finishm 0.0.1

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Files changed (554) hide show
  1. checksums.yaml +7 -0
  2. data/.document +5 -0
  3. data/.gitmodules +3 -0
  4. data/.rspec +1 -0
  5. data/Gemfile +31 -0
  6. data/LICENSE.txt +20 -0
  7. data/README.md +59 -0
  8. data/Rakefile +51 -0
  9. data/VERSION +1 -0
  10. data/bin/assembly_visualiser +106 -0
  11. data/bin/check_primer_combinations.rb +73 -0
  12. data/bin/contig_joiner.rb +244 -0
  13. data/bin/contigs_against_assembly.rb +153 -0
  14. data/bin/finishm +143 -0
  15. data/bin/finishm_assembler +55 -0
  16. data/bin/finishm_gap_closer.rb +241 -0
  17. data/bin/kmer_abundance_file_tool.rb +49 -0
  18. data/bin/kmer_pattern_to_assembly.rb +377 -0
  19. data/bin/kmer_profile_finder.rb +92 -0
  20. data/bin/kmers_count_parse.d +52 -0
  21. data/bin/kmers_count_tabulate.d +123 -0
  22. data/bin/kmers_count_tabulate.rb +84 -0
  23. data/bin/pcr_result_parser.rb +108 -0
  24. data/bin/primer_finder.rb +119 -0
  25. data/bin/read_selection_by_kmer.d +174 -0
  26. data/bin/scaffold_by_pattern.rb +119 -0
  27. data/bin/scaffold_connection_possibilities_to_knowns.rb +193 -0
  28. data/bin/scaffold_end_coverages.rb +69 -0
  29. data/bin/trail_validator.rb +84 -0
  30. data/ext/mkrf_conf.rb +56 -0
  31. data/ext/src/Makefile +140 -0
  32. data/ext/src/src/allocArray.c +305 -0
  33. data/ext/src/src/allocArray.h +86 -0
  34. data/ext/src/src/autoOpen.c +107 -0
  35. data/ext/src/src/autoOpen.h +18 -0
  36. data/ext/src/src/binarySequences.c +813 -0
  37. data/ext/src/src/binarySequences.h +125 -0
  38. data/ext/src/src/concatenatedGraph.c +233 -0
  39. data/ext/src/src/concatenatedGraph.h +30 -0
  40. data/ext/src/src/concatenatedPreGraph.c +262 -0
  41. data/ext/src/src/concatenatedPreGraph.h +29 -0
  42. data/ext/src/src/correctedGraph.c +2643 -0
  43. data/ext/src/src/correctedGraph.h +32 -0
  44. data/ext/src/src/dfib.c +509 -0
  45. data/ext/src/src/dfib.h +69 -0
  46. data/ext/src/src/dfibHeap.c +89 -0
  47. data/ext/src/src/dfibHeap.h +39 -0
  48. data/ext/src/src/dfibpriv.h +105 -0
  49. data/ext/src/src/fib.c +628 -0
  50. data/ext/src/src/fib.h +78 -0
  51. data/ext/src/src/fibHeap.c +79 -0
  52. data/ext/src/src/fibHeap.h +41 -0
  53. data/ext/src/src/fibpriv.h +110 -0
  54. data/ext/src/src/globals.h +154 -0
  55. data/ext/src/src/graph.c +3932 -0
  56. data/ext/src/src/graph.h +233 -0
  57. data/ext/src/src/graphReConstruction.c +1472 -0
  58. data/ext/src/src/graphReConstruction.h +30 -0
  59. data/ext/src/src/graphStats.c +2167 -0
  60. data/ext/src/src/graphStats.h +72 -0
  61. data/ext/src/src/graphStructures.h +52 -0
  62. data/ext/src/src/kmer.c +652 -0
  63. data/ext/src/src/kmer.h +73 -0
  64. data/ext/src/src/kmerOccurenceTable.c +236 -0
  65. data/ext/src/src/kmerOccurenceTable.h +44 -0
  66. data/ext/src/src/kseq.h +223 -0
  67. data/ext/src/src/locallyCorrectedGraph.c +557 -0
  68. data/ext/src/src/locallyCorrectedGraph.h +40 -0
  69. data/ext/src/src/passageMarker.c +677 -0
  70. data/ext/src/src/passageMarker.h +137 -0
  71. data/ext/src/src/preGraph.c +1717 -0
  72. data/ext/src/src/preGraph.h +106 -0
  73. data/ext/src/src/preGraphConstruction.c +990 -0
  74. data/ext/src/src/preGraphConstruction.h +26 -0
  75. data/ext/src/src/probe_node_finder.c +84 -0
  76. data/ext/src/src/probe_node_finder.h +6 -0
  77. data/ext/src/src/readCoherentGraph.c +557 -0
  78. data/ext/src/src/readCoherentGraph.h +30 -0
  79. data/ext/src/src/readSet.c +1734 -0
  80. data/ext/src/src/readSet.h +67 -0
  81. data/ext/src/src/readToNode.c +218 -0
  82. data/ext/src/src/readToNode.h +35 -0
  83. data/ext/src/src/recycleBin.c +199 -0
  84. data/ext/src/src/recycleBin.h +58 -0
  85. data/ext/src/src/roadMap.c +342 -0
  86. data/ext/src/src/roadMap.h +65 -0
  87. data/ext/src/src/run.c +318 -0
  88. data/ext/src/src/run.h +52 -0
  89. data/ext/src/src/run2.c +744 -0
  90. data/ext/src/src/runReadToNode.c +29 -0
  91. data/ext/src/src/scaffold.c +1876 -0
  92. data/ext/src/src/scaffold.h +64 -0
  93. data/ext/src/src/shortReadPairs.c +1243 -0
  94. data/ext/src/src/shortReadPairs.h +32 -0
  95. data/ext/src/src/splay.c +259 -0
  96. data/ext/src/src/splay.h +43 -0
  97. data/ext/src/src/splayTable.c +1315 -0
  98. data/ext/src/src/splayTable.h +31 -0
  99. data/ext/src/src/tightString.c +362 -0
  100. data/ext/src/src/tightString.h +82 -0
  101. data/ext/src/src/utility.c +199 -0
  102. data/ext/src/src/utility.h +98 -0
  103. data/ext/src/third-party/zlib-1.2.3/ChangeLog +855 -0
  104. data/ext/src/third-party/zlib-1.2.3/FAQ +339 -0
  105. data/ext/src/third-party/zlib-1.2.3/INDEX +51 -0
  106. data/ext/src/third-party/zlib-1.2.3/Makefile +154 -0
  107. data/ext/src/third-party/zlib-1.2.3/Makefile.in +154 -0
  108. data/ext/src/third-party/zlib-1.2.3/README +125 -0
  109. data/ext/src/third-party/zlib-1.2.3/adler32.c +149 -0
  110. data/ext/src/third-party/zlib-1.2.3/adler32.o +0 -0
  111. data/ext/src/third-party/zlib-1.2.3/algorithm.txt +209 -0
  112. data/ext/src/third-party/zlib-1.2.3/amiga/Makefile.pup +66 -0
  113. data/ext/src/third-party/zlib-1.2.3/amiga/Makefile.sas +65 -0
  114. data/ext/src/third-party/zlib-1.2.3/as400/bndsrc +132 -0
  115. data/ext/src/third-party/zlib-1.2.3/as400/compile.clp +123 -0
