be resumed later). If the stop watch was not running an exception is thrown.
OpenMS::DefaultParamHandler::setParameters
void setParameters(const Param &param)
Sets the parameters.
OpenMS::MSSpectrum::setMSLevel
void setMSLevel(UInt ms_level)
Sets the MS level.
OpenMS::Plot3DWidget::canvas
Plot3DCanvas * canvas()
This method is overwritten to make the class specific members accessible.
Definition: Plot3DWidget.h:66
OpenMS::DefaultParamHandler::getDefaults
const Param & getDefaults() const
Non-mutable access to the default parameters.
OpenMS::String::toQString
QString toQString() const
Conversion to Qt QString.
OpenMS::TOPPViewBase::showCurrentPeaksAs3D
void showCurrentPeaksAs3D()
Shows the current peak data of the active layer in 3D.
Definition: TOPPViewBase.cpp:2229
OpenMS::String::hasSuffix
bool hasSuffix(const String &string) const
true if String ends with string, false otherwise
OpenMS::TOPPViewBase::layerDeactivated
void layerDeactivated()
gets called if a layer got deactivated
Definition: TOPPViewBase.cpp:1432
OpenMS::TOPPViewBase::toggleInterestingMZs
void toggleInterestingMZs() const
Toggles drawing of interesting MZs.
Definition: TOPPViewBase.cpp:2446
OpenMS::File::path
static String path(const String &file)
OpenMS::EnhancedTabBar
Convenience tab bar implementation.
Definition: EnhancedTabBar.h:60
OpenMS::VersionInfo::getVersion
static String getVersion()
Return the version number of OpenMS.
OpenMS::EnhancedTabBarWidgetInterface::getWindowId
Int getWindowId() const
get the EnhancedTabBar unique window id
OpenMS::TOPPViewBase::layerStatistics
void layerStatistics() const
Shows statistics (count,min,max,avg) about Intensity, Quality, Charge and meta data.
Definition: TOPPViewBase.cpp:1054
OpenMS::PeakMap
MSExperiment PeakMap
Two-dimensional map of raw data points or peaks.
Definition: StandardTypes.h:61
OpenMS::LayerAnnotatorBase::annotateWithFileDialog
bool annotateWithFileDialog(LayerDataBase &layer, LogWindow &log, const String &current_path) const
OpenMS::PlotCanvas::saveCurrentLayer
virtual void saveCurrentLayer(bool visible)=0
Saves the current layer data.
OpenMS::SpectraTreeTab::getSelectedScan
bool getSelectedScan(MSExperiment &exp, LayerDataBase::DataType &current_type) const
OpenMS::Plot2DWidget::getVerticalProjection
const Plot1DWidget * getVerticalProjection() const
const reference to the vertical projection
OpenMS::Internal::FilterList::filterChanged
void filterChanged(const DataFilters &filters)
emitted when the user has edited/added/removed a filter
OpenMS::TOPPViewBase::chooseFilesDialog_
QStringList chooseFilesDialog_(const String &path_overwrite="")
Shows a dialog where the user can select files.
Definition: TOPPViewBase.cpp:1661
FilterList.h
OpenMS::Plot2DCanvas
Canvas for 2D-visualization of peak map, feature map and consensus map data.
Definition: Plot2DCanvas.h:70
OpenMS::Plot2DWidget::toggleProjections
void toggleProjections()
Shows/hides the projections.
OpenMS::Plot1DWidget
Widget for visualization of several spectra.
Definition: Plot1DWidget.h:65
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:82
QMainWindow
OpenMS::Plot1DWidget::canvas
Plot1DCanvas * canvas()
This method is overwritten to make the class specific members accessible.
Definition: Plot1DWidget.h:77
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::FeatureXMLFile::store
void store(const String &filename, const FeatureMap &feature_map)
stores the map feature_map in file with name filename.
OpenMS::TOPPViewBase::getActive2DWidget
Plot2DWidget * getActive2DWidget() const
returns a pointer to the active Plot2DWidget (0 the active window is no Plot2DWidget or there is no a...
Definition: TOPPViewBase.cpp:1537
OpenMS::SpectrumAlignmentDialog
Lets the user select two spectra and set the parameters for the spectrum alignment.
