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OpenMS
2.4.0
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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;
254 void updateCurrentPath();
258 void openFileDialog();
260 void openExampleDialog();
262 void showGoToDialog();
264 void preferencesDialog();
266 void layerStatistics();
270 void layerActivated();
272 void layerZoomChanged();
276 void layerDeactivated();
280 void updateToolBar();
282 void updateLayerBar();
284 void updateViewBar();
286 void viewChanged(
int);
288 void viewTabwidgetDoubleClicked(
int);
290 void updateFilterBar();
294 void updateTabBar(QMdiSubWindow* w);
298 void tileHorizontal();
305 void showStatusMessage(std::string msg,
OpenMS::UInt time);
307 void showCursorStatus(
double mz,
double rt);
309 void showCursorStatusInvert(
double mz,
double rt);
311 void showTOPPDialog();
313 void annotateWithID();
315 void showSpectrumGenerationDialog();
317 void showSpectrumAlignmentDialog();
319 void showSpectrumAs1D(
int index);
320 void showSpectrumAs1D(std::vector<
int, std::allocator<int> > indices);
322 void showCurrentPeaksAs2D();
324 void showCurrentPeaksAs3D();
326 void showCurrentPeaksAsIonMobility();
328 void showCurrentPeaksAsDIA();
330 void showAboutDialog();
334 void saveLayerVisible();
336 void toggleGridLines();
338 void toggleAxisLegends();
340 void showPreferences();
342 void metadataFileDialog();
347 void setDrawMode1D(
int);
348 void setIntensityMode(
int);
349 void changeLayerFlag(
bool);
350 void changeLabel(QAction*);
351 void changeUnassigned(QAction*);
353 void toggleProjections();
357 void loadFile(QString);
363 void layerSelectionChange(
int);
366 void layerFilterVisibilityChange(
bool);
368 void layerContextMenu(
const QPoint& pos);
370 void logContextMenu(
const QPoint& pos);
372 void layerVisibilityChange(QListWidgetItem* item);
374 void filterContextMenu(
const QPoint& pos);
376 void filterEdit(QListWidgetItem* item);
378 void layerEdit(QListWidgetItem* );
382 void finishTOPPToolExecution(
int exitCode, QProcess::ExitStatus exitStatus);
384 void abortTOPPTool();
386 void rerunTOPPTool();
388 void showSpectrumBrowser();
390 void showSpectrumMetaData(
int spectrum_index);
395 void closeByTab(
int id);
398 void enhancedWorkspaceWindowChanged(
int id);
400 void openRecentFile();
402 void copyLayer(
const QMimeData* data,
QWidget* source,
int id = -1);
406 void updateProcessLog();
409 void fileChanged_(
const String&);
412 void initializeDefaultParameters_();
416 bool annotateMS1FromMassFingerprinting_(
const FeatureMap& identifications);
419 std::set<String> getFilenamesOfOpenFiles_();
424 QStringList getFileList_(
const String& path_overwrite =
"");
503 QLabel* message_label_;
513 void addRecentFile_(
const String& filename);
516 void updateRecentMenu_();
546 void checkPreferences_();
549 void closeEvent(QCloseEvent* event)
override;
560 void showLogMessage_(LogState state,
const String& heading,
const String& body);
566 void showTOPPDialog_(
bool visible);
586 static bool containsIMData(
const MSSpectrum& s);
QActionGroup * group_label_2d_
Definition: TOPPViewBase.h:486
void changeVisibility(Size i, bool b)
change the visibility of a layer
bool mirrorModeActive()
Returns whether this widget is currently in mirror mode.
const char * tool_name
Definition: TOPPView.cpp:78
void showStatusMessage(std::string msg, OpenMS::UInt time)
Shows a status message in the status bar.
Definition: TOPPViewBase.cpp:1688
OpenMS identification format (.idXML)
Definition: FileTypes.h:66
void filterContextMenu(const QPoint &pos)
slot for filter manager context menu
Definition: TOPPViewBase.cpp:2230
SpectraViewWidget * spectra_view_widget_
Definition: TOPPViewBase.h:438
String out
Definition: TOPPViewBase.h:534
FilterType field
Field to filter.
Definition: DataFilters.h:80
void setVisibleArea(AreaType area)
Sets the visible area.
Shows intensities normalized by layer maximum: f(x)=x/max(x)*100.
Definition: SpectrumCanvas.h:152
Definition: EnhancedWorkspace.h:49
std::vector< PeptideIdentification > peptides
peptide identifications
Definition: LayerData.h:418
String name
layer name
Definition: LayerData.h:412
void removeAll(const String &prefix)
Remove all entries that start with prefix.
Param copy(const String &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
QTabWidget * views_tabwidget_
Tabwidget that hold the different views on the loaded data.
Definition: TOPPViewBase.h:573
void resetZoom()
Definition: TOPPViewBase.cpp:1738
bool isDataDIA() const
Returns if the data is DIA / SWATH-MS data.
void setIntensityMode(int)
Definition: TOPPViewBase.cpp:1747
void resetZoom(bool repaint=true)
Zooms fully out and resets the zoom stack.
boost::shared_ptr< ExperimentType > ExperimentSharedPtrType
SharedPtr on MSExperiment.
Definition: LayerData.h:147
Size spectrum_id
Definition: TOPPViewBase.h:538
void removeFile(const String &path)
removes a file from the watcher
Definition: FileWatcher.h:90
void setMetadataOnly(bool only)
sets whether or not to load only meta data
static const String CAPTION_3D_SUFFIX_
Suffix appended to caption of tabs when layer is shown in 3D.
