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 +1,328 @@
1
+ ------------------------------------------------------------------------------
2
+ -- ZLib for Ada thick binding. --
3
+ -- --
4
+ -- Copyright (C) 2002-2004 Dmitriy Anisimkov --
5
+ -- --
6
+ -- This library is free software; you can redistribute it and/or modify --
7
+ -- it under the terms of the GNU General Public License as published by --
8
+ -- the Free Software Foundation; either version 2 of the License, or (at --
9
+ -- your option) any later version. --
10
+ -- --
11
+ -- This library is distributed in the hope that it will be useful, but --
12
+ -- WITHOUT ANY WARRANTY; without even the implied warranty of --
13
+ -- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU --
14
+ -- General Public License for more details. --
15
+ -- --
16
+ -- You should have received a copy of the GNU General Public License --
17
+ -- along with this library; if not, write to the Free Software Foundation, --
18
+ -- Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. --
19
+ -- --
20
+ -- As a special exception, if other files instantiate generics from this --
21
+ -- unit, or you link this unit with other files to produce an executable, --
22
+ -- this unit does not by itself cause the resulting executable to be --
23
+ -- covered by the GNU General Public License. This exception does not --
24
+ -- however invalidate any other reasons why the executable file might be --
25
+ -- covered by the GNU Public License. --
26
+ ------------------------------------------------------------------------------
27
+
28
+ -- $Id: zlib.ads,v 1.26 2004/09/06 06:53:19 vagul Exp $
29
+
30
+ with Ada.Streams;
31
+
32
+ with Interfaces;
33
+
34
+ package ZLib is
35
+
36
+ ZLib_Error : exception;
37
+ Status_Error : exception;
38
+
39
+ type Compression_Level is new Integer range -1 .. 9;
40
+
41
+ type Flush_Mode is private;
42
+
43
+ type Compression_Method is private;
44
+
45
+ type Window_Bits_Type is new Integer range 8 .. 15;
46
+
47
+ type Memory_Level_Type is new Integer range 1 .. 9;
48
+
49
+ type Unsigned_32 is new Interfaces.Unsigned_32;
50
+
51
+ type Strategy_Type is private;
52
+
53
+ type Header_Type is (None, Auto, Default, GZip);
54
+ -- Header type usage have a some limitation for inflate.
55
+ -- See comment for Inflate_Init.
56
+
57
+ subtype Count is Ada.Streams.Stream_Element_Count;
58
+
59
+ Default_Memory_Level : constant Memory_Level_Type := 8;
60
+ Default_Window_Bits : constant Window_Bits_Type := 15;
61
+
62
+ ----------------------------------
63
+ -- Compression method constants --
64
+ ----------------------------------
65
+
66
+ Deflated : constant Compression_Method;
67
+ -- Only one method allowed in this ZLib version
68
+
69
+ ---------------------------------
70
+ -- Compression level constants --
71
+ ---------------------------------
72
+
73
+ No_Compression : constant Compression_Level := 0;
74
+ Best_Speed : constant Compression_Level := 1;
75
+ Best_Compression : constant Compression_Level := 9;
76
+ Default_Compression : constant Compression_Level := -1;
77
+
78
+ --------------------------
79
+ -- Flush mode constants --
80
+ --------------------------
81
+
82
+ No_Flush : constant Flush_Mode;
83
+ -- Regular way for compression, no flush
84
+
85
+ Partial_Flush : constant Flush_Mode;
86
+ -- Will be removed, use Z_SYNC_FLUSH instead
87
+
88
+ Sync_Flush : constant Flush_Mode;
89
+ -- All pending output is flushed to the output buffer and the output
90
+ -- is aligned on a byte boundary, so that the decompressor can get all
91
+ -- input data available so far. (In particular avail_in is zero after the
92
+ -- call if enough output space has been provided before the call.)
93
+ -- Flushing may degrade compression for some compression algorithms and so
94
+ -- it should be used only when necessary.
95
+
96
+ Block_Flush : constant Flush_Mode;
97
+ -- Z_BLOCK requests that inflate() stop
98
+ -- if and when it get to the next deflate block boundary. When decoding the
99
+ -- zlib or gzip format, this will cause inflate() to return immediately
100
+ -- after the header and before the first block. When doing a raw inflate,
101
+ -- inflate() will go ahead and process the first block, and will return
102
+ -- when it gets to the end of that block, or when it runs out of data.
