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Algorithm BRZ included

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This commit is contained in:
fc_botelho 2005-07-27 21:13:02 +00:00
parent 9a12ab1456
commit 2948f675d5
10 changed files with 508 additions and 19 deletions
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3
src/Makefile.am
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@ -15,7 +15,8 @@ libcmph_la_SOURCES = debug.h\
cmph.h cmph.c\
cmph_structs.h cmph_structs.c\
chm.h chm_structs.h chm.c\
bmz.h bmz_structs.h bmz.c
bmz.h bmz_structs.h bmz.c\
brz.h brz_structs.h brz.c
libcmph_la_LDFLAGS = -version-info 0:0:0

2
src/bmz.c
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@ -175,7 +175,7 @@ cmph_t *bmz_new(cmph_config_t *mph, float c)
if (iterations_map == 0) return NULL;
mphf = (cmph_t *)malloc(sizeof(cmph_t));
mphf->algo = mph->algo;
bmzf = (bmz_data_t *)malloc(sizeof(bmz_config_data_t));
bmzf = (bmz_data_t *)malloc(sizeof(bmz_data_t));
bmzf->g = bmz->g;
bmz->g = NULL; //transfer memory ownership
bmzf->hashes = bmz->hashes;

1
src/bmz_structs.h
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@ -11,6 +11,7 @@ struct __bmz_data_t
hash_state_t **hashes;
};
struct __bmz_config_data_t
{
CMPH_HASH hashfuncs[2];

408
src/brz.c Executable file
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@ -0,0 +1,408 @@
#include "graph.h"
#include "bmz.h"
#include "bmz_structs.h"
#include "brz.h"
#include "cmph_structs.h"
#include "brz_structs.h"
#include "cmph.h"
#include "hash.h"
#include "bitbool.h"
#include <math.h>
#include <stdlib.h>
#include <stdio.h>
#include <assert.h>
#include <string.h>
//#define DEBUG
#include "debug.h"
static int brz_before_gen_graphs(cmph_config_t *mph, cmph_uint32 * disksize, cmph_uint32 * diskoffset);
static void brz_gen_graphs(cmph_config_t *mph, cmph_uint32 * disksize, cmph_uint32 * diskoffset, FILE * graphs_fd);
static char ** brz_read_keys_vd(FILE * graphs_fd, cmph_uint8 nkeys);
static void brz_destroy_keys_vd(char ** keys_vd, cmph_uint8 nkeys);
static void brz_copy_partial_mphf(brz_config_data_t *brz, bmz_data_t * bmzf, cmph_uint32 index);
brz_config_data_t *brz_config_new()
{
brz_config_data_t *brz = NULL;
brz = (brz_config_data_t *)malloc(sizeof(brz_config_data_t));
brz->hashfuncs[0] = CMPH_HASH_JENKINS;
brz->hashfuncs[1] = CMPH_HASH_JENKINS;
brz->hashfuncs[2] = CMPH_HASH_JENKINS;
brz->size = NULL;
brz->offset = NULL;
brz->g = NULL;
brz->h1 = NULL;
brz->h2 = NULL;
brz->h3 = NULL;
assert(brz);
return brz;
}
void brz_config_destroy(cmph_config_t *mph)
{
brz_config_data_t *data = (brz_config_data_t *)mph->data;
DEBUGP("Destroying algorithm dependent data\n");
free(data);
}
void brz_config_set_hashfuncs(cmph_config_t *mph, CMPH_HASH *hashfuncs)
{
brz_config_data_t *brz = (brz_config_data_t *)mph->data;
CMPH_HASH *hashptr = hashfuncs;
cmph_uint32 i = 0;
while(*hashptr != CMPH_HASH_COUNT)
{
if (i >= 3) break; //brz only uses three hash functions
brz->hashfuncs[i] = *hashptr;
++i, ++hashptr;
}
}
cmph_t *brz_new(cmph_config_t *mph, float c)
{
cmph_t *mphf = NULL;
brz_data_t *brzf = NULL;
cmph_uint32 i;
cmph_uint32 iterations = 20;
cmph_uint32 * disksize = NULL;
cmph_uint32 * diskoffset = NULL;
cmph_io_adapter_t *source = NULL;
cmph_config_t *config = NULL;
cmph_t *mphf_tmp = NULL;
char ** keys_vd = NULL;
FILE * graphs_fd = NULL;
DEBUGP("c: %f\n", c);
brz_config_data_t *brz = (brz_config_data_t *)mph->data;
brz->m = mph->key_source->nkeys;
DEBUGP("m: %f\n", brz->m);
brz->k = ceil(brz->m/128);
DEBUGP("k: %f\n", brz->k);
brz->size = (cmph_uint8 *) malloc(sizeof(cmph_uint8)*brz->k);
brz->offset = (cmph_uint32 *)malloc(sizeof(cmph_uint32)*brz->k);
disksize = (cmph_uint32 *)malloc(sizeof(cmph_uint32)*brz->k);
diskoffset = (cmph_uint32 *)malloc(sizeof(cmph_uint32)*brz->k);
for(i = 0; i < brz->k; ++i)
{
brz->size[i] = 0;
brz->offset[i] = 0;
disksize[i] = 0;
diskoffset[i] = 0;
}
// Creating the external graphs.
