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 +1,235 @@
1
+ /* zip.h -- IO for compress .zip files using zlib
2
+ Version 1.01e, February 12th, 2005
3
+
4
+ Copyright (C) 1998-2005 Gilles Vollant
5
+
6
+ This unzip package allow creates .ZIP file, compatible with PKZip 2.04g
7
+ WinZip, InfoZip tools and compatible.
8
+ Multi volume ZipFile (span) are not supported.
9
+ Encryption compatible with pkzip 2.04g only supported
10
+ Old compressions used by old PKZip 1.x are not supported
11
+
12
+ For uncompress .zip file, look at unzip.h
13
+
14
+
15
+ I WAIT FEEDBACK at mail info@winimage.com
16
+ Visit also http://www.winimage.com/zLibDll/unzip.html for evolution
17
+
18
+ Condition of use and distribution are the same than zlib :
19
+
20
+ This software is provided 'as-is', without any express or implied
21
+ warranty. In no event will the authors be held liable for any damages
22
+ arising from the use of this software.
23
+
24
+ Permission is granted to anyone to use this software for any purpose,
25
+ including commercial applications, and to alter it and redistribute it
26
+ freely, subject to the following restrictions:
27
+
28
+ 1. The origin of this software must not be misrepresented; you must not
29
+ claim that you wrote the original software. If you use this software
30
+ in a product, an acknowledgment in the product documentation would be
31
+ appreciated but is not required.
32
+ 2. Altered source versions must be plainly marked as such, and must not be
33
+ misrepresented as being the original software.
34
+ 3. This notice may not be removed or altered from any source distribution.
35
+
36
+
37
+ */
38
+
39
+ /* for more info about .ZIP format, see
40
+ http://www.info-zip.org/pub/infozip/doc/appnote-981119-iz.zip
41
+ http://www.info-zip.org/pub/infozip/doc/
42
+ PkWare has also a specification at :
43
+ ftp://ftp.pkware.com/probdesc.zip
44
+ */
45
+
46
+ #ifndef _zip_H
47
+ #define _zip_H
48
+
49
+ #ifdef __cplusplus
50
+ extern "C" {
51
+ #endif
52
+
53
+ #ifndef _ZLIB_H
54
+ #include "zlib.h"
55
+ #endif
56
+
57
+ #ifndef _ZLIBIOAPI_H
58
+ #include "ioapi.h"
59
+ #endif
60
+
61
+ #if defined(STRICTZIP) || defined(STRICTZIPUNZIP)
62
+ /* like the STRICT of WIN32, we define a pointer that cannot be converted
63
+ from (void*) without cast */
64
+ typedef struct TagzipFile__ { int unused; } zipFile__;
65
+ typedef zipFile__ *zipFile;
66
+ #else
67
+ typedef voidp zipFile;
68
+ #endif
69
+
70
+ #define ZIP_OK (0)
71
+ #define ZIP_EOF (0)
72
+ #define ZIP_ERRNO (Z_ERRNO)
73
+ #define ZIP_PARAMERROR (-102)
74
+ #define ZIP_BADZIPFILE (-103)
75
+ #define ZIP_INTERNALERROR (-104)
76
+
77
+ #ifndef DEF_MEM_LEVEL
78
+ # if MAX_MEM_LEVEL >= 8
79
+ # define DEF_MEM_LEVEL 8
80
+ # else
81
+ # define DEF_MEM_LEVEL MAX_MEM_LEVEL
82
+ # endif
83
+ #endif
84
+ /* default memLevel */
85
+
86
+ /* tm_zip contain date/time info */
87
+ typedef struct tm_zip_s
88
+ {
89
+ uInt tm_sec; /* seconds after the minute - [0,59] */
90
+ uInt tm_min; /* minutes after the hour - [0,59] */
91
+ uInt tm_hour; /* hours since midnight - [0,23] */
92
+ uInt tm_mday; /* day of the month - [1,31] */
93
+ uInt tm_mon; /* months since January - [0,11] */
94
+ uInt tm_year; /* years - [1980..2044] */
95
+ } tm_zip;
96
+
97
+ typedef struct
98
+ {
99
+ tm_zip tmz_date; /* date in understandable format */
100
+ uLong dosDate; /* if dos_date == 0, tmu_date is used */
101
+ /* uLong flag; */ /* general purpose bit flag 2 bytes */
102
+
103
+ uLong internal_fa; /* internal file attributes 2 bytes */
104
+ uLong external_fa; /* external file attributes 4 bytes */
105
+ } zip_fileinfo;
106
+
107
+ typedef const char* zipcharpc;
108
+
109
+
110
+ #define APPEND_STATUS_CREATE (0)
111
+ #define APPEND_STATUS_CREATEAFTER (1)
112
+ #define APPEND_STATUS_ADDINZIP (2)
113
+
114
+ extern zipFile ZEXPORT zipOpen OF((const char *pathname, int append));
115
+ /*
116
+ Create a zipfile.