103
+
104
+ Full_Flush : constant Flush_Mode;
105
+ -- All output is flushed as with SYNC_FLUSH, and the compression state
106
+ -- is reset so that decompression can restart from this point if previous
107
+ -- compressed data has been damaged or if random access is desired. Using
108
+ -- Full_Flush too often can seriously degrade the compression.
109
+
110
+ Finish : constant Flush_Mode;
111
+ -- Just for tell the compressor that input data is complete.
112
+
113
+ ------------------------------------
114
+ -- Compression strategy constants --
115
+ ------------------------------------
116
+
117
+ -- RLE stategy could be used only in version 1.2.0 and later.
118
+
119
+ Filtered : constant Strategy_Type;
120
+ Huffman_Only : constant Strategy_Type;
121
+ RLE : constant Strategy_Type;
122
+ Default_Strategy : constant Strategy_Type;
123
+
124
+ Default_Buffer_Size : constant := 4096;
125
+
126
+ type Filter_Type is tagged limited private;
127
+ -- The filter is for compression and for decompression.
128
+ -- The usage of the type is depend of its initialization.
129
+
130
+ function Version return String;
131
+ pragma Inline (Version);
132
+ -- Return string representation of the ZLib version.
133
+
134
+ procedure Deflate_Init
135
+ (Filter : in out Filter_Type;
136
+ Level : in Compression_Level := Default_Compression;
137
+ Strategy : in Strategy_Type := Default_Strategy;
138
+ Method : in Compression_Method := Deflated;
139
+ Window_Bits : in Window_Bits_Type := Default_Window_Bits;
140
+ Memory_Level : in Memory_Level_Type := Default_Memory_Level;
141
+ Header : in Header_Type := Default);
142
+ -- Compressor initialization.
143
+ -- When Header parameter is Auto or Default, then default zlib header
144
+ -- would be provided for compressed data.
145
+ -- When Header is GZip, then gzip header would be set instead of
146
+ -- default header.
147
+ -- When Header is None, no header would be set for compressed data.
148
+
149
+ procedure Inflate_Init
150
+ (Filter : in out Filter_Type;
151
+ Window_Bits : in Window_Bits_Type := Default_Window_Bits;
152
+ Header : in Header_Type := Default);
153
+ -- Decompressor initialization.
154
+ -- Default header type mean that ZLib default header is expecting in the
155
+ -- input compressed stream.
156
+ -- Header type None mean that no header is expecting in the input stream.
157
+ -- GZip header type mean that GZip header is expecting in the
158
+ -- input compressed stream.
159
+ -- Auto header type mean that header type (GZip or Native) would be
160
+ -- detected automatically in the input stream.
161
+ -- Note that header types parameter values None, GZip and Auto are
162
+ -- supported for inflate routine only in ZLib versions 1.2.0.2 and later.
163
+ -- Deflate_Init is supporting all header types.
164
+
165
+ function Is_Open (Filter : in Filter_Type) return Boolean;
166
+ pragma Inline (Is_Open);
167
+ -- Is the filter opened for compression or decompression.
168
+
169
+ procedure Close
170
+ (Filter : in out Filter_Type;
171
+ Ignore_Error : in Boolean := False);
172
+ -- Closing the compression or decompressor.
173
+ -- If stream is closing before the complete and Ignore_Error is False,
174
+ -- The exception would be raised.
175
+
176
+ generic
177
+ with procedure Data_In
178
+ (Item : out Ada.Streams.Stream_Element_Array;
179
+ Last : out Ada.Streams.Stream_Element_Offset);
180
+ with procedure Data_Out
181
+ (Item : in Ada.Streams.Stream_Element_Array);
182
+ procedure Generic_Translate
183
+ (Filter : in out Filter_Type;
184
+ In_Buffer_Size : in Integer := Default_Buffer_Size;
185
+ Out_Buffer_Size : in Integer := Default_Buffer_Size);
186
+ -- Compress/decompress data fetch from Data_In routine and pass the result
187
+ -- to the Data_Out routine. User should provide Data_In and Data_Out
188
+ -- for compression/decompression data flow.