Definition: SpectrumAlignmentDialog.h:56
OpenMS::ConsensusXMLFile::load
void load(const String &filename, ConsensusMap &map)
Loads a consensus map from file and calls updateRanges.
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::IMDataConverter::splitByIonMobility
static MSExperiment splitByIonMobility(MSSpectrum im_frame, UInt number_of_bins=-1)
Split a (TimsTOF) ion mobility frame (i.e. a spectrum concatenated from multiple spectra with differe...
OpenMS::PlotCanvas::showGridLines
void showGridLines(bool show)
Whether or not to show grid lines.
OpenMS::TOPPViewMenu::update
void update(const FS_TV status, const LayerDataBase::DataType layer_type)
enable/disable entries according to a given state of TOPPViewBase
OpenMS::LayerDataBase::getPeakData
const ConstExperimentSharedPtrType getPeakData() const
Returns a const reference to the current in-memory peak data.
OpenMS::TOPPViewBase::openFilesByDialog
void openFilesByDialog(const String &initial_directory="")
shows the file dialog for opening files (a starting directory, e.g. for the example files can be prov...
Definition: TOPPViewBase.cpp:1685
OpenMS::TOPPViewOpenDialog::disableLocation
void disableLocation(bool window)
Disables opening location section and sets the selected option.
OpenMS::TOPPViewBase::savePreferences
void savePreferences()
Stores the preferences (used when this window is closed)
Definition: TOPPViewBase.cpp:1626
OpenMS::TOPPViewBase::updateProcessLog
void updateProcessLog()
Appends process output to log window.
Definition: TOPPViewBase.cpp:2313
OpenMS::StopWatch
This class is used to determine the current process' CPU (user and/or kernel) and wall time.
Definition: StopWatch.h:65
OpenMS::DataSelectionTabs
A tabbed view, to browse lists of spectra or identifications.
Definition: DataSelectionTabs.h:75
OpenMS::MzIdentMLFile::load
void load(const String &filename, std::vector< ProteinIdentification > &poid, std::vector< PeptideIdentification > &peid)
Loads the identifications from a MzIdentML file.
OpenMS::TOPPViewBase::projections_2d_
QAction * projections_2d_
Definition: TOPPViewBase.h:475
Annotation1DPeakItem.h
Precursor.h
OpenMS::MetaDataBrowser
A meta data visualization widget.
Definition: MetaDataBrowser.h:104
OpenMS::TOPPViewBase::topp_
struct OpenMS::TOPPViewBase::@19 topp_
Information needed for execution of TOPP tools.
OpenMS::TOPPViewBase::recent_files_
RecentFilesMenu recent_files_
manages recent list of filenames and the menu that goes with it
Definition: TOPPViewBase.h:488
OpenMS::LayerDataBase::F_HULLS
Features: Convex hulls of single mass traces.
Definition: LayerDataBase.h:118
OpenMS::SpectrumAlignmentDialog::isPPM
bool isPPM() const
OpenMS::ParamValue::toString
std::string toString(bool full_precision=true) const
Convert ParamValue to string.
OpenMS::FileWatcher::fileChanged
void fileChanged(const String &)
Delayed file change signal.
OpenMS::TOPPViewBase::showCursorStatus
void showCursorStatus(double mz, double rt)
shows m/z and rt in the status bar
Definition: TOPPViewBase.cpp:1078
MSExperiment.h
OpenMS::StringUtils::fillLeft
static String & fillLeft(String &this_s, char c, UInt size)
Definition: StringUtilsSimple.h:93
OpenMS::TOPPViewBase::addDataFile
LOAD_RESULT addDataFile(const String &filename, bool show_options, bool add_to_recent, String caption="", UInt window_id=0, Size spectrum_id=0)
Opens and displays data from a file.
Definition: TOPPViewBase.cpp:538
OpenMS::Internal::TOPPViewPrefDialog::getParam
Param getParam() const
FilterList
OpenMS::Internal::FilterList FilterList
Definition: FilterList.h:94
OpenMS::File::getUserDirectory
static String getUserDirectory()
OpenMS::Plot1DWidget::showCurrentPeaksAsIonMobility
void showCurrentPeaksAsIonMobility()
Requests to display the whole spectrum in ion mobility view.