  116. data/ext/src/third-party/zlib-1.2.3/as400/readme.txt +111 -0
  117. data/ext/src/third-party/zlib-1.2.3/as400/zlib.inc +331 -0
  118. data/ext/src/third-party/zlib-1.2.3/compress.c +79 -0
  119. data/ext/src/third-party/zlib-1.2.3/compress.o +0 -0
  120. data/ext/src/third-party/zlib-1.2.3/configure +459 -0
  121. data/ext/src/third-party/zlib-1.2.3/contrib/README.contrib +71 -0
  122. data/ext/src/third-party/zlib-1.2.3/contrib/ada/buffer_demo.adb +106 -0
  123. data/ext/src/third-party/zlib-1.2.3/contrib/ada/mtest.adb +156 -0
  124. data/ext/src/third-party/zlib-1.2.3/contrib/ada/read.adb +156 -0
  125. data/ext/src/third-party/zlib-1.2.3/contrib/ada/readme.txt +65 -0
  126. data/ext/src/third-party/zlib-1.2.3/contrib/ada/test.adb +463 -0
  127. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-streams.adb +225 -0
  128. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-streams.ads +114 -0
  129. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-thin.adb +141 -0
  130. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-thin.ads +450 -0
  131. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib.adb +701 -0
  132. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib.ads +328 -0
  133. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib.gpr +20 -0
  134. data/ext/src/third-party/zlib-1.2.3/contrib/asm586/README.586 +43 -0
  135. data/ext/src/third-party/zlib-1.2.3/contrib/asm586/match.S +364 -0
  136. data/ext/src/third-party/zlib-1.2.3/contrib/asm686/README.686 +34 -0
  137. data/ext/src/third-party/zlib-1.2.3/contrib/asm686/match.S +329 -0
  138. data/ext/src/third-party/zlib-1.2.3/contrib/blast/Makefile +8 -0
  139. data/ext/src/third-party/zlib-1.2.3/contrib/blast/README +4 -0
  140. data/ext/src/third-party/zlib-1.2.3/contrib/blast/blast.c +444 -0
  141. data/ext/src/third-party/zlib-1.2.3/contrib/blast/blast.h +71 -0
  142. data/ext/src/third-party/zlib-1.2.3/contrib/blast/test.pk +0 -0
  143. data/ext/src/third-party/zlib-1.2.3/contrib/blast/test.txt +1 -0
  144. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/ZLib.pas +557 -0
  145. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/ZLibConst.pas +11 -0
  146. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/readme.txt +76 -0
  147. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/zlibd32.mak +93 -0
  148. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.build +33 -0
  149. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.chm +0 -0
  150. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.sln +21 -0
  151. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/AssemblyInfo.cs +58 -0
  152. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/ChecksumImpl.cs +202 -0
  153. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/CircularBuffer.cs +83 -0
  154. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/CodecBase.cs +198 -0
  155. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/Deflater.cs +106 -0
  156. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/DotZLib.cs +288 -0
  157. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/DotZLib.csproj +141 -0
  158. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/GZipStream.cs +301 -0
  159. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/Inflater.cs +105 -0
  160. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/UnitTests.cs +274 -0
  161. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/LICENSE_1_0.txt +23 -0
  162. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/readme.txt +58 -0
  163. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/README +1 -0
  164. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/infback9.c +608 -0
  165. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/infback9.h +37 -0
  166. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inffix9.h +107 -0
  167. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inflate9.h +47 -0
  168. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inftree9.c +323 -0
  169. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inftree9.h +55 -0
  170. data/ext/src/third-party/zlib-1.2.3/contrib/inflate86/inffas86.c +1157 -0
  171. data/ext/src/third-party/zlib-1.2.3/contrib/inflate86/inffast.S +1368 -0
  172. data/ext/src/third-party/zlib-1.2.3/contrib/iostream/test.cpp +24 -0
  173. data/ext/src/third-party/zlib-1.2.3/contrib/iostream/zfstream.cpp +329 -0
  174. data/ext/src/third-party/zlib-1.2.3/contrib/iostream/zfstream.h +128 -0
  175. data/ext/src/third-party/zlib-1.2.3/contrib/iostream2/zstream.h +307 -0
  176. data/ext/src/third-party/zlib-1.2.3/contrib/iostream2/zstream_test.cpp +25 -0
  177. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/README +35 -0
  178. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/TODO +17 -0
  179. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/test.cc +50 -0
  180. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/zfstream.cc +479 -0
  181. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/zfstream.h +466 -0
  182. data/ext/src/third-party/zlib-1.2.3/contrib/masm686/match.asm +413 -0
  183. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/bld_ml64.bat +2 -0
  184. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/gvmat64.asm +513 -0
