#ifndef __COGAPS_GAPS_STATISTICS_H__
 #define __COGAPS_GAPS_STATISTICS_H__

 
 #include "GibbsSampler.h"

 #include "data_structures/Matrix.h"

 enum PumpThreshold
 {
     PUMP_UNIQUE=1,
     PUMP_CUT=2
 };
 

 class GapsStatistics
 {
 private:
 
     ColMatrix mAMeanMatrix;
     ColMatrix mAStdMatrix;
     RowMatrix mPMeanMatrix;
     RowMatrix mPStdMatrix;
     

     unsigned mStatUpdates;
     unsigned mNumPatterns;

     ColMatrix mPumpMatrix;
     PumpThreshold mPumpThreshold;
     unsigned mPumpStatUpdates;
 

 public:
 

     GapsStatistics(unsigned nRow, unsigned nCol, unsigned nFactor, PumpThreshold t=PUMP_CUT);

     Rcpp::NumericMatrix AMean() const;
     Rcpp::NumericMatrix AStd() const;
     Rcpp::NumericMatrix PMean() const;
     Rcpp::NumericMatrix PStd() const;

     Rcpp::NumericMatrix pumpMatrix() const;
     Rcpp::NumericMatrix meanPattern();

     float meanChiSq(const AmplitudeGibbsSampler &ASampler) const;

 
     void update(const AmplitudeGibbsSampler &ASampler,
         const PatternGibbsSampler &PSampler);

 
     void updatePump(const AmplitudeGibbsSampler &ASampler,
         const PatternGibbsSampler &PSampler);
 

     void patternMarkers(ColMatrix normedA, RowMatrix normedP, ColMatrix &statMatrix);
 

     // serialization
     friend Archive& operator<<(Archive &ar, GapsStatistics &stat);
     friend Archive& operator>>(Archive &ar, GapsStatistics &stat);

 };
 
 #endif