117
+ pathname contain on Windows XP a filename like "c:\\zlib\\zlib113.zip" or on
118
+ an Unix computer "zlib/zlib113.zip".
119
+ if the file pathname exist and append==APPEND_STATUS_CREATEAFTER, the zip
120
+ will be created at the end of the file.
121
+ (useful if the file contain a self extractor code)
122
+ if the file pathname exist and append==APPEND_STATUS_ADDINZIP, we will
123
+ add files in existing zip (be sure you don't add file that doesn't exist)
124
+ If the zipfile cannot be opened, the return value is NULL.
125
+ Else, the return value is a zipFile Handle, usable with other function
126
+ of this zip package.
127
+ */
128
+
129
+ /* Note : there is no delete function into a zipfile.
130
+ If you want delete file into a zipfile, you must open a zipfile, and create another
131
+ Of couse, you can use RAW reading and writing to copy the file you did not want delte
132
+ */
133
+
134
+ extern zipFile ZEXPORT zipOpen2 OF((const char *pathname,
135
+ int append,
136
+ zipcharpc* globalcomment,
137
+ zlib_filefunc_def* pzlib_filefunc_def));
138
+
139
+ extern int ZEXPORT zipOpenNewFileInZip OF((zipFile file,
140
+ const char* filename,
141
+ const zip_fileinfo* zipfi,
142
+ const void* extrafield_local,
143
+ uInt size_extrafield_local,
144
+ const void* extrafield_global,
145
+ uInt size_extrafield_global,
146
+ const char* comment,
147
+ int method,
148
+ int level));
149
+ /*
150
+ Open a file in the ZIP for writing.
151
+ filename : the filename in zip (if NULL, '-' without quote will be used
152
+ *zipfi contain supplemental information
153
+ if extrafield_local!=NULL and size_extrafield_local>0, extrafield_local
154
+ contains the extrafield data the the local header
155
+ if extrafield_global!=NULL and size_extrafield_global>0, extrafield_global
156
+ contains the extrafield data the the local header
157
+ if comment != NULL, comment contain the comment string
158
+ method contain the compression method (0 for store, Z_DEFLATED for deflate)
159
+ level contain the level of compression (can be Z_DEFAULT_COMPRESSION)
160
+ */
161
+
162
+
163
+ extern int ZEXPORT zipOpenNewFileInZip2 OF((zipFile file,
164
+ const char* filename,
165
+ const zip_fileinfo* zipfi,
166
+ const void* extrafield_local,
167
+ uInt size_extrafield_local,
168
+ const void* extrafield_global,
169
+ uInt size_extrafield_global,
170
+ const char* comment,
171
+ int method,
172
+ int level,
173
+ int raw));
174
+
175
+ /*
176
+ Same than zipOpenNewFileInZip, except if raw=1, we write raw file
177
+ */
178
+
179
+ extern int ZEXPORT zipOpenNewFileInZip3 OF((zipFile file,
180
+ const char* filename,
181
+ const zip_fileinfo* zipfi,
182
+ const void* extrafield_local,
183
+ uInt size_extrafield_local,
184
+ const void* extrafield_global,
185
+ uInt size_extrafield_global,
186
+ const char* comment,
187
+ int method,
188
+ int level,
189
+ int raw,
190
+ int windowBits,
191
+ int memLevel,
192
+ int strategy,
193
+ const char* password,
194
+ uLong crcForCtypting));
195
+
196
+ /*
197
+ Same than zipOpenNewFileInZip2, except
198
+ windowBits,memLevel,,strategy : see parameter strategy in deflateInit2
199
+ password : crypting password (NULL for no crypting)
200
+ crcForCtypting : crc of file to compress (needed for crypting)
201
+ */
202
+
203
+
204
+ extern int ZEXPORT zipWriteInFileInZip OF((zipFile file,
205
+ const void* buf,
206
+ unsigned len));
207
+ /*
208
+ Write data in the zipfile
209
+ */
210
+
211
+ extern int ZEXPORT zipCloseFileInZip OF((zipFile file));
212
+ /*
213
+ Close the current file in the zipfile
214
+ */
215
+
216
+ extern int ZEXPORT zipCloseFileInZipRaw OF((zipFile file,
217
+ uLong uncompressed_size,
218
+ uLong crc32));
219
+ /*
220
+ Close the current file in the zipfile, for fiel opened with
221
+ parameter raw=1 in zipOpenNewFileInZip2
222
+ uncompressed_size and crc32 are value for the uncompressed size
223
+ */
224
+
225
+ extern int ZEXPORT zipClose OF((zipFile file,
226
+ const char* global_comment));
227
+ /*
228
+ Close the zipfile
229
+ */
230
+
231
+ #ifdef __cplusplus
232
+ }
233
+ #endif
234
+
235
+ #endif /* _zip_H */
@@ -0,0 +1,599 @@
1
+ (* example.c -- usage example of the zlib compression library
2
+ * Copyright (C) 1995-2003 Jean-loup Gailly.
