bio-velvet_underground 0.0.1
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- checksums.yaml +7 -0
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- data/ext/src/third-party/zlib-1.2.3/uncompr.c +61 -0
- data/ext/src/third-party/zlib-1.2.3/win32/DLL_FAQ.txt +397 -0
- data/ext/src/third-party/zlib-1.2.3/win32/Makefile.bor +107 -0
- data/ext/src/third-party/zlib-1.2.3/win32/Makefile.emx +69 -0
- data/ext/src/third-party/zlib-1.2.3/win32/Makefile.gcc +141 -0
- data/ext/src/third-party/zlib-1.2.3/win32/Makefile.msc +126 -0
- data/ext/src/third-party/zlib-1.2.3/win32/VisualC.txt +3 -0
- data/ext/src/third-party/zlib-1.2.3/win32/zlib.def +60 -0
- data/ext/src/third-party/zlib-1.2.3/win32/zlib1.rc +39 -0
- data/ext/src/third-party/zlib-1.2.3/zconf.h +332 -0
- data/ext/src/third-party/zlib-1.2.3/zconf.in.h +332 -0
- data/ext/src/third-party/zlib-1.2.3/zlib.3 +159 -0
- data/ext/src/third-party/zlib-1.2.3/zlib.h +1357 -0
- data/ext/src/third-party/zlib-1.2.3/zutil.c +318 -0
- data/ext/src/third-party/zlib-1.2.3/zutil.h +269 -0
- data/lib/bio-velvet_underground.rb +12 -0
- data/lib/bio-velvet_underground/external/VERSION +1 -0
- data/lib/bio-velvet_underground/velvet_underground.rb +72 -0
- data/spec/binary_sequence_store_spec.rb +27 -0
- data/spec/data/1/CnyUnifiedSeq +0 -0
- data/spec/spec_helper.rb +31 -0
- metadata +456 -0
@@ -0,0 +1,115 @@
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/* inflate.h -- internal inflate state definition
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* Copyright (C) 1995-2004 Mark Adler
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* For conditions of distribution and use, see copyright notice in zlib.h
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*/
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/* WARNING: this file should *not* be used by applications. It is
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part of the implementation of the compression library and is
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subject to change. Applications should only use zlib.h.
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*/
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/* define NO_GZIP when compiling if you want to disable gzip header and
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trailer decoding by inflate(). NO_GZIP would be used to avoid linking in
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the crc code when it is not needed. For shared libraries, gzip decoding
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should be left enabled. */
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#ifndef NO_GZIP
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# define GUNZIP
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#endif
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/* Possible inflate modes between inflate() calls */
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typedef enum {
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HEAD, /* i: waiting for magic header */
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FLAGS, /* i: waiting for method and flags (gzip) */
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TIME, /* i: waiting for modification time (gzip) */
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OS, /* i: waiting for extra flags and operating system (gzip) */
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EXLEN, /* i: waiting for extra length (gzip) */
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EXTRA, /* i: waiting for extra bytes (gzip) */
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NAME, /* i: waiting for end of file name (gzip) */
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COMMENT, /* i: waiting for end of comment (gzip) */
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HCRC, /* i: waiting for header crc (gzip) */
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DICTID, /* i: waiting for dictionary check value */
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DICT, /* waiting for inflateSetDictionary() call */
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TYPE, /* i: waiting for type bits, including last-flag bit */
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TYPEDO, /* i: same, but skip check to exit inflate on new block */
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STORED, /* i: waiting for stored size (length and complement) */
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COPY, /* i/o: waiting for input or output to copy stored block */
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TABLE, /* i: waiting for dynamic block table lengths */
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LENLENS, /* i: waiting for code length code lengths */
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CODELENS, /* i: waiting for length/lit and distance code lengths */
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LEN, /* i: waiting for length/lit code */
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LENEXT, /* i: waiting for length extra bits */
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DIST, /* i: waiting for distance code */
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DISTEXT, /* i: waiting for distance extra bits */
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MATCH, /* o: waiting for output space to copy string */
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LIT, /* o: waiting for output space to write literal */
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CHECK, /* i: waiting for 32-bit check value */
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LENGTH, /* i: waiting for 32-bit length (gzip) */
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DONE, /* finished check, done -- remain here until reset */
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BAD, /* got a data error -- remain here until reset */
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MEM, /* got an inflate() memory error -- remain here until reset */
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SYNC /* looking for synchronization bytes to restart inflate() */
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} inflate_mode;
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/*
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State transitions between above modes -
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(most modes can go to the BAD or MEM mode -- not shown for clarity)
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Process header:
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HEAD -> (gzip) or (zlib)
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(gzip) -> FLAGS -> TIME -> OS -> EXLEN -> EXTRA -> NAME
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NAME -> COMMENT -> HCRC -> TYPE
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(zlib) -> DICTID or TYPE
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DICTID -> DICT -> TYPE
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Read deflate blocks:
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TYPE -> STORED or TABLE or LEN or CHECK
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STORED -> COPY -> TYPE
