diff --git a/Hash_Table.cpp b/Hash_Table.cpp index eb0c87a..60d0bcf 100644 --- a/Hash_Table.cpp +++ b/Hash_Table.cpp @@ -1016,12 +1016,12 @@ void merge_k_mer_pos_list_alloc_heap_sort(k_mer_pos_list_alloc* list, Candidates void init_Count_Table(Count_Table** table) { - *table = kh_init(COUNT64); + *table = ha_ct_init(); } void init_Pos_Table(Pos_Table** table) { - *table = kh_init(POS64); + *table = ha_pt_init(); } void init_Total_Count_Table(int k, Total_Count_Table* TCB) @@ -1091,7 +1091,7 @@ void destory_Total_Count_Table(Total_Count_Table* TCB) int i; for (i = 0; i < TCB->size; i++) { - kh_destroy(COUNT64, TCB->sub_h[i]); + ha_ct_destroy(TCB->sub_h[i]); } free(TCB->sub_h); free(TCB->sub_h_lock); @@ -1107,12 +1107,12 @@ void destory_Total_Pos_Table(Total_Pos_Table* TCB) int i; for (i = 0; i < TCB->size; i++) { - kh_destroy(POS64, TCB->sub_h[i]); + ha_pt_destroy(TCB->sub_h[i]); } free(TCB->sub_h); } - +/* void write_Total_Pos_Table(Total_Pos_Table* TCB, char* read_file_name) { fprintf(stderr, "Writing index to disk... \n"); @@ -1212,6 +1212,7 @@ int load_Total_Pos_Table(Total_Pos_Table* TCB, char* read_file_name) return 1; } +*/ typedef struct { @@ -1268,7 +1269,7 @@ void get_peak_debug(Total_Count_Table* TCB, long long* min, long long* max) for (i = 0; i < TCB->size; i++) { h = TCB->sub_h[i]; - for (k = kh_begin(h); k != kh_end(h); ++k) + for (k = 0; k != kh_end(h); ++k) { if (kh_exist(h, k)) // test if a bucket contains data { @@ -1308,7 +1309,7 @@ void get_peak_debug(Total_Count_Table* TCB, long long* min, long long* max) ///get_Total_Count_Table(&TCB, &k_code, k_mer_length); - c_count = kh_value(h, k); + c_count = kh_val(h, k); if(get_Total_Count_Table(TCB, &code, asm_opt.k_mer_length) != c_count) { @@ -1436,7 +1437,7 @@ void get_peak(Total_Count_Table* TCB, long long* min, long long* max, long long* for (i = 0; i < TCB->size; i++) { h = TCB->sub_h[i]; - for (k = kh_begin(h); k != kh_end(h); ++k) + for (k = 0; k != kh_end(h); ++k) { if (kh_exist(h, k)) // test if a bucket contains data { @@ -1548,7 +1549,7 @@ void Traverse_Counting_Table(Total_Count_Table* TCB, Total_Pos_Table* PCB, int k for (i = 0; i < TCB->size; i++) { h = TCB->sub_h[i]; - for (k = kh_begin(h); k != kh_end(h); ++k) + for (k = 0; k != kh_end(h); ++k) { if (kh_exist(h, k)) // test if a bucket contains data { @@ -1558,22 +1559,22 @@ void Traverse_Counting_Table(Total_Count_Table* TCB, Total_Pos_Table* PCB, int k if (count>=k_mer_min_freq && count<=k_mer_max_freq) { - t = kh_put(POS64, PCB->sub_h[sub_ID], sub_key, &absent); + t = ha_pt_put(PCB->sub_h[sub_ID], sub_key, &absent); if (absent) { - ///kh_value(PCB->sub_h[sub_ID], t) = useful_k_mer + total_occ; - kh_value(PCB->sub_h[sub_ID], t) = PCB->useful_k_mer; + ///kh_val(PCB->sub_h[sub_ID], t) = useful_k_mer + total_occ; + kh_val(PCB->sub_h[sub_ID], t) = PCB->useful_k_mer; } else { - ///kh_value(PCB->sub_h[sub_ID], t)++; + ///kh_val(PCB->sub_h[sub_ID], t)++; fprintf(stderr, "ERROR\n"); } PCB->useful_k_mer++; - PCB->total_occ = PCB->total_occ + kh_value(h, k); + PCB->total_occ = PCB->total_occ + kh_val(h, k); } } } @@ -1593,7 +1594,7 @@ void Traverse_Counting_Table(Total_Count_Table* TCB, Total_Pos_Table* PCB, int k for (i = 0; i < TCB->size; i++) { h = TCB->sub_h[i]; - for (k = kh_begin(h); k != kh_end(h); ++k) + for (k = 0; k != kh_end(h); ++k) { if (kh_exist(h, k)) // test if a bucket contains data { @@ -1601,11 +1602,11 @@ void Traverse_Counting_Table(Total_Count_Table* TCB, Total_Pos_Table* PCB, int k sub_key = kh_key(h, k); get_total_freq(TCB, sub_ID, sub_key, &count); - ///if (kh_value(h, k)>=k_mer_min_freq && kh_value(h, k)<=k_mer_max_freq) + ///if (kh_val(h, k)>=k_mer_min_freq && kh_val(h, k)<=k_mer_max_freq) if (count>=k_mer_min_freq && count<=k_mer_max_freq) { PCB->useful_k_mer++; - PCB->total_occ = PCB->total_occ + kh_value(h, k); + PCB->total_occ = PCB->total_occ + kh_val(h, k); PCB->k_mer_index[PCB->useful_k_mer] = PCB->total_occ; } } @@ -1849,4 +1850,4 @@ void resize_window_list_alloc(window_list_alloc* x, long long size) x->length = 0; -} \ No newline at end of file +} diff --git a/Hash_Table.h b/Hash_Table.h index 29f8827..cff1453 100644 --- a/Hash_Table.h +++ b/Hash_Table.h @@ -1,13 +1,10 @@ #ifndef __HASHTABLE__ #define __HASHTABLE__ -#include "khash.h" +#include "khashl.h" #include "kmer.h" -KHASH_MAP_INIT_INT64(COUNT64, int) -typedef khash_t(COUNT64) Count_Table; - -KHASH_MAP_INIT_INT64(POS64, uint64_t) -typedef khash_t(POS64) Pos_Table; +KHASHL_MAP_INIT(static inline, Count_Table, ha_ct, uint64_t, int, kh_hash_dummy, kh_eq_generic) +KHASHL_MAP_INIT(static inline, Pos_Table, ha_pt, uint64_t, uint64_t, kh_hash_dummy, kh_eq_generic) #define PREFIX_BITS 16 #define MAX_SUFFIX_BITS 64 @@ -295,15 +292,15 @@ inline int insert_Total_Count_Table(Total_Count_Table* TCB, Hash_code* code, int while (TCB->sub_h_lock[sub_ID].lock); } - t = kh_put(COUNT64, TCB->sub_h[sub_ID], sub_key, &absent); + t = ha_ct_put(TCB->sub_h[sub_ID], sub_key, &absent); if (absent) { - kh_value(TCB->sub_h[sub_ID], t) = 1; + kh_val(TCB->sub_h[sub_ID], t) = 1; } else { //kh_value(TCB->sub_h[sub_ID], t) = kh_value(TCB->sub_h[sub_ID], t) + 1; - kh_value(TCB->sub_h[sub_ID], t)++; + kh_val(TCB->sub_h[sub_ID], t)++; } __sync_lock_release(&TCB->sub_h_lock[sub_ID].lock); @@ -323,11 +320,11 @@ inline int get_Total_Count_Table(Total_Count_Table* TCB, Hash_code* code, int k) khint_t t; ///query hash table，key is k - t = kh_get(COUNT64, TCB->sub_h[sub_ID], sub_key); + t = ha_ct_get(TCB->sub_h[sub_ID], sub_key); if (t != kh_end(TCB->sub_h[sub_ID])) { - return kh_value(TCB->sub_h[sub_ID], t); + return kh_val(TCB->sub_h[sub_ID], t); } else { @@ -351,12 +348,12 @@ inline uint64_t get_Total_Pos_Table(Total_Pos_Table* PCB, Hash_code* code, int k khint_t t; ///query hash table，key is k - t = kh_get(POS64, PCB->sub_h[sub_ID], sub_key); + t = ha_pt_get(PCB->sub_h[sub_ID], sub_key); if (t != kh_end(PCB->sub_h[sub_ID])) { *r_sub_ID = sub_ID; - return kh_value(PCB->sub_h[sub_ID], t); + return kh_val(PCB->sub_h[sub_ID], t); } else { diff --git a/Makefile b/Makefile index 59d1aef..d8e1773 100644 --- a/Makefile +++ b/Makefile @@ -31,26 +31,27 @@ depend: # DO NOT DELETE -Assembly.o: Assembly.h Process_Read.h kseq.h Overlaps.h kvec.h kdq.h -Assembly.o: CommandLines.h kmer.h Hash_Table.h khash.h POA.h Correct.h +Assembly.o: Assembly.h CommandLines.h Process_Read.h kseq.h Overlaps.h kvec.h +Assembly.o: kdq.h kmer.h Hash_Table.h khashl.h POA.h Correct.h Assembly.o: Levenshtein_distance.h Output.h Trio.h CommandLines.o: CommandLines.h ketopt.h -Correct.o: Correct.h Hash_Table.h khash.h kmer.h Process_Read.h kseq.h +Correct.o: Correct.h Hash_Table.h khashl.h kmer.h Process_Read.h kseq.h Correct.o: Overlaps.h kvec.h kdq.h CommandLines.h Levenshtein_distance.h -Correct.o: POA.h Assembly.h #ksw2.h -Hash_Table.o: Hash_Table.h khash.h kmer.h Process_Read.h kseq.h Overlaps.h +Correct.o: POA.h Assembly.h +Hash_Table.o: Hash_Table.h khashl.h kmer.h Process_Read.h kseq.h Overlaps.h Hash_Table.o: kvec.h kdq.h CommandLines.h Correct.h Levenshtein_distance.h Hash_Table.o: POA.h ksort.h Levenshtein_distance.o: Levenshtein_distance.h Output.o: Output.h CommandLines.h Overlaps.o: Overlaps.h kvec.h kdq.h ksort.h Process_Read.h kseq.h -Overlaps.o: CommandLines.h -POA.o: POA.h Hash_Table.h khash.h kmer.h Process_Read.h kseq.h Overlaps.h +Overlaps.o: CommandLines.h Hash_Table.h khashl.h kmer.h