3
+ * For conditions of distribution and use, see copyright notice in zlib.h
4
+ *
5
+ * Pascal translation
6
+ * Copyright (C) 1998 by Jacques Nomssi Nzali.
7
+ * For conditions of distribution and use, see copyright notice in readme.txt
8
+ *
9
+ * Adaptation to the zlibpas interface
10
+ * Copyright (C) 2003 by Cosmin Truta.
11
+ * For conditions of distribution and use, see copyright notice in readme.txt
12
+ *)
13
+
14
+ program example;
15
+
16
+ {$DEFINE TEST_COMPRESS}
17
+ {DO NOT $DEFINE TEST_GZIO}
18
+ {$DEFINE TEST_DEFLATE}
19
+ {$DEFINE TEST_INFLATE}
20
+ {$DEFINE TEST_FLUSH}
21
+ {$DEFINE TEST_SYNC}
22
+ {$DEFINE TEST_DICT}
23
+
24
+ uses SysUtils, zlibpas;
25
+
26
+ const TESTFILE = 'foo.gz';
27
+
28
+ (* "hello world" would be more standard, but the repeated "hello"
29
+ * stresses the compression code better, sorry...
30
+ *)
31
+ const hello: PChar = 'hello, hello!';
32
+
33
+ const dictionary: PChar = 'hello';
34
+
35
+ var dictId: LongInt; (* Adler32 value of the dictionary *)
36
+
37
+ procedure CHECK_ERR(err: Integer; msg: String);
38
+ begin
39
+ if err <> Z_OK then
40
+ begin
41
+ WriteLn(msg, ' error: ', err);
42
+ Halt(1);
43
+ end;
44
+ end;
45
+
46
+ procedure EXIT_ERR(const msg: String);
47
+ begin
48
+ WriteLn('Error: ', msg);
49
+ Halt(1);
50
+ end;
51
+
52
+ (* ===========================================================================
53
+ * Test compress and uncompress
54
+ *)
55
+ {$IFDEF TEST_COMPRESS}
56
+ procedure test_compress(compr: Pointer; comprLen: LongInt;
57
+ uncompr: Pointer; uncomprLen: LongInt);
58
+ var err: Integer;
59
+ len: LongInt;
60
+ begin
61
+ len := StrLen(hello)+1;
62
+
63
+ err := compress(compr, comprLen, hello, len);
64
+ CHECK_ERR(err, 'compress');
65
+
66
+ StrCopy(PChar(uncompr), 'garbage');
67
+
68
+ err := uncompress(uncompr, uncomprLen, compr, comprLen);
69
+ CHECK_ERR(err, 'uncompress');
70
+
71
+ if StrComp(PChar(uncompr), hello) <> 0 then
72
+ EXIT_ERR('bad uncompress')
73
+ else
74
+ WriteLn('uncompress(): ', PChar(uncompr));
75
+ end;
76
+ {$ENDIF}
77
+
78
+ (* ===========================================================================
79
+ * Test read/write of .gz files
80
+ *)
81
+ {$IFDEF TEST_GZIO}
82
+ procedure test_gzio(const fname: PChar; (* compressed file name *)
83
+ uncompr: Pointer;
84
+ uncomprLen: LongInt);
85
+ var err: Integer;
86
+ len: Integer;
87
+ zfile: gzFile;
88
+ pos: LongInt;
89
+ begin
90
+ len := StrLen(hello)+1;
91
+
92
+ zfile := gzopen(fname, 'wb');
93
+ if zfile = NIL then
94
+ begin
95
+ WriteLn('gzopen error');
96
+ Halt(1);
97
+ end;
98
+ gzputc(zfile, 'h');
99
+ if gzputs(zfile, 'ello') <> 4 then
100
+ begin
101
+ WriteLn('gzputs err: ', gzerror(zfile, err));
102
+ Halt(1);
103
+ end;
104
+ {$IFDEF GZ_FORMAT_STRING}
105
+ if gzprintf(zfile, ', %s!', 'hello') <> 8 then
106
+ begin
107
+ WriteLn('gzprintf err: ', gzerror(zfile, err));
108
+ Halt(1);
109
+ end;
110
+ {$ELSE}
111
+ if gzputs(zfile, ', hello!') <> 8 then
