bio-velvet_underground 0.0.1
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- checksums.yaml +7 -0
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- data/ext/src/third-party/zlib-1.2.3/win32/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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// � Copyright Henrik Ravn 2004
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//
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// Use, modification and distribution are subject to the Boost Software License, Version 1.0.
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// (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
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//
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using System;
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using System.IO;
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using System.Runtime.InteropServices;
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namespace DotZLib
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{
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/// <summary>
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/// Implements a compressed <see cref="Stream"/>, in GZip (.gz) format.
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/// </summary>
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public class GZipStream : Stream, IDisposable
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{
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#region Dll Imports
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[DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl, CharSet=CharSet.Ansi)]
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private static extern IntPtr gzopen(string name, string mode);
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[DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
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private static extern int gzclose(IntPtr gzFile);
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[DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
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private static extern int gzwrite(IntPtr gzFile, int data, int length);
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[DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
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private static extern int gzread(IntPtr gzFile, int data, int length);
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[DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
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private static extern int gzgetc(IntPtr gzFile);
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[DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
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private static extern int gzputc(IntPtr gzFile, int c);
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#endregion
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#region Private data
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private IntPtr _gzFile;
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private bool _isDisposed = false;
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private bool _isWriting;
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#endregion
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#region Constructors
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/// <summary>
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/// Creates a new file as a writeable GZipStream
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/// </summary>
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/// <param name="fileName">The name of the compressed file to create</param>
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/// <param name="level">The compression level to use when adding data</param>
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/// <exception cref="ZLibException">If an error occurred in the internal zlib function</exception>
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public GZipStream(string fileName, CompressLevel level)
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{
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_isWriting = true;
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_gzFile = gzopen(fileName, String.Format("wb{0}", (int)level));
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throw new ZLibException(-1, "Could not open " + fileName);
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}
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/// <summary>
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/// Opens an existing file as a readable GZipStream
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/// </summary>
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/// <param name="fileName">The name of the file to open</param>
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/// <exception cref="ZLibException">If an error occurred in the internal zlib function</exception>
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public GZipStream(string fileName)
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{
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_isWriting = false;
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_gzFile = gzopen(fileName, "rb");
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if (_gzFile == IntPtr.Zero)
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throw new ZLibException(-1, "Could not open " + fileName);
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}
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#endregion
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#region Access properties
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/// <summary>
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/// Returns true of this stream can be read from, false otherwise
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/// </summary>
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public override bool CanRead
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{
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get
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}
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}
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/// <summary>
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/// Returns false.
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/// </summary>
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public override bool CanSeek
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{
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get
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{
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return false;
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}
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}
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/// <summary>
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/// Returns true if this tsream is writeable, false otherwise
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/// </summary>
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public override bool CanWrite
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{
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get
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{
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return _isWriting;
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}
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}
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#endregion
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#region Destructor & IDispose stuff
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/// <summary>
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/// Destroys this instance
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/// </summary>
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~GZipStream()
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{
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cleanUp(false);
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}
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/// <summary>
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/// Closes the external file handle
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/// </summary>
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public void Dispose()
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{
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cleanUp(true);
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}
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// Does the actual closing of the file handle.
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private void cleanUp(bool isDisposing)
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{
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if (!_isDisposed)
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{
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gzclose(_gzFile);
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_isDisposed = true;
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}
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}
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#endregion
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#region Basic reading and writing
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/// <summary>
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/// Attempts to read a number of bytes from the stream.