Definition: TOPPViewBase.h:599
void getVisibleFeatureData(FeatureMapType &map) const
Fills the handed over map with the visible features of the current layer.
void setYLabel(const QString &l)
Definition: Spectrum3DOpenGLCanvas.h:101
void store(const String &filename, const ConsensusMap &consensus_map)
Stores a consensus map to file.
void addRecentFile_(const String &filename)
adds a Filename to the recent files
Definition: TOPPViewBase.cpp:1556
QLabel * mz_label_
m/z label for messages in the status bar
Definition: TOPPViewBase.h:506
bool modified
Flag that indicates that the layer data was modified since loading it.
Definition: LayerData.h:439
Param param
Definition: TOPPViewBase.h:531
static const std::string NamesOfLabelType[SIZE_OF_LABEL_TYPE]
Label names.
Definition: LayerData.h:129
bool getParsingSuccess() const
Returns whether parsing was successful.
static void openURL(const QString &target)
boost::shared_ptr< FeatureMap > FeatureMapSharedPtrType
SharedPtr on feature map.
Definition: LayerData.h:135
CoordinateType minX() const
Accessor for min_ coordinate minimum.
Definition: DIntervalBase.h:240
static bool containsIMData(const MSSpectrum &s)
Returns true if contains ion mobility data.
Definition: TOPPViewBase.cpp:682
String getSequence() const
Consensus feature data.
Definition: LayerData.h:95
virtual void activateBehavior()
Slot for behavior activation.
boost::shared_ptr< ConsensusMap > ConsensusMapSharedPtrType
SharedPtr on consensus features.
Definition: LayerData.h:141
void runTOPPTool_()
Runs the TOPP tool according to the information in topp_.
Definition: TOPPViewBase.cpp:2928
Int getMergeLayer() const
Returns the index of the selected merge layer. If the option is not selected -1 is returned.
Size getLayerCount() const
Returns the number of layers.
Definition: SpectrumCanvas.h:338
Fatal error.
Definition: TOPPViewBase.h:557
void setLabel(LayerData::LabelType label)
Definition: SpectrumCanvas.h:295
QButtonGroup * intensity_button_group_
Definition: TOPPViewBase.h:471
static String basename(const String &file)
Returns the basename of the file (without the path).
Invalid value exception.
Definition: Exception.h:335
void store(const String &filename, const PeakMap &map) const
Stores a map in an MzML file.
Dialog for creating and changing a DataFilter.
Definition: DataFilterDialog.h:56
void setMZ(CoordinateType mz)
Mutable access to m/z.
Definition: Peak1D.h:119
void disableDimension(bool as_2d)
Disables view dimension section and sets the selected option.
int addTab(const String &text, int id)
Adds a new tab with the name text and the identifier id.
Logarithmic mode.
Definition: SpectrumCanvas.h:154
MzML file (.mzML)
Definition: FileTypes.h:72
LayerData::FeatureMapSharedPtrType FeatureMapSharedPtrType
Definition: TOPPViewBase.h:138
void changeLayerFilterState(Size i, bool b)
change if the defined data filters are used
No label is displayed.
Definition: LayerData.h:120
void setValue(const String &key, const DataValue &value, const String &description="", const StringList &tags=StringList())
Sets a value.
QString toQString() const
Conversion to QString.
const ODExperimentSharedPtrType & getOnDiscPeakData() const
Returns a mutable reference to the on-disc data.
Definition: LayerData.h:248
void addFile(const String &path)
Adds a file to the watcher.
Definition: FileWatcher.h:84
Dataset opening options for TOPPView.
Definition: TOPPViewOpenDialog.h:60
File adapter for MzML files.
Definition: MzMLFile.h:55
QTextEdit * log_
Log output window.
Definition: TOPPViewBase.h:463
A more convenient string class.
Definition: String.h:57
void tileHorizontal()
tile the open windows horizontally
Definition: TOPPViewBase.cpp:2369
Representation of a peak/feature filter combining FilterType, FilterOperation and a value.
Definition: DataFilters.h:74
File not found exception.
Definition: Exception.h:523
Canvas for visualization of one or several spectra.
Definition: Spectrum1DCanvas.h:67
void setValidStrings(const String &key, const std::vector< String > &strings)
Sets the valid strings for the parameter key.
LayerData::FeatureMapType FeatureMapType
Definition: TOPPViewBase.h:136
String current_path_
Definition: TOPPViewBase.h:570
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
const std::vector< Precursor > & getPrecursors() const
returns a const reference to the precursors
OpenMS consensus map format (.consensusXML)
Definition: FileTypes.h:67
void abortTOPPTool()
aborts the execution of a TOPP tool
Definition: TOPPViewBase.cpp:3766
Main window of TOPPView tool.
Definition: TOPPViewBase.h:124
void setMaxInt(const String &key, Int max)
Sets the maximum value for the integer or integer list parameter key.
void fileChanged_(const String &)
Called if a data file has been externally changed.
Definition: TOPPViewBase.cpp:4133
void disableCutoff(bool cutoff_on)
Disables cutoff section and sets the selected option.
Extension to the QApplication for running TOPPs GUI tools.
Definition: QApplicationTOPP.h:50
void enhancedWorkspaceWindowChanged(int id)
Raises the window corresponding to the data of the tab with identifier id.
Definition: TOPPViewBase.cpp:1623
OpenMS parameters file (.ini)
Definition: FileTypes.h:69
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
QActionGroup * group_unassigned_2d_
Definition: TOPPViewBase.h:488
double getMonoWeight(Residue::ResidueType type=Residue::Full, Int charge=0) const
const AreaType & getVisibleArea() const
Returns the currently visible area.
Definition: SpectrumCanvas.h:312
const FeatureMapSharedPtrType & getFeatureMap() const
Returns a const reference to the current feature data.
Definition: LayerData.h:187
FilterOperation op
Filter operation.