189
+ -- Compression or decompression depend on Filter initialization.
190
+
191
+ function Total_In (Filter : in Filter_Type) return Count;
192
+ pragma Inline (Total_In);
193
+ -- Returns total number of input bytes read so far
194
+
195
+ function Total_Out (Filter : in Filter_Type) return Count;
196
+ pragma Inline (Total_Out);
197
+ -- Returns total number of bytes output so far
198
+
199
+ function CRC32
200
+ (CRC : in Unsigned_32;
201
+ Data : in Ada.Streams.Stream_Element_Array)
202
+ return Unsigned_32;
203
+ pragma Inline (CRC32);
204
+ -- Compute CRC32, it could be necessary for make gzip format
205
+
206
+ procedure CRC32
207
+ (CRC : in out Unsigned_32;
208
+ Data : in Ada.Streams.Stream_Element_Array);
209
+ pragma Inline (CRC32);
210
+ -- Compute CRC32, it could be necessary for make gzip format
211
+
212
+ -------------------------------------------------
213
+ -- Below is more complex low level routines. --
214
+ -------------------------------------------------
215
+
216
+ procedure Translate
217
+ (Filter : in out Filter_Type;
218
+ In_Data : in Ada.Streams.Stream_Element_Array;
219
+ In_Last : out Ada.Streams.Stream_Element_Offset;
220
+ Out_Data : out Ada.Streams.Stream_Element_Array;
221
+ Out_Last : out Ada.Streams.Stream_Element_Offset;
222
+ Flush : in Flush_Mode);
223
+ -- Compress/decompress the In_Data buffer and place the result into
224
+ -- Out_Data. In_Last is the index of last element from In_Data accepted by
225
+ -- the Filter. Out_Last is the last element of the received data from
226
+ -- Filter. To tell the filter that incoming data are complete put the
227
+ -- Flush parameter to Finish.
228
+
229
+ function Stream_End (Filter : in Filter_Type) return Boolean;
230
+ pragma Inline (Stream_End);
231
+ -- Return the true when the stream is complete.
232
+
233
+ procedure Flush
234
+ (Filter : in out Filter_Type;
235
+ Out_Data : out Ada.Streams.Stream_Element_Array;
236
+ Out_Last : out Ada.Streams.Stream_Element_Offset;
237
+ Flush : in Flush_Mode);
238
+ pragma Inline (Flush);
239
+ -- Flushing the data from the compressor.
240
+
241
+ generic
242
+ with procedure Write
243
+ (Item : in Ada.Streams.Stream_Element_Array);
244
+ -- User should provide this routine for accept
245
+ -- compressed/decompressed data.
246
+
247
+ Buffer_Size : in Ada.Streams.Stream_Element_Offset
248
+ := Default_Buffer_Size;
249
+ -- Buffer size for Write user routine.
250
+
251
+ procedure Write
252
+ (Filter : in out Filter_Type;
253
+ Item : in Ada.Streams.Stream_Element_Array;
254
+ Flush : in Flush_Mode := No_Flush);
255
+ -- Compress/Decompress data from Item to the generic parameter procedure
256
+ -- Write. Output buffer size could be set in Buffer_Size generic parameter.
257
+
258
+ generic
259
+ with procedure Read
260
+ (Item : out Ada.Streams.Stream_Element_Array;
261
+ Last : out Ada.Streams.Stream_Element_Offset);
262
+ -- User should provide data for compression/decompression
263
+ -- thru this routine.
264
+
265
+ Buffer : in out Ada.Streams.Stream_Element_Array;
266
+ -- Buffer for keep remaining data from the previous
267
+ -- back read.
268
+
269
+ Rest_First, Rest_Last : in out Ada.Streams.Stream_Element_Offset;
270
+ -- Rest_First have to be initialized to Buffer'Last + 1
271
+ -- Rest_Last have to be initialized to Buffer'Last
272
+ -- before usage.
273
+
274
+ Allow_Read_Some : in Boolean := False;
275
+ -- Is it allowed to return Last < Item'Last before end of data.
