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 +1,307 @@
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/*
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*
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* Copyright (c) 1997
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* Christian Michelsen Research AS
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* Advanced Computing
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* Fantoftvegen 38, 5036 BERGEN, Norway
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* http://www.cmr.no
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*
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* Permission to use, copy, modify, distribute and sell this software
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* and its documentation for any purpose is hereby granted without fee,
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* provided that the above copyright notice appear in all copies and
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* that both that copyright notice and this permission notice appear
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* in supporting documentation. Christian Michelsen Research AS makes no
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* representations about the suitability of this software for any
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* purpose. It is provided "as is" without express or implied warranty.
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*
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*/
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#ifndef ZSTREAM__H
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#define ZSTREAM__H
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/*
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* zstream.h - C++ interface to the 'zlib' general purpose compression library
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* $Id: zstream.h 1.1 1997-06-25 12:00:56+02 tyge Exp tyge $
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*/
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#include <strstream.h>
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#include <string.h>
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#include <stdio.h>
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#include "zlib.h"
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#if defined(_WIN32)
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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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class zstringlen {
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public:
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zstringlen(class izstream&);
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zstringlen(class ozstream&, const char*);
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size_t value() const { return val.word; }
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private:
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struct Val { unsigned char byte; size_t word; } val;
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};
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// ----------------------------- izstream -----------------------------
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class izstream
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{
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public:
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izstream() : m_fp(0) {}
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izstream(FILE* fp) : m_fp(0) { open(fp); }
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izstream(const char* name) : m_fp(0) { open(name); }
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~izstream() { close(); }
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/* Opens a gzip (.gz) file for reading.
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* open() can be used to read a file which is not in gzip format;
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* in this case read() will directly read from the file without
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* decompression. errno can be checked to distinguish two error
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* cases (if errno is zero, the zlib error is Z_MEM_ERROR).
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*/
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void open(const char* name) {
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if (m_fp) close();
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m_fp = ::gzopen(name, "rb");
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}
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void open(FILE* fp) {
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SET_BINARY_MODE(fp);
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if (m_fp) close();
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m_fp = ::gzdopen(fileno(fp), "rb");
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}
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/* Flushes all pending input if necessary, closes the compressed file
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* and deallocates all the (de)compression state. The return value is
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* the zlib error number (see function error() below).
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*/
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int close() {
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int r = ::gzclose(m_fp);
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m_fp = 0; return r;
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}
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/* Binary read the given number of bytes from the compressed file.
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*/
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int read(void* buf, size_t len) {
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return ::gzread(m_fp, buf, len);
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}
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/* Returns the error message for the last error which occurred on the
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* given compressed file. errnum is set to zlib error number. If an
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* error occurred in the file system and not in the compression library,
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* errnum is set to Z_ERRNO and the application may consult errno
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* to get the exact error code.
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*/
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const char* error(int* errnum) {
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return ::gzerror(m_fp, errnum);
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}
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gzFile fp() { return m_fp; }
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private:
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gzFile m_fp;
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};
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/*
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* Binary read the given (array of) object(s) from the compressed file.
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* If the input file was not in gzip format, read() copies the objects number
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* of bytes into the buffer.
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* returns the number of uncompressed bytes actually read
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* (0 for end of file, -1 for error).
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*/
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template <class T, class Items>
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inline int read(izstream& zs, T* x, Items items) {
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return ::gzread(zs.fp(), x, items*sizeof(T));
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}
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/*
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* Binary input with the '>' operator.
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*/
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template <class T>
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inline izstream& operator>(izstream& zs, T& x) {
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::gzread(zs.fp(), &x, sizeof(T));
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return zs;
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}
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inline zstringlen::zstringlen(izstream& zs) {
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zs > val.byte;
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if (val.byte == 255) zs > val.word;
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else val.word = val.byte;
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}
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/*
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* Read length of string + the string with the '>' operator.
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*/
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inline izstream& operator>(izstream& zs, char* x) {
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zstringlen len(zs);
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::gzread(zs.fp(), x, len.value());
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x[len.value()] = '\0';
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return zs;
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}
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inline char* read_string(izstream& zs) {
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zstringlen len(zs);
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char* x = new char[len.value()+1];
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::gzread(zs.fp(), x, len.value());
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x[len.value()] = '\0';
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return x;
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}
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// ----------------------------- ozstream -----------------------------
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class ozstream
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{
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public:
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ozstream() : m_fp(0), m_os(0) {
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}
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ozstream(FILE* fp, int level = Z_DEFAULT_COMPRESSION)
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: m_fp(0), m_os(0) {
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open(fp, level);
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}
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ozstream(const char* name, int level = Z_DEFAULT_COMPRESSION)
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: m_fp(0), m_os(0) {
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open(name, level);
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}
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~ozstream() {
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close();
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}
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/* Opens a gzip (.gz) file for writing.