while(1)
{
int ok;
DEBUGP("hash function 3\n");
brz->h3 = hash_state_new(brz->hashfuncs[2], brz->k);
DEBUGP("Generating graphs\n");
ok = brz_before_gen_graphs(mph, disksize, diskoffset);
if (!ok)
{
--iterations;
hash_state_destroy(brz->h3);
brz->h3 = NULL;
DEBUGP("%u iterations remaining to create the graphs in a external file\n", iterations);
if (mph->verbosity)
{
fprintf(stderr, "Failure: A graph with more than 255 keys was created - %u iterations remaining\n", iterations);
}
if (iterations == 0) break;
}
else break;
}
if (iterations == 0)
{
DEBUGP("Graphs with more than 255 keys were created in all 20 iterations\n");
free(brz->size);
free(brz->offset);
free(disksize);
free(diskoffset);
return NULL;
}
graphs_fd = fopen("/colecao/fbotelho/cmph.tmp", "wb+");
if (graphs_fd == NULL)
{
free(brz->size);
free(brz->offset);
free(disksize);
free(diskoffset);
fprintf(stderr, "Unable to open file %s\n", "/colecao/fbotelho/cmph.tmp");
return NULL;
}
// Clustering the keys by graph id.
brz_gen_graphs(mph, disksize, diskoffset, graphs_fd);
free(disksize);
free(diskoffset);
// codigo do algoritmo...
brz->h1 = (hash_state_t **)malloc(sizeof(hash_state_t *)*brz->k);
brz->h2 = (hash_state_t **)malloc(sizeof(hash_state_t *)*brz->k);
brz->g = (cmph_uint8 **) malloc(sizeof(cmph_uint8 *) *brz->k);
for(i = 0; i < brz->k; i++)
{
bmz_data_t * bmzf = NULL;
if (brz->size[i] == 0) continue;
keys_vd = brz_read_keys_vd(graphs_fd, brz->size[i]);
// Source of keys
source = cmph_io_vector_adapter(keys_vd, (cmph_uint32)brz->size[i]);
config = cmph_config_new(source);
cmph_config_set_algo(config, CMPH_BMZ);
cmph_config_set_graphsize(config, c);
mphf_tmp = cmph_new(config);
bmzf = (bmz_data_t *)mphf_tmp->data;
brz_copy_partial_mphf(brz, bmzf, i); // implementar
cmph_config_destroy(config);
brz_destroy_keys_vd(keys_vd, brz->size[i]);
free(keys_vd);
cmph_destroy(mphf_tmp);
free(source);
}
fclose(graphs_fd);
// Generating a mphf
mphf = (cmph_t *)malloc(sizeof(cmph_t));
mphf->algo = mph->algo;
brzf = (brz_data_t *)malloc(sizeof(brz_data_t));
brzf->g = brz->g;
brz->g = NULL; //transfer memory ownership
brzf->h1 = brz->h1;
brz->h1 = NULL; //transfer memory ownership
brzf->h2 = brz->h2;
brz->h2 = NULL; //transfer memory ownership
brzf->h3 = brz->h3;
brz->h3 = NULL; //transfer memory ownership
brzf->size = brz->size;
brz->size = NULL; //transfer memory ownership
brzf->offset = brz->offset;
brz->offset = NULL; //transfer memory ownership
brzf->k = brz->k;
brzf->m = brz->m;
mphf->data = brzf;
mphf->size = brz->m;
DEBUGP("Successfully generated minimal perfect hash\n");
if (mph->verbosity)
{
fprintf(stderr, "Successfully generated minimal perfect hash function\n");
}
return mphf;
}
static int brz_before_gen_graphs(cmph_config_t *mph, cmph_uint32 * disksize, cmph_uint32 * diskoffset)
{
cmph_uint32 e;
brz_config_data_t *brz = (brz_config_data_t *)mph->data;
mph->key_source->rewind(mph->key_source->data);
DEBUGP("Generating information before the keys partition\n");
for (e = 0; e < brz->m; ++e)
{