Definition: DataFilters.h:82
A widget witch allows constructing gradients of multiple colors.
Definition: MultiGradientSelector.h:67
bool loadFeatures(const String &filename, FeatureMap &map, FileTypes::Type force_type=FileTypes::UNKNOWN)
Loads a file into a FeatureMap.
void add(const DataFilter &filter)
Adds a filter.
#define LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:454
void closeEvent(QCloseEvent *event) override
Definition: TOPPViewBase.cpp:650
The file pendant of the Param class used to load and store the param datastructure as paramXML.
Definition: ParamXMLFile.h:49
virtual void removeLayer(Size layer_index)=0
removes the layer with index layer_index
void setDrawMode1D(int)
Definition: TOPPViewBase.cpp:1757
void openFileDialog()
shows the file dialog for opening files
Definition: TOPPViewBase.cpp:2854
void updateViewBar()
adapts view bar to the active window
Definition: TOPPViewBase.cpp:2022
bool isCutoffEnabled() const
Returns if the low intensity peaks should be hidden.
void updateMenu()
enabled/disabled menu entries depending on the current state
Definition: TOPPViewBase.cpp:3784
DataFilters filters
Filters to apply before painting.
Definition: LayerData.h:427
String prefix(SizeType length) const
returns the prefix of length length
void layerContextMenu(const QPoint &pos)
slot for layer manager context menu
Definition: TOPPViewBase.cpp:2134
void toggleProjections()
Definition: TOPPViewBase.cpp:3125
void setMaxX(CoordinateType const c)
Mutator for min_ coordinate of the larger point.
Definition: DIntervalBase.h:278
double value
Value for comparison.
Definition: DataFilters.h:84
SpectrumWidget * getActiveSpectrumWidget() const
returns a pointer to the active SpectrumWidget (0 if none is active)
Definition: TOPPViewBase.cpp:2683
draw data as peak
Definition: Spectrum1DCanvas.h:90
const DataValue & getValue(const String &key) const
Returns a value of a parameter.
Int get1stLayerIndex()
Returns the index of the selected non-flipped layer.
mzIdentML (HUPO PSI AnalysisXML followup format) (.mzid)
Definition: FileTypes.h:77
QToolBar * tool_bar_
Definition: TOPPViewBase.h:468
bool flipped
if this layer is flipped (1d mirror view)
Definition: LayerData.h:406
virtual void getSpectrum(PeakSpectrum &spec, const AASequence &peptide, Int min_charge, Int max_charge) const
returns a spectrum with the ion types, that are set in the tool parameters
QStringList recent_files_
list of the recently opened files
Definition: TOPPViewBase.h:518
static bool remove(const String &file)
Removes a file (if it exists).
void setLayerName(Size i, const String &name)
Sets the name of layer i.
static String getUniqueName(bool include_hostname=true)
Returns a string, consisting of date, time, hostname, process id, and a incrementing number....
void addData(FeatureMapSharedPtrType feature_map, ConsensusMapSharedPtrType consensus_map, std::vector< PeptideIdentification > &peptides, ExperimentSharedPtrType peak_map, ODExperimentSharedPtrType on_disc_peak_map, LayerData::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:1334
PeakFileOptions & getOptions()
Mutable access to the options for loading/storing.
IntensityModes
Display modes of intensity.
Definition: SpectrumCanvas.h:149
CoordinateType minY() const
Accessor for max_ coordinate minimum.
Definition: DIntervalBase.h:246
Canvas for 3D-visualization of peak map data.
Definition: Spectrum3DCanvas.h:66
Unknown file extension.
Definition: FileTypes.h:60
void linkZoom()
link the zoom of individual windows
Definition: TOPPViewBase.cpp:2444
Spectrum1DWidget * getActive1DWidget() const
returns a pointer to the active Spectrum1DWidget (0 the active window is no Spectrum1DWidget or there...
Definition: TOPPViewBase.cpp:2706
void showGridLines(bool show)
Whether or not to show grid lines.
EnhancedWorkspace * ws_
Main workspace.
Definition: TOPPViewBase.h:495
EnhancedTabBar * tab_bar_
Tab bar. The address of the corresponding window to a tab is stored as an int in tabData()
Definition: TOPPViewBase.h:498
void showAboutDialog()
Shows the 'About' dialog.
Definition: TOPPViewBase.cpp:3743
void layerVisibilityChange(QListWidgetItem *item)
slot for layer manager visibility change (check box)
Definition: TOPPViewBase.cpp:2342
bool hasSubstring(const String &string) const
true if String contains the string, false otherwise
DrawModes getDrawMode() const
Returns the draw mode of the current layer.
Size size() const
Definition: MSExperiment.h:127
Feature data.
Definition: LayerData.h:94
void layerSelectionChange(int)
slot for layer manager selection change
Definition: TOPPViewBase.cpp:2124
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
The element number is used.
Definition: LayerData.h:121
String layer_name
Definition: TOPPViewBase.h:536
Size activeLayerIndex() const
Returns the index of the active layer.
const LayerData & getCurrentLayer() const
returns the layer data of the active layer
Definition: SpectrumCanvas.h:244
static DateTime now()
Returns the current date and time.
QToolButton * dm_unassigned_2d_
Definition: TOPPViewBase.h:487
static bool writable(const String &file)
Return true if the file is writable.
void load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)
Loads the identifications of an idXML file without identifier.
Exception indicating that an invalid parameter was handed over to an algorithm.
Definition: Exception.h:347
void closeByTab(int id)
Closes the window corresponding to the data of the tab with identifier id.
Definition: TOPPViewBase.cpp:1612
void openRecentFile()
Opens a file from the recent files menu.