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TABLE -> LENLENS -> CODELENS -> LEN
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Read deflate codes:
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LEN -> LENEXT or LIT or TYPE
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LENEXT -> DIST -> DISTEXT -> MATCH -> LEN
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LIT -> LEN
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Process trailer:
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CHECK -> LENGTH -> DONE
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*/
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/* state maintained between inflate() calls. Approximately 7K bytes. */
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struct inflate_state {
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inflate_mode mode; /* current inflate mode */
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int last; /* true if processing last block */
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int wrap; /* bit 0 true for zlib, bit 1 true for gzip */
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int havedict; /* true if dictionary provided */
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int flags; /* gzip header method and flags (0 if zlib) */
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unsigned dmax; /* zlib header max distance (INFLATE_STRICT) */
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unsigned long check; /* protected copy of check value */
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unsigned long total; /* protected copy of output count */
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gz_headerp head; /* where to save gzip header information */
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/* sliding window */
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unsigned wbits; /* log base 2 of requested window size */
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unsigned wsize; /* window size or zero if not using window */
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unsigned whave; /* valid bytes in the window */
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unsigned write; /* window write index */
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unsigned char FAR *window; /* allocated sliding window, if needed */
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/* bit accumulator */
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unsigned long hold; /* input bit accumulator */
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unsigned bits; /* number of bits in "in" */
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/* for string and stored block copying */
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unsigned length; /* literal or length of data to copy */
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unsigned offset; /* distance back to copy string from */
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/* for table and code decoding */
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unsigned extra; /* extra bits needed */
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/* fixed and dynamic code tables */
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code const FAR *lencode; /* starting table for length/literal codes */
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code const FAR *distcode; /* starting table for distance codes */
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unsigned lenbits; /* index bits for lencode */
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unsigned distbits; /* index bits for distcode */
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/* dynamic table building */
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unsigned ncode; /* number of code length code lengths */
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unsigned nlen; /* number of length code lengths */
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unsigned ndist; /* number of distance code lengths */
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unsigned have; /* number of code lengths in lens[] */
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code FAR *next; /* next available space in codes[] */
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unsigned short lens[320]; /* temporary storage for code lengths */
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unsigned short work[288]; /* work area for code table building */
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code codes[ENOUGH]; /* space for code tables */
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};
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/* inftrees.c -- generate Huffman trees for efficient decoding
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* Copyright (C) 1995-2005 Mark Adler
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* For conditions of distribution and use, see copyright notice in zlib.h
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*/
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#include "zutil.h"
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#include "inftrees.h"
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#define MAXBITS 15
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const char inflate_copyright[] =
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" inflate 1.2.3 Copyright 1995-2005 Mark Adler ";
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/*
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If you use the zlib library in a product, an acknowledgment is welcome
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in the documentation of your product. If for some reason you cannot
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include such an acknowledgment, I would appreciate that you keep this
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copyright string in the executable of your product.
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*/
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/*
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Build a set of tables to decode the provided canonical Huffman code.
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The code lengths are lens[0..codes-1]. The result starts at *table,
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whose indices are 0..2^bits-1. work is a writable array of at least
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lens shorts, which is used as a work area. type is the type of code
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to be generated, CODES, LENS, or DISTS. On return, zero is success,
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-1 is an invalid code, and +1 means that ENOUGH isn't enough. table
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on return points to the next available entry's address. bits is the
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requested root table index bits, and on return it is the actual root
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table index bits. It will differ if the request is greater than the
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longest code or if it is less than the shortest code.
