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 +1,837 @@
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/*
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* puff.c
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* Copyright (C) 2002-2004 Mark Adler
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* For conditions of distribution and use, see copyright notice in puff.h
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* version 1.8, 9 Jan 2004
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*
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* puff.c is a simple inflate written to be an unambiguous way to specify the
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* deflate format. It is not written for speed but rather simplicity. As a
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* side benefit, this code might actually be useful when small code is more
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* important than speed, such as bootstrap applications. For typical deflate
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* data, zlib's inflate() is about four times as fast as puff(). zlib's
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* inflate compiles to around 20K on my machine, whereas puff.c compiles to
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* around 4K on my machine (a PowerPC using GNU cc). If the faster decode()
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* function here is used, then puff() is only twice as slow as zlib's
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* inflate().
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*
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* All dynamically allocated memory comes from the stack. The stack required
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* is less than 2K bytes. This code is compatible with 16-bit int's and
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* assumes that long's are at least 32 bits. puff.c uses the short data type,
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* assumed to be 16 bits, for arrays in order to to conserve memory. The code
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* works whether integers are stored big endian or little endian.
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*
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* In the comments below are "Format notes" that describe the inflate process
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* and document some of the less obvious aspects of the format. This source
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* code is meant to supplement RFC 1951, which formally describes the deflate
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* format:
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*
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* http://www.zlib.org/rfc-deflate.html
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*/
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/*
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* Change history:
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*
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* 1.0 10 Feb 2002 - First version
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* 1.1 17 Feb 2002 - Clarifications of some comments and notes
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* - Update puff() dest and source pointers on negative
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* errors to facilitate debugging deflators
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* - Remove longest from struct huffman -- not needed
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* - Simplify offs[] index in construct()
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* - Add input size and checking, using longjmp() to
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* maintain easy readability
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* - Use short data type for large arrays
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* - Use pointers instead of long to specify source and
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* destination sizes to avoid arbitrary 4 GB limits
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* 1.2 17 Mar 2002 - Add faster version of decode(), doubles speed (!),
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* but leave simple version for readabilty
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* - Make sure invalid distances detected if pointers
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* are 16 bits
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* - Fix fixed codes table error
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* - Provide a scanning mode for determining size of
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* uncompressed data
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* 1.3 20 Mar 2002 - Go back to lengths for puff() parameters [Jean-loup]
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* - Add a puff.h file for the interface
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* - Add braces in puff() for else do [Jean-loup]
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* - Use indexes instead of pointers for readability
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* 1.4 31 Mar 2002 - Simplify construct() code set check
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* - Fix some comments
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* - Add FIXLCODES #define
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* 1.5 6 Apr 2002 - Minor comment fixes
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* 1.6 7 Aug 2002 - Minor format changes
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* 1.7 3 Mar 2003 - Added test code for distribution
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* - Added zlib-like license
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* 1.8 9 Jan 2004 - Added some comments on no distance codes case
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*/
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#include <setjmp.h> /* for setjmp(), longjmp(), and jmp_buf */
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#include "puff.h" /* prototype for puff() */
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#define local static /* for local function definitions */
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#define NIL ((unsigned char *)0) /* for no output option */
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/*
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* Maximums for allocations and loops. It is not useful to change these --
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* they are fixed by the deflate format.
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*/
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#define MAXBITS 15 /* maximum bits in a code */
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#define MAXLCODES 286 /* maximum number of literal/length codes */
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#define MAXDCODES 30 /* maximum number of distance codes */
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#define MAXCODES (MAXLCODES+MAXDCODES) /* maximum codes lengths to read */
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#define FIXLCODES 288 /* number of fixed literal/length codes */
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/* input and output state */
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struct state {
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/* output state */
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unsigned char *out; /* output buffer */
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unsigned long outlen; /* available space at out */
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unsigned long outcnt; /* bytes written to out so far */
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/* input state */
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unsigned char *in; /* input buffer */
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unsigned long inlen; /* available input at in */
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unsigned long incnt; /* bytes read so far */
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int bitbuf; /* bit buffer */
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int bitcnt; /* number of bits in bit buffer */
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/* input limit error return state for bits() and decode() */
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jmp_buf env;
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};
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/*
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* Return need bits from the input stream. This always leaves less than
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* eight bits in the buffer. bits() works properly for need == 0.
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*
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* Format notes:
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*
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* - Bits are stored in bytes from the least significant bit to the most
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* significant bit. Therefore bits are dropped from the bottom of the bit
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* buffer, using shift right, and new bytes are appended to the top of the
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* bit buffer, using shift left.
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*/
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local int bits(struct state *s, int need)
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{
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long val; /* bit accumulator (can use up to 20 bits) */
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/* load at least need bits into val */
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val = s->bitbuf;
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while (s->bitcnt < need) {
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if (s->incnt == s->inlen) longjmp(s->env, 1); /* out of input */
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val |= (long)(s->in[s->incnt++]) << s->bitcnt; /* load eight bits */
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s->bitcnt += 8;
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}
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/* drop need bits and update buffer, always zero to seven bits left */
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s->bitbuf = (int)(val >> need);
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s->bitcnt -= need;
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/* return need bits, zeroing the bits above that */
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return (int)(val & ((1L << need) - 1));
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}
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/*
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* Process a stored block.
