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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ZLib for Ada thick binding (ZLib.Ada)
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Release 1.3
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ZLib.Ada is a thick binding interface to the popular ZLib data
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compression library, available at http://www.gzip.org/zlib/.
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It provides Ada-style access to the ZLib C library.
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Here are the main changes since ZLib.Ada 1.2:
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- Attension: ZLib.Read generic routine have a initialization requirement
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for Read_Last parameter now. It is a bit incompartible with previous version,
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but extends functionality, we could use new parameters Allow_Read_Some and
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Flush now.
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- Added Is_Open routines to ZLib and ZLib.Streams packages.
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- Add pragma Assert to check Stream_Element is 8 bit.
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- Fix extraction to buffer with exact known decompressed size. Error reported by
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Steve Sangwine.
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- Fix definition of ULong (changed to unsigned_long), fix regression on 64 bits
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computers. Patch provided by Pascal Obry.
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- Add Status_Error exception definition.
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- Add pragma Assertion that Ada.Streams.Stream_Element size is 8 bit.
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How to build ZLib.Ada under GNAT
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You should have the ZLib library already build on your computer, before
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building ZLib.Ada. Make the directory of ZLib.Ada sources current and
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issue the command:
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gnatmake test -largs -L<directory where libz.a is> -lz
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Or use the GNAT project file build for GNAT 3.15 or later:
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gnatmake -Pzlib.gpr -L<directory where libz.a is>
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How to build ZLib.Ada under Aonix ObjectAda for Win32 7.2.2
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1. Make a project with all *.ads and *.adb files from the distribution.
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2. Build the libz.a library from the ZLib C sources.
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3. Rename libz.a to z.lib.
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4. Add the library z.lib to the project.
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5. Add the libc.lib library from the ObjectAda distribution to the project.
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6. Build the executable using test.adb as a main procedure.
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How to use ZLib.Ada
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The source files test.adb and read.adb are small demo programs that show
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the main functionality of ZLib.Ada.
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The routines from the package specifications are commented.
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Homepage: http://zlib-ada.sourceforge.net/
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Author: Dmitriy Anisimkov <anisimkov@yahoo.com>
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Contributors: Pascal Obry <pascal@obry.org>, Steve Sangwine <sjs@essex.ac.uk>
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----------------------------------------------------------------
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-- ZLib for Ada thick binding. --
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-- --
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-- Copyright (C) 2002-2003 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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-- $Id: test.adb,v 1.17 2003/08/12 12:13:30 vagul Exp $
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-- The program has a few aims.
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-- 1. Test ZLib.Ada95 thick binding functionality.
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-- 2. Show the example of use main functionality of the ZLib.Ada95 binding.
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-- 3. Build this program automatically compile all ZLib.Ada95 packages under
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-- GNAT Ada95 compiler.
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with ZLib.Streams;
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with Ada.Streams.Stream_IO;
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with Ada.Numerics.Discrete_Random;
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with Ada.Text_IO;
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with Ada.Calendar;
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procedure Test is
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use Ada.Streams;
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use Stream_IO;
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------------------------------------
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-- Test configuration parameters --
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------------------------------------
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File_Size : Count := 100_000;
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Continuous : constant Boolean := False;
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Header : constant ZLib.Header_Type := ZLib.Default;
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-- ZLib.None;
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-- ZLib.Auto;
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-- ZLib.GZip;
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-- Do not use Header other then Default in ZLib versions 1.1.4
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-- and older.
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Strategy : constant ZLib.Strategy_Type := ZLib.Default_Strategy;
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Init_Random : constant := 10;
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-- End --
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In_File_Name : constant String := "testzlib.in";
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-- Name of the input file
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Z_File_Name : constant String := "testzlib.zlb";
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-- Name of the compressed file.
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Out_File_Name : constant String := "testzlib.out";
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-- Name of the decompressed file.
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File_In : File_Type;
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File_Out : File_Type;
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File_Back : File_Type;
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File_Z : ZLib.Streams.Stream_Type;
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Filter : ZLib.Filter_Type;
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Time_Stamp : Ada.Calendar.Time;
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procedure Generate_File;
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-- Generate file of spetsified size with some random data.
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-- The random data is repeatable, for the good compression.
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procedure Compare_Streams
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(Left, Right : in out Root_Stream_Type'Class);
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-- The procedure compearing data in 2 streams.
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-- It is for compare data before and after compression/decompression.
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procedure Compare_Files (Left, Right : String);
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-- Compare files. Based on the Compare_Streams.
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procedure Copy_Streams
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(Source, Target : in out Root_Stream_Type'Class;
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Buffer_Size : in Stream_Element_Offset := 1024);
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-- Copying data from one stream to another. It is for test stream
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-- interface of the library.
