OpenMS
StablePairFinder.h
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34 
35 #ifndef OPENMS_ANALYSIS_MAPMATCHING_STABLEPAIRFINDER_H
36 #define OPENMS_ANALYSIS_MAPMATCHING_STABLEPAIRFINDER_H
37 
39 
40 namespace OpenMS
41 {
42  class AASequence;
43 
109  class OPENMS_DLLAPI StablePairFinder :
110  public BaseGroupFinder
111  {
112 public:
113 
116 
119 
121  ~StablePairFinder() override
122  {
123  }
124 
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  {
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 
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  */
Representation of a peptide/protein sequence.
Definition: AASequence.h:112
The base class of all element group finding algorithms.
Definition: BaseGroupFinder.h:64
A consensus feature spanning multiple LC-MS/MS experiments.
Definition: ConsensusFeature.h:71
A container for consensus elements.
Definition: ConsensusMap.h:92
@ MZ
Mass-to-charge dimension id (1 if used as a const int)
Definition: Peak2D.h:76
@ RT
Retention time dimension id (0 if used as a const int)
Definition: Peak2D.h:75
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:65
This class implements a pair finding algorithm for consensus features.
Definition: StablePairFinder.h:111
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
~StablePairFinder() override
Destructor.
Definition: StablePairFinder.h:121
bool use_IDs_
Only match if peptide IDs are compatible?
Definition: StablePairFinder.h:175
StablePairFinder()
Constructor.
bool compatibleIDs_(const ConsensusFeature &feat1, const ConsensusFeature &feat2) const
Checks if the peptide IDs of two features are compatible.
void run(const std::vector< ConsensusMap > &input_maps, ConsensusMap &result_map) override
Run the algorithm.
void updateMembers_() override
This method is used to update extra member variables at the end of the setParameters() method.
const AASequence & getBestHitSequence_(const PeptideIdentification &peptideIdentification) const
Returns the highest scoring peptide hit in the the given peptide identification.
BaseGroupFinder Base
Base class.
Definition: StablePairFinder.h:115
static BaseGroupFinder * create()
Returns an instance of this class.
Definition: StablePairFinder.h:126
static const String getProductName()
Returns the name of this module.
Definition: StablePairFinder.h:132
A more convenient string class.
Definition: String.h:60
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48
@ RT
RT in seconds.