  185. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/gvmat64.obj +0 -0
  186. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/inffas8664.c +186 -0
  187. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/inffasx64.asm +392 -0
  188. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/inffasx64.obj +0 -0
  189. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/readme.txt +28 -0
  190. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/bld_ml32.bat +2 -0
  191. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/gvmat32.asm +972 -0
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  193. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/gvmat32c.c +62 -0
  194. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/inffas32.asm +1083 -0
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  196. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/mkasm.bat +3 -0
  197. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/readme.txt +21 -0
  198. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/ChangeLogUnzip +67 -0
  199. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/Makefile +25 -0
  200. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/crypt.h +132 -0
  201. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/ioapi.c +177 -0
  202. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/ioapi.h +75 -0
  203. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/iowin32.c +270 -0
  204. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/iowin32.h +21 -0
  205. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/miniunz.c +585 -0
  206. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/minizip.c +420 -0
  207. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/mztools.c +281 -0
  208. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/mztools.h +31 -0
  209. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/unzip.c +1598 -0
  210. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/unzip.h +354 -0
  211. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/zip.c +1219 -0
  212. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/zip.h +235 -0
  213. data/ext/src/third-party/zlib-1.2.3/contrib/pascal/example.pas +599 -0
  214. data/ext/src/third-party/zlib-1.2.3/contrib/pascal/readme.txt +76 -0
  215. data/ext/src/third-party/zlib-1.2.3/contrib/pascal/zlibd32.mak +93 -0
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  217. data/ext/src/third-party/zlib-1.2.3/contrib/puff/Makefile +8 -0
  218. data/ext/src/third-party/zlib-1.2.3/contrib/puff/README +63 -0
  219. data/ext/src/third-party/zlib-1.2.3/contrib/puff/puff.c +837 -0
  220. data/ext/src/third-party/zlib-1.2.3/contrib/puff/puff.h +31 -0
  221. data/ext/src/third-party/zlib-1.2.3/contrib/puff/zeros.raw +0 -0
  222. data/ext/src/third-party/zlib-1.2.3/contrib/testzlib/testzlib.c +275 -0
  223. data/ext/src/third-party/zlib-1.2.3/contrib/testzlib/testzlib.txt +10 -0
  224. data/ext/src/third-party/zlib-1.2.3/contrib/untgz/Makefile +14 -0
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  226. data/ext/src/third-party/zlib-1.2.3/contrib/untgz/untgz.c +674 -0
  227. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/readme.txt +73 -0
  228. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/miniunz.vcproj +126 -0
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  245. data/ext/src/third-party/zlib-1.2.3/crc32.c +423 -0
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  248. data/ext/src/third-party/zlib-1.2.3/deflate.c +1736 -0
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  251. data/ext/src/third-party/zlib-1.2.3/example +0 -0
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  253. data/ext/src/third-party/zlib-1.2.3/examples/README.examples +42 -0
  254. data/ext/src/third-party/zlib-1.2.3/examples/fitblk.c +233 -0
  255. data/ext/src/third-party/zlib-1.2.3/examples/gun.c +693 -0
  256. data/ext/src/third-party/zlib-1.2.3/examples/gzappend.c +500 -0
  257. data/ext/src/third-party/zlib-1.2.3/examples/gzjoin.c +448 -0
  258. data/ext/src/third-party/zlib-1.2.3/examples/gzlog.c +413 -0
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@@ -0,0 +1,37 @@
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+ /* infback9.h -- header for using inflateBack9 functions
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+ * Copyright (C) 2003 Mark Adler
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+ * For conditions of distribution and use, see copyright notice in zlib.h
4
+ */
5
+
6
+ /*
7
+ * This header file and associated patches provide a decoder for PKWare's
8
+ * undocumented deflate64 compression method (method 9). Use with infback9.c,
9
+ * inftree9.h, inftree9.c, and inffix9.h. These patches are not supported.
10
+ * This should be compiled with zlib, since it uses zutil.h and zutil.o.
11
+ * This code has not yet been tested on 16-bit architectures. See the
12
+ * comments in zlib.h for inflateBack() usage. These functions are used
13
+ * identically, except that there is no windowBits parameter, and a 64K
14
+ * window must be provided. Also if int's are 16 bits, then a zero for
15
+ * the third parameter of the "out" function actually means 65536UL.
16
+ * zlib.h must be included before this header file.
