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 +1,322 @@
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/* minigzip.c -- simulate gzip using the zlib compression library
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* Copyright (C) 1995-2005 Jean-loup Gailly.
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* For conditions of distribution and use, see copyright notice in zlib.h
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*/
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/*
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* minigzip is a minimal implementation of the gzip utility. This is
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* only an example of using zlib and isn't meant to replace the
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* full-featured gzip. No attempt is made to deal with file systems
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* limiting names to 14 or 8+3 characters, etc... Error checking is
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* very limited. So use minigzip only for testing; use gzip for the
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* real thing. On MSDOS, use only on file names without extension
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* or in pipe mode.
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*/
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/* @(#) $Id$ */
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#include <stdio.h>
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#include "zlib.h"
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#ifdef STDC
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# include <string.h>
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# include <stdlib.h>
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#endif
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#ifdef USE_MMAP
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# include <sys/types.h>
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# include <sys/mman.h>
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# include <sys/stat.h>
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#endif
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#if defined(MSDOS) || defined(OS2) || defined(WIN32) || defined(__CYGWIN__)
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# include <fcntl.h>
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# include <io.h>
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# define SET_BINARY_MODE(file) setmode(fileno(file), O_BINARY)
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#else
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# define SET_BINARY_MODE(file)
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#endif
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#ifdef VMS
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# define unlink delete
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# define GZ_SUFFIX "-gz"
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#endif
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#ifdef RISCOS
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# define unlink remove
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# define GZ_SUFFIX "-gz"
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# define fileno(file) file->__file
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#endif
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#if defined(__MWERKS__) && __dest_os != __be_os && __dest_os != __win32_os
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# include <unix.h> /* for fileno */
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#endif
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#ifndef WIN32 /* unlink already in stdio.h for WIN32 */
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extern int unlink OF((const char *));
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#endif
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#ifndef GZ_SUFFIX
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# define GZ_SUFFIX ".gz"
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#endif
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#define SUFFIX_LEN (sizeof(GZ_SUFFIX)-1)
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#define BUFLEN 16384
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#define MAX_NAME_LEN 1024
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#ifdef MAXSEG_64K
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# define local static
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/* Needed for systems with limitation on stack size. */
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#else
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# define local
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#endif
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char *prog;
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void error OF((const char *msg));
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void gz_compress OF((FILE *in, gzFile out));
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#ifdef USE_MMAP
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int gz_compress_mmap OF((FILE *in, gzFile out));
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#endif
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void gz_uncompress OF((gzFile in, FILE *out));
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void file_compress OF((char *file, char *mode));
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void file_uncompress OF((char *file));
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int main OF((int argc, char *argv[]));
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/* ===========================================================================
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* Display error message and exit
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*/
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void error(msg)
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const char *msg;
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{
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fprintf(stderr, "%s: %s\n", prog, msg);
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exit(1);
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}
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/* ===========================================================================
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* Compress input to output then close both files.
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*/
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void gz_compress(in, out)
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FILE *in;
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gzFile out;
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{
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local char buf[BUFLEN];
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int len;
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int err;
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#ifdef USE_MMAP
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/* Try first compressing with mmap. If mmap fails (minigzip used in a
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* pipe), use the normal fread loop.
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*/
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if (gz_compress_mmap(in, out) == Z_OK) return;
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#endif
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for (;;) {
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len = (int)fread(buf, 1, sizeof(buf), in);
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if (ferror(in)) {
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perror("fread");
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exit(1);
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}
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if (len == 0) break;
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if (gzwrite(out, buf, (unsigned)len) != len) error(gzerror(out, &err));
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}
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fclose(in);
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if (gzclose(out) != Z_OK) error("failed gzclose");
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}
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#ifdef USE_MMAP /* MMAP version, Miguel Albrecht <malbrech@eso.org> */
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/* Try compressing the input file at once using mmap. Return Z_OK if
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* if success, Z_ERRNO otherwise.