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*
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* Format notes:
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*
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* - After the two-bit stored block type (00), the stored block length and
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* stored bytes are byte-aligned for fast copying. Therefore any leftover
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* bits in the byte that has the last bit of the type, as many as seven, are
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* discarded. The value of the discarded bits are not defined and should not
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* be checked against any expectation.
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*
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* - The second inverted copy of the stored block length does not have to be
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* checked, but it's probably a good idea to do so anyway.
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*
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* - A stored block can have zero length. This is sometimes used to byte-align
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* subsets of the compressed data for random access or partial recovery.
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*/
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local int stored(struct state *s)
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{
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unsigned len; /* length of stored block */
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/* discard leftover bits from current byte (assumes s->bitcnt < 8) */
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s->bitbuf = 0;
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s->bitcnt = 0;
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/* get length and check against its one's complement */
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if (s->incnt + 4 > s->inlen) return 2; /* not enough input */
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len = s->in[s->incnt++];
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len |= s->in[s->incnt++] << 8;
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if (s->in[s->incnt++] != (~len & 0xff) ||
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s->in[s->incnt++] != ((~len >> 8) & 0xff))
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return -2; /* didn't match complement! */
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/* copy len bytes from in to out */
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if (s->incnt + len > s->inlen) return 2; /* not enough input */
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if (s->out != NIL) {
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if (s->outcnt + len > s->outlen)
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return 1; /* not enough output space */
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while (len--)
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s->out[s->outcnt++] = s->in[s->incnt++];
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}
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else { /* just scanning */
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s->outcnt += len;
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s->incnt += len;
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}
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/* done with a valid stored block */
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return 0;
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}
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/*
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* Huffman code decoding tables. count[1..MAXBITS] is the number of symbols of
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* each length, which for a canonical code are stepped through in order.
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* symbol[] are the symbol values in canonical order, where the number of
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* entries is the sum of the counts in count[]. The decoding process can be
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* seen in the function decode() below.
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*/
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struct huffman {
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short *count; /* number of symbols of each length */
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short *symbol; /* canonically ordered symbols */
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};
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/*
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* Decode a code from the stream s using huffman table h. Return the symbol or
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* a negative value if there is an error. If all of the lengths are zero, i.e.
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* an empty code, or if the code is incomplete and an invalid code is received,
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* then -9 is returned after reading MAXBITS bits.
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*
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* Format notes:
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*
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* - The codes as stored in the compressed data are bit-reversed relative to
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* a simple integer ordering of codes of the same lengths. Hence below the
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* bits are pulled from the compressed data one at a time and used to
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* build the code value reversed from what is in the stream in order to
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* permit simple integer comparisons for decoding. A table-based decoding
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* scheme (as used in zlib) does not need to do this reversal.
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*
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* - The first code for the shortest length is all zeros. Subsequent codes of
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* the same length are simply integer increments of the previous code. When
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* moving up a length, a zero bit is appended to the code. For a complete
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* code, the last code of the longest length will be all ones.
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*
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* - Incomplete codes are handled by this decoder, since they are permitted
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* in the deflate format. See the format notes for fixed() and dynamic().
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*/
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#ifdef SLOW
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local int decode(struct state *s, struct huffman *h)
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{
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int len; /* current number of bits in code */
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int code; /* len bits being decoded */
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int first; /* first code of length len */
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int count; /* number of codes of length len */
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int index; /* index of first code of length len in symbol table */
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code = first = index = 0;
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for (len = 1; len <= MAXBITS; len++) {
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code |= bits(s, 1); /* get next bit */
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count = h->count[len];
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if (code < first + count) /* if length len, return symbol */
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return h->symbol[index + (code - first)];
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index += count; /* else update for next length */
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first += count;
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first <<= 1;
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code <<= 1;
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}
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return -9; /* ran out of codes */
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}
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/*
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* A faster version of decode() for real applications of this code. It's not
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* as readable, but it makes puff() twice as fast. And it only makes the code
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* a few percent larger.
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*/
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#else /* !SLOW */
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local int decode(struct state *s, struct huffman *h)
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{
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int len; /* current number of bits in code */
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int code; /* len bits being decoded */
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int first; /* first code of length len */
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int count; /* number of codes of length len */
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int index; /* index of first code of length len in symbol table */
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int bitbuf; /* bits from stream */
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int left; /* bits left in next or left to process */
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short *next; /* next number of codes */
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bitbuf = s->bitbuf;
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left = s->bitcnt;
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code = first = index = 0;
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len = 1;
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next = h->count + 1;
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while (1) {
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while (left--) {
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code |= bitbuf & 1;
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bitbuf >>= 1;
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count = *next++;
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if (code < first + count) { /* if length len, return symbol */
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s->bitbuf = bitbuf;
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s->bitcnt = (s->bitcnt - len) & 7;
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return h->symbol[index + (code - first)];
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}
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index += count; /* else update for next length */
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first += count;
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first <<= 1;
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code <<= 1;
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len++;
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}
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left = (MAXBITS+1) - len;
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if (left == 0) break;
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if (s->incnt == s->inlen) longjmp(s->env, 1); /* out of input */
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bitbuf = s->in[s->incnt++];
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if (left > 8) left = 8;
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}
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return -9; /* ran out of codes */
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}
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#endif /* SLOW */
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/*
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* Given the list of code lengths length[0..n-1] representing a canonical
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* Huffman code for n symbols, construct the tables required to decode those
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* codes. Those tables are the number of codes of each length, and the symbols
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* sorted by length, retaining their original order within each length. The
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* return value is zero for a complete code set, negative for an over-
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* subscribed code set, and positive for an incomplete code set. The tables
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* can be used if the return value is zero or positive, but they cannot be used
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* if the return value is negative. If the return value is zero, it is not
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* possible for decode() using that table to return an error--any stream of
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* enough bits will resolve to a symbol. If the return value is positive, then
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* it is possible for decode() using that table to return an error for received
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* codes past the end of the incomplete lengths.