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* The compression level parameter should be in 0..9
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* errno can be checked to distinguish two error cases
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* (if errno is zero, the zlib error is Z_MEM_ERROR).
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*/
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void open(const char* name, int level = Z_DEFAULT_COMPRESSION) {
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char mode[4] = "wb\0";
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if (level != Z_DEFAULT_COMPRESSION) mode[2] = '0'+level;
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if (m_fp) close();
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m_fp = ::gzopen(name, mode);
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}
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/* open from a FILE pointer.
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*/
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void open(FILE* fp, int level = Z_DEFAULT_COMPRESSION) {
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SET_BINARY_MODE(fp);
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char mode[4] = "wb\0";
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if (level != Z_DEFAULT_COMPRESSION) mode[2] = '0'+level;
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if (m_fp) close();
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m_fp = ::gzdopen(fileno(fp), mode);
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}
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/* Flushes all pending output if necessary, closes the compressed file
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* and deallocates all the (de)compression state. The return value is
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* the zlib error number (see function error() below).
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*/
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int close() {
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if (m_os) {
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::gzwrite(m_fp, m_os->str(), m_os->pcount());
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delete[] m_os->str(); delete m_os; m_os = 0;
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}
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int r = ::gzclose(m_fp); m_fp = 0; return r;
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}
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/* Binary write the given number of bytes into the compressed file.
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*/
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int write(const void* buf, size_t len) {
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return ::gzwrite(m_fp, (voidp) buf, len);
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}
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/* Flushes all pending output into the compressed file. The parameter
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* _flush is as in the deflate() function. The return value is the zlib
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* error number (see function gzerror below). flush() returns Z_OK if
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* the flush_ parameter is Z_FINISH and all output could be flushed.
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* flush() should be called only when strictly necessary because it can
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* degrade compression.
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*/
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int flush(int _flush) {
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os_flush();
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return ::gzflush(m_fp, _flush);
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}
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/* Returns the error message for the last error which occurred on the
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* given compressed file. errnum is set to zlib error number. If an
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* error occurred in the file system and not in the compression library,
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* errnum is set to Z_ERRNO and the application may consult errno
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* to get the exact error code.
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*/
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const char* error(int* errnum) {
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return ::gzerror(m_fp, errnum);
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}
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gzFile fp() { return m_fp; }
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ostream& os() {
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if (m_os == 0) m_os = new ostrstream;
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return *m_os;
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}
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void os_flush() {
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if (m_os && m_os->pcount()>0) {
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ostrstream* oss = new ostrstream;
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oss->fill(m_os->fill());
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oss->flags(m_os->flags());
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oss->precision(m_os->precision());
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oss->width(m_os->width());
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::gzwrite(m_fp, m_os->str(), m_os->pcount());
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delete[] m_os->str(); delete m_os; m_os = oss;
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}
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}
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private:
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gzFile m_fp;
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ostrstream* m_os;
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};
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/*
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* Binary write the given (array of) object(s) into the compressed file.
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* returns the number of uncompressed bytes actually written
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* (0 in case of error).
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*/
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template <class T, class Items>
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inline int write(ozstream& zs, const T* x, Items items) {
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return ::gzwrite(zs.fp(), (voidp) x, items*sizeof(T));
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}
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/*
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* Binary output with the '<' operator.
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*/
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template <class T>
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inline ozstream& operator<(ozstream& zs, const T& x) {
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::gzwrite(zs.fp(), (voidp) &x, sizeof(T));
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return zs;
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}
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inline zstringlen::zstringlen(ozstream& zs, const char* x) {
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val.byte = 255; val.word = ::strlen(x);
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if (val.word < 255) zs < (val.byte = val.word);
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else zs < val;
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}
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/*
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* Write length of string + the string with the '<' operator.
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*/
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inline ozstream& operator<(ozstream& zs, const char* x) {
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zstringlen len(zs, x);
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::gzwrite(zs.fp(), (voidp) x, len.value());
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return zs;
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}
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#ifdef _MSC_VER
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inline ozstream& operator<(ozstream& zs, char* const& x) {
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return zs < (const char*) x;
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}
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#endif
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/*
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* Ascii write with the << operator;
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*/
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template <class T>
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inline ostream& operator<<(ozstream& zs, const T& x) {
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zs.os_flush();
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return zs.os() << x;
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}
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#endif
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@@ -0,0 +1,25 @@
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#include "zstream.h"
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#include <math.h>
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#include <stdlib.h>
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#include <iomanip.h>
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5
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|
6
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void main() {
|
7
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char h[256] = "Hello";
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char* g = "Goodbye";
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ozstream out("temp.gz");
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out < "This works well" < h < g;
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out.close();
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izstream in("temp.gz"); // read it back
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char *x = read_string(in), *y = new char[256], z[256];
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in > y > z;
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in.close();
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cout << x << endl << y << endl << z << endl;
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out.open("temp.gz"); // try ascii output; zcat temp.gz to see the results
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out << setw(50) << setfill('#') << setprecision(20) << x << endl << y << endl << z << endl;
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out << z << endl << y << endl << x << endl;
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out << 1.1234567890123456789 << endl;
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delete[] x; delete[] y;
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}
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@@ -0,0 +1,35 @@
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1
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These classes provide a C++ stream interface to the zlib library. It allows you
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2
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to do things like:
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3
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4
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gzofstream outf("blah.gz");
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5
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outf << "These go into the gzip file " << 123 << endl;
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7
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It does this by deriving a specialized stream buffer for gzipped files, which is
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the way Stroustrup would have done it. :->
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The gzifstream and gzofstream classes were originally written by Kevin Ruland
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and made available in the zlib contrib/iostream directory. The older version still
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compiles under gcc 2.xx, but not under gcc 3.xx, which sparked the development of
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this version.
