RefMARepresentor

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KEYWORD

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RefMARepresentor();

  RefMARepresentor();

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RefMARepresentor(const MultipleResult& multipleResult) ;

  RefMARepresentor(const MultipleResult& multipleResult) ;

Function is currently defined inline.

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class FeatureTriplet ;

  class FeatureTriplet {
  public:
    FeatureTriplet(const Feature* feature1, const Feature* feature2, const Feature* feature3, unsigned int id) :
      feature1_(feature1), feature2_(feature2), feature3_(feature3), id_(id) {
      RigidTrans3 trans(feature1_->getCenter(), feature2_->getCenter(), feature3_->getCenter());
      trans_ = !trans;
      featuresCode_ = encodeFeatureTypes();
      triangleSideLengths_ = triangleSideLengths();
      transformedFeatureCenters_[0] = trans_*feature1_->getCenter();
      transformedFeatureCenters_[1] = trans_*feature2_->getCenter();
      transformedFeatureCenters_[2] = trans_*feature3_->getCenter();
    }

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class VoteTable ;

  class VoteTable : public hash_map< int, hash_map< int, unsigned int> > { // key1 = base1, key2=base2, data=num of votes
  public:   
    void incVote(const int base1, const int base2, int acc) {
      hash_map<int, hash_map<int, unsigned int> >::iterator iter1 = find(base1);
      if(iter1 != end()) {
	hash_map<int, unsigned int>& hashMap = iter1->second;
	hash_map<int, unsigned int>::iterator iter2 = hashMap.find(base2);
	if(iter2 != hashMap.end()) { // pair already exists, increment vote only
	  iter2->second += acc;
	} else { // only first base exists, add second
	  hashMap[base2] = acc;
	}
      } else { // the given pair is a new one
	(*this)[base1][base2] = acc;
      }
    }

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unsigned int commonFeatures(const MultipleResult& multipleResult, RigidTrans3& trans, float& rmsd) const;

Returns number of common features, alignment transformation and rmsd on features for an input MA

  unsigned int commonFeatures(const MultipleResult& multipleResult, RigidTrans3& trans, float& rmsd) const;

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unsigned int numOfFeatures() const ;

  unsigned int numOfFeatures() const                                            
;

Function is currently defined inline.

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unsigned int numOfMolecules() const ;

  unsigned int numOfMolecules() const                                             
;

Function is currently defined inline.

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friend ostream& operator<<(ostream& s, const RefMARepresentor& refMA)

  friend ostream& operator<<(ostream& s, const RefMARepresentor& refMA)                                                                                                                                            

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void init();

  void init();

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unsigned int actualMatchSize(const RigidTrans3& trans, vector< const Feature *>& features, float featureMatchThr);

  unsigned int actualMatchSize(const RigidTrans3& trans, vector< const Feature *>& features, float featureMatchThr);

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unsigned int buildTriplets(const vector< const Feature *>& features, vector< FeatureTriplet>& triplets, bool ordered) const;

  unsigned int buildTriplets(const vector< const Feature *>& features, vector< FeatureTriplet>& triplets, bool ordered) const;

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float calculateRmsd(const RigidTrans3& trans, vector< const Feature *>& features);

  float calculateRmsd(const RigidTrans3& trans, vector< const Feature *>& features);

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const MultipleResult& multipleResult_;

  const MultipleResult& multipleResult_;

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vector< const Feature *> features_;

  vector< const Feature *> features_;

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vector< FeatureTriplet> featureTriplets_;

  vector< FeatureTriplet> featureTriplets_;

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GeomHash< HashKey, HashData> geomHash_;

  GeomHash< HashKey, HashData> geomHash_;

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GeomHash< FeatureTriplet, unsigned int> tripletHash_;

  GeomHash< FeatureTriplet, unsigned int> tripletHash_;

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BipartiteMatcher *bipartiteMatcher_;

  static BipartiteMatcher *bipartiteMatcher_;

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GeomHash< Vector3, unsigned int> featuresHash_;

  GeomHash< Vector3, unsigned int> featuresHash_; // key=feature center, data=feature index in features_ array

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