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*
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* Not used by decode(), but used for error checking, h->count[0] is the number
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* of the n symbols not in the code. So n - h->count[0] is the number of
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* codes. This is useful for checking for incomplete codes that have more than
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* one symbol, which is an error in a dynamic block.
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*
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* Assumption: for all i in 0..n-1, 0 <= length[i] <= MAXBITS
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* This is assured by the construction of the length arrays in dynamic() and
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* fixed() and is not verified by construct().
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*
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* Format notes:
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*
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* - Permitted and expected examples of incomplete codes are one of the fixed
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* codes and any code with a single symbol which in deflate is coded as one
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* bit instead of zero bits. See the format notes for fixed() and dynamic().
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*
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* - Within a given code length, the symbols are kept in ascending order for
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* the code bits definition.
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*/
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local int construct(struct huffman *h, short *length, int n)
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{
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int symbol; /* current symbol when stepping through length[] */
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int len; /* current length when stepping through h->count[] */
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+
int left; /* number of possible codes left of current length */
|
324
|
+
short offs[MAXBITS+1]; /* offsets in symbol table for each length */
|
325
|
+
|
326
|
+
/* count number of codes of each length */
|
327
|
+
for (len = 0; len <= MAXBITS; len++)
|
328
|
+
h->count[len] = 0;
|
329
|
+
for (symbol = 0; symbol < n; symbol++)
|
330
|
+
(h->count[length[symbol]])++; /* assumes lengths are within bounds */
|
331
|
+
if (h->count[0] == n) /* no codes! */
|
332
|
+
return 0; /* complete, but decode() will fail */
|
333
|
+
|
334
|
+
/* check for an over-subscribed or incomplete set of lengths */
|
335
|
+
left = 1; /* one possible code of zero length */
|
336
|
+
for (len = 1; len <= MAXBITS; len++) {
|
337
|
+
left <<= 1; /* one more bit, double codes left */
|
338
|
+
left -= h->count[len]; /* deduct count from possible codes */
|
339
|
+
if (left < 0) return left; /* over-subscribed--return negative */
|
340
|
+
} /* left > 0 means incomplete */
|
341
|
+
|
342
|
+
/* generate offsets into symbol table for each length for sorting */
|
343
|
+
offs[1] = 0;
|
344
|
+
for (len = 1; len < MAXBITS; len++)
|
345
|
+
offs[len + 1] = offs[len] + h->count[len];
|
346
|
+
|
347
|
+
/*
|
348
|
+
* put symbols in table sorted by length, by symbol order within each
|
349
|
+
* length
|
350
|
+
*/
|
351
|
+
for (symbol = 0; symbol < n; symbol++)
|
352
|
+
if (length[symbol] != 0)
|
353
|
+
h->symbol[offs[length[symbol]]++] = symbol;
|
354
|
+
|
355
|
+
/* return zero for complete set, positive for incomplete set */
|
356
|
+
return left;
|
357
|
+
}
|
358
|
+
|
359
|
+
/*
|
360
|
+
* Decode literal/length and distance codes until an end-of-block code.
|
361
|
+
*
|
362
|
+
* Format notes:
|
363
|
+
*
|
364
|
+
* - Compressed data that is after the block type if fixed or after the code
|
365
|
+
* description if dynamic is a combination of literals and length/distance
|
366
|
+
* pairs terminated by and end-of-block code. Literals are simply Huffman
|
367
|
+
* coded bytes. A length/distance pair is a coded length followed by a
|
368
|
+
* coded distance to represent a string that occurs earlier in the
|
369
|
+
* uncompressed data that occurs again at the current location.
|
370
|
+
*
|
371
|
+
* - Literals, lengths, and the end-of-block code are combined into a single
|
372
|
+
* code of up to 286 symbols. They are 256 literals (0..255), 29 length
|
373
|
+
* symbols (257..285), and the end-of-block symbol (256).
|
374
|
+
*
|
375
|
+
* - There are 256 possible lengths (3..258), and so 29 symbols are not enough
|
376
|
+
* to represent all of those. Lengths 3..10 and 258 are in fact represented
|
377
|
+
* by just a length symbol. Lengths 11..257 are represented as a symbol and
|
378
|
+
* some number of extra bits that are added as an integer to the base length
|
379
|
+
* of the length symbol. The number of extra bits is determined by the base
|
380
|
+
* length symbol. These are in the static arrays below, lens[] for the base
|
381
|
+
* lengths and lext[] for the corresponding number of extra bits.