Definition: TOPPViewBase.cpp:2819
virtual void deactivateBehavior()
Slot for behavior deactivation.
Size size() const
Filter count.
Precursor meta information.
Definition: Precursor.h:57
QListWidget * layer_manager_
Layer management widget.
Definition: TOPPViewBase.h:443
void print_usage()
Definition: TOPPView.cpp:84
void metadataFileDialog()
dialog for inspecting database meta data
Definition: TOPPViewBase.cpp:4000
File adapter for MzIdentML files.
Definition: MzIdentMLFile.h:67
int Int
Signed integer type.
Definition: Types.h:102
Forward const iterator for the Param class.
Definition: Param.h:181
const ConstExperimentSharedPtrType getPeakData() const
Returns a const reference to the current in-memory peak data.
static bool exists(const String &file)
Method used to test if a file exists.
void setMergeLayers(const Map< Size, String > &layers)
Sets the possible merge layers (index and name) and activates the option.
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
QButtonGroup * draw_group_1d_
Definition: TOPPViewBase.h:475
bool toBool() const
Conversion to bool.
Spectrum2DWidget * getActive2DWidget() const
returns a pointer to the active Spectrum2DWidget (0 the active window is no Spectrum2DWidget or there...
Definition: TOPPViewBase.cpp:2711
Spectrum profile or centroided data.
Definition: LayerData.h:93
static String number(double d, UInt n)
returns a string for d with exactly n decimal places
void addSpectrum(const MSSpectrum &spectrum)
adds a spectrum to the list
const LayerData & getLayer(Size index) const
returns the layer data with index index
Definition: SpectrumCanvas.h:237
Behavior of TOPPView in spectra view mode.
Definition: TOPPViewSpectraViewBehavior.h:48
static bool containsMS1Scans(const ExperimentType &exp)
Returns true if contains at least one MS1 spectrum.
Definition: TOPPViewBase.cpp:666
QDockWidget * filter_dock_widget_
Definition: TOPPViewBase.h:433
QMenu * add_2d_context_
Additional context menu for 2D layers.
Definition: TOPPViewBase.h:563
EnhancedWorkspace * getWorkspace() const
returns a pointer to the EnhancedWorkspace containing SpectrumWidgets
Definition: TOPPViewBase.cpp:2678
Features: Unassigned peptide hits.
Definition: LayerData.h:106
void showCurrentPeaksAs2D()
Shows the current peak data of the active layer in 2D.
Definition: TOPPViewBase.cpp:3476
std::vector< QAction * > recent_actions_
list of the recently opened files actions (menu entries)
Definition: TOPPViewBase.h:520
OpenMS feature file (.featureXML)
Definition: FileTypes.h:65
void changeLabel(QAction *)
Definition: TOPPViewBase.cpp:1766
Peptide identification data.
Definition: LayerData.h:97
String filename
file name of the file the data comes from (if available)
Definition: LayerData.h:415
void updateRecentMenu_()
update the recent files menu
Definition: TOPPViewBase.cpp:1574
QLabel * rt_label_
RT label for messages in the status bar.
Definition: TOPPViewBase.h:508
bool viewMapAs1D() const
Returns true, if 1D mode is to be used for maps.
void remove_chromatogram_flag()
remove the chromatogram flag
Definition: LayerData.h:379
const LayerData * getCurrentLayer() const
Returns the active Layer data (0 if no layer is active)
Definition: TOPPViewBase.cpp:3115
bool exists(const String &key) const
Tests if a parameter is set (expecting its fully qualified name, e.g., TextExporter:1:proteins_only)
LogState
Log message states.
Definition: TOPPViewBase.h:553
void copyLayer(const QMimeData *data, QWidget *source, int id=-1)
Slot for drag-and-drop of layer manager to tabbar.
Definition: TOPPViewBase.cpp:4033
void loadPreferences(String filename="")
Loads the preferences from the filename given.
Definition: TOPPViewBase.cpp:2721
void setLayerFlag(LayerData::Flags f, bool value)
sets a layer flag of the current layer
Definition: SpectrumCanvas.h:270
Filter the intensity value.
Definition: DataFilters.h:58
ExperimentType::SpectrumType SpectrumType
Peak spectrum type.
Definition: TOPPViewBase.h:152
void initializeDefaultParameters_()
Initializes the default parameters on TOPPView construction.
Definition: TOPPViewBase.cpp:602
double getClockTime() const
QDockWidget * views_dockwidget_
Definition: TOPPViewBase.h:432
const ExperimentType::SpectrumType & getCurrentSpectrum() const
Returns a const reference to the current spectrum (1D view)
static void showAboutDialog(QWidget *parent, const QString &toolname)
Show the About-Dialog with License and Citation for all GUI tools.
Definition: QApplicationTOPP.cpp:131
LayerData::ConsensusMapSharedPtrType ConsensusMapSharedPtrType
Definition: TOPPViewBase.h:143
Class that stores the data for one layer.
Definition: LayerData.h:85
QCheckBox * filters_check_box_
Definition: TOPPViewBase.h:448
void getVisibleConsensusData(ConsensusMapType &map) const
Fills the handed over map with the visible consensus features of the current layer.
void parseCommandLine(const int argc, const char **argv, const String &prefix="")
Parses command line arguments.
void setMinInt(const String &key, Int min)
Sets the minimum value for the integer or integer list parameter key.
Facilitates file handling by file type recognition.
Definition: FileHandler.h:62
Shows the maximum displayed intensity as if it was the overall maximum intensity.
Definition: SpectrumCanvas.h:153
QToolButton * dm_label_2d_
Definition: TOPPViewBase.h:485
void tileVertical()
tile the open windows vertically
Definition: TOPPViewBase.cpp:2407
Representation of a mass spectrometry experiment on disk.