112
+ begin
113
+ WriteLn('gzputs err: ', gzerror(zfile, err));
114
+ Halt(1);
115
+ end;
116
+ {$ENDIF}
117
+ gzseek(zfile, 1, SEEK_CUR); (* add one zero byte *)
118
+ gzclose(zfile);
119
+
120
+ zfile := gzopen(fname, 'rb');
121
+ if zfile = NIL then
122
+ begin
123
+ WriteLn('gzopen error');
124
+ Halt(1);
125
+ end;
126
+
127
+ StrCopy(PChar(uncompr), 'garbage');
128
+
129
+ if gzread(zfile, uncompr, uncomprLen) <> len then
130
+ begin
131
+ WriteLn('gzread err: ', gzerror(zfile, err));
132
+ Halt(1);
133
+ end;
134
+ if StrComp(PChar(uncompr), hello) <> 0 then
135
+ begin
136
+ WriteLn('bad gzread: ', PChar(uncompr));
137
+ Halt(1);
138
+ end
139
+ else
140
+ WriteLn('gzread(): ', PChar(uncompr));
141
+
142
+ pos := gzseek(zfile, -8, SEEK_CUR);
143
+ if (pos <> 6) or (gztell(zfile) <> pos) then
144
+ begin
145
+ WriteLn('gzseek error, pos=', pos, ', gztell=', gztell(zfile));
146
+ Halt(1);
147
+ end;
148
+
149
+ if gzgetc(zfile) <> ' ' then
150
+ begin
151
+ WriteLn('gzgetc error');
152
+ Halt(1);
153
+ end;
154
+
155
+ if gzungetc(' ', zfile) <> ' ' then
156
+ begin
157
+ WriteLn('gzungetc error');
158
+ Halt(1);
159
+ end;
160
+
161
+ gzgets(zfile, PChar(uncompr), uncomprLen);
162
+ uncomprLen := StrLen(PChar(uncompr));
163
+ if uncomprLen <> 7 then (* " hello!" *)
164
+ begin
165
+ WriteLn('gzgets err after gzseek: ', gzerror(zfile, err));
166
+ Halt(1);
167
+ end;
168
+ if StrComp(PChar(uncompr), hello + 6) <> 0 then
169
+ begin
170
+ WriteLn('bad gzgets after gzseek');
171
+ Halt(1);
172
+ end
173
+ else
174
+ WriteLn('gzgets() after gzseek: ', PChar(uncompr));
175
+
176
+ gzclose(zfile);
177
+ end;
178
+ {$ENDIF}
179
+
180
+ (* ===========================================================================
181
+ * Test deflate with small buffers
182
+ *)
183
+ {$IFDEF TEST_DEFLATE}
184
+ procedure test_deflate(compr: Pointer; comprLen: LongInt);
185
+ var c_stream: z_stream; (* compression stream *)
186
+ err: Integer;
187
+ len: LongInt;
188
+ begin
189
+ len := StrLen(hello)+1;
190
+
191
+ c_stream.zalloc := NIL;
192
+ c_stream.zfree := NIL;
193
+ c_stream.opaque := NIL;
194
+
195
+ err := deflateInit(c_stream, Z_DEFAULT_COMPRESSION);
196
+ CHECK_ERR(err, 'deflateInit');
197
+
198
+ c_stream.next_in := hello;
199
+ c_stream.next_out := compr;
200
+
201
+ while (c_stream.total_in <> len) and
202
+ (c_stream.total_out < comprLen) do
203
+ begin
204
+ c_stream.avail_out := 1; { force small buffers }
205
+ c_stream.avail_in := 1;
206
+ err := deflate(c_stream, Z_NO_FLUSH);
207
+ CHECK_ERR(err, 'deflate');
208
+ end;
209
+
210
+ (* Finish the stream, still forcing small buffers: *)
211
+ while TRUE do
212
+ begin
213
+ c_stream.avail_out := 1;
214
+ err := deflate(c_stream, Z_FINISH);
215
+ if err = Z_STREAM_END then
216
+ break;
217
+ CHECK_ERR(err, 'deflate');
218
+ end;
219
+
220
+ err := deflateEnd(c_stream);
221
+ CHECK_ERR(err, 'deflateEnd');
222
+ end;
223
+ {$ENDIF}
224
+
225
