OpenMS GUI
TOPPView, TOPPAS, INIFileEditor and the OpenMS_GUI library
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OpenMS Namespace Reference

Namespaces

namespace  GUIHelpers
 
namespace  Internal
 Namespace used to hide implementation details from users.
 

Classes

class  AcquisitionInfoVisualizer
 Class that displays all meta information for AcquisitionInfo objects. More...
 
class  AcquisitionVisualizer
 Class that displays all meta information for Acquisition objects. More...
 
class  Annotation1DCaret
 An annotation item which paints a set of carets on the canvas. More...
 
class  Annotation1DDistanceItem
 An annotation item which represents a measured distance between two peaks. More...
 
class  Annotation1DItem
 An abstract class acting as an interface for the different 1D annotation items. More...
 
class  Annotation1DPeakItem
 A peak annotation item. More...
 
class  Annotation1DTextItem
 An annotation item which represents an arbitrary text on the canvas. More...
 
class  Annotation1DVerticalLineItem
 An annotation item which represents a vertical line (or more precisely a line along the gravity axis, i.e. it could also be horizontal) and text label on top. More...
 
class  Annotations1DContainer
 Container for annotations to content of Plot1DCanvas. More...
 
class  AxisPainter
 Draws a coordinate axis. It has only static methods, that's why the constructor is private. More...
 
class  AxisTickCalculator
 Calculates ticks for a given value range. More...
 
class  AxisWidget
 Widget that represents an axis of a graph. More...
 
class  BaseVisualizer
 A base class for all visualizer classes. More...
 
class  BaseVisualizerGUI
 A base class for all visualizer classes. More...
 
class  ColorSelector
 A widget for selecting a color. More...
 
class  ContactPersonVisualizer
 Class that displays all meta information for ContactPerson objects. More...
 
class  DataFilterDialog
 Dialog for creating and changing a DataFilter. More...
 
class  DataProcessingVisualizer
 Class that displays all meta information for DataProcessing objects. More...
 
class  DataSelectionTabs
 A tabbed view, to browse lists of spectra or identifications. More...
 
class  DataTabBase
 all tabs need to implement this interface More...
 
class  DIATreeTab
 Hierarchical visualization and selection of spectra. More...
 
class  DimMapper
 
class  DocumentIdentifierVisualizer
 Class that displays all meta information for DocumentIdentifier objects. More...
 
class  EnhancedTabBar
 Convenience tab bar implementation. More...
 
class  EnhancedTabBarWidgetInterface
 Widgets that are placed into an EnhancedTabBar must implement this interface. More...
 
class  EnhancedWorkspace
 
class  ExperimentalSettingsVisualizer
 Class that displays all meta information for ExperimentalSettings objects. More...
 
class  ExternalProcessMBox
 A wrapper around ExternalProcess to conveniently show a MessageBox when an error occurs. More...
 
class  FakeProcess
 A FakeProcess class. More...
 
class  FeatureEditDialog
 Dialog for editing a feature. More...
 
class  FileWatcher
 Watcher that monitors file changes. More...
 
class  GradientVisualizer
 GradientVisualizer is a visualizer class for objects of type gradient. More...
 
class  Gravitator
 Manipulates X or Y component of points in the X-Y plane, by assuming one axis (either X or Y axis) has gravity acting upon it. More...
 
class  GUIProgressLoggerImpl
 Implements a GUI version of the ProgressLoggerImpl. More...
 
class  HistogramDialog
 Dialog that show a HistogramWidget. More...
 
class  HistogramWidget
 
class  HPLCVisualizer
 Class that displays all meta information for HPLC objects. More...
 
class  INIFileEditorWindow
 shows the ParamEditor widget in a QMainWindow with a toolbar More...
 
class  InputFile
 A simple widget with a line-edit and a browse button to choose filenames. More...
 
class  InstrumentSettingsVisualizer
 Class that displays all meta information for InstrumentSettings objects. More...
 
class  InstrumentVisualizer
 Class that displays all meta information for an MS instrument. More...
 