|
382
|
+
*
|
383
|
+
* - The reason that 258 gets its own symbol is that the longest length is used
|
384
|
+
* often in highly redundant files. Note that 258 can also be coded as the
|
385
|
+
* base value 227 plus the maximum extra value of 31. While a good deflate
|
386
|
+
* should never do this, it is not an error, and should be decoded properly.
|
387
|
+
*
|
388
|
+
* - If a length is decoded, including its extra bits if any, then it is
|
389
|
+
* followed a distance code. There are up to 30 distance symbols. Again
|
390
|
+
* there are many more possible distances (1..32768), so extra bits are added
|
391
|
+
* to a base value represented by the symbol. The distances 1..4 get their
|
392
|
+
* own symbol, but the rest require extra bits. The base distances and
|
393
|
+
* corresponding number of extra bits are below in the static arrays dist[]
|
394
|
+
* and dext[].
|
395
|
+
*
|
396
|
+
* - Literal bytes are simply written to the output. A length/distance pair is
|
397
|
+
* an instruction to copy previously uncompressed bytes to the output. The
|
398
|
+
* copy is from distance bytes back in the output stream, copying for length
|
399
|
+
* bytes.
|
400
|
+
*
|
401
|
+
* - Distances pointing before the beginning of the output data are not
|
402
|
+
* permitted.
|
403
|
+
*
|
404
|
+
* - Overlapped copies, where the length is greater than the distance, are
|
405
|
+
* allowed and common. For example, a distance of one and a length of 258
|
406
|
+
* simply copies the last byte 258 times. A distance of four and a length of
|
407
|
+
* twelve copies the last four bytes three times. A simple forward copy
|
408
|
+
* ignoring whether the length is greater than the distance or not implements
|
409
|
+
* this correctly. You should not use memcpy() since its behavior is not
|
410
|
+
* defined for overlapped arrays. You should not use memmove() or bcopy()
|
411
|
+
* since though their behavior -is- defined for overlapping arrays, it is
|
412
|
+
* defined to do the wrong thing in this case.
|
413
|
+
*/
|
414
|
+
local int codes(struct state *s,
|
415
|
+
struct huffman *lencode,
|
416
|
+
struct huffman *distcode)
|
417
|
+
{
|
418
|
+
int symbol; /* decoded symbol */
|
419
|
+
int len; /* length for copy */
|
420
|
+
unsigned dist; /* distance for copy */
|
421
|
+
static const short lens[29] = { /* Size base for length codes 257..285 */
|
422
|
+
3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 15, 17, 19, 23, 27, 31,
|
423
|
+
35, 43, 51, 59, 67, 83, 99, 115, 131, 163, 195, 227, 258};
|
424
|
+
static const short lext[29] = { /* Extra bits for length codes 257..285 */
|
425
|
+
0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 2, 2, 2, 2,
|
426
|
+
3, 3, 3, 3, 4, 4, 4, 4, 5, 5, 5, 5, 0};
|
427
|
+
static const short dists[30] = { /* Offset base for distance codes 0..29 */
|
428
|
+
1, 2, 3, 4, 5, 7, 9, 13, 17, 25, 33, 49, 65, 97, 129, 193,
|
429
|
+
257, 385, 513, 769, 1025, 1537, 2049, 3073, 4097, 6145,
|
430
|
+
8193, 12289, 16385, 24577};
|
431
|
+
static const short dext[30] = { /* Extra bits for distance codes 0..29 */
|
432
|
+
0, 0, 0, 0, 1, 1, 2, 2, 3, 3, 4, 4, 5, 5, 6, 6,
|
433
|
+
7, 7, 8, 8, 9, 9, 10, 10, 11, 11,
|
434
|
+
12, 12, 13, 13};
|
435
|
+
|
436
|
+
/* decode literals and length/distance pairs */
|
437
|
+
do {
|
438
|
+
symbol = decode(s, lencode);
|
439
|
+
if (symbol < 0) return symbol; /* invalid symbol */
|
440
|
+
if (symbol < 256) { /* literal: symbol is the byte */
|
441
|
+
/* write out the literal */
|
442
|
+
if (s->out != NIL) {
|
443
|
+
if (s->outcnt == s->outlen) return 1;
|
444
|
+
s->out[s->outcnt] = symbol;
|
445
|
+
}
|
446
|
+
s->outcnt++;
|
447
|
+
}
|
448
|
+
else if (symbol > 256) { /* length */
|
449
|
+
/* get and compute length */
|
450
|
+
symbol -= 257;
|
451
|
+
if (symbol >= 29) return -9; /* invalid fixed code */
|
452
|
+
len = lens[symbol] + bits(s, lext[symbol]);
|
453
|
+
|
454
|
+
/* get and check distance */
|
455
|
+
symbol = decode(s, distcode);
|
456
|
+
if (symbol < 0) return symbol; /* invalid symbol */
|
457
|
+
dist = dists[symbol] + bits(s, dext[symbol]);
|
458
|
+
if (dist > s->outcnt)
|
459
|
+
return -10; /* distance too far back */
|
460
|
+
|
461
|
+
/* copy length bytes from distance bytes back */
|
462
|
+
if (s->out != NIL) {
|
463
|
+
if (s->outcnt + len > s->outlen) return 1;
|
464
|
+
while (len--) {
|
465
|
+
s->out[s->outcnt] = s->out[s->outcnt - dist];
|
466
|
+
s->outcnt++;
|
467
|
+
}
|
468
|
+
}
|
469
|
+
else
|
470
|
+
s->outcnt += len;
|
471
|
+
}
|
472
|
+
} while (symbol != 256); /* end of block symbol */
|
473
|
+
|
474
|
+
/* done with a valid fixed or dynamic block */
|
475
|
+
return 0;
|
476
|
+
}
|
477
|
+
|
478
|
+
/*
|
479
|
+
* Process a fixed codes block.