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+
The new classes are as standard-compliant as possible, closely following the
|
16
|
+
approach of the standard library's fstream classes. It compiles under gcc versions
|
17
|
+
3.2 and 3.3, but not under gcc 2.xx. This is mainly due to changes in the standard
|
18
|
+
library naming scheme. The new version of gzifstream/gzofstream/gzfilebuf differs
|
19
|
+
from the previous one in the following respects:
|
20
|
+
- added showmanyc
|
21
|
+
- added setbuf, with support for unbuffered output via setbuf(0,0)
|
22
|
+
- a few bug fixes of stream behavior
|
23
|
+
- gzipped output file opened with default compression level instead of maximum level
|
24
|
+
- setcompressionlevel()/strategy() members replaced by single setcompression()
|
25
|
+
|
26
|
+
The code is provided "as is", with the permission to use, copy, modify, distribute
|
27
|
+
and sell it for any purpose without fee.
|
28
|
+
|
29
|
+
Ludwig Schwardt
|
30
|
+
<schwardt@sun.ac.za>
|
31
|
+
|
32
|
+
DSP Lab
|
33
|
+
Electrical & Electronic Engineering Department
|
34
|
+
University of Stellenbosch
|
35
|
+
South Africa
|
@@ -0,0 +1,17 @@
|
|
1
|
+
Possible upgrades to gzfilebuf:
|
2
|
+
|
3
|
+
- The ability to do putback (e.g. putbackfail)
|
4
|
+
|
5
|
+
- The ability to seek (zlib supports this, but could be slow/tricky)
|
6
|
+
|
7
|
+
- Simultaneous read/write access (does it make sense?)
|
8
|
+
|
9
|
+
- Support for ios_base::ate open mode
|
10
|
+
|
11
|
+
- Locale support?
|
12
|
+
|
13
|
+
- Check public interface to see which calls give problems
|
14
|
+
(due to dependence on library internals)
|
15
|
+
|
16
|
+
- Override operator<<(ostream&, gzfilebuf*) to allow direct copying
|
17
|
+
of stream buffer to stream ( i.e. os << is.rdbuf(); )
|
@@ -0,0 +1,50 @@
|
|
1
|
+
/*
|
2
|
+
* Test program for gzifstream and gzofstream
|
3
|
+
*
|
4
|
+
* by Ludwig Schwardt <schwardt@sun.ac.za>
|
5
|
+
* original version by Kevin Ruland <kevin@rodin.wustl.edu>
|
6
|
+
*/
|
7
|
+
|
8
|
+
#include "zfstream.h"
|
9
|
+
#include <iostream> // for cout
|
10
|
+
|
11
|
+
int main() {
|
12
|
+
|
13
|
+
gzofstream outf;
|
14
|
+
gzifstream inf;
|
15
|
+
char buf[80];
|
16
|
+
|
17
|
+
outf.open("test1.txt.gz");
|
18
|
+
outf << "The quick brown fox sidestepped the lazy canine\n"
|
19
|
+
<< 1.3 << "\nPlan " << 9 << std::endl;
|
20
|
+
outf.close();
|
21
|
+
std::cout << "Wrote the following message to 'test1.txt.gz' (check with zcat or zless):\n"
|
22
|
+
<< "The quick brown fox sidestepped the lazy canine\n"
|
23
|
+
<< 1.3 << "\nPlan " << 9 << std::endl;
|
24
|
+
|
25
|
+
std::cout << "\nReading 'test1.txt.gz' (buffered) produces:\n";
|
26
|
+
inf.open("test1.txt.gz");
|
27
|
+
while (inf.getline(buf,80,'\n')) {
|
28
|
+
std::cout << buf << "\t(" << inf.rdbuf()->in_avail() << " chars left in buffer)\n";
|
29
|
+
}
|
30
|
+
inf.close();
|
31
|
+
|
32
|
+
outf.rdbuf()->pubsetbuf(0,0);
|
33
|
+
outf.open("test2.txt.gz");
|
34
|
+
outf << setcompression(Z_NO_COMPRESSION)
|
35
|
+
<< "The quick brown fox sidestepped the lazy canine\n"
|
36
|
+
<< 1.3 << "\nPlan " << 9 << std::endl;
|
37
|
+
outf.close();
|
38
|
+
std::cout << "\nWrote the same message to 'test2.txt.gz' in uncompressed form";
|
39
|
+
|
40
|
+
std::cout << "\nReading 'test2.txt.gz' (unbuffered) produces:\n";
|
41
|
+
inf.rdbuf()->pubsetbuf(0,0);
|
42
|
+
inf.open("test2.txt.gz");
|
43
|
+
while (inf.getline(buf,80,'\n')) {
|
44
|
+
std::cout << buf << "\t(" << inf.rdbuf()->in_avail() << " chars left in buffer)\n";
|
45
|
+
}
|
46