class  InteractiveSplashScreen
 A QSplashScreen which stays responsive and can be dismissed early by the user. More...
 
class  IonDetectorVisualizer
 Class that displays all meta information for IonDetector objects. More...
 
class  IonSourceVisualizer
 Class that displays all meta information for IonSource objects. More...
 
class  IPeptideIds
 Abstract base class which defines an interface for PeptideIdentifications. More...
 
class  LayerAnnotatorAMS
 
class  LayerAnnotatorBase
 
class  LayerAnnotatorOSW
 
class  LayerAnnotatorPeptideID
 
class  LayerData1DBase
 Base class for all 1D layers, a special case of LayerData. More...
 
class  LayerData1DChrom
 
class  LayerData1DIonMobility
 
class  LayerData1DPeak
 
class  LayerDataBase
 Class that stores the data for one layer. More...
 
class  LayerDataChrom
 Class that stores the data for one layer of type Chromatogram. More...
 
class  LayerDataConsensus
 Class that stores the data for one layer of type ConsensusMap. More...
 
struct  LayerDataDefs
 
class  LayerDataFeature
 Class that stores the data for one layer of type FeatureMap. More...
 
class  LayerDataIdent
 Class that stores the data for one layer of type PeptideIdentifications. More...
 
class  LayerDataIonMobility
 Class that stores the data for one layer of type IonMobility. More...
 
class  LayerDataPeak
 Class that stores the data for one layer of type PeakMap. More...
 
class  LayerListView
 Pimped QListView for Layers of a Canvas. More...
 
class  LayerStack
 
class  LayerStatistics
 Compute summary statistics (count/min/max/avg) about a container, e.g. intensity, charge, meta values, ... More...
 
class  LayerStatisticsConsensusMap
 Computes statistics and distributions for a PeakMap. More...
 
class  LayerStatisticsDialog
 Dialog showing statistics about the data of the current layer. More...
 
class  LayerStatisticsFeatureMap
 Computes statistics and distributions for a PeakMap. More...
 
class  LayerStatisticsIdent
 Computes statistics and distributions for a vector<PeptideIdentifications> More...
 
class  LayerStatisticsPeakMap
 Computes statistics and distributions for a PeakMap
More...
 
class  LayerStoreData
 Base class to store either the currently visible or all data of a canvas. More...
 
class  LayerStoreDataConsensusMapAll
 Visitor which can save a full ConsensusMap; subsequently the data can be stored to a file. More...
 
class  LayerStoreDataConsensusMapVisible
 Visitor which can save a visible piece of data; subsequently the data can be stored to a file. More...
 
class  LayerStoreDataFeatureMapAll
 Visitor which can save a full FeatureMap; subsequently the data can be stored to a file. More...
 
class  LayerStoreDataFeatureMapVisible
 Visitor which can save a visible piece of data; subsequently the data can be stored to a file. More...
 
class  LayerStoreDataIdentAll
 Visitor which can save a full set of Identifications; subsequently the data can be stored to a file. More...
 
class  LayerStoreDataIdentVisible
 Visitor which can save a visible piece of data; subsequently the data can be stored to a file. More...
 
class  LayerStoreDataPeakMapAll
 Visitor which can save a full experiment; subsequently the data can be stored to a file. More...
 
class  LayerStoreDataPeakMapVisible
 Visitor which can save a visible piece of data; subsequently the data can be stored to a file. More...
 
class  ListEditor
 Editor for editing int, double and string lists (including output and input file lists) More...
 
class  ListFilterDialog
 Dialog for creating and changing a DataFilter. More...
 
class  LogWindow
 A log window (QTextEdit) with convenience functions. More...
 
class  MassAnalyzerVisualizer
 Class that displays all meta information for MassAnalyzer objects. More...
 
class  MetaDataBrowser
 A meta data visualization widget. More...
 
class  MetaInfoDescriptionVisualizer
 Class that displays all meta information for MetaInfoDescription objects. More...
 