17
+ */
18
+
19
+ #ifdef __cplusplus
20
+ extern "C" {
21
+ #endif
22
+
23
+ ZEXTERN int ZEXPORT inflateBack9 OF((z_stream FAR *strm,
24
+ in_func in, void FAR *in_desc,
25
+ out_func out, void FAR *out_desc));
26
+ ZEXTERN int ZEXPORT inflateBack9End OF((z_stream FAR *strm));
27
+ ZEXTERN int ZEXPORT inflateBack9Init_ OF((z_stream FAR *strm,
28
+ unsigned char FAR *window,
29
+ const char *version,
30
+ int stream_size));
31
+ #define inflateBack9Init(strm, window) \
32
+ inflateBack9Init_((strm), (window), \
33
+ ZLIB_VERSION, sizeof(z_stream))
34
+
35
+ #ifdef __cplusplus
36
+ }
37
+ #endif
@@ -0,0 +1,107 @@
1
+ /* inffix9.h -- table for decoding deflate64 fixed codes
2
+ * Generated automatically by makefixed9().
3
+ */
4
+
5
+ /* WARNING: this file should *not* be used by applications.
6
+ It is part of the implementation of this library and is
7
+ subject to change. Applications should only use zlib.h.
8
+ */
9
+
10
+ static const code lenfix[512] = {
11
+ {96,7,0},{0,8,80},{0,8,16},{132,8,115},{130,7,31},{0,8,112},
12
+ {0,8,48},{0,9,192},{128,7,10},{0,8,96},{0,8,32},{0,9,160},
13
+ {0,8,0},{0,8,128},{0,8,64},{0,9,224},{128,7,6},{0,8,88},
14
+ {0,8,24},{0,9,144},{131,7,59},{0,8,120},{0,8,56},{0,9,208},
15
+ {129,7,17},{0,8,104},{0,8,40},{0,9,176},{0,8,8},{0,8,136},
16
+ {0,8,72},{0,9,240},{128,7,4},{0,8,84},{0,8,20},{133,8,227},
17
+ {131,7,43},{0,8,116},{0,8,52},{0,9,200},{129,7,13},{0,8,100},
18
+ {0,8,36},{0,9,168},{0,8,4},{0,8,132},{0,8,68},{0,9,232},
19
+ {128,7,8},{0,8,92},{0,8,28},{0,9,152},{132,7,83},{0,8,124},
20
+ {0,8,60},{0,9,216},{130,7,23},{0,8,108},{0,8,44},{0,9,184},
21
+ {0,8,12},{0,8,140},{0,8,76},{0,9,248},{128,7,3},{0,8,82},
22
+ {0,8,18},{133,8,163},{131,7,35},{0,8,114},{0,8,50},{0,9,196},
23
+ {129,7,11},{0,8,98},{0,8,34},{0,9,164},{0,8,2},{0,8,130},
24
+ {0,8,66},{0,9,228},{128,7,7},{0,8,90},{0,8,26},{0,9,148},
25
+ {132,7,67},{0,8,122},{0,8,58},{0,9,212},{130,7,19},{0,8,106},
26
+ {0,8,42},{0,9,180},{0,8,10},{0,8,138},{0,8,74},{0,9,244},
27
+ {128,7,5},{0,8,86},{0,8,22},{65,8,0},{131,7,51},{0,8,118},
28
+ {0,8,54},{0,9,204},{129,7,15},{0,8,102},{0,8,38},{0,9,172},
29
+ {0,8,6},{0,8,134},{0,8,70},{0,9,236},{128,7,9},{0,8,94},
30
+ {0,8,30},{0,9,156},{132,7,99},{0,8,126},{0,8,62},{0,9,220},
31
+ {130,7,27},{0,8,110},{0,8,46},{0,9,188},{0,8,14},{0,8,142},
32
+ {0,8,78},{0,9,252},{96,7,0},{0,8,81},{0,8,17},{133,8,131},
33
+ {130,7,31},{0,8,113},{0,8,49},{0,9,194},{128,7,10},{0,8,97},
34
+ {0,8,33},{0,9,162},{0,8,1},{0,8,129},{0,8,65},{0,9,226},
35
+ {128,7,6},{0,8,89},{0,8,25},{0,9,146},{131,7,59},{0,8,121},
36
+ {0,8,57},{0,9,210},{129,7,17},{0,8,105},{0,8,41},{0,9,178},
37
+ {0,8,9},{0,8,137},{0,8,73},{0,9,242},{128,7,4},{0,8,85},
38
+ {0,8,21},{144,8,3},{131,7,43},{0,8,117},{0,8,53},{0,9,202},
39
+ {129,7,13},{0,8,101},{0,8,37},{0,9,170},{0,8,5},{0,8,133},
40
+ {0,8,69},{0,9,234},{128,7,8},{0,8,93},{0,8,29},{0,9,154},
41
+ {132,7,83},{0,8,125},{0,8,61},{0,9,218},{130,7,23},{0,8,109},
42
+ {0,8,45},{0,9,186},{0,8,13},{0,8,141},{0,8,77},{0,9,250},
43
+ {128,7,3},{0,8,83},{0,8,19},{133,8,195},{131,7,35},{0,8,115},
44
+ {0,8,51},{0,9,198},{129,7,11},{0,8,99},{0,8,35},{0,9,166},
45
+ {0,8,3},{0,8,131},{0,8,67},{0,9,230},{128,7,7},{0,8,91},
46
+ {0,8,27},{0,9,150},{132,7,67},{0,8,123},{0,8,59},{0,9,214},
47
+ {130,7,19},{0,8,107},{0,8,43},{0,9,182},{0,8,11},{0,8,139},
48
+ {0,8,75},{0,9,246},{128,7,5},{0,8,87},{0,8,23},{77,8,0},
49
+ {131,7,51},{0,8,119},{0,8,55},{0,9,206},{129,7,15},{0,8,103},
50
+ {0,8,39},{0,9,174},{0,8,7},{0,8,135},{0,8,71},{0,9,238},
51
+ {128,7,9},{0,8,95},{0,8,31},{0,9,158},{132,7,99},{0,8,127},
52
+ {0,8,63},{0,9,222},{130,7,27},{0,8,111},{0,8,47},{0,9,190},
