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Spectrum visualization widgets

Spectrum visualization widgets. More...

Classes

class  LayerData
 Class that stores the data for one layer. More...
 
class  SpectraViewWidget
 Hierarchical visualization and selection of spectra. More...
 
class  Spectrum1DCanvas
 Canvas for visualization of one or several spectra. More...
 
class  Spectrum1DWidget
 Widget for visualization of several spectra. More...
 
class  Spectrum2DCanvas
 Canvas for 2D-visualization of peak map, feature map and consensus map data. More...
 
class  Spectrum2DWidget
 Widget for 2D-visualization of peak map and feature map data. More...
 
class  Spectrum3DCanvas
 Canvas for 3D-visualization of peak map data. More...
 
class  Spectrum3DOpenGLCanvas
 OpenGL Canvas for 3D-visualization of map data. More...
 
class  Spectrum3DWidget
 Widget for 3D-visualization of map data. More...
 
class  SpectrumCanvas
 Base class for visualization canvas classes. More...
 

Enumerations

enum  LabelMode { LM_XABSOLUTE_YABSOLUTE, LM_XPERCENT_YABSOLUTE, LM_XABSOLUTE_YPERCENT, LM_XPERCENT_YPERCENT }
 Label modes (percentage or absolute) of x axis and y axis. More...
 
enum  DrawModes { DM_PEAKS, DM_CONNECTEDLINES }
 Enumerate all available paint styles. More...
 
enum  ShadeModes { SHADE_FLAT = 0, SHADE_SMOOTH = 1 }
 Different shade modes. More...
 

Type definitions

enum  DataType {
  DT_PEAK, DT_FEATURE, DT_CONSENSUS, DT_CHROMATOGRAM,
  DT_IDENT, DT_UNKNOWN
}
 Dataset types. More...
 
enum  Flags {
  F_HULL, F_HULLS, F_UNASSIGNED, P_PRECURSORS,
  P_PROJECTIONS, C_ELEMENTS, I_PEPTIDEMZ, SIZE_OF_FLAGS
}
 Flags that determine which information is shown. More...
 
enum  LabelType {
  L_NONE, L_INDEX, L_META_LABEL, L_ID,
  L_ID_ALL, SIZE_OF_LABEL_TYPE
}
 Label used in visualization. More...
 
typedef FeatureMap FeatureMapType
 Features. More...
 
typedef boost::shared_ptr< FeatureMap > FeatureMapSharedPtrType
 SharedPtr on feature map. More...
 
typedef ConsensusMap ConsensusMapType
 consensus features More...
 
typedef boost::shared_ptr< ConsensusMap > ConsensusMapSharedPtrType
 SharedPtr on consensus features. More...
 
typedef MSExperiment ExperimentType
 Main data type (experiment) More...
 
typedef boost::shared_ptr< ExperimentType > ExperimentSharedPtrType
 SharedPtr on MSExperiment. More...
 
std::bitset< SIZE_OF_FLAGS > flags
 Actual state of each flag. More...
 
static const std::string NamesOfLabelType [SIZE_OF_LABEL_TYPE]
 Label names. More...
 

Type definitions

enum  ActionModes { AM_TRANSLATE, AM_ZOOM, AM_MEASURE }
 Mouse action modes. More...
 
enum  IntensityModes { IM_NONE, IM_PERCENTAGE, IM_SNAP, IM_LOG }
 Display modes of intensity. More...
 
typedef LayerData::ExperimentType ExperimentType
 Main data type (experiment) More...
 
typedef LayerData::ExperimentSharedPtrType ExperimentSharedPtrType
 Main managed data type (experiment) More...
 
typedef LayerData::FeatureMapType FeatureMapType
 Main data type (features) More...
 
typedef LayerData::FeatureMapSharedPtrType FeatureMapSharedPtrType
 Main managed data type (features) More...
 
typedef LayerData::ConsensusMapType ConsensusMapType
 Main data type (consensus features) More...
 
typedef LayerData::ConsensusMapSharedPtrType ConsensusMapSharedPtrType
 Main managed data type (consensus features) More...
 
typedef ExperimentType::SpectrumType SpectrumType
 Spectrum type. More...
 
typedef SpectrumType::ConstIterator SpectrumConstIteratorType
 Spectrum iterator type (iterates over peaks) More...
 
typedef SpectrumType::PeakType PeakType
 Peak type. More...
 
typedef FeatureMapType::FeatureType FeatureType
 Feature type. More...
 
typedef DPosition< 2 > PointType
 Type of the Points. More...
 
typedef DRange< 2 > AreaType
 Types of Ranges/Areas. More...
 

