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
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/*
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* A C++ I/O streams interface to the zlib gz* functions
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*
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* by Ludwig Schwardt <schwardt@sun.ac.za>
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* original version by Kevin Ruland <kevin@rodin.wustl.edu>
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*
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* This version is standard-compliant and compatible with gcc 3.x.
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*/
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#ifndef ZFSTREAM_H
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#define ZFSTREAM_H
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#include <istream> // not iostream, since we don't need cin/cout
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#include <ostream>
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#include "zlib.h"
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/*****************************************************************************/
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/**
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* @brief Gzipped file stream buffer class.
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*
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* This class implements basic_filebuf for gzipped files. It doesn't yet support
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* seeking (allowed by zlib but slow/limited), putback and read/write access
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* (tricky). Otherwise, it attempts to be a drop-in replacement for the standard
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* file streambuf.
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*/
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class gzfilebuf : public std::streambuf
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{
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public:
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// Default constructor.
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gzfilebuf();
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// Destructor.
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virtual
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~gzfilebuf();
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/**
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* @brief Set compression level and strategy on the fly.
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* @param comp_level Compression level (see zlib.h for allowed values)
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* @param comp_strategy Compression strategy (see zlib.h for allowed values)
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* @return Z_OK on success, Z_STREAM_ERROR otherwise.
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*
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* Unfortunately, these parameters cannot be modified separately, as the
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* previous zfstream version assumed. Since the strategy is seldom changed,
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* it can default and setcompression(level) then becomes like the old
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* setcompressionlevel(level).
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*/
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int
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setcompression(int comp_level,
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int comp_strategy = Z_DEFAULT_STRATEGY);
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/**
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* @brief Check if file is open.
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* @return True if file is open.
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*/
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bool
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is_open() const { return (file != NULL); }
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/**
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* @brief Open gzipped file.
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* @param name File name.
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* @param mode Open mode flags.
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* @return @c this on success, NULL on failure.
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*/
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gzfilebuf*
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open(const char* name,
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std::ios_base::openmode mode);
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/**
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* @brief Attach to already open gzipped file.
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* @param fd File descriptor.
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* @param mode Open mode flags.
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* @return @c this on success, NULL on failure.
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*/
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gzfilebuf*
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attach(int fd,
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std::ios_base::openmode mode);
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/**
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* @brief Close gzipped file.
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* @return @c this on success, NULL on failure.
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*/
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gzfilebuf*
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close();
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protected:
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/**
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* @brief Convert ios open mode int to mode string used by zlib.
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* @return True if valid mode flag combination.
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*/
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bool
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open_mode(std::ios_base::openmode mode,
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char* c_mode) const;
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/**
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* @brief Number of characters available in stream buffer.
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* @return Number of characters.
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*
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* This indicates number of characters in get area of stream buffer.
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* These characters can be read without accessing the gzipped file.
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*/
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virtual std::streamsize
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showmanyc();
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/**
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* @brief Fill get area from gzipped file.
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* @return First character in get area on success, EOF on error.
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*
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* This actually reads characters from gzipped file to stream
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* buffer. Always buffered.
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*/
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virtual int_type
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underflow();
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/**
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* @brief Write put area to gzipped file.
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* @param c Extra character to add to buffer contents.
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* @return Non-EOF on success, EOF on error.
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*
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* This actually writes characters in stream buffer to
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* gzipped file. With unbuffered output this is done one
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* character at a time.
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*/
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virtual int_type
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overflow(int_type c = traits_type::eof());
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/**
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* @brief Installs external stream buffer.
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* @param p Pointer to char buffer.
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* @param n Size of external buffer.
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* @return @c this on success, NULL on failure.
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*
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* Call setbuf(0,0) to enable unbuffered output.
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*/
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virtual std::streambuf*
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setbuf(char_type* p,
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std::streamsize n);
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/**
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* @brief Flush stream buffer to file.
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* @return 0 on success, -1 on error.
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*
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* This calls underflow(EOF) to do the job.
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*/
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virtual int
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sync();
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//
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// Some future enhancements
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//
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// virtual int_type uflow();
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// virtual int_type pbackfail(int_type c = traits_type::eof());
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// virtual pos_type
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// seekoff(off_type off,
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// std::ios_base::seekdir way,
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// std::ios_base::openmode mode = std::ios_base::in|std::ios_base::out);
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// virtual pos_type
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// seekpos(pos_type sp,
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// std::ios_base::openmode mode = std::ios_base::in|std::ios_base::out);
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private:
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/**
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* @brief Allocate internal buffer.