|
480
|
+
*
|
481
|
+
* Format notes:
|
482
|
+
*
|
483
|
+
* - This block type can be useful for compressing small amounts of data for
|
484
|
+
* which the size of the code descriptions in a dynamic block exceeds the
|
485
|
+
* benefit of custom codes for that block. For fixed codes, no bits are
|
486
|
+
* spent on code descriptions. Instead the code lengths for literal/length
|
487
|
+
* codes and distance codes are fixed. The specific lengths for each symbol
|
488
|
+
* can be seen in the "for" loops below.
|
489
|
+
*
|
490
|
+
* - The literal/length code is complete, but has two symbols that are invalid
|
491
|
+
* and should result in an error if received. This cannot be implemented
|
492
|
+
* simply as an incomplete code since those two symbols are in the "middle"
|
493
|
+
* of the code. They are eight bits long and the longest literal/length\
|
494
|
+
* code is nine bits. Therefore the code must be constructed with those
|
495
|
+
* symbols, and the invalid symbols must be detected after decoding.
|
496
|
+
*
|
497
|
+
* - The fixed distance codes also have two invalid symbols that should result
|
498
|
+
* in an error if received. Since all of the distance codes are the same
|
499
|
+
* length, this can be implemented as an incomplete code. Then the invalid
|
500
|
+
* codes are detected while decoding.
|
501
|
+
*/
|
502
|
+
local int fixed(struct state *s)
|
503
|
+
{
|
504
|
+
static int virgin = 1;
|
505
|
+
static short lencnt[MAXBITS+1], lensym[FIXLCODES];
|
506
|
+
static short distcnt[MAXBITS+1], distsym[MAXDCODES];
|
507
|
+
static struct huffman lencode = {lencnt, lensym};
|
508
|
+
static struct huffman distcode = {distcnt, distsym};
|
509
|
+
|
510
|
+
/* build fixed huffman tables if first call (may not be thread safe) */
|
511
|
+
if (virgin) {
|
512
|
+
int symbol;
|
513
|
+
short lengths[FIXLCODES];
|
514
|
+
|
515
|
+
/* literal/length table */
|
516
|
+
for (symbol = 0; symbol < 144; symbol++)
|
517
|
+
lengths[symbol] = 8;
|
518
|
+
for (; symbol < 256; symbol++)
|
519
|
+
lengths[symbol] = 9;
|
520
|
+
for (; symbol < 280; symbol++)
|
521
|
+
lengths[symbol] = 7;
|
522
|
+
for (; symbol < FIXLCODES; symbol++)
|
523
|
+
lengths[symbol] = 8;
|
524
|
+
construct(&lencode, lengths, FIXLCODES);
|
525
|
+
|
526
|
+
/* distance table */
|
527
|
+
for (symbol = 0; symbol < MAXDCODES; symbol++)
|
528
|
+
lengths[symbol] = 5;
|
529
|
+
construct(&distcode, lengths, MAXDCODES);
|
530
|
+
|
531
|
+
/* do this just once */
|
532
|
+
virgin = 0;
|
533
|
+
}
|
534
|
+
|
535
|
+
/* decode data until end-of-block code */
|
536
|
+
return codes(s, &lencode, &distcode);
|
537
|
+
}
|
538
|
+
|
539
|
+
/*
|
540
|
+
* Process a dynamic codes block.
|
541
|
+
*
|
542
|
+
* Format notes:
|
543
|
+
*
|
544
|
+
* - A dynamic block starts with a description of the literal/length and
|
545
|
+
* distance codes for that block. New dynamic blocks allow the compressor to
|
546
|
+
* rapidly adapt to changing data with new codes optimized for that data.
|
547
|
+
*
|
548
|
+
* - The codes used by the deflate format are "canonical", which means that
|
549
|
+
* the actual bits of the codes are generated in an unambiguous way simply
|
550
|
+
* from the number of bits in each code. Therefore the code descriptions
|
551
|
+
* are simply a list of code lengths for each symbol.
|
552
|
+
*
|
553
|
+
* - The code lengths are stored in order for the symbols, so lengths are
|
554
|
+
* provided for each of the literal/length symbols, and for each of the
|
555
|
+
* distance symbols.
|
556
|
+
*
|
557
|
+
* - If a symbol is not used in the block, this is represented by a zero as
|
558
|
+
* as the code length. This does not mean a zero-length code, but rather
|
559
|
+
* that no code should be created for this symbol. There is no way in the
|
560
|
+
* deflate format to represent a zero-length code.
|
561
|
+
*
|
562
|
+
* - The maximum number of bits in a code is 15, so the possible lengths for
|
563
|
+
* any code are 1..15.