+ (* ===========================================================================
226
+ * Test inflate with small buffers
227
+ *)
228
+ {$IFDEF TEST_INFLATE}
229
+ procedure test_inflate(compr: Pointer; comprLen : LongInt;
230
+ uncompr: Pointer; uncomprLen : LongInt);
231
+ var err: Integer;
232
+ d_stream: z_stream; (* decompression stream *)
233
+ begin
234
+ StrCopy(PChar(uncompr), 'garbage');
235
+
236
+ d_stream.zalloc := NIL;
237
+ d_stream.zfree := NIL;
238
+ d_stream.opaque := NIL;
239
+
240
+ d_stream.next_in := compr;
241
+ d_stream.avail_in := 0;
242
+ d_stream.next_out := uncompr;
243
+
244
+ err := inflateInit(d_stream);
245
+ CHECK_ERR(err, 'inflateInit');
246
+
247
+ while (d_stream.total_out < uncomprLen) and
248
+ (d_stream.total_in < comprLen) do
249
+ begin
250
+ d_stream.avail_out := 1; (* force small buffers *)
251
+ d_stream.avail_in := 1;
252
+ err := inflate(d_stream, Z_NO_FLUSH);
253
+ if err = Z_STREAM_END then
254
+ break;
255
+ CHECK_ERR(err, 'inflate');
256
+ end;
257
+
258
+ err := inflateEnd(d_stream);
259
+ CHECK_ERR(err, 'inflateEnd');
260
+
261
+ if StrComp(PChar(uncompr), hello) <> 0 then
262
+ EXIT_ERR('bad inflate')
263
+ else
264
+ WriteLn('inflate(): ', PChar(uncompr));
265
+ end;
266
+ {$ENDIF}
267
+
268
+ (* ===========================================================================
269
+ * Test deflate with large buffers and dynamic change of compression level
270
+ *)
271
+ {$IFDEF TEST_DEFLATE}
272
+ procedure test_large_deflate(compr: Pointer; comprLen: LongInt;
273
+ uncompr: Pointer; uncomprLen: LongInt);
274
+ var c_stream: z_stream; (* compression stream *)
275
+ err: Integer;
276
+ begin
277
+ c_stream.zalloc := NIL;
278
+ c_stream.zfree := NIL;
279
+ c_stream.opaque := NIL;
280
+
281
+ err := deflateInit(c_stream, Z_BEST_SPEED);
282
+ CHECK_ERR(err, 'deflateInit');
283
+
284
+ c_stream.next_out := compr;
285
+ c_stream.avail_out := Integer(comprLen);
286
+
287
+ (* At this point, uncompr is still mostly zeroes, so it should compress
288
+ * very well:
289
+ *)
290
+ c_stream.next_in := uncompr;
291
+ c_stream.avail_in := Integer(uncomprLen);
292
+ err := deflate(c_stream, Z_NO_FLUSH);
293
+ CHECK_ERR(err, 'deflate');
294
+ if c_stream.avail_in <> 0 then
295
+ EXIT_ERR('deflate not greedy');
296
+
297
+ (* Feed in already compressed data and switch to no compression: *)
298
+ deflateParams(c_stream, Z_NO_COMPRESSION, Z_DEFAULT_STRATEGY);
299
+ c_stream.next_in := compr;
300
+ c_stream.avail_in := Integer(comprLen div 2);
301
+ err := deflate(c_stream, Z_NO_FLUSH);
302
+ CHECK_ERR(err, 'deflate');
303
+
304
+ (* Switch back to compressing mode: *)
305
+ deflateParams(c_stream, Z_BEST_COMPRESSION, Z_FILTERED);
306
+ c_stream.next_in := uncompr;
307
+ c_stream.avail_in := Integer(uncomprLen);
308
+ err := deflate(c_stream, Z_NO_FLUSH);
309
+ CHECK_ERR(err, 'deflate');
310
+
311
+ err := deflate(c_stream, Z_FINISH);
312
+ if err <> Z_STREAM_END then
313
