bio-velvet_underground 0.0.1

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Files changed (286) hide show
  1. checksums.yaml +7 -0
  2. data/.document +5 -0
  3. data/.gitmodules +3 -0
  4. data/.travis.yml +13 -0
  5. data/Gemfile +19 -0
  6. data/LICENSE.txt +20 -0
  7. data/README.md +53 -0
  8. data/Rakefile +51 -0
  9. data/VERSION +1 -0
  10. data/ext/bioruby.patch +60 -0
  11. data/ext/mkrf_conf.rb +50 -0
  12. data/ext/src/Makefile +125 -0
  13. data/ext/src/src/allocArray.c +305 -0
  14. data/ext/src/src/allocArray.h +86 -0
  15. data/ext/src/src/autoOpen.c +107 -0
  16. data/ext/src/src/autoOpen.h +18 -0
  17. data/ext/src/src/binarySequences.c +813 -0
  18. data/ext/src/src/binarySequences.h +125 -0
  19. data/ext/src/src/concatenatedGraph.c +233 -0
  20. data/ext/src/src/concatenatedGraph.h +30 -0
  21. data/ext/src/src/concatenatedPreGraph.c +262 -0
  22. data/ext/src/src/concatenatedPreGraph.h +29 -0
  23. data/ext/src/src/correctedGraph.c +2642 -0
  24. data/ext/src/src/correctedGraph.h +32 -0
  25. data/ext/src/src/dfib.c +509 -0
  26. data/ext/src/src/dfib.h +69 -0
  27. data/ext/src/src/dfibHeap.c +89 -0
  28. data/ext/src/src/dfibHeap.h +39 -0
  29. data/ext/src/src/dfibpriv.h +105 -0
  30. data/ext/src/src/fib.c +628 -0
  31. data/ext/src/src/fib.h +78 -0
  32. data/ext/src/src/fibHeap.c +79 -0
  33. data/ext/src/src/fibHeap.h +41 -0
  34. data/ext/src/src/fibpriv.h +110 -0
  35. data/ext/src/src/globals.h +153 -0
  36. data/ext/src/src/graph.c +3983 -0
  37. data/ext/src/src/graph.h +233 -0
  38. data/ext/src/src/graphReConstruction.c +1472 -0
  39. data/ext/src/src/graphReConstruction.h +30 -0
  40. data/ext/src/src/graphStats.c +2167 -0
  41. data/ext/src/src/graphStats.h +72 -0
  42. data/ext/src/src/kmer.c +652 -0
  43. data/ext/src/src/kmer.h +73 -0
  44. data/ext/src/src/kmerOccurenceTable.c +236 -0
  45. data/ext/src/src/kmerOccurenceTable.h +44 -0
  46. data/ext/src/src/kseq.h +223 -0
  47. data/ext/src/src/locallyCorrectedGraph.c +557 -0
  48. data/ext/src/src/locallyCorrectedGraph.h +40 -0
  49. data/ext/src/src/passageMarker.c +677 -0
  50. data/ext/src/src/passageMarker.h +137 -0
  51. data/ext/src/src/preGraph.c +1717 -0
  52. data/ext/src/src/preGraph.h +106 -0
  53. data/ext/src/src/preGraphConstruction.c +990 -0
  54. data/ext/src/src/preGraphConstruction.h +26 -0
  55. data/ext/src/src/readCoherentGraph.c +557 -0
  56. data/ext/src/src/readCoherentGraph.h +30 -0
  57. data/ext/src/src/readSet.c +1734 -0
  58. data/ext/src/src/readSet.h +67 -0
  59. data/ext/src/src/recycleBin.c +199 -0
  60. data/ext/src/src/recycleBin.h +58 -0
  61. data/ext/src/src/roadMap.c +342 -0
  62. data/ext/src/src/roadMap.h +65 -0
  63. data/ext/src/src/run.c +318 -0
  64. data/ext/src/src/run.h +52 -0
  65. data/ext/src/src/run2.c +712 -0
  66. data/ext/src/src/scaffold.c +1876 -0
  67. data/ext/src/src/scaffold.h +64 -0
  68. data/ext/src/src/shortReadPairs.c +1243 -0
  69. data/ext/src/src/shortReadPairs.h +32 -0
  70. data/ext/src/src/splay.c +259 -0
  71. data/ext/src/src/splay.h +43 -0
  72. data/ext/src/src/splayTable.c +1315 -0
  73. data/ext/src/src/splayTable.h +31 -0
  74. data/ext/src/src/tightString.c +362 -0
  75. data/ext/src/src/tightString.h +82 -0
  76. data/ext/src/src/utility.c +199 -0
  77. data/ext/src/src/utility.h +98 -0
