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/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
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/* gzlog.h
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Copyright (C) 2004 Mark Adler, all rights reserved
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version 1.0, 26 Nov 2004
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This software is provided 'as-is', without any express or implied
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warranty. In no event will the author be held liable for any damages
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arising from the use of this software.
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Permission is granted to anyone to use this software for any purpose,
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including commercial applications, and to alter it and redistribute it
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freely, subject to the following restrictions:
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1. The origin of this software must not be misrepresented; you must not
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claim that you wrote the original software. If you use this software
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in a product, an acknowledgment in the product documentation would be
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appreciated but is not required.
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2. Altered source versions must be plainly marked as such, and must not be
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misrepresented as being the original software.
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3. This notice may not be removed or altered from any source distribution.
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Mark Adler madler@alumni.caltech.edu
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*/
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/*
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The gzlog object allows writing short messages to a gzipped log file,
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opening the log file locked for small bursts, and then closing it. The log
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object works by appending stored data to the gzip file until 1 MB has been
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accumulated. At that time, the stored data is compressed, and replaces the
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uncompressed data in the file. The log file is truncated to its new size at
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that time. After closing, the log file is always valid gzip file that can
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decompressed to recover what was written.
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A gzip header "extra" field contains two file offsets for appending. The
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first points to just after the last compressed data. The second points to
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the last stored block in the deflate stream, which is empty. All of the
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data between those pointers is uncompressed.
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*/
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/* Open a gzlog object, creating the log file if it does not exist. Return
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NULL on error. Note that gzlog_open() could take a long time to return if
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there is difficulty in locking the file. */
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void *gzlog_open(char *path);
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/* Write to a gzlog object. Return non-zero on error. This function will
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simply write data to the file uncompressed. Compression of the data
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will not occur until gzlog_close() is called. It is expected that
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gzlog_write() is used for a short message, and then gzlog_close() is
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called. If a large amount of data is to be written, then the application
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should write no more than 1 MB at a time with gzlog_write() before
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calling gzlog_close() and then gzlog_open() again. */
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int gzlog_write(void *log, char *data, size_t len);
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/* Close a gzlog object. Return non-zero on error. The log file is locked
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until this function is called. This function will compress stored data
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at the end of the gzip file if at least 1 MB has been accumulated. Note
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that the file will not be a valid gzip file until this function completes.
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*/
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int gzlog_close(void *log);
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"
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"http://www.w3.org/TR/REC-html40/loose.dtd">
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<html>
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<head>
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<meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1">
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<title>zlib Usage Example</title>
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<!-- Copyright (c) 2004 Mark Adler. -->
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</head>
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<body bgcolor="#FFFFFF" text="#000000" link="#0000FF" vlink="#00A000">
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<h2 align="center"> zlib Usage Example </h2>
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We often get questions about how the <tt>deflate()</tt> and <tt>inflate()</tt> functions should be used.
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Users wonder when they should provide more input, when they should use more output,
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what to do with a <tt>Z_BUF_ERROR</tt>, how to make sure the process terminates properly, and
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so on. So for those who have read <tt>zlib.h</tt> (a few times), and
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would like further edification, below is an annotated example in C of simple routines to compress and decompress
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from an input file to an output file using <tt>deflate()</tt> and <tt>inflate()</tt> respectively. The
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annotations are interspersed between lines of the code. So please read between the lines.
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We hope this helps explain some of the intricacies of <em>zlib</em>.
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<p>
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Without further adieu, here is the program <a href="zpipe.c"><tt>zpipe.c</tt></a>:
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<pre><b>
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/* zpipe.c: example of proper use of zlib's inflate() and deflate()
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Not copyrighted -- provided to the public domain
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Version 1.2 9 November 2004 Mark Adler */
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/* Version history:
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1.0 30 Oct 2004 First version
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1.1 8 Nov 2004 Add void casting for unused return values
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Use switch statement for inflate() return values
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1.2 9 Nov 2004 Add assertions to document zlib guarantees
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*/
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</b></pre><!-- -->
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We now include the header files for the required definitions. From
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<tt>stdio.h</tt> we use <tt>fopen()</tt>, <tt>fread()</tt>, <tt>fwrite()</tt>,
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<tt>feof()</tt>, <tt>ferror()</tt>, and <tt>fclose()</tt> for file i/o, and
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<tt>fputs()</tt> for error messages. From <tt>string.h</tt> we use
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<tt>strcmp()</tt> for command line argument processing.
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From <tt>assert.h</tt> we use the <tt>assert()</tt> macro.
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From <tt>zlib.h</tt>
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we use the basic compression functions <tt>deflateInit()</tt>,
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<tt>deflate()</tt>, and <tt>deflateEnd()</tt>, and the basic decompression
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functions <tt>inflateInit()</tt>, <tt>inflate()</tt>, and
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<tt>inflateEnd()</tt>.