class  MetaInfoVisualizer
 MetaInfoVisualizer is a visualizer class for all classes that use one MetaInfo object as member. More...
 
class  MultiGradient
 A gradient of multiple colors and arbitrary distances between colors. More...
 
class  MultiGradientSelector
 A widget witch allows constructing gradients of multiple colors. More...
 
class  OutputDirectory
 A simple widget with a line-edit and a browse button to choose filenames. More...
 
class  Painter1DBase
 A base class for painting all items from a data layer (as supported by class derived from here) onto a 1D Canvas. More...
 
class  Painter1DChrom
 Painter1D for chromatograms. More...
 
class  Painter1DIonMobility
 Painter1D for mobilograms. More...
 
class  Painter1DPeak
 Painter1D for spectra. More...
 
class  Painter2DBase
 A base class for painting all items from a data layer (as supported by class derived from here) onto a 2D Canvas. More...
 
class  Painter2DChrom
 Painter2D for chromatograms. More...
 
class  Painter2DConsensus
 Painter2D for ConsensusFeatures. More...
 
class  Painter2DFeature
 Painter2D for Features. More...
 
class  Painter2DIdent
 Painter2D for Identifications. More...
 
class  Painter2DIonMobility
 Painter2D for ion mobilograms. More...
 
class  Painter2DPeak
 Painter2D for spectra. More...
 
class  PainterBase
 An empty base class with some static convenience functions. More...
 
class  ParamEditor
 A GUI for editing or viewing a Param object. More...
 
class  PeptideHitVisualizer
 Class that displays all meta information for PeptideHit objects. More...
 
class  PeptideIdentificationVisualizer
 Class that displays all meta information for PeptideIdentification objects. More...
 
class  Plot1DCanvas
 Canvas for visualization of one or several spectra. More...
 
class  Plot1DGoToDialog
 simple goto/set visible area dialog for exact placement of the viewing window More...
 
class  Plot1DWidget
 Widget for visualization of several spectra. More...
 
class  Plot2DCanvas
 Canvas for 2D-visualization of peak map, feature map and consensus map data. More...
 
class  Plot2DGoToDialog
 GoTo dialog used to zoom to a m/z and retention time range or to a feature. More...
 
class  Plot2DWidget
 Widget for 2D-visualization of peak map and feature map data. More...
 
class  Plot3DCanvas
 Canvas for 3D-visualization of peak map data. More...
 
class  Plot3DOpenGLCanvas
 OpenGL Canvas for 3D-visualization of map data. More...
 
class  Plot3DWidget
 Widget for 3D-visualization of map data. More...
 
class  PlotCanvas
 Base class for visualization canvas classes. More...
 
class  PlotWidget
 Base class for spectrum widgets. More...
 
class  PrecursorVisualizer
 Class that displays all meta information for Precursor objects. More...
 
class  ProductVisualizer
 Class that displays all meta information for Product objects. More...
 
class  ProteinHitVisualizer
 Class that displays all meta information for ProteinHit objects. More...
 
class  ProteinIdentificationVisualizer
 Class that displays all meta information for ProteinIdentification objects. More...
 
class  QApplicationTOPP
 Extension to the QApplication for running TOPPs GUI tools. More...
 
struct  RangeStats
 Struct representing the statistics about a set of values. More...
 
struct  RangeStatsType
 Origin and name of a statistic. More...
 
class  RecentFilesMenu
 Manages recent files opened by the user and provides a QMenu to go with it. More...
 
class  SampleVisualizer
 Class that displays all meta information of sample objects. More...
 
class  SaveImageDialog
 Dialog for saving an image. More...
 
class  ScanWindowVisualizer
 Class that displays all meta information for ScanWindow objects. More...
 
class  SignalProvider
 provides a signal mechanism (by deriving from QObject) for classes which are not allowed to have signals themselves. More...
 
class  SoftwareVisualizer
 Class that displays all meta information for Software objects. More...
 
class  SourceFileVisualizer
 Class that displays all meta information for SourceFile objects. More...
 