|
564
|
+
*
|
565
|
+
* - The fact that a length of zero is not permitted for a code has an
|
566
|
+
* interesting consequence. Normally if only one symbol is used for a given
|
567
|
+
* code, then in fact that code could be represented with zero bits. However
|
568
|
+
* in deflate, that code has to be at least one bit. So for example, if
|
569
|
+
* only a single distance base symbol appears in a block, then it will be
|
570
|
+
* represented by a single code of length one, in particular one 0 bit. This
|
571
|
+
* is an incomplete code, since if a 1 bit is received, it has no meaning,
|
572
|
+
* and should result in an error. So incomplete distance codes of one symbol
|
573
|
+
* should be permitted, and the receipt of invalid codes should be handled.
|
574
|
+
*
|
575
|
+
* - It is also possible to have a single literal/length code, but that code
|
576
|
+
* must be the end-of-block code, since every dynamic block has one. This
|
577
|
+
* is not the most efficient way to create an empty block (an empty fixed
|
578
|
+
* block is fewer bits), but it is allowed by the format. So incomplete
|
579
|
+
* literal/length codes of one symbol should also be permitted.
|
580
|
+
*
|
581
|
+
* - If there are only literal codes and no lengths, then there are no distance
|
582
|
+
* codes. This is represented by one distance code with zero bits.
|
583
|
+
*
|
584
|
+
* - The list of up to 286 length/literal lengths and up to 30 distance lengths
|
585
|
+
* are themselves compressed using Huffman codes and run-length encoding. In
|
586
|
+
* the list of code lengths, a 0 symbol means no code, a 1..15 symbol means
|
587
|
+
* that length, and the symbols 16, 17, and 18 are run-length instructions.
|
588
|
+
* Each of 16, 17, and 18 are follwed by extra bits to define the length of
|
589
|
+
* the run. 16 copies the last length 3 to 6 times. 17 represents 3 to 10
|
590
|
+
* zero lengths, and 18 represents 11 to 138 zero lengths. Unused symbols
|
591
|
+
* are common, hence the special coding for zero lengths.
|
592
|
+
*
|
593
|
+
* - The symbols for 0..18 are Huffman coded, and so that code must be
|
594
|
+
* described first. This is simply a sequence of up to 19 three-bit values
|
595
|
+
* representing no code (0) or the code length for that symbol (1..7).
|
596
|
+
*
|
597
|
+
* - A dynamic block starts with three fixed-size counts from which is computed
|
598
|
+
* the number of literal/length code lengths, the number of distance code
|
599
|
+
* lengths, and the number of code length code lengths (ok, you come up with
|
600
|
+
* a better name!) in the code descriptions. For the literal/length and
|
601
|
+
* distance codes, lengths after those provided are considered zero, i.e. no
|
602
|
+
* code. The code length code lengths are received in a permuted order (see
|
603
|
+
* the order[] array below) to make a short code length code length list more
|
604
|
+
* likely. As it turns out, very short and very long codes are less likely
|
605
|
+
* to be seen in a dynamic code description, hence what may appear initially
|
606
|
+
* to be a peculiar ordering.
|
607
|
+
*
|
608
|
+
* - Given the number of literal/length code lengths (nlen) and distance code
|
609
|
+
* lengths (ndist), then they are treated as one long list of nlen + ndist
|
610
|
+
* code lengths. Therefore run-length coding can and often does cross the
|
611
|
+
* boundary between the two sets of lengths.
|
612
|
+
*
|
613
|
+
* - So to summarize, the code description at the start of a dynamic block is
|
614
|
+
* three counts for the number of code lengths for the literal/length codes,
|
615
|
+
* the distance codes, and the code length codes. This is followed by the
|
616
|
+
* code length code lengths, three bits each. This is used to construct the
|
617
|
+
* code length code which is used to read the remainder of the lengths. Then
|
618
|
+
* the literal/length code lengths and distance lengths are read as a single
|
619
|
+
* set of lengths using the code length codes. Codes are constructed from
|
620
|
+
* the resulting two sets of lengths, and then finally you can start
|
621
|
+
* decoding actual compressed data in the block.
|
622
|
+
*
|
623
|
+
* - For reference, a "typical" size for the code description in a dynamic
|
624
|
+
* block is around 80 bytes.