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<pre><b>
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#include <stdio.h>
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#include <string.h>
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#include <assert.h>
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#include "zlib.h"
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</b></pre><!-- -->
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<tt>CHUNK</tt> is simply the buffer size for feeding data to and pulling data
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from the <em>zlib</em> routines. Larger buffer sizes would be more efficient,
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especially for <tt>inflate()</tt>. If the memory is available, buffers sizes
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on the order of 128K or 256K bytes should be used.
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<pre><b>
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#define CHUNK 16384
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</b></pre><!-- -->
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The <tt>def()</tt> routine compresses data from an input file to an output file. The output data
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will be in the <em>zlib</em> format, which is different from the <em>gzip</em> or <em>zip</em>
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formats. The <em>zlib</em> format has a very small header of only two bytes to identify it as
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a <em>zlib</em> stream and to provide decoding information, and a four-byte trailer with a fast
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check value to verify the integrity of the uncompressed data after decoding.
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<pre><b>
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/* Compress from file source to file dest until EOF on source.
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def() returns Z_OK on success, Z_MEM_ERROR if memory could not be
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allocated for processing, Z_STREAM_ERROR if an invalid compression
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level is supplied, Z_VERSION_ERROR if the version of zlib.h and the
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version of the library linked do not match, or Z_ERRNO if there is
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an error reading or writing the files. */
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int def(FILE *source, FILE *dest, int level)
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{
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</b></pre>
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Here are the local variables for <tt>def()</tt>. <tt>ret</tt> will be used for <em>zlib</em>
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return codes. <tt>flush</tt> will keep track of the current flushing state for <tt>deflate()</tt>,
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which is either no flushing, or flush to completion after the end of the input file is reached.
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<tt>have</tt> is the amount of data returned from <tt>deflate()</tt>. The <tt>strm</tt> structure
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is used to pass information to and from the <em>zlib</em> routines, and to maintain the
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<tt>deflate()</tt> state. <tt>in</tt> and <tt>out</tt> are the input and output buffers for
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<tt>deflate()</tt>.
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<pre><b>
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int ret, flush;
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unsigned have;
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z_stream strm;
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char in[CHUNK];
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char out[CHUNK];
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</b></pre><!-- -->
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The first thing we do is to initialize the <em>zlib</em> state for compression using
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<tt>deflateInit()</tt>. This must be done before the first use of <tt>deflate()</tt>.
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The <tt>zalloc</tt>, <tt>zfree</tt>, and <tt>opaque</tt> fields in the <tt>strm</tt>
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structure must be initialized before calling <tt>deflateInit()</tt>. Here they are
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set to the <em>zlib</em> constant <tt>Z_NULL</tt> to request that <em>zlib</em> use
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the default memory allocation routines. An application may also choose to provide
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custom memory allocation routines here. <tt>deflateInit()</tt> will allocate on the
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order of 256K bytes for the internal state.
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(See <a href="zlib_tech.html"><em>zlib Technical Details</em></a>.)
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<p>
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<tt>deflateInit()</tt> is called with a pointer to the structure to be initialized and
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the compression level, which is an integer in the range of -1 to 9. Lower compression
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levels result in faster execution, but less compression. Higher levels result in
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greater compression, but slower execution. The <em>zlib</em> constant Z_DEFAULT_COMPRESSION,
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equal to -1,
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provides a good compromise between compression and speed and is equivalent to level 6.
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Level 0 actually does no compression at all, and in fact expands the data slightly to produce
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the <em>zlib</em> format (it is not a byte-for-byte copy of the input).
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More advanced applications of <em>zlib</em>
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may use <tt>deflateInit2()</tt> here instead. Such an application may want to reduce how
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much memory will be used, at some price in compression. Or it may need to request a
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<em>gzip</em> header and trailer instead of a <em>zlib</em> header and trailer, or raw
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encoding with no header or trailer at all.
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<p>
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We must check the return value of <tt>deflateInit()</tt> against the <em>zlib</em> constant
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<tt>Z_OK</tt> to make sure that it was able to
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allocate memory for the internal state, and that the provided arguments were valid.
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<tt>deflateInit()</tt> will also check that the version of <em>zlib</em> that the <tt>zlib.h</tt>
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file came from matches the version of <em>zlib</em> actually linked with the program. This
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is especially important for environments in which <em>zlib</em> is a shared library.
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<p>
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Note that an application can initialize multiple, independent <em>zlib</em> streams, which can
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operate in parallel. The state information maintained in the structure allows the <em>zlib</em>
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routines to be reentrant.
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<pre><b>
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/* allocate deflate state */
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strm.zalloc = Z_NULL;
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strm.zfree = Z_NULL;
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strm.opaque = Z_NULL;
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ret = deflateInit(&strm, level);
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if (ret != Z_OK)
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return ret;
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</b></pre><!-- -->
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With the pleasantries out of the way, now we can get down to business. The outer <tt>do</tt>-loop
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reads all of the input file and exits at the bottom of the loop once end-of-file is reached.