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*/
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int inflate_table(type, lens, codes, table, bits, work)
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codetype type;
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unsigned short FAR *lens;
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unsigned codes;
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code FAR * FAR *table;
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unsigned FAR *bits;
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unsigned short FAR *work;
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{
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unsigned len; /* a code's length in bits */
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unsigned sym; /* index of code symbols */
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unsigned min, max; /* minimum and maximum code lengths */
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unsigned root; /* number of index bits for root table */
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unsigned curr; /* number of index bits for current table */
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unsigned drop; /* code bits to drop for sub-table */
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int left; /* number of prefix codes available */
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unsigned used; /* code entries in table used */
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unsigned huff; /* Huffman code */
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unsigned incr; /* for incrementing code, index */
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unsigned fill; /* index for replicating entries */
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unsigned low; /* low bits for current root entry */
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unsigned mask; /* mask for low root bits */
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code this; /* table entry for duplication */
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code FAR *next; /* next available space in table */
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const unsigned short FAR *base; /* base value table to use */
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const unsigned short FAR *extra; /* extra bits table to use */
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int end; /* use base and extra for symbol > end */
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unsigned short count[MAXBITS+1]; /* number of codes of each length */
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unsigned short offs[MAXBITS+1]; /* offsets in table for each length */
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static const unsigned short lbase[31] = { /* Length codes 257..285 base */
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3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 15, 17, 19, 23, 27, 31,
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35, 43, 51, 59, 67, 83, 99, 115, 131, 163, 195, 227, 258, 0, 0};
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static const unsigned short lext[31] = { /* Length codes 257..285 extra */
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16, 16, 16, 16, 16, 16, 16, 16, 17, 17, 17, 17, 18, 18, 18, 18,
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19, 19, 19, 19, 20, 20, 20, 20, 21, 21, 21, 21, 16, 201, 196};
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static const unsigned short dbase[32] = { /* Distance codes 0..29 base */
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1, 2, 3, 4, 5, 7, 9, 13, 17, 25, 33, 49, 65, 97, 129, 193,
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257, 385, 513, 769, 1025, 1537, 2049, 3073, 4097, 6145,
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8193, 12289, 16385, 24577, 0, 0};
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static const unsigned short dext[32] = { /* Distance codes 0..29 extra */
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16, 16, 16, 16, 17, 17, 18, 18, 19, 19, 20, 20, 21, 21, 22, 22,
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23, 23, 24, 24, 25, 25, 26, 26, 27, 27,
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28, 28, 29, 29, 64, 64};
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/*
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Process a set of code lengths to create a canonical Huffman code. The
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code lengths are lens[0..codes-1]. Each length corresponds to the
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symbols 0..codes-1. The Huffman code is generated by first sorting the
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symbols by length from short to long, and retaining the symbol order
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for codes with equal lengths. Then the code starts with all zero bits
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for the first code of the shortest length, and the codes are integer
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increments for the same length, and zeros are appended as the length
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increases. For the deflate format, these bits are stored backwards
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from their more natural integer increment ordering, and so when the
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decoding tables are built in the large loop below, the integer codes
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are incremented backwards.
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|
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This routine assumes, but does not check, that all of the entries in
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lens[] are in the range 0..MAXBITS. The caller must assure this.
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1..MAXBITS is interpreted as that code length. zero means that that
|
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symbol does not occur in this code.
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|
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The codes are sorted by computing a count of codes for each length,
|
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creating from that a table of starting indices for each length in the
|
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sorted table, and then entering the symbols in order in the sorted
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table. The sorted table is work[], with that space being provided by
|
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the caller.
|
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|
99
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The length counts are used for other purposes as well, i.e. finding
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100
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the minimum and maximum length codes, determining if there are any
|
101
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codes at all, checking for a valid set of lengths, and looking ahead
|
102
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at length counts to determine sub-table sizes when building the
|
103
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decoding tables.
