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 +1,71 @@
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All files under this contrib directory are UNSUPPORTED. There were
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provided by users of zlib and were not tested by the authors of zlib.
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Use at your own risk. Please contact the authors of the contributions
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for help about these, not the zlib authors. Thanks.
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ada/ by Dmitriy Anisimkov <anisimkov@yahoo.com>
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Support for Ada
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See http://zlib-ada.sourceforge.net/
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asm586/
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asm686/ by Brian Raiter <breadbox@muppetlabs.com>
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asm code for Pentium and PPro/PII, using the AT&T (GNU as) syntax
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See http://www.muppetlabs.com/~breadbox/software/assembly.html
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blast/ by Mark Adler <madler@alumni.caltech.edu>
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Decompressor for output of PKWare Data Compression Library (DCL)
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delphi/ by Cosmin Truta <cosmint@cs.ubbcluj.ro>
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Support for Delphi and C++ Builder
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dotzlib/ by Henrik Ravn <henrik@ravn.com>
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Support for Microsoft .Net and Visual C++ .Net
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infback9/ by Mark Adler <madler@alumni.caltech.edu>
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Unsupported diffs to infback to decode the deflate64 format
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inflate86/ by Chris Anderson <christop@charm.net>
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Tuned x86 gcc asm code to replace inflate_fast()
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iostream/ by Kevin Ruland <kevin@rodin.wustl.edu>
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A C++ I/O streams interface to the zlib gz* functions
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iostream2/ by Tyge L�vset <Tyge.Lovset@cmr.no>
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Another C++ I/O streams interface
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iostream3/ by Ludwig Schwardt <schwardt@sun.ac.za>
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and Kevin Ruland <kevin@rodin.wustl.edu>
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Yet another C++ I/O streams interface
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masm686/ by Dan Higdon <hdan@kinesoft.com>
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and Chuck Walbourn <chuckw@kinesoft.com>
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asm code for Pentium Pro/PII, using the MASM syntax
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masmx64/ by Gilles Vollant <info@winimage.com>
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x86 64-bit (AMD64 and Intel EM64t) code for x64 assembler to
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replace longest_match() and inflate_fast()
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masmx86/ by Gilles Vollant <info@winimage.com>
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x86 asm code to replace longest_match() and inflate_fast(),
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for Visual C++ and MASM
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minizip/ by Gilles Vollant <info@winimage.com>
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Mini zip and unzip based on zlib
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See http://www.winimage.com/zLibDll/unzip.html
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pascal/ by Bob Dellaca <bobdl@xtra.co.nz> et al.
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Support for Pascal
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puff/ by Mark Adler <madler@alumni.caltech.edu>
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Small, low memory usage inflate. Also serves to provide an
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unambiguous description of the deflate format.
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testzlib/ by Gilles Vollant <info@winimage.com>
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Example of the use of zlib
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untgz/ by Pedro A. Aranda Gutierrez <paag@tid.es>
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A very simple tar.gz file extractor using zlib
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vstudio/ by Gilles Vollant <info@winimage.com>
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Building a minizip-enhanced zlib with Microsoft Visual Studio
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----------------------------------------------------------------
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-- ZLib for Ada thick binding. --
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-- --
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-- Copyright (C) 2002-2004 Dmitriy Anisimkov --
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-- --
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-- Open source license information is in the zlib.ads file. --
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----------------------------------------------------------------
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--
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-- $Id: buffer_demo.adb,v 1.3 2004/09/06 06:55:35 vagul Exp $
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-- This demo program provided by Dr Steve Sangwine <sjs@essex.ac.uk>
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--
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-- Demonstration of a problem with Zlib-Ada (already fixed) when a buffer
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-- of exactly the correct size is used for decompressed data, and the last
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-- few bytes passed in to Zlib are checksum bytes.
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-- This program compresses a string of text, and then decompresses the
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-- compressed text into a buffer of the same size as the original text.