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/// </summary>
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/// <param name="buffer">The destination data buffer</param>
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/// <param name="offset">The index of the first destination byte in <c>buffer</c></param>
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/// <param name="count">The number of bytes requested</param>
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/// <returns>The number of bytes read</returns>
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/// <exception cref="ArgumentNullException">If <c>buffer</c> is null</exception>
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/// <exception cref="ArgumentOutOfRangeException">If <c>count</c> or <c>offset</c> are negative</exception>
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/// <exception cref="ArgumentException">If <c>offset</c> + <c>count</c> is > buffer.Length</exception>
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/// <exception cref="NotSupportedException">If this stream is not readable.</exception>
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/// <exception cref="ObjectDisposedException">If this stream has been disposed.</exception>
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public override int Read(byte[] buffer, int offset, int count)
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{
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if (!CanRead) throw new NotSupportedException();
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if (buffer == null) throw new ArgumentNullException();
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if (offset < 0 || count < 0) throw new ArgumentOutOfRangeException();
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if ((offset+count) > buffer.Length) throw new ArgumentException();
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if (_isDisposed) throw new ObjectDisposedException("GZipStream");
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GCHandle h = GCHandle.Alloc(buffer, GCHandleType.Pinned);
|
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int result;
|
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try
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{
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result = gzread(_gzFile, h.AddrOfPinnedObject().ToInt32() + offset, count);
|
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if (result < 0)
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throw new IOException();
|
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}
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finally
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{
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h.Free();
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}
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return result;
|
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}
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/// <summary>
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/// Attempts to read a single byte from the stream.
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/// </summary>
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/// <returns>The byte that was read, or -1 in case of error or End-Of-File</returns>
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public override int ReadByte()
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{
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if (!CanRead) throw new NotSupportedException();
|
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if (_isDisposed) throw new ObjectDisposedException("GZipStream");
|
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return gzgetc(_gzFile);
|
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}
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/// <summary>
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/// Writes a number of bytes to the stream
|
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/// </summary>
|
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/// <param name="buffer"></param>
|
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/// <param name="offset"></param>
|
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/// <param name="count"></param>
|
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/// <exception cref="ArgumentNullException">If <c>buffer</c> is null</exception>
|
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/// <exception cref="ArgumentOutOfRangeException">If <c>count</c> or <c>offset</c> are negative</exception>
|
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/// <exception cref="ArgumentException">If <c>offset</c> + <c>count</c> is > buffer.Length</exception>
|
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/// <exception cref="NotSupportedException">If this stream is not writeable.</exception>
|
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/// <exception cref="ObjectDisposedException">If this stream has been disposed.</exception>
|
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public override void Write(byte[] buffer, int offset, int count)
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{
|
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if (!CanWrite) throw new NotSupportedException();
|
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if (buffer == null) throw new ArgumentNullException();
|
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if (offset < 0 || count < 0) throw new ArgumentOutOfRangeException();
|
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if ((offset+count) > buffer.Length) throw new ArgumentException();
|
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if (_isDisposed) throw new ObjectDisposedException("GZipStream");
|
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|
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GCHandle h = GCHandle.Alloc(buffer, GCHandleType.Pinned);
|
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try
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{
|
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int result = gzwrite(_gzFile, h.AddrOfPinnedObject().ToInt32() + offset, count);
|
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if (result < 0)
|
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throw new IOException();
|
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}
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finally
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{
|
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|
+
h.Free();
|
217
|
+
}
|
218
|
+
}
|
219
|
+
|
220
|
+
/// <summary>
|
221
|
+
/// Writes a single byte to the stream
|
222
|
+
/// </summary>
|
223
|
+
/// <param name="value">The byte to add to the stream.</param>
|
224
|
+
/// <exception cref="NotSupportedException">If this stream is not writeable.</exception>
|
225
|
+
/// <exception cref="ObjectDisposedException">If this stream has been disposed.</exception>
|
226
|
+
public override void WriteByte(byte value)
|
227
|
+
{
|
228
|
+
if (!CanWrite) throw new NotSupportedException();
|
229
|
+
if (_isDisposed) throw new ObjectDisposedException("GZipStream");
|
230
|
+
|
231
|
+
int result = gzputc(_gzFile, (int)value);
|
232
|
+
if (result < 0)
|
233
|
+
throw new IOException();
|
234
|
+
}
|
235
|
+
#endregion
|
236
|
+
|
237
|
+
#region Position & length stuff
|
238
|
+
/// <summary>
|
239
|
+
/// Not supported.