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This loop contains the only call of <tt>deflate()</tt>. So we must make sure that all of the
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input data has been processed and that all of the output data has been generated and consumed
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before we fall out of the loop at the bottom.
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<pre><b>
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/* compress until end of file */
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do {
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</b></pre>
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We start off by reading data from the input file. The number of bytes read is put directly
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into <tt>avail_in</tt>, and a pointer to those bytes is put into <tt>next_in</tt>. We also
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check to see if end-of-file on the input has been reached. If we are at the end of file, then <tt>flush</tt> is set to the
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<em>zlib</em> constant <tt>Z_FINISH</tt>, which is later passed to <tt>deflate()</tt> to
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indicate that this is the last chunk of input data to compress. We need to use <tt>feof()</tt>
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to check for end-of-file as opposed to seeing if fewer than <tt>CHUNK</tt> bytes have been read. The
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reason is that if the input file length is an exact multiple of <tt>CHUNK</tt>, we will miss
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the fact that we got to the end-of-file, and not know to tell <tt>deflate()</tt> to finish
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up the compressed stream. If we are not yet at the end of the input, then the <em>zlib</em>
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constant <tt>Z_NO_FLUSH</tt> will be passed to <tt>deflate</tt> to indicate that we are still
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in the middle of the uncompressed data.
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<p>
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If there is an error in reading from the input file, the process is aborted with
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<tt>deflateEnd()</tt> being called to free the allocated <em>zlib</em> state before returning
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the error. We wouldn't want a memory leak, now would we? <tt>deflateEnd()</tt> can be called
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at any time after the state has been initialized. Once that's done, <tt>deflateInit()</tt> (or
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<tt>deflateInit2()</tt>) would have to be called to start a new compression process. There is
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no point here in checking the <tt>deflateEnd()</tt> return code. The deallocation can't fail.
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<pre><b>
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strm.avail_in = fread(in, 1, CHUNK, source);
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if (ferror(source)) {
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(void)deflateEnd(&strm);
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return Z_ERRNO;
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}
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flush = feof(source) ? Z_FINISH : Z_NO_FLUSH;
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strm.next_in = in;
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</b></pre><!-- -->
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The inner <tt>do</tt>-loop passes our chunk of input data to <tt>deflate()</tt>, and then
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keeps calling <tt>deflate()</tt> until it is done producing output. Once there is no more
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new output, <tt>deflate()</tt> is guaranteed to have consumed all of the input, i.e.,
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<tt>avail_in</tt> will be zero.
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<pre><b>
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/* run deflate() on input until output buffer not full, finish
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compression if all of source has been read in */
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do {
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</b></pre>
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Output space is provided to <tt>deflate()</tt> by setting <tt>avail_out</tt> to the number
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of available output bytes and <tt>next_out</tt> to a pointer to that space.
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<pre><b>
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strm.avail_out = CHUNK;
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strm.next_out = out;
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</b></pre>
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Now we call the compression engine itself, <tt>deflate()</tt>. It takes as many of the
|
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<tt>avail_in</tt> bytes at <tt>next_in</tt> as it can process, and writes as many as
|
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<tt>avail_out</tt> bytes to <tt>next_out</tt>. Those counters and pointers are then
|
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updated past the input data consumed and the output data written. It is the amount of
|
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|
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output space available that may limit how much input is consumed.
|
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Hence the inner loop to make sure that
|
|
186
|
+
all of the input is consumed by providing more output space each time. Since <tt>avail_in</tt>
|
|
187
|
+
and <tt>next_in</tt> are updated by <tt>deflate()</tt>, we don't have to mess with those
|
|
188
|
+
between <tt>deflate()</tt> calls until it's all used up.
|
|
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<p>
|
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|
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The parameters to <tt>deflate()</tt> are a pointer to the <tt>strm</tt> structure containing
|
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191
|
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the input and output information and the internal compression engine state, and a parameter
|
|
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+
indicating whether and how to flush data to the output. Normally <tt>deflate</tt> will consume
|
|
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|
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several K bytes of input data before producing any output (except for the header), in order
|
|
194
|
+
to accumulate statistics on the data for optimum compression. It will then put out a burst of
|
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195
|
+
compressed data, and proceed to consume more input before the next burst. Eventually,
|
|
196
|
+
<tt>deflate()</tt>
|
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197
|
+
must be told to terminate the stream, complete the compression with provided input data, and
|
|
198
|
+
write out the trailer check value. <tt>deflate()</tt> will continue to compress normally as long
|
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199
|
+
as the flush parameter is <tt>Z_NO_FLUSH</tt>. Once the <tt>Z_FINISH</tt> parameter is provided,
|
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200
|
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<tt>deflate()</tt> will begin to complete the compressed output stream. However depending on how
|
|
201
|
+
much output space is provided, <tt>deflate()</tt> may have to be called several times until it
|
|
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|
+
has provided the complete compressed stream, even after it has consumed all of the input. The flush
|
|
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|
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parameter must continue to be <tt>Z_FINISH</tt> for those subsequent calls.
