OpenMS
LayerDataPeak.h
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1 // Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Chris Bielow $
6 // $Authors: Chris Bielow $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
13 
16 
17 #include <vector>
18 
19 namespace OpenMS
20 {
21  class Annotation1DItem;
22 
28  class OPENMS_GUI_DLLAPI LayerDataPeak : public virtual LayerDataBase
29  {
30  public:
31 
34 
38  LayerDataPeak(const LayerDataPeak& ld) = default;
40  LayerDataPeak& operator=(const LayerDataPeak& ld) = delete;
41 
42  std::unique_ptr<Painter2DBase> getPainter2D() const override;
43 
44  std::unique_ptr<LayerData1DBase> to1DLayer() const override;
45 
46  std::unique_ptr<LayerStoreData> storeVisibleData(const RangeAllType& visible_range, const DataFilters& layer_filters) const override;
47 
48  std::unique_ptr<LayerStoreData> storeFullData() const override;
49 
50  ProjectionData getProjection(const DIM_UNIT unit_x, const DIM_UNIT unit_y, const RangeAllType& area) const override;
51 
52  PeakIndex findHighestDataPoint(const RangeAllType& area) const override;
53 
54  void updateRanges() override
55  {
56  peak_map_->updateRanges();
57  // on_disc_peaks_->updateRanges(); // note: this is not going to work since its on disk! We currently don't have a good way to access these ranges
58  }
59 
60  RangeAllType getRange() const override
61  {
62  RangeAllType r;
63  r.assign(*peak_map_);
64  return r;
65  }
66 
67  PointXYType peakIndexToXY(const PeakIndex& peak, const DimMapper<2>& mapper) const override;
68 
69  String getDataArrayDescription(const PeakIndex& peak_index) override;
70 
71  std::unique_ptr<LayerStatistics> getStats() const override;
72 
73  bool annotate(const std::vector<PeptideIdentification>& identifications, const std::vector<ProteinIdentification>& protein_identifications) override;
74 
75  const ExperimentType::SpectrumType& getSpectrum(Size spectrum_idx) const
76  {
77  if ((*peak_map_)[spectrum_idx].size() > 0)
78  {
79  return (*peak_map_)[spectrum_idx];
80  }
81  if (!on_disc_peaks_->empty())
82  {
83  static MSSpectrum local_spec;
84  local_spec = on_disc_peaks_->getSpectrum(spectrum_idx);
85  return local_spec;
86  }
87  return (*peak_map_)[spectrum_idx];
88  }
89 
100 
111  {
112  return peak_map_;
113  }
114 
119  {
120  peak_map_ = p;
121  }
122 
125  {
126  on_disc_peaks_ = p;
127  }
128 
131  {
132  return on_disc_peaks_;
133  }
134 
135 
136 
138  bool isIonMobilityData() const
139  {
140  return this->getPeakData()->size() > 0 && this->getPeakData()->metaValueExists("is_ion_mobility") && this->getPeakData()->getMetaValue("is_ion_mobility").toBool();
141  }
142 
144  {
145  peak_map_->setMetaValue("is_ion_mobility", "true");
146  }
147 
149  bool isDIAData() const
150  {
151  return this->getPeakData()->size() > 0 && this->getPeakData()->metaValueExists("is_dia_data") && this->getPeakData()->getMetaValue("is_dia_data").toBool();
152  }
153 
156  {
157  peak_map_->setMetaValue("is_dia_data", "true");
158  }
159 
169  {
170  return this->getPeakData()->size() > 0 && this->getPeakData()->metaValueExists("is_chromatogram") && this->getPeakData()->getMetaValue("is_chromatogram").toBool();
171  }
172 
175  {
176  peak_map_->setMetaValue("is_chromatogram", "true");
177  }
178 
181  {
182  if (this->chromatogram_flag_set())
183  {
184  peak_map_->removeMetaValue("is_chromatogram");
185  }
186  }
187 
188 
189  protected:
192 
195  };
196 
197 }// namespace OpenMS
DataFilter array providing some convenience functions.
Definition: DataFilters.h:27
Class that stores the data for one layer.
Definition: LayerDataBase.h:169
Class that stores the data for one layer of type PeakMap.