|
625
|
+
*/
|
626
|
+
local int dynamic(struct state *s)
|
627
|
+
{
|
628
|
+
int nlen, ndist, ncode; /* number of lengths in descriptor */
|
629
|
+
int index; /* index of lengths[] */
|
630
|
+
int err; /* construct() return value */
|
631
|
+
short lengths[MAXCODES]; /* descriptor code lengths */
|
632
|
+
short lencnt[MAXBITS+1], lensym[MAXLCODES]; /* lencode memory */
|
633
|
+
short distcnt[MAXBITS+1], distsym[MAXDCODES]; /* distcode memory */
|
634
|
+
struct huffman lencode = {lencnt, lensym}; /* length code */
|
635
|
+
struct huffman distcode = {distcnt, distsym}; /* distance code */
|
636
|
+
static const short order[19] = /* permutation of code length codes */
|
637
|
+
{16, 17, 18, 0, 8, 7, 9, 6, 10, 5, 11, 4, 12, 3, 13, 2, 14, 1, 15};
|
638
|
+
|
639
|
+
/* get number of lengths in each table, check lengths */
|
640
|
+
nlen = bits(s, 5) + 257;
|
641
|
+
ndist = bits(s, 5) + 1;
|
642
|
+
ncode = bits(s, 4) + 4;
|
643
|
+
if (nlen > MAXLCODES || ndist > MAXDCODES)
|
644
|
+
return -3; /* bad counts */
|
645
|
+
|
646
|
+
/* read code length code lengths (really), missing lengths are zero */
|
647
|
+
for (index = 0; index < ncode; index++)
|
648
|
+
lengths[order[index]] = bits(s, 3);
|
649
|
+
for (; index < 19; index++)
|
650
|
+
lengths[order[index]] = 0;
|
651
|
+
|
652
|
+
/* build huffman table for code lengths codes (use lencode temporarily) */
|
653
|
+
err = construct(&lencode, lengths, 19);
|
654
|
+
if (err != 0) return -4; /* require complete code set here */
|
655
|
+
|
656
|
+
/* read length/literal and distance code length tables */
|
657
|
+
index = 0;
|
658
|
+
while (index < nlen + ndist) {
|
659
|
+
int symbol; /* decoded value */
|
660
|
+
int len; /* last length to repeat */
|
661
|
+
|
662
|
+
symbol = decode(s, &lencode);
|
663
|
+
if (symbol < 16) /* length in 0..15 */
|
664
|
+
lengths[index++] = symbol;
|
665
|
+
else { /* repeat instruction */
|
666
|
+
len = 0; /* assume repeating zeros */
|
667
|
+
if (symbol == 16) { /* repeat last length 3..6 times */
|
668
|
+
if (index == 0) return -5; /* no last length! */
|
669
|
+
len = lengths[index - 1]; /* last length */
|
670
|
+
symbol = 3 + bits(s, 2);
|
671
|
+
}
|
672
|
+
else if (symbol == 17) /* repeat zero 3..10 times */
|
673
|
+
symbol = 3 + bits(s, 3);
|
674
|
+
else /* == 18, repeat zero 11..138 times */
|
675
|
+
symbol = 11 + bits(s, 7);
|
676
|
+
if (index + symbol > nlen + ndist)
|
677
|
+
return -6; /* too many lengths! */
|
678
|
+
while (symbol--) /* repeat last or zero symbol times */
|
679
|
+
lengths[index++] = len;
|
680
|
+
}
|
681
|
+
}
|
682
|
+
|
683
|
+
/* build huffman table for literal/length codes */
|
684
|
+
err = construct(&lencode, lengths, nlen);
|
685
|
+
if (err < 0 || (err > 0 && nlen - lencode.count[0] != 1))
|
686
|
+
return -7; /* only allow incomplete codes if just one code */
|
687
|
+
|
688
|
+
/* build huffman table for distance codes */
|
689
|
+
err = construct(&distcode, lengths + nlen, ndist);
|
690
|
+
if (err < 0 || (err > 0 && ndist - distcode.count[0] != 1))
|
691
|
+
return -8; /* only allow incomplete codes if just one code */
|
692
|
+
|
693
|
+
/* decode data until end-of-block code */
|
694
|
+
return codes(s, &lencode, &distcode);
|
695
|
+
}
|
696
|
+
|
697
|
+
/*
|
698
|
+
* Inflate source to dest. On return, destlen and sourcelen are updated to the
|
699
|
+
* size of the uncompressed data and the size of the deflate data respectively.
|
700
|
+
* On success, the return value of puff() is zero. If there is an error in the
|
701
|
+
* source data, i.e. it is not in the deflate format, then a negative value is
|
702
|
+
* returned. If there is not enough input available or there is not enough
|
703
|
+
* output space, then a positive error is returned. In that case, destlen and
|
704
|
+
* sourcelen are not updated to facilitate retrying from the beginning with the
|
705
|
+
* provision of more input data or more output space. In the case of invalid
|
706
|
+
* inflate data (a negative error), the dest and source pointers are updated to
|
707
|
+
* facilitate the debugging of deflators.
|
708
|
+
*
|
709
|
+
* puff() also has a mode to determine the size of the uncompressed output with
|
710
|
+
* no output written. For this dest must be (unsigned char *)0. In this case,
|
711
|
+
* the input value of *destlen is ignored, and on return *destlen is set to the
|
712
|
+
* size of the uncompressed output.
|
713
|
+
*
|
714
|
+
* The return codes are:
|
715
|
+
*
|
716
|
+
* 2: available inflate data did not terminate
|
717
|
+
* 1: output space exhausted before completing inflate
|
718
|
+
* 0: successful inflate
|
719
|
+
* -1: invalid block type (type == 3)
|
720
|
+
* -2: stored block length did not match one's complement
|
721
|
+
* -3: dynamic block code description: too many length or distance codes
|
722
|
+
* -4: dynamic block code description: code lengths codes incomplete
|
723
|
+
* -5: dynamic block code description: repeat lengths with no first length
|
724
|
+
* -6: dynamic block code description: repeat more than specified lengths
|
725
|
+
* -7: dynamic block code description: invalid literal/length code lengths
|
726
|
+
* -8: dynamic block code description: invalid distance code lengths
|
727
|
+
* -9: invalid literal/length or distance code in fixed or dynamic block
|
728
|
+
* -10: distance is too far back in fixed or dynamic block
|
729
|
+
*
|
730
|
+
* Format notes:
|
731
|
+
*
|
732
|
+
* - Three bits are read for each block to determine the kind of block and
|
733
|
+
* whether or not it is the last block. Then the block is decoded and the
|
734
|
+
* process repeated if it was not the last block.