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with Ada.Streams; use Ada.Streams;
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with Ada.Text_IO;
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with ZLib; use ZLib;
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procedure Buffer_Demo is
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EOL : Character renames ASCII.LF;
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Text : constant String
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:= "Four score and seven years ago our fathers brought forth," & EOL &
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"upon this continent, a new nation, conceived in liberty," & EOL &
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"and dedicated to the proposition that `all men are created equal'.";
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Source : Stream_Element_Array (1 .. Text'Length);
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for Source'Address use Text'Address;
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begin
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Ada.Text_IO.Put (Text);
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Ada.Text_IO.New_Line;
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Ada.Text_IO.Put_Line
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("Uncompressed size : " & Positive'Image (Text'Length) & " bytes");
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declare
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Compressed_Data : Stream_Element_Array (1 .. Text'Length);
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L : Stream_Element_Offset;
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begin
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Compress : declare
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Compressor : Filter_Type;
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I : Stream_Element_Offset;
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begin
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Deflate_Init (Compressor);
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-- Compress the whole of T at once.
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Translate (Compressor, Source, I, Compressed_Data, L, Finish);
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pragma Assert (I = Source'Last);
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Close (Compressor);
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Ada.Text_IO.Put_Line
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("Compressed size : "
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& Stream_Element_Offset'Image (L) & " bytes");
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end Compress;
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+
|
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-- Now we decompress the data, passing short blocks of data to Zlib
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-- (because this demonstrates the problem - the last block passed will
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-- contain checksum information and there will be no output, only a
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-- check inside Zlib that the checksum is correct).
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+
|
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Decompress : declare
|
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Decompressor : Filter_Type;
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+
|
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Uncompressed_Data : Stream_Element_Array (1 .. Text'Length);
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+
|
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Block_Size : constant := 4;
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-- This makes sure that the last block contains
|
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-- only Adler checksum data.
|
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+
|
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P : Stream_Element_Offset := Compressed_Data'First - 1;
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O : Stream_Element_Offset;
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begin
|
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Inflate_Init (Decompressor);
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|
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loop
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Translate
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(Decompressor,
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Compressed_Data
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(P + 1 .. Stream_Element_Offset'Min (P + Block_Size, L)),
|
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P,
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Uncompressed_Data
|
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(Total_Out (Decompressor) + 1 .. Uncompressed_Data'Last),
|
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O,
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No_Flush);
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+
|
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Ada.Text_IO.Put_Line
|
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("Total in : " & Count'Image (Total_In (Decompressor)) &
|
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", out : " & Count'Image (Total_Out (Decompressor)));
|
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+
|
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exit when P = L;
|
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end loop;
|
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+
|
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Ada.Text_IO.New_Line;
|
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Ada.Text_IO.Put_Line
|
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("Decompressed text matches original text : "
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& Boolean'Image (Uncompressed_Data = Source));
|
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end Decompress;
|
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end;
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end Buffer_Demo;
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----------------------------------------------------------------
|
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-- ZLib for Ada thick binding. --
|
3
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-- --
|
4
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-- Copyright (C) 2002-2003 Dmitriy Anisimkov --
|
5
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-- --
|
6
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-- Open source license information is in the zlib.ads file. --
|
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----------------------------------------------------------------
|
8
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-- Continuous test for ZLib multithreading. If the test would fail
|
9
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-- we should provide thread safe allocation routines for the Z_Stream.