53
+ {0,8,15},{0,8,143},{0,8,79},{0,9,254},{96,7,0},{0,8,80},
54
+ {0,8,16},{132,8,115},{130,7,31},{0,8,112},{0,8,48},{0,9,193},
55
+ {128,7,10},{0,8,96},{0,8,32},{0,9,161},{0,8,0},{0,8,128},
56
+ {0,8,64},{0,9,225},{128,7,6},{0,8,88},{0,8,24},{0,9,145},
57
+ {131,7,59},{0,8,120},{0,8,56},{0,9,209},{129,7,17},{0,8,104},
58
+ {0,8,40},{0,9,177},{0,8,8},{0,8,136},{0,8,72},{0,9,241},
59
+ {128,7,4},{0,8,84},{0,8,20},{133,8,227},{131,7,43},{0,8,116},
60
+ {0,8,52},{0,9,201},{129,7,13},{0,8,100},{0,8,36},{0,9,169},
61
+ {0,8,4},{0,8,132},{0,8,68},{0,9,233},{128,7,8},{0,8,92},
62
+ {0,8,28},{0,9,153},{132,7,83},{0,8,124},{0,8,60},{0,9,217},
63
+ {130,7,23},{0,8,108},{0,8,44},{0,9,185},{0,8,12},{0,8,140},
64
+ {0,8,76},{0,9,249},{128,7,3},{0,8,82},{0,8,18},{133,8,163},
65
+ {131,7,35},{0,8,114},{0,8,50},{0,9,197},{129,7,11},{0,8,98},
66
+ {0,8,34},{0,9,165},{0,8,2},{0,8,130},{0,8,66},{0,9,229},
67
+ {128,7,7},{0,8,90},{0,8,26},{0,9,149},{132,7,67},{0,8,122},
68
+ {0,8,58},{0,9,213},{130,7,19},{0,8,106},{0,8,42},{0,9,181},
69
+ {0,8,10},{0,8,138},{0,8,74},{0,9,245},{128,7,5},{0,8,86},
70
+ {0,8,22},{65,8,0},{131,7,51},{0,8,118},{0,8,54},{0,9,205},
71
+ {129,7,15},{0,8,102},{0,8,38},{0,9,173},{0,8,6},{0,8,134},
72
+ {0,8,70},{0,9,237},{128,7,9},{0,8,94},{0,8,30},{0,9,157},
73
+ {132,7,99},{0,8,126},{0,8,62},{0,9,221},{130,7,27},{0,8,110},
74
+ {0,8,46},{0,9,189},{0,8,14},{0,8,142},{0,8,78},{0,9,253},
75
+ {96,7,0},{0,8,81},{0,8,17},{133,8,131},{130,7,31},{0,8,113},
76
+ {0,8,49},{0,9,195},{128,7,10},{0,8,97},{0,8,33},{0,9,163},
77
+ {0,8,1},{0,8,129},{0,8,65},{0,9,227},{128,7,6},{0,8,89},
78
+ {0,8,25},{0,9,147},{131,7,59},{0,8,121},{0,8,57},{0,9,211},
79
+ {129,7,17},{0,8,105},{0,8,41},{0,9,179},{0,8,9},{0,8,137},
80
+ {0,8,73},{0,9,243},{128,7,4},{0,8,85},{0,8,21},{144,8,3},
81
+ {131,7,43},{0,8,117},{0,8,53},{0,9,203},{129,7,13},{0,8,101},
82
+ {0,8,37},{0,9,171},{0,8,5},{0,8,133},{0,8,69},{0,9,235},
83
+ {128,7,8},{0,8,93},{0,8,29},{0,9,155},{132,7,83},{0,8,125},
84
+ {0,8,61},{0,9,219},{130,7,23},{0,8,109},{0,8,45},{0,9,187},
85
+ {0,8,13},{0,8,141},{0,8,77},{0,9,251},{128,7,3},{0,8,83},
86
+ {0,8,19},{133,8,195},{131,7,35},{0,8,115},{0,8,51},{0,9,199},
87
+ {129,7,11},{0,8,99},{0,8,35},{0,9,167},{0,8,3},{0,8,131},
88
+ {0,8,67},{0,9,231},{128,7,7},{0,8,91},{0,8,27},{0,9,151},
89
+ {132,7,67},{0,8,123},{0,8,59},{0,9,215},{130,7,19},{0,8,107},
90
+ {0,8,43},{0,9,183},{0,8,11},{0,8,139},{0,8,75},{0,9,247},
91
+ {128,7,5},{0,8,87},{0,8,23},{77,8,0},{131,7,51},{0,8,119},
92
+ {0,8,55},{0,9,207},{129,7,15},{0,8,103},{0,8,39},{0,9,175},
93
+ {0,8,7},{0,8,135},{0,8,71},{0,9,239},{128,7,9},{0,8,95},
94
+ {0,8,31},{0,9,159},{132,7,99},{0,8,127},{0,8,63},{0,9,223},
95
+ {130,7,27},{0,8,111},{0,8,47},{0,9,191},{0,8,15},{0,8,143},
96
+ {0,8,79},{0,9,255}
97
+ };
98
+
99
+ static const code distfix[32] = {
100
+ {128,5,1},{135,5,257},{131,5,17},{139,5,4097},{129,5,5},
101
+ {137,5,1025},{133,5,65},{141,5,16385},{128,5,3},{136,5,513},
102
+ {132,5,33},{140,5,8193},{130,5,9},{138,5,2049},{134,5,129},
103
+ {142,5,32769},{128,5,2},{135,5,385},{131,5,25},{139,5,6145},
104
+ {129,5,7},{137,5,1537},{133,5,97},{141,5,24577},{128,5,4},
105
+ {136,5,769},{132,5,49},{140,5,12289},{130,5,13},{138,5,3073},
106
+ {134,5,193},{142,5,49153}
107
+ };
@@ -0,0 +1,47 @@
1
+ /* inflate9.h -- internal inflate state definition
2
+ * Copyright (C) 1995-2003 Mark Adler
3
+ * For conditions of distribution and use, see copyright notice in zlib.h
4
+ */
5
+
6
+ /* WARNING: this file should *not* be used by applications. It is
7
+ part of the implementation of the compression library and is
8
+ subject to change. Applications should only use zlib.h.