Correct.h +Overlaps.o: Levenshtein_distance.h POA.h +POA.o: POA.h Hash_Table.h khashl.h kmer.h Process_Read.h kseq.h Overlaps.h POA.o: kvec.h kdq.h CommandLines.h Correct.h Levenshtein_distance.h Process_Read.o: Process_Read.h kseq.h Overlaps.h kvec.h kdq.h CommandLines.h +Trio.o: khashl.h kthread.h Process_Read.h kseq.h Overlaps.h kvec.h kdq.h +Trio.o: CommandLines.h Trio.h kmer.o: kmer.h Process_Read.h kseq.h Overlaps.h kvec.h kdq.h CommandLines.h +kthread.o: kthread.h main.o: CommandLines.h Process_Read.h kseq.h Overlaps.h kvec.h kdq.h main.o: Assembly.h Levenshtein_distance.h -Trio.o: Trio.h khashl.h kthread.h Process_Read.h CommandLines.h -kthread.o: kthread.h -#ksw2_extz2_sse.o: ksw2.h \ No newline at end of file diff --git a/khash.h b/khash.h deleted file mode 100644 index 71b1e3e..0000000 --- a/khash.h +++ /dev/null @@ -1,669 +0,0 @@ -/* The MIT License - - Copyright (c) 2008, 2009, 2011 by Attractive Chaos - - Permission is hereby granted, free of charge, to any person obtaining - a copy of this software and associated documentation files (the - "Software"), to deal in the Software without restriction, including - without limitation the rights to use, copy, modify, merge, publish, - distribute, sublicense, and/or sell copies of the Software, and to - permit persons to whom the Software is furnished to do so, subject to - the following conditions: - - The above copyright notice and this permission notice shall be - included in all copies or substantial portions of the Software. - - THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, - EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF - MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND - NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS - BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN - ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN - CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE - SOFTWARE. -*/ - -/* - An example: - -#include "khash.h" -KHASH_MAP_INIT_INT(32, char) -int main() { - int ret, is_missing; - khiter_t k; - khash_t(32) *h = kh_init(32); - k = kh_put(32, h, 5, &ret); - kh_value(h, k) = 10; - k = kh_get(32, h, 10); - is_missing = (k == kh_end(h)); - k = kh_get(32, h, 5); - kh_del(32, h, k); - for (k = kh_begin(h); k != kh_end(h); ++k) - if (kh_exist(h, k)) kh_value(h, k) = 1; - kh_destroy(32, h); - return 0; -} -*/ - -/* - 2013-05-02 (0.2.8): - - * Use quadratic probing. When the capacity is power of 2, stepping function - i*(i+1)/2 guarantees to traverse each bucket. It is better than double - hashing on cache performance and is more robust than linear probing. - - In theory, double hashing should be more robust than quadratic probing. - However, my implementation is probably not for large hash tables, because - the second hash function is closely tied to the first hash function, - which reduce the effectiveness of double hashing. - - Reference: http://research.cs.vt.edu/AVresearch/hashing/quadratic.php - - 2011-12-29 (0.2.7): - - * Minor code clean up; no actual effect. - - 2011-09-16 (0.2.6): - - * The capacity is a power of 2. This seems to dramatically improve the - speed for simple keys. Thank Zilong Tan for the suggestion. Reference: - - - http://code.google.com/p/ulib/ - - http://nothings.org/computer/judy/ - - * Allow to optionally use linear probing which usually has better - performance for random input. Double hashing is still the default as it - is more robust to certain non-random input. - - * Added Wang's integer hash function (not used by default). This hash - function is more robust to certain non-random input. - - 2011-02-14 (0.2.5): - - * Allow to declare global functions. - - 2009-09-26 (0.2.4): - - * Improve portability - - 2008-09-19 (0.2.3): - - * Corrected the example - * Improved interfaces - - 2008-09-11 (0.2.2): - - * Improved speed a little in kh_put() - - 2008-09-10 (0.2.1): - - * Added kh_clear() - * Fixed a compiling error - - 2008-09-02 (0.2.0): - - * Changed to token concatenation which increases flexibility. - - 2008-08-31 (0.1.2): - - * Fixed a bug in kh_get(), which has not been tested previously. - - 2008-08-31 (0.1.1): - - * Added destructor -*/ - - -#ifndef __AC_KHASH_H -#define __AC_KHASH_H - -/*! - @header - - Generic hash table library. - */ - -#define AC_VERSION_KHASH_H "0.2.8" - -#include -#include -#include -#include - - -/* compiler specific configuration */ - -#if UINT_MAX == 0xffffffffu -typedef unsigned int khint32_t; -#elif ULONG_MAX == 0xffffffffu -typedef unsigned long khint32_t; -#endif - -#if ULONG_MAX == ULLONG_MAX -typedef unsigned long khint64_t; -#else -typedef unsigned long long khint64_t; -#endif - -#ifndef kh_inline -#ifdef _MSC_VER -#define kh_inline __inline -#else -#define kh_inline inline -#endif -#endif /* kh_inline */ - -#ifndef klib_unused -#if (defined __clang__ && __clang_major__ >= 3) || (defined __GNUC__ && __GNUC__ >= 3) -#define klib_unused __attribute__ ((__unused__)) -#else -#define klib_unused -#endif -#endif /* klib_unused */ - -typedef khint32_t khint_t; -typedef khint_t khiter_t; - -#define __ac_isempty(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&2) -#define __ac_isdel(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&1) -#define __ac_iseither(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&3) -#define __ac_set_isdel_false(flag, i) (flag[i>>4]&=~(1ul<<((i&0xfU)<<1))) -#define __ac_set_isempty_false(flag, i) (flag[i>>4]&=~(2ul<<((i&0xfU)<<1))) -#define __ac_set_isboth_false(flag, i) (flag[i>>4]&=~(3ul<<((i&0xfU)<<1))) -#define __ac_set_isdel_true(flag, i) (flag[i>>4]|=1ul<<((i&0xfU)<<1)) - -#define __ac_fsize(m) ((m) < 16? 1 : (m)>>4) - -#ifndef kroundup32 -#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x)) -#endif - -#ifndef kcalloc -#define kcalloc(N,Z) calloc(N,Z) -#endif -#ifndef kmalloc -#define kmalloc(Z) malloc(Z) -#endif -#ifndef krealloc -#define krealloc(P,Z) realloc(P,Z) -#endif -#ifndef kfree -#define kfree(P) free(P) -#endif - -static const double __ac_HASH_UPPER = 0.77; - -#define __KHASH_TYPE(name, khkey_t, khval_t) \ - typedef struct kh_##name##_s { \ - khint_t n_buckets, size, n_occupied, upper_bound; \ - khint32_t *flags; \ - khkey_t *keys; \ - khval_t *vals; \ - } kh_##name##_t; - -#define __KHASH_PROTOTYPES(name, khkey_t, khval_t) \ - extern kh_##name##_t *kh_init_##name(void); \ - extern void kh_destroy_##name(kh_##name##_t *h); \ - extern void kh_clear_##name(kh_##name##_t *h); \ - extern khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key); \ - extern int kh_resize_##name(kh_##name##_t *h, khint_t new_n_buckets); \ - extern khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret); \ - extern void kh_del_##name(kh_##name##_t *h, khint_t x);\ - extern void kh_write_##name(kh_##name##_t *h, FILE* fp);\ - extern void kh_load_##name(kh_##name##_t *h, FILE* fp); - -#define __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) \ - SCOPE kh_##name##_t *kh_init_##name(void) { \ - return (kh_##name##_t*)kcalloc(1, sizeof(kh_##name##_t)); \ - } \ - SCOPE void kh_destroy_##name(kh_##name##_t *h) \ - { \ - if (h) { \ - kfree((void *)h->keys); kfree(h->flags); \ - kfree((void *)h->vals); \ - kfree(h); \ - } \ - } \ - SCOPE void kh_clear_##name(kh_##name##_t *h) \ - { \ - if (h && h->flags) { \ - memset(h->flags, 0xaa, __ac_fsize(h->n_buckets) * sizeof(khint32_t)); \ - h->size = h->n_occupied = 0; \ - } \ - } \ - SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ - { \ - if (h->n_buckets) { \ - khint_t k, i, last, mask, step = 0; \ - mask = h->n_buckets - 1; \ - k = __hash_func(key); i = k & mask; \ - last = i; \ - while (!