  78. data/ext/src/third-party/zlib-1.2.3/ChangeLog +855 -0
  79. data/ext/src/third-party/zlib-1.2.3/FAQ +339 -0
  80. data/ext/src/third-party/zlib-1.2.3/INDEX +51 -0
  81. data/ext/src/third-party/zlib-1.2.3/Makefile +154 -0
  82. data/ext/src/third-party/zlib-1.2.3/Makefile.in +154 -0
  83. data/ext/src/third-party/zlib-1.2.3/README +125 -0
  84. data/ext/src/third-party/zlib-1.2.3/adler32.c +149 -0
  85. data/ext/src/third-party/zlib-1.2.3/algorithm.txt +209 -0
  86. data/ext/src/third-party/zlib-1.2.3/amiga/Makefile.pup +66 -0
  87. data/ext/src/third-party/zlib-1.2.3/amiga/Makefile.sas +65 -0
  88. data/ext/src/third-party/zlib-1.2.3/as400/bndsrc +132 -0
  89. data/ext/src/third-party/zlib-1.2.3/as400/compile.clp +123 -0
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  92. data/ext/src/third-party/zlib-1.2.3/compress.c +79 -0
  93. data/ext/src/third-party/zlib-1.2.3/configure +459 -0
  94. data/ext/src/third-party/zlib-1.2.3/contrib/README.contrib +71 -0
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  107. data/ext/src/third-party/zlib-1.2.3/contrib/asm586/README.586 +43 -0
  108. data/ext/src/third-party/zlib-1.2.3/contrib/asm586/match.S +364 -0
  109. data/ext/src/third-party/zlib-1.2.3/contrib/asm686/README.686 +34 -0
  110. data/ext/src/third-party/zlib-1.2.3/contrib/asm686/match.S +329 -0
  111. data/ext/src/third-party/zlib-1.2.3/contrib/blast/Makefile +8 -0
  112. data/ext/src/third-party/zlib-1.2.3/contrib/blast/README +4 -0
  113. data/ext/src/third-party/zlib-1.2.3/contrib/blast/blast.c +444 -0
  114. data/ext/src/third-party/zlib-1.2.3/contrib/blast/blast.h +71 -0
  115. data/ext/src/third-party/zlib-1.2.3/contrib/blast/test.pk +0 -0
  116. data/ext/src/third-party/zlib-1.2.3/contrib/blast/test.txt +1 -0
  117. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/ZLib.pas +557 -0
  118. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/ZLibConst.pas +11 -0
  119. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/readme.txt +76 -0
  120. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/zlibd32.mak +93 -0
  121. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.build +33 -0
  122. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.chm +0 -0
  123. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.sln +21 -0
  124. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/AssemblyInfo.cs +58 -0
  125. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/ChecksumImpl.cs +202 -0
  126. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/CircularBuffer.cs +83 -0
  127. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/CodecBase.cs +198 -0
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  129. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/DotZLib.cs +288 -0
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  131. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/GZipStream.cs +301 -0
  132. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/Inflater.cs +105 -0
  133. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/UnitTests.cs +274 -0
  134. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/LICENSE_1_0.txt +23 -0
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  136. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/README +1 -0