|
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<p>
|
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|
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There are other values of the flush parameter that are used in more advanced applications. You can
|
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|
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force <tt>deflate()</tt> to produce a burst of output that encodes all of the input data provided
|
|
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|
+
so far, even if it wouldn't have otherwise, for example to control data latency on a link with
|
|
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|
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compressed data. You can also ask that <tt>deflate()</tt> do that as well as erase any history up to
|
|
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|
+
that point so that what follows can be decompressed independently, for example for random access
|
|
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|
+
applications. Both requests will degrade compression by an amount depending on how often such
|
|
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|
+
requests are made.
|
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|
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<p>
|
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|
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<tt>deflate()</tt> has a return value that can indicate errors, yet we do not check it here. Why
|
|
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|
+
not? Well, it turns out that <tt>deflate()</tt> can do no wrong here. Let's go through
|
|
215
|
+
<tt>deflate()</tt>'s return values and dispense with them one by one. The possible values are
|
|
216
|
+
<tt>Z_OK</tt>, <tt>Z_STREAM_END</tt>, <tt>Z_STREAM_ERROR</tt>, or <tt>Z_BUF_ERROR</tt>. <tt>Z_OK</tt>
|
|
217
|
+
is, well, ok. <tt>Z_STREAM_END</tt> is also ok and will be returned for the last call of
|
|
218
|
+
<tt>deflate()</tt>. This is already guaranteed by calling <tt>deflate()</tt> with <tt>Z_FINISH</tt>
|
|
219
|
+
until it has no more output. <tt>Z_STREAM_ERROR</tt> is only possible if the stream is not
|
|
220
|
+
initialized properly, but we did initialize it properly. There is no harm in checking for
|
|
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|
+
<tt>Z_STREAM_ERROR</tt> here, for example to check for the possibility that some
|
|
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|
+
other part of the application inadvertently clobbered the memory containing the <em>zlib</em> state.
|
|
223
|
+
<tt>Z_BUF_ERROR</tt> will be explained further below, but
|
|
224
|
+
suffice it to say that this is simply an indication that <tt>deflate()</tt> could not consume
|
|
225
|
+
more input or produce more output. <tt>deflate()</tt> can be called again with more output space
|
|
226
|
+
or more available input, which it will be in this code.
|
|
227
|
+
<pre><b>
|
|
228
|
+
ret = deflate(&strm, flush); /* no bad return value */
|
|
229
|
+
assert(ret != Z_STREAM_ERROR); /* state not clobbered */
|
|
230
|
+
</b></pre>
|
|
231
|
+
Now we compute how much output <tt>deflate()</tt> provided on the last call, which is the
|
|
232
|
+
difference between how much space was provided before the call, and how much output space
|
|
233
|
+
is still available after the call. Then that data, if any, is written to the output file.
|
|
234
|
+
We can then reuse the output buffer for the next call of <tt>deflate()</tt>. Again if there
|
|
235
|
+
is a file i/o error, we call <tt>deflateEnd()</tt> before returning to avoid a memory leak.
|
|
236
|
+
<pre><b>
|
|
237
|
+
have = CHUNK - strm.avail_out;
|
|
238
|
+
if (fwrite(out, 1, have, dest) != have || ferror(dest)) {
|
|
239
|
+
(void)deflateEnd(&strm);
|
|
240
|
+
return Z_ERRNO;
|
|
241
|
+
}
|
|
242
|
+
</b></pre>
|
|
243
|
+
The inner <tt>do</tt>-loop is repeated until the last <tt>deflate()</tt> call fails to fill the
|
|
244
|
+
provided output buffer. Then we know that <tt>deflate()</tt> has done as much as it can with
|
|
245
|
+
the provided input, and that all of that input has been consumed. We can then fall out of this
|
|
246
|
+
loop and reuse the input buffer.
|
|
247
|
+
<p>
|
|
248
|
+
The way we tell that <tt>deflate()</tt> has no more output is by seeing that it did not fill
|
|
249
|
+
the output buffer, leaving <tt>avail_out</tt> greater than zero. However suppose that
|
|
250
|
+
<tt>deflate()</tt> has no more output, but just so happened to exactly fill the output buffer!
|
|
251
|
+
<tt>avail_out</tt> is zero, and we can't tell that <tt>deflate()</tt> has done all it can.
|
|
252
|
+
As far as we know, <tt>deflate()</tt>
|
|
253
|
+
has more output for us. So we call it again. But now <tt>deflate()</tt> produces no output
|
|
254
|
+
at all, and <tt>avail_out</tt> remains unchanged as <tt>CHUNK</tt>. That <tt>deflate()</tt> call
|
|
255
|
+
wasn't able to do anything, either consume input or produce output, and so it returns
|
|
256
|
+
<tt>Z_BUF_ERROR</tt>. (See, I told you I'd cover this later.) However this is not a problem at
|
|
257
|
+
all. Now we finally have the desired indication that <tt>deflate()</tt> is really done,
|
|
258
|
+
and so we drop out of the inner loop to provide more input to <tt>deflate()</tt>.