9
+ */
10
+
11
+ /* Possible inflate modes between inflate() calls */
12
+ typedef enum {
13
+ TYPE, /* i: waiting for type bits, including last-flag bit */
14
+ STORED, /* i: waiting for stored size (length and complement) */
15
+ TABLE, /* i: waiting for dynamic block table lengths */
16
+ LEN, /* i: waiting for length/lit code */
17
+ DONE, /* finished check, done -- remain here until reset */
18
+ BAD /* got a data error -- remain here until reset */
19
+ } inflate_mode;
20
+
21
+ /*
22
+ State transitions between above modes -
23
+
24
+ (most modes can go to the BAD mode -- not shown for clarity)
25
+
26
+ Read deflate blocks:
27
+ TYPE -> STORED or TABLE or LEN or DONE
28
+ STORED -> TYPE
29
+ TABLE -> LENLENS -> CODELENS -> LEN
30
+ Read deflate codes:
31
+ LEN -> LEN or TYPE
32
+ */
33
+
34
+ /* state maintained between inflate() calls. Approximately 7K bytes. */
35
+ struct inflate_state {
36
+ /* sliding window */
37
+ unsigned char FAR *window; /* allocated sliding window, if needed */
38
+ /* dynamic table building */
39
+ unsigned ncode; /* number of code length code lengths */
40
+ unsigned nlen; /* number of length code lengths */
41
+ unsigned ndist; /* number of distance code lengths */
42
+ unsigned have; /* number of code lengths in lens[] */
43
+ code FAR *next; /* next available space in codes[] */
44
+ unsigned short lens[320]; /* temporary storage for code lengths */
45
+ unsigned short work[288]; /* work area for code table building */
46
+ code codes[ENOUGH]; /* space for code tables */
47
+ };
@@ -0,0 +1,323 @@
1
+ /* inftree9.c -- generate Huffman trees for efficient decoding
2
+ * Copyright (C) 1995-2005 Mark Adler
3
+ * For conditions of distribution and use, see copyright notice in zlib.h
4
+ */
5
+
6
+ #include "zutil.h"
7
+ #include "inftree9.h"
8
+
9
+ #define MAXBITS 15
10
+
11
+ const char inflate9_copyright[] =
12
+ " inflate9 1.2.3 Copyright 1995-2005 Mark Adler ";
13
+ /*
14
+ If you use the zlib library in a product, an acknowledgment is welcome
15
+ in the documentation of your product. If for some reason you cannot
16
+ include such an acknowledgment, I would appreciate that you keep this
17
+ copyright string in the executable of your product.
18
+ */
19
+
20
+ /*
21
+ Build a set of tables to decode the provided canonical Huffman code.
22
+ The code lengths are lens[0..codes-1]. The result starts at *table,
23
+ whose indices are 0..2^bits-1. work is a writable array of at least
24
+ lens shorts, which is used as a work area. type is the type of code
25
+ to be generated, CODES, LENS, or DISTS. On return, zero is success,
26
+ -1 is an invalid code, and +1 means that ENOUGH isn't enough. table
27
+ on return points to the next available entry's address. bits is the
28
+ requested root table index bits, and on return it is the actual root
29
+ table index bits. It will differ if the request is greater than the
30
+ longest code or if it is less than the shortest code.