OpenMS::TOPPViewBase::tool_bar_2d_feat_
QToolBar * tool_bar_2d_feat_
Definition: TOPPViewBase.h:464
OpenMS::PlotCanvas::getVisibleFeatureData
void getVisibleFeatureData(FeatureMapType &map) const
Fills the handed over map with the visible features of the current layer.
OpenMS::ToolsDialog
TOPP tool selection dialog.
Definition: ToolsDialog.h:69
OpenMS::LayerDataBase::I_LABELS
Identifications: Show labels (not sequences)
Definition: LayerDataBase.h:124
TOPPViewPrefDialog.h
FileWatcher.h
OpenMS::Param::removeAll
void removeAll(const std::string &prefix)
Remove all entries that start with prefix.
OpenMS::File::absolutePath
static String absolutePath(const String &file)
Replaces the relative path in the argument with the absolute path.
OpenMS::PlotCanvas::preferencesChange
void preferencesChange()
Emitted when the layer preferences have changed.
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:98
OpenMS::Plot2DWidget::canvas
Plot2DCanvas * canvas()
This method is overwritten to make the class specific members accessible.
Definition: Plot2DWidget.h:77
OpenMS::Exception::ParseError
Parse Error exception.
Definition: Exception.h:622
OpenMS::Plot3DWidget
Widget for 3D-visualization of map data.
Definition: Plot3DWidget.h:53
OpenMS::DataFilters
DataFilter array providing some convenience functions.
Definition: DataFilters.h:51
AASequence.h
OpenMS::PlotCanvas::updateLayer
virtual void updateLayer(Size i)=0
Updates layer i when the data in the corresponding file changes.
OpenMS::TOPPViewBase::tool_scanner_
TVToolDiscovery tool_scanner_
Scans for tools/utils and generates a param for each.
Definition: TOPPViewBase.h:448
Plot2DCanvas.h
OpenMS::TOPPViewBase::tool_bar_2d_ident_
QToolBar * tool_bar_2d_ident_
Definition: TOPPViewBase.h:466
OpenMS::TOPPViewBase::showCurrentPeaksAsIonMobility
void showCurrentPeaksAsIonMobility()
Shows the current peak data of the active layer as ion mobility.
Definition: TOPPViewBase.cpp:2113
OpenMS::LayerDataBase::isDIAData
bool isDIAData() const
Check whether the current layer contains DIA (SWATH-MS) data.
Definition: LayerDataBase.h:370
OpenMS::Param::copy
Param copy(const std::string &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
OpenMS::TOPPViewBase::LOAD_RESULT::OK
OpenMS::TOPPViewBase::loadFiles
void loadFiles(const StringList &list, QSplashScreen *splash_screen)
Opens all the files in the string list.
Definition: TOPPViewBase.cpp:2343
OpenMS::FileWatcher
Watcher that monitors file changes.
Definition: FileWatcher.h:65
OpenMS::TOPPViewBase::ConsensusMapType
LayerDataBase::ConsensusMapType ConsensusMapType
Definition: TOPPViewBase.h:143
OpenMS::FileTypeList::contains
bool contains(const FileTypes::Type &type) const
check if type is contained in this array
OpenMS::EnhancedTabBarWidgetInterface::addToTabBar
void addToTabBar(EnhancedTabBar *const parent, const String &caption, const bool make_active_tab=true)
OpenMS::TOPPViewBase::showSpectrumGenerationDialog
void showSpectrumGenerationDialog()
Shows the theoretical spectrum generation dialog.
Definition: TOPPViewBase.cpp:2026
OpenMS::FlagSet< TV_STATUS >
OpenMS::TOPPViewOpenDialog::setMergeLayers
void setMergeLayers(const std::map< Size, String > &layers)
Sets the possible merge layers (index and name) and activates the option.