276
+
277
+ procedure Read
278
+ (Filter : in out Filter_Type;
279
+ Item : out Ada.Streams.Stream_Element_Array;
280
+ Last : out Ada.Streams.Stream_Element_Offset;
281
+ Flush : in Flush_Mode := No_Flush);
282
+ -- Compress/Decompress data from generic parameter procedure Read to the
283
+ -- Item. User should provide Buffer and initialized Rest_First, Rest_Last
284
+ -- indicators. If Allow_Read_Some is True, Read routines could return
285
+ -- Last < Item'Last only at end of stream.
286
+
287
+ private
288
+
289
+ use Ada.Streams;
290
+
291
+ pragma Assert (Ada.Streams.Stream_Element'Size = 8);
292
+ pragma Assert (Ada.Streams.Stream_Element'Modulus = 2**8);
293
+
294
+ type Flush_Mode is new Integer range 0 .. 5;
295
+
296
+ type Compression_Method is new Integer range 8 .. 8;
297
+
298
+ type Strategy_Type is new Integer range 0 .. 3;
299
+
300
+ No_Flush : constant Flush_Mode := 0;
301
+ Partial_Flush : constant Flush_Mode := 1;
302
+ Sync_Flush : constant Flush_Mode := 2;
303
+ Full_Flush : constant Flush_Mode := 3;
304
+ Finish : constant Flush_Mode := 4;
305
+ Block_Flush : constant Flush_Mode := 5;
306
+
307
+ Filtered : constant Strategy_Type := 1;
308
+ Huffman_Only : constant Strategy_Type := 2;
309
+ RLE : constant Strategy_Type := 3;
310
+ Default_Strategy : constant Strategy_Type := 0;
311
+
312
+ Deflated : constant Compression_Method := 8;
313
+
314
+ type Z_Stream;
315
+
316
+ type Z_Stream_Access is access all Z_Stream;
317
+
318
+ type Filter_Type is tagged limited record
319
+ Strm : Z_Stream_Access;
320
+ Compression : Boolean;
321
+ Stream_End : Boolean;
322
+ Header : Header_Type;
323
+ CRC : Unsigned_32;
324
+ Offset : Stream_Element_Offset;
325
+ -- Offset for gzip header/footer output.
326
+ end record;
327
+
328
+ end ZLib;
@@ -0,0 +1,20 @@
1
+ project Zlib is
2
+
3
+ for Languages use ("Ada");
4
+ for Source_Dirs use (".");
5
+ for Object_Dir use ".";
6
+ for Main use ("test.adb", "mtest.adb", "read.adb", "buffer_demo");
7
+
8
+ package Compiler is
9
+ for Default_Switches ("ada") use ("-gnatwcfilopru", "-gnatVcdfimorst", "-gnatyabcefhiklmnoprst");
10
+ end Compiler;
11
+
12
+ package Linker is
13
+ for Default_Switches ("ada") use ("-lz");
14
+ end Linker;
15
+
16
+ package Builder is
17
+ for Default_Switches ("ada") use ("-s", "-gnatQ");
18
+ end Builder;
19
+
20
+ end Zlib;
@@ -0,0 +1,43 @@
1
+ This is a patched version of zlib modified to use
2
+ Pentium-optimized assembly code in the deflation algorithm. The files
3
+ changed/added by this patch are:
4
+
5
+ README.586
6
+ match.S
7
+
8
+ The effectiveness of these modifications is a bit marginal, as the the
9
+ program's bottleneck seems to be mostly L1-cache contention, for which
10
+ there is no real way to work around without rewriting the basic
11
+ algorithm. The speedup on average is around 5-10% (which is generally
12
+ less than the amount of variance between subsequent executions).
13
+ However, when used at level 9 compression, the cache contention can
14
+ drop enough for the assembly version to achieve 10-20% speedup (and
15
+ sometimes more, depending on the amount of overall redundancy in the
16
+ files). Even here, though, cache contention can still be the limiting
17
+ factor, depending on the nature of the program using the zlib library.
18
+ This may also mean that better improvements will be seen on a Pentium
19
+ with MMX, which suffers much less from L1-cache contention, but I have
20
+ not yet verified this.
21
+
22
+ Note that this code has been tailored for the Pentium in particular,
23
+ and will not perform well on the Pentium Pro (due to the use of a
24
+ partial register in the inner loop).