31
+ */
32
+ int inflate_table9(type, lens, codes, table, bits, work)
33
+ codetype type;
34
+ unsigned short FAR *lens;
35
+ unsigned codes;
36
+ code FAR * FAR *table;
37
+ unsigned FAR *bits;
38
+ unsigned short FAR *work;
39
+ {
40
+ unsigned len; /* a code's length in bits */
41
+ unsigned sym; /* index of code symbols */
42
+ unsigned min, max; /* minimum and maximum code lengths */
43
+ unsigned root; /* number of index bits for root table */
44
+ unsigned curr; /* number of index bits for current table */
45
+ unsigned drop; /* code bits to drop for sub-table */
46
+ int left; /* number of prefix codes available */
47
+ unsigned used; /* code entries in table used */
48
+ unsigned huff; /* Huffman code */
49
+ unsigned incr; /* for incrementing code, index */
50
+ unsigned fill; /* index for replicating entries */
51
+ unsigned low; /* low bits for current root entry */
52
+ unsigned mask; /* mask for low root bits */
53
+ code this; /* table entry for duplication */
54
+ code FAR *next; /* next available space in table */
55
+ const unsigned short FAR *base; /* base value table to use */
56
+ const unsigned short FAR *extra; /* extra bits table to use */
57
+ int end; /* use base and extra for symbol > end */
58
+ unsigned short count[MAXBITS+1]; /* number of codes of each length */
59
+ unsigned short offs[MAXBITS+1]; /* offsets in table for each length */
60
+ static const unsigned short lbase[31] = { /* Length codes 257..285 base */
61
+ 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 15, 17,
62
+ 19, 23, 27, 31, 35, 43, 51, 59, 67, 83, 99, 115,
63
+ 131, 163, 195, 227, 3, 0, 0};
64
+ static const unsigned short lext[31] = { /* Length codes 257..285 extra */
65
+ 128, 128, 128, 128, 128, 128, 128, 128, 129, 129, 129, 129,
66
+ 130, 130, 130, 130, 131, 131, 131, 131, 132, 132, 132, 132,
67
+ 133, 133, 133, 133, 144, 201, 196};
68
+ static const unsigned short dbase[32] = { /* Distance codes 0..31 base */
69
+ 1, 2, 3, 4, 5, 7, 9, 13, 17, 25, 33, 49,
70
+ 65, 97, 129, 193, 257, 385, 513, 769, 1025, 1537, 2049, 3073,
71
+ 4097, 6145, 8193, 12289, 16385, 24577, 32769, 49153};
72
+ static const unsigned short dext[32] = { /* Distance codes 0..31 extra */
73
+ 128, 128, 128, 128, 129, 129, 130, 130, 131, 131, 132, 132,
74
+ 133, 133, 134, 134, 135, 135, 136, 136, 137, 137, 138, 138,
75
+ 139, 139, 140, 140, 141, 141, 142, 142};
76
+
77
+ /*
78
+ Process a set of code lengths to create a canonical Huffman code. The
79
+ code lengths are lens[0..codes-1]. Each length corresponds to the
80
+ symbols 0..codes-1. The Huffman code is generated by first sorting the
81
+ symbols by length from short to long, and retaining the symbol order
82
+ for codes with equal lengths. Then the code starts with all zero bits
83
+ for the first code of the shortest length, and the codes are integer
84
+ increments for the same length, and zeros are appended as the length
85
+ increases. For the deflate format, these bits are stored backwards
86
+ from their more natural integer increment ordering, and so when the
87
+ decoding tables are built in the large loop below, the integer codes
88
+ are incremented backwards.
89
+
90
+ This routine assumes, but does not check, that all of the entries in
91
+ lens[] are in the range 0..MAXBITS. The caller must assure this.
92
+ 1..MAXBITS is interpreted as that code length. zero means that that
93
+ symbol does not occur in this code.
94
+
95
+ The codes are sorted by computing a count of codes for each length,
96
+ creating from that a table of starting indices for each length in the
97
+ sorted table, and then entering the symbols in order in the sorted
98
+ table. The sorted table is work[], with that space being provided by
99
+ the caller.
100
+
101
+ The length counts are used for other purposes as well, i.e. finding
102
+ the minimum and maximum length codes, determining if there are any
103
+ codes at all, checking for a valid set of lengths, and looking ahead
104
+ at length counts to determine sub-table sizes when building the
105
+ decoding tables.
106
+ */
107
+
108
+ /* accumulate lengths for codes (assumes lens[] all in 0..MAXBITS) */
109
+ for (len = 0; len <= MAXBITS; len++)
110
+ count[len] = 0;
111
+ for (sym = 0; sym < codes; sym++)
112
+ count[lens[sym]]++;
113
+
114
+ /* bound code lengths, force root to be within code lengths */
115
+ root = *bits;
116
+ for (max = MAXBITS; max >= 1; max--)
117
+ if (count[max] != 0) break;
118
+ if (root > max) root = max;
119
+ if (max == 0) return -1; /* no codes! */
120
+ for (min = 1; min <= MAXBITS; min++)
121
+ if (count[min] != 0) break;
122
+ if (root < min) root = min;
123
+
124
+ /* check for an over-subscribed or incomplete set of lengths */
125
+ left = 1;
126
+ for (len = 1; len <= MAXBITS; len++) {
127
+ left <<= 1;
128
+ left -= count[len];
129
+ if (left < 0) return -1; /* over-subscribed */
130
+ }
131
+ if (left > 0 && (type == CODES || max != 1))
132
+ return -1; /* incomplete set */
133
+
134
+ /* generate offsets into symbol table for each length for sorting */
135
+ offs[1] = 0;
136
+ for (len = 1; len < MAXBITS; len++)
137
+ offs[len + 1] = offs[len] + count[len];
138
+
139
+ /* sort symbols by length, by symbol order within each length */
140
+ for (sym = 0; sym < codes; sym++)
141
+ if (lens[sym] != 0) work[offs[lens[sym]]++] = (unsigned short)sym;
142
+
143
+ /*
144
+ Create and fill in decoding tables. In this loop, the table being
145
+ filled is at next and has curr index bits. The code being used is huff
146
+ with length len. That code is converted to an index by dropping drop
147
+ bits off of the bottom. For codes where len is less than drop + curr,
148
+ those top drop + curr - len bits are incremented through all values to
149
+ fill the table with replicated entries.
150
+
151
+ root is the number of index bits for the root table. When len exceeds
152
+ root, sub-tables are created pointed to by the root entry with an index
153
+ of the low root bits of huff. This is saved in low to check for when a
154
+ new sub-table should be started. drop is zero when the root table is
155
+ being filled, and drop is root when sub-tables are being filled.
156
+
157
+ When a new sub-table is needed, it is necessary to look ahead in the
158
+ code lengths to determine what size sub-table is needed. The length
159
+ counts are used for this, and so count[] is decremented as codes are
160
+ entered in the tables.
161
+
162
+ used keeps track of how many table entries have been allocated from the
163
+ provided *table space. It is checked when a LENS table is being made
164
+ against the space in *table, ENOUGH, minus the maximum space needed by
165
+ the worst case distance code, MAXD. This should never happen, but the
166
+ sufficiency of ENOUGH has not been proven exhaustively, hence the check.