OpenMS::TOPPViewBase::dm_ident_2d_
QAction * dm_ident_2d_
Definition: TOPPViewBase.h:476
OpenMS::TVToolDiscovery::findPluginExecutable
std::string findPluginExecutable(const std::string &name)
Returns the path to the plugin executable or an empty string if the plugin name is unknown.
OpenMS::DataSelectionTabs::currentTabChanged
void currentTabChanged(int tab_index)
invoked when user changes the active tab to tab_index
OpenMS::TV_STATUS::TOPP_IDLE
OpenMS::TOPPViewBase::saveLayerVisible
void saveLayerVisible() const
Saves the visible layer data.
Definition: TOPPViewBase.cpp:2431
OpenMS::TOPPViewBase::showTOPPDialog_
void showTOPPDialog_(bool visible)
Apply TOPP tool. If visible is true, only the visible data is used, otherwise the whole layer is used...
Definition: TOPPViewBase.cpp:1699
OpenMS::PlotCanvas::layerModficationChange
void layerModficationChange(Size layer, bool modified)
Signal emitted whenever the modification status of a layer changes (editing and storing)
OpenMS::LayerDataBase::SIZE_OF_LABEL_TYPE
Definition: LayerDataBase.h:139
OpenMS::TOPPViewBase::updateLayerBar
void updateLayerBar()
adapts the layer bar to the active window
Definition: TOPPViewBase.cpp:1332
OpenMS::TOPPViewBase::showTOPPDialog
void showTOPPDialog()
Apply TOPP tool.
Definition: TOPPViewBase.cpp:1693
OpenMS::EnhancedTabBar::dropOnTab
void dropOnTab(const QMimeData *data, QWidget *source, int id)
Signal that is emitted, when a drag-and-drop action ends on a tab.
OpenMS::FeatureXMLFile
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:62
OpenMS::File::readable
static bool readable(const String &file)
Return true if the file exists and is readable.
OpenMS::TOPPViewBase::updateBarsAndMenus
void updateBarsAndMenus()
calls update*Bar and updateMenu_() to make sure the interface matches the current data
Definition: TOPPViewBase.cpp:1247
OpenMS::Plot1DCanvas::mirrorModeActive
bool mirrorModeActive() const
Returns whether this widget is currently in mirror mode.
OpenMS::LayerDataBase::ConsensusMapSharedPtrType
boost::shared_ptr< ConsensusMap > ConsensusMapSharedPtrType
SharedPtr on consensus features.
Definition: LayerDataBase.h:155
OpenMS::PlotCanvas::IM_SNAP
Shows the maximum displayed intensity as if it was the overall maximum intensity.
Definition: PlotCanvas.h:188
OpenMS::LayerAnnotatorPeptideID
Definition: LayerDataBase.h:574
OpenMS::PlotCanvas::getVisibleArea
const AreaType & getVisibleArea() const
Returns the currently visible area.
Definition: PlotCanvas.h:342
IPeptideIds.h
OpenMS::PlotCanvas::layerZoomChanged
void layerZoomChanged(QWidget *w)
Signal emitted whenever the zoom changed.
OpenMS::TOPPViewBase::preferencesDialog
void preferencesDialog()
shows the preferences dialog
Definition: TOPPViewBase.cpp:523
OpenMS::TOPPViewBase::tool_bar_2d_peak_
QToolBar * tool_bar_2d_peak_
Definition: TOPPViewBase.h:463
OpenMS::FilterLayout::BOTH
combine COMPACT and ONE_BY_ONE
OpenMS::PlotCanvas::getLayerFlag
bool getLayerFlag(LayerDataBase::Flags f) const
returns a layer flag of the current layer
Definition: PlotCanvas.h:300
OpenMS::TOPPViewBase::updateFilterBar
void updateFilterBar()
adapts the filter bar to the active window
Definition: TOPPViewBase.cpp:1369
OpenMS::PlotCanvas::getVisibleConsensusData
void getVisibleConsensusData(ConsensusMapType &map) const
Fills the handed over map with the visible consensus features of the current layer.
OpenMS::TOPPViewBase::changeUnassigned
void changeUnassigned(QAction *)
Definition: TOPPViewBase.cpp:1169
OpenMS::LayerDataBase::FeatureMapSharedPtrType
boost::shared_ptr< FeatureMap > FeatureMapSharedPtrType
SharedPtr on feature map.