25
+
26
+ If you are using an assembler other than GNU as, you will have to
27
+ translate match.S to use your assembler's syntax. (Have fun.)
28
+
29
+ Brian Raiter
30
+ breadbox@muppetlabs.com
31
+ April, 1998
32
+
33
+
34
+ Added for zlib 1.1.3:
35
+
36
+ The patches come from
37
+ http://www.muppetlabs.com/~breadbox/software/assembly.html
38
+
39
+ To compile zlib with this asm file, copy match.S to the zlib directory
40
+ then do:
41
+
42
+ CFLAGS="-O3 -DASMV" ./configure
43
+ make OBJA=match.o
@@ -0,0 +1,364 @@
1
+ /* match.s -- Pentium-optimized version of longest_match()
2
+ * Written for zlib 1.1.2
3
+ * Copyright (C) 1998 Brian Raiter <breadbox@muppetlabs.com>
4
+ *
5
+ * This is free software; you can redistribute it and/or modify it
6
+ * under the terms of the GNU General Public License.
7
+ */
8
+
9
+ #ifndef NO_UNDERLINE
10
+ #define match_init _match_init
11
+ #define longest_match _longest_match
12
+ #endif
13
+
14
+ #define MAX_MATCH (258)
15
+ #define MIN_MATCH (3)
16
+ #define MIN_LOOKAHEAD (MAX_MATCH + MIN_MATCH + 1)
17
+ #define MAX_MATCH_8 ((MAX_MATCH + 7) & ~7)
18
+
19
+ /* stack frame offsets */
20
+
21
+ #define wmask 0 /* local copy of s->wmask */
22
+ #define window 4 /* local copy of s->window */
23
+ #define windowbestlen 8 /* s->window + bestlen */
24
+ #define chainlenscanend 12 /* high word: current chain len */
25
+ /* low word: last bytes sought */
26
+ #define scanstart 16 /* first two bytes of string */
27
+ #define scanalign 20 /* dword-misalignment of string */
28
+ #define nicematch 24 /* a good enough match size */
29
+ #define bestlen 28 /* size of best match so far */
30
+ #define scan 32 /* ptr to string wanting match */
31
+
32
+ #define LocalVarsSize (36)
33
+ /* saved ebx 36 */
34
+ /* saved edi 40 */
35
+ /* saved esi 44 */
36
+ /* saved ebp 48 */
37
+ /* return address 52 */
38
+ #define deflatestate 56 /* the function arguments */
39
+ #define curmatch 60
40
+
41
+ /* Offsets for fields in the deflate_state structure. These numbers
42
+ * are calculated from the definition of deflate_state, with the
43
+ * assumption that the compiler will dword-align the fields. (Thus,
44
+ * changing the definition of deflate_state could easily cause this
45
+ * program to crash horribly, without so much as a warning at
46
+ * compile time. Sigh.)
47
+ */
48
+
49
+ /* All the +zlib1222add offsets are due to the addition of fields
50
+ * in zlib in the deflate_state structure since the asm code was first written
51
+ * (if you compile with zlib 1.0.4 or older, use "zlib1222add equ (-4)").
52
+ * (if you compile with zlib between 1.0.5 and 1.2.2.1, use "zlib1222add equ 0").
53
+ * if you compile with zlib 1.2.2.2 or later , use "zlib1222add equ 8").