+ EXIT_ERR('deflate should report Z_STREAM_END');
314
+
315
+ err := deflateEnd(c_stream);
316
+ CHECK_ERR(err, 'deflateEnd');
317
+ end;
318
+ {$ENDIF}
319
+
320
+ (* ===========================================================================
321
+ * Test inflate with large buffers
322
+ *)
323
+ {$IFDEF TEST_INFLATE}
324
+ procedure test_large_inflate(compr: Pointer; comprLen: LongInt;
325
+ uncompr: Pointer; uncomprLen: LongInt);
326
+ var err: Integer;
327
+ d_stream: z_stream; (* decompression stream *)
328
+ begin
329
+ StrCopy(PChar(uncompr), 'garbage');
330
+
331
+ d_stream.zalloc := NIL;
332
+ d_stream.zfree := NIL;
333
+ d_stream.opaque := NIL;
334
+
335
+ d_stream.next_in := compr;
336
+ d_stream.avail_in := Integer(comprLen);
337
+
338
+ err := inflateInit(d_stream);
339
+ CHECK_ERR(err, 'inflateInit');
340
+
341
+ while TRUE do
342
+ begin
343
+ d_stream.next_out := uncompr; (* discard the output *)
344
+ d_stream.avail_out := Integer(uncomprLen);
345
+ err := inflate(d_stream, Z_NO_FLUSH);
346
+ if err = Z_STREAM_END then
347
+ break;
348
+ CHECK_ERR(err, 'large inflate');
349
+ end;
350
+
351
+ err := inflateEnd(d_stream);
352
+ CHECK_ERR(err, 'inflateEnd');
353
+
354
+ if d_stream.total_out <> 2 * uncomprLen + comprLen div 2 then
355
+ begin
356
+ WriteLn('bad large inflate: ', d_stream.total_out);
357
+ Halt(1);
358
+ end
359
+ else
360
+ WriteLn('large_inflate(): OK');
361
+ end;
362
+ {$ENDIF}
363
+
364
+ (* ===========================================================================
365
+ * Test deflate with full flush
366
+ *)
367
+ {$IFDEF TEST_FLUSH}
368
+ procedure test_flush(compr: Pointer; var comprLen : LongInt);
369
+ var c_stream: z_stream; (* compression stream *)
370
+ err: Integer;
371
+ len: Integer;
372
+ begin
373
+ len := StrLen(hello)+1;
374
+
375
+ c_stream.zalloc := NIL;
376
+ c_stream.zfree := NIL;
377
+ c_stream.opaque := NIL;
378
+
379
+ err := deflateInit(c_stream, Z_DEFAULT_COMPRESSION);
380
+ CHECK_ERR(err, 'deflateInit');
381
+
382
+ c_stream.next_in := hello;
383
+ c_stream.next_out := compr;
384
+ c_stream.avail_in := 3;
385
+ c_stream.avail_out := Integer(comprLen);
386
+ err := deflate(c_stream, Z_FULL_FLUSH);
387
+ CHECK_ERR(err, 'deflate');
388
+
389
+ Inc(PByteArray(compr)^[3]); (* force an error in first compressed block *)
390
+ c_stream.avail_in := len - 3;
391
+
392
+ err := deflate(c_stream, Z_FINISH);
393
+ if err <> Z_STREAM_END then
394
+ CHECK_ERR(err, 'deflate');
395
+
396
+ err := deflateEnd(c_stream);
397
+ CHECK_ERR(err, 'deflateEnd');
398
+
399
+ comprLen := c_stream.total_out;
400
+ end;
401
+ {$ENDIF}
402
+
403
+ (* ===========================================================================
404
+ * Test inflateSync()
405
+ *)
406
+ {$IFDEF TEST_SYNC}
407
+ procedure test_sync(compr: Pointer; comprLen: LongInt;
408
+ uncompr: Pointer; uncomprLen : LongInt);
409
+ var err: Integer;
410
+ d_stream: z_stream; (* decompression stream *)
411
+ begin
