OpenMS  3.0.0
FeatureGroupingAlgorithmUnlabeled.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 2002-2022.
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: $
33 // --------------------------------------------------------------------------
34 
35 #pragma once
36 
38 
40 
41 namespace OpenMS
42 {
61  class OPENMS_DLLAPI FeatureGroupingAlgorithmUnlabeled :
63  {
64 public:
67 
70 
78  template <typename MapType>
79  void setReference(int map_id, const MapType & map)
80  {
81  MapConversion::convert(map_id, map, pairfinder_input_[0]);
82  }
83 
88  {
89  return pairfinder_input_[0];
90  }
91 
97  void group(const std::vector<FeatureMap > & maps, ConsensusMap & out) override;
98 
109  void addToGroup(int map_id, const FeatureMap & feature_map);
110 
113  {
115  }
116 
119  {
120  return "unlabeled";
121  }
122 
123 private:
124 
125  // This vector should always have 2 elements
126  // - the first element is the currently computed consensus map.
127  // After initialization of the algorithm, it will consist of the reference
128  // map alone, after adding all maps through addToGroup it will contain the
129  // final result (e.g. the consensus result of all maps).
130  // - the second element is the map which was last added to the consensus map
131  std::vector<ConsensusMap> pairfinder_input_;
132 
137 
138  };
139 
140 } // namespace OpenMS
141 
OpenMS::FeatureGroupingAlgorithm
Base class for all feature grouping algorithms.
Definition: FeatureGroupingAlgorithm.h:49
ConversionHelper.h
OpenMS::MapConversion::convert
static void convert(UInt64 const input_map_index, PeakMap &input_map, ConsensusMap &output_map, Size n=-1)
Similar to convert for FeatureMaps.
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS::FeatureGroupingAlgorithmUnlabeled::create
static FeatureGroupingAlgorithm * create()
Creates a new instance of this class (for Factory)
Definition: FeatureGroupingAlgorithmUnlabeled.h:112
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::FeatureGroupingAlgorithmUnlabeled::getProductName
static String getProductName()
Returns the product name (for the Factory)
Definition: FeatureGroupingAlgorithmUnlabeled.h:118
OpenMS::FeatureGroupingAlgorithmUnlabeled::setReference
void setReference(int map_id, const MapType &map)
Sets the reference map for the algorithm.
Definition: FeatureGroupingAlgorithmUnlabeled.h:79
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:82
FeatureGroupingAlgorithm.h
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:98
OpenMS::FeatureGroupingAlgorithmUnlabeled::pairfinder_input_
std::vector< ConsensusMap > pairfinder_input_
Definition: FeatureGroupingAlgorithmUnlabeled.h:131
OpenMS::FeatureGroupingAlgorithmUnlabeled
A map feature grouping algorithm for unlabeled data.
Definition: FeatureGroupingAlgorithmUnlabeled.h:61
OpenMS::FeatureGroupingAlgorithmUnlabeled::getResultMap
ConsensusMap & getResultMap()
Returns the computed consensus map (after calling addToGroup with all maps)
Definition: FeatureGroupingAlgorithmUnlabeled.h:87