family.h

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#ifndef __FAMILIY_H__
#define __FAMILIY_H__

#include<tree.h>
#include<birthdeath.h>
#include "input_values.h"

#define FAMILYSIZEMAX   1000

typedef struct {
    int min;
    int max;
    int root_min;
    int root_max;
} family_size_range;

typedef struct 
{
    Tree    super;
    family_size_range range;    
    double  lambda;
    double mu;
    int branch_params_cnt;
    int k;
    int     size_of_factor;
    int     rfsize;
}CafeTree;
typedef CafeTree* pCafeTree;


typedef struct
{
    char* errorfilename;
    int fromdiff;
    int todiff;
    int maxfamilysize;
    double** errormatrix;
}ErrorStruct;
typedef ErrorStruct* pErrorStruct;       

struct probabilities
{
    double  lambda;
    double  mu;
    double* param_lambdas;
    double* param_mus;
};

void free_probabilities(struct probabilities *probs);

typedef struct
{
    PhylogenyNode super;
    double** k_likelihoods;
    double* likelihoods;
    int*    viterbi;
    
    int familysize; 


    struct probabilities birth_death_probabilities;

    struct square_matrix* birthdeath_matrix;
    pArrayList k_bd;
    pErrorStruct errormodel;
}CafeNode;
typedef CafeNode*   pCafeNode;


typedef struct
{
    char** species;             
    int   num_species;          
    int*  index;                
    pErrorStruct* error_ptr;    
    int   max_size;
    pArrayList flist;   
    pArrayList errors;  
    int** countbackup;  
}CafeFamily;
typedef CafeFamily* pCafeFamily;

void init_family_size(family_size_range* fs, int max);
void copy_range_to_tree(pCafeTree tree, family_size_range* range);

typedef struct tagCafeParam CafeParam;
typedef CafeParam* pCafeParam;
typedef void (*param_func)(pCafeParam param, double* parameters);
enum OPTIMIZER_INIT_TYPE { UNKNOWN, DO_NOTHING, LAMBDA_ONLY, LAMBDA_MU };
void cafe_shell_set_lambdas(pCafeParam param, double* lambda);

struct tagCafeParam
{
    FILE *fout, *flog;
    pString str_fdata;

    pCafeTree pcafe;        

    pCafeFamily pfamily;    
    
    int eqbg;
    int posterior;

    double* ML;

    double* MAP;

    double* prior_rfsize;

    input_values input;

    int num_params;

    enum OPTIMIZER_INIT_TYPE optimizer_init_type;

    double* lambda;
    pTree lambda_tree;
    int num_lambdas;

    double* mu;
    int num_mus;
    
    int parameterized_k_value;
    double* k_weights;
    double** p_z_membership;
    int fixcluster0;

    int checkconv;
    int* old_branchlength;
    double max_branch_length;
    double sum_branch_length;
    int num_branches;

    family_size_range family_size;
    
    int* root_dist;

    double pvalue;
    
    int  num_threads;

    double** likelihoodRatios;

    int quiet;
};


/****************************************************************************
 * Cafe Main
****************************************************************************/

extern void thread_run_with_arraylist(int numthreads, void* (*run)(void*), pArrayList pal );
// cafe tree
extern void cafe_tree_set_birthdeath(pCafeTree pcafe, int max_family_size);
#endif