412
+ StrCopy(PChar(uncompr), 'garbage');
413
+
414
+ d_stream.zalloc := NIL;
415
+ d_stream.zfree := NIL;
416
+ d_stream.opaque := NIL;
417
+
418
+ d_stream.next_in := compr;
419
+ d_stream.avail_in := 2; (* just read the zlib header *)
420
+
421
+ err := inflateInit(d_stream);
422
+ CHECK_ERR(err, 'inflateInit');
423
+
424
+ d_stream.next_out := uncompr;
425
+ d_stream.avail_out := Integer(uncomprLen);
426
+
427
+ inflate(d_stream, Z_NO_FLUSH);
428
+ CHECK_ERR(err, 'inflate');
429
+
430
+ d_stream.avail_in := Integer(comprLen-2); (* read all compressed data *)
431
+ err := inflateSync(d_stream); (* but skip the damaged part *)
432
+ CHECK_ERR(err, 'inflateSync');
433
+
434
+ err := inflate(d_stream, Z_FINISH);
435
+ if err <> Z_DATA_ERROR then
436
+ EXIT_ERR('inflate should report DATA_ERROR');
437
+ (* Because of incorrect adler32 *)
438
+
439
+ err := inflateEnd(d_stream);
440
+ CHECK_ERR(err, 'inflateEnd');
441
+
442
+ WriteLn('after inflateSync(): hel', PChar(uncompr));
443
+ end;
444
+ {$ENDIF}
445
+
446
+ (* ===========================================================================
447
+ * Test deflate with preset dictionary
448
+ *)
449
+ {$IFDEF TEST_DICT}
450
+ procedure test_dict_deflate(compr: Pointer; comprLen: LongInt);
451
+ var c_stream: z_stream; (* compression stream *)
452
+ err: Integer;
453
+ begin
454
+ c_stream.zalloc := NIL;
455
+ c_stream.zfree := NIL;
456
+ c_stream.opaque := NIL;
457
+
458
+ err := deflateInit(c_stream, Z_BEST_COMPRESSION);
459
+ CHECK_ERR(err, 'deflateInit');
460
+
461
+ err := deflateSetDictionary(c_stream, dictionary, StrLen(dictionary));
462
+ CHECK_ERR(err, 'deflateSetDictionary');
463
+
464
+ dictId := c_stream.adler;
465
+ c_stream.next_out := compr;
466
+ c_stream.avail_out := Integer(comprLen);
467
+
468
+ c_stream.next_in := hello;
469
+ c_stream.avail_in := StrLen(hello)+1;
470
+
471
+ err := deflate(c_stream, Z_FINISH);
472
+ if err <> Z_STREAM_END then
473
+ EXIT_ERR('deflate should report Z_STREAM_END');
474
+
475
+ err := deflateEnd(c_stream);
476
+ CHECK_ERR(err, 'deflateEnd');
477
+ end;
478
+ {$ENDIF}
479
+
480
+ (* ===========================================================================
481
+ * Test inflate with a preset dictionary
482
+ *)
483
+ {$IFDEF TEST_DICT}
484
+ procedure test_dict_inflate(compr: Pointer; comprLen: LongInt;
485
+ uncompr: Pointer; uncomprLen: LongInt);
486
+ var err: Integer;
487
+ d_stream: z_stream; (* decompression stream *)
488
+ begin
489
+ StrCopy(PChar(uncompr), 'garbage');
490
+
491
+ d_stream.zalloc := NIL;
492
+ d_stream.zfree := NIL;
493
+ d_stream.opaque := NIL;
494
+
495
+ d_stream.next_in := compr;
496
+ d_stream.avail_in := Integer(comprLen);
497
+
498
+ err := inflateInit(d_stream);
499
+ CHECK_ERR(err, 'inflateInit');
500
+
501
+ d_stream.next_out := uncompr;
502
+ d_stream.avail_out := Integer(uncomprLen);
503
+
504
+ while TRUE do
505
+ begin
506
+ err := inflate(d_stream, Z_NO_FLUSH);
507