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procedure Data_In
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(Item : out Stream_Element_Array;
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Last : out Stream_Element_Offset);
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-- this procedure is for generic instantiation of
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-- ZLib.Generic_Translate.
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-- reading data from the File_In.
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procedure Data_Out (Item : in Stream_Element_Array);
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-- this procedure is for generic instantiation of
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-- ZLib.Generic_Translate.
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-- writing data to the File_Out.
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procedure Stamp;
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-- Store the timestamp to the local variable.
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procedure Print_Statistic (Msg : String; Data_Size : ZLib.Count);
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-- Print the time statistic with the message.
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procedure Translate is new ZLib.Generic_Translate
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(Data_In => Data_In,
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Data_Out => Data_Out);
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-- This procedure is moving data from File_In to File_Out
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-- with compression or decompression, depend on initialization of
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-- Filter parameter.
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-------------------
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-- Compare_Files --
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-------------------
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procedure Compare_Files (Left, Right : String) is
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Left_File, Right_File : File_Type;
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begin
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Open (Left_File, In_File, Left);
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Open (Right_File, In_File, Right);
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Compare_Streams (Stream (Left_File).all, Stream (Right_File).all);
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Close (Left_File);
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Close (Right_File);
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end Compare_Files;
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---------------------
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-- Compare_Streams --
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---------------------
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procedure Compare_Streams
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(Left, Right : in out Ada.Streams.Root_Stream_Type'Class)
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is
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Left_Buffer, Right_Buffer : Stream_Element_Array (0 .. 16#FFF#);
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Left_Last, Right_Last : Stream_Element_Offset;
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begin
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loop
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Read (Left, Left_Buffer, Left_Last);
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Read (Right, Right_Buffer, Right_Last);
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if Left_Last /= Right_Last then
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Ada.Text_IO.Put_Line ("Compare error :"
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& Stream_Element_Offset'Image (Left_Last)
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& " /= "
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& Stream_Element_Offset'Image (Right_Last));
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raise Constraint_Error;
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elsif Left_Buffer (0 .. Left_Last)
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/= Right_Buffer (0 .. Right_Last)
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then
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Ada.Text_IO.Put_Line ("ERROR: IN and OUT files is not equal.");
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raise Constraint_Error;
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end if;
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exit when Left_Last < Left_Buffer'Last;
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end loop;
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end Compare_Streams;
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------------------
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-- Copy_Streams --
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------------------
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procedure Copy_Streams
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(Source, Target : in out Ada.Streams.Root_Stream_Type'Class;
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Buffer_Size : in Stream_Element_Offset := 1024)
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is
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Buffer : Stream_Element_Array (1 .. Buffer_Size);
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Last : Stream_Element_Offset;
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begin
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loop
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Read (Source, Buffer, Last);
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Write (Target, Buffer (1 .. Last));
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exit when Last < Buffer'Last;
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end loop;
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end Copy_Streams;
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-------------
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-- Data_In --
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-------------
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procedure Data_In
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(Item : out Stream_Element_Array;
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Last : out Stream_Element_Offset) is
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begin
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Read (File_In, Item, Last);
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end Data_In;
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--------------
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-- Data_Out --
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--------------
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procedure Data_Out (Item : in Stream_Element_Array) is
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begin
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Write (File_Out, Item);
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end Data_Out;
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-------------------
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-- Generate_File --
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-------------------
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procedure Generate_File is
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subtype Visible_Symbols is Stream_Element range 16#20# .. 16#7E#;
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+
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package Random_Elements is
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new Ada.Numerics.Discrete_Random (Visible_Symbols);
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Gen : Random_Elements.Generator;
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Buffer : Stream_Element_Array := (1 .. 77 => 16#20#) & 10;
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Buffer_Count : constant Count := File_Size / Buffer'Length;
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-- Number of same buffers in the packet.
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Density : constant Count := 30; -- from 0 to Buffer'Length - 2;
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procedure Fill_Buffer (J, D : in Count);
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-- Change the part of the buffer.
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+
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-----------------
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-- Fill_Buffer --
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-----------------
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221
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222
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procedure Fill_Buffer (J, D : in Count) is
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begin
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for K in 0 .. D loop
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Buffer
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(Stream_Element_Offset ((J + K) mod (Buffer'Length - 1) + 1))
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:= Random_Elements.Random (Gen);
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end loop;
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end Fill_Buffer;
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231
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|
232
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begin
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233
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Random_Elements.Reset (Gen, Init_Random);
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+
|
235
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Create (File_In, Out_File, In_File_Name);
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236
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+
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237
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Fill_Buffer (1, Buffer'Length - 2);
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238
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+
|
239
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for J in 1 .. Buffer_Count loop
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240
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Write (File_In, Buffer);
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241
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+
|
242
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Fill_Buffer (J, Density);
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243
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+
end loop;
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244
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+
|
245
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+
-- fill remain size.