class  SpectraIDViewTab
 Tabular visualization / selection of identified spectra. More...
 
class  SpectraTreeTab
 Hierarchical visualization and selection of spectra. More...
 
class  SpectrumAlignmentDialog
 Lets the user select two spectra and set the parameters for the spectrum alignment. More...
 
class  SpectrumSettingsVisualizer
 Class that displays all meta information for SpectrumSettings objects. More...
 
struct  StatsCounter
 a simple counting struct, for non-numerical occurrences of meta-values More...
 
class  TableView
 A better QTable for TOPPView, which supports exporting to TSV and conveniently adding data to cells and headers. More...
 
class  TheoreticalSpectrumGenerationDialog
 Dialog which allows to enter an AA or NA sequence and generates a theoretical spectrum for it. More...
 
class  ToolsDialog
 TOPP tool selection dialog. More...
 
class  TOPPASBase
 Main window of the TOPPAS tool. More...
 
class  TOPPASEdge
 An edge representing a data flow in TOPPAS. More...
 
class  TOPPASInputFileDialog
 Dialog which allows to specify an input file. More...
 
class  TOPPASInputFileListVertex
 A vertex representing an input file list. More...
 
class  TOPPASInputFilesDialog
 Dialog which allows to specify a list of input files. More...
 
class  TOPPASIOMappingDialog
 Dialog which allows to configure the input/output parameter mapping of an edge. More...
 
class  TOPPASMergerVertex
 A special vertex that allows to merge several inputs. More...
 
class  TOPPASOutputFileListVertex
 A vertex representing an output file list. More...
 
class  TOPPASOutputFilesDialog
 Dialog which allows to specify the directory for the output files. More...
 
class  TOPPASOutputFolderVertex
 A vertex representing an output folder. More...
 
class  TOPPASOutputVertex
 A vertex representing an output, either folder or files(s) More...
 
class  TOPPASResource
 Represents a data resource for TOPPAS workflows. More...
 
class  TOPPASResources
 A dictionary mapping string keys to lists of TOPPASResource objects. More...
 
class  TOPPASScene
 
class  TOPPASSplitterVertex
 A special vertex that allows to split a list of inputs. More...
 
class  TOPPASToolConfigDialog
 TOPP tool configuration dialog. More...
 
class  TOPPASToolVertex
 A vertex representing a TOPP tool. More...
 
class  TOPPASTreeView
 Tree view implementation for the list of TOPP tools. More...
 
class  TOPPASVertex
 The base class of the different vertex classes. More...
 
class  TOPPASVertexNameDialog
 Dialog which allows to change the name of an input/output vertex. More...
 
class  TOPPASWidget
 Widget visualizing and allowing to edit TOPP pipelines. More...
 
class  TOPPViewBase
 Main window of TOPPView tool. More...
 
class  TOPPViewMenu
 The file menu items for TOPPView. More...
 
class  TOPPViewOpenDialog
 Dataset opening options for TOPPView. More...
 
class  TreeView
 A better QTreeWidget for TOPPView, which supports header context menu and conveniently adding/getting headers names. More...
 
class  TVControllerBase
 Base behavior for different visualizaton modules in TOPPView. More...
 
class  TVDIATreeTabController
 Behavior of TOPPView in spectra view mode. More...
 
class  TVIdentificationViewController
 Behavior of TOPPView in identification mode. More...
 
class  TVSpectraViewController
 Behavior of TOPPView in spectra view mode. More...
 
class  TVToolDiscovery
 Scans for tools and generates a param for each asynchronously. More...
 