cmph_uint32 h3;
cmph_uint32 keylen;
char *key;
mph->key_source->read(mph->key_source->data, &key, &keylen);
h3 = hash(brz->h3, key, keylen) % brz->k;
mph->key_source->dispose(mph->key_source->data, key, keylen);
if (brz->size[h3] == 255) return 0;
brz->size[h3] = brz->size[h3] + 1;
disksize[h3] = disksize[h3] + keylen + 1;
}
for (e = 1; e < brz->k; ++e)
{
brz->offset[e] = brz->size[e-1] + brz->size[e];
diskoffset[e] = disksize[e-1] + disksize[e];
}
return 1;
}
// disksize nao esta sendo usado ainda. Sera usado qd incluir os buffers.
static void brz_gen_graphs(cmph_config_t *mph, cmph_uint32 * disksize, cmph_uint32 * diskoffset, FILE * graphs_fd)
{
cmph_uint32 e;
brz_config_data_t *brz = (brz_config_data_t *)mph->data;
mph->key_source->rewind(mph->key_source->data);
DEBUGP("Generating graphs from %u keys\n", brz->m);
for (e = 0; e < brz->m; ++e)
{
cmph_uint32 h3;
cmph_uint32 keylen;
char *key;
mph->key_source->read(mph->key_source->data, &key, &keylen);
h3 = hash(brz->h3, key, keylen) % brz->k;
mph->key_source->dispose(mph->key_source->data, key, keylen);
fseek(graphs_fd, diskoffset[h3], SEEK_SET);
fwrite(key, sizeof(char), keylen + 1, graphs_fd);
diskoffset[h3] = diskoffset[h3] + keylen + 1;
}
}
static char ** brz_read_keys_vd(FILE * graphs_fd, cmph_uint8 nkeys)
{
char ** keys_vd = (char **)malloc(sizeof(char *)*nkeys);
cmph_uint8 i;
for(i = 0; i < nkeys; i++)
{
char * buf = (char *)malloc(BUFSIZ);
cmph_uint32 buf_pos = 0;
char c;
while(1)
{
fread(&c, sizeof(char), 1, graphs_fd);
buf[buf_pos++] = c;
if(c == '\0') break;
if(buf_pos % BUFSIZ == 0) buf = (char *)realloc(buf, buf_pos + BUFSIZ);
}
keys_vd[i] = (char *)malloc(strlen(buf) + 1);
strcpy(keys_vd[i], buf);
free(buf);
}
return keys_vd;
}
static void brz_destroy_keys_vd(char ** keys_vd, cmph_uint8 nkeys)
{
cmph_uint8 i;
for(i = 0; i < nkeys; i++) free(keys_vd[i]);
}
static void brz_copy_partial_mphf(brz_config_data_t *brz, bmz_data_t * bmzf, cmph_uint32 index)
{
cmph_uint32 i;
brz->g[index] = (cmph_uint8 *)malloc(sizeof(cmph_uint8)*bmzf->m);
for(i = 0; i < bmzf->m; i++)
{
brz->g[index][i] = (cmph_uint8) bmzf->g[i];
}
brz->h1[index] = bmzf->hashes[0];
brz->h2[index] = bmzf->hashes[1];
}
int brz_dump(cmph_t *mphf, FILE *fd)
{
/*char *buf = NULL;
cmph_uint32 buflen;
cmph_uint32 nbuflen;
cmph_uint32 i;
cmph_uint32 two = 2; //number of hash functions
brz_data_t *data = (brz_data_t *)mphf->data;
cmph_uint32 nn, nm;
__cmph_dump(mphf, fd);
fwrite(&two, sizeof(cmph_uint32), 1, fd);
hash_state_dump(data->hashes[0], &buf, &buflen);
DEBUGP("Dumping hash state with %u bytes to disk\n", buflen);
fwrite(&buflen, sizeof(cmph_uint32), 1, fd);
fwrite(buf, buflen, 1, fd);
free(buf);
hash_state_dump(data->hashes[1], &buf, &buflen);
DEBUGP("Dumping hash state with %u bytes to disk\n", buflen);
fwrite(&buflen, sizeof(cmph_uint32), 1, fd);
fwrite(buf, buflen, 1, fd);
free(buf);
fwrite(&(data->n), sizeof(cmph_uint32), 1, fd);
fwrite(&(data->m), sizeof(cmph_uint32), 1, fd);
fwrite(data->g, sizeof(cmph_uint32)*(data->n), 1, fd);