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*
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* This function is safe to call multiple times. It will ensure
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* that a proper internal buffer exists if it is required. If the
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* buffer already exists or is external, the buffer pointers will be
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* reset to their original state.
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*/
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void
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enable_buffer();
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/**
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* @brief Destroy internal buffer.
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*
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* This function is safe to call multiple times. It will ensure
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* that the internal buffer is deallocated if it exists. In any
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* case, it will also reset the buffer pointers.
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*/
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void
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disable_buffer();
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/**
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* Underlying file pointer.
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*/
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gzFile file;
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/**
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* Mode in which file was opened.
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*/
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std::ios_base::openmode io_mode;
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/**
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* @brief True if this object owns file descriptor.
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*
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* This makes the class responsible for closing the file
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* upon destruction.
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*/
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bool own_fd;
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/**
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* @brief Stream buffer.
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*
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* For simplicity this remains allocated on the free store for the
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* entire life span of the gzfilebuf object, unless replaced by setbuf.
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*/
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char_type* buffer;
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/**
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* @brief Stream buffer size.
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*
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* Defaults to system default buffer size (typically 8192 bytes).
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* Modified by setbuf.
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*/
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std::streamsize buffer_size;
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/**
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* @brief True if this object owns stream buffer.
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*
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* This makes the class responsible for deleting the buffer
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* upon destruction.
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*/
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bool own_buffer;
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};
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/*****************************************************************************/
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/**
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* @brief Gzipped file input stream class.
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*
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* This class implements ifstream for gzipped files. Seeking and putback
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* is not supported yet.
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*/
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class gzifstream : public std::istream
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{
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public:
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// Default constructor
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gzifstream();
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/**
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* @brief Construct stream on gzipped file to be opened.
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* @param name File name.
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* @param mode Open mode flags (forced to contain ios::in).
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*/
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explicit
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gzifstream(const char* name,
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std::ios_base::openmode mode = std::ios_base::in);
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/**
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* @brief Construct stream on already open gzipped file.
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* @param fd File descriptor.
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* @param mode Open mode flags (forced to contain ios::in).
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*/
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explicit
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gzifstream(int fd,
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std::ios_base::openmode mode = std::ios_base::in);
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/**
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* Obtain underlying stream buffer.
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*/
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gzfilebuf*
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rdbuf() const
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{ return const_cast<gzfilebuf*>(&sb); }
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/**
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* @brief Check if file is open.
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* @return True if file is open.
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*/
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bool
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is_open() { return sb.is_open(); }
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/**
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* @brief Open gzipped file.
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* @param name File name.
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* @param mode Open mode flags (forced to contain ios::in).
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*
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* Stream will be in state good() if file opens successfully;
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* otherwise in state fail(). This differs from the behavior of
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* ifstream, which never sets the state to good() and therefore
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* won't allow you to reuse the stream for a second file unless
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* you manually clear() the state. The choice is a matter of
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* convenience.
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*/
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void
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open(const char* name,
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std::ios_base::openmode mode = std::ios_base::in);
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/**
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* @brief Attach to already open gzipped file.
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* @param fd File descriptor.
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* @param mode Open mode flags (forced to contain ios::in).
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*
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* Stream will be in state good() if attach succeeded; otherwise
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* in state fail().
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*/
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void
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attach(int fd,
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std::ios_base::openmode mode = std::ios_base::in);
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/**
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* @brief Close gzipped file.
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*
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* Stream will be in state fail() if close failed.
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*/
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void
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close();
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private:
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/**
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* Underlying stream buffer.
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*/
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gzfilebuf sb;
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};
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/*****************************************************************************/
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/**
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* @brief Gzipped file output stream class.
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*
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* This class implements ofstream for gzipped files. Seeking and putback
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* is not supported yet.
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*/
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class gzofstream : public std::ostream
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{
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public:
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// Default constructor
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gzofstream();
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/**
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* @brief Construct stream on gzipped file to be opened.
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* @param name File name.
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* @param mode Open mode flags (forced to contain ios::out).
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*/
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explicit
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gzofstream(const char* name,
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std::ios_base::openmode mode = std::ios_base::out);
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/**
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* @brief Construct stream on already open gzipped file.
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* @param fd File descriptor.
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* @param mode Open mode flags (forced to contain ios::out).
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*/
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explicit
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gzofstream(int fd,
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std::ios_base::openmode mode = std::ios_base::out);
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/**
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* Obtain underlying stream buffer.
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*/
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gzfilebuf*
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rdbuf() const
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{ return const_cast<gzfilebuf*>(&sb); }
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/**
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* @brief Check if file is open.
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* @return True if file is open.