Definition: LayerDataBase.h:149
OpenMS::TOPPViewBase::LOAD_RESULT::LOAD_ERROR
an error occurred while loading the file
OpenMS::LayerDataBase::remove_chromatogram_flag
void remove_chromatogram_flag()
remove the chromatogram flag
Definition: LayerDataBase.h:405
OpenMS::LayerDataBase::getConsensusMap
const ConsensusMapSharedPtrType & getConsensusMap() const
Returns a const reference to the consensus feature data.
Definition: LayerDataBase.h:204
OpenMS::EnhancedTabBar::dropOnWidget
void dropOnWidget(const QMimeData *data, QWidget *source)
Signal that is emitted, when a drag-and-drop action ends on the unused space on the right side of the...
OpenMS::DefaultParamHandler::defaults_
Param defaults_
Container for default parameters. This member should be filled in the constructor of derived classes!
Definition: DefaultParamHandler.h:173
OpenMS::PlotWidget::sendStatusMessage
void sendStatusMessage(std::string, OpenMS::UInt)
Emits a status message that should be displayed for time ms. If time is 0 the message should be displ...
OpenMS::Plot1DWidget::performAlignment
void performAlignment(Size layer_index_1, Size layer_index_2, const Param &param)
Performs an alignment of the layers with layer_index_1 and layer_index_2.
OpenMS::FileHandler::stripExtension
static String stripExtension(const String &filename)
If filename contains an extension, it will be removed (including the '.'). Special extensions,...
OpenMS::TVToolDiscovery::loadToolParams
void loadToolParams()
Start creating params for each tool/util asynchronously.
OpenMS::Exception::BaseException::getFile
const char * getFile() const noexcept
Returns the file where it occurred.
OpenMS::TOPPViewBase::updateCurrentPath
void updateCurrentPath()
changes the current path according to the currently active window/layer
Definition: TOPPViewBase.cpp:2562
SignalToNoiseEstimator.h
OpenMS::DefaultParamHandler::defaultsToParam_
void defaultsToParam_()
Updates the parameters after the defaults have been set in the constructor.
OpenMS::TOPPViewBase::toggleGridLines
void toggleGridLines() const
Toggles the grid lines.
Definition: TOPPViewBase.cpp:2436
OpenMS::supported_types
const FileTypeList supported_types({ FileTypes::MZML, FileTypes::MZXML, FileTypes::MZDATA, FileTypes::SQMASS, FileTypes::FEATUREXML, FileTypes::CONSENSUSXML, FileTypes::IDXML, FileTypes::DTA, FileTypes::DTA2D, FileTypes::MGF, FileTypes::MS2, FileTypes::MSP, FileTypes::BZ2, FileTypes::GZ })
supported types which can be opened with File–>Open
OpenMS::LayerDataBase::getOnDiscPeakData
const ODExperimentSharedPtrType & getOnDiscPeakData() const
Returns a mutable reference to the on-disc data.
Definition: LayerDataBase.h:256
OpenMS::TOPPViewBase::dm_elements_2d_
QAction * dm_elements_2d_
Definition: TOPPViewBase.h:474
OpenMS::ProgressLogger::GUI
Progress dialog.
Definition: ProgressLogger.h:71
OpenMS::Internal::FilterList
A widget which shows a list of DataFilter items.
Definition: FilterList.h:60
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:69
TOPPViewOpenDialog.h
OpenMS::File::getTempDirectory
static String getTempDirectory()
OpenMS::FileTypeList::toFileDialogFilter
String toFileDialogFilter(const FilterLayout style, bool add_all_filter) const
QTreeWidget
OpenMS::TOPPViewBase::closeTab
void closeTab()
closes the active window
Definition: TOPPViewBase.cpp:1035
OpenMS::TOPPViewBase::annotateWithID
void annotateWithID()
Annotates current layer with ID data.
Definition: TOPPViewBase.cpp:2002
OpenMS::TOPPViewBase::layer_dock_widget_
QDockWidget * layer_dock_widget_
Definition: TOPPViewBase.h:418
OpenMS::DataFilters::GREATER_EQUAL
Greater than the value or equal to the value.