54
+ */
55
+
56
+ #define zlib1222add (8)
57
+
58
+ #define dsWSize (36+zlib1222add)
59
+ #define dsWMask (44+zlib1222add)
60
+ #define dsWindow (48+zlib1222add)
61
+ #define dsPrev (56+zlib1222add)
62
+ #define dsMatchLen (88+zlib1222add)
63
+ #define dsPrevMatch (92+zlib1222add)
64
+ #define dsStrStart (100+zlib1222add)
65
+ #define dsMatchStart (104+zlib1222add)
66
+ #define dsLookahead (108+zlib1222add)
67
+ #define dsPrevLen (112+zlib1222add)
68
+ #define dsMaxChainLen (116+zlib1222add)
69
+ #define dsGoodMatch (132+zlib1222add)
70
+ #define dsNiceMatch (136+zlib1222add)
71
+
72
+
73
+ .file "match.S"
74
+
75
+ .globl match_init, longest_match
76
+
77
+ .text
78
+
79
+ /* uInt longest_match(deflate_state *deflatestate, IPos curmatch) */
80
+
81
+ longest_match:
82
+
83
+ /* Save registers that the compiler may be using, and adjust %esp to */
84
+ /* make room for our stack frame. */
85
+
86
+ pushl %ebp
87
+ pushl %edi
88
+ pushl %esi
89
+ pushl %ebx
90
+ subl $LocalVarsSize, %esp
91
+
92
+ /* Retrieve the function arguments. %ecx will hold cur_match */
93
+ /* throughout the entire function. %edx will hold the pointer to the */
94
+ /* deflate_state structure during the function's setup (before */
95
+ /* entering the main loop). */
96
+
97
+ movl deflatestate(%esp), %edx
98
+ movl curmatch(%esp), %ecx
99
+
100
+ /* if ((uInt)nice_match > s->lookahead) nice_match = s->lookahead; */
101
+
102
+ movl dsNiceMatch(%edx), %eax
103
+ movl dsLookahead(%edx), %ebx
104
+ cmpl %eax, %ebx
105
+ jl LookaheadLess
106
+ movl %eax, %ebx
107
+ LookaheadLess: movl %ebx, nicematch(%esp)
108
+
109
+ /* register Bytef *scan = s->window + s->strstart; */
110
+
111
+ movl dsWindow(%edx), %esi
112
+ movl %esi, window(%esp)
113
+ movl dsStrStart(%edx), %ebp
114
+ lea (%esi,%ebp), %edi
115
+ movl %edi, scan(%esp)
116
+
117
+ /* Determine how many bytes the scan ptr is off from being */
118
+ /* dword-aligned. */
119
+
120
+ movl %edi, %eax
121
+ negl %eax
122
+ andl $3, %eax
123
+ movl %eax, scanalign(%esp)
124
+
125
+ /* IPos limit = s->strstart > (IPos)MAX_DIST(s) ? */
126
+ /* s->strstart - (IPos)MAX_DIST(s) : NIL; */
127
+
128
+ movl dsWSize(%edx), %eax
129
+ subl $MIN_LOOKAHEAD, %eax
130
+ subl %eax, %ebp
131
+ jg LimitPositive
132
+ xorl %ebp, %ebp
133
+ LimitPositive:
134
+
135
+ /* unsigned chain_length = s->max_chain_length; */
136
+ /* if (s->prev_length >= s->good_match) { */
137
+ /* chain_length >>= 2; */
138
+ /* } */
139
+
140
+ movl dsPrevLen(%edx), %eax
141
+ movl dsGoodMatch(%edx), %ebx
142
+ cmpl %ebx, %eax
143
+ movl dsMaxChainLen(%edx), %ebx
144
+ jl LastMatchGood
145
+ shrl $2, %ebx
146
+ LastMatchGood:
147
+
148
+ /* chainlen is decremented once beforehand so that the function can */
149
+ /* use the sign flag instead of the zero flag for the exit test. */
150
+ /* It is then shifted into the high word, to make room for the scanend */
151
+ /* scanend value, which it will always accompany. */
152
+
153
+ decl %ebx
154
+ shll $16, %ebx
155
+
156
+ /* int best_len = s->prev_length; */
157
+
158
+ movl dsPrevLen(%edx), %eax
159
+ movl %eax, bestlen(%esp)
160
+
161
+ /* Store the sum of s->window + best_len in %esi locally, and in %esi. */
162
+
163
+ addl %eax, %esi
164
+ movl %esi, windowbestlen(%esp)
165
+
166
+ /* register ush scan_start = *(ushf*)scan; */
167
+ /* register ush scan_end = *(ushf*)(scan+best_len-1); */
168
+
169
+ movw (%edi), %bx
170
+ movw %bx, scanstart(%esp)
171
+ movw -1(%edi,%eax), %bx
172
+ movl %ebx, chainlenscanend(%esp)
173
+
174
+ /* Posf *prev = s->prev; */
175
+ /* uInt wmask = s->w_mask; */
176
+
177
+ movl dsPrev(%edx), %edi
178
+ movl dsWMask(%edx), %edx
179
+ mov %edx, wmask(%esp)
180
+
181
+ /* Jump into the main loop. */
182
+
183
+ jmp LoopEntry
184
+
185
+ .balign 16
186
+
187
+ /* do {
188
+ * match = s->window + cur_match;
189
+ * if (*(ushf*)(match+best_len-1) != scan_end ||
190
+ * *(ushf*)match != scan_start) continue;
191
+ * [...]