|
10
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--
|
11
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-- $Id: mtest.adb,v 1.4 2004/07/23 07:49:54 vagul Exp $
|
12
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+
|
13
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with ZLib;
|
14
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with Ada.Streams;
|
15
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with Ada.Numerics.Discrete_Random;
|
16
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with Ada.Text_IO;
|
17
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with Ada.Exceptions;
|
18
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with Ada.Task_Identification;
|
19
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+
|
20
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procedure MTest is
|
21
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use Ada.Streams;
|
22
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use ZLib;
|
23
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+
|
24
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Stop : Boolean := False;
|
25
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+
|
26
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pragma Atomic (Stop);
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27
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+
|
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subtype Visible_Symbols is Stream_Element range 16#20# .. 16#7E#;
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+
|
30
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package Random_Elements is
|
31
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new Ada.Numerics.Discrete_Random (Visible_Symbols);
|
32
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+
|
33
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task type Test_Task;
|
34
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+
|
35
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task body Test_Task is
|
36
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Buffer : Stream_Element_Array (1 .. 100_000);
|
37
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Gen : Random_Elements.Generator;
|
38
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+
|
39
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Buffer_First : Stream_Element_Offset;
|
40
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Compare_First : Stream_Element_Offset;
|
41
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+
|
42
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+
Deflate : Filter_Type;
|
43
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Inflate : Filter_Type;
|
44
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+
|
45
|
+
procedure Further (Item : in Stream_Element_Array);
|
46
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+
|
47
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procedure Read_Buffer
|
48
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(Item : out Ada.Streams.Stream_Element_Array;
|
49
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Last : out Ada.Streams.Stream_Element_Offset);
|
50
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+
|
51
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-------------
|
52
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-- Further --
|
53
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-------------
|
54
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|
55
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procedure Further (Item : in Stream_Element_Array) is
|
56
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+
|
57
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procedure Compare (Item : in Stream_Element_Array);
|
58
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|
59
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-------------
|
60
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-- Compare --
|
61
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-------------
|
62
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+
|
63
|
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procedure Compare (Item : in Stream_Element_Array) is
|
64
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+
Next_First : Stream_Element_Offset := Compare_First + Item'Length;
|
65
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+
begin
|
66
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+
if Buffer (Compare_First .. Next_First - 1) /= Item then
|
67
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raise Program_Error;
|
68
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+
end if;
|
69
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+
|
70
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+
Compare_First := Next_First;