Typedefs

typedef std::shared_ptr< OSWData > OSWDataSharedPtrType
 SharedPtr on OSWData.
 
using PointXYType = DPosition< 2U >
 Type of the Points in a 'flat' canvas (1D and 2D)
 
using LayerDataBaseUPtr = std::unique_ptr< LayerDataBase >
 
using LayerDataChromUPtr = std::unique_ptr< LayerDataChrom >
 
using LayerDataPeakUPtr = std::unique_ptr< LayerDataPeak >
 
using LayerDataFeatureUPtr = std::unique_ptr< LayerDataFeature >
 
using LayerDataConsensusUPtr = std::unique_ptr< LayerDataConsensus >
 
using FS_TV = FlagSet< TV_STATUS >
 
using FS_LAYER = FlagSet< LayerDataBase::DataType >
 
using RangeStatsInt = RangeStats< int >
 
using RangeStatsDouble = RangeStats< double >
 
using RangeStatsVariant = std::variant< RangeStatsInt, RangeStatsDouble >
 
using StatsMap = std::map< RangeStatsType, RangeStatsVariant >
 collection of Min/Max/Avg statistics from different sources. Note: must be sorted, i.e. do not switch to unordered_map!
 
using StatsCounterMap = std::map< std::string, StatsCounter >
 collection of MetaValues which are not numeric (counts only the number of occurrences per metavalue)
 

Enumerations

enum class  CheckBoxState { HIDDEN , ENABLED , PRECHECKED }
 state of an ion (and its intensity) More...
 
enum class  WidgetHeader { VISIBLE_ONLY , WITH_INVISIBLE }
 Enum to decide which headers(=column) names should be get/set in a table/tree widget. More...
 
enum class  ShapeIcon { DIAMOND , SQUARE , CIRCLE , TRIANGLE }
 
enum class  TV_STATUS {
  HAS_CANVAS , HAS_LAYER , HAS_MIRROR_MODE , IS_1D_VIEW ,
  TOPP_IDLE
}
 
enum class  RangeStatsSource { CORE , METAINFO , ARRAYINFO , SIZE_OF_STATSSOURCE }
 Where did a statistic come from? Useful for display to user, and for internal dispatch when user requests a more detailed value distribution. More...
 

Functions

std::ostream & operator<< (std::ostream &os, const LayerDataBase &rhs)
 Print the contents to a stream.
 
template<typename T , template< typename > typename C>
QSet< T > toQSet (const C< T > &container)
 Drop-in for QT5's QStringList::toSet.
 
std::vector< std::string > fromQStringList (const QStringList &rhs)
 Convert QStringList to StringList (replaces StringListUtils::fromQStringList)
 
QString toQString (const std::string &s)
 Convert std::string to QString (replaces String::toQString())
 
std::string fromQString (const QString &s)
 Construct std::string from QString (replaces StringUtils::toStr(const QString&))
 
FS_TV operator+ (const TV_STATUS left, const TV_STATUS right)
 allow + operations on the enum, e.g. 'HAS_CANVAS + HAS_LAYER + IS_1D_VIEW'
 
FS_LAYER operator+ (const LayerDataBase::DataType left, const LayerDataBase::DataType right)
 allow + operations on the enum, e.g. 'DT_PEAK + DT_FEATURE'
 
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
 

Variables

static const std::array< const char *,(size_t) RangeStatsSource::SIZE_OF_STATSSOURCE > StatsSourceNames = {"core statistics", "meta values", "data arrays"}
 Names corresponding to elements of enum RangeStatsSource.
 
const std::string user_section = "preferences:user:"
 

Class Documentation

◆ OpenMS::DimMapper

class OpenMS::DimMapper
template<int D>
class OpenMS::DimMapper< D >

◆ OpenMS::StatsCounter

struct OpenMS::StatsCounter

a simple counting struct, for non-numerical occurrences of meta-values

Class Members
size_t counter {0}

Typedef Documentation

◆ FS_LAYER

◆ FS_TV

using FS_TV = FlagSet<TV_STATUS>

◆ LayerDataBaseUPtr

using LayerDataBaseUPtr = std::unique_ptr<LayerDataBase>

◆ LayerDataChromUPtr

using LayerDataChromUPtr = std::unique_ptr<LayerDataChrom>

◆ LayerDataConsensusUPtr

using LayerDataConsensusUPtr = std::unique_ptr<LayerDataConsensus>

◆ LayerDataFeatureUPtr

using LayerDataFeatureUPtr = std::unique_ptr<LayerDataFeature>

◆ LayerDataPeakUPtr

using LayerDataPeakUPtr = std::unique_ptr<LayerDataPeak>

◆ OSWDataSharedPtrType

typedef std::shared_ptr<OSWData> OSWDataSharedPtrType

SharedPtr on OSWData.

