OpenMS  2.8.0
MapAlignmentEvaluationAlgorithm.h
Go to the documentation of this file.
1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2021.
6 //
7 // This software is released under a three-clause BSD license:
8 // * Redistributions of source code must retain the above copyright
9 // notice, this list of conditions and the following disclaimer.
10 // * Redistributions in binary form must reproduce the above copyright
11 // notice, this list of conditions and the following disclaimer in the
12 // documentation and/or other materials provided with the distribution.
13 // * Neither the name of any author or any participating institution
14 // may be used to endorse or promote products derived from this software
15 // without specific prior written permission.
16 // For a full list of authors, refer to the file AUTHORS.
17 // --------------------------------------------------------------------------
18 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19 // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
21 // ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
22 // INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
23 // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
24 // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
25 // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
26 // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
27 // OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
28 // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Katharina Albers $
33 // --------------------------------------------------------------------------
34 
35 #pragma once
36 
38 
39 namespace OpenMS
40 {
41 
47  class OPENMS_DLLAPI MapAlignmentEvaluationAlgorithm
48  {
49 
50 protected:
51  typedef ConsensusFeature::HandleSetType::const_iterator HandleIterator;
52 
53 public:
54 
57 
60 
61 
63  virtual void evaluate(const ConsensusMap & conensus_map_in, const ConsensusMap & consensus_map_gt, const double & rt_dev, const double & mz_dev, const Peak2D::IntensityType & int_dev, const bool use_charge, double & out) = 0;
64 
66  bool isSameHandle(const FeatureHandle & lhs, const FeatureHandle & rhs, const double & rt_dev, const double & mz_dev, const Peak2D::IntensityType & int_dev, const bool use_charge);
67 
69  static void registerChildren();
70 
71 private:
76 
77  };
78 
79 } // namespace OpenMS
80 
A container for consensus elements.
Definition: ConsensusMap.h:90
Representation of a Peak2D, RichPeak2D or Feature .
Definition: FeatureHandle.h:60
Base class for all Caap evaluation algorithms.
Definition: MapAlignmentEvaluationAlgorithm.h:48
virtual void evaluate(const ConsensusMap &conensus_map_in, const ConsensusMap &consensus_map_gt, const double &rt_dev, const double &mz_dev, const Peak2D::IntensityType &int_dev, const bool use_charge, double &out)=0
Applies the algorithm. The input consensus map is compared to the ground truth.
ConsensusFeature::HandleSetType::const_iterator HandleIterator
Definition: MapAlignmentEvaluationAlgorithm.h:51
MapAlignmentEvaluationAlgorithm(const MapAlignmentEvaluationAlgorithm &)
Copy constructor is not implemented -> private.
MapAlignmentEvaluationAlgorithm()
Default constructor.
bool isSameHandle(const FeatureHandle &lhs, const FeatureHandle &rhs, const double &rt_dev, const double &mz_dev, const Peak2D::IntensityType &int_dev, const bool use_charge)
Decides if two features are the same, based on maximum allowed deviations for retention time,...
static void registerChildren()
Register all derived classes in this method.
MapAlignmentEvaluationAlgorithm & operator=(const MapAlignmentEvaluationAlgorithm &)
Assignment operator is not implemented -> private.
virtual ~MapAlignmentEvaluationAlgorithm()
Destructor.
float IntensityType
Intensity type.
Definition: Peak2D.h:62
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47