Class that stores the data for one layer of type PeakMap. More...
#include <OpenMS/VISUAL/LayerDataPeak.h>
Public Member Functions | |
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... | |
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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... | |
virtual PeakIndex | findClosestDataPoint (const RangeAllType &) const |
Find the closest datapoint within the given range and return a proxy to that datapoint. 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... | |
virtual String | getDecoratedName () const |
get name augmented with attributes, e.g. '*' if modified More... | |
Protected Attributes | |
ExperimentSharedPtrType | peak_map_ = ExperimentSharedPtrType(new ExperimentType()) |
peak data More... | |
ODExperimentSharedPtrType | on_disc_peaks_ = ODExperimentSharedPtrType(new OnDiscMSExperiment()) |
on disc peak data More... | |
Additional Inherited Members | |
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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 |
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static const std::string | NamesOfLabelType [SIZE_OF_LABEL_TYPE] |
Label names. More... | |
Class that stores the data for one layer of type PeakMap.
using PeakType = SpectrumType::PeakType |
LayerDataPeak | ( | ) |
Default constructor.
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default |
Copy-ctor.
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overridevirtual |
add peptide identifications to the layer Only supported for DT_PEAK, DT_FEATURE and DT_CONSENSUS. Will return false otherwise.
Reimplemented from LayerDataBase.
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inline |
Check whether the current layer is a chromatogram.
This is needed because type will *not* distinguish properly between chromatogram and spectra data. This is due to the fact that we store chromatograms for display in 1D in a data layer using MSSpectrum and so the layer looks like PEAK data to tools.
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overridevirtual |
Find the datapoint with the highest intensity 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.
Get name and value of all data-arrays corresponding to the given datapoint.
Empty (or shorter) data-arrays are skipped.
peak_index | The datapoint |
Reimplemented from LayerDataBase.
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inline |
Returns a mutable reference to the on-disc data.
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overridevirtual |
Obtain a painter which can draw the layer on a 2D canvas.
Implements LayerDataBase.
const ConstExperimentSharedPtrType getPeakData | ( | ) | const |
Returns a const reference to the current in-memory peak data.
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inline |
Returns a mutable reference to the current in-memory peak data.
Referenced by TOPPViewBase::showCurrentPeaksAs2D().
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overridevirtual |
Calculate a projection of the current layer for the given unit and the given area. E.g. the area might be restricted in RT and m/z, and then requested projection should return the XIC (unit
== RT) It is up to the implementation to decide on binning.
Implements LayerDataBase.
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inlineoverridevirtual |
Returns the data range of the whole layer (i.e. all scans/chroms/etc) in all known dimensions. 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 a 1D view (i.e. only a single spec/chrom/etc), call 'LayerDataBase1D::getRange1D()'
Implements LayerDataBase.
References RangeManager< RangeBases >::assign().
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inline |
Referenced by LayerData1DPeak::getCurrentSpectrum().
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overridevirtual |
Compute layer statistics (via visitor)
Implements LayerDataBase.
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inline |
Check whether the current layer contains DIA (SWATH-MS) data.
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inline |
Check whether the current layer should be represented as ion mobility.
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inline |
Label the current layer as DIA (SWATH-MS) data.
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inline |
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delete |
no assignment operator (should not be needed)
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overridevirtual |
Convert a PeakIndex to a XY coordinate (via mapper
).
peak | The Peak to convert |
mapper | Converts the internal representation (e.g. Peak1D) to an XY coordinate |
Implements LayerDataBase.
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inline |
remove the chromatogram flag
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inline |
set the chromatogram flag
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inline |
Set the current on-disc data.
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inline |
Set the current in-memory peak data.
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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.
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overridevirtual |
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)
Implements LayerDataBase.
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inlineoverridevirtual |
Update ranges of the underlying data.
Implements LayerDataBase.
Referenced by LayerData1DPeak::updateRanges().
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protected |
on disc peak data
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protected |
peak data