cafe.h

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#ifndef __CAFE_TREE_H__
#define __CAFE_TREE_H__

#include<family.h>
#include<gmatrix.h>
#include <chooseln_cache.h>

typedef struct
{
    char* id;

    int*  count;
    char* desc;
    int   maxlh;
    int   ref;
    double*  lambda;
    double*  mu;
    double*  z_membership;
    int   holder;
}CafeFamilyItem;

typedef CafeFamilyItem* pCafeFamilyItem;


typedef enum 
{
    CAFE_REPORT_TEXT = 0,
    CAFE_REPORT_HTML,
    CAFE_REPORT_PDF,
}enumCafeReport;

/****************************************************************************
 * Cafe Tree
****************************************************************************/

extern pCafeTree cafe_tree_new(const char* sztree, family_size_range* range, double lambda, double mu);
extern pTreeNode cafe_tree_new_empty_node(pTree pcafe);
extern void cafe_tree_set_parameters(pCafeTree pcafe, family_size_range* range, double lambda);
extern pCafeTree cafe_tree_copy(pCafeTree psrc);
extern pCafeTree cafe_tree_split(pCafeTree pcafe, int idx );
extern void cafe_tree_free(pCafeTree pcafe);
extern void __cafe_tree_free_node(pTree ptree, pTreeNode ptnode, va_list ap);
extern void cafe_tree_string_name(pString pstr, pPhylogenyNode ptnode);
extern pString cafe_tree_string_with_lambda(pCafeTree pcafe);
extern pString cafe_tree_string_with_id(pCafeTree pcafe);
extern pString cafe_tree_string(pCafeTree pcafe);
extern pString cafe_tree_string_with_familysize_lambda(pCafeTree pcafe);
extern pString cafe_tree_string_with_familysize(pCafeTree pcafe);
extern void cafe_tree_string_print(pCafeTree pcafe);
void compute_internal_node_likelihood(pTree ptree, pTreeNode ptnode);

extern void compute_tree_likelihoods(pCafeTree pcafe);
extern double* get_likelihoods(const pCafeTree pcafe);
extern void cafe_tree_node_free_clustered_likelihoods (pCafeParam param);
extern double** cafe_tree_clustered_likelihood(pCafeTree pcafe, struct chooseln_cache *ln_cache);
extern void cafe_tree_viterbi(pCafeTree pcafe);
extern void cafe_tree_clustered_viterbi(pCafeTree pcafe, int num_likelihoods);
extern void cafe_tree_viterbi_posterior(pCafeTree pcafe, pCafeParam param);
void initialize_leaf_likelihood_clustered(pTree ptree, pTreeNode ptnode);

extern double cafe_tree_mp_remark(pString str, pTree ptree, pMetapostConfig pmc, va_list ap);
extern int cafe_tree_random_familysize(pCafeTree pcafe, int rootFamilysize, int maxFamilySize);
void node_set_birthdeath_matrix(pCafeNode pcnode, pBirthDeathCacheArray cache, int num_lambdas);
void add_key(pArrayList arr, double branchlength, double lambda, double mu);

/****************************************************************************
 * Cafe Family
****************************************************************************/
void cafe_family_set_size(pCafeFamily pcf, pCafeFamilyItem pitem, pCafeTree pcafe);
extern int cafe_family_set_species_index(pCafeFamily pcf, pCafeTree pcafe );
extern int cafe_family_get_species_index(pCafeFamily pcf, char* speciesname); 
extern void cafe_family_set_size_with_family(pCafeFamily pcf, int idx, pCafeTree pcafe );
extern void cafe_family_set_truesize_with_family(pCafeFamily pcf, int idx, pCafeTree pcafe );
extern void cafe_family_set_size_by_species(char* speciesname, int size, pCafeTree pcafe);
extern int cafe_family_get_index(pCafeFamily pcf, const char* szid);
extern void cafe_family_set_size_with_family_forced(pCafeFamily pcf, int idx, pCafeTree pcafe);
extern void cafe_family_filter( pCafeParam param );
extern void cafe_family_reset_maxlh(pCafeFamily pcf);
extern int cafe_family_split_cvfiles_byfamily(pCafeParam param, int cv_fold);
extern void cafe_family_split_cvfiles_byspecies(pCafeParam param);

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

extern void cafe_log(pCafeParam param, const char* msg, ... );
extern void reset_birthdeath_cache(pCafeTree tree, int k_value, family_size_range* range);
extern double* cafe_best_lambda_by_fminsearch(pCafeParam param, int lambda_len, int k);
extern double* cafe_each_best_lambda_by_fminsearch(pCafeParam param, int lambda_len );
extern void cafe_lambda_set_default(pCafeParam param, double* lambda);

extern void cafe_free_birthdeath_cache(pCafeTree pcafe);
extern void cafe_likelihood_ratio_test(pCafeParam param, double *maximumPvalues);
void input_values_randomize(input_values *vals, int lambda_len, int mu_len, int k,
    int kfix, double max_branch_length, double *k_weights);

void initialize_leaf_likelihoods_for_viterbi(double **matrix, int num_rows, int range, int familysize, int num_cols, pErrorStruct errormodel);
void reset_k_likelihoods(pCafeNode pcnode, int k, int num_factors);

double cafe_get_clustered_posterior(pCafeParam param, double *ML, double *MAP, double *prior_rfsize);

#define E_NOT_SYNCHRONIZED 1
#define E_INCONSISTENT_SIZE 2
int sync_sanity_check(pCafeFamily pcf, pCafeTree pcafe);

#endif