__ac_isempty(h->flags, i) && (__ac_isdel(h->flags, i) || !__hash_equal(h->keys[i], key))) { \ - i = (i + (++step)) & mask; \ - if (i == last) return h->n_buckets; \ - } \ - return __ac_iseither(h->flags, i)? h->n_buckets : i; \ - } else return 0; \ - } \ - SCOPE int kh_resize_##name(kh_##name##_t *h, khint_t new_n_buckets) \ - { /* This function uses 0.25*n_buckets bytes of working space instead of [sizeof(key_t+val_t)+.25]*n_buckets. */ \ - khint32_t *new_flags = 0; \ - khint_t j = 1; \ - { \ - kroundup32(new_n_buckets); \ - if (new_n_buckets < 4) new_n_buckets = 4; \ - if (h->size >= (khint_t)(new_n_buckets * __ac_HASH_UPPER + 0.5)) j = 0; /* requested size is too small */ \ - else { /* hash table size to be changed (shrink or expand); rehash */ \ - new_flags = (khint32_t*)kmalloc(__ac_fsize(new_n_buckets) * sizeof(khint32_t)); \ - if (!new_flags) return -1; \ - memset(new_flags, 0xaa, __ac_fsize(new_n_buckets) * sizeof(khint32_t)); \ - if (h->n_buckets < new_n_buckets) { /* expand */ \ - khkey_t *new_keys = (khkey_t*)krealloc((void *)h->keys, new_n_buckets * sizeof(khkey_t)); \ - if (!new_keys) { kfree(new_flags); return -1; } \ - h->keys = new_keys; \ - if (kh_is_map) { \ - khval_t *new_vals = (khval_t*)krealloc((void *)h->vals, new_n_buckets * sizeof(khval_t)); \ - if (!new_vals) { kfree(new_flags); return -1; } \ - h->vals = new_vals; \ - } \ - } /* otherwise shrink */ \ - } \ - } \ - if (j) { /* rehashing is needed */ \ - for (j = 0; j != h->n_buckets; ++j) { \ - if (__ac_iseither(h->flags, j) == 0) { \ - khkey_t key = h->keys[j]; \ - khval_t val; \ - khint_t new_mask; \ - new_mask = new_n_buckets - 1; \ - if (kh_is_map) val = h->vals[j]; \ - __ac_set_isdel_true(h->flags, j); \ - while (1) { /* kick-out process; sort of like in Cuckoo hashing */ \ - khint_t k, i, step = 0; \ - k = __hash_func(key); \ - i = k & new_mask; \ - while (!__ac_isempty(new_flags, i)) i = (i + (++step)) & new_mask; \ - __ac_set_isempty_false(new_flags, i); \ - if (i < h->n_buckets && __ac_iseither(h->flags, i) == 0) { /* kick out the existing element */ \ - { khkey_t tmp = h->keys[i]; h->keys[i] = key; key = tmp; } \ - if (kh_is_map) { khval_t tmp = h->vals[i]; h->vals[i] = val; val = tmp; } \ - __ac_set_isdel_true(h->flags, i); /* mark it as deleted in the old hash table */ \ - } else { /* write the element and jump out of the loop */ \ - h->keys[i] = key; \ - if (kh_is_map) h->vals[i] = val; \ - break; \ - } \ - } \ - } \ - } \ - if (h->n_buckets > new_n_buckets) { /* shrink the hash table */ \ - h->keys = (khkey_t*)krealloc((void *)h->keys, new_n_buckets * sizeof(khkey_t)); \ - if (kh_is_map) h->vals = (khval_t*)krealloc((void *)h->vals, new_n_buckets * sizeof(khval_t)); \ - } \ - kfree(h->flags); /* free the working space */ \ - h->flags = new_flags; \ - h->n_buckets = new_n_buckets; \ - h->n_occupied = h->size; \ - h->upper_bound = (khint_t)(h->n_buckets * __ac_HASH_UPPER + 0.5); \ - } \ - return 0; \ - } \ - SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \ - { \ - khint_t x; \ - if (h->n_occupied >= h->upper_bound) { /* update the hash table */ \ - if (h->n_buckets > (h->size<<1)) { \ - if (kh_resize_##name(h, h->n_buckets - 1) < 0) { /* clear "deleted" elements */ \ - *ret = -1; return h->n_buckets; \ - } \ - } else if (kh_resize_##name(h, h->n_buckets + 1) < 0) { /* expand the hash table */ \ - *ret = -1; return h->n_buckets; \ - } \ - } /* TODO: to implement automatically shrinking; resize() already support shrinking */ \ - { \ - khint_t k, i, site, last, mask = h->n_buckets - 1, step = 0; \ - x = site = h->n_buckets; k = __hash_func(key); i = k & mask; \ - if (__ac_isempty(h->flags, i)) x = i; /* for speed up */ \ - else { \ - last = i; \ - while (!