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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 {
107  class OPENMS_DLLAPI StablePairFinder :
108  public BaseGroupFinder
109  {
110 public:
111 
114 
117 
120  {
121  }
122 
125  {
126  return new StablePairFinder();
127  }
128 
130  static const String getProductName()
131  {
132  return "stable";
133  }
134 
142  void run(const std::vector<ConsensusMap>& input_maps,
143  ConsensusMap& result_map);
144 
145 protected:
146 
148 
149  enum
150  {
153  };
155 
156  //docu in base class
157  virtual void updateMembers_();
158 
166  bool compatibleIDs_(const ConsensusFeature& feat1,
167  const ConsensusFeature& feat2) const;
168 
171 
173  bool use_IDs_;
174 
180  const AASequence& getBestHitSequence_(const PeptideIdentification& peptideIdentification) const;
181  };
182 
183 } // namespace OpenMS
184 
185 #endif // OPENMS_ANALYSIS_MAPMATCHING_STABLEPAIRFINDER_H
186 
187 /*
188 
189  gnuplot history - how the plot was created - please do not delete this receipt
190 
191  f(x,intercept,exponent)=1/(1+(abs(x)*intercept)**exponent)
192  set terminal postscript enhanced color
193  set output "choosingstablepairfinderparams.ps"
194  set size ratio .3
195  plot [-3:3] [0:1] f(x,1,1), f(x,2,1), f(x,1,2), f(x,2,2)
196 
197  */
This class implements a pair finding algorithm for consensus features.
Definition: StablePairFinder.h:107
A more convenient string class.
Definition: String.h:56
Retention time dimension id (0 if used as a const int)
Definition: Peak2D.h:76
A container for consensus elements.
Definition: ConsensusMap.h:60
Mass-to-charge dimension id (1 if used as a const int)
Definition: Peak2D.h:77
Representation of a peptide/protein sequence.
Definition: AASequence.h:84
The base class of all element group finding algorithms.
Definition: BaseGroupFinder.h:59
bool use_IDs_
Only match if peptide IDs are compatible?
Definition: StablePairFinder.h:173
virtual ~StablePairFinder()
Destructor.
Definition: StablePairFinder.h:119
BaseGroupFinder Base
Base class.
Definition: StablePairFinder.h:113
DoubleReal 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:170
static BaseGroupFinder * create()
Returns an instance of this class.
Definition: StablePairFinder.h:124
static const String getProductName()
Returns the name of this module.
Definition: StablePairFinder.h:130
A 2-dimensional consensus feature.
Definition: ConsensusFeature.h:59
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:63

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:21 using doxygen 1.8.5