#ifdef DEBUG
fprintf(stderr, "G: ");
for (i = 0; i < data->n; ++i) fprintf(stderr, "%u ", data->g[i]);
fprintf(stderr, "\n");
#endif
*/
return 1;
}
void brz_load(FILE *f, cmph_t *mphf)
{
/* cmph_uint32 nhashes;
char *buf = NULL;
cmph_uint32 buflen;
cmph_uint32 i;
brz_data_t *brz = (brz_data_t *)malloc(sizeof(brz_data_t));
DEBUGP("Loading brz mphf\n");
mphf->data = brz;
fread(&nhashes, sizeof(cmph_uint32), 1, f);
brz->hashes = (hash_state_t **)malloc(sizeof(hash_state_t *)*(nhashes + 1));
brz->hashes[nhashes] = NULL;
DEBUGP("Reading %u hashes\n", nhashes);
for (i = 0; i < nhashes; ++i)
{
hash_state_t *state = NULL;
fread(&buflen, sizeof(cmph_uint32), 1, f);
DEBUGP("Hash state has %u bytes\n", buflen);
buf = (char *)malloc(buflen);
fread(buf, buflen, 1, f);
state = hash_state_load(buf, buflen);
brz->hashes[i] = state;
free(buf);
}
DEBUGP("Reading m and n\n");
fread(&(brz->n), sizeof(cmph_uint32), 1, f);
fread(&(brz->m), sizeof(cmph_uint32), 1, f);
brz->g = (cmph_uint32 *)malloc(sizeof(cmph_uint32)*brz->n);
fread(brz->g, brz->n*sizeof(cmph_uint32), 1, f);
#ifdef DEBUG
fprintf(stderr, "G: ");
for (i = 0; i < brz->n; ++i) fprintf(stderr, "%u ", brz->g[i]);
fprintf(stderr, "\n");
#endif
return;
*/
}
cmph_uint32 brz_search(cmph_t *mphf, const char *key, cmph_uint32 keylen)
{
/* brz_data_t *brz = mphf->data;
cmph_uint32 h1 = hash(brz->hashes[0], key, keylen) % brz->n;
cmph_uint32 h2 = hash(brz->hashes[1], key, keylen) % brz->n;
DEBUGP("key: %s h1: %u h2: %u\n", key, h1, h2);
if (h1 == h2 && ++h2 > brz->n) h2 = 0;
DEBUGP("key: %s g[h1]: %u g[h2]: %u edges: %u\n", key, brz->g[h1], brz->g[h2], brz->m);
return brz->g[h1] + brz->g[h2];
*/
return 0;
}
void brz_destroy(cmph_t *mphf)
{
cmph_uint32 i;
brz_data_t *data = (brz_data_t *)mphf->data;
for(i = 0; i < data->k; i++)
{
free(data->g[i]);
hash_state_destroy(data->h1[i]);
hash_state_destroy(data->h2[i]);
}
hash_state_destroy(data->h3);
free(data->g);
free(data->h1);
free(data->h2);
free(data->size);
free(data->offset);
free(data);
free(mphf);
}

18
src/brz.h Normal file
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@ -0,0 +1,18 @@
#ifndef __CMPH_BRZ_H__
#define __CMPH_BRZ_H__
#include "cmph.h"
typedef struct __brz_data_t brz_data_t;
typedef struct __brz_config_data_t brz_config_data_t;
brz_config_data_t *brz_config_new();
void brz_config_set_hashfuncs(cmph_config_t *mph, CMPH_HASH *hashfuncs);
void brz_config_destroy(cmph_config_t *mph);
cmph_t *brz_new(cmph_config_t *mph, float c);
void brz_load(FILE *f, cmph_t *mphf);
int brz_dump(cmph_t *mphf, FILE *f);
void brz_destroy(cmph_t *mphf);
cmph_uint32 brz_search(cmph_t *mphf, const char *key, cmph_uint32 keylen);
#endif

31
src/brz_structs.h Executable file
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@ -0,0 +1,31 @@
#ifndef __CMPH_BRZ_STRUCTS_H__
#define __CMPH_BRZ_STRUCTS_H__
#include "hash_state.h"
struct __brz_data_t
{
cmph_uint32 m; // edges (words) count
cmph_uint8 *size; // size[i] stores the number of edges represented by g[i][...].
