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

Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/deflate_interlaced.h	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,116 @@
+#ifndef _DEFLATE_SIMPLE_H_
+#define _DEFLATE_SIMPLE_H_
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/* inlined codes */
+#define CODE_INLINE	  0   
+
+/* predefined codes */
+#define CODE_DNA	  1   /* DNA, uppercase only */
+#define CODE_DNA_AMBIG	  2   /* DNA, uc with ambiguity codes */
+#define CODE_ENGLISH      3   /* English text */
+#define NCODES_STATIC     4   /* Cheat, but we count from 0 for ease */
+
+/* predefined elsewhere in HUFF chunks, 128 onwards */
+#define CODE_USER	  128 
+
+#define MAX_CODE_LEN	  15 /* maximum allowed by RFC 1951 */
+
+#ifndef ZTR_FORM_STHUFF
+#  define ZTR_FORM_STHUFF  77
+#endif
+
+/* A single symbol and it's encoding */
+typedef struct {
+    signed int symbol; /* 0-255 character, 256 = exception code, 257 = EOF */
+    int nbits;
+    unsigned int code;
+    int freq;
+} huffman_code_t;
+
+/* A collection of huffman_code_t along with decoding optimisations */
+typedef struct {
+    huffman_code_t *codes;
+    int ncodes;
+    int codes_static;
+    huffman_code_t lookup[258]; /* Mapping of symbol character to code */
+    int max_code_len;
+} huffman_codes_t;
+
+/* Use for store_bits() and get_bits() */
+typedef struct block {
+    unsigned char *data;
+    size_t alloc;
+    size_t byte;
+    int bit;
+} block_t;
+
+/* Tree and jump-table data structures used for fast decoding. */
+typedef struct {
+    /* Graph construction */
+    unsigned short c[2]; /* child node */
+      signed short l[2]; /* symbol to emit on transition. -1 => none */
+} htree_t;
+
+typedef struct {
+    /* Byte-wise jumping table */
+    unsigned short jump;
+    unsigned char symbol[4];
+    unsigned char nsymbols;
+    unsigned char top_bit;   /* bit 9 of symbol[] */
+} h_jump4_t;
+
+
+/* A collection of huffman_codes_t, for use with the multi-code codec */
+typedef struct {
+    huffman_codes_t **codes;
+    int ncodes;
+    int code_set; /* (128-255) The user specified number for this encoding */
+
+    /* Cached binary version of codeset, assumes last block */
+    block_t *blk;
+    int      bit_num; /* if 1st block, which bit will stored codes end on */
+
+    /* Cache huffman_multi_decode parameters */
+    h_jump4_t (*decode_J4)[16];
+    htree_t *decode_t;
+} huffman_codeset_t;
+
+block_t *block_create(unsigned char *data, size_t size);
+void block_destroy(block_t *blk, int keep_data);
+int block_resize(block_t *blk, size_t size);
+void store_bytes(block_t *block, unsigned char *val, int nbytes);
+
+
+int huffman_encode(block_t *blk, huffman_codes_t *c, int code_set,
+		   unsigned char *data, int len);
+
+block_t *huffman_decode(block_t *in, huffman_codes_t *c);
+
+int huffman_multi_encode(block_t *blk, huffman_codeset_t *cs,
+			 int code_set, unsigned char *data, int len);
+
+block_t *huffman_multi_decode(block_t *in, huffman_codeset_t *cs);
+
+huffman_codeset_t *codes2codeset(huffman_code_t *codes, int ncodes,
+				 int code_num);
+huffman_codeset_t *generate_code_set(int code_set, int ncodes,
+				     unsigned char *data, int len,
+				     int eof, int max_code_len,
+				     int all_codes);
+
+int store_codes(block_t *out,
+		huffman_codeset_t *c,
+		int last_block);
+huffman_codeset_t *restore_codes(block_t *block, int *bfinal);
+void huffman_codes_destroy(huffman_codes_t *c);
+void huffman_codeset_destroy(huffman_codeset_t *cs);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _DEFLATE_SIMPLE_H_ */