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*/
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int gz_compress_mmap(in, out)
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FILE *in;
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gzFile out;
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{
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int len;
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int err;
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int ifd = fileno(in);
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caddr_t buf; /* mmap'ed buffer for the entire input file */
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off_t buf_len; /* length of the input file */
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struct stat sb;
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/* Determine the size of the file, needed for mmap: */
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if (fstat(ifd, &sb) < 0) return Z_ERRNO;
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buf_len = sb.st_size;
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if (buf_len <= 0) return Z_ERRNO;
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/* Now do the actual mmap: */
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buf = mmap((caddr_t) 0, buf_len, PROT_READ, MAP_SHARED, ifd, (off_t)0);
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if (buf == (caddr_t)(-1)) return Z_ERRNO;
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/* Compress the whole file at once: */
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len = gzwrite(out, (char *)buf, (unsigned)buf_len);
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if (len != (int)buf_len) error(gzerror(out, &err));
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munmap(buf, buf_len);
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fclose(in);
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if (gzclose(out) != Z_OK) error("failed gzclose");
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return Z_OK;
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}
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#endif /* USE_MMAP */
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/* ===========================================================================
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* Uncompress input to output then close both files.
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*/
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void gz_uncompress(in, out)
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gzFile in;
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FILE *out;
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{
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local char buf[BUFLEN];
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int len;
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int err;
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for (;;) {
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len = gzread(in, buf, sizeof(buf));
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if (len < 0) error (gzerror(in, &err));
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if (len == 0) break;
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if ((int)fwrite(buf, 1, (unsigned)len, out) != len) {
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error("failed fwrite");
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}
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}
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if (fclose(out)) error("failed fclose");
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if (gzclose(in) != Z_OK) error("failed gzclose");
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}
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/* ===========================================================================
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* Compress the given file: create a corresponding .gz file and remove the
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* original.
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*/
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void file_compress(file, mode)
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char *file;
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char *mode;
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{
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local char outfile[MAX_NAME_LEN];
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FILE *in;
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gzFile out;
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strcpy(outfile, file);
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strcat(outfile, GZ_SUFFIX);
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in = fopen(file, "rb");
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if (in == NULL) {
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perror(file);
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exit(1);
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}
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out = gzopen(outfile, mode);
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if (out == NULL) {
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fprintf(stderr, "%s: can't gzopen %s\n", prog, outfile);
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exit(1);
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}
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gz_compress(in, out);
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unlink(file);
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}
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/* ===========================================================================
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* Uncompress the given file and remove the original.
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*/
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void file_uncompress(file)
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char *file;
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{
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local char buf[MAX_NAME_LEN];
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char *infile, *outfile;
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FILE *out;
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gzFile in;
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uInt len = (uInt)strlen(file);
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strcpy(buf, file);
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if (len > SUFFIX_LEN && strcmp(file+len-SUFFIX_LEN, GZ_SUFFIX) == 0) {
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infile = file;
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outfile = buf;
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outfile[len-3] = '\0';
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} else {
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outfile = file;
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infile = buf;
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strcat(infile, GZ_SUFFIX);
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}
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in = gzopen(infile, "rb");
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if (in == NULL) {
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fprintf(stderr, "%s: can't gzopen %s\n", prog, infile);
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exit(1);
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}
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out = fopen(outfile, "wb");
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if (out == NULL) {
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perror(file);
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exit(1);
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}
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gz_uncompress(in, out);
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unlink(infile);
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}
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/* ===========================================================================
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* Usage: minigzip [-d] [-f] [-h] [-r] [-1 to -9] [files...]