|
735
|
+
*
|
736
|
+
* - The leftover bits in the last byte of the deflate data after the last
|
737
|
+
* block (if it was a fixed or dynamic block) are undefined and have no
|
738
|
+
* expected values to check.
|
739
|
+
*/
|
740
|
+
int puff(unsigned char *dest, /* pointer to destination pointer */
|
741
|
+
unsigned long *destlen, /* amount of output space */
|
742
|
+
unsigned char *source, /* pointer to source data pointer */
|
743
|
+
unsigned long *sourcelen) /* amount of input available */
|
744
|
+
{
|
745
|
+
struct state s; /* input/output state */
|
746
|
+
int last, type; /* block information */
|
747
|
+
int err; /* return value */
|
748
|
+
|
749
|
+
/* initialize output state */
|
750
|
+
s.out = dest;
|
751
|
+
s.outlen = *destlen; /* ignored if dest is NIL */
|
752
|
+
s.outcnt = 0;
|
753
|
+
|
754
|
+
/* initialize input state */
|
755
|
+
s.in = source;
|
756
|
+
s.inlen = *sourcelen;
|
757
|
+
s.incnt = 0;
|
758
|
+
s.bitbuf = 0;
|
759
|
+
s.bitcnt = 0;
|
760
|
+
|
761
|
+
/* return if bits() or decode() tries to read past available input */
|
762
|
+
if (setjmp(s.env) != 0) /* if came back here via longjmp() */
|
763
|
+
err = 2; /* then skip do-loop, return error */
|
764
|
+
else {
|
765
|
+
/* process blocks until last block or error */
|
766
|
+
do {
|
767
|
+
last = bits(&s, 1); /* one if last block */
|
768
|
+
type = bits(&s, 2); /* block type 0..3 */
|
769
|
+
err = type == 0 ? stored(&s) :
|
770
|
+
(type == 1 ? fixed(&s) :
|
771
|
+
(type == 2 ? dynamic(&s) :
|
772
|
+
-1)); /* type == 3, invalid */
|
773
|
+
if (err != 0) break; /* return with error */
|
774
|
+
} while (!last);
|
775
|
+
}
|
776
|
+
|
777
|
+
/* update the lengths and return */
|
778
|
+
if (err <= 0) {
|
779
|
+
*destlen = s.outcnt;
|
780
|
+
*sourcelen = s.incnt;
|
781
|
+
}
|
782
|
+
return err;
|
783
|
+
}
|
784
|
+
|
785
|
+
#ifdef TEST
|
786
|
+
/* Example of how to use puff() */
|
787
|
+
#include <stdio.h>
|
788
|
+
#include <stdlib.h>
|
789
|
+
#include <sys/types.h>
|
790
|
+
#include <sys/stat.h>
|
791
|
+
|
792
|
+
local unsigned char *yank(char *name, unsigned long *len)
|
793
|
+
{
|
794
|
+
unsigned long size;
|
795
|
+
unsigned char *buf;
|
796
|
+
FILE *in;
|
797
|
+
struct stat s;
|
798
|
+
|
799
|
+
*len = 0;
|
800
|
+
if (stat(name, &s)) return NULL;
|
801
|
+
if ((s.st_mode & S_IFMT) != S_IFREG) return NULL;
|
802
|
+
size = (unsigned long)(s.st_size);
|
803
|
+
if (size == 0 || (off_t)size != s.st_size) return NULL;
|
804
|
+
in = fopen(name, "r");
|
805
|
+
if (in == NULL) return NULL;
|
806
|
+
buf = malloc(size);
|
807
|
+
if (buf != NULL && fread(buf, 1, size, in) != size) {
|
808
|
+
free(buf);
|
809
|
+
buf = NULL;
|
810
|
+
}
|
811
|
+
fclose(in);
|
812
|
+
*len = size;
|
813
|
+
return buf;
|
814
|
+
}
|
815
|
+
|
816
|
+
int main(int argc, char **argv)
|
817
|
+
{
|
818
|
+
int ret;
|
819
|
+
unsigned char *source;
|
820
|
+
unsigned long len, sourcelen, destlen;
|
821
|
+
|
822
|
+
if (argc < 2) return 2;
|
823
|
+
source = yank(argv[1], &len);
|
824
|
+
if (source == NULL) return 2;
|
825
|
+
sourcelen = len;
|
826
|
+
ret = puff(NIL, &destlen, source, &sourcelen);
|
827
|
+
if (ret)
|
828
|
+
printf("puff() failed with return code %d\n", ret);
|
829
|
+
else {
|
830
|
+
printf("puff() succeeded uncompressing %lu bytes\n", destlen);
|
831
|
+
if (sourcelen < len) printf("%lu compressed bytes unused\n",
|
832
|
+
len - sourcelen);
|
833
|
+
}
|
834
|
+
free(source);
|
835
|
+
return ret;
|
836
|
+
}
|
837
|
+
#endif
|