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104
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*/
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105
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|
106
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/* accumulate lengths for codes (assumes lens[] all in 0..MAXBITS) */
|
107
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for (len = 0; len <= MAXBITS; len++)
|
108
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count[len] = 0;
|
109
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for (sym = 0; sym < codes; sym++)
|
110
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count[lens[sym]]++;
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111
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+
|
112
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/* bound code lengths, force root to be within code lengths */
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root = *bits;
|
114
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for (max = MAXBITS; max >= 1; max--)
|
115
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if (count[max] != 0) break;
|
116
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if (root > max) root = max;
|
117
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if (max == 0) { /* no symbols to code at all */
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118
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this.op = (unsigned char)64; /* invalid code marker */
|
119
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this.bits = (unsigned char)1;
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120
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this.val = (unsigned short)0;
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121
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*(*table)++ = this; /* make a table to force an error */
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122
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*(*table)++ = this;
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*bits = 1;
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return 0; /* no symbols, but wait for decoding to report error */
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125
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}
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126
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for (min = 1; min <= MAXBITS; min++)
|
127
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if (count[min] != 0) break;
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if (root < min) root = min;
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129
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+
|
130
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/* check for an over-subscribed or incomplete set of lengths */
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131
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left = 1;
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132
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for (len = 1; len <= MAXBITS; len++) {
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133
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left <<= 1;
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134
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left -= count[len];
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135
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if (left < 0) return -1; /* over-subscribed */
|
136
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}
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137
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if (left > 0 && (type == CODES || max != 1))
|
138
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return -1; /* incomplete set */
|
139
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+
|
140
|
+
/* generate offsets into symbol table for each length for sorting */
|
141
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+
offs[1] = 0;
|
142
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+
for (len = 1; len < MAXBITS; len++)
|
143
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+
offs[len + 1] = offs[len] + count[len];
|
144
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+
|
145
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+
/* sort symbols by length, by symbol order within each length */
|
146
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+
for (sym = 0; sym < codes; sym++)
|
147
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+
if (lens[sym] != 0) work[offs[lens[sym]]++] = (unsigned short)sym;
|
148
|
+
|
149
|
+
/*
|
150
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+
Create and fill in decoding tables. In this loop, the table being
|
151
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filled is at next and has curr index bits. The code being used is huff
|
152
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with length len. That code is converted to an index by dropping drop
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153
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bits off of the bottom. For codes where len is less than drop + curr,
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154
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those top drop + curr - len bits are incremented through all values to
|
155
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fill the table with replicated entries.
|
156
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+
|
157
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root is the number of index bits for the root table. When len exceeds
|
158
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root, sub-tables are created pointed to by the root entry with an index
|
159
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of the low root bits of huff. This is saved in low to check for when a
|
160
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new sub-table should be started. drop is zero when the root table is
|
161
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being filled, and drop is root when sub-tables are being filled.
|
162
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+
|
163
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When a new sub-table is needed, it is necessary to look ahead in the
|
164
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code lengths to determine what size sub-table is needed. The length
|
165
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counts are used for this, and so count[] is decremented as codes are
|
166
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entered in the tables.
|
167
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+
|
168
|
+
used keeps track of how many table entries have been allocated from the
|
169
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+
provided *table space. It is checked when a LENS table is being made
|
170
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against the space in *table, ENOUGH, minus the maximum space needed by
|
171
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the worst case distance code, MAXD. This should never happen, but the
|
172
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sufficiency of ENOUGH has not been proven exhaustively, hence the check.
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173
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This assumes that when type == LENS, bits == 9.
|
174
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+
|
175
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+
sym increments through all symbols, and the loop terminates when
|
176
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+
all codes of length max, i.e. all codes, have been processed. This
|
177
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+
routine permits incomplete codes, so another loop after this one fills
|
178
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+
in the rest of the decoding tables with invalid code markers.