Detailed Description

Spectrum visualization widgets.

The spectrum widgets allow spectrum data to be visualized in different manners. There are predefined widgets for 1D, 2D and 3D visualization. For each type of view, at least two new classes must be defined:

Typedef Documentation

typedef DRange<2> AreaType

Types of Ranges/Areas.

typedef boost::shared_ptr<ConsensusMap> ConsensusMapSharedPtrType

SharedPtr on consensus features.

typedef LayerData::ConsensusMapSharedPtrType ConsensusMapSharedPtrType

Main managed data type (consensus features)

typedef ConsensusMap ConsensusMapType

consensus features

typedef LayerData::ConsensusMapType ConsensusMapType

Main data type (consensus features)

typedef LayerData::ExperimentSharedPtrType ExperimentSharedPtrType

Main managed data type (experiment)

typedef boost::shared_ptr<ExperimentType> ExperimentSharedPtrType

SharedPtr on MSExperiment.

typedef LayerData::ExperimentType ExperimentType

Main data type (experiment)

typedef MSExperiment ExperimentType

Main data type (experiment)

typedef boost::shared_ptr<FeatureMap > FeatureMapSharedPtrType

SharedPtr on feature map.

typedef LayerData::FeatureMapSharedPtrType FeatureMapSharedPtrType

Main managed data type (features)

typedef FeatureMap FeatureMapType

Features.

typedef LayerData::FeatureMapType FeatureMapType

Main data type (features)

typedef FeatureMapType::FeatureType FeatureType

Feature type.

typedef SpectrumType::PeakType PeakType

Peak type.

typedef DPosition<2> PointType

Type of the Points.

typedef SpectrumType::ConstIterator SpectrumConstIteratorType

Spectrum iterator type (iterates over peaks)

typedef ExperimentType::SpectrumType SpectrumType

Spectrum type.

Enumeration Type Documentation

enum ActionModes

Mouse action modes.

Enumerator
AM_TRANSLATE 

translate

AM_ZOOM 

zoom

AM_MEASURE 

measure

enum DataType

Dataset types.

Enumerator
DT_PEAK 

Spectrum profile or centroided data.

DT_FEATURE 

Feature data.

DT_CONSENSUS 

Consensus feature data.

DT_CHROMATOGRAM 

Chromatogram data.

DT_IDENT 

Peptide identification data.

DT_UNKNOWN 

Undefined data type indicating an error.

enum DrawModes

Enumerate all available paint styles.

Enumerator
DM_PEAKS 
DM_CONNECTEDLINES 
enum Flags

Flags that determine which information is shown.

Enumerator
F_HULL 

Features: Overall convex hull.

F_HULLS 

Features: Convex hulls of single mass traces.

F_UNASSIGNED 

Features: Unassigned peptide hits.

P_PRECURSORS 

Peaks: Mark precursor peaks of MS/MS scans.

P_PROJECTIONS 

Peaks: Show projections.

C_ELEMENTS 

Consensus features: Show elements.

I_PEPTIDEMZ 

Identifications: m/z source.

SIZE_OF_FLAGS 
enum IntensityModes

Display modes of intensity.

Enumerator
IM_NONE 

Normal mode: f(x)=x.

IM_PERCENTAGE 

Shows intensities normalized by layer maximum: f(x)=x/max(x)*100.

IM_SNAP 

Shows the maximum displayed intensity as if it was the overall maximum intensity.

IM_LOG 

Logarithmic mode.

enum LabelMode

Label modes (percentage or absolute) of x axis and y axis.

Enumerator
LM_XABSOLUTE_YABSOLUTE 
LM_XPERCENT_YABSOLUTE 
LM_XABSOLUTE_YPERCENT 
LM_XPERCENT_YPERCENT 
enum LabelType

Label used in visualization.

Enumerator
L_NONE 

No label is displayed.

L_INDEX 

The element number is used.

L_META_LABEL 

The 'label' meta information is used.

L_ID 

The best peptide hit of the first identification run is used.

L_ID_ALL 

All peptide hits of the first identification run are used.

SIZE_OF_LABEL_TYPE 
enum ShadeModes

Different shade modes.

Enumerator
SHADE_FLAT 
SHADE_SMOOTH 

Variable Documentation

std::bitset<SIZE_OF_FLAGS> flags

Actual state of each flag.

const std::string NamesOfLabelType[SIZE_OF_LABEL_TYPE]
static

OpenMS / TOPP release 2.0.0 Documentation generated on Sat May 16 2015 16:13:43 using doxygen 1.8.9.1