|
+
inf.close();
|
47
|
+
|
48
|
+
return 0;
|
49
|
+
|
50
|
+
}
|
@@ -0,0 +1,479 @@
|
|
1
|
+
/*
|
2
|
+
* A C++ I/O streams interface to the zlib gz* functions
|
3
|
+
*
|
4
|
+
* by Ludwig Schwardt <schwardt@sun.ac.za>
|
5
|
+
* original version by Kevin Ruland <kevin@rodin.wustl.edu>
|
6
|
+
*
|
7
|
+
* This version is standard-compliant and compatible with gcc 3.x.
|
8
|
+
*/
|
9
|
+
|
10
|
+
#include "zfstream.h"
|
11
|
+
#include <cstring> // for strcpy, strcat, strlen (mode strings)
|
12
|
+
#include <cstdio> // for BUFSIZ
|
13
|
+
|
14
|
+
// Internal buffer sizes (default and "unbuffered" versions)
|
15
|
+
#define BIGBUFSIZE BUFSIZ
|
16
|
+
#define SMALLBUFSIZE 1
|
17
|
+
|
18
|
+
/*****************************************************************************/
|
19
|
+
|
20
|
+
// Default constructor
|
21
|
+
gzfilebuf::gzfilebuf()
|
22
|
+
: file(NULL), io_mode(std::ios_base::openmode(0)), own_fd(false),
|
23
|
+
buffer(NULL), buffer_size(BIGBUFSIZE), own_buffer(true)
|
24
|
+
{
|
25
|
+
// No buffers to start with
|
26
|
+
this->disable_buffer();
|
27
|
+
}
|
28
|
+
|
29
|
+
// Destructor
|
30
|
+
gzfilebuf::~gzfilebuf()
|
31
|
+
{
|
32
|
+
// Sync output buffer and close only if responsible for file
|
33
|
+
// (i.e. attached streams should be left open at this stage)
|
34
|
+
this->sync();
|
35
|
+
if (own_fd)
|
36
|
+
this->close();
|
37
|
+
// Make sure internal buffer is deallocated
|
38
|
+
this->disable_buffer();
|
39
|
+
}
|
40
|
+
|
41
|
+
// Set compression level and strategy
|
42
|
+
int
|
43
|
+
gzfilebuf::setcompression(int comp_level,
|
44
|
+
int comp_strategy)
|
45
|
+
{
|
46
|
+
return gzsetparams(file, comp_level, comp_strategy);
|
47
|
+
}
|
48
|
+
|
49
|
+
// Open gzipped file
|
50
|
+
gzfilebuf*
|
51
|
+
gzfilebuf::open(const char *name,
|
52
|
+
std::ios_base::openmode mode)
|
53
|
+
{
|
54
|
+
// Fail if file already open
|
55
|
+
if (this->is_open())
|
56
|
+
return NULL;
|
57
|
+
// Don't support simultaneous read/write access (yet)
|
58
|
+
if ((mode & std::ios_base::in) && (mode & std::ios_base::out))
|
59
|
+
return NULL;
|
60
|
+
|
61
|
+
// Build mode string for gzopen and check it [27.8.1.3.2]
|
62
|
+
char char_mode[6] = "\0\0\0\0\0";
|
63
|
+
if (!this->open_mode(mode, char_mode))
|
64
|
+
return NULL;
|
65
|
+
|
66
|
+
// Attempt to open file
|
67
|
+
if ((file = gzopen(name, char_mode)) == NULL)
|
68
|
+
return NULL;
|
69
|
+
|
70
|
+
// On success, allocate internal buffer and set flags
|
71
|
+
this->enable_buffer();
|
72
|
+
io_mode = mode;
|
73
|
+
own_fd = true;
|
74
|
+
return this;
|
75
|
+
}
|
76
|
+
|
77
|
+
// Attach to gzipped file
|
78
|
+
gzfilebuf*
|
79
|
+
gzfilebuf::attach(int fd,
|
80
|
+
std::ios_base::openmode mode)
|
81
|
+
{
|
82
|
+
// Fail if file already open
|
83
|
+
if (this->is_open())
|
84
|
+
return NULL;
|
85
|
+
// Don't support simultaneous read/write access (yet)
|
86
|
+
if ((mode & std::ios_base::in) && (mode & std::ios_base::out))
|
87
|
+
return NULL;
|
88
|
+
|
89
|
+
// Build mode string for gzdopen and check it [27.8.1.3.2]
|
90
|
+
char char_mode[6] = "\0\0\0\0\0";
|
91
|
+
if (!this->open_mode(mode, char_mode))
|
92
|
+
return NULL;
|
93
|
+
|
94
|
+
// Attempt to attach to file
|
95
|
+
if ((file = gzdopen(fd, char_mode)) == NULL)
|
96
|
+
return NULL;
|
97
|
+
|
98
|
+
// On success, allocate internal buffer and set flags
|
99
|
+
this->enable_buffer();
|
100
|
+
io_mode = mode;
|
101
|
+
own_fd = false;
|
102
|
+
return this;
|
103
|
+
}
|
104
|
+
|
105
|
+
// Close gzipped file
|
106
|
+
gzfilebuf*
|
107
|
+