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246
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+
|
247
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Write
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(File_In,
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Buffer
|
250
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(1 .. Stream_Element_Offset
|
251
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+
(File_Size - Buffer'Length * Buffer_Count)));
|
252
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+
|
253
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Flush (File_In);
|
254
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Close (File_In);
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255
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+
end Generate_File;
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256
|
+
|
257
|
+
---------------------
|
258
|
+
-- Print_Statistic --
|
259
|
+
---------------------
|
260
|
+
|
261
|
+
procedure Print_Statistic (Msg : String; Data_Size : ZLib.Count) is
|
262
|
+
use Ada.Calendar;
|
263
|
+
use Ada.Text_IO;
|
264
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+
|
265
|
+
package Count_IO is new Integer_IO (ZLib.Count);
|
266
|
+
|
267
|
+
Curr_Dur : Duration := Clock - Time_Stamp;
|
268
|
+
begin
|
269
|
+
Put (Msg);
|
270
|
+
|
271
|
+
Set_Col (20);
|
272
|
+
Ada.Text_IO.Put ("size =");
|
273
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+
|
274
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+
Count_IO.Put
|
275
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+
(Data_Size,
|
276
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+
Width => Stream_IO.Count'Image (File_Size)'Length);
|
277
|
+
|
278
|
+
Put_Line (" duration =" & Duration'Image (Curr_Dur));
|
279
|
+
end Print_Statistic;
|
280
|
+
|
281
|
+
-----------
|
282
|
+
-- Stamp --
|
283
|
+
-----------
|
284
|
+
|
285
|
+
procedure Stamp is
|
286
|
+
begin
|
287
|
+
Time_Stamp := Ada.Calendar.Clock;
|
288
|
+
end Stamp;
|
289
|
+
|
290
|
+
begin
|
291
|
+
Ada.Text_IO.Put_Line ("ZLib " & ZLib.Version);
|
292
|
+
|
293
|
+
loop
|
294
|
+
Generate_File;
|
295
|
+
|
296
|
+
for Level in ZLib.Compression_Level'Range loop
|
297
|
+
|
298
|
+
Ada.Text_IO.Put_Line ("Level ="
|
299
|
+
& ZLib.Compression_Level'Image (Level));
|
300
|
+
|
301
|
+
-- Test generic interface.
|
302
|
+
Open (File_In, In_File, In_File_Name);
|
303
|
+
Create (File_Out, Out_File, Z_File_Name);
|
304
|
+
|
305
|
+
Stamp;
|
306
|
+
|
307
|
+
-- Deflate using generic instantiation.
|
308
|
+
|
309
|
+
ZLib.Deflate_Init
|
310
|
+
(Filter => Filter,
|
311
|
+
Level => Level,
|
312
|
+
Strategy => Strategy,
|
313
|
+
Header => Header);
|
314
|
+
|
315
|
+
Translate (Filter);
|
316
|
+
Print_Statistic ("Generic compress", ZLib.Total_Out (Filter));
|
317
|
+
ZLib.Close (Filter);
|
318
|
+
|
319
|
+
Close (File_In);
|
320
|
+
Close (File_Out);
|
321
|
+
|
322
|
+
Open (File_In, In_File, Z_File_Name);
|
323
|
+
Create (File_Out, Out_File, Out_File_Name);
|
324
|
+
|
325
|
+
Stamp;
|
326
|
+
|
327
|
+
-- Inflate using generic instantiation.
|
328
|
+
|
329
|
+
ZLib.Inflate_Init (Filter, Header => Header);
|
330
|
+
|
331
|
+
Translate (Filter);
|
332
|
+
Print_Statistic ("Generic decompress", ZLib.Total_Out (Filter));
|
333
|
+
|
334
|
+
ZLib.Close (Filter);
|
335
|
+
|
336
|
+
Close (File_In);
|
337
|
+
Close (File_Out);
|
338
|
+
|
339
|
+
Compare_Files (In_File_Name, Out_File_Name);
|
340
|
+
|
341
|
+
-- Test stream interface.
|
342
|
+
|
343
|
+
-- Compress to the back stream.
|
344
|
+
|
345
|
+
Open (File_In, In_File, In_File_Name);
|
346
|
+
Create (File_Back, Out_File, Z_File_Name);
|
347
|
+
|
348
|
+
Stamp;
|
349
|
+
|
350
|
+
ZLib.Streams.Create
|
351
|
+
(Stream => File_Z,
|
352
|
+
Mode => ZLib.Streams.Out_Stream,
|
353
|
+
Back => ZLib.Streams.Stream_Access
|
354
|
+
(Stream (File_Back)),
|
355
|
+
Back_Compressed => True,
|
356
|
+
Level => Level,
|
357
|
+
Strategy => Strategy,
|
358
|
+
Header => Header);
|
359
|
+
|
360
|
+
Copy_Streams
|
361
|
+
(Source => Stream (File_In).all,
|
362
|
+
Target => File_Z);
|
363
|
+
|
364
|
+
-- Flushing internal buffers to the back stream.
