mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-09-25 04:18:11 +08:00
replaced khash with khashl
This commit is contained in:
Heng Li
+19
-18
@@ -1016,12 +1016,12 @@ void merge_k_mer_pos_list_alloc_heap_sort(k_mer_pos_list_alloc* list, Candidates
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void init_Count_Table(Count_Table** table)
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{
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*table = kh_init(COUNT64);
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*table = ha_ct_init();
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}
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void init_Pos_Table(Pos_Table** table)
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{
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*table = kh_init(POS64);
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*table = ha_pt_init();
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}
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void init_Total_Count_Table(int k, Total_Count_Table* TCB)
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@@ -1091,7 +1091,7 @@ void destory_Total_Count_Table(Total_Count_Table* TCB)
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int i;
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for (i = 0; i < TCB->size; i++)
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{
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kh_destroy(COUNT64, TCB->sub_h[i]);
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ha_ct_destroy(TCB->sub_h[i]);
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}
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free(TCB->sub_h);
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free(TCB->sub_h_lock);
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@@ -1107,12 +1107,12 @@ void destory_Total_Pos_Table(Total_Pos_Table* TCB)
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int i;
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for (i = 0; i < TCB->size; i++)
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{
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kh_destroy(POS64, TCB->sub_h[i]);
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ha_pt_destroy(TCB->sub_h[i]);
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}
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free(TCB->sub_h);
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}
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/*
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void write_Total_Pos_Table(Total_Pos_Table* TCB, char* read_file_name)
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{
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fprintf(stderr, "Writing index to disk... \n");
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@@ -1212,6 +1212,7 @@ int load_Total_Pos_Table(Total_Pos_Table* TCB, char* read_file_name)
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return 1;
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}
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*/
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typedef struct
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{
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@@ -1268,7 +1269,7 @@ void get_peak_debug(Total_Count_Table* TCB, long long* min, long long* max)
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for (i = 0; i < TCB->size; i++)
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{
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h = TCB->sub_h[i];
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for (k = kh_begin(h); k != kh_end(h); ++k)
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for (k = 0; k != kh_end(h); ++k)
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{
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if (kh_exist(h, k)) // test if a bucket contains data
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{
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@@ -1308,7 +1309,7 @@ void get_peak_debug(Total_Count_Table* TCB, long long* min, long long* max)
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///get_Total_Count_Table(&TCB, &k_code, k_mer_length);
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c_count = kh_value(h, k);
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c_count = kh_val(h, k);
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if(get_Total_Count_Table(TCB, &code, asm_opt.k_mer_length) != c_count)
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{
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@@ -1436,7 +1437,7 @@ void get_peak(Total_Count_Table* TCB, long long* min, long long* max, long long*
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for (i = 0; i < TCB->size; i++)
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{
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h = TCB->sub_h[i];
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for (k = kh_begin(h); k != kh_end(h); ++k)
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for (k = 0; k != kh_end(h); ++k)
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{
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if (kh_exist(h, k)) // test if a bucket contains data
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{
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@@ -1548,7 +1549,7 @@ void Traverse_Counting_Table(Total_Count_Table* TCB, Total_Pos_Table* PCB, int k
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for (i = 0; i < TCB->size; i++)
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{
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h = TCB->sub_h[i];
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for (k = kh_begin(h); k != kh_end(h); ++k)
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for (k = 0; k != kh_end(h); ++k)
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{
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if (kh_exist(h, k)) // test if a bucket contains data
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{
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@@ -1558,22 +1559,22 @@ void Traverse_Counting_Table(Total_Count_Table* TCB, Total_Pos_Table* PCB, int k
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if (count>=k_mer_min_freq && count<=k_mer_max_freq)
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{
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t = kh_put(POS64, PCB->sub_h[sub_ID], sub_key, &absent);
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t = ha_pt_put(PCB->sub_h[sub_ID], sub_key, &absent);