__ac_isempty(h->flags, i) && (__ac_isdel(h->flags, i) || !__hash_equal(h->keys[i], key))) { \ - if (__ac_isdel(h->flags, i)) site = i; \ - i = (i + (++step)) & mask; \ - if (i == last) { x = site; break; } \ - } \ - if (x == h->n_buckets) { \ - if (__ac_isempty(h->flags, i) && site != h->n_buckets) x = site; \ - else x = i; \ - } \ - } \ - } \ - if (__ac_isempty(h->flags, x)) { /* not present at all */ \ - h->keys[x] = key; \ - __ac_set_isboth_false(h->flags, x); \ - ++h->size; ++h->n_occupied; \ - *ret = 1; \ - } else if (__ac_isdel(h->flags, x)) { /* deleted */ \ - h->keys[x] = key; \ - __ac_set_isboth_false(h->flags, x); \ - ++h->size; \ - *ret = 2; \ - } else *ret = 0; /* Don't touch h->keys[x] if present and not deleted */ \ - return x; \ - } \ - SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ - { \ - if (x != h->n_buckets && !__ac_iseither(h->flags, x)) { \ - __ac_set_isdel_true(h->flags, x); \ - --h->size; \ - } \ - } \ - SCOPE void kh_write_##name(kh_##name##_t *h, FILE* fp)\ - {\ - fwrite(&(h->n_buckets), sizeof(khint_t), 1, fp);\ - fwrite(&(h->size), sizeof(khint_t), 1, fp);\ - fwrite(&(h->n_occupied), sizeof(khint_t), 1, fp);\ - fwrite(&(h->upper_bound), sizeof(khint_t), 1, fp);\ - if (h->n_buckets)\ - {\ - fwrite(h->flags, sizeof(khint32_t), __ac_fsize(h->n_buckets), fp);\ - fwrite(h->keys, sizeof(khkey_t), h->n_buckets, fp);\ - fwrite(h->vals, sizeof(khval_t), h->n_buckets, fp);\ - }\ - } \ - SCOPE void kh_load_##name(kh_##name##_t *h, FILE* fp)\ - {\ - int f_flag;\ - f_flag = fread(&(h->n_buckets), sizeof(khint_t), 1, fp);\ - f_flag += fread(&(h->size), sizeof(khint_t), 1, fp);\ - f_flag += fread(&(h->n_occupied), sizeof(khint_t), 1, fp);\ - f_flag += fread(&(h->upper_bound), sizeof(khint_t), 1, fp);\ - if (h->n_buckets)\ - {\ - h->flags = (khint32_t*)kmalloc(__ac_fsize(h->n_buckets) * sizeof(khint32_t));\ - f_flag += fread(h->flags, sizeof(khint32_t), __ac_fsize(h->n_buckets), fp);\ - h->keys = (khkey_t*)kmalloc(sizeof(khkey_t)*h->n_buckets);\ - f_flag += fread(h->keys, sizeof(khkey_t), h->n_buckets, fp);\ - h->vals = (khval_t*)kmalloc(sizeof(khval_t)*h->n_buckets);\ - f_flag += fread(h->vals, sizeof(khval_t), h->n_buckets, fp);\ - }\ - } - -#define KHASH_DECLARE(name, khkey_t, khval_t) \ - __KHASH_TYPE(name, khkey_t, khval_t) \ - __KHASH_PROTOTYPES(name, khkey_t, khval_t) - -#define KHASH_INIT2(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) \ - __KHASH_TYPE(name, khkey_t, khval_t) \ - __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) - -#define KHASH_INIT(name, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) \ - KHASH_INIT2(name, static kh_inline klib_unused, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) - -/* --- BEGIN OF HASH FUNCTIONS --- */ - -/*! @function - @abstract Integer hash function - @param key The integer [khint32_t] - @return The hash value [khint_t] - */ -#define kh_int_hash_func(key) (khint32_t)(key) -/*! @function - @abstract Integer comparison function - */ -#define kh_int_hash_equal(a, b) ((a) == (b)) -/*! @function - @abstract 64-bit integer hash function - @param key The integer [khint64_t] - @return The hash value [khint_t] - */ -#define kh_int64_hash_func(key) (khint32_t)((key)>>33^(key)^(key)<<11) -/*! @function - @abstract 64-bit integer comparison function - */ -#define kh_int64_hash_equal(a, b) ((a) == (b)) -/*! @function - @abstract const char* hash function - @param s Pointer to a null terminated string - @return The hash value - */ -static kh_inline khint_t __ac_X31_hash_string(const char *s) -{ - khint_t h = (khint_t)*s; - if (h) for (++s ; *s; ++s) h = (h << 5) - h + (khint_t)*s; - return h; -} -/*! @function - @abstract Another interface to const char* hash function - @param key Pointer to a null terminated string [const char*] - @return The hash value [khint_t] - */ -#define kh_str_hash_func(key) __ac_X31_hash_string(key) -/*! @function - @abstract Const char* comparison function - */ -#define kh_str_hash_equal(a, b) (strcmp(a, b) == 0) - -static kh_inline khint_t __ac_Wang_hash(khint_t key) -{ - key += ~(key << 15); - key ^= (key >> 10); - key += (key << 3); - key ^= (key >> 6); - key += ~(key << 11); - key ^= (key >> 16); - return key; -} -#define kh_int_hash_func2(key) __ac_Wang_hash((khint_t)key) - -/* --- END OF HASH FUNCTIONS --- */ - -/* Other convenient macros... */ - -/*! - @abstract Type of the hash table. - @param name Name of the hash table [symbol] - */ -#define khash_t(name) kh_##name##_t - -/*! @function - @abstract Initiate a hash table. - @param name Name of the hash table [symbol] - @return Pointer to the hash table [khash_t(name)*] - */ -#define kh_init(name) kh_init_##name() - -/*! @function - @abstract Destroy a hash table. - @param name Name of the hash table [symbol] - @param h Pointer to the hash table [khash_t(name)*] - */ -#define kh_destroy(name, h) kh_destroy_##name(h) - -/*! @function - @abstract Reset a hash table without deallocating memory. - @param name Name of the hash table [symbol] - @param h Pointer to the hash table [khash_t(name)*] - */ -#define kh_clear(name, h) kh_clear_##name(h) - -/*! @function - @abstract Resize a hash table. - @param name Name of the hash table [symbol] - @param h Pointer to the hash table [khash_t(name)*] - @param s New size [khint_t] - */ -#define kh_resize(name, h, s) kh_resize_##name(h, s) - -/*! @function - @abstract Insert a key to the hash table. - @param name Name of the hash table [symbol] - @param h Pointer to the hash table [khash_t(name)*] - @param k Key [type of keys] - @param r Extra return code: -1 if the operation failed; - 0 if the key is present in the hash table; - 1 if the bucket is empty (never used); 2 if the element in - the bucket has been deleted [int*] - @return Iterator to the inserted element [khint_t] - */ -#define kh_put(name, h, k, r) kh_put_##name(h, k, r) - -/*! @function - @abstract Retrieve a key from the hash table. - @param name Name of the hash table [symbol] - @param h Pointer to the hash table [khash_t(name)*] - @param k Key [type of keys] - @return Iterator to the found element, or kh_end(h) if the element is absent [khint_t] - */ -#define kh_get(name, h, k) kh_get_##name(h, k) - -/*! @function - @abstract Remove a key from the hash table. - @param name Name of the hash table [symbol] - @param h Pointer to the hash table [khash_t(name)*] - @param k Iterator to the element to be deleted [khint_t] - */ -#define kh_del(name, h, k) kh_del_##name(h, k) - -/*! @function - @abstract Test whether a bucket contains data. - @param h Pointer to the hash table [khash_t(name)*] - @param x Iterator to the bucket [khint_t] - @return 1 if containing data; 0 otherwise [int] - */ -#define kh_exist(h, x) (!