Mercurial > repos > dawe > srf2fastq

comparison srf2fastq/io_lib-1.12.2/io_lib/deflate_interlaced.h @ 0:d901c9f41a6a default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
author dawe
date Tue, 07 Jun 2011 17:48:05 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:d901c9f41a6a
1 #ifndef _DEFLATE_SIMPLE_H_
2 #define _DEFLATE_SIMPLE_H_
3
4 #ifdef __cplusplus
5 extern "C" {
6 #endif
7
8 /* inlined codes */
9 #define CODE_INLINE 0
10
11 /* predefined codes */
12 #define CODE_DNA 1 /* DNA, uppercase only */
13 #define CODE_DNA_AMBIG 2 /* DNA, uc with ambiguity codes */
14 #define CODE_ENGLISH 3 /* English text */
15 #define NCODES_STATIC 4 /* Cheat, but we count from 0 for ease */
16
17 /* predefined elsewhere in HUFF chunks, 128 onwards */
18 #define CODE_USER 128
19
20 #define MAX_CODE_LEN 15 /* maximum allowed by RFC 1951 */
21
22 #ifndef ZTR_FORM_STHUFF
23 # define ZTR_FORM_STHUFF 77
24 #endif
25
26 /* A single symbol and it's encoding */
27 typedef struct {
28 signed int symbol; /* 0-255 character, 256 = exception code, 257 = EOF */
29 int nbits;
30 unsigned int code;
31 int freq;
32 } huffman_code_t;
33
34 /* A collection of huffman_code_t along with decoding optimisations */
35 typedef struct {
36 huffman_code_t *codes;
37 int ncodes;
38 int codes_static;
39 huffman_code_t lookup[258]; /* Mapping of symbol character to code */
40 int max_code_len;
41 } huffman_codes_t;
42
43 /* Use for store_bits() and get_bits() */
44 typedef struct block {
45 unsigned char *data;
46 size_t alloc;
47 size_t byte;
48 int bit;
49 } block_t;
50
51 /* Tree and jump-table data structures used for fast decoding. */
52 typedef struct {
53 /* Graph construction */
54 unsigned short c[2]; /* child node */
55 signed short l[2]; /* symbol to emit on transition. -1 => none */
56 } htree_t;
57
58 typedef struct {
59 /* Byte-wise jumping table */
60 unsigned short jump;
61 unsigned char symbol[4];
62 unsigned char nsymbols;
63 unsigned char top_bit; /* bit 9 of symbol[] */
64 } h_jump4_t;
65
66
67 /* A collection of huffman_codes_t, for use with the multi-code codec */
68 typedef struct {
69 huffman_codes_t **codes;
70 int ncodes;
71 int code_set; /* (128-255) The user specified number for this encoding */
72
73 /* Cached binary version of codeset, assumes last block */
74 block_t *blk;
75 int bit_num; /* if 1st block, which bit will stored codes end on */
76
77 /* Cache huffman_multi_decode parameters */
78 h_jump4_t (*decode_J4)[16];
79 htree_t *decode_t;
80 } huffman_codeset_t;
81
82 block_t *block_create(unsigned char *data, size_t size);
83 void block_destroy(block_t *blk, int keep_data);
84 int block_resize(block_t *blk, size_t size);
85 void store_bytes(block_t *block, unsigned char *val, int nbytes);
86
87
88 int huffman_encode(block_t *blk, huffman_codes_t *c, int code_set,
89 unsigned char *data, int len);
90
91 block_t *huffman_decode(block_t *in, huffman_codes_t *c);
92
93 int huffman_multi_encode(block_t *blk, huffman_codeset_t *cs,
94 int code_set, unsigned char *data, int len);
95
96 block_t *huffman_multi_decode(block_t *in, huffman_codeset_t *cs);
97
98 huffman_codeset_t *codes2codeset(huffman_code_t *codes, int ncodes,
99 int code_num);
100 huffman_codeset_t *generate_code_set(int code_set, int ncodes,
101 unsigned char *data, int len,
102 int eof, int max_code_len,
103 int all_codes);
104
105 int store_codes(block_t *out,
106 huffman_codeset_t *c,
107 int last_block);
108 huffman_codeset_t *restore_codes(block_t *block, int *bfinal);
109 void huffman_codes_destroy(huffman_codes_t *c);
110 void huffman_codeset_destroy(huffman_codeset_t *cs);
111
112 #ifdef __cplusplus
113 }
114 #endif
115
116 #endif /* _DEFLATE_SIMPLE_H_ */