|
240
|
+
/// </summary>
|
241
|
+
/// <param name="value"></param>
|
242
|
+
/// <exception cref="NotSupportedException">Always thrown</exception>
|
243
|
+
public override void SetLength(long value)
|
244
|
+
{
|
245
|
+
throw new NotSupportedException();
|
246
|
+
}
|
247
|
+
|
248
|
+
/// <summary>
|
249
|
+
/// Not suppported.
|
250
|
+
/// </summary>
|
251
|
+
/// <param name="offset"></param>
|
252
|
+
/// <param name="origin"></param>
|
253
|
+
/// <returns></returns>
|
254
|
+
/// <exception cref="NotSupportedException">Always thrown</exception>
|
255
|
+
public override long Seek(long offset, SeekOrigin origin)
|
256
|
+
{
|
257
|
+
throw new NotSupportedException();
|
258
|
+
}
|
259
|
+
|
260
|
+
/// <summary>
|
261
|
+
/// Flushes the <c>GZipStream</c>.
|
262
|
+
/// </summary>
|
263
|
+
/// <remarks>In this implementation, this method does nothing. This is because excessive
|
264
|
+
/// flushing may degrade the achievable compression rates.</remarks>
|
265
|
+
public override void Flush()
|
266
|
+
{
|
267
|
+
// left empty on purpose
|
268
|
+
}
|
269
|
+
|
270
|
+
/// <summary>
|
271
|
+
/// Gets/sets the current position in the <c>GZipStream</c>. Not suppported.
|
272
|
+
/// </summary>
|
273
|
+
/// <remarks>In this implementation this property is not supported</remarks>
|
274
|
+
/// <exception cref="NotSupportedException">Always thrown</exception>
|
275
|
+
public override long Position
|
276
|
+
{
|
277
|
+
get
|
278
|
+
{
|
279
|
+
throw new NotSupportedException();
|
280
|
+
}
|
281
|
+
set
|
282
|
+
{
|
283
|
+
throw new NotSupportedException();
|
284
|
+
}
|
285
|
+
}
|
286
|
+
|
287
|
+
/// <summary>
|
288
|
+
/// Gets the size of the stream. Not suppported.
|
289
|
+
/// </summary>
|
290
|
+
/// <remarks>In this implementation this property is not supported</remarks>
|
291
|
+
/// <exception cref="NotSupportedException">Always thrown</exception>
|
292
|
+
public override long Length
|
293
|
+
{
|
294
|
+
get
|
295
|
+
{
|
296
|
+
throw new NotSupportedException();
|
297
|
+
}
|
298
|
+
}
|
299
|
+
#endregion
|
300
|
+
}
|
301
|
+
}
|
@@ -0,0 +1,105 @@
|
|
1
|
+
//
|
2
|
+
// � Copyright Henrik Ravn 2004
|
3
|
+
//
|
4
|
+
// Use, modification and distribution are subject to the Boost Software License, Version 1.0.