__ac_iseither((h)->flags, (x))) - -/*! @function - @abstract Get key given an iterator - @param h Pointer to the hash table [khash_t(name)*] - @param x Iterator to the bucket [khint_t] - @return Key [type of keys] - */ -#define kh_key(h, x) ((h)->keys[x]) - -/*! @function - @abstract Get value given an iterator - @param h Pointer to the hash table [khash_t(name)*] - @param x Iterator to the bucket [khint_t] - @return Value [type of values] - @discussion For hash sets, calling this results in segfault. - */ -#define kh_val(h, x) ((h)->vals[x]) - -/*! @function - @abstract Alias of kh_val() - */ -#define kh_value(h, x) ((h)->vals[x]) - -/*! @function - @abstract Get the start iterator - @param h Pointer to the hash table [khash_t(name)*] - @return The start iterator [khint_t] - */ -#define kh_begin(h) (khint_t)(0) - -/*! @function - @abstract Get the end iterator - @param h Pointer to the hash table [khash_t(name)*] - @return The end iterator [khint_t] - */ -#define kh_end(h) ((h)->n_buckets) - -/*! @function - @abstract Get the number of elements in the hash table - @param h Pointer to the hash table [khash_t(name)*] - @return Number of elements in the hash table [khint_t] - */ -#define kh_size(h) ((h)->size) - -/*! @function - @abstract Get the number of buckets in the hash table - @param h Pointer to the hash table [khash_t(name)*] - @return Number of buckets in the hash table [khint_t] - */ -#define kh_n_buckets(h) ((h)->n_buckets) - -/*! @function - @abstract Iterate over the entries in the hash table - @param h Pointer to the hash table [khash_t(name)*] - @param kvar Variable to which key will be assigned - @param vvar Variable to which value will be assigned - @param code Block of code to execute - */ -#define kh_foreach(h, kvar, vvar, code) { khint_t __i; \ - for (__i = kh_begin(h); __i != kh_end(h); ++__i) { \ - if (!kh_exist(h,__i)) continue; \ - (kvar) = kh_key(h,__i); \ - (vvar) = kh_val(h,__i); \ - code; \ - } } - -/*! @function - @abstract Iterate over the values in the hash table - @param h Pointer to the hash table [khash_t(name)*] - @param vvar Variable to which value will be assigned - @param code Block of code to execute - */ -#define kh_foreach_value(h, vvar, code) { khint_t __i; \ - for (__i = kh_begin(h); __i != kh_end(h); ++__i) { \ - if (!kh_exist(h,__i)) continue; \ - (vvar) = kh_val(h,__i); \ - code; \ - } } - -/* More convenient interfaces */ - -/*! @function - @abstract Instantiate a hash set containing integer keys - @param name Name of the hash table [symbol] - */ -#define KHASH_SET_INIT_INT(name) \ - KHASH_INIT(name, khint32_t, char, 0, kh_int_hash_func, kh_int_hash_equal) - -/*! @function - @abstract Instantiate a hash map containing integer keys - @param name Name of the hash table [symbol] - @param khval_t Type of values [type] - */ -#define KHASH_MAP_INIT_INT(name, khval_t) \ - KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) - -/*! @function - @abstract Instantiate a hash set containing 64-bit integer keys - @param name Name of the hash table [symbol] - */ -#define KHASH_SET_INIT_INT64(name) \ - KHASH_INIT(name, khint64_t, char, 0, kh_int64_hash_func, kh_int64_hash_equal) - -/*! @function - @abstract Instantiate a hash map containing 64-bit integer keys - @param name Name of the hash table [symbol] - @param khval_t Type of values [type] - */ -#define KHASH_MAP_INIT_INT64(name, khval_t) \ - KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal) - -typedef const char *kh_cstr_t; -/*! @function - @abstract Instantiate a hash map containing const char* keys - @param name Name of the hash table [symbol] - */ -#define KHASH_SET_INIT_STR(name) \ - KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal) - -/*! @function - @abstract Instantiate a hash map containing const char* keys - @param name Name of the hash table [symbol] - @param khval_t Type of values [type] - */ -#define KHASH_MAP_INIT_STR(name, khval_t) \ - KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) - - - - -#define kh_write(name, h, fp) kh_write_##name(h, fp) - -#define kh_load(name, h, fp) kh_load_##name(h, fp) - - -#endif /* __AC_KHASH_H */