cmph_uint32 *offset; // offset[i] stores the sum: size[0] + size[1] + ... size[i-1].
cmph_uint8 **g; // g function.
cmph_uint32 k; // number of components
hash_state_t **h1;
hash_state_t **h2;
hash_state_t * h3;
};
struct __brz_config_data_t
{
CMPH_HASH hashfuncs[3];
cmph_uint32 m; // edges (words) count
cmph_uint8 *size; // size[i] stores the number of edges represented by g[i][...].
cmph_uint32 *offset; // offset[i] stores the sum: size[0] + size[1] + ... size[i-1].
cmph_uint8 **g; // g function.
cmph_uint32 k; // number of components
hash_state_t **h1;
hash_state_t **h2;
hash_state_t * h3;
};
#endif

2
src/chm.c
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@ -124,7 +124,7 @@ cmph_t *chm_new(cmph_config_t *mph, float c)
mphf = (cmph_t *)malloc(sizeof(cmph_t));
mphf->algo = mph->algo;
chmf = (chm_data_t *)malloc(sizeof(chm_config_data_t));
chmf = (chm_data_t *)malloc(sizeof(chm_data_t));
chmf->g = chm->g;
chm->g = NULL; //transfer memory ownership
chmf->hashes = chm->hashes;

58
src/cmph.c
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@ -2,7 +2,7 @@
#include "cmph_structs.h"
#include "chm.h"
#include "bmz.h"
//#include "bmz.h" /* included -- Fabiano */
#include "brz.h" /* included -- Fabiano */
#include <stdlib.h>
#include <assert.h>
@ -10,7 +10,7 @@
//#define DEBUG
#include "debug.h"
const char *cmph_names[] = { "bmz", "chm", NULL }; /* included -- Fabiano */
const char *cmph_names[] = { "bmz", "chm", "brz", NULL }; /* included -- Fabiano */
static cmph_uint32 position; // access position when data is a vector
@ -107,7 +107,7 @@ cmph_io_adapter_t *cmph_io_nlnkfile_adapter(FILE * keys_fd, cmph_uint32 nkeys)
return key_source;
}
cmph_io_adapter_t *cmph_io_vector_adapter(const char ** vector, cmph_uint32 nkeys)
cmph_io_adapter_t *cmph_io_vector_adapter(char ** vector, cmph_uint32 nkeys)
{
cmph_io_adapter_t * key_source = malloc(sizeof(cmph_io_adapter_t));
assert(key_source);
@ -136,24 +136,30 @@ void cmph_config_set_algo(cmph_config_t *mph, CMPH_ALGO algo)
switch (mph->algo)
{
case CMPH_CHM:
chm_config_destroy(mph->data);
break;
chm_config_destroy(mph->data);
break;
case CMPH_BMZ:
bmz_config_destroy(mph->data);
break;
bmz_config_destroy(mph->data);
break;
case CMPH_BRZ:
brz_config_destroy(mph->data);
break;
default:
assert(0);
assert(0);
}
switch(algo)
{
case CMPH_CHM:
mph->data = chm_config_new();
break;
mph->data = chm_config_new();
break;
case CMPH_BMZ:
mph->data = bmz_config_new();
break;
mph->data = bmz_config_new();
break;
case CMPH_BRZ:
mph->data = brz_config_new();
break;
default:
assert(0);
assert(0);
}
}
mph->algo = algo;
@ -168,7 +174,10 @@ void cmph_config_destroy(cmph_config_t *mph)
chm_config_destroy(mph);
break;
case CMPH_BMZ: /* included -- Fabiano */
bmz_config_destroy(mph);