167
+ This assumes that when type == LENS, bits == 9.
168
+
169
+ sym increments through all symbols, and the loop terminates when
170
+ all codes of length max, i.e. all codes, have been processed. This
171
+ routine permits incomplete codes, so another loop after this one fills
172
+ in the rest of the decoding tables with invalid code markers.
173
+ */
174
+
175
+ /* set up for code type */
176
+ switch (type) {
177
+ case CODES:
178
+ base = extra = work; /* dummy value--not used */
179
+ end = 19;
180
+ break;
181
+ case LENS:
182
+ base = lbase;
183
+ base -= 257;
184
+ extra = lext;
185
+ extra -= 257;
186
+ end = 256;
187
+ break;
188
+ default: /* DISTS */
189
+ base = dbase;
190
+ extra = dext;
191
+ end = -1;
192
+ }
193
+
194
+ /* initialize state for loop */
195
+ huff = 0; /* starting code */
196
+ sym = 0; /* starting code symbol */
197
+ len = min; /* starting code length */
198
+ next = *table; /* current table to fill in */
199
+ curr = root; /* current table index bits */
200
+ drop = 0; /* current bits to drop from code for index */
201
+ low = (unsigned)(-1); /* trigger new sub-table when len > root */
202
+ used = 1U << root; /* use root table entries */
203
+ mask = used - 1; /* mask for comparing low */
204
+
205
+ /* check available table space */
206
+ if (type == LENS && used >= ENOUGH - MAXD)
207
+ return 1;
208
+
209
+ /* process all codes and make table entries */
210
+ for (;;) {
211
+ /* create table entry */
212
+ this.bits = (unsigned char)(len - drop);
213
+ if ((int)(work[sym]) < end) {
214
+ this.op = (unsigned char)0;
215
+ this.val = work[sym];
216
+ }
217
+ else if ((int)(work[sym]) > end) {
218
+ this.op = (unsigned char)(extra[work[sym]]);
219
+ this.val = base[work[sym]];
220
+ }
221
+ else {
222
+ this.op = (unsigned char)(32 + 64); /* end of block */
223
+ this.val = 0;
224
+ }
225
+
226
+ /* replicate for those indices with low len bits equal to huff */
227
+ incr = 1U << (len - drop);
228
+ fill = 1U << curr;
229
+ do {
230
+ fill -= incr;
231
+ next[(huff >> drop) + fill] = this;
232
+ } while (fill != 0);
233
+
234
+ /* backwards increment the len-bit code huff */
235
+ incr = 1U << (len - 1);
236
+ while (huff & incr)
237
+ incr >>= 1;
238
+ if (incr != 0) {
239
+ huff &= incr - 1;
240
+ huff += incr;
241
+ }
242
+ else
243
+ huff = 0;
244
+
245
+ /* go to next symbol, update count, len */
246
+ sym++;
247
+ if (--(count[len]) == 0) {
248
+ if (len == max) break;
249
+ len = lens[work[sym]];
250
+ }
251
+
252
+ /* create new sub-table if needed */
253
+ if (len > root && (huff & mask) != low) {
254
+ /* if first time, transition to sub-tables */
255
+ if (drop == 0)
256
+ drop = root;
257
+
258
+ /* increment past last table */
259
+ next += 1U << curr;
260
+
261
+ /* determine length of next table */
262
+ curr = len - drop;
263
+ left = (int)(1 << curr);
264
+ while (curr + drop < max) {
265
+ left -= count[curr + drop];
266
+ if (left <= 0) break;
267
+ curr++;
268
+ left <<= 1;
269
+ }
270
+
271
+ /* check for enough space */
272
+ used += 1U << curr;
273
+ if (type == LENS && used >= ENOUGH - MAXD)
274
+ return 1;
275
+
276
+ /* point entry in root table to sub-table */
277
+ low = huff & mask;
278
+ (*table)[low].op = (unsigned char)curr;
279
+ (*table)[low].bits = (unsigned char)root;
280
+ (*table)[low].val = (unsigned short)(next - *table);
281
+ }
282
+ }
283
+
284
+ /*
285
+ Fill in rest of table for incomplete codes. This loop is similar to the
286
+ loop above in incrementing huff for table indices. It is assumed that
287
+ len is equal to curr + drop, so there is no loop needed to increment
288
+ through high index bits. When the current sub-table is filled, the loop
289
+ drops back to the root table to fill in any remaining entries there.
290
+ */
291
+ this.op = (unsigned char)64; /* invalid code marker */
292
+ this.bits = (unsigned char)(len - drop);
293
+ this.val = (unsigned short)0;
294
+ while (huff != 0) {
295
+ /* when done with sub-table, drop back to root table */
296
+ if (drop != 0 && (huff & mask) != low) {
297
+ drop = 0;
298
+ len = root;
299
+ next = *table;
300
+ curr = root;
301
+ this.bits = (unsigned char)len;
302
+ }
303
+
304
+ /* put invalid code marker in table */
305
+ next[huff >> drop] = this;
306
+
307
+ /* backwards increment the len-bit code huff */
308
+ incr = 1U << (len - 1);
309
+ while (huff & incr)
310
+ incr >>= 1;
311
+ if (incr != 0) {
312
+ huff &= incr - 1;
313
+ huff += incr;
314
+ }
315
+ else
316
+ huff = 0;
317
+ }
318
+
319
+ /* set return parameters */
320
+ *table += used;
321
+ *bits = root;
322
+ return 0;
323
+ }