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neighborj.h
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neighborj.h
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#ifndef NEIGHBORJ_H
#define NEIGHBORJ_H
#include "structs.h"
#include "const_tree.h"
double neighborj_SN ( struct genome_struct *genomes, int num_genes,
int num_genomes, distmem_t * distmem, int CIRCULAR,
int verbose );
double neighborj_SK ( struct genome_struct *genomes, int num_genes,
int num_genomes, distmem_t * distmem, int CIRCULAR,
int verbose );
double neighborj_SK_tree ( struct genome_struct *genomes, int num_genes,
int num_genomes, distmem_t * distmem, int CIRCULAR,
char *constTree );
/* constTree holds the string of the constraint tree and is preallocated */
int neighborj_score_string ( const char *constTree,
struct genome_struct *genome_list, int num_genes,
int num_genomes,
distmem_t * distmem, int CIRCULAR,
struct tNode *tpool, int *edgepool,
struct genome_struct *labels,
int initmethod, int COND,
struct qNode *qpool,
struct adj_struct *adj_list,
struct adj_struct *adj_pool,
int *stack, int *degree, int *otherEnd,
intpair_t * neighbors,
smalledge_t * smalledges,
edge_t * edges,
int *outcycle, int *pred1, int *pred2,
int *picked, int *decode, int inittspsolver,
triple_t * triple, int *incycle, int tspsolver,
int distmethod, int thresh, int **weights,
int **status, int *best_so_far,
env_t * const_env, int *genes,
int *condense_succ, int *condense_decode,
int orig_num_genes, int correction,
char *treeString );
int neighborj_score_one ( struct genome_struct *genome_list, int num_genes,
int num_genomes,
distmem_t * distmem, int CIRCULAR,
struct tNode *tpool, int *edgepool,
struct genome_struct *labels,
int initmethod, int COND,
struct qNode *qpool,
struct adj_struct *adj_list,
struct adj_struct *adj_pool, int *stack,
int *degree, int *otherEnd, intpair_t * neighbors,
smalledge_t * smalledges, edge_t * edges,
int *outcycle, int *pred1, int *pred2, int *picked,
int *decode, int inittspsolver, triple_t * triple,
int *incycle, int tspsolver, int distmethod,
int thresh, int **weights, int **status,
env_t * const_env, int *genes, int *condense_succ,
int *condense_decode, int orig_num_genes,
int correction );
void neighborj_SK_trees ( struct genome_struct *genome_list,
int num_genes, int num_genomes,
distmem_t * distmem, int CIRCULAR,
struct tNode *tpool, int *edgepool,
struct genome_struct *labels,
int initmethod, int COND,
struct qNode *qpool, struct adj_struct *adj_list,
struct adj_struct *adj_pool,
int *stack, int *degree, int *otherEnd,
intpair_t * neighbors,
smalledge_t * smalledges,
edge_t * edges,
int *outcycle, int *pred1, int *pred2, int *picked,
int *decode, int inittspsolver,
triple_t * triple, int *incycle, int tspsolver,
int distmethod, int thresh, int **weights,
int **status, int num_clusters, double **orig_D,
int *orig_valid, char **orig_branch,
int maxConstSize, int *best_so_far, int *score,
env_t * const_env, int *genes, int *condense_succ,
int *condense_decode, int orig_num_genes,
int correction, char *treeString );
int neighborj_score ( struct genome_struct *genome_list, int num_genes,
int num_genomes,
distmem_t * distmem, int CIRCULAR,
struct tNode *tpool, int *edgepool,
struct genome_struct *labels,
int initmethod, int COND,
struct qNode *qpool,
struct adj_struct *adj_list,
struct adj_struct *adj_pool, int *stack, int *degree,
int *otherEnd, intpair_t * neighbors,
smalledge_t * smalledges, edge_t * edges, int *outcycle,
int *pred1, int *pred2, int *picked, int *decode,
int inittspsolver, triple_t * triple, int *incycle,
int tspsolver, int distmethod, int thresh,
int **weights, int **status, env_t * const_env,
int *genes, int *condense_succ, int *condense_decode,
int orig_num_genes, int correction, char *treeString );
#endif