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* -d : decompress
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* -f : compress with Z_FILTERED
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* -h : compress with Z_HUFFMAN_ONLY
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265
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* -r : compress with Z_RLE
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* -1 to -9 : compression level
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*/
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int main(argc, argv)
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int argc;
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char *argv[];
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{
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int uncompr = 0;
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gzFile file;
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char outmode[20];
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strcpy(outmode, "wb6 ");
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prog = argv[0];
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argc--, argv++;
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281
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282
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while (argc > 0) {
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if (strcmp(*argv, "-d") == 0)
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uncompr = 1;
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285
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else if (strcmp(*argv, "-f") == 0)
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outmode[3] = 'f';
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else if (strcmp(*argv, "-h") == 0)
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outmode[3] = 'h';
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289
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else if (strcmp(*argv, "-r") == 0)
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290
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outmode[3] = 'R';
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291
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else if ((*argv)[0] == '-' && (*argv)[1] >= '1' && (*argv)[1] <= '9' &&
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292
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(*argv)[2] == 0)
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293
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outmode[2] = (*argv)[1];
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else
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break;
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296
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argc--, argv++;
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297
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}
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298
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if (outmode[3] == ' ')
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outmode[3] = 0;
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300
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if (argc == 0) {
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301
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SET_BINARY_MODE(stdin);
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302
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SET_BINARY_MODE(stdout);
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303
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if (uncompr) {
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304
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file = gzdopen(fileno(stdin), "rb");
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305
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if (file == NULL) error("can't gzdopen stdin");
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306
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gz_uncompress(file, stdout);
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307
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} else {
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308
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file = gzdopen(fileno(stdout), outmode);
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309
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if (file == NULL) error("can't gzdopen stdout");
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310
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gz_compress(stdin, file);
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311
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}
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312
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} else {
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313
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do {
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314
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if (uncompr) {
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315
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file_uncompress(*argv);
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316