|
71
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+
end Compare;
|
72
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+
|
73
|
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procedure Compare_Write is new ZLib.Write (Write => Compare);
|
74
|
+
begin
|
75
|
+
Compare_Write (Inflate, Item, No_Flush);
|
76
|
+
end Further;
|
77
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+
|
78
|
+
-----------------
|
79
|
+
-- Read_Buffer --
|
80
|
+
-----------------
|
81
|
+
|
82
|
+
procedure Read_Buffer
|
83
|
+
(Item : out Ada.Streams.Stream_Element_Array;
|
84
|
+
Last : out Ada.Streams.Stream_Element_Offset)
|
85
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+
is
|
86
|
+
Buff_Diff : Stream_Element_Offset := Buffer'Last - Buffer_First;
|
87
|
+
Next_First : Stream_Element_Offset;
|
88
|
+
begin
|
89
|
+
if Item'Length <= Buff_Diff then
|
90
|
+
Last := Item'Last;
|
91
|
+
|
92
|
+
Next_First := Buffer_First + Item'Length;
|
93
|
+
|
94
|
+
Item := Buffer (Buffer_First .. Next_First - 1);
|
95
|
+
|
96
|
+
Buffer_First := Next_First;
|
97
|
+
else
|
98
|
+
Last := Item'First + Buff_Diff;
|
99
|
+
Item (Item'First .. Last) := Buffer (Buffer_First .. Buffer'Last);
|
100
|
+
Buffer_First := Buffer'Last + 1;
|
101
|
+
end if;
|
102
|
+
end Read_Buffer;
|
103
|
+
|
104
|
+
procedure Translate is new Generic_Translate
|
105
|
+
(Data_In => Read_Buffer,
|
106
|
+
Data_Out => Further);
|
107
|
+
|
108
|
+
begin
|
109
|
+
Random_Elements.Reset (Gen);
|
110
|
+
|
111
|
+
Buffer := (others => 20);
|
112
|
+
|
113
|
+
Main : loop
|
114
|
+
for J in Buffer'Range loop
|
115
|
+
Buffer (J) := Random_Elements.Random (Gen);
|
116
|
+
|
117
|
+
Deflate_Init (Deflate);
|
118
|
+
Inflate_Init (Inflate);
|
119
|
+
|
120
|
+
Buffer_First := Buffer'First;
|
121
|
+
Compare_First := Buffer'First;
|
122
|
+
|
123
|
+
Translate (Deflate);
|
124
|
+
|
125
|
+
if Compare_First /= Buffer'Last + 1 then
|
126
|
+
raise Program_Error;
|
127
|
+
end if;
|
128
|
+
|
129
|
+
Ada.Text_IO.Put_Line
|
130
|
+
(Ada.Task_Identification.Image
|
131
|
+
(Ada.Task_Identification.Current_Task)
|
132
|
+
& Stream_Element_Offset'Image (J)
|
133
|
+
& ZLib.Count'Image (Total_Out (Deflate)));
|
134
|
+
|
135
|
+
Close (Deflate);
|
136
|
+
Close (Inflate);
|
137
|
+
|
138
|
+
exit Main when Stop;
|
139
|
+
end loop;
|
140
|
+
end loop Main;
|
141
|
+
exception
|
142
|
+
when E : others =>
|
143
|
+
Ada.Text_IO.Put_Line (Ada.Exceptions.Exception_Information (E));
|
144
|
+
Stop := True;
|
145
|
+
end Test_Task;
|
146
|
+
|
147
|
+
Test : array (1 .. 4) of Test_Task;
|
148
|
+
|
149
|
+
pragma Unreferenced (Test);
|
150
|
+
|
151
|
+
Dummy : Character;
|
152
|
+
|
153
|
+
begin
|
154
|
+
Ada.Text_IO.Get_Immediate (Dummy);
|
155
|
+
Stop := True;
|
156
|
+
end MTest;
|
@@ -0,0 +1,156 @@
|
|
1
|
+
----------------------------------------------------------------
|
2
|
+
-- ZLib for Ada thick binding. --
|
3
|
+
-- --
|
4
|
+
-- Copyright (C) 2002-2003 Dmitriy Anisimkov --
|
5
|
+
-- --
|
6
|
+
-- Open source license information is in the zlib.ads file. --
|
7
|
+
----------------------------------------------------------------
|
8
|
+
|
9
|
+
-- $Id: read.adb,v 1.8 2004/05/31 10:53:40 vagul Exp $
|
10
|
+
|
11
|
+
-- Test/demo program for the generic read interface.
|
12
|
+
|
13
|
+
with Ada.Numerics.Discrete_Random;
|
14
|
+
with Ada.Streams;
|
15
|
+
with Ada.Text_IO;
|
16
|
+
|
17
|
+
with ZLib;
|
18
|
+
|
19
|
+
procedure Read is
|
20
|
+
|
21
|
+
use Ada.Streams;
|
22
|
+
|
23
|
+
------------------------------------
|
24
|
+
-- Test configuration parameters --
|
25
|
+
------------------------------------
|
26
|
+
|
27
|
+
File_Size : Stream_Element_Offset := 100_000;
|
28
|
+
|
29
|
+
Continuous : constant Boolean := False;
|
30
|
+
-- If this constant is True, the test would be repeated again and again,
|
31
|
+
-- with increment File_Size for every iteration.
|
32
|
+
|
33
|
+
Header : constant ZLib.Header_Type := ZLib.Default;
|
34
|
+
-- Do not use Header other than Default in ZLib versions 1.1.4 and older.
|
35
|
+
|
36
|
+
Init_Random : constant := 8;
|
37
|
+
-- We are using the same random sequence, in case of we catch bug,
|
38
|
+
-- so we would be able to reproduce it.
|
39
|
+
|
40
|
+
-- End --
|
41
|
+
|
42
|
+
Pack_Size : Stream_Element_Offset;
|
43
|
+
Offset : Stream_Element_Offset;
|
44
|
+
|
45
|
+
Filter : ZLib.Filter_Type;
|
46
|
+
|
47
|
+
subtype Visible_Symbols
|
48
|
+
is Stream_Element range 16#20# .. 16#7E#;
|
49
|
+
|
50
|
+
package Random_Elements is new
|
51
|
+
Ada.Numerics.Discrete_Random (Visible_Symbols);
|
52
|
+
|
53
|
+
Gen : Random_Elements.Generator;
|
54
|
+
Period : constant Stream_Element_Offset := 200;
|
55
|
+
-- Period constant variable for random generator not to be very random.
|
56
|
+
-- Bigger period, harder random.