|
179
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+
*/
|
180
|
+
|
181
|
+
/* set up for code type */
|
182
|
+
switch (type) {
|
183
|
+
case CODES:
|
184
|
+
base = extra = work; /* dummy value--not used */
|
185
|
+
end = 19;
|
186
|
+
break;
|
187
|
+
case LENS:
|
188
|
+
base = lbase;
|
189
|
+
base -= 257;
|
190
|
+
extra = lext;
|
191
|
+
extra -= 257;
|
192
|
+
end = 256;
|
193
|
+
break;
|
194
|
+
default: /* DISTS */
|
195
|
+
base = dbase;
|
196
|
+
extra = dext;
|
197
|
+
end = -1;
|
198
|
+
}
|
199
|
+
|
200
|
+
/* initialize state for loop */
|
201
|
+
huff = 0; /* starting code */
|
202
|
+
sym = 0; /* starting code symbol */
|
203
|
+
len = min; /* starting code length */
|
204
|
+
next = *table; /* current table to fill in */
|
205
|
+
curr = root; /* current table index bits */
|
206
|
+
drop = 0; /* current bits to drop from code for index */
|
207
|
+
low = (unsigned)(-1); /* trigger new sub-table when len > root */
|
208
|
+
used = 1U << root; /* use root table entries */
|
209
|
+
mask = used - 1; /* mask for comparing low */
|
210
|
+
|
211
|
+
/* check available table space */
|
212
|
+
if (type == LENS && used >= ENOUGH - MAXD)
|
213
|
+
return 1;
|
214
|
+
|
215
|
+
/* process all codes and make table entries */
|
216
|
+
for (;;) {
|
217
|
+
/* create table entry */
|
218
|
+
this.bits = (unsigned char)(len - drop);
|
219
|
+
if ((int)(work[sym]) < end) {
|
220
|
+
this.op = (unsigned char)0;
|
221
|
+
this.val = work[sym];
|
222
|
+
}
|
223
|
+
else if ((int)(work[sym]) > end) {
|
224
|
+
this.op = (unsigned char)(extra[work[sym]]);
|
225
|
+
this.val = base[work[sym]];
|
226
|
+
}
|
227
|
+
else {
|
228
|
+
this.op = (unsigned char)(32 + 64); /* end of block */
|
229
|
+
this.val = 0;
|
230
|
+
}
|
231
|
+
|
232
|
+
/* replicate for those indices with low len bits equal to huff */
|
233
|
+
incr = 1U << (len - drop);
|
234
|
+
fill = 1U << curr;
|
235
|
+
min = fill; /* save offset to next table */
|
236
|
+
do {
|
237
|
+
fill -= incr;
|
238
|
+
next[(huff >> drop) + fill] = this;
|
239
|
+
} while (fill != 0);
|
240
|
+
|
241
|
+
/* backwards increment the len-bit code huff */
|
242
|
+
incr = 1U << (len - 1);
|
243
|
+
while (huff & incr)
|
244
|
+
incr >>= 1;
|
245
|
+
if (incr != 0) {
|
246
|
+
huff &= incr - 1;
|
247
|
+
huff += incr;
|
248
|
+
}
|
249
|
+
else
|
250
|
+
huff = 0;
|
251
|
+
|
252
|
+
/* go to next symbol, update count, len */
|
253
|
+
sym++;
|
254
|
+
if (--(count[len]) == 0) {
|
255
|
+
if (len == max) break;
|
256
|
+
len = lens[work[sym]];
|
257
|
+
}
|
258
|
+
|
259
|
+
/* create new sub-table if needed */
|
260
|
+
if (len > root && (huff & mask) != low) {
|
261
|
+
/* if first time, transition to sub-tables */
|
262
|
+
if (drop == 0)
|
263
|
+
drop = root;
|
264
|
+
|
265
|
+
/* increment past last table */
|
266
|
+
next += min; /* here min is 1 << curr */
|
267
|
+
|
268
|
+
/* determine length of next table */
|
269
|
+
curr = len - drop;
|
270
|
+
left = (int)(1 << curr);
|
271
|
+
while (curr + drop < max) {
|
272
|
+
left -= count[curr + drop];
|
273
|
+
if (left <= 0) break;
|
274
|
+
curr++;
|
275
|
+
left <<= 1;
|
276
|
+
}
|
277
|
+
|
278
|
+
/* check for enough space */
|
279
|
+
used += 1U << curr;
|
280
|
+
if (type == LENS && used >= ENOUGH - MAXD)
|
281
|
+
return 1;
|
282
|
+
|
283
|
+
/* point entry in root table to sub-table */
|
284
|
+
low = huff & mask;
|
285
|
+
(*table)[low].op = (unsigned char)curr;
|
286
|
+
(*table)[low].bits = (unsigned char)root;
|
287
|
+
(*table)[low].val = (unsigned short)(next - *table);
|
288
|
+
}
|
289
|
+
}
|
290
|
+
|
291
|
+
/*
|
292
|
+
Fill in rest of table for incomplete codes. This loop is similar to the
|
293
|
+
loop above in incrementing huff for table indices. It is assumed that
|
294
|
+
len is equal to curr + drop, so there is no loop needed to increment
|
295
|
+
through high index bits. When the current sub-table is filled, the loop
|
296
|
+
drops back to the root table to fill in any remaining entries there.