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} else {
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317
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file_compress(*argv, outmode);
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318
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}
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319
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} while (argv++, --argc);
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320
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}
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321
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return 0;
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322
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}
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@@ -0,0 +1,109 @@
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1
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# Makefile for zlib
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2
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# Borland C++
|
3
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# Last updated: 15-Mar-2003
|
4
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+
|
5
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# To use, do "make -fmakefile.bor"
|
6
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# To compile in small model, set below: MODEL=s
|
7
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+
|
8
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# WARNING: the small model is supported but only for small values of
|
9
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+
# MAX_WBITS and MAX_MEM_LEVEL. For example:
|
10
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# -DMAX_WBITS=11 -DDEF_WBITS=11 -DMAX_MEM_LEVEL=3
|
11
|
+
# If you wish to reduce the memory requirements (default 256K for big
|
12
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+
# objects plus a few K), you can add to the LOC macro below:
|
13
|
+
# -DMAX_MEM_LEVEL=7 -DMAX_WBITS=14
|
14
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+
# See zconf.h for details about the memory requirements.
|
15
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+
|
16
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+
# ------------ Turbo C++, Borland C++ ------------
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17
|
+
|
18
|
+
# Optional nonstandard preprocessor flags (e.g. -DMAX_MEM_LEVEL=7)
|
19
|
+
# should be added to the environment via "set LOCAL_ZLIB=-DFOO" or added
|
20
|
+
# to the declaration of LOC here:
|
21
|
+
LOC = $(LOCAL_ZLIB)
|
22
|
+
|
23
|
+
# type for CPU required: 0: 8086, 1: 80186, 2: 80286, 3: 80386, etc.
|
24
|
+
CPU_TYP = 0
|
25
|
+
|
26
|
+
# memory model: one of s, m, c, l (small, medium, compact, large)
|
27
|
+
MODEL=l
|
28
|
+
|
29
|
+
# replace bcc with tcc for Turbo C++ 1.0, with bcc32 for the 32 bit version
|
30
|
+
CC=bcc
|
31
|
+
LD=bcc
|
32
|
+
AR=tlib
|
33
|
+
|
34
|
+
# compiler flags
|
35
|
+
# replace "-O2" by "-O -G -a -d" for Turbo C++ 1.0
|
36
|
+
CFLAGS=-O2 -Z -m$(MODEL) $(LOC)
|
37
|
+
|
38
|
+
LDFLAGS=-m$(MODEL) -f-
|
39
|
+
|
40
|
+
|
41
|
+
# variables
|
42
|
+
ZLIB_LIB = zlib_$(MODEL).lib
|
43
|
+
|
44
|
+
OBJ1 = adler32.obj compress.obj crc32.obj deflate.obj gzio.obj infback.obj
|
45
|
+
OBJ2 = inffast.obj inflate.obj inftrees.obj trees.obj uncompr.obj zutil.obj
|
46
|
+
OBJP1 = +adler32.obj+compress.obj+crc32.obj+deflate.obj+gzio.obj+infback.obj
|
47
|
+
OBJP2 = +inffast.obj+inflate.obj+inftrees.obj+trees.obj+uncompr.obj+zutil.obj
|
48
|
+
|
49
|
+
|
50
|
+
# targets
|
51
|
+
all: $(ZLIB_LIB) example.exe minigzip.exe
|
52
|
+
|
53
|
+
.c.obj:
|
54
|
+
$(CC) -c $(CFLAGS) $*.c
|
55
|
+
|
56
|
+
adler32.obj: adler32.c zlib.h zconf.h
|
57
|
+
|
58
|
+
compress.obj: compress.c zlib.h zconf.h
|
59
|
+
|
60
|
+
crc32.obj: crc32.c zlib.h zconf.h crc32.h
|
61
|
+
|
62
|
+
deflate.obj: deflate.c deflate.h zutil.h zlib.h zconf.h
|
63
|
+
|
64
|
+
gzio.obj: gzio.c zutil.h zlib.h zconf.h
|
65
|
+
|
66
|
+
infback.obj: infback.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
|
67
|
+
inffast.h inffixed.h
|
68
|
+
|
69
|
+
inffast.obj: inffast.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
|
70
|
+
inffast.h
|
71
|
+
|
72
|
+
inflate.obj: inflate.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
|
73
|
+
inffast.h inffixed.h
|
74
|
+
|
75
|
+
inftrees.obj: inftrees.c zutil.h zlib.h zconf.h inftrees.h
|
76
|
+
|
77
|
+
trees.obj: trees.c zutil.h zlib.h zconf.h deflate.h trees.h
|
78
|
+
|
79
|
+
uncompr.obj: uncompr.c zlib.h zconf.h
|
80
|
+
|
81
|
+
zutil.obj: zutil.c zutil.h zlib.h zconf.h
|
82
|
+
|
83
|
+
example.obj: example.c zlib.h zconf.h
|
84
|
+
|
85
|
+
minigzip.obj: minigzip.c zlib.h zconf.h
|
86
|
+
|
87
|
+
|
88
|
+
# the command line is cut to fit in the MS-DOS 128 byte limit:
|
89
|
+
$(ZLIB_LIB): $(OBJ1) $(OBJ2)
|
90
|
+
-del $(ZLIB_LIB)
|
91
|
+
$(AR) $(ZLIB_LIB) $(OBJP1)
|
92
|
+
$(AR) $(ZLIB_LIB) $(OBJP2)
|
93
|
+
|
94
|
+
example.exe: example.obj $(ZLIB_LIB)
|
95
|
+
$(LD) $(LDFLAGS) example.obj $(ZLIB_LIB)
|
96
|
+
|
97
|
+
minigzip.exe: minigzip.obj $(ZLIB_LIB)
|
98
|
+
$(LD) $(LDFLAGS) minigzip.obj $(ZLIB_LIB)
|
99
|
+
|
100
|
+
test: example.exe minigzip.exe
|
101
|
+
example
|
102
|
+
echo hello world | minigzip | minigzip -d
|
103
|
+
|
104
|
+
clean:
