OpenMS
LayerDataFeature.h
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1 // Copyright (c) 2002-2023, 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 
14 namespace OpenMS
15 {
16 
22  class OPENMS_GUI_DLLAPI LayerDataFeature : public virtual LayerDataBase, public IPeptideIds
23  {
24  public:
28  LayerDataFeature(const LayerDataFeature& ld) = delete;
31 
32  std::unique_ptr<Painter2DBase> getPainter2D() const override;
33 
34  std::unique_ptr<LayerData1DBase> to1DLayer() const override
35  {
36  throw Exception::NotImplemented(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
37  }
38 
39 
40  std::unique_ptr<LayerStoreData> storeVisibleData(const RangeAllType& visible_range, const DataFilters& layer_filters) const override;
41 
42  std::unique_ptr<LayerStoreData> storeFullData() const override;
43 
44  ProjectionData getProjection(const DIM_UNIT /*unit_x*/, const DIM_UNIT /*unit_y*/, const RangeAllType& /*area*/) const override
45  { // currently only a stub
46  ProjectionData proj;
47  return proj;
48  }
49 
50  PeakIndex findHighestDataPoint(const RangeAllType& area) const override;
51 
52  PointXYType peakIndexToXY(const PeakIndex& peak, const DimMapper<2>& mapper) const override;
53 
54  void updateRanges() override
55  {
56  features_->updateRanges();
57  }
58 
59  RangeAllType getRange() const override
60  {
61  RangeAllType r;
62  r.assign(*getFeatureMap());
63  return r;
64  }
65 
66  std::unique_ptr<LayerStatistics> getStats() const override;
67 
68  bool annotate(const std::vector<PeptideIdentification>& identifications, const std::vector<ProteinIdentification>& protein_identifications) override;
69 
70  const PepIds& getPeptideIds() const override
71  {
72  return getFeatureMap()->getUnassignedPeptideIdentifications();
73  }
74  PepIds& getPeptideIds() override
75  {
76  return getFeatureMap()->getUnassignedPeptideIdentifications();
77  }
78 
79  void setPeptideIds(const PepIds& ids) override
80  {
81  getFeatureMap()->getUnassignedPeptideIdentifications() = ids;
82  }
83  void setPeptideIds(PepIds&& ids) override
84  {
85  getFeatureMap()->getUnassignedPeptideIdentifications() = std::move(ids);
86  }
87 
88 
91  {
92  return features_;
93  }
94 
97  {
98  return features_;
99  }
100 
101  protected:
104  };
105 
106 }// namespace OpenMS
DataFilter array providing some convenience functions.
Definition: DataFilters.h:27
Not implemented exception.
Definition: Exception.h:404
A container for features.
Definition: FeatureMap.h:80
Abstract base class which defines an interface for PeptideIdentifications.
Definition: IPeptideIds.h:23
std::vector< PeptideIdentification > PepIds
Definition: IPeptideIds.h:25
Class that stores the data for one layer.
Definition: LayerDataBase.h:169
Class that stores the data for one layer of type FeatureMap.
Definition: LayerDataFeature.h:23
std::unique_ptr< LayerStatistics > getStats() const override
Compute layer statistics (via visitor)
LayerDataFeature & operator=(const LayerDataFeature &ld)=delete
no assignment operator (should not be needed)
void setPeptideIds(const PepIds &ids) override
overwrite the peptide IDs for this layer
Definition: LayerDataFeature.h:79
ProjectionData getProjection(const DIM_UNIT, const DIM_UNIT, const RangeAllType &) const override
Definition: LayerDataFeature.h:44
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...
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 FeatureMapSharedPtrType & getFeatureMap() const
Returns a const reference to the current feature data.
Definition: LayerDataFeature.h:90
std::unique_ptr< LayerData1DBase > to1DLayer() const override
Create a shallow copy (i.e. shared experimental data using shared_ptr) of the current layer,...
Definition: LayerDataFeature.h:34
const PepIds & getPeptideIds() const override
get the peptide IDs for this layer
Definition: LayerDataFeature.h:70
PointXYType peakIndexToXY(const PeakIndex &peak, const DimMapper< 2 > &mapper) const override
Convert a PeakIndex to a XY coordinate (via mapper).
PepIds & getPeptideIds() override
Definition: LayerDataFeature.h:74
FeatureMapSharedPtrType & getFeatureMap()
Returns a const reference to the current feature data.
Definition: LayerDataFeature.h:96
RangeAllType getRange() const override
Definition: LayerDataFeature.h:59
void setPeptideIds(PepIds &&ids) override
Definition: LayerDataFeature.h:83
LayerDataFeature()
Default constructor.
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.
LayerDataFeature(const LayerDataFeature &ld)=delete
no Copy-ctor (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: LayerDataFeature.h:54
auto & assign(const RangeManager< RangeBasesOther... > &rhs)
Definition: RangeManager.h:586
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:22
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< FeatureMap > FeatureMapSharedPtrType
SharedPtr on feature map.
Definition: LayerDataBase.h:114
Index of a peak or feature.
Definition: PeakIndex.h:25