|
365
|
+
|
366
|
+
ZLib.Streams.Flush (File_Z, ZLib.Finish);
|
367
|
+
|
368
|
+
Print_Statistic ("Write compress",
|
369
|
+
ZLib.Streams.Write_Total_Out (File_Z));
|
370
|
+
|
371
|
+
ZLib.Streams.Close (File_Z);
|
372
|
+
|
373
|
+
Close (File_In);
|
374
|
+
Close (File_Back);
|
375
|
+
|
376
|
+
-- Compare reading from original file and from
|
377
|
+
-- decompression stream.
|
378
|
+
|
379
|
+
Open (File_In, In_File, In_File_Name);
|
380
|
+
Open (File_Back, In_File, Z_File_Name);
|
381
|
+
|
382
|
+
ZLib.Streams.Create
|
383
|
+
(Stream => File_Z,
|
384
|
+
Mode => ZLib.Streams.In_Stream,
|
385
|
+
Back => ZLib.Streams.Stream_Access
|
386
|
+
(Stream (File_Back)),
|
387
|
+
Back_Compressed => True,
|
388
|
+
Header => Header);
|
389
|
+
|
390
|
+
Stamp;
|
391
|
+
Compare_Streams (Stream (File_In).all, File_Z);
|
392
|
+
|
393
|
+
Print_Statistic ("Read decompress",
|
394
|
+
ZLib.Streams.Read_Total_Out (File_Z));
|
395
|
+
|
396
|
+
ZLib.Streams.Close (File_Z);
|
397
|
+
Close (File_In);
|
398
|
+
Close (File_Back);
|
399
|
+
|
400
|
+
-- Compress by reading from compression stream.
|
401
|
+
|
402
|
+
Open (File_Back, In_File, In_File_Name);
|
403
|
+
Create (File_Out, Out_File, Z_File_Name);
|
404
|
+
|
405
|
+
ZLib.Streams.Create
|
406
|
+
(Stream => File_Z,
|
407
|
+
Mode => ZLib.Streams.In_Stream,
|
408
|
+
Back => ZLib.Streams.Stream_Access
|
409
|
+
(Stream (File_Back)),
|
410
|
+
Back_Compressed => False,
|
411
|
+
Level => Level,
|
412
|
+
Strategy => Strategy,
|
413
|
+
Header => Header);
|
414
|
+
|
415
|
+
Stamp;
|
416
|
+
Copy_Streams
|
417
|
+
(Source => File_Z,
|
418
|
+
Target => Stream (File_Out).all);
|
419
|
+
|
420
|
+
Print_Statistic ("Read compress",
|
421
|
+
ZLib.Streams.Read_Total_Out (File_Z));
|
422
|
+
|
423
|
+
ZLib.Streams.Close (File_Z);
|
424
|
+
|
425
|
+
Close (File_Out);
|
426
|
+
Close (File_Back);
|
427
|
+
|
428
|
+
-- Decompress to decompression stream.
|
429
|
+
|
430
|
+
Open (File_In, In_File, Z_File_Name);
|
431
|
+
Create (File_Back, Out_File, Out_File_Name);
|
432
|
+
|
433
|
+
ZLib.Streams.Create
|
434
|
+
(Stream => File_Z,
|
435
|
+
Mode => ZLib.Streams.Out_Stream,
|
436
|
+
Back => ZLib.Streams.Stream_Access
|
437
|
+
(Stream (File_Back)),
|
438
|
+
Back_Compressed => False,
|
439
|
+
Header => Header);
|
440
|
+
|
441
|
+
Stamp;
|
442
|
+
|
443
|
+
Copy_Streams
|
444
|
+
(Source => Stream (File_In).all,
|
445
|
+
Target => File_Z);
|
446
|
+
|
447
|
+
Print_Statistic ("Write decompress",
|
448
|
+
ZLib.Streams.Write_Total_Out (File_Z));
|
449
|
+
|
450
|
+
ZLib.Streams.Close (File_Z);
|
451
|
+
Close (File_In);
|
452
|
+
Close (File_Back);
|
453
|
+
|
454
|
+
Compare_Files (In_File_Name, Out_File_Name);
|
455
|
+
end loop;
|
456
|
+
|
457
|
+
Ada.Text_IO.Put_Line (Count'Image (File_Size) & " Ok.");
|
458
|
+
|
459
|
+
exit when not Continuous;
|
460
|
+
|
461
|
+
File_Size := File_Size + 1;
|
462
|
+
end loop;
|
463
|
+
end Test;
|