OpenMS
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#include <OpenMS/VISUAL/LayerData1DPeak.h>
Public Member Functions | |
LayerData1DPeak () | |
LayerData1DPeak (const LayerDataPeak &base) | |
std::unique_ptr< LayerStoreData > | storeVisibleData (const RangeAllType &visible_range, const DataFilters &layer_filters) const override |
Returns a visitor which contains the current visible data and can write the data to disk. More... | |
std::unique_ptr< LayerStoreData > | storeFullData () const override |
Returns a visitor which contains the the full data of the layer and can write the data to disk in the appropriate format (e.g. mzML) More... | |
std::unique_ptr< Painter1DBase > | getPainter1D () const override |
Obtain a painter which can draw the layer on a canvas. More... | |
bool | hasIndex (Size index) const override |
Does the layer have at least index items (e.g. spectra, chroms, etc), so a call to setCurrentIndex() is valid? More... | |
RangeAllType | getRangeForArea (const RangeAllType partial_range) const override |
Given a partial_range for the current 1D layer (e.g. an m/z range), fill in the other dimensions (usually intensity) from all data points which are within the input range. More... | |
const ExperimentType::SpectrumType & | getCurrentSpectrum () const |
void | updateRanges () override |
Update ranges of the underlying data. More... | |
RangeAllType | getRange1D () const override |
QMenu * | getContextMenuAnnotation (Annotation1DItem *annot_item, bool &need_repaint) override |
Get a context menu (with lambda actions included) for this 1D layer, when a Annotation1DItem was right-clicked. More... | |
PeakIndex | findClosestDataPoint (const RangeAllType &area) const override |
Find the closest datapoint within the given range and return a proxy to that datapoint. More... | |
Annotation1DItem * | addPeakAnnotation (const PeakIndex &peak_index, const QString &text, const QColor &color) override |
Add a Annotation1DPeakItem to getCurrentAnnotations(). The specific type is determined by the derived class (e.g. Peak1D, ChromatogramPeak1D, etc) More... | |
void | synchronizePeakAnnotations () |
void | removePeakAnnotationsFromPeptideHit (const std::vector< Annotation1DItem * > &selected_annotations) |
remove peak annotations in the given list from the currently active PeptideHit More... | |
void | updatePeptideHitAnnotations_ (PeptideHit &hit) |
updates the PeakAnnotations in the current PeptideHit with manually changed annotations More... | |
Public Member Functions inherited from LayerDataPeak | |
LayerDataPeak () | |
Default constructor. More... | |
LayerDataPeak (const LayerDataPeak &ld)=default | |
Copy-ctor. More... | |
LayerDataPeak & | operator= (const LayerDataPeak &ld)=delete |
no assignment operator (should not be needed) More... | |
std::unique_ptr< Painter2DBase > | getPainter2D () const override |
Obtain a painter which can draw the layer on a 2D canvas. More... | |
std::unique_ptr< LayerData1DBase > | to1DLayer () const override |
Create a shallow copy (i.e. shared experimental data using shared_ptr) of the current layer, and make it 1D (i.e. support showing a single spec/chrom etc) More... | |
std::unique_ptr< LayerStoreData > | storeVisibleData (const RangeAllType &visible_range, const DataFilters &layer_filters) const override |
Returns a visitor which contains the current visible data and can write the data to disk. More... | |
std::unique_ptr< LayerStoreData > | storeFullData () const override |
Returns a visitor which contains the the full data of the layer and can write the data to disk in the appropriate format (e.g. mzML) More... | |
ProjectionData | getProjection (const DIM_UNIT unit_x, const DIM_UNIT unit_y, const RangeAllType &area) const override |
PeakIndex | findHighestDataPoint (const RangeAllType &area) const override |
Find the datapoint with the highest intensity within the given range and return a proxy to that datapoint. More... | |
void | updateRanges () override |
Update ranges of the underlying data. More... | |
RangeAllType | getRange () const override |
PointXYType | peakIndexToXY (const PeakIndex &peak, const DimMapper< 2 > &mapper) const override |
Convert a PeakIndex to a XY coordinate (via mapper ). More... | |
String | getDataArrayDescription (const PeakIndex &peak_index) override |
Get name and value of all data-arrays corresponding to the given datapoint. More... | |
std::unique_ptr< LayerStatistics > | getStats () const override |
Compute layer statistics (via visitor) More... | |
bool | annotate (const std::vector< PeptideIdentification > &identifications, const std::vector< ProteinIdentification > &protein_identifications) override |
const ExperimentType::SpectrumType & | getSpectrum (Size spectrum_idx) const |
const ConstExperimentSharedPtrType | getPeakData () const |
Returns a const reference to the current in-memory peak data. More... | |
const ExperimentSharedPtrType & | getPeakDataMuteable () |
Returns a mutable reference to the current in-memory peak data. More... | |