|
57
|
+
|
58
|
+
Read_Buffer : Stream_Element_Array (1 .. 2048);
|
59
|
+
Read_First : Stream_Element_Offset;
|
60
|
+
Read_Last : Stream_Element_Offset;
|
61
|
+
|
62
|
+
procedure Reset;
|
63
|
+
|
64
|
+
procedure Read
|
65
|
+
(Item : out Stream_Element_Array;
|
66
|
+
Last : out Stream_Element_Offset);
|
67
|
+
-- this procedure is for generic instantiation of
|
68
|
+
-- ZLib.Read
|
69
|
+
-- reading data from the File_In.
|
70
|
+
|
71
|
+
procedure Read is new ZLib.Read
|
72
|
+
(Read,
|
73
|
+
Read_Buffer,
|
74
|
+
Rest_First => Read_First,
|
75
|
+
Rest_Last => Read_Last);
|
76
|
+
|
77
|
+
----------
|
78
|
+
-- Read --
|
79
|
+
----------
|
80
|
+
|
81
|
+
procedure Read
|
82
|
+
(Item : out Stream_Element_Array;
|
83
|
+
Last : out Stream_Element_Offset) is
|
84
|
+
begin
|
85
|
+
Last := Stream_Element_Offset'Min
|
86
|
+
(Item'Last,
|
87
|
+
Item'First + File_Size - Offset);
|
88
|
+
|
89
|
+
for J in Item'First .. Last loop
|
90
|
+
if J < Item'First + Period then
|
91
|
+
Item (J) := Random_Elements.Random (Gen);
|
92
|
+
else
|
93
|
+
Item (J) := Item (J - Period);
|
94
|
+
end if;
|
95
|
+
|
96
|
+
Offset := Offset + 1;
|
97
|
+
end loop;
|
98
|
+
end Read;
|
99
|
+
|
100
|
+
-----------
|
101
|
+
-- Reset --
|
102
|
+
-----------
|
103
|
+
|
104
|
+
procedure Reset is
|
105
|
+
begin
|
106
|
+
Random_Elements.Reset (Gen, Init_Random);
|
107
|
+
Pack_Size := 0;
|
108
|
+
Offset := 1;
|
109
|
+
Read_First := Read_Buffer'Last + 1;
|
110
|
+
Read_Last := Read_Buffer'Last;
|
111
|
+
end Reset;
|
112
|
+
|
113
|
+
begin
|
114
|
+
Ada.Text_IO.Put_Line ("ZLib " & ZLib.Version);
|
115
|
+
|
116
|
+
loop
|
117
|
+
for Level in ZLib.Compression_Level'Range loop
|
118
|
+
|
119
|
+
Ada.Text_IO.Put ("Level ="
|
120
|
+
& ZLib.Compression_Level'Image (Level));
|
121
|
+
|
122
|
+
-- Deflate using generic instantiation.
|
123
|
+
|
124
|
+
ZLib.Deflate_Init
|
125
|
+
(Filter,
|
126
|
+
Level,
|
127
|
+
Header => Header);
|
128
|
+
|
129
|
+
Reset;
|
130
|
+
|
131
|
+
Ada.Text_IO.Put
|
132
|
+
(Stream_Element_Offset'Image (File_Size) & " ->");
|
133
|
+
|
134
|
+
loop
|
135
|
+
declare
|
136
|
+
Buffer : Stream_Element_Array (1 .. 1024);
|
137
|
+
Last : Stream_Element_Offset;
|
138
|
+
begin
|
139
|
+
Read (Filter, Buffer, Last);
|
140
|
+
|
141
|
+
Pack_Size := Pack_Size + Last - Buffer'First + 1;
|
142
|
+
|
143
|
+
exit when Last < Buffer'Last;
|
144
|
+
end;
|
145
|
+
end loop;
|
146
|
+
|
147
|
+
Ada.Text_IO.Put_Line (Stream_Element_Offset'Image (Pack_Size));
|
148
|
+
|
149
|
+
ZLib.Close (Filter);
|
150
|
+
end loop;
|
151
|
+
|
152
|
+
exit when not Continuous;
|
153
|
+
|
154
|
+
File_Size := File_Size + 1;
|
155
|
+
end loop;
|
156
|
+
end Read;
|