Definition: DataFilters.h:68
OpenMS::Internal::IndexedMzMLHandler::getNrSpectra
size_t getNrSpectra() const
Returns the number of spectra available.
OpenMS::LayerDataBase::ODExperimentSharedPtrType
boost::shared_ptr< OnDiscMSExperiment > ODExperimentSharedPtrType
SharedPtr on On-Disc MSExperiment.
Definition: LayerDataBase.h:166
OpenMS::LayerDataBase::getCurrentSpectrumIndex
Size getCurrentSpectrumIndex() const
Get the index of the current spectrum (1D view)
Definition: LayerDataBase.h:331
OpenMS::LayerDataBase
Class that stores the data for one layer.
Definition: LayerDataBase.h:97
OpenMS::TOPPViewBase::watcher_
FileWatcher * watcher_
Watcher that tracks file changes (in order to update the data in the different views)
Definition: TOPPViewBase.h:434
OpenMS::ParamXMLFile::store
void store(const String &filename, const Param &param) const
Write XML file.
OpenMS::TOPPViewBase::ExperimentType
LayerDataBase::ExperimentType ExperimentType
Definition: TOPPViewBase.h:148
OpenMS::Internal::FilterList::set
void set(const DataFilters &filters)
OpenMS::Plot1DCanvas::DM_PEAKS
draw data as peak
Definition: Plot1DCanvas.h:115
TheoreticalSpectrumGenerator.h
OpenMS::TOPPViewBase::showSpectrumAlignmentDialog
void showSpectrumAlignmentDialog()
Shows the spectrum alignment dialog.
Definition: TOPPViewBase.cpp:2049
OpenMS::TOPPViewBase::ODExperimentSharedPtrType
LayerDataBase::ODExperimentSharedPtrType ODExperimentSharedPtrType
Definition: TOPPViewBase.h:152
OpenMS::Internal::TOPPViewPrefDialog
Preferences dialog for TOPPView.
Definition: TOPPViewPrefDialog.h:58
OpenMS::Exception::MissingInformation
Not all required information provided.
Definition: Exception.h:186
ToolsDialog.h
OpenMS::TOPPViewBase::finishTOPPToolExecution
void finishTOPPToolExecution(int exitCode, QProcess::ExitStatus exitStatus)
slot for the finished signal of the TOPP tools execution
Definition: TOPPViewBase.cpp:1909
OpenMS::TOPPViewBase::getCanvasParameters
Param getCanvasParameters(UInt dim) const
Returns the parameters for a PlotCanvas of dimension dim.
Definition: TOPPViewBase.cpp:2318
OPENMS_LOG_INFO
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
OpenMS::TOPPViewBase::layerFilterVisibilityChange
void layerFilterVisibilityChange(bool) const
Enables/disables the data filters for the current layer.
Definition: TOPPViewBase.cpp:1381
SpectraIDViewTab.h
OpenMS::PlotCanvas::resetZoom
void resetZoom(bool repaint=true)
Zooms fully out and resets the zoom stack.
OpenMS::Plot1DCanvas::getAlignmentScore
double getAlignmentScore() const
Returns the score of the alignment.
main
int main(int argc, const char **argv)
Definition: TOPPView.cpp:110
QApplicationTOPP.h
OpenMS::TheoreticalSpectrumGenerationDialog
Dialog which allows to enter an AA or NA sequence and generates a theoretical spectrum for it.
Definition: TheoreticalSpectrumGenerationDialog.h:73
OpenMS::PlotCanvas::getCurrentLayerIndex
Size getCurrentLayerIndex() const
returns the index of the active layer
Definition: PlotCanvas.h:294
OpenMS::TOPPViewBase::getActive1DWidget
Plot1DWidget * getActive1DWidget() const
returns a pointer to the active Plot1DWidget (0 the active window is no Plot1DWidget or there is no a...
Definition: TOPPViewBase.cpp:1532
IndexedMzMLHandler.h
OpenMS::Exception::FileEmpty
File is empty.