Definition: OnDiscMSExperiment.h:68
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.
void load(const String &filename, FeatureMap &feature_map)
loads the file with name filename into map and calls updateRanges().
TOPPViewIdentificationViewBehavior * identificationview_behavior_
TOPPView behavior for the identification view.
Definition: TOPPViewBase.h:576
size_t getNrChromatograms() const
Returns the number of chromatograms available.
Type
Actual file types enum.
Definition: FileTypes.h:58
Unable to create file exception.
Definition: Exception.h:636
bool openAsNewWindow() const
Returns true, if the data should be opened in a new window.
void layerEdit(QListWidgetItem *)
slot for editing the preferences of the current layer
Definition: TOPPViewBase.cpp:2306
const ConsensusMapSharedPtrType & getConsensusMap() const
Returns a const reference to the consensus feature data.
Definition: LayerData.h:199
void layerZoomChanged()
gets called when a layer changes in zoom
Definition: TOPPViewBase.cpp:2464
QAction * dm_hulls_2d_
Definition: TOPPViewBase.h:484
QToolBar * tool_bar_1d_
Definition: TOPPViewBase.h:474
QLabel * message_label_
Label for messages in the status bar.
Definition: TOPPViewBase.h:504
QAction * dm_precursors_2d_
Definition: TOPPViewBase.h:482
QProcess * process
Definition: TOPPViewBase.h:539
Identifications: m/z source.
Definition: LayerData.h:110
double getAlignmentScore()
Returns the score of the alignment.
const ExperimentSharedPtrType & getPeakDataMuteable()
Returns a mutable reference to the current in-memory peak data.
Definition: LayerData.h:230
LayerData::ExperimentType ExperimentType
Definition: TOPPViewBase.h:146
static FileTypes::Type getType(const String &filename)
Tries to determine the file type (by name or content)
Size size() const
Returns the number of entries (leafs).
bool addLayer(ExperimentSharedPtrType map, ODExperimentSharedPtrType od_map, const String &filename="")
Add a peak data layer.
LayerData::ExperimentSharedPtrType ExperimentSharedPtrType
Definition: TOPPViewBase.h:148
Consensus features: Show elements.
Definition: LayerData.h:109
void getTime(UInt &hour, UInt &minute, UInt &second) const
Fills the arguments with the time.
QToolBar * tool_bar_2d_cons_
Definition: TOPPViewBase.h:480
SpectrumCanvas * getActiveCanvas() const
returns a pointer to the active SpectrumCanvas (0 if none is active)
Definition: TOPPViewBase.cpp:2692
void openFile(String filename)
Open a file.
Exception base class.
Definition: Exception.h:89
void setPrecursors(const std::vector< Precursor > &precursors)
sets the precursors
void setCurrentId(int id)
Selects the tab with identifier id.
LayerData::ConsensusMapType ConsensusMapType
Definition: TOPPViewBase.h:141
Size getCurrentSpectrumIndex() const
Get the index of the current spectrum (1D view)
Definition: LayerData.h:318
virtual void updateLayer(Size i)=0
Updates layer i when the data in the corresponding file changes.
void setParameters(const Param ¶m)
Sets the parameters.
void setMSLevel(UInt ms_level)
Sets the MS level.
void setMinX(CoordinateType const c)
Mutator for min_ coordinate of the smaller point.
Definition: DIntervalBase.h:264
const Param & getDefaults() const
Non-mutable access to the default parameters.
QAction * linkZoom_action_
Definition: TOPPViewBase.h:460
EnhancedTabBarWidgetInterface * window_(int id) const
Returns the enhanced tabbar widget with id id.
Definition: TOPPViewBase.cpp:1598
QString toQString() const
Conversion to Qt QString.
void showCurrentPeaksAs3D()
Shows the current peak data of the active layer in 3D.
Definition: TOPPViewBase.cpp:3660
bool hasSuffix(const String &string) const
true if String ends with string, false otherwise
bool visible
if this layer is visible
Definition: LayerData.h:403
void layerDeactivated()
gets called if a layer got deactivated
Definition: TOPPViewBase.cpp:2596
static String path(const String &file)
Returns the path of the file (without the file name).
Convenience tab bar implementation.
Definition: EnhancedTabBar.h:60
static String getVersion()
Return the version number of OpenMS.
const Param & getParameters() const
Non-mutable access to the parameters.
void setCurrentLayerParameters(const Param ¶m)
Sets the parameters of the current layer.
Definition: SpectrumCanvas.h:472
Not implemented exception.
Definition: Exception.h:436
bool empty() const
Definition: MSExperiment.h:137
bool chromatogram_flag_set() const
Check whether the current layer is a chromatogram.
Definition: LayerData.h:365
void showPreferences()
Shows current layer preferences.
Definition: TOPPViewBase.cpp:3995
MSExperiment PeakMap
Two-dimensional map of raw data points or peaks.
Definition: StandardTypes.h:61
void toggleGridLines()
Toggles the grid lines.
Definition: TOPPViewBase.cpp:3985
virtual void saveCurrentLayer(bool visible)=0
Saves the current layer data.
DrawModes
Enumerate all available paint styles.
Definition: Spectrum1DCanvas.h:88
SpectraIdentificationViewWidget * spectra_identification_view_widget_
Definition: TOPPViewBase.h:439
Normal mode: f(x)=x.
Definition: SpectrumCanvas.h:151
String file_name
Definition: TOPPViewBase.h:535
IntensityModes getIntensityMode() const
Returns the intensity mode.
Definition: SpectrumCanvas.h:206
A container for consensus elements.
Definition: ConsensusMap.h:75
void mergeIntoLayer(Size i, FeatureMapSharedPtrType map)
Merges the features in map into the features layer i.