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if (absent)
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{
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///kh_value(PCB->sub_h[sub_ID], t) = useful_k_mer + total_occ;
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kh_value(PCB->sub_h[sub_ID], t) = PCB->useful_k_mer;
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///kh_val(PCB->sub_h[sub_ID], t) = useful_k_mer + total_occ;
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kh_val(PCB->sub_h[sub_ID], t) = PCB->useful_k_mer;
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}
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else
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{
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///kh_value(PCB->sub_h[sub_ID], t)++;
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///kh_val(PCB->sub_h[sub_ID], t)++;
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fprintf(stderr, "ERROR\n");
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}
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PCB->useful_k_mer++;
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PCB->total_occ = PCB->total_occ + kh_value(h, k);
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PCB->total_occ = PCB->total_occ + kh_val(h, k);
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}
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}
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}
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@@ -1593,7 +1594,7 @@ void Traverse_Counting_Table(Total_Count_Table* TCB, Total_Pos_Table* PCB, int k
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for (i = 0; i < TCB->size; i++)
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{
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h = TCB->sub_h[i];
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for (k = kh_begin(h); k != kh_end(h); ++k)
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for (k = 0; k != kh_end(h); ++k)
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{
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if (kh_exist(h, k)) // test if a bucket contains data
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{
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@@ -1601,11 +1602,11 @@ void Traverse_Counting_Table(Total_Count_Table* TCB, Total_Pos_Table* PCB, int k
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sub_key = kh_key(h, k);
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get_total_freq(TCB, sub_ID, sub_key, &count);
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///if (kh_value(h, k)>=k_mer_min_freq && kh_value(h, k)<=k_mer_max_freq)
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///if (kh_val(h, k)>=k_mer_min_freq && kh_val(h, k)<=k_mer_max_freq)
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if (count>=k_mer_min_freq && count<=k_mer_max_freq)
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{
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PCB->useful_k_mer++;
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PCB->total_occ = PCB->total_occ + kh_value(h, k);
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PCB->total_occ = PCB->total_occ + kh_val(h, k);
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PCB->k_mer_index[PCB->useful_k_mer] = PCB->total_occ;
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}
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}
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@@ -1849,4 +1850,4 @@ void resize_window_list_alloc(window_list_alloc* x, long long size)
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x->length = 0;
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}
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}
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+10
-13
@@ -1,13 +1,10 @@
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#ifndef __HASHTABLE__
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#define __HASHTABLE__
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#include "khash.h"
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#include "khashl.h"
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#include "kmer.h"
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KHASH_MAP_INIT_INT64(COUNT64, int)
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typedef khash_t(COUNT64) Count_Table;
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KHASH_MAP_INIT_INT64(POS64, uint64_t)
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typedef khash_t(POS64) Pos_Table;
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KHASHL_MAP_INIT(static inline, Count_Table, ha_ct, uint64_t, int, kh_hash_dummy, kh_eq_generic)
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KHASHL_MAP_INIT(static inline, Pos_Table, ha_pt, uint64_t, uint64_t, kh_hash_dummy, kh_eq_generic)
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#define PREFIX_BITS 16
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#define MAX_SUFFIX_BITS 64
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@@ -295,15 +292,15 @@ inline int insert_Total_Count_Table(Total_Count_Table* TCB, Hash_code* code, int
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while (TCB->sub_h_lock[sub_ID].lock);
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}
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t = kh_put(COUNT64, TCB->sub_h[sub_ID], sub_key, &absent);
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t = ha_ct_put(TCB->sub_h[sub_ID], sub_key, &absent);
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if (absent)
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{
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kh_value(TCB->sub_h[sub_ID], t) = 1;
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kh_val(TCB->sub_h[sub_ID], t) = 1;
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}
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else
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{
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//kh_value(TCB->sub_h[sub_ID], t) = kh_value(TCB->sub_h[sub_ID], t) + 1;
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kh_value(TCB->sub_h[sub_ID], t)++;
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kh_val(TCB->sub_h[sub_ID], t)++;
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}
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__sync_lock_release(&TCB->sub_h_lock[sub_ID].lock);
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@@ -323,11 +320,11 @@ inline int get_Total_Count_Table(Total_Count_Table* TCB, Hash_code* code, int k)