void | setPeakData (ExperimentSharedPtrType p) |
Set the current in-memory peak data. More... | |
void | setOnDiscPeakData (ODExperimentSharedPtrType p) |
Set the current on-disc data. More... | |
const ODExperimentSharedPtrType & | getOnDiscPeakData () const |
Returns a mutable reference to the on-disc data. More... | |
bool | isIonMobilityData () const |
Check whether the current layer should be represented as ion mobility. More... | |
void | labelAsIonMobilityData () const |
bool | isDIAData () const |
Check whether the current layer contains DIA (SWATH-MS) data. More... | |
void | labelAsDIAData () |
Label the current layer as DIA (SWATH-MS) data. More... | |
bool | chromatogram_flag_set () const |
Check whether the current layer is a chromatogram. More... | |
void | set_chromatogram_flag () |
set the chromatogram flag More... | |
void | remove_chromatogram_flag () |
remove the chromatogram flag More... | |
Public Member Functions inherited from LayerDataBase | |
LayerDataBase ()=delete | |
Default constructor (for virtual inheritance) More... | |
LayerDataBase (const DataType type) | |
C'tor for child classes. More... | |
LayerDataBase (const LayerDataBase &ld)=default | |
Copy-C'tor. More... | |
LayerDataBase & | operator= (const LayerDataBase &ld)=delete |
Assignment operator. More... | |
LayerDataBase (LayerDataBase &&ld)=delete | |
LayerDataBase & | operator= (LayerDataBase &&ld)=delete |
Move assignment – deleted, by same argument as for move c'tor. More... | |
virtual | ~LayerDataBase ()=default |
D'tor. More... | |
float | getMinIntensity () const |
Returns the minimum intensity of the internal data, depending on type. More... | |
float | getMaxIntensity () const |
Returns the maximum intensity of the internal data, depending on type. More... | |
const String & | getName () const |
The name of the layer, usually the basename of the file. More... | |
void | setName (const String &new_name) |
Set the name of the layer, usually the basename of the file. More... | |
const String & | getNameSuffix () const |
get the extra annotation to the layers name, e.g. '[39]' for which chromatogram index is currently shown in 1D More... | |
void | setNameSuffix (const String &decorator) |
set an extra annotation as suffix to the layers name, e.g. '[39]' for which chromatogram index is currently shown in 1D More... | |
Public Member Functions inherited from LayerData1DBase | |
String | getDecoratedName () const override |
get name augmented with attributes, e.g. '*' if modified More... | |
const Annotations1DContainer & | getCurrentAnnotations () const |
Returns a const reference to the annotations of the current spectrum (1D view) More... | |
Annotations1DContainer & | getCurrentAnnotations () |
Returns a mutable reference to the annotations of the current spectrum (1D view) More... | |
const Annotations1DContainer & | getAnnotations (Size spectrum_index) const |
Returns a const reference to the annotations of the spectrum_index's spectrum (1D view) More... | |
Annotations1DContainer & | getAnnotations (Size spectrum_index) |
Returns a mutable reference to the annotations of the spectrum_index's spectrum (1D view) More... | |
Size | getCurrentIndex () const |
Get the index of the current spectrum (1D view) More... | |
void | setCurrentIndex (Size index) |
Set the index of the current spectrum (1D view) – and prepares annotations. More... | |
Additional Inherited Members | |
Public Types inherited from LayerDataPeak | |
using | SpectrumType = ExperimentType::SpectrumType |
using | PeakType = SpectrumType::PeakType |
Public Types inherited from LayerDataBase | |
using | RangeAllType = RangeManager< RangeRT, RangeMZ, RangeIntensity, RangeMobility > |
Public Types inherited from LayerDataDefs | |
enum | DataType { DT_PEAK , DT_CHROMATOGRAM , DT_FEATURE , DT_CONSENSUS , DT_IDENT , DT_UNKNOWN } |
enum | Flags { F_HULL , F_HULLS , F_UNASSIGNED , P_PRECURSORS , P_PROJECTIONS , C_ELEMENTS , I_PEPTIDEMZ , I_LABELS , 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 PeakMap | ExperimentType |
Main data type (experiment) More... | |
typedef boost::shared_ptr< ExperimentType > | ExperimentSharedPtrType |
SharedPtr on MSExperiment. More... | |
typedef boost::shared_ptr< const ExperimentType > | ConstExperimentSharedPtrType |
typedef boost::shared_ptr< OnDiscMSExperiment > | ODExperimentSharedPtrType |
SharedPtr on On-Disc MSExperiment. More... | |
typedef boost::shared_ptr< OSWData > | OSWDataSharedPtrType |
SharedPtr on OSWData. More... | |
Public Attributes inherited from LayerDataBase | |
std::bitset< SIZE_OF_FLAGS > | flags |
Actual state of each flag. More... | |
bool | visible = true |
if this layer is visible More... | |
DataType | type = DT_UNKNOWN |
data type (peak or feature data, etc) More... | |
String | filename |
file name of the file the data comes from (if available) More... | |
Param | param |
Layer parameters. More... | |
MultiGradient | gradient |
Gradient for 2D and 3D views. More... | |
DataFilters | filters |
Filters to apply before painting. More... | |