Definition: Exception.h:594
OpenMS::PlotCanvas::showCurrentLayerPreferences
virtual void showCurrentLayerPreferences()=0
Shows the preferences dialog of the active layer.
OpenMS::EnhancedTabBar::removeId
void removeId(int id)
Remove the tab with identifier id.
OpenMS::AxisWidget::setLegend
void setLegend(const String &legend)
sets the legend text
DataSelectionTabs.h
OpenMS::ParamXMLFile::load
void load(const String &filename, Param &param)
Read XML file.
OpenMS::TOPPViewBase::~TOPPViewBase
~TOPPViewBase() override
Destructor.
Definition: TOPPViewBase.cpp:2726
OpenMS::LogWindow::addNewline
void addNewline()
appends a line break (same as append(""))
OpenMS::TOPPViewBase::TOOL_SCAN::SCAN_IF_NEWER_VERSION
Only generate params for each tool/util if TOPPView's last ini file has an older version....
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
OpenMS::TOPPViewMenu::addWindowToggle
void addWindowToggle(QAction *const window_toggle)
add a menu entry at 'Windows -> [Windowname]' to allow hiding/showing a TOPPView subwindow (e....
OpenMS::Plot2DCanvas::mergeIntoLayer
void mergeIntoLayer(Size i, FeatureMapSharedPtrType map)
Merges the features in map into the features layer i.
OpenMS::TOPPViewBase::showCurrentPeaksAsDIA
void showCurrentPeaksAsDIA()
Shows the current peak data of the active layer as DIA data.
Definition: TOPPViewBase.cpp:2145
OpenMS::TOPPViewBase::layerActivated
void layerActivated()
gets called if a layer got activated
Definition: TOPPViewBase.cpp:1389
OpenMS::PlotCanvas::setLayerFlag
void setLayerFlag(LayerDataBase::Flags f, bool value)
sets a layer flag of the current layer
Definition: PlotCanvas.h:306
OpenMS::TOPPViewBase::updateToolBar
void updateToolBar()
updates the toolbar
Definition: TOPPViewBase.cpp:1254
OpenMS::Param::getValue
const ParamValue & getValue(const std::string &key) const
Returns a value of a parameter.
OpenMS::DefaultParamHandler::subsections_
std::vector< String > subsections_
Container for registered subsections. This member should be filled in the constructor of derived clas...
Definition: DefaultParamHandler.h:180
OnDiscMSExperiment.h
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:437
OpenMS::PlotCanvas::addLayer
bool addLayer(ExperimentSharedPtrType map, ODExperimentSharedPtrType od_map, const String &filename="")
Add a peak data layer.
OpenMS::Exception::FileNotReadable
File not readable exception.
Definition: Exception.h:523
OpenMS::SpectrumAlignmentDialog::getTolerance
double getTolerance() const
OpenMS::Param::remove
void remove(const std::string &key)
Remove the entry key or a section key (when suffix is ':')
OpenMS::PlotCanvas::getCurrentLayer
const LayerDataBase & getCurrentLayer() const
returns the layer data of the active layer
Definition: PlotCanvas.h:283
OpenMS::LayerDataBase::LabelType
LabelType
Label used in visualization.
Definition: LayerDataBase.h:132
OpenMS::Param::setValidStrings
void setValidStrings(const std::string &key, const std::vector< std::string > &strings)
Sets the valid strings for the parameter key.
OpenMS::TOPPViewBase::showSpectrumBrowser
void showSpectrumBrowser()
shows the spectrum browser and updates it
Definition: TOPPViewBase.cpp:2580
StandardTypes.h
QLineEdit
OpenMS::TOPPViewBase::ConsensusMapSharedPtrType
LayerDataBase::ConsensusMapSharedPtrType ConsensusMapSharedPtrType
Definition: TOPPViewBase.h:145
OpenMS::PlotCanvas::ODExperimentSharedPtrType
LayerDataBase::ODExperimentSharedPtrType ODExperimentSharedPtrType
Definition: PlotCanvas.h:150
OpenMS::LayerDataBase::chromatogram_flag_set
bool chromatogram_flag_set() const
Check whether the current layer is a chromatogram.