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khint_t t;
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///query hash table，key is k
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t = kh_get(COUNT64, TCB->sub_h[sub_ID], sub_key);
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t = ha_ct_get(TCB->sub_h[sub_ID], sub_key);
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if (t != kh_end(TCB->sub_h[sub_ID]))
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{
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return kh_value(TCB->sub_h[sub_ID], t);
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return kh_val(TCB->sub_h[sub_ID], t);
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}
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else
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{
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@@ -351,12 +348,12 @@ inline uint64_t get_Total_Pos_Table(Total_Pos_Table* PCB, Hash_code* code, int k
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khint_t t;
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///query hash table，key is k
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t = kh_get(POS64, PCB->sub_h[sub_ID], sub_key);
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t = ha_pt_get(PCB->sub_h[sub_ID], sub_key);
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if (t != kh_end(PCB->sub_h[sub_ID]))
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{
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*r_sub_ID = sub_ID;
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return kh_value(PCB->sub_h[sub_ID], t);
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return kh_val(PCB->sub_h[sub_ID], t);
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}
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else
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{
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@@ -31,26 +31,27 @@ depend:
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# DO NOT DELETE
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Assembly.o: Assembly.h Process_Read.h kseq.h Overlaps.h kvec.h kdq.h
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Assembly.o: CommandLines.h kmer.h Hash_Table.h khash.h POA.h Correct.h
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Assembly.o: Assembly.h CommandLines.h Process_Read.h kseq.h Overlaps.h kvec.h
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Assembly.o: kdq.h kmer.h Hash_Table.h khashl.h POA.h Correct.h
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Assembly.o: Levenshtein_distance.h Output.h Trio.h
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CommandLines.o: CommandLines.h ketopt.h
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Correct.o: Correct.h Hash_Table.h khash.h kmer.h Process_Read.h kseq.h
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Correct.o: Correct.h Hash_Table.h khashl.h kmer.h Process_Read.h kseq.h
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Correct.o: Overlaps.h kvec.h kdq.h CommandLines.h Levenshtein_distance.h
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Correct.o: POA.h Assembly.h #ksw2.h
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Hash_Table.o: Hash_Table.h khash.h kmer.h Process_Read.h kseq.h Overlaps.h
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Correct.o: POA.h Assembly.h
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Hash_Table.o: Hash_Table.h khashl.h kmer.h Process_Read.h kseq.h Overlaps.h
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Hash_Table.o: kvec.h kdq.h CommandLines.h Correct.h Levenshtein_distance.h
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Hash_Table.o: POA.h ksort.h
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Levenshtein_distance.o: Levenshtein_distance.h
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Output.o: Output.h CommandLines.h
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Overlaps.o: Overlaps.h kvec.h kdq.h ksort.h Process_Read.h kseq.h
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Overlaps.o: CommandLines.h
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POA.o: POA.h Hash_Table.h khash.h kmer.h Process_Read.h kseq.h Overlaps.h
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Overlaps.o: CommandLines.h Hash_Table.h khashl.h kmer.h Correct.h
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Overlaps.o: Levenshtein_distance.h POA.h
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POA.o: POA.h Hash_Table.h khashl.h kmer.h Process_Read.h kseq.h Overlaps.h
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POA.o: kvec.h kdq.h CommandLines.h Correct.h Levenshtein_distance.h
|
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Process_Read.o: Process_Read.h kseq.h Overlaps.h kvec.h kdq.h CommandLines.h
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Trio.o: khashl.h kthread.h Process_Read.h kseq.h Overlaps.h kvec.h kdq.h
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Trio.o: CommandLines.h Trio.h
|
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kmer.o: kmer.h Process_Read.h kseq.h Overlaps.h kvec.h kdq.h CommandLines.h
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kthread.o: kthread.h
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main.o: CommandLines.h Process_Read.h kseq.h Overlaps.h kvec.h kdq.h
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main.o: Assembly.h Levenshtein_distance.h
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Trio.o: Trio.h khashl.h kthread.h Process_Read.h CommandLines.h
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kthread.o: kthread.h
|
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#ksw2_extz2_sse.o: ksw2.h
|
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@@ -1,669 +0,0 @@
|
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/* The MIT License
|
||||
|
||||
Copyright (c) 2008, 2009, 2011 by Attractive Chaos <attractor@live.co.uk>
|
||||
|
||||
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"
|
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KHASH_MAP_INIT_INT(32, char)
|
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int main() {
|
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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,
|
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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 <stdlib.h>
|
||||
#include <string.h>
|
||||
#include <limits.h>
|
||||
#include <stdio.h>
|
||||
|
||||
|
||||
/* 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 */
|
||||
Reference in New Issue
Block a user