  137. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/infback9.c +608 -0
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  141. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inftree9.c +323 -0
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  145. data/ext/src/third-party/zlib-1.2.3/contrib/iostream/test.cpp +24 -0
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  250. data/ext/src/third-party/zlib-1.2.3/old/README +3 -0
  251. data/ext/src/third-party/zlib-1.2.3/old/descrip.mms +48 -0
  252. data/ext/src/third-party/zlib-1.2.3/old/os2/Makefile.os2 +136 -0
  253. data/ext/src/third-party/zlib-1.2.3/old/os2/zlib.def +51 -0
  254. data/ext/src/third-party/zlib-1.2.3/old/visual-basic.txt +160 -0
  255. data/ext/src/third-party/zlib-1.2.3/old/zlib.html +971 -0
  256. data/ext/src/third-party/zlib-1.2.3/projects/README.projects +41 -0
  257. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/README.txt +73 -0
  258. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/example.dsp +278 -0
  259. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/minigzip.dsp +278 -0
  260. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/zlib.dsp +609 -0
  261. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/zlib.dsw +59 -0
  262. data/ext/src/third-party/zlib-1.2.3/qnx/package.qpg +141 -0
  263. data/ext/src/third-party/zlib-1.2.3/trees.c +1219 -0
  264. data/ext/src/third-party/zlib-1.2.3/trees.h +128 -0
  265. data/ext/src/third-party/zlib-1.2.3/uncompr.c +61 -0
  266. data/ext/src/third-party/zlib-1.2.3/win32/DLL_FAQ.txt +397 -0
  267. data/ext/src/third-party/zlib-1.2.3/win32/Makefile.bor +107 -0
  268. data/ext/src/third-party/zlib-1.2.3/win32/Makefile.emx +69 -0
  269. data/ext/src/third-party/zlib-1.2.3/win32/Makefile.gcc +141 -0
  270. data/ext/src/third-party/zlib-1.2.3/win32/Makefile.msc +126 -0
  271. data/ext/src/third-party/zlib-1.2.3/win32/VisualC.txt +3 -0
  272. data/ext/src/third-party/zlib-1.2.3/win32/zlib.def +60 -0
  273. data/ext/src/third-party/zlib-1.2.3/win32/zlib1.rc +39 -0
  274. data/ext/src/third-party/zlib-1.2.3/zconf.h +332 -0
  275. data/ext/src/third-party/zlib-1.2.3/zconf.in.h +332 -0
  276. data/ext/src/third-party/zlib-1.2.3/zlib.3 +159 -0
  277. data/ext/src/third-party/zlib-1.2.3/zlib.h +1357 -0
  278. data/ext/src/third-party/zlib-1.2.3/zutil.c +318 -0
  279. data/ext/src/third-party/zlib-1.2.3/zutil.h +269 -0
  280. data/lib/bio-velvet_underground.rb +12 -0
  281. data/lib/bio-velvet_underground/external/VERSION +1 -0
  282. data/lib/bio-velvet_underground/velvet_underground.rb +72 -0
  283. data/spec/binary_sequence_store_spec.rb +27 -0
  284. data/spec/data/1/CnyUnifiedSeq +0 -0
  285. data/spec/spec_helper.rb +31 -0
  286. metadata +456 -0
@@ -0,0 +1,65 @@
1
+ ZLib for Ada thick binding (ZLib.Ada)
2
+ Release 1.3
3
+
4
+ ZLib.Ada is a thick binding interface to the popular ZLib data
5
+ compression library, available at http://www.gzip.org/zlib/.
6
+ It provides Ada-style access to the ZLib C library.
7
+
8
+
9
+ Here are the main changes since ZLib.Ada 1.2:
10
+
11
+ - Attension: ZLib.Read generic routine have a initialization requirement
12
+ for Read_Last parameter now. It is a bit incompartible with previous version,
13
+ but extends functionality, we could use new parameters Allow_Read_Some and
14
+ Flush now.