gzfilebuf::close()
|
108
|
+
{
|
109
|
+
// Fail immediately if no file is open
|
110
|
+
if (!this->is_open())
|
111
|
+
return NULL;
|
112
|
+
// Assume success
|
113
|
+
gzfilebuf* retval = this;
|
114
|
+
// Attempt to sync and close gzipped file
|
115
|
+
if (this->sync() == -1)
|
116
|
+
retval = NULL;
|
117
|
+
if (gzclose(file) < 0)
|
118
|
+
retval = NULL;
|
119
|
+
// File is now gone anyway (postcondition [27.8.1.3.8])
|
120
|
+
file = NULL;
|
121
|
+
own_fd = false;
|
122
|
+
// Destroy internal buffer if it exists
|
123
|
+
this->disable_buffer();
|
124
|
+
return retval;
|
125
|
+
}
|
126
|
+
|
127
|
+
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
|
128
|
+
|
129
|
+
// Convert int open mode to mode string
|
130
|
+
bool
|
131
|
+
gzfilebuf::open_mode(std::ios_base::openmode mode,
|
132
|
+
char* c_mode) const
|
133
|
+
{
|
134
|
+
bool testb = mode & std::ios_base::binary;
|
135
|
+
bool testi = mode & std::ios_base::in;
|
136
|
+
bool testo = mode & std::ios_base::out;
|
137
|
+
bool testt = mode & std::ios_base::trunc;
|
138
|
+
bool testa = mode & std::ios_base::app;
|
139
|
+
|
140
|
+
// Check for valid flag combinations - see [27.8.1.3.2] (Table 92)
|
141
|
+
// Original zfstream hardcoded the compression level to maximum here...
|
142
|
+
// Double the time for less than 1% size improvement seems
|
143
|
+
// excessive though - keeping it at the default level
|
144
|
+
// To change back, just append "9" to the next three mode strings
|
145
|
+
if (!testi && testo && !testt && !testa)
|
146
|
+
strcpy(c_mode, "w");
|
147
|
+
if (!testi && testo && !testt && testa)
|
148
|
+
strcpy(c_mode, "a");
|
149
|
+
if (!testi && testo && testt && !testa)
|
150
|
+
strcpy(c_mode, "w");
|
151
|
+
if (testi && !testo && !testt && !testa)
|
152
|
+
strcpy(c_mode, "r");
|
153
|
+
// No read/write mode yet
|
154
|
+
// if (testi && testo && !testt && !testa)
|
155
|
+
// strcpy(c_mode, "r+");
|
156
|
+
// if (testi && testo && testt && !testa)
|
157
|
+
// strcpy(c_mode, "w+");
|
158
|
+
|
159
|
+
// Mode string should be empty for invalid combination of flags
|
160
|
+
if (strlen(c_mode) == 0)
|
161
|
+
return false;
|
162
|
+
if (testb)
|
163
|
+
strcat(c_mode, "b");
|
164
|
+
return true;
|
165
|
+
}
|
166
|
+
|
167
|
+
// Determine number of characters in internal get buffer
|
168
|
+
std::streamsize
|
169
|
+
gzfilebuf::showmanyc()
|
170
|
+
{
|
171
|
+
// Calls to underflow will fail if file not opened for reading
|
172
|
+
if (!this->is_open() || !(io_mode & std::ios_base::in))
|
173
|
+
return -1;
|
174
|
+
// Make sure get area is in use
|
175
|
+
if (this->gptr() && (this->gptr() < this->egptr()))
|
176
|
+
return std::streamsize(this->egptr() - this->gptr());
|
177
|
+
else
|
178
|
+
return 0;
|
179
|
+
}
|
180
|
+
|
181
|
+
// Fill get area from gzipped file
|
182
|
+
gzfilebuf::int_type
|
183
|
+
gzfilebuf::underflow()
|
184
|
+
{
|
185
|
+
// If something is left in the get area by chance, return it
|
186
|
+
// (this shouldn't normally happen, as underflow is only supposed
|
187
|
+
// to be called when gptr >= egptr, but it serves as error check)
|
188
|
+
if (this->gptr() && (this->gptr() < this->egptr()))
|
189
|
+
return traits_type::to_int_type(*(this->gptr()));
|
190
|
+
|
191
|
+
// If the file hasn't been opened for reading, produce error
|
192
|
+
if (!this->is_open() || !(io_mode & std::ios_base::in))
|
193
|
+
return traits_type::eof();
|
194
|
+
|
195
|
+
// Attempt to fill internal buffer from gzipped file
|
196
|
+
// (buffer must be guaranteed to exist...)