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:73
void store(const String &filename, const FeatureMap &feature_map)
stores the map feature_map in file with name filename.
Lets the user select two spectra and set the parameters for the spectrum alignment.
Definition: SpectrumAlignmentDialog.h:56
void load(const String &filename, ConsensusMap &map)
Loads a consensus map from file and calls updateRanges.
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
const FloatDataArrays & getFloatDataArrays() const
Returns a const reference to the float meta data arrays.
void disableLocation(bool window)
Disables opening location section and sets the selected option.
void showGoToDialog()
shows the DB dialog for opening files
Definition: TOPPViewBase.cpp:2669
void savePreferences()
Stores the preferences (used when this window is closed)
Definition: TOPPViewBase.cpp:2794
void updateProcessLog()
Appends process output to log window.
Definition: TOPPViewBase.cpp:3748
void showSpectrumAs1D(int index)
Shows the spectrum with index index of the active layer in 1D.
Definition: TOPPViewBase.cpp:3424
StopWatch Class.
Definition: StopWatch.h:59
void load(const String &filename, std::vector< ProteinIdentification > &poid, std::vector< PeptideIdentification > &peid)
Loads the identifications from a MzIdentML file.
QAction * projections_2d_
Definition: TOPPViewBase.h:490
bool visible
Definition: TOPPViewBase.h:541
LayerData::ODExperimentSharedPtrType ODExperimentSharedPtrType
Definition: TOPPViewBase.h:150
QStringList getFileList_(const String &path_overwrite="")
Shows a dialog where the user can select files.
Definition: TOPPViewBase.cpp:2829
SpectraIdentificationViewWidget * getSpectraIdentificationViewWidget()
returns a pointer to the SpectraIdentificationViewWidget
Definition: TOPPViewBase.cpp:4023
CoordinateType maxY() const
Accessor for max_ coordinate maximum.
Definition: DIntervalBase.h:258
void viewTabwidgetDoubleClicked(int)
adds empty ID structure to allow manual annotations
Definition: TOPPViewBase.cpp:2099
void showCursorStatus(double mz, double rt)
shows m/z and rt in the status bar
Definition: TOPPViewBase.cpp:1707
Behavior of TOPPView in identification mode.
Definition: TOPPViewIdentificationViewBehavior.h:49
Param param
Layer parameters.
Definition: LayerData.h:421
Features: Convex hulls of single mass traces.
Definition: LayerData.h:105
QToolBar * tool_bar_2d_feat_
Definition: TOPPViewBase.h:479
void 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:1102
void showSpectrumMetaData(int spectrum_index)
shows the spectrum metadata
Definition: TOPPViewBase.cpp:4028
QTime timer
Definition: TOPPViewBase.h:540
void setSectionDescription(const String &key, const String &description)
Sets a description for an existing section.
Generates theoretical spectra with various options.
Definition: TheoreticalSpectrumGenerator.h:63
bool getLayerFlag(LayerData::Flags f) const
returns a layer flag of the current layer
Definition: SpectrumCanvas.h:264
ParamIterator end() const
End iterator for the internal tree.
static String absolutePath(const String &file)
Replaces the relative path in the argument with the absolute path.
ParamIterator begin() const
Begin iterator for the internal tree.
A container for features.
Definition: FeatureMap.h:93
String tool
Definition: TOPPViewBase.h:532
void toggleAxisLegends()
Toggles the axis legends.
Definition: TOPPViewBase.cpp:3990
Parse Error exception.
Definition: Exception.h:622
DataFilter array providing some convenience functions.
Definition: DataFilters.h:50
struct OpenMS::TOPPViewBase::@22 topp_
Information needed for execution of TOPP tools.
bool isIonMobilityData() const
Check whether the current layer should be represented as ion mobility.
Definition: LayerData.h:331
Size getAlignmentSize()
Returns the number of aligned pairs of peaks.
QToolBar * tool_bar_2d_ident_
Definition: TOPPViewBase.h:481
void showCurrentPeaksAsIonMobility()
Shows the current peak data of the active layer as ion mobility.
Definition: TOPPViewBase.cpp:3505
static bool hasMS1Zeros(const ExperimentType &exp)
Returns true of experiment has at least one exact zero valued peak in any of its MS1 spectra.
Definition: TOPPViewBase.cpp:728
void loadFiles(const StringList &list, QSplashScreen *splash_screen)
Opens all the files in the string list.
Definition: TOPPViewBase.cpp:3869
void activateSpectrum(Size index, bool repaint=true)
Sets current spectrum index of current layer to index.
Watcher that monitors file changes.
Definition: FileWatcher.h:65
Iterator end()
Definition: MSExperiment.h:167
draw as connected lines
Definition: Spectrum1DCanvas.h:91
void showSpectrumGenerationDialog()
Shows the theoretical spectrum generation dialog.
Definition: TOPPViewBase.cpp:3292
A widget for selecting a color.
Definition: ColorSelector.h:60
QAction * dm_ident_2d_
Definition: TOPPViewBase.h:491
Canvas for 2D-visualization of peak map, feature map and consensus map data.
Definition: Spectrum2DCanvas.h:70
virtual void activateLayer(Size layer_index)=0
change the active layer (the one that is used for selecting and so on)
Spectrum3DWidget * getActive3DWidget() const
returns a pointer to the active Spectrum3DWidget (0 the active window is no Spectrum2DWidget or there...
Definition: TOPPViewBase.cpp:2716
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:2898
virtual void deactivateBehavior()
Slot for behavior deactivation.
static String getOpenMSDataPath()
Returns the OpenMS data path (environment variable overwrites the default installation path)
std::set< String > getFilenamesOfOpenFiles_()
unique list of files referenced by all layers
Definition: TOPPViewBase.cpp:1079
void updateLayerBar()
adapts the layer bar to the active window
Definition: TOPPViewBase.cpp:1968
void showTOPPDialog()
Apply TOPP tool.