15
+
16
+ - Added Is_Open routines to ZLib and ZLib.Streams packages.
17
+
18
+ - Add pragma Assert to check Stream_Element is 8 bit.
19
+
20
+ - Fix extraction to buffer with exact known decompressed size. Error reported by
21
+ Steve Sangwine.
22
+
23
+ - Fix definition of ULong (changed to unsigned_long), fix regression on 64 bits
24
+ computers. Patch provided by Pascal Obry.
25
+
26
+ - Add Status_Error exception definition.
27
+
28
+ - Add pragma Assertion that Ada.Streams.Stream_Element size is 8 bit.
29
+
30
+
31
+ How to build ZLib.Ada under GNAT
32
+
33
+ You should have the ZLib library already build on your computer, before
34
+ building ZLib.Ada. Make the directory of ZLib.Ada sources current and
35
+ issue the command:
36
+
37
+ gnatmake test -largs -L<directory where libz.a is> -lz
38
+
39
+ Or use the GNAT project file build for GNAT 3.15 or later:
40
+
41
+ gnatmake -Pzlib.gpr -L<directory where libz.a is>
42
+
43
+
44
+ How to build ZLib.Ada under Aonix ObjectAda for Win32 7.2.2
45
+
46
+ 1. Make a project with all *.ads and *.adb files from the distribution.
47
+ 2. Build the libz.a library from the ZLib C sources.
48
+ 3. Rename libz.a to z.lib.
49
+ 4. Add the library z.lib to the project.
50
+ 5. Add the libc.lib library from the ObjectAda distribution to the project.
51
+ 6. Build the executable using test.adb as a main procedure.
52
+
53
+
54
+ How to use ZLib.Ada
55
+
56
+ The source files test.adb and read.adb are small demo programs that show
57
+ the main functionality of ZLib.Ada.
58
+
59
+ The routines from the package specifications are commented.
60
+
61
+
62
+ Homepage: http://zlib-ada.sourceforge.net/
63
+ Author: Dmitriy Anisimkov <anisimkov@yahoo.com>
64
+
65
+ Contributors: Pascal Obry <pascal@obry.org>, Steve Sangwine <sjs@essex.ac.uk>
@@ -0,0 +1,463 @@
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: test.adb,v 1.17 2003/08/12 12:13:30 vagul Exp $
10
+
11
+ -- The program has a few aims.
12
+ -- 1. Test ZLib.Ada95 thick binding functionality.
13
+ -- 2. Show the example of use main functionality of the ZLib.Ada95 binding.
14
+ -- 3. Build this program automatically compile all ZLib.Ada95 packages under
15
+ -- GNAT Ada95 compiler.
16
+
17
+ with ZLib.Streams;
18
+ with Ada.Streams.Stream_IO;
19
+ with Ada.Numerics.Discrete_Random;
20
+
21
+ with Ada.Text_IO;
22
+
23
+ with Ada.Calendar;
24
+
25
+ procedure Test is
26
+
27
+ use Ada.Streams;
28
+ use Stream_IO;
29
+
30
+ ------------------------------------
31
+ -- Test configuration parameters --
32
+ ------------------------------------
33
+
34
+ File_Size : Count := 100_000;
35
+ Continuous : constant Boolean := False;
36
+
37
+ Header : constant ZLib.Header_Type := ZLib.Default;
38
+ -- ZLib.None;
39
+ -- ZLib.Auto;
40
+ -- ZLib.GZip;
41
+ -- Do not use Header other then Default in ZLib versions 1.1.4
42
+ -- and older.
43
+
44
+ Strategy : constant ZLib.Strategy_Type := ZLib.Default_Strategy;
45
+ Init_Random : constant := 10;
46
+
47
+ -- End --
48
+
49
+ In_File_Name : constant String := "testzlib.in";
50
+ -- Name of the input file
51
+
52
+ Z_File_Name : constant String := "testzlib.zlb";
53
+ -- Name of the compressed file.
