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
  192. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/gvmat32.obj +0 -0
  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
  195. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/inffas32.obj +0 -0
  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
  216. data/ext/src/third-party/zlib-1.2.3/contrib/pascal/zlibpas.pas +236 -0
  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
  225. data/ext/src/third-party/zlib-1.2.3/contrib/untgz/Makefile.msc +17 -0
  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
  229. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/minizip.vcproj +126 -0
  230. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/testzlib.vcproj +126 -0
  231. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlib.rc +32 -0
  232. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlibstat.vcproj +246 -0
  233. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlibvc.def +92 -0
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  236. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/miniunz.vcproj +566 -0
  237. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/minizip.vcproj +563 -0
  238. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/testzlib.vcproj +948 -0
  239. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/testzlibdll.vcproj +567 -0
  240. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlib.rc +32 -0
  241. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlibstat.vcproj +870 -0
  242. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlibvc.def +92 -0
  243. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlibvc.sln +144 -0
  244. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlibvc.vcproj +1219 -0
  245. data/ext/src/third-party/zlib-1.2.3/crc32.c +423 -0
  246. data/ext/src/third-party/zlib-1.2.3/crc32.h +441 -0
  247. data/ext/src/third-party/zlib-1.2.3/crc32.o +0 -0
  248. data/ext/src/third-party/zlib-1.2.3/deflate.c +1736 -0
  249. data/ext/src/third-party/zlib-1.2.3/deflate.h +331 -0
  250. data/ext/src/third-party/zlib-1.2.3/deflate.o +0 -0
  251. data/ext/src/third-party/zlib-1.2.3/example +0 -0
  252. data/ext/src/third-party/zlib-1.2.3/example.c +565 -0
  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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  550. data/spec/wander_spec.rb +119 -0
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@@ -0,0 +1,71 @@
1
+ /* blast.h -- interface for blast.c
2
+ Copyright (C) 2003 Mark Adler
3
+ version 1.1, 16 Feb 2003
4
+
5
+ This software is provided 'as-is', without any express or implied
6
+ warranty. In no event will the author be held liable for any damages
7
+ arising from the use of this software.
8
+
9
+ Permission is granted to anyone to use this software for any purpose,
10
+ including commercial applications, and to alter it and redistribute it
11
+ freely, subject to the following restrictions:
12
+
13
+ 1. The origin of this software must not be misrepresented; you must not
14
+ claim that you wrote