|
5
|
+
// (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
|
6
|
+
//
|
7
|
+
|
8
|
+
using System;
|
9
|
+
using System.Diagnostics;
|
10
|
+
using System.Runtime.InteropServices;
|
11
|
+
|
12
|
+
namespace DotZLib
|
13
|
+
{
|
14
|
+
|
15
|
+
/// <summary>
|
16
|
+
/// Implements a data decompressor, using the inflate algorithm in the ZLib dll
|
17
|
+
/// </summary>
|
18
|
+
public class Inflater : CodecBase
|
19
|
+
{
|
20
|
+
#region Dll imports
|
21
|
+
[DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl, CharSet=CharSet.Ansi)]
|
22
|
+
private static extern int inflateInit_(ref ZStream sz, string vs, int size);
|
23
|
+
|
24
|
+
[DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
|
25
|
+
private static extern int inflate(ref ZStream sz, int flush);
|
26
|
+
|
27
|
+
[DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
|
28
|
+
private static extern int inflateReset(ref ZStream sz);
|
29
|
+
|
30
|
+
[DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
|
31
|
+
private static extern int inflateEnd(ref ZStream sz);
|
32
|
+
#endregion
|
33
|
+
|
34
|
+
/// <summary>
|
35
|
+
/// Constructs an new instance of the <c>Inflater</c>
|
36
|
+
/// </summary>
|
37
|
+
public Inflater() : base()
|
38
|
+
{
|
39
|
+
int retval = inflateInit_(ref _ztream, Info.Version, Marshal.SizeOf(_ztream));
|
40
|
+
if (retval != 0)
|
41
|
+
throw new ZLibException(retval, "Could not initialize inflater");
|
42
|
+
|
43
|
+
resetOutput();
|
44
|
+
}
|
45
|
+
|
46
|
+
|
47
|
+
/// <summary>
|
48
|
+
/// Adds more data to the codec to be processed.
|
49
|
+
/// </summary>
|
50
|
+
/// <param name="data">Byte array containing the data to be added to the codec</param>
|
51
|
+
/// <param name="offset">The index of the first byte to add from <c>data</c></param>
|
52
|
+
/// <param name="count">The number of bytes to add</param>
|
53
|
+
/// <remarks>Adding data may, or may not, raise the <c>DataAvailable</c> event</remarks>
|
54
|
+
public override void Add(byte[] data, int offset, int count)
|
55
|
+
{
|
56
|
+
if (data == null) throw new ArgumentNullException();
|
57
|
+
if (offset < 0 || count < 0) throw new ArgumentOutOfRangeException();
|
58
|
+
if ((offset+count) > data.Length) throw new ArgumentException();
|
59
|
+
|
60
|
+
int total = count;
|
61
|
+
int inputIndex = offset;
|
62
|
+
int err = 0;
|
63
|
+
|
64
|
+
while (err >= 0 && inputIndex < total)
|
65
|
+
{
|
66
|
+
copyInput(data, inputIndex, Math.Min(total - inputIndex, kBufferSize));
|
67
|
+
err = inflate(ref _ztream, (int)FlushTypes.None);
|
68
|
+
if (err == 0)
|
69
|
+
while (_ztream.avail_out == 0)
|
70
|
+
{
|
71
|
+
OnDataAvailable();
|
72
|
+
err = inflate(ref _ztream, (int)FlushTypes.None);
|
73
|
+
}
|
74
|
+
|
75
|
+
inputIndex += (int)_ztream.total_in;
|
76
|
+
}
|
77
|
+
setChecksum( _ztream.adler );
|
78
|
+
}
|
79
|
+
|
80
|
+
|
81
|
+
/// <summary>
|
82
|
+
/// Finishes up any pending data that needs to be processed and handled.
|
83
|
+
/// </summary>
|
84
|
+
public override void Finish()
|
85
|
+
{
|
86
|
+
int err;
|
87
|
+
do
|
88
|
+
{
|
89
|
+
err = inflate(ref _ztream, (int)FlushTypes.Finish);
|
90
|
+
OnDataAvailable();
|
91
|
+
}
|
92
|
+
while (err == 0);
|
93
|
+
setChecksum( _ztream.adler );
|
94
|
+
inflateReset(ref _ztream);
|
95
|
+
resetOutput();
|
96
|
+
}
|
97
|
+
|
98
|
+
/// <summary>
|
99
|
+
/// Closes the internal zlib inflate stream
|
100
|
+
/// </summary>
|
101
|
+
protected override void CleanUp() { inflateEnd(ref _ztream); }
|
102
|
+
|
103
|
+
|
104
|
+
}
|
105
|
+
}
|