bool | modifiable = false |
Flag that indicates if the layer data can be modified (so far used for features only) More... | |
bool | modified = false |
Flag that indicates that the layer data was modified since loading it. More... | |
LabelType | label = L_NONE |
Label type. More... | |
int | peptide_id_index = -1 |
Selected peptide id and hit index (-1 if none is selected) More... | |
int | peptide_hit_index = -1 |
Public Attributes inherited from LayerData1DBase | |
bool | flipped = false |
if this layer is flipped (1d mirror view) More... | |
std::vector< QColor > | peak_colors_1d |
Peak colors of the currently shown spectrum. More... | |
Static Public Attributes inherited from LayerDataDefs | |
static const std::string | NamesOfLabelType [SIZE_OF_LABEL_TYPE] |
Label names. More... | |
Protected Attributes inherited from LayerDataPeak | |
ExperimentSharedPtrType | peak_map_ = ExperimentSharedPtrType(new ExperimentType()) |
peak data More... | |
ODExperimentSharedPtrType | on_disc_peaks_ = ODExperimentSharedPtrType(new OnDiscMSExperiment()) |
on disc peak data More... | |
Protected Attributes inherited from LayerData1DBase | |
Size | current_idx_ = 0 |
Index of the current spectrum/chromatogram etc (by default, show the first one) More... | |
std::vector< Annotations1DContainer > | annotations_1d_ = std::vector<Annotations1DContainer>(1) |
Annotations of all spectra of the experiment (1D view) More... | |
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inline |
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inline |
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overridevirtual |
Add a Annotation1DPeakItem to getCurrentAnnotations(). The specific type is determined by the derived class (e.g. Peak1D, ChromatogramPeak1D, etc)
peak_index | Which peak should be annotated? |
text | Text to annotate with |
color | Color of the text |
Implements LayerData1DBase.
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overridevirtual |
Find the closest datapoint within the given range and return a proxy to that datapoint.
area | Range to search in. Only dimensions used in the canvas are populated. |
Reimplemented from LayerDataBase.
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overridevirtual |
Get a context menu (with lambda actions included) for this 1D layer, when a Annotation1DItem was right-clicked.
annot_item | The annotation item clicked on |
need_repaint | Reference of bool in calling function, which must know if the action requires repainting the canvas |
Implements LayerData1DBase.
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inline |
References LayerDataPeak::getSpectrum().
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overridevirtual |
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inlineoverridevirtual |
Returns the data range in all known dimensions for the data of the currently active index (i.e. only a single spec/chrom/etc). If a layer does not support the dimension (or the layer is empty) the dimension will be empty If you need the data range for the whole layer (i.e. all specs/chroms/etc), call 'LayerDataBase::getRange()'
Implements LayerData1DBase.
References RangeManager< RangeBases >::assign().
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inlineoverridevirtual |
Given a partial_range
for the current 1D layer (e.g. an m/z range), fill in the other dimensions (usually intensity) from all data points which are within the input range.
partial_range | Range with at least one dimension populated (which is used to filter the current spectrum/chrom/...) |
Implements LayerData1DBase.
References RangeManager< RangeBases >::assign().
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inlineoverridevirtual |
Does the layer have at least index
items (e.g. spectra, chroms, etc), so a call to setCurrentIndex() is valid?
Implements LayerData1DBase.
void removePeakAnnotationsFromPeptideHit | ( | const std::vector< Annotation1DItem * > & | selected_annotations | ) |
remove peak annotations in the given list from the currently active PeptideHit
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overridevirtual |
Returns a visitor which contains the the full data of the layer and can write the data to disk in the appropriate format (e.g. mzML)
Reimplemented from LayerDataBase.
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overridevirtual |
Returns a visitor which contains the current visible data and can write the data to disk.
Reimplemented from LayerDataBase.
void synchronizePeakAnnotations | ( | ) |
updates the PeakAnnotations in the current PeptideHit with manually changed annotations if no PeptideIdentification or PeptideHit for the spectrum exist, it is generated
void updatePeptideHitAnnotations_ | ( | PeptideHit & | hit | ) |
updates the PeakAnnotations in the current PeptideHit with manually changed annotations
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inlineoverridevirtual |
Update ranges of the underlying data.
Implements LayerDataBase.
References LayerDataPeak::updateRanges().