192
+ * } while ((cur_match = prev[cur_match & wmask]) > limit
193
+ * && --chain_length != 0);
194
+ *
195
+ * Here is the inner loop of the function. The function will spend the
196
+ * majority of its time in this loop, and majority of that time will
197
+ * be spent in the first ten instructions.
198
+ *
199
+ * Within this loop:
200
+ * %ebx = chainlenscanend - i.e., ((chainlen << 16) | scanend)
201
+ * %ecx = curmatch
202
+ * %edx = curmatch & wmask
203
+ * %esi = windowbestlen - i.e., (window + bestlen)
204
+ * %edi = prev
205
+ * %ebp = limit
206
+ *
207
+ * Two optimization notes on the choice of instructions:
208
+ *
209
+ * The first instruction uses a 16-bit address, which costs an extra,
210
+ * unpairable cycle. This is cheaper than doing a 32-bit access and
211
+ * zeroing the high word, due to the 3-cycle misalignment penalty which
212
+ * would occur half the time. This also turns out to be cheaper than
213
+ * doing two separate 8-bit accesses, as the memory is so rarely in the
214
+ * L1 cache.
215
+ *
216
+ * The window buffer, however, apparently spends a lot of time in the
217
+ * cache, and so it is faster to retrieve the word at the end of the
218
+ * match string with two 8-bit loads. The instructions that test the
219
+ * word at the beginning of the match string, however, are executed
220
+ * much less frequently, and there it was cheaper to use 16-bit
221
+ * instructions, which avoided the necessity of saving off and
222
+ * subsequently reloading one of the other registers.
223
+ */
224
+ LookupLoop:
225
+ /* 1 U & V */
226
+ movw (%edi,%edx,2), %cx /* 2 U pipe */
227
+ movl wmask(%esp), %edx /* 2 V pipe */
228
+ cmpl %ebp, %ecx /* 3 U pipe */
229
+ jbe LeaveNow /* 3 V pipe */
230
+ subl $0x00010000, %ebx /* 4 U pipe */
231
+ js LeaveNow /* 4 V pipe */
232
+ LoopEntry: movb -1(%esi,%ecx), %al /* 5 U pipe */
233
+ andl %ecx, %edx /* 5 V pipe */
234
+ cmpb %bl, %al /* 6 U pipe */
235
+ jnz LookupLoop /* 6 V pipe */
236
+ movb (%esi,%ecx), %ah
237
+ cmpb %bh, %ah
238
+ jnz LookupLoop
239
+ movl window(%esp), %eax
240
+ movw (%eax,%ecx), %ax
241
+ cmpw scanstart(%esp), %ax
242
+ jnz LookupLoop
243
+
244
+ /* Store the current value of chainlen. */
245
+
246
+ movl %ebx, chainlenscanend(%esp)
247
+
248
+ /* Point %edi to the string under scrutiny, and %esi to the string we */
249
+ /* are hoping to match it up with. In actuality, %esi and %edi are */
250
+ /* both pointed (MAX_MATCH_8 - scanalign) bytes ahead, and %edx is */
251
+ /* initialized to -(MAX_MATCH_8 - scanalign). */
252
+
253
+ movl window(%esp), %esi
254
+ movl scan(%esp), %edi
255
+ addl %ecx, %esi
256
+ movl scanalign(%esp), %eax
257
+ movl $(-MAX_MATCH_8), %edx
258
+ lea MAX_MATCH_8(%edi,%eax), %edi
259
+ lea MAX_MATCH_8(%esi,%eax), %esi
260
+
261
+ /* Test the strings for equality, 8 bytes at a time. At the end,
262
+ * adjust %edx so that it is offset to the exact byte that mismatched.