|
|
259
|
+
<p>
|
|
260
|
+
With <tt>flush</tt> set to <tt>Z_FINISH</tt>, this final set of <tt>deflate()</tt> calls will
|
|
261
|
+
complete the output stream. Once that is done, subsequent calls of <tt>deflate()</tt> would return
|
|
262
|
+
<tt>Z_STREAM_ERROR</tt> if the flush parameter is not <tt>Z_FINISH</tt>, and do no more processing
|
|
263
|
+
until the state is reinitialized.
|
|
264
|
+
<p>
|
|
265
|
+
Some applications of <em>zlib</em> have two loops that call <tt>deflate()</tt>
|
|
266
|
+
instead of the single inner loop we have here. The first loop would call
|
|
267
|
+
without flushing and feed all of the data to <tt>deflate()</tt>. The second loop would call
|
|
268
|
+
<tt>deflate()</tt> with no more
|
|
269
|
+
data and the <tt>Z_FINISH</tt> parameter to complete the process. As you can see from this
|
|
270
|
+
example, that can be avoided by simply keeping track of the current flush state.
|
|
271
|
+
<pre><b>
|
|
272
|
+
} while (strm.avail_out == 0);
|
|
273
|
+
assert(strm.avail_in == 0); /* all input will be used */
|
|
274
|
+
</b></pre><!-- -->
|
|
275
|
+
Now we check to see if we have already processed all of the input file. That information was
|
|
276
|
+
saved in the <tt>flush</tt> variable, so we see if that was set to <tt>Z_FINISH</tt>. If so,
|
|
277
|
+
then we're done and we fall out of the outer loop. We're guaranteed to get <tt>Z_STREAM_END</tt>
|
|
278
|
+
from the last <tt>deflate()</tt> call, since we ran it until the last chunk of input was
|
|
279
|
+
consumed and all of the output was generated.
|
|
280
|
+
<pre><b>
|
|
281
|
+
/* done when last data in file processed */
|
|
282
|
+
} while (flush != Z_FINISH);
|
|
283
|
+
assert(ret == Z_STREAM_END); /* stream will be complete */
|
|
284
|
+
</b></pre><!-- -->
|
|
285
|
+
The process is complete, but we still need to deallocate the state to avoid a memory leak
|
|
286
|
+
(or rather more like a memory hemorrhage if you didn't do this). Then
|
|
287
|
+
finally we can return with a happy return value.
|
|
288
|
+
<pre><b>
|
|
289
|
+
/* clean up and return */
|
|
290
|
+
(void)deflateEnd(&strm);
|
|
291
|
+
return Z_OK;
|
|
292
|
+
}
|
|
293
|
+
</b></pre><!-- -->
|
|
294
|
+
Now we do the same thing for decompression in the <tt>inf()</tt> routine. <tt>inf()</tt>
|
|
295
|
+
decompresses what is hopefully a valid <em>zlib</em> stream from the input file and writes the
|
|
296
|
+
uncompressed data to the output file. Much of the discussion above for <tt>def()</tt>
|
|
297
|
+
applies to <tt>inf()</tt> as well, so the discussion here will focus on the differences between
|
|
298
|
+
the two.
|
|
299
|
+
<pre><b>
|
|
300
|
+
/* Decompress from file source to file dest until stream ends or EOF.
|
|
301
|
+
inf() returns Z_OK on success, Z_MEM_ERROR if memory could not be
|
|
302
|
+
allocated for processing, Z_DATA_ERROR if the deflate data is
|
|
303
|
+
invalid or incomplete, Z_VERSION_ERROR if the version of zlib.h and
|
|
304
|
+
the version of the library linked do not match, or Z_ERRNO if there
|
|
305
|
+
is an error reading or writing the files. */
|
|
306
|
+
int inf(FILE *source, FILE *dest)
|
|
307
|
+
{
|
|
308
|
+
</b></pre>
|
|
309
|
+
The local variables have the same functionality as they do for <tt>def()</tt>. The
|
|
310
|
+
only difference is that there is no <tt>flush</tt> variable, since <tt>inflate()</tt>
|
|
311
|
+
can tell from the <em>zlib</em> stream itself when the stream is complete.