54
+
55
+ Out_File_Name : constant String := "testzlib.out";
56
+ -- Name of the decompressed file.
57
+
58
+ File_In : File_Type;
59
+ File_Out : File_Type;
60
+ File_Back : File_Type;
61
+ File_Z : ZLib.Streams.Stream_Type;
62
+
63
+ Filter : ZLib.Filter_Type;
64
+
65
+ Time_Stamp : Ada.Calendar.Time;
66
+
67
+ procedure Generate_File;
68
+ -- Generate file of spetsified size with some random data.
69
+ -- The random data is repeatable, for the good compression.
70
+
71
+ procedure Compare_Streams
72
+ (Left, Right : in out Root_Stream_Type'Class);
73
+ -- The procedure compearing data in 2 streams.
74
+ -- It is for compare data before and after compression/decompression.
75
+
76
+ procedure Compare_Files (Left, Right : String);
77
+ -- Compare files. Based on the Compare_Streams.
78
+
79
+ procedure Copy_Streams
80
+ (Source, Target : in out Root_Stream_Type'Class;
81
+ Buffer_Size : in Stream_Element_Offset := 1024);
82
+ -- Copying data from one stream to another. It is for test stream
83
+ -- interface of the library.
84
+
85
+ procedure Data_In
86
+ (Item : out Stream_Element_Array;
87
+ Last : out Stream_Element_Offset);
88
+ -- this procedure is for generic instantiation of
89
+ -- ZLib.Generic_Translate.
90
+ -- reading data from the File_In.
91
+
92
+ procedure Data_Out (Item : in Stream_Element_Array);
93
+ -- this procedure is for generic instantiation of
94
+ -- ZLib.Generic_Translate.
95
+ -- writing data to the File_Out.
96
+
97
+ procedure Stamp;
98
+ -- Store the timestamp to the local variable.
99
+
100
+ procedure Print_Statistic (Msg : String; Data_Size : ZLib.Count);
101
+ -- Print the time statistic with the message.
102
+
103
+ procedure Translate is new ZLib.Generic_Translate
104
+ (Data_In => Data_In,
105
+ Data_Out => Data_Out);
106
+ -- This procedure is moving data from File_In to File_Out
107
+ -- with compression or decompression, depend on initialization of
108
+ -- Filter parameter.
109
+
110
+ -------------------
111
+ -- Compare_Files --
112
+ -------------------
113
+
114
+ procedure Compare_Files (Left, Right : String) is
115
+ Left_File, Right_File : File_Type;
116
+ begin
117
+ Open (Left_File, In_File, Left);
118
+ Open (Right_File, In_File, Right);
119
+ Compare_Streams (Stream (Left_File).all, Stream (Right_File).all);
120
+ Close (Left_File);
121
+ Close (Right_File);
122
+ end Compare_Files;
123
+
124
+ ---------------------
125
+ -- Compare_Streams --
126
+ ---------------------
127
+
128
+ procedure Compare_Streams
129
+ (Left, Right : in out Ada.Streams.Root_Stream_Type'Class)
130
+ is
131
+ Left_Buffer, Right_Buffer : Stream_Element_Array (0 .. 16#FFF#);
132
+ Left_Last, Right_Last : Stream_Element_Offset;
133
+ begin
134
+ loop
135
+ Read (Left, Left_Buffer, Left_Last);
136
+ Read (Right, Right_Buffer, Right_Last);
137
+
138
+ if Left_Last /= Right_Last then
139
+ Ada.Text_IO.Put_Line ("Compare error :"
140
+ & Stream_Element_Offset'Image (Left_Last)
141
+ & " /= "
142
+ & Stream_Element_Offset'Image (Right_Last));
143
+
144
+ raise Constraint_Error;
