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 +1,225 @@
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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: zlib-streams.adb,v 1.10 2004/05/31 10:53:40 vagul Exp $
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with Ada.Unchecked_Deallocation;
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package body ZLib.Streams is
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-----------
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-- Close --
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-----------
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procedure Close (Stream : in out Stream_Type) is
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procedure Free is new Ada.Unchecked_Deallocation
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(Stream_Element_Array, Buffer_Access);
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begin
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if Stream.Mode = Out_Stream or Stream.Mode = Duplex then
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-- We should flush the data written by the writer.
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Flush (Stream, Finish);
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Close (Stream.Writer);
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end if;
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if Stream.Mode = In_Stream or Stream.Mode = Duplex then
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Close (Stream.Reader);
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Free (Stream.Buffer);
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end if;
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end Close;
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------------
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-- Create --
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------------
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procedure Create
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(Stream : out Stream_Type;
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Mode : in Stream_Mode;
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Back : in Stream_Access;
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Back_Compressed : in Boolean;
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Level : in Compression_Level := Default_Compression;
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Strategy : in Strategy_Type := Default_Strategy;
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Header : in Header_Type := Default;
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Read_Buffer_Size : in Ada.Streams.Stream_Element_Offset
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:= Default_Buffer_Size;
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Write_Buffer_Size : in Ada.Streams.Stream_Element_Offset
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:= Default_Buffer_Size)
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is
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subtype Buffer_Subtype is Stream_Element_Array (1 .. Read_Buffer_Size);
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procedure Init_Filter
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(Filter : in out Filter_Type;
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Compress : in Boolean);
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-----------------
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-- Init_Filter --
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-----------------
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procedure Init_Filter
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(Filter : in out Filter_Type;
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Compress : in Boolean) is
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begin
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if Compress then
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Deflate_Init
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(Filter, Level, Strategy, Header => Header);
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else
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Inflate_Init (Filter, Header => Header);
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end if;
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end Init_Filter;
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begin
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Stream.Back := Back;
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Stream.Mode := Mode;
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if Mode = Out_Stream or Mode = Duplex then
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Init_Filter (Stream.Writer, Back_Compressed);
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Stream.Buffer_Size := Write_Buffer_Size;
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else
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Stream.Buffer_Size := 0;
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end if;
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if Mode = In_Stream or Mode = Duplex then
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Init_Filter (Stream.Reader, not Back_Compressed);
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Stream.Buffer := new Buffer_Subtype;
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Stream.Rest_First := Stream.Buffer'Last + 1;
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Stream.Rest_Last := Stream.Buffer'Last;
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end if;
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end Create;
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-----------
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-- Flush --
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-----------
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procedure Flush
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(Stream : in out Stream_Type;
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Mode : in Flush_Mode := Sync_Flush)
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is
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Buffer : Stream_Element_Array (1 .. Stream.Buffer_Size);
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Last : Stream_Element_Offset;
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begin
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loop
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Flush (Stream.Writer, Buffer, Last, Mode);
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Ada.Streams.Write (Stream.Back.all, Buffer (1 .. Last));
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exit when Last < Buffer'Last;
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end loop;
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end Flush;
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-------------
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-- Is_Open --
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-------------
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function Is_Open (Stream : Stream_Type) return Boolean is
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begin
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return Is_Open (Stream.Reader) or else Is_Open (Stream.Writer);
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end Is_Open;
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----------
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-- Read --
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----------
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procedure Read
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(Stream : in out Stream_Type;
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Item : out Stream_Element_Array;
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Last : out Stream_Element_Offset)
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is
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procedure Read
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(Item : out Stream_Element_Array;
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Last : out Stream_Element_Offset);
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----------
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-- Read --
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----------
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procedure Read
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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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Ada.Streams.Read (Stream.Back.all, Item, Last);
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end Read;
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procedure Read is new ZLib.Read
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(Read => Read,
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Buffer => Stream.Buffer.all,
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Rest_First => Stream.Rest_First,
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Rest_Last => Stream.Rest_Last);
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begin
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Read (Stream.Reader, Item, Last);
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end Read;
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-------------------
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-- Read_Total_In --
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-------------------
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function Read_Total_In (Stream : in Stream_Type) return Count is
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begin
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return Total_In (Stream.Reader);
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end Read_Total_In;
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--------------------
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-- Read_Total_Out --
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--------------------
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function Read_Total_Out (Stream : in Stream_Type) return Count is
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begin
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return Total_Out (Stream.Reader);
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end Read_Total_Out;
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-----------
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-- Write --
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-----------
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procedure Write
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(Stream : in out Stream_Type;
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Item : in Stream_Element_Array)
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is
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procedure Write (Item : in Stream_Element_Array);
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-----------
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-- Write --
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-----------
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procedure Write (Item : in Stream_Element_Array) is
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begin
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Ada.Streams.Write (Stream.Back.all, Item);
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end Write;
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procedure Write is new ZLib.Write
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(Write => Write,
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Buffer_Size => Stream.Buffer_Size);
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begin
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Write (Stream.Writer, Item, No_Flush);
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end Write;
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--------------------
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-- Write_Total_In --
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--------------------
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function Write_Total_In (Stream : in Stream_Type) return Count is
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begin
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return Total_In (Stream.Writer);
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end Write_Total_In;
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---------------------
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-- Write_Total_Out --
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---------------------
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function Write_Total_Out (Stream : in Stream_Type) return Count is
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begin
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return Total_Out (Stream.Writer);
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end Write_Total_Out;
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end ZLib.Streams;
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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: zlib-streams.ads,v 1.12 2004/05/31 10:53:40 vagul Exp $
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package ZLib.Streams is
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type Stream_Mode is (In_Stream, Out_Stream, Duplex);
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type Stream_Access is access all Ada.Streams.Root_Stream_Type'Class;
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type Stream_Type is
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new Ada.Streams.Root_Stream_Type with private;
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procedure Read
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(Stream : in out Stream_Type;
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Item : out Ada.Streams.Stream_Element_Array;
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Last : out Ada.Streams.Stream_Element_Offset);
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procedure Write
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(Stream : in out Stream_Type;
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Item : in Ada.Streams.Stream_Element_Array);
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procedure Flush
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(Stream : in out Stream_Type;
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Mode : in Flush_Mode := Sync_Flush);
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-- Flush the written data to the back stream,
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-- all data placed to the compressor is flushing to the Back stream.