|
|
312
|
+
<pre><b>
|
|
313
|
+
int ret;
|
|
314
|
+
unsigned have;
|
|
315
|
+
z_stream strm;
|
|
316
|
+
char in[CHUNK];
|
|
317
|
+
char out[CHUNK];
|
|
318
|
+
</b></pre><!-- -->
|
|
319
|
+
The initialization of the state is the same, except that there is no compression level,
|
|
320
|
+
of course, and two more elements of the structure are initialized. <tt>avail_in</tt>
|
|
321
|
+
and <tt>next_in</tt> must be initialized before calling <tt>inflateInit()</tt>. This
|
|
322
|
+
is because the application has the option to provide the start of the zlib stream in
|
|
323
|
+
order for <tt>inflateInit()</tt> to have access to information about the compression
|
|
324
|
+
method to aid in memory allocation. In the current implementation of <em>zlib</em>
|
|
325
|
+
(up through versions 1.2.x), the method-dependent memory allocations are deferred to the first call of
|
|
326
|
+
<tt>inflate()</tt> anyway. However those fields must be initialized since later versions
|
|
327
|
+
of <em>zlib</em> that provide more compression methods may take advantage of this interface.
|
|
328
|
+
In any case, no decompression is performed by <tt>inflateInit()</tt>, so the
|
|
329
|
+
<tt>avail_out</tt> and <tt>next_out</tt> fields do not need to be initialized before calling.
|
|
330
|
+
<p>
|
|
331
|
+
Here <tt>avail_in</tt> is set to zero and <tt>next_in</tt> is set to <tt>Z_NULL</tt> to
|
|
332
|
+
indicate that no input data is being provided.
|
|
333
|
+
<pre><b>
|
|
334
|
+
/* allocate inflate state */
|
|
335
|
+
strm.zalloc = Z_NULL;
|
|
336
|
+
strm.zfree = Z_NULL;
|
|
337
|
+
strm.opaque = Z_NULL;
|
|
338
|
+
strm.avail_in = 0;
|
|
339
|
+
strm.next_in = Z_NULL;
|
|
340
|
+
ret = inflateInit(&strm);
|
|
341
|
+
if (ret != Z_OK)
|
|
342
|
+
return ret;
|
|
343
|
+
</b></pre><!-- -->
|
|
344
|
+
The outer <tt>do</tt>-loop decompresses input until <tt>inflate()</tt> indicates
|
|
345
|
+
that it has reached the end of the compressed data and has produced all of the uncompressed
|
|
346
|
+
output. This is in contrast to <tt>def()</tt> which processes all of the input file.
|
|
347
|
+
If end-of-file is reached before the compressed data self-terminates, then the compressed
|
|
348
|
+
data is incomplete and an error is returned.
|
|
349
|
+
<pre><b>
|
|
350
|
+
/* decompress until deflate stream ends or end of file */
|
|
351
|
+
do {
|
|
352
|
+
</b></pre>
|
|
353
|
+
We read input data and set the <tt>strm</tt> structure accordingly. If we've reached the
|
|
354
|
+
end of the input file, then we leave the outer loop and report an error, since the
|
|
355
|
+
compressed data is incomplete. Note that we may read more data than is eventually consumed
|
|
356
|
+
by <tt>inflate()</tt>, if the input file continues past the <em>zlib</em> stream.
|
|
357
|
+
For applications where <em>zlib</em> streams are embedded in other data, this routine would
|
|
358
|
+
need to be modified to return the unused data, or at least indicate how much of the input
|
|
359
|
+
data was not used, so the application would know where to pick up after the <em>zlib</em> stream.
|
|
360
|
+
<pre><b>
|
|
361
|
+
strm.avail_in = fread(in, 1, CHUNK, source);
|
|
362
|
+
if (ferror(source)) {
|
|
363
|
+
(void)inflateEnd(&strm);
|
|
364
|
+
return Z_ERRNO;
|
|
365
|
+
}
|
|
366
|
+
if (strm.avail_in == 0)
|
|
367
|
+
break;
|
|
368
|
+
strm.next_in = in;
|
|
369
|
+
</b></pre><!-- -->
|
|
370
|
+
The inner <tt>do</tt>-loop has the same function it did in <tt>def()</tt>, which is to
|
|
371
|
+
keep calling <tt>inflate()</tt> until has generated all of the output it can with the
|
|
372
|
+
provided input.
|
|
373
|
+
<pre><b>
|
|
374
|
+
/* run inflate() on input until output buffer not full */
|
|
375
|
+
do {
|
|
376
|
+
</b></pre>
|
|
377
|
+
Just like in <tt>def()</tt>, the same output space is provided for each call of <tt>inflate()</tt>.
|
|
378
|
+
<pre><b>
|
|
379
|
+
strm.avail_out = CHUNK;
|
|
380
|
+
strm.next_out = out;
|
|
381
|
+
</b></pre>
|
|
382
|
+
Now we run the decompression engine itself. There is no need to adjust the flush parameter, since
|
|
383
|
+
the <em>zlib</em> format is self-terminating. The main difference here is that there are
|
|
384
|
+
return values that we need to pay attention to. <tt>Z_DATA_ERROR</tt>
|
|
385
|
+
indicates that <tt>inflate()</tt> detected an error in the <em>zlib</em> compressed data format,
|
|
386
|
+
which means that either the data is not a <em>zlib</em> stream to begin with, or that the data was
|
|
387
|
+
corrupted somewhere along the way since it was compressed. The other error to be processed is
|
|
388
|
+
<tt>Z_MEM_ERROR</tt>, which can occur since memory allocation is deferred until <tt>inflate()</tt>
|
|
389
|
+
needs it, unlike <tt>deflate()</tt>, whose memory is allocated at the start by <tt>deflateInit()</tt>.