Definition: LayerDataPeak.h:29
void remove_chromatogram_flag()
remove the chromatogram flag
Definition: LayerDataPeak.h:180
LayerDataPeak()
Default constructor.
std::unique_ptr< LayerStatistics > getStats() const override
Compute layer statistics (via visitor)
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...
bool isDIAData() const
Check whether the current layer contains DIA (SWATH-MS) data.
Definition: LayerDataPeak.h:149
void set_chromatogram_flag()
set the chromatogram flag
Definition: LayerDataPeak.h:174
void setOnDiscPeakData(ODExperimentSharedPtrType p)
Set the current on-disc data.
Definition: LayerDataPeak.h:124
const ConstExperimentSharedPtrType getPeakData() const
Returns a const reference to the current in-memory peak data.
bool isIonMobilityData() const
Check whether the current layer should be represented as ion mobility.
Definition: LayerDataPeak.h:138
PeakIndex findHighestDataPoint(const RangeAllType &area) const override
Find the datapoint with the highest intensity within the given range and return a proxy to that datap...
bool annotate(const std::vector< PeptideIdentification > &identifications, const std::vector< ProteinIdentification > &protein_identifications) override
const ExperimentSharedPtrType & getPeakDataMuteable()
Returns a mutable reference to the current in-memory peak data.
Definition: LayerDataPeak.h:110
bool chromatogram_flag_set() const
Check whether the current layer is a chromatogram.
Definition: LayerDataPeak.h:168
std::unique_ptr< LayerData1DBase > to1DLayer() const override
Create a shallow copy (i.e. shared experimental data using shared_ptr) of the current layer,...
void setPeakData(ExperimentSharedPtrType p)
Set the current in-memory peak data.
Definition: LayerDataPeak.h:118
const ODExperimentSharedPtrType & getOnDiscPeakData() const
Returns a mutable reference to the on-disc data.
Definition: LayerDataPeak.h:130
void labelAsIonMobilityData() const
Definition: LayerDataPeak.h:143
PointXYType peakIndexToXY(const PeakIndex &peak, const DimMapper< 2 > &mapper) const override
Convert a PeakIndex to a XY coordinate (via mapper).
const ExperimentType::SpectrumType & getSpectrum(Size spectrum_idx) const
Definition: LayerDataPeak.h:75
ProjectionData getProjection(const DIM_UNIT unit_x, const DIM_UNIT unit_y, const RangeAllType &area) const override
RangeAllType getRange() const override
Definition: LayerDataPeak.h:60
LayerDataPeak(const LayerDataPeak &ld)=default
Copy-ctor.
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.
LayerDataPeak & operator=(const LayerDataPeak &ld)=delete
no assignment operator (should not be needed)
std::unique_ptr< Painter2DBase > getPainter2D() const override
Obtain a painter which can draw the layer on a 2D canvas.
void updateRanges() override
Update ranges of the underlying data.
Definition: LayerDataPeak.h:54
String getDataArrayDescription(const PeakIndex &peak_index) override
Get name and value of all data-arrays corresponding to the given datapoint.
void labelAsDIAData()
Label the current layer as DIA (SWATH-MS) data.
Definition: LayerDataPeak.h:155
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:45
The representation of a 1D spectrum.
Definition: MSSpectrum.h:44
OpenMS::Peak1D PeakType
Peak type.
Definition: MSSpectrum.h:86
Representation of a mass spectrometry experiment on disk.
Definition: OnDiscMSExperiment.h:41
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:28
auto & assign(const RangeManager< RangeBasesOther... > &rhs)
Definition: RangeManager.h:593
A more convenient string class.
Definition: String.h:34
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:97
MSSpectrum SpectrumType
Definition: MzDataHandler.h:34
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19
DIM_UNIT
Definition: CommonEnums.h:20
Result of computing a projection on X and Y axis in a 2D Canvas; see LayerDataBase::getProjection()
Definition: LayerDataBase.h:51
boost::shared_ptr< ExperimentType > ExperimentSharedPtrType
SharedPtr on MSExperiment.
Definition: LayerDataBase.h:126
boost::shared_ptr< OnDiscMSExperiment > ODExperimentSharedPtrType
SharedPtr on On-Disc MSExperiment.
Definition: LayerDataBase.h:131
boost::shared_ptr< const ExperimentType > ConstExperimentSharedPtrType
Definition: LayerDataBase.h:128
Index of a peak or feature.
Definition: PeakIndex.h:25