bmz_config_destroy(mph);
break;
case CMPH_BRZ: /* included -- Fabiano */
brz_config_destroy(mph);
break;
default:
assert(0);
@ -191,6 +200,9 @@ void cmph_config_set_hashfuncs(cmph_config_t *mph, CMPH_HASH *hashfuncs)
case CMPH_BMZ: /* included -- Fabiano */
bmz_config_set_hashfuncs(mph, hashfuncs);
break;
case CMPH_BRZ: /* included -- Fabiano */
brz_config_set_hashfuncs(mph, hashfuncs);
break;
default:
break;
}
@ -220,6 +232,11 @@ cmph_t *cmph_new(cmph_config_t *mph)
if (c == 0) c = 1.15;
mphf = bmz_new(mph, c);
break;
case CMPH_BRZ: /* included -- Fabiano */
DEBUGP("Creating brz hash\n");
if (c == 0) c = 1.15;
mphf = brz_new(mph, c);
break;
default:
assert(0);
}
@ -236,6 +253,9 @@ int cmph_dump(cmph_t *mphf, FILE *f)
case CMPH_BMZ: /* included -- Fabiano */
return bmz_dump(mphf, f);
break;
case CMPH_BRZ: /* included -- Fabiano */
return brz_dump(mphf, f);
break;
default:
assert(0);
}
@ -259,6 +279,10 @@ cmph_t *cmph_load(FILE *f)
DEBUGP("Loading bmz algorithm dependent parts\n");
bmz_load(f, mphf);
break;
case CMPH_BRZ: /* included -- Fabiano */
DEBUGP("Loading brz algorithm dependent parts\n");
brz_load(f, mphf);
break;
default:
assert(0);
}
@ -277,6 +301,9 @@ cmph_uint32 cmph_search(cmph_t *mphf, const char *key, cmph_uint32 keylen)
case CMPH_BMZ: /* included -- Fabiano */
DEBUGP("bmz algorithm search\n");
return bmz_search(mphf, key, keylen);
case CMPH_BRZ: /* included -- Fabiano */
DEBUGP("brz algorithm search\n");
return brz_search(mphf, key, keylen);
default:
assert(0);
}
@ -299,6 +326,9 @@ void cmph_destroy(cmph_t *mphf)
case CMPH_BMZ: /* included -- Fabiano */
bmz_destroy(mphf);
return;
case CMPH_BRZ: /* included -- Fabiano */
brz_destroy(mphf);
return;
default:
assert(0);
}

2
src/cmph.h
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@ -27,7 +27,7 @@ typedef struct
/* please call free() in the created adapters */
cmph_io_adapter_t *cmph_io_nlfile_adapter(FILE * keys_fd);
cmph_io_adapter_t *cmph_io_nlnkfile_adapter(FILE * keys_fd, cmph_uint32 nkeys);
cmph_io_adapter_t *cmph_io_vector_adapter(const char ** vector, cmph_uint32 nkeys);
cmph_io_adapter_t *cmph_io_vector_adapter(char ** vector, cmph_uint32 nkeys);
/** Hash configuration API **/
cmph_config_t *cmph_config_new(cmph_io_adapter_t *key_source);

2
src/cmph_types.h
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@ -8,7 +8,7 @@ typedef unsigned int cmph_uint32;
typedef enum { CMPH_HASH_DJB2, CMPH_HASH_FNV, CMPH_HASH_JENKINS,
CMPH_HASH_SDBM, CMPH_HASH_COUNT } CMPH_HASH;
extern const char *cmph_hash_names[];
typedef enum { CMPH_BMZ, CMPH_CHM, CMPH_COUNT } CMPH_ALGO; /* included -- Fabiano */
typedef enum { CMPH_BMZ, CMPH_CHM, CMPH_BRZ, CMPH_COUNT } CMPH_ALGO; /* included -- Fabiano */
extern const char *cmph_names[];
#endif