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-- Should not be used untill necessary, becouse it is decreasing
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-- compression.
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function Read_Total_In (Stream : in Stream_Type) return Count;
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pragma Inline (Read_Total_In);
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-- Return total number of bytes read from back stream so far.
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function Read_Total_Out (Stream : in Stream_Type) return Count;
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pragma Inline (Read_Total_Out);
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-- Return total number of bytes read so far.
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function Write_Total_In (Stream : in Stream_Type) return Count;
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pragma Inline (Write_Total_In);
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-- Return total number of bytes written so far.
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|
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function Write_Total_Out (Stream : in Stream_Type) return Count;
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pragma Inline (Write_Total_Out);
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-- Return total number of bytes written to the back stream.
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|
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procedure Create
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(Stream : out Stream_Type;
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Mode : in Stream_Mode;
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Back : in Stream_Access;
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Back_Compressed : in Boolean;
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Level : in Compression_Level := Default_Compression;
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Strategy : in Strategy_Type := Default_Strategy;
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Header : in Header_Type := Default;
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Read_Buffer_Size : in Ada.Streams.Stream_Element_Offset
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:= Default_Buffer_Size;
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Write_Buffer_Size : in Ada.Streams.Stream_Element_Offset
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:= Default_Buffer_Size);
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-- Create the Comression/Decompression stream.
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-- If mode is In_Stream then Write operation is disabled.
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-- If mode is Out_Stream then Read operation is disabled.
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-- If Back_Compressed is true then
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-- Data written to the Stream is compressing to the Back stream
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-- and data read from the Stream is decompressed data from the Back stream.
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72
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-- If Back_Compressed is false then
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-- Data written to the Stream is decompressing to the Back stream
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75
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-- and data read from the Stream is compressed data from the Back stream.
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76
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|
77
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-- !!! When the Need_Header is False ZLib-Ada is using undocumented
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-- ZLib 1.1.4 functionality to do not create/wait for ZLib headers.
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79
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|
80
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function Is_Open (Stream : Stream_Type) return Boolean;
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81
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|
82
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procedure Close (Stream : in out Stream_Type);
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83
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|
84
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private
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85
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|
86
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use Ada.Streams;
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87
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|
88
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type Buffer_Access is access all Stream_Element_Array;
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89
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|
90
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type Stream_Type
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91
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is new Root_Stream_Type with
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92
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record
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93
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Mode : Stream_Mode;
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94
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|
95
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Buffer : Buffer_Access;
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96
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Rest_First : Stream_Element_Offset;
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97
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Rest_Last : Stream_Element_Offset;
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98
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-- Buffer for Read operation.
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99
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-- We need to have this buffer in the record
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100
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-- becouse not all read data from back stream
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101
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-- could be processed during the read operation.
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102
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+
|
103
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Buffer_Size : Stream_Element_Offset;
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104
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-- Buffer size for write operation.
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105
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-- We do not need to have this buffer
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106
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-- in the record becouse all data could be
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-- processed in the write operation.
