OpenMS
LayerDataConsensus.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 
12 
13 #include <vector>
14 
15 namespace OpenMS
16 {
17 
23  class OPENMS_GUI_DLLAPI LayerDataConsensus : public virtual LayerDataBase
24  {
25  public:
32 
33  std::unique_ptr<Painter2DBase> getPainter2D() const override;
34 
35  std::unique_ptr<LayerData1DBase> to1DLayer() const override
36  {
37  throw Exception::NotImplemented(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
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  consensus_map_->updateRanges();
57  }
58 
59  RangeAllType getRange() const override
60  {
61  RangeAllType r;
62  r.assign(*getConsensusMap());
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 
72  {
73  return consensus_map_;
74  }
75 
78  {
79  return consensus_map_;
80  }
81  protected:
84  };
85 
86 }// namespace OpenMS
A container for consensus elements.
Definition: ConsensusMap.h:66
DataFilter array providing some convenience functions.
Definition: DataFilters.h:27
Not implemented exception.
Definition: Exception.h:399
Class that stores the data for one layer.
Definition: LayerDataBase.h:169
Class that stores the data for one layer of type ConsensusMap.
Definition: LayerDataConsensus.h:24
LayerDataConsensus(const LayerDataConsensus &ld)=delete
no Copy-ctor (should not be needed)
std::unique_ptr< LayerStatistics > getStats() const override
Compute layer statistics (via visitor)
ProjectionData getProjection(const DIM_UNIT, const DIM_UNIT, const RangeAllType &) const override
Definition: LayerDataConsensus.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
std::unique_ptr< LayerData1DBase > to1DLayer() const override
Create a shallow copy (i.e. shared experimental data using shared_ptr) of the current layer,...
Definition: LayerDataConsensus.h:35
const ConsensusMapSharedPtrType & getConsensusMap() const
Returns a const reference to the consensus feature data.
Definition: LayerDataConsensus.h:71
PointXYType peakIndexToXY(const PeakIndex &peak, const DimMapper< 2 > &mapper) const override
Convert a PeakIndex to a XY coordinate (via mapper).
LayerDataConsensus & operator=(const LayerDataConsensus &ld)=delete
no assignment operator (should not be needed)
RangeAllType getRange() const override
Definition: LayerDataConsensus.h:59
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.
ConsensusMapSharedPtrType & getConsensusMap()
Returns current consensus map (mutable)
Definition: LayerDataConsensus.h:77
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: LayerDataConsensus.h:54
LayerDataConsensus(ConsensusMapSharedPtrType &map)
Default constructor.
auto & assign(const RangeManager< RangeBasesOther... > &rhs)
Definition: RangeManager.h:593
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< ConsensusMap > ConsensusMapSharedPtrType
SharedPtr on consensus features.
Definition: LayerDataBase.h:120
Index of a peak or feature.
Definition: PeakIndex.h:25