+ if err = Z_STREAM_END then
508
+ break;
509
+ if err = Z_NEED_DICT then
510
+ begin
511
+ if d_stream.adler <> dictId then
512
+ EXIT_ERR('unexpected dictionary');
513
+ err := inflateSetDictionary(d_stream, dictionary, StrLen(dictionary));
514
+ end;
515
+ CHECK_ERR(err, 'inflate with dict');
516
+ end;
517
+
518
+ err := inflateEnd(d_stream);
519
+ CHECK_ERR(err, 'inflateEnd');
520
+
521
+ if StrComp(PChar(uncompr), hello) <> 0 then
522
+ EXIT_ERR('bad inflate with dict')
523
+ else
524
+ WriteLn('inflate with dictionary: ', PChar(uncompr));
525
+ end;
526
+ {$ENDIF}
527
+
528
+ var compr, uncompr: Pointer;
529
+ comprLen, uncomprLen: LongInt;
530
+
531
+ begin
532
+ if zlibVersion^ <> ZLIB_VERSION[1] then
533
+ EXIT_ERR('Incompatible zlib version');
534
+
535
+ WriteLn('zlib version: ', zlibVersion);
536
+ WriteLn('zlib compile flags: ', Format('0x%x', [zlibCompileFlags]));
537
+
538
+ comprLen := 10000 * SizeOf(Integer); (* don't overflow on MSDOS *)
539
+ uncomprLen := comprLen;
540
+ GetMem(compr, comprLen);
541
+ GetMem(uncompr, uncomprLen);
542
+ if (compr = NIL) or (uncompr = NIL) then
543
+ EXIT_ERR('Out of memory');
544
+ (* compr and uncompr are cleared to avoid reading uninitialized
545
+ * data and to ensure that uncompr compresses well.
546
+ *)
547
+ FillChar(compr^, comprLen, 0);
548
+ FillChar(uncompr^, uncomprLen, 0);
549
+
550
+ {$IFDEF TEST_COMPRESS}
551
+ WriteLn('** Testing compress');
552
+ test_compress(compr, comprLen, uncompr, uncomprLen);
553
+ {$ENDIF}
554
+
555
+ {$IFDEF TEST_GZIO}
556
+ WriteLn('** Testing gzio');
557
+ if ParamCount >= 1 then
558
+ test_gzio(ParamStr(1), uncompr, uncomprLen)
559
+ else
560
+ test_gzio(TESTFILE, uncompr, uncomprLen);
561
+ {$ENDIF}
562
+
563
+ {$IFDEF TEST_DEFLATE}
564
+ WriteLn('** Testing deflate with small buffers');
565
+ test_deflate(compr, comprLen);
566
+ {$ENDIF}
567
+ {$IFDEF TEST_INFLATE}
568
+ WriteLn('** Testing inflate with small buffers');
569
+ test_inflate(compr, comprLen, uncompr, uncomprLen);
570
+ {$ENDIF}
571
+
572
+ {$IFDEF TEST_DEFLATE}
573
+ WriteLn('** Testing deflate with large buffers');
574
+ test_large_deflate(compr, comprLen, uncompr, uncomprLen);
575
+ {$ENDIF}
576
+ {$IFDEF TEST_INFLATE}
577
+ WriteLn('** Testing inflate with large buffers');
578
+ test_large_inflate(compr, comprLen, uncompr, uncomprLen);
579
+ {$ENDIF}
580
+
581
+ {$IFDEF TEST_FLUSH}
582
+ WriteLn('** Testing deflate with full flush');
583
+ test_flush(compr, comprLen);
584
+ {$ENDIF}
585
+ {$IFDEF TEST_SYNC}
586
+ WriteLn('** Testing inflateSync');
587
+ test_sync(compr, comprLen, uncompr, uncomprLen);
588
+ {$ENDIF}
589
+ comprLen := uncomprLen;
590
+
591
+ {$IFDEF TEST_DICT}
592
+ WriteLn('** Testing deflate and inflate with preset dictionary');
593
+ test_dict_deflate(compr, comprLen);
594
+ test_dict_inflate(compr, comprLen, uncompr, uncomprLen);
595
+ {$ENDIF}
596
+
597
+ FreeMem(compr, comprLen);
598
+ FreeMem(uncompr, uncomprLen);
599
+ end.