viterbi.h

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#ifndef VITERBI_H_A08989A1_B4B4_461C_B863_A1AE2FE9BD98
#define VITERBI_H_A08989A1_B4B4_461C_B863_A1AE2FE9BD98

#include <vector>
#include <map>

extern "C"
{
#include <family.h>
#include <cafe.h>
void compute_viterbis(pCafeNode node, int k, double *factors, int rootfamilysize_start, int rootfamilysize_end, int familysize_start, int familysize_end);
}

class Globals;

struct change
{
    change(int e, int r, int d) : expand(e), remain(r), decrease(d)
    {

    }
    change() : expand(0), remain(0), decrease(0)
    {

    }
    int expand;
    int remain;
    int decrease;
};

class viterbi_parameters
{
public:
    int num_nodes;

    int num_rows;

    std::vector<change> expandRemainDecrease;

    // first value is node ID
  using NodeFamilyKey = std::pair<int, pCafeFamilyItem>;

  std::map<NodeFamilyKey, int> viterbiNodeFamilysizes;

  std::map<NodeFamilyKey, double> viterbiPvalues;

    double* maximumPvalues;
    std::vector<double> averageExpansion;
    double** cutPvalues;

  void set_node_familysize(pCafeTree tree, pCafeFamilyItem pItem);
  void compute_size_deltas(pTree ptree, pCafeFamilyItem pitem);
  void clear(int nnodes);
} ;

void viterbi_parameters_init(viterbi_parameters *viterbi, int nnodes, int nrows);

void viterbi_set_max_pvalue(viterbi_parameters* viterbi, int index, const std::vector<double>& values );

void cafe_viterbi(Globals& globals, viterbi_parameters& viterbi, std::vector<std::vector<double> >* pCD);
void viterbi_sum_probabilities(viterbi_parameters *viterbi, pCafeTree pcafe, pCafeFamilyItem pitem);
void* __cafe_viterbi_thread_func(void* ptr);
void viterbi_family_print(pCafeTree pcafe, pCafeFamily pfamily, int idx);

struct ViterbiParam
{
    pCafeFamily pfamily;
    pCafeTree pcafe;
    int num_threads;
    viterbi_parameters *viterbi;
    int num_random_samples;
    double pvalue;

    std::vector<std::vector<double> >* pCD;
    int from;
};


#endif