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108
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+
|
109
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Back : Stream_Access;
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110
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Reader : Filter_Type;
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111
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Writer : Filter_Type;
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112
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end record;
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113
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114
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end ZLib.Streams;
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@@ -0,0 +1,141 @@
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1
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----------------------------------------------------------------
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2
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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. --
|
7
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----------------------------------------------------------------
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8
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|
9
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-- $Id: zlib-thin.adb,v 1.8 2003/12/14 18:27:31 vagul Exp $
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10
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+
|
11
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package body ZLib.Thin is
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12
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+
|
13
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ZLIB_VERSION : constant Chars_Ptr := zlibVersion;
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14
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+
|
15
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Z_Stream_Size : constant Int := Z_Stream'Size / System.Storage_Unit;
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16
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+
|
17
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--------------
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18
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-- Avail_In --
|
19
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--------------
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20
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+
|
21
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function Avail_In (Strm : in Z_Stream) return UInt is
|
22
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begin
|
23
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return Strm.Avail_In;
|
24
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+
end Avail_In;
|
25
|
+
|
26
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---------------
|
27
|
+
-- Avail_Out --
|
28
|
+
---------------
|
29
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+
|
30
|
+
function Avail_Out (Strm : in Z_Stream) return UInt is
|
31
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+
begin
|
32
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+
return Strm.Avail_Out;
|
33
|
+
end Avail_Out;
|
34
|
+
|
35
|
+
------------------
|
36
|
+
-- Deflate_Init --
|
37
|
+
------------------
|
38
|
+
|
39
|
+
function Deflate_Init
|
40
|
+
(strm : Z_Streamp;
|
41
|
+
level : Int;
|
42
|
+
method : Int;
|
43
|
+
windowBits : Int;
|
44
|
+
memLevel : Int;
|
45
|
+
strategy : Int)
|
46
|
+
return Int is
|
47
|
+
begin
|
48
|
+
return deflateInit2
|
49
|
+
(strm,
|
50
|
+
level,
|
51
|
+
method,
|
52
|
+
windowBits,
|
53
|
+
memLevel,
|
54
|
+
strategy,
|
55
|
+
ZLIB_VERSION,
|
56
|
+
Z_Stream_Size);
|
57
|
+
end Deflate_Init;
|
58
|
+
|
59
|
+
------------------
|
60
|
+
-- Inflate_Init --
|
61
|
+
------------------
|
62
|
+
|
63
|
+
function Inflate_Init (strm : Z_Streamp; windowBits : Int) return Int is
|
64
|
+
begin
|
65
|
+
return inflateInit2 (strm, windowBits, ZLIB_VERSION, Z_Stream_Size);
|
66
|
+
end Inflate_Init;
|
67
|
+
|
68
|
+
------------------------
|
69
|
+
-- Last_Error_Message --
|
70
|
+
------------------------
|
71
|
+
|
72
|
+
function Last_Error_Message (Strm : in Z_Stream) return String is
|
73
|
+
use Interfaces.C.Strings;
|
74
|
+
begin
|
75
|
+
if Strm.msg = Null_Ptr then
|
76
|
+
return "";
|
77
|
+
else
|
78
|
+
return Value (Strm.msg);
|
79
|
+
end if;
|
80
|
+
end Last_Error_Message;
|
81
|
+
|
82
|
+
------------
|
83
|
+
-- Set_In --
|
84
|
+
------------
|
85
|
+
|
86
|
+
procedure Set_In
|
87
|
+
(Strm : in out Z_Stream;
|
88
|
+
Buffer : in Voidp;
|
89
|
+
Size : in UInt) is
|
90
|
+
begin
|
91
|
+
Strm.Next_In := Buffer;
|
92
|
+
Strm.Avail_In := Size;
|
93
|
+
end Set_In;
|
94
|
+
|
95
|
+
------------------
|
96
|
+
-- Set_Mem_Func --
|
97
|
+
------------------
|
98
|
+
|
99
|
+
procedure Set_Mem_Func
|
100
|
+
(Strm : in out Z_Stream;
|
101
|
+
Opaque : in Voidp;
|
102
|
+
Alloc : in alloc_func;
|
103
|
+
Free : in free_func) is
|
104
|
+
begin
|
105
|
+
Strm.opaque := Opaque;
|
106
|
+
Strm.zalloc := Alloc;
|
107
|
+
Strm.zfree := Free;
|
108
|
+
end Set_Mem_Func;
|
109
|
+
|
110
|
+
-------------
|
111
|
+
-- Set_Out --
|
112
|
+
-------------
|
113
|
+
|
114
|
+
procedure Set_Out
|
115
|
+
(Strm : in out Z_Stream;
|
116
|
+
Buffer : in Voidp;
|
117
|
+
Size : in UInt) is
|
118
|
+
begin
|
119
|
+
Strm.Next_Out := Buffer;
|
120
|
+
Strm.Avail_Out := Size;
|
121
|
+
end Set_Out;
|
122
|
+
|
123
|
+
--------------
|
124
|
+
-- Total_In --
|
125
|
+
--------------
|
126
|
+
|
127
|
+
function Total_In (Strm : in Z_Stream) return ULong is
|
128
|
+
begin
|
129
|
+
return Strm.Total_In;
|
130
|
+
end Total_In;
|
131
|
+
|
132
|
+
---------------
|
133
|
+
-- Total_Out --
|
134
|
+
---------------
|
135
|
+
|
136
|
+
function Total_Out (Strm : in Z_Stream) return ULong is
|
137
|
+
begin
|
138
|
+
return Strm.Total_Out;
|
139
|
+
end Total_Out;
|
140
|
+
|
141
|
+
end ZLib.Thin;
|