Definition: TOPPViewBase.cpp:2892
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:68
static bool readable(const String &file)
Return true if the file exists and is readable.
QListWidget * filters_
Definition: TOPPViewBase.h:447
Size getCurrentLayerIndex() const
returns the index of the active layer
Definition: SpectrumCanvas.h:251
Param getSpectrumParameters(UInt dim)
Returns the parameters for a SpectrumCanvas of dimension dim.
Definition: TOPPViewBase.cpp:3759
void preferencesDialog()
shows the preferences dialog
Definition: TOPPViewBase.cpp:765
QToolBar * tool_bar_2d_peak_
Definition: TOPPViewBase.h:478
void updateFilterBar()
adapts the filter bar to the active window
Definition: TOPPViewBase.cpp:2311
bool flippedLayersExist()
Returns whether flipped layers exist or not.
void changeUnassigned(QAction *)
Definition: TOPPViewBase.cpp:1798
LabelType label
Label type.
Definition: LayerData.h:442
void replace(Size index, const DataFilter &filter)
Replaces the filter corresponding to index.
String toString() const
Conversion to String.
Definition: LayerData.h:125
DataType
Dataset types.
Definition: LayerData.h:91
Notice.
Definition: TOPPViewBase.h:555
Param defaults_
Container for default parameters. This member should be filled in the constructor of derived classes!
Definition: DefaultParamHandler.h:156
CoordinateType maxX() const
Accessor for min_ coordinate maximum.
Definition: DIntervalBase.h:252
const char * getFile() const noexcept
Returns the file where it occurred.
void updateCurrentPath()
changes the current path according to the currently active window/layer
Definition: TOPPViewBase.cpp:4109
void defaultsToParam_()
Updates the parameters after the defaults have been set in the constructor.
QAction * dm_elements_2d_
Definition: TOPPViewBase.h:489
void setMirrorModeActive(bool b)
Sets whether this widget is currently in mirror mode.
Progress dialog.
Definition: ProgressLogger.h:73
void getVisiblePeakData(ExperimentType &map) const
Fills the handed over map with the visible peaks of the current layer.
Management and storage of parameters / INI files.
Definition: Param.h:74
void saveLayerAll()
Saves the whole current layer data.
Definition: TOPPViewBase.cpp:3975
static String findExecutable(const String &toolName)
Searches for an executable with the given name.
void annotateWithID()
Annotates current layer with ID data.
Definition: TOPPViewBase.cpp:3167
QDockWidget * layer_dock_widget_
Definition: TOPPViewBase.h:431
void remove(Size index)
Removes the filter corresponding to index.
bool isActive() const
Returns if the filters are enabled.
Definition: DataFilters.h:151
Representation of a peptide/protein sequence.
Definition: AASequence.h:107
Greater than the value or equal to the value.
Definition: DataFilters.h:67
size_t getNrSpectra() const
Returns the number of spectra available.
void layerStatistics()
Shows statistics (count,min,max,avg) about Intensity, Quality, Charge and meta data.
Definition: TOPPViewBase.cpp:1682
Base class for visualization canvas classes.
Definition: SpectrumCanvas.h:100
void showURL()
shows the URL stored in the data of the sender QAction
Definition: TOPPViewBase.cpp:659
const char * what() const noexcept override
Returns the error message of the exception.
Warning.
Definition: TOPPViewBase.h:556
FileWatcher * watcher_
Watcher that tracks file changes (in order to update the data in the different views)
Definition: TOPPViewBase.h:452
void store(const String &filename, const Param ¶m) const
Write XML file.
void setDrawMode(DrawModes mode)
Sets draw mode of the current layer.
static AASequence fromString(const String &s, bool permissive=true)
create AASequence object by parsing an OpenMS string
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50
void showSpectrumAlignmentDialog()
Shows the spectrum alignment dialog.
Definition: TOPPViewBase.cpp:3387
void setCharge(Int charge)
Mutable access to the charge.
Preferences dialog for TOPPView.
Definition: TOPPViewPrefDialog.h:55
void finishTOPPToolExecution(int exitCode, QProcess::ExitStatus exitStatus)
slot for the finished signal of the TOPP tools execution
Definition: TOPPViewBase.cpp:3074
bool annotateMS1FromMassFingerprinting_(const FeatureMap &identifications)
Definition: TOPPViewBase.cpp:3148
void updateTabBar(QMdiSubWindow *w)
brings the tab corresponding to the active window in front
Definition: TOPPViewBase.cpp:2359
UInt window_id
Definition: TOPPViewBase.h:537
int main(int argc, const char **argv)
Definition: TOPPView.cpp:108
DataType type
data type (peak or feature data)
Definition: LayerData.h:409
void flipLayer(Size index)
Flips the layer with index up/downwards.
Dialog which allows to enter an AA sequence and generates a theoretical spectrum for it.
Definition: TheoreticalSpectrumGenerationDialog.h:55
LayerData::ODExperimentSharedPtrType ODExperimentSharedPtrType
Definition: SpectrumCanvas.h:115
void filterEdit(QListWidgetItem *item)
slot for editing a filter
Definition: TOPPViewBase.cpp:2293
ContainerType::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSSpectrum.h:103
File is empty.
Definition: Exception.h:594
void removeId(int id)
Remove the tab with identifier id.
Spectrum3DOpenGLCanvas * openglwidget()
returns the Spectrum3DOpenGLcanvas
LabelType
Label used in visualization.
Definition: LayerData.h:118
void load(const String &filename, Param ¶m)
Read XML file.