|
197
|
+
int bytes_read = gzread(file, buffer, buffer_size);
|
198
|
+
// Indicates error or EOF
|
199
|
+
if (bytes_read <= 0)
|
200
|
+
{
|
201
|
+
// Reset get area
|
202
|
+
this->setg(buffer, buffer, buffer);
|
203
|
+
return traits_type::eof();
|
204
|
+
}
|
205
|
+
// Make all bytes read from file available as get area
|
206
|
+
this->setg(buffer, buffer, buffer + bytes_read);
|
207
|
+
|
208
|
+
// Return next character in get area
|
209
|
+
return traits_type::to_int_type(*(this->gptr()));
|
210
|
+
}
|
211
|
+
|
212
|
+
// Write put area to gzipped file
|
213
|
+
gzfilebuf::int_type
|
214
|
+
gzfilebuf::overflow(int_type c)
|
215
|
+
{
|
216
|
+
// Determine whether put area is in use
|
217
|
+
if (this->pbase())
|
218
|
+
{
|
219
|
+
// Double-check pointer range
|
220
|
+
if (this->pptr() > this->epptr() || this->pptr() < this->pbase())
|
221
|
+
return traits_type::eof();
|
222
|
+
// Add extra character to buffer if not EOF
|
223
|
+
if (!traits_type::eq_int_type(c, traits_type::eof()))
|
224
|
+
{
|
225
|
+
*(this->pptr()) = traits_type::to_char_type(c);
|
226
|
+
this->pbump(1);
|
227
|
+
}
|
228
|
+
// Number of characters to write to file
|
229
|
+
int bytes_to_write = this->pptr() - this->pbase();
|
230
|
+
// Overflow doesn't fail if nothing is to be written
|
231
|
+
if (bytes_to_write > 0)
|
232
|
+
{
|
233
|
+
// If the file hasn't been opened for writing, produce error
|
234
|
+
if (!this->is_open() || !(io_mode & std::ios_base::out))
|
235
|
+
return traits_type::eof();
|
236
|
+
// If gzipped file won't accept all bytes written to it, fail
|
237
|
+
if (gzwrite(file, this->pbase(), bytes_to_write) != bytes_to_write)
|
238
|
+
return traits_type::eof();
|
239
|
+
// Reset next pointer to point to pbase on success
|
240
|
+
this->pbump(-bytes_to_write);
|
241
|
+
}
|
242
|
+
}
|
243
|
+
// Write extra character to file if not EOF
|
244
|
+
else if (!traits_type::eq_int_type(c, traits_type::eof()))
|
245
|
+
{
|
246
|
+
// If the file hasn't been opened for writing, produce error
|
247
|
+
if (!this->is_open() || !(io_mode & std::ios_base::out))
|
248
|
+
return traits_type::eof();
|
249
|
+
// Impromptu char buffer (allows "unbuffered" output)
|
250
|
+
char_type last_char = traits_type::to_char_type(c);
|
251
|
+
// If gzipped file won't accept this character, fail
|
252
|
+
if (gzwrite(file, &last_char, 1) != 1)
|
253
|
+
return traits_type::eof();
|
254
|
+
}
|
255
|
+
|
256
|
+
// If you got here, you have succeeded (even if c was EOF)
|
257
|
+
// The return value should therefore be non-EOF
|
258
|
+
if (traits_type::eq_int_type(c, traits_type::eof()))
|
259
|
+
return traits_type::not_eof(c);
|
260
|
+
else
|
261
|
+
return c;
|
262
|
+
}
|
263
|
+
|
264
|
+
// Assign new buffer
|
265
|
+
std::streambuf*
|
266
|
+
gzfilebuf::setbuf(char_type* p,
|
267
|
+
std::streamsize n)
|
268
|
+
{
|
269
|
+
// First make sure stuff is sync'ed, for safety
|
270
|
+
if (this->sync() == -1)
|
271
|
+
return NULL;
|
272
|
+
// If buffering is turned off on purpose via setbuf(0,0), still allocate one...