|
|
390
|
+
<p>
|
|
391
|
+
Advanced applications may use
|
|
392
|
+
<tt>deflateSetDictionary()</tt> to prime <tt>deflate()</tt> with a set of likely data to improve the
|
|
393
|
+
first 32K or so of compression. This is noted in the <em>zlib</em> header, so <tt>inflate()</tt>
|
|
394
|
+
requests that that dictionary be provided before it can start to decompress. Without the dictionary,
|
|
395
|
+
correct decompression is not possible. For this routine, we have no idea what the dictionary is,
|
|
396
|
+
so the <tt>Z_NEED_DICT</tt> indication is converted to a <tt>Z_DATA_ERROR</tt>.
|
|
397
|
+
<p>
|
|
398
|
+
<tt>inflate()</tt> can also return <tt>Z_STREAM_ERROR</tt>, which should not be possible here,
|
|
399
|
+
but could be checked for as noted above for <tt>def()</tt>. <tt>Z_BUF_ERROR</tt> does not need to be
|
|
400
|
+
checked for here, for the same reasons noted for <tt>def()</tt>. <tt>Z_STREAM_END</tt> will be
|
|
401
|
+
checked for later.
|
|
402
|
+
<pre><b>
|
|
403
|
+
ret = inflate(&strm, Z_NO_FLUSH);
|
|
404
|
+
assert(ret != Z_STREAM_ERROR); /* state not clobbered */
|
|
405
|
+
switch (ret) {
|
|
406
|
+
case Z_NEED_DICT:
|
|
407
|
+
ret = Z_DATA_ERROR; /* and fall through */
|
|
408
|
+
case Z_DATA_ERROR:
|
|
409
|
+
case Z_MEM_ERROR:
|
|
410
|
+
(void)inflateEnd(&strm);
|
|
411
|
+
return ret;
|
|
412
|
+
}
|
|
413
|
+
</b></pre>
|
|
414
|
+
The output of <tt>inflate()</tt> is handled identically to that of <tt>deflate()</tt>.
|
|
415
|
+
<pre><b>
|
|
416
|
+
have = CHUNK - strm.avail_out;
|
|
417
|
+
if (fwrite(out, 1, have, dest) != have || ferror(dest)) {
|
|
418
|
+
(void)inflateEnd(&strm);
|
|
419
|
+
return Z_ERRNO;
|
|
420
|
+
}
|
|
421
|
+
</b></pre>
|
|
422
|
+
The inner <tt>do</tt>-loop ends when <tt>inflate()</tt> has no more output as indicated
|
|
423
|
+
by not filling the output buffer, just as for <tt>deflate()</tt>. In this case, we cannot
|
|
424
|
+
assert that <tt>strm.avail_in</tt> will be zero, since the deflate stream may end before the file
|
|
425
|
+
does.
|
|
426
|
+
<pre><b>
|
|
427
|
+
} while (strm.avail_out == 0);
|
|
428
|
+
</b></pre><!-- -->
|
|
429
|
+
The outer <tt>do</tt>-loop ends when <tt>inflate()</tt> reports that it has reached the
|
|
430
|
+
end of the input <em>zlib</em> stream, has completed the decompression and integrity
|
|
431
|
+
check, and has provided all of the output. This is indicated by the <tt>inflate()</tt>
|
|
432
|
+
return value <tt>Z_STREAM_END</tt>. The inner loop is guaranteed to leave <tt>ret</tt>
|
|
433
|
+
equal to <tt>Z_STREAM_END</tt> if the last chunk of the input file read contained the end
|
|
434
|
+
of the <em>zlib</em> stream. So if the return value is not <tt>Z_STREAM_END</tt>, the
|
|
435
|
+
loop continues to read more input.
|
|
436
|
+
<pre><b>
|
|
437
|
+
/* done when inflate() says it's done */
|
|
438
|
+
} while (ret != Z_STREAM_END);
|
|
439
|
+
</b></pre><!-- -->
|
|
440
|
+
At this point, decompression successfully completed, or we broke out of the loop due to no
|
|
441
|
+
more data being available from the input file. If the last <tt>inflate()</tt> return value
|
|
442
|
+
is not <tt>Z_STREAM_END</tt>, then the <em>zlib</em> stream was incomplete and a data error
|
|
443
|
+
is returned. Otherwise, we return with a happy return value. Of course, <tt>inflateEnd()</tt>
|
|
444
|
+
is called first to avoid a memory leak.