~TOPPViewBase() override
Destructor.
Definition: TOPPViewBase.cpp:4316
void showSpectrumWidgetInWindow(SpectrumWidget *sw, const String &caption)
Opens the provided spectrum widget in a new window.
Definition: TOPPViewBase.cpp:2601
Annotates an MSExperiment, FeatureMap or ConsensusMap with peptide identifications.
Definition: IDMapper.h:66
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
void showCurrentPeaksAsDIA()
Shows the current peak data of the active layer as DIA data.
Definition: TOPPViewBase.cpp:3573
void layerActivated()
gets called if a layer got activated
Definition: TOPPViewBase.cpp:2457
void openExampleDialog()
shows the file dialog for opening example files
Definition: TOPPViewBase.cpp:2864
void updateToolBar()
updates the toolbar
Definition: TOPPViewBase.cpp:1874
void saveLayerVisible()
Saves the visible layer data.
Definition: TOPPViewBase.cpp:3980
virtual void showSpectrumAs1D(int index)
Behavior for showSpectrumAs1D.
std::vector< String > subsections_
Container for registered subsections. This member should be filled in the constructor of derived clas...
Definition: DefaultParamHandler.h:163
void closeFile()
closes the active window
Definition: TOPPViewBase.cpp:1662
bool watcher_msgbox_
Holds the messageboxes for each layer that are currently popped up (to avoid popping them up again,...
Definition: TOPPViewBase.h:455
Features: Overall convex hull.
Definition: LayerData.h:104
boost::shared_ptr< OnDiscMSExperiment > ODExperimentSharedPtrType
SharedPtr on On-Disc MSExperiment.
Definition: LayerData.h:152
virtual void activateBehavior()
Slot for behavior activation.
File not readable exception.
Definition: Exception.h:537
virtual void showCurrentLayerPreferences()=0
Shows the preferences dialog of the active layer.
double getTolerance() const
void insert(const String &prefix, const Param ¶m)
void loadFile(QString)
Loads a file given by the passed string.
Definition: TOPPViewBase.cpp:3143
TOPPViewSpectraViewBehavior * spectraview_behavior_
TOPPView behavior for the spectra view.
Definition: TOPPViewBase.h:578
static bool hasPeptideIdentifications(const ExperimentType &map)
Returns true if the experiment map contains peptide identifications.
Definition: TOPPViewBase.cpp:753
void showSpectrumBrowser()
shows the spectrum browser and updates it
Definition: TOPPViewBase.cpp:4127
String toString(T i)
toString functions (single argument)
Definition: StringUtils.h:68
DateTime Class.
Definition: DateTime.h:54
String in
Definition: TOPPViewBase.h:533
void rerunTOPPTool()
returns the last invoked TOPP tool with the same parameters
Definition: TOPPViewBase.cpp:2875
virtual void setFilters(const DataFilters &filters)
Sets the filters applied to the data before drawing (for the current layer)
QAction * dm_hull_2d_
Definition: TOPPViewBase.h:483
Int get2ndLayerIndex()
Returns the index of the selected flipped layer.
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
void logContextMenu(const QPoint &pos)
slot for log window context menu
Definition: TOPPViewBase.cpp:2215
void editMetadata()
lets the user edit the meta data of a layer
Definition: TOPPViewBase.cpp:1668
Peaks: Mark precursor peaks of MS/MS scans.
Definition: LayerData.h:107
void changeLayerFlag(bool)
Definition: TOPPViewBase.cpp:1842
bool isDIAData() const
Check whether the current layer contains DIA (SWATH-MS) data.
Definition: LayerData.h:344
const std::vector< ProteinIdentification > & getProteinIdentifications() const
non-mutable access to the protein identifications
void showLogMessage_(LogState state, const String &heading, const String &body)
Shows a log message in the log_ window.
Definition: TOPPViewBase.cpp:3951
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLFile.h:61
Used to load and store idXML files.
Definition: IdXMLFile.h:63
float estimateNoiseFromRandomMS1Scans(const ExperimentType &exp, UInt n_scans=10)
Estimates the noise by evaluating n_scans random scans of MS level 1. Assumes that 4/5 of intensities...
Definition: TOPPViewBase.cpp:695
static String typeToName(Type type)
Returns the name/extension of the type.
void layerFilterVisibilityChange(bool)
Enables/disables the data filters for the current layer.
Definition: TOPPViewBase.cpp:2334
void viewChanged(int)
changes the behavior according to the selected view in the spectra view bar and calls updateSpectraVi...
Definition: TOPPViewBase.cpp:2069
A low-level class to read an indexedmzML file.
Definition: IndexedMzMLHandler.h:78
virtual void showSpectrumAs1D(int spectrum_index, int peptide_id_index, int peptide_hit_index)
Behavior for showSpectrumAs1D.
Param param_
Container for current parameters.
Definition: DefaultParamHandler.h:149
void annotate(PeakMap &map, const std::vector< PeptideIdentification > &peptide_ids, const std::vector< ProteinIdentification > &protein_ids, const bool clear_ids=false, const bool mapMS1=false)
Mapping method for peak maps.
Definition: IDMapper.h:96
Chromatogram data.
Definition: LayerData.h:96
bool zoom_together_
Stores whether the individual windows should zoom together (be linked) or not.
Definition: TOPPViewBase.h:458
virtual void showMetaData(bool modifiable=false, Int index=-1)
Shows a dialog with the meta data.
void showCursorStatusInvert(double mz, double rt)
shows m/z and rt in the status bar (inverting RT and m/z)
Definition: TOPPViewBase.cpp:1701
int getLine() const noexcept
Returns the line number where it occurred.
bool viewMapAs2D() const
Returns true, if 2D mode is to be used for maps.