◆ PointXYType

using PointXYType = DPosition<2U>

Type of the Points in a 'flat' canvas (1D and 2D)

◆ RangeStatsDouble

using RangeStatsDouble = RangeStats<double>

◆ RangeStatsInt

using RangeStatsInt = RangeStats<int>

◆ RangeStatsVariant

◆ StatsCounterMap

using StatsCounterMap = std::map<std::string, StatsCounter>

collection of MetaValues which are not numeric (counts only the number of occurrences per metavalue)

◆ StatsMap

collection of Min/Max/Avg statistics from different sources. Note: must be sorted, i.e. do not switch to unordered_map!

Enumeration Type Documentation

◆ CheckBoxState

enum class CheckBoxState
strong

state of an ion (and its intensity)

Enumerator
HIDDEN 

check box hidden (invisible)

ENABLED 

check box enabled (visible, but not checked)

PRECHECKED 

check box enabled and checked by default

◆ RangeStatsSource

enum class RangeStatsSource
strong

Where did a statistic come from? Useful for display to user, and for internal dispatch when user requests a more detailed value distribution.

Enumerator
CORE 

statistic was obtained from a core data structure of the container, e.g. intensity

METAINFO 

statistic was obtained from MetaInfoInterface of container elements, e.g. "FWHM" for FeatureMaps

ARRAYINFO 

statistic was obtained from Float/IntegerArrays of the container elements, e.g. "IonMobility" for PeakMap

SIZE_OF_STATSSOURCE 

◆ ShapeIcon

enum class ShapeIcon
strong
Enumerator
DIAMOND 
SQUARE 
CIRCLE 
TRIANGLE 

◆ TV_STATUS

enum class TV_STATUS
strong
Enumerator
HAS_CANVAS 
HAS_LAYER 
HAS_MIRROR_MODE 
IS_1D_VIEW 
TOPP_IDLE 

◆ WidgetHeader

enum class WidgetHeader
strong

Enum to decide which headers(=column) names should be get/set in a table/tree widget.

Enumerator
VISIBLE_ONLY 
WITH_INVISIBLE 

Function Documentation

◆ fromQString()

◆ fromQStringList()

std::vector< std::string > fromQStringList ( const QStringList &  rhs)
inline

Convert QStringList to StringList (replaces StringListUtils::fromQStringList)

◆ operator+() [1/2]

FS_LAYER operator+ ( const LayerDataBase::DataType  left,
const LayerDataBase::DataType  right 
)

allow + operations on the enum, e.g. 'DT_PEAK + DT_FEATURE'

◆ operator+() [2/2]

FS_TV operator+ ( const TV_STATUS  left,
const TV_STATUS  right 
)

allow + operations on the enum, e.g. 'HAS_CANVAS + HAS_LAYER + IS_1D_VIEW'

◆ operator<<()

std::ostream & operator<< ( std::ostream &  os,
const LayerDataBase &  rhs 
)

Print the contents to a stream.

◆ 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

Referenced by TOPPViewBase::addDataFile(), and TOPPViewBase::chooseFilesDialog_().

◆ toQSet()

template<typename T , template< typename > typename C>
QSet< T > toQSet ( const C< T > &  container)

Drop-in for QT5's QStringList::toSet.

◆ toQString()

Variable Documentation

◆ StatsSourceNames

const std::array<const char*, (size_t)RangeStatsSource::SIZE_OF_STATSSOURCE> StatsSourceNames = {"core statistics", "meta values", "data arrays"}
static

Names corresponding to elements of enum RangeStatsSource.

◆ user_section