Definition: LayerDataBase.h:391
File.h
MzIdentMLFile.h
OpenMS::TOPPViewBase::rerunTOPPTool
void rerunTOPPTool()
returns the last invoked TOPP tool with the same parameters
Definition: TOPPViewBase.cpp:1737
OpenMS::TOPPViewBase::dm_hull_2d_
QAction * dm_hull_2d_
Definition: TOPPViewBase.h:468
OpenMS::PlotCanvas::IM_NONE
Normal mode: f(x)=x.
Definition: PlotCanvas.h:186
OpenMS::SpectrumAlignmentDialog::get2ndLayerIndex
Int get2ndLayerIndex()
Returns the index of the selected flipped layer.
OpenMS::ProgressLogger::setLogType
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
OpenMS::TOPPViewBase::editMetadata
void editMetadata()
lets the user edit the meta data of a layer
Definition: TOPPViewBase.cpp:1040
OpenMS::File::findSiblingTOPPExecutable
static String findSiblingTOPPExecutable(const String &toolName)
Searches for an executable with the given name.
OpenMS::TOPPViewBase::changeLayerFlag
void changeLayerFlag(bool)
Definition: TOPPViewBase.cpp:1215
EnhancedWorkspace.h
OpenMS::RecentFilesMenu::getAsParam
Param getAsParam() const
Convert current file list to Param. Their names are just numbers, starting at "0"....
MSSpectrum.h
OpenMS::TOPPViewBase::FeatureMapType
LayerDataBase::FeatureMapType FeatureMapType
Definition: TOPPViewBase.h:138
TOPPViewMenu.h
OpenMS::estimateNoiseFromRandomScans
float estimateNoiseFromRandomScans(const MSExperiment &exp, const UInt ms_level, const UInt n_scans=10, const double percentile=80)
OpenMS::ConsensusXMLFile
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLFile.h:58
OpenMS::IdXMLFile
Used to load and store idXML files.
Definition: IdXMLFile.h:68
OpenMS::FileTypes::typeToName
static String typeToName(Type type)
Returns the name/extension of the type.
OpenMS::Internal::IndexedMzMLHandler
A low-level class to read an indexedmzML file.
Definition: IndexedMzMLHandler.h:79
OpenMS::DefaultParamHandler::param_
Param param_
Container for current parameters.
Definition: DefaultParamHandler.h:166
OpenMS::TOPPViewBase::LOAD_RESULT::FILETYPE_UNKNOWN
file exists, but type could no be determined
OpenMS::TOPPViewBase::zoom_together_
bool zoom_together_
Stores whether the individual windows should zoom together (be linked) or not.
Definition: TOPPViewBase.h:440
OpenMS::DefaultParamHandler::getName
const String & getName() const
Non-mutable access to the name.
OpenMS::LayerDataBase::getPeakDataMuteable
const ExperimentSharedPtrType & getPeakDataMuteable()
Returns a mutable reference to the current in-memory peak data.
Definition: LayerDataBase.h:235
OpenMS::FileHandler::swapExtension
static String swapExtension(const String &filename, const FileTypes::Type new_type)
Tries to find and remove a known file extension, and append the new one.
OpenMS::TOPPViewBase::showCursorStatusInvert
void showCursorStatusInvert(double mz, double rt)
shows m/z and rt in the status bar (inverting RT and m/z)
Definition: TOPPViewBase.cpp:1072
OpenMS::DataSelectionTabs::callUpdateEntries
void callUpdateEntries()
OpenMS::LogWindow::appendText
void appendText(const QString &text)
appends text without adding line breaks and shows the log-window
OpenMS::Exception::BaseException::getLine
int getLine() const noexcept
Returns the line number where it occurred.
OpenMS::PlotCanvas::getLayer
const LayerDataBase & getLayer(Size index) const
returns the layer data with index index
Definition: PlotCanvas.h:272
OpenMS::FileTypeList
holds a vector of known file types, e.g. as a way to specify supported input formats
Definition: FileTypes.h:149
OpenMS::TOPPViewOpenDialog::viewMapAs2D
bool viewMapAs2D() const
Returns true, if 2D mode is to be used for maps.
EnhancedTabBar.h