OpenMS  3.0.0
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  {
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  */
BaseGroupFinder.h
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::StablePairFinder::~StablePairFinder
~StablePairFinder() override
Destructor.
Definition: StablePairFinder.h:121
OpenMS::DIM_UNIT::MZ
m/z
OpenMS::Peak2D::MZ
Mass-to-charge dimension id (1 if used as a const int)
Definition: Peak2D.h:76
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::StablePairFinder
This class implements a pair finding algorithm for consensus features.
Definition: StablePairFinder.h:109
OpenMS::ConsensusFeature
A consensus feature spanning multiple LC-MS/MS experiments.
Definition: ConsensusFeature.h:69
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:82
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::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:63
OpenMS::StablePairFinder::getProductName
static const String getProductName()
Returns the name of this module.
Definition: StablePairFinder.h:132
OpenMS::Peak2D::RT
Retention time dimension id (0 if used as a const int)
Definition: Peak2D.h:75
OpenMS::StablePairFinder::Base
BaseGroupFinder Base
Base class.
Definition: StablePairFinder.h:115
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:111
OpenMS::BaseGroupFinder
The base class of all element group finding algorithms.
Definition: BaseGroupFinder.h:61
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
OpenMS::DIM_UNIT::RT
RT in seconds.