|
273
|
+
// "Unbuffered" only really refers to put [27.8.1.4.10], while get needs at
|
274
|
+
// least a buffer of size 1 (very inefficient though, therefore make it bigger?)
|
275
|
+
// This follows from [27.5.2.4.3]/12 (gptr needs to point at something, it seems)
|
276
|
+
if (!p || !n)
|
277
|
+
{
|
278
|
+
// Replace existing buffer (if any) with small internal buffer
|
279
|
+
this->disable_buffer();
|
280
|
+
buffer = NULL;
|
281
|
+
buffer_size = 0;
|
282
|
+
own_buffer = true;
|
283
|
+
this->enable_buffer();
|
284
|
+
}
|
285
|
+
else
|
286
|
+
{
|
287
|
+
// Replace existing buffer (if any) with external buffer
|
288
|
+
this->disable_buffer();
|
289
|
+
buffer = p;
|
290
|
+
buffer_size = n;
|
291
|
+
own_buffer = false;
|
292
|
+
this->enable_buffer();
|
293
|
+
}
|
294
|
+
return this;
|
295
|
+
}
|
296
|
+
|
297
|
+
// Write put area to gzipped file (i.e. ensures that put area is empty)
|
298
|
+
int
|
299
|
+
gzfilebuf::sync()
|
300
|
+
{
|
301
|
+
return traits_type::eq_int_type(this->overflow(), traits_type::eof()) ? -1 : 0;
|
302
|
+
}
|
303
|
+
|
304
|
+
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
|
305
|
+
|
306
|
+
// Allocate internal buffer
|
307
|
+
void
|
308
|
+
gzfilebuf::enable_buffer()
|
309
|
+
{
|
310
|
+
// If internal buffer required, allocate one
|
311
|
+
if (own_buffer && !buffer)
|
312
|
+
{
|
313
|
+
// Check for buffered vs. "unbuffered"
|
314
|
+
if (buffer_size > 0)
|
315
|
+
{
|
316
|
+
// Allocate internal buffer
|
317
|
+
buffer = new char_type[buffer_size];
|
318
|
+
// Get area starts empty and will be expanded by underflow as need arises
|
319
|
+
this->setg(buffer, buffer, buffer);
|
320
|
+
// Setup entire internal buffer as put area.
|
321
|
+
// The one-past-end pointer actually points to the last element of the buffer,
|
322
|
+
// so that overflow(c) can safely add the extra character c to the sequence.
|
323
|
+
// These pointers remain in place for the duration of the buffer
|
324
|
+
this->setp(buffer, buffer + buffer_size - 1);
|
325
|
+
}
|
326
|
+
else
|
327
|
+
{
|
328
|
+
// Even in "unbuffered" case, (small?) get buffer is still required
|
329
|
+
buffer_size = SMALLBUFSIZE;
|
330
|
+
buffer = new char_type[buffer_size];
|
331
|
+
this->setg(buffer, buffer, buffer);
|
332
|
+
// "Unbuffered" means no put buffer
|
333
|
+
this->setp(0, 0);
|
334
|
+
}
|
335
|
+
}
|
336
|
+
else
|
337
|
+
{
|
338
|
+
// If buffer already allocated, reset buffer pointers just to make sure no
|
339
|
+
// stale chars are lying around
|
340
|
+
this->setg(buffer, buffer, buffer);
|
341
|
+
this->setp(buffer, buffer + buffer_size - 1);
|
342
|
+
}
|
343
|
+
}
|
344
|
+
|
345
|
+
// Destroy internal buffer
|
346
|
+
void
|
347
|
+
gzfilebuf::disable_buffer()
|
348
|
+
{
|
349
|
+
// If internal buffer exists, deallocate it
|
350
|
+
if (own_buffer && buffer)
|
351
|
+
{
|
352
|
+
// Preserve unbuffered status by zeroing size
|
353
|
+
if (!this->pbase())
|
354
|
+
buffer_size = 0;
|
355
|
+
delete[] buffer;
|
356
|
+
buffer = NULL;
|
357
|
+
this->setg(0, 0, 0);
|
358
|
+
this->setp(0, 0);
|
359
|
+
}
|
360
|
+
else
|
361
|
+
{
|
362
|
+
// Reset buffer pointers to initial state if external buffer exists
|
363
|
+
this->setg(buffer, buffer, buffer);
|
364
|
+
if (buffer)
|
365
|
+
this->setp(buffer, buffer + buffer_size - 1);
|
366
|
+
else
|
367
|
+
this->setp(0, 0);
|
368