263
+ *
264
+ * We already know at this point that the first three bytes of the
265
+ * strings match each other, and they can be safely passed over before
266
+ * starting the compare loop. So what this code does is skip over 0-3
267
+ * bytes, as much as necessary in order to dword-align the %edi
268
+ * pointer. (%esi will still be misaligned three times out of four.)
269
+ *
270
+ * It should be confessed that this loop usually does not represent
271
+ * much of the total running time. Replacing it with a more
272
+ * straightforward "rep cmpsb" would not drastically degrade
273
+ * performance.
274
+ */
275
+ LoopCmps:
276
+ movl (%esi,%edx), %eax
277
+ movl (%edi,%edx), %ebx
278
+ xorl %ebx, %eax
279
+ jnz LeaveLoopCmps
280
+ movl 4(%esi,%edx), %eax
281
+ movl 4(%edi,%edx), %ebx
282
+ xorl %ebx, %eax
283
+ jnz LeaveLoopCmps4
284
+ addl $8, %edx
285
+ jnz LoopCmps
286
+ jmp LenMaximum
287
+ LeaveLoopCmps4: addl $4, %edx
288
+ LeaveLoopCmps: testl $0x0000FFFF, %eax
289
+ jnz LenLower
290
+ addl $2, %edx
291
+ shrl $16, %eax
292
+ LenLower: subb $1, %al
293
+ adcl $0, %edx
294
+
295
+ /* Calculate the length of the match. If it is longer than MAX_MATCH, */
296
+ /* then automatically accept it as the best possible match and leave. */
297
+
298
+ lea (%edi,%edx), %eax
299
+ movl scan(%esp), %edi
300
+ subl %edi, %eax
301
+ cmpl $MAX_MATCH, %eax
302
+ jge LenMaximum
303
+
304
+ /* If the length of the match is not longer than the best match we */
305
+ /* have so far, then forget it and return to the lookup loop. */
306
+
307
+ movl deflatestate(%esp), %edx
308
+ movl bestlen(%esp), %ebx
309
+ cmpl %ebx, %eax
310
+ jg LongerMatch
311
+ movl chainlenscanend(%esp), %ebx
312
+ movl windowbestlen(%esp), %esi
313
+ movl dsPrev(%edx), %edi
314
+ movl wmask(%esp), %edx
315
+ andl %ecx, %edx
316
+ jmp LookupLoop
317
+
318
+ /* s->match_start = cur_match; */
319
+ /* best_len = len; */
320
+ /* if (len >= nice_match) break; */
321
+ /* scan_end = *(ushf*)(scan+best_len-1); */
322
+
323
+ LongerMatch: movl nicematch(%esp), %ebx
324
+ movl %eax, bestlen(%esp)
325
+ movl %ecx, dsMatchStart(%edx)
326
+ cmpl %ebx, %eax
327
+ jge LeaveNow
328
+ movl window(%esp), %esi
329
+ addl %eax, %esi
330
+ movl %esi, windowbestlen(%esp)
331
+ movl chainlenscanend(%esp), %ebx
332
+ movw -1(%edi,%eax), %bx
333
+ movl dsPrev(%edx), %edi
334
+ movl %ebx, chainlenscanend(%esp)
335
+ movl wmask(%esp), %edx
336
+ andl %ecx, %edx
337
+ jmp LookupLoop
338
+
339
+ /* Accept the current string, with the maximum possible length. */
340
+
341
+ LenMaximum: movl deflatestate(%esp), %edx
342
+ movl $MAX_MATCH, bestlen(%esp)
343
+ movl %ecx, dsMatchStart(%edx)
344
+
345
+ /* if ((uInt)best_len <= s->lookahead) return (uInt)best_len; */
346
+ /* return s->lookahead; */
347
+
348
+ LeaveNow:
349
+ movl deflatestate(%esp), %edx
350
+ movl bestlen(%esp), %ebx
351
+ movl dsLookahead(%edx), %eax
352
+ cmpl %eax, %ebx
353
+ jg LookaheadRet
354
+ movl %ebx, %eax
355
+ LookaheadRet:
356
+
357
+ /* Restore the stack and return from whence we came. */
358
+
359
+ addl $LocalVarsSize, %esp
360
+ popl %ebx
361
+ popl %esi
362
+ popl %edi
363
+ popl %ebp
364
+ match_init: ret