145
+
146
+ elsif Left_Buffer (0 .. Left_Last)
147
+ /= Right_Buffer (0 .. Right_Last)
148
+ then
149
+ Ada.Text_IO.Put_Line ("ERROR: IN and OUT files is not equal.");
150
+ raise Constraint_Error;
151
+
152
+ end if;
153
+
154
+ exit when Left_Last < Left_Buffer'Last;
155
+ end loop;
156
+ end Compare_Streams;
157
+
158
+ ------------------
159
+ -- Copy_Streams --
160
+ ------------------
161
+
162
+ procedure Copy_Streams
163
+ (Source, Target : in out Ada.Streams.Root_Stream_Type'Class;
164
+ Buffer_Size : in Stream_Element_Offset := 1024)
165
+ is
166
+ Buffer : Stream_Element_Array (1 .. Buffer_Size);
167
+ Last : Stream_Element_Offset;
168
+ begin
169
+ loop
170
+ Read (Source, Buffer, Last);
171
+ Write (Target, Buffer (1 .. Last));
172
+
173
+ exit when Last < Buffer'Last;
174
+ end loop;
175
+ end Copy_Streams;
176
+
177
+ -------------
178
+ -- Data_In --
179
+ -------------
180
+
181
+ procedure Data_In
182
+ (Item : out Stream_Element_Array;
183
+ Last : out Stream_Element_Offset) is
184
+ begin
185
+ Read (File_In, Item, Last);
186
+ end Data_In;
187
+
188
+ --------------
189
+ -- Data_Out --
190
+ --------------
191
+
192
+ procedure Data_Out (Item : in Stream_Element_Array) is
193
+ begin
194
+ Write (File_Out, Item);
195
+ end Data_Out;
196
+
197
+ -------------------
198
+ -- Generate_File --
199
+ -------------------
200
+
201
+ procedure Generate_File is
202
+ subtype Visible_Symbols is Stream_Element range 16#20# .. 16#7E#;
203
+
204
+ package Random_Elements is
205
+ new Ada.Numerics.Discrete_Random (Visible_Symbols);
206
+
207
+ Gen : Random_Elements.Generator;
208
+ Buffer : Stream_Element_Array := (1 .. 77 => 16#20#) & 10;
209
+
210
+ Buffer_Count : constant Count := File_Size / Buffer'Length;
211
+ -- Number of same buffers in the packet.
212
+
213
+ Density : constant Count := 30; -- from 0 to Buffer'Length - 2;
214
+
215
+ procedure Fill_Buffer (J, D : in Count);
216
+ -- Change the part of the buffer.
217
+
218
+ -----------------
219
+ -- Fill_Buffer --
220
+ -----------------
221
+
222
+ procedure Fill_Buffer (J, D : in Count) is
223
+ begin
224
+ for K in 0 .. D loop
225
+ Buffer
226
+ (Stream_Element_Offset ((J + K) mod (Buffer'Length - 1) + 1))
227
+ := Random_Elements.Random (Gen);
228
+
229
+ end loop;
230
+ end Fill_Buffer;
231
+
232
+ begin
233
+ Random_Elements.Reset (Gen, Init_Random);
234
+
235
+ Create (File_In, Out_File, In_File_Name);
236
+
237
+ Fill_Buffer (1, Buffer'Length - 2);
238
+
239
+ for J in 1 .. Buffer_Count loop
240
+ Write (File_In, Buffer);
241
+
242
+ Fill_Buffer (J, Density);
243
+ end loop;
244
+
245
+ -- fill remain size.
246
+
247
+ Write
248
+ (File_In,
249
+ Buffer
250
+ (1 .. Stream_Element_Offset
251
+ (File_Size - Buffer'Length * Buffer_Count)));
252
+
253
+ Flush (File_In);
254
+ Close (File_In);
255
+ end Generate_File;
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
+
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
+
274
+ Count_IO.Put
275
+ (Data_Size,
276
+ 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;