| OpenMS 2.5.0

StablePairFinder.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: $
33 // --------------------------------------------------------------------------
34
35 #ifndef OPENMS_ANALYSIS_MAPMATCHING_STABLEPAIRFINDER_H
36 #define OPENMS_ANALYSIS_MAPMATCHING_STABLEPAIRFINDER_H
37
38 #include <OpenMS/ANALYSIS/MAPMATCHING/BaseGroupFinder.h>
39
40 namespace OpenMS
41 {
42 class AASequence;
43
109 class OPENMS_DLLAPI StablePairFinder :
110 public BaseGroupFinder
111 {
112 public:
113
115 typedef BaseGroupFinder Base;
116
118 StablePairFinder();
119
121 ~StablePairFinder() override
122 {
123 }
124
126 static BaseGroupFinder* create()
127 {
128 return new StablePairFinder();
129 }
130
132 static const String getProductName()
133 {
134 return "stable";
135 }
136
144 void run(const std::vector<ConsensusMap>& input_maps,
145 ConsensusMap& result_map) override;
146
147 protected:
148
150
151 enum
152 {
153 RT = Peak2D::RT,
154 MZ = Peak2D::MZ
155 };
157
158 //docu in base class
159 void updateMembers_() override;
160
168 bool compatibleIDs_(const ConsensusFeature& feat1,
169 const ConsensusFeature& feat2) const;
170
172 double second_nearest_gap_;
173
175 bool use_IDs_;
176
182 const AASequence& getBestHitSequence_(const PeptideIdentification& peptideIdentification) const;
183 };
184
185 } // namespace OpenMS
186
187 #endif // OPENMS_ANALYSIS_MAPMATCHING_STABLEPAIRFINDER_H
188
189 /*
190
191 gnuplot history - how the plot was created - please do not delete this receipt
192
193 f(x,intercept,exponent)=1/(1+(abs(x)*intercept)**exponent)
194 set terminal postscript enhanced color
195 set output "choosingstablepairfinderparams.ps"
196 set size ratio .3
197 plot [-3:3] [0:1] f(x,1,1), f(x,2,1), f(x,1,2), f(x,2,2)
198
199 */
OpenMS::StablePairFinder
This class implements a pair finding algorithm for consensus features.
Definition: StablePairFinder.h:109
OpenMS::BaseGroupFinder
The base class of all element group finding algorithms.
Definition: BaseGroupFinder.h:61
BaseGroupFinder.h
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::StablePairFinder::Base
BaseGroupFinder Base
Base class.
Definition: StablePairFinder.h:115
OpenMS::Peak2D::RT
Retention time dimension id (0 if used as a const int)
Definition: Peak2D.h:75
OpenMS::ConsensusFeature
A consensus feature spanning multiple LC-MS/MS experiments.
Definition: ConsensusFeature.h:69
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::Peak2D::MZ
Mass-to-charge dimension id (1 if used as a const int)
Definition: Peak2D.h:76
OpenMS::StablePairFinder::~StablePairFinder
~StablePairFinder() override
Destructor.
Definition: StablePairFinder.h:121
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:79
OpenMS::StablePairFinder::getProductName
static const String getProductName()
Returns the name of this module.
Definition: StablePairFinder.h:132
OpenMS::StablePairFinder::second_nearest_gap_
double second_nearest_gap_
The distance to the second nearest neighbors must be by this factor larger than the distance to the m...
Definition: StablePairFinder.h:172
OpenMS::StablePairFinder::create
static BaseGroupFinder * create()
Returns an instance of this class.
Definition: StablePairFinder.h:126
OpenMS::StablePairFinder::use_IDs_
bool use_IDs_
Only match if peptide IDs are compatible?
Definition: StablePairFinder.h:175