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*/
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bool
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is_open() { return sb.is_open(); }
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/**
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* @brief Open gzipped file.
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* @param name File name.
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* @param mode Open mode flags (forced to contain ios::out).
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*
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* Stream will be in state good() if file opens successfully;
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* otherwise in state fail(). This differs from the behavior of
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* ofstream, which never sets the state to good() and therefore
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* won't allow you to reuse the stream for a second file unless
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* you manually clear() the state. The choice is a matter of
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* convenience.
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*/
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void
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open(const char* name,
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std::ios_base::openmode mode = std::ios_base::out);
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/**
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* @brief Attach to already open gzipped file.
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* @param fd File descriptor.
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* @param mode Open mode flags (forced to contain ios::out).
|
381
|
+
*
|
382
|
+
* Stream will be in state good() if attach succeeded; otherwise
|
383
|
+
* in state fail().
|
384
|
+
*/
|
385
|
+
void
|
386
|
+
attach(int fd,
|
387
|
+
std::ios_base::openmode mode = std::ios_base::out);
|
388
|
+
|
389
|
+
/**
|
390
|
+
* @brief Close gzipped file.
|
391
|
+
*
|
392
|
+
* Stream will be in state fail() if close failed.
|
393
|
+
*/
|
394
|
+
void
|
395
|
+
close();
|
396
|
+
|
397
|
+
private:
|
398
|
+
/**
|
399
|
+
* Underlying stream buffer.
|
400
|
+
*/
|
401
|
+
gzfilebuf sb;
|
402
|
+
};
|
403
|
+
|
404
|
+
/*****************************************************************************/
|
405
|
+
|
406
|
+
/**
|
407
|
+
* @brief Gzipped file output stream manipulator class.
|
408
|
+
*
|
409
|
+
* This class defines a two-argument manipulator for gzofstream. It is used
|
410
|
+
* as base for the setcompression(int,int) manipulator.
|
411
|
+
*/
|
412
|
+
template<typename T1, typename T2>
|
413
|
+
class gzomanip2
|
414
|
+
{
|
415
|
+
public:
|
416
|
+
// Allows insertor to peek at internals
|
417
|
+
template <typename Ta, typename Tb>
|
418
|
+
friend gzofstream&
|
419
|
+
operator<<(gzofstream&,
|
420
|
+
const gzomanip2<Ta,Tb>&);
|
421
|
+
|
422
|
+
// Constructor
|
423
|
+
gzomanip2(gzofstream& (*f)(gzofstream&, T1, T2),
|
424
|
+
T1 v1,
|
425
|
+
T2 v2);
|
426
|
+
private:
|
427
|
+
// Underlying manipulator function
|
428
|
+
gzofstream&
|
429
|
+
(*func)(gzofstream&, T1, T2);
|
430
|
+
|
431
|
+
// Arguments for manipulator function
|
432
|
+
T1 val1;
|
433
|
+
T2 val2;
|
434
|
+
};
|
435
|
+
|
436
|
+
/*****************************************************************************/
|
437
|
+
|
438
|
+
// Manipulator function thunks through to stream buffer
|
439
|
+
inline gzofstream&
|
440
|
+
setcompression(gzofstream &gzs, int l, int s = Z_DEFAULT_STRATEGY)
|
441
|
+
{
|
442
|
+
(gzs.rdbuf())->setcompression(l, s);
|
443
|
+
return gzs;
|
444
|
+
}
|
445
|
+
|
446
|
+
// Manipulator constructor stores arguments
|
447
|
+
template<typename T1, typename T2>
|
448
|
+
inline
|
449
|
+
gzomanip2<T1,T2>::gzomanip2(gzofstream &(*f)(gzofstream &, T1, T2),
|
450
|
+
T1 v1,
|
451
|
+
T2 v2)
|
452
|
+
: func(f), val1(v1), val2(v2)
|
453
|
+
{ }
|
454
|
+
|
455
|
+
// Insertor applies underlying manipulator function to stream
|
456
|
+
template<typename T1, typename T2>
|
457
|
+
inline gzofstream&
|
458
|
+
operator<<(gzofstream& s, const gzomanip2<T1,T2>& m)
|
459
|
+
{ return (*m.func)(s, m.val1, m.val2); }
|
460
|
+
|
461
|
+
// Insert this onto stream to simplify setting of compression level
|
462
|
+
inline gzomanip2<int,int>
|
463
|
+
setcompression(int l, int s = Z_DEFAULT_STRATEGY)
|
464
|
+
{ return gzomanip2<int,int>(&setcompression, l, s); }
|
465
|
+
|
466
|
+
#endif // ZFSTREAM_H
|