|
105
|
+
-del *.obj
|
106
|
+
-del *.lib
|
107
|
+
-del *.exe
|
108
|
+
-del zlib_*.bak
|
109
|
+
-del foo.gz
|
@@ -0,0 +1,104 @@
|
|
1
|
+
# Makefile for zlib. Modified for djgpp v2.0 by F. J. Donahoe, 3/15/96.
|
2
|
+
# Copyright (C) 1995-1998 Jean-loup Gailly.
|
3
|
+
# For conditions of distribution and use, see copyright notice in zlib.h
|
4
|
+
|
5
|
+
# To compile, or to compile and test, type:
|
6
|
+
#
|
7
|
+
# make -fmakefile.dj2; make test -fmakefile.dj2
|
8
|
+
#
|
9
|
+
# To install libz.a, zconf.h and zlib.h in the djgpp directories, type:
|
10
|
+
#
|
11
|
+
# make install -fmakefile.dj2
|
12
|
+
#
|
13
|
+
# after first defining LIBRARY_PATH and INCLUDE_PATH in djgpp.env as
|
14
|
+
# in the sample below if the pattern of the DJGPP distribution is to
|
15
|
+
# be followed. Remember that, while <sp>'es around <=> are ignored in
|
16
|
+
# makefiles, they are *not* in batch files or in djgpp.env.
|
17
|
+
# - - - - -
|
18
|
+
# [make]
|
19
|
+
# INCLUDE_PATH=%\>;INCLUDE_PATH%%\DJDIR%\include
|
20
|
+
# LIBRARY_PATH=%\>;LIBRARY_PATH%%\DJDIR%\lib
|
21
|
+
# BUTT=-m486
|
22
|
+
# - - - - -
|
23
|
+
# Alternately, these variables may be defined below, overriding the values
|
24
|
+
# in djgpp.env, as
|
25
|
+
# INCLUDE_PATH=c:\usr\include
|
26
|
+
# LIBRARY_PATH=c:\usr\lib
|
27
|
+
|
28
|
+
CC=gcc
|
29
|
+
|
30
|
+
#CFLAGS=-MMD -O
|
31
|
+
#CFLAGS=-O -DMAX_WBITS=14 -DMAX_MEM_LEVEL=7
|
32
|
+
#CFLAGS=-MMD -g -DDEBUG
|
33
|
+
CFLAGS=-MMD -O3 $(BUTT) -Wall -Wwrite-strings -Wpointer-arith -Wconversion \
|
34
|
+
-Wstrict-prototypes -Wmissing-prototypes
|
35
|
+
|
36
|
+
# If cp.exe is available, replace "copy /Y" with "cp -fp" .
|
37
|
+
CP=copy /Y
|
38
|
+
# If gnu install.exe is available, replace $(CP) with ginstall.
|
39
|
+
INSTALL=$(CP)
|
40
|
+
# The default value of RM is "rm -f." If "rm.exe" is found, comment out:
|
41
|
+
RM=del
|
42
|
+
LDLIBS=-L. -lz
|
43
|
+
LD=$(CC) -s -o
|
44
|
+
LDSHARED=$(CC)
|
45
|
+
|
46
|
+
INCL=zlib.h zconf.h
|
47
|
+
LIBS=libz.a
|
48
|
+
|
49
|
+
AR=ar rcs
|
50
|
+
|
51
|
+
prefix=/usr/local
|
52
|
+
exec_prefix = $(prefix)
|
53
|
+
|
54
|
+
OBJS = adler32.o compress.o crc32.o gzio.o uncompr.o deflate.o trees.o \
|
55
|
+
zutil.o inflate.o infback.o inftrees.o inffast.o
|
56
|
+
|
57
|
+
OBJA =
|
58
|
+
# to use the asm code: make OBJA=match.o
|
59
|
+
|
60
|
+
TEST_OBJS = example.o minigzip.o
|
61
|
+
|
62
|
+
all: example.exe minigzip.exe
|
63
|
+
|
64
|
+
check: test
|
65
|
+
test: all
|
66
|
+
./example
|
67
|
+
echo hello world | .\minigzip | .\minigzip -d
|
68
|
+
|
69
|
+
%.o : %.c
|
70
|
+
$(CC) $(CFLAGS) -c $< -o $@
|
71
|
+
|
72
|
+
libz.a: $(OBJS) $(OBJA)
|
73
|
+
$(AR) $@ $(OBJS) $(OBJA)
|
74
|
+
|
75
|
+
%.exe : %.o $(LIBS)
|
76
|
+
$(LD) $@ $< $(LDLIBS)
|
77
|
+
|
78
|
+
# INCLUDE_PATH and LIBRARY_PATH were set for [make] in djgpp.env .
|
79
|
+
|
80
|
+
.PHONY : uninstall clean
|
81
|
+
|
82
|
+
install: $(INCL) $(LIBS)
|
83
|
+
-@if not exist $(INCLUDE_PATH)\nul mkdir $(INCLUDE_PATH)
|
84
|
+
-@if not exist $(LIBRARY_PATH)\nul mkdir $(LIBRARY_PATH)
|
85
|
+
$(INSTALL) zlib.h $(INCLUDE_PATH)
|
86
|
+
$(INSTALL) zconf.h $(INCLUDE_PATH)
|
87
|
+
$(INSTALL) libz.a $(LIBRARY_PATH)
|
88
|
+
|
89
|
+
uninstall:
|
90
|
+
$(RM) $(INCLUDE_PATH)\zlib.h
|
91
|
+
$(RM) $(INCLUDE_PATH)\zconf.h
|
92
|
+
$(RM) $(LIBRARY_PATH)\libz.a
|
93
|
+
|
94
|
+
clean:
|
95
|
+
$(RM) *.d
|
96
|
+
$(RM) *.o
|
97
|
+
$(RM) *.exe
|
98
|
+
$(RM) libz.a
|
99
|
+
$(RM) foo.gz
|
100
|
+
|
101
|
+
DEPS := $(wildcard *.d)
|
102
|
+
ifneq ($(DEPS),)
|
103
|
+
include $(DEPS)
|
104
|
+
endif
|