|
+
}
|
369
|
+
}
|
370
|
+
|
371
|
+
/*****************************************************************************/
|
372
|
+
|
373
|
+
// Default constructor initializes stream buffer
|
374
|
+
gzifstream::gzifstream()
|
375
|
+
: std::istream(NULL), sb()
|
376
|
+
{ this->init(&sb); }
|
377
|
+
|
378
|
+
// Initialize stream buffer and open file
|
379
|
+
gzifstream::gzifstream(const char* name,
|
380
|
+
std::ios_base::openmode mode)
|
381
|
+
: std::istream(NULL), sb()
|
382
|
+
{
|
383
|
+
this->init(&sb);
|
384
|
+
this->open(name, mode);
|
385
|
+
}
|
386
|
+
|
387
|
+
// Initialize stream buffer and attach to file
|
388
|
+
gzifstream::gzifstream(int fd,
|
389
|
+
std::ios_base::openmode mode)
|
390
|
+
: std::istream(NULL), sb()
|
391
|
+
{
|
392
|
+
this->init(&sb);
|
393
|
+
this->attach(fd, mode);
|
394
|
+
}
|
395
|
+
|
396
|
+
// Open file and go into fail() state if unsuccessful
|
397
|
+
void
|
398
|
+
gzifstream::open(const char* name,
|
399
|
+
std::ios_base::openmode mode)
|
400
|
+
{
|
401
|
+
if (!sb.open(name, mode | std::ios_base::in))
|
402
|
+
this->setstate(std::ios_base::failbit);
|
403
|
+
else
|
404
|
+
this->clear();
|
405
|
+
}
|
406
|
+
|
407
|
+
// Attach to file and go into fail() state if unsuccessful
|
408
|
+
void
|
409
|
+
gzifstream::attach(int fd,
|
410
|
+
std::ios_base::openmode mode)
|
411
|
+
{
|
412
|
+
if (!sb.attach(fd, mode | std::ios_base::in))
|
413
|
+
this->setstate(std::ios_base::failbit);
|
414
|
+
else
|
415
|
+
this->clear();
|
416
|
+
}
|
417
|
+
|
418
|
+
// Close file
|
419
|
+
void
|
420
|
+
gzifstream::close()
|
421
|
+
{
|
422
|
+
if (!sb.close())
|
423
|
+
this->setstate(std::ios_base::failbit);
|
424
|
+
}
|
425
|
+
|
426
|
+
/*****************************************************************************/
|
427
|
+
|
428
|
+
// Default constructor initializes stream buffer
|
429
|
+
gzofstream::gzofstream()
|
430
|
+
: std::ostream(NULL), sb()
|
431
|
+
{ this->init(&sb); }
|
432
|
+
|
433
|
+
// Initialize stream buffer and open file
|
434
|
+
gzofstream::gzofstream(const char* name,
|
435
|
+
std::ios_base::openmode mode)
|
436
|
+
: std::ostream(NULL), sb()
|
437
|
+
{
|
438
|
+
this->init(&sb);
|
439
|
+
this->open(name, mode);
|
440
|
+
}
|
441
|
+
|
442
|
+
// Initialize stream buffer and attach to file
|
443
|
+
gzofstream::gzofstream(int fd,
|
444
|
+
std::ios_base::openmode mode)
|
445
|
+
: std::ostream(NULL), sb()
|
446
|
+
{
|
447
|
+
this->init(&sb);
|
448
|
+
this->attach(fd, mode);
|
449
|
+
}
|
450
|
+
|
451
|
+
// Open file and go into fail() state if unsuccessful
|
452
|
+
void
|
453
|
+
gzofstream::open(const char* name,
|
454
|
+
std::ios_base::openmode mode)
|
455
|
+
{
|
456
|
+
if (!sb.open(name, mode | std::ios_base::out))
|
457
|
+
this->setstate(std::ios_base::failbit);
|
458
|
+
else
|
459
|
+
this->clear();
|
460
|
+
}
|
461
|
+
|
462
|
+
// Attach to file and go into fail() state if unsuccessful
|
463
|
+
void
|
464
|
+
gzofstream::attach(int fd,
|
465
|
+
std::ios_base::openmode mode)
|
466
|
+
{
|
467
|
+
if (!sb.attach(fd, mode | std::ios_base::out))
|
468
|
+
this->setstate(std::ios_base::failbit);
|
469
|
+
else
|
470
|
+
this->clear();
|
471
|
+
}
|
472
|
+
|
473
|
+
// Close file
|
474
|
+
void
|
475
|
+
gzofstream::close()
|
476
|
+
{
|
477
|
+
if (!sb.close())
|
478
|
+
this->setstate(std::ios_base::failbit);
|
479
|
+
}
|