|
297
|
+
*/
|
298
|
+
this.op = (unsigned char)64; /* invalid code marker */
|
299
|
+
this.bits = (unsigned char)(len - drop);
|
300
|
+
this.val = (unsigned short)0;
|
301
|
+
while (huff != 0) {
|
302
|
+
/* when done with sub-table, drop back to root table */
|
303
|
+
if (drop != 0 && (huff & mask) != low) {
|
304
|
+
drop = 0;
|
305
|
+
len = root;
|
306
|
+
next = *table;
|
307
|
+
this.bits = (unsigned char)len;
|
308
|
+
}
|
309
|
+
|
310
|
+
/* put invalid code marker in table */
|
311
|
+
next[huff >> drop] = this;
|
312
|
+
|
313
|
+
/* backwards increment the len-bit code huff */
|
314
|
+
incr = 1U << (len - 1);
|
315
|
+
while (huff & incr)
|
316
|
+
incr >>= 1;
|
317
|
+
if (incr != 0) {
|
318
|
+
huff &= incr - 1;
|
319
|
+
huff += incr;
|
320
|
+
}
|
321
|
+
else
|
322
|
+
huff = 0;
|
323
|
+
}
|
324
|
+
|
325
|
+
/* set return parameters */
|
326
|
+
*table += used;
|
327
|
+
*bits = root;
|
328
|
+
return 0;
|
329
|
+
}
|
@@ -0,0 +1,55 @@
|
|
1
|
+
/* inftrees.h -- header to use inftrees.c
|
2
|
+
* Copyright (C) 1995-2005 Mark Adler
|
3
|
+
* For conditions of distribution and use, see copyright notice in zlib.h
|
4
|
+
*/
|
5
|
+
|
6
|
+
/* WARNING: this file should *not* be used by applications. It is
|
7
|
+
part of the implementation of the compression library and is
|
8
|
+
subject to change. Applications should only use zlib.h.
|
9
|
+
*/
|
10
|
+
|
11
|
+
/* Structure for decoding tables. Each entry provides either the
|
12
|
+
information needed to do the operation requested by the code that
|
13
|
+
indexed that table entry, or it provides a pointer to another
|
14
|
+
table that indexes more bits of the code. op indicates whether
|
15
|
+
the entry is a pointer to another table, a literal, a length or
|
16
|
+
distance, an end-of-block, or an invalid code. For a table
|
17
|
+
pointer, the low four bits of op is the number of index bits of
|
18
|
+
that table. For a length or distance, the low four bits of op
|
19
|
+
is the number of extra bits to get after the code. bits is
|
20
|
+
the number of bits in this code or part of the code to drop off
|
21
|
+
of the bit buffer. val is the actual byte to output in the case
|
22
|
+
of a literal, the base length or distance, or the offset from
|
23
|
+
the current table to the next table. Each entry is four bytes. */
|
24
|
+
typedef struct {
|
25
|
+
unsigned char op; /* operation, extra bits, table bits */
|
26
|
+
unsigned char bits; /* bits in this part of the code */
|
27
|
+
unsigned short val; /* offset in table or code value */
|
28
|
+
} code;
|
29
|
+
|
30
|
+
/* op values as set by inflate_table():
|
31
|
+
00000000 - literal
|
32
|
+
0000tttt - table link, tttt != 0 is the number of table index bits
|
33
|
+
0001eeee - length or distance, eeee is the number of extra bits
|
34
|
+
01100000 - end of block
|
35
|
+
01000000 - invalid code
|
36
|
+
*/
|
37
|
+
|
38
|
+
/* Maximum size of dynamic tree. The maximum found in a long but non-
|
39
|
+
exhaustive search was 1444 code structures (852 for length/literals
|
40
|
+
and 592 for distances, the latter actually the result of an
|
41
|
+
exhaustive search). The true maximum is not known, but the value
|
42
|
+
below is more than safe. */
|
43
|
+
#define ENOUGH 2048
|
44
|
+
#define MAXD 592
|
45
|
+
|
46
|
+
/* Type of code to build for inftable() */
|
47
|
+
typedef enum {
|
48
|
+
CODES,
|
49
|
+
LENS,
|
50
|
+
DISTS
|
51
|
+
} codetype;
|
52
|
+
|
53
|
+
extern int inflate_table OF((codetype type, unsigned short FAR *lens,
|
54
|
+
unsigned codes, code FAR * FAR *table,
|
55
|
+
unsigned FAR *bits, unsigned short FAR *work));
|