|
|
445
|
+
<pre><b>
|
|
446
|
+
/* clean up and return */
|
|
447
|
+
(void)inflateEnd(&strm);
|
|
448
|
+
return ret == Z_STREAM_END ? Z_OK : Z_DATA_ERROR;
|
|
449
|
+
}
|
|
450
|
+
</b></pre><!-- -->
|
|
451
|
+
That ends the routines that directly use <em>zlib</em>. The following routines make this
|
|
452
|
+
a command-line program by running data through the above routines from <tt>stdin</tt> to
|
|
453
|
+
<tt>stdout</tt>, and handling any errors reported by <tt>def()</tt> or <tt>inf()</tt>.
|
|
454
|
+
<p>
|
|
455
|
+
<tt>zerr()</tt> is used to interpret the possible error codes from <tt>def()</tt>
|
|
456
|
+
and <tt>inf()</tt>, as detailed in their comments above, and print out an error message.
|
|
457
|
+
Note that these are only a subset of the possible return values from <tt>deflate()</tt>
|
|
458
|
+
and <tt>inflate()</tt>.
|
|
459
|
+
<pre><b>
|
|
460
|
+
/* report a zlib or i/o error */
|
|
461
|
+
void zerr(int ret)
|
|
462
|
+
{
|
|
463
|
+
fputs("zpipe: ", stderr);
|
|
464
|
+
switch (ret) {
|
|
465
|
+
case Z_ERRNO:
|
|
466
|
+
if (ferror(stdin))
|
|
467
|
+
fputs("error reading stdin\n", stderr);
|
|
468
|
+
if (ferror(stdout))
|
|
469
|
+
fputs("error writing stdout\n", stderr);
|
|
470
|
+
break;
|
|
471
|
+
case Z_STREAM_ERROR:
|
|
472
|
+
fputs("invalid compression level\n", stderr);
|
|
473
|
+
break;
|
|
474
|
+
case Z_DATA_ERROR:
|
|
475
|
+
fputs("invalid or incomplete deflate data\n", stderr);
|
|
476
|
+
break;
|
|
477
|
+
case Z_MEM_ERROR:
|
|
478
|
+
fputs("out of memory\n", stderr);
|
|
479
|
+
break;
|
|
480
|
+
case Z_VERSION_ERROR:
|
|
481
|
+
fputs("zlib version mismatch!\n", stderr);
|
|
482
|
+
}
|
|
483
|
+
}
|
|
484
|
+
</b></pre><!-- -->
|
|
485
|
+
Here is the <tt>main()</tt> routine used to test <tt>def()</tt> and <tt>inf()</tt>. The
|
|
486
|
+
<tt>zpipe</tt> command is simply a compression pipe from <tt>stdin</tt> to <tt>stdout</tt>, if
|
|
487
|
+
no arguments are given, or it is a decompression pipe if <tt>zpipe -d</tt> is used. If any other
|
|
488
|
+
arguments are provided, no compression or decompression is performed. Instead a usage
|
|
489
|
+
message is displayed. Examples are <tt>zpipe < foo.txt > foo.txt.z</tt> to compress, and
|
|
490
|
+
<tt>zpipe -d < foo.txt.z > foo.txt</tt> to decompress.
|
|
491
|
+
<pre><b>
|
|
492
|
+
/* compress or decompress from stdin to stdout */
|
|
493
|
+
int main(int argc, char **argv)
|
|
494
|
+
{
|
|
495
|
+
int ret;
|
|
496
|
+
|
|
497
|
+
/* do compression if no arguments */
|
|
498
|
+
if (argc == 1) {
|
|
499
|
+
ret = def(stdin, stdout, Z_DEFAULT_COMPRESSION);
|
|
500
|
+
if (ret != Z_OK)
|
|
501
|
+
zerr(ret);
|
|
502
|
+
return ret;
|
|
503
|
+
}
|
|
504
|
+
|
|
505
|
+
/* do decompression if -d specified */
|
|
506
|
+
else if (argc == 2 && strcmp(argv[1], "-d") == 0) {
|
|
507
|
+
ret = inf(stdin, stdout);
|
|
508
|
+
if (ret != Z_OK)
|
|
509
|
+
zerr(ret);
|
|
510
|
+
return ret;
|
|
511
|
+
}
|
|
512
|
+
|
|
513
|
+
/* otherwise, report usage */
|
|
514
|
+
else {
|
|
515
|
+
fputs("zpipe usage: zpipe [-d] < source > dest\n", stderr);
|
|
516
|
+
return 1;
|
|
517
|
+
}
|
|
518
|
+
}
|
|
519
|
+
</b></pre>
|
|
520
|
+
<hr>
|
|
521
|
+
<i>Copyright (c) 2004 by Mark Adler<br>Last modified 13 November 2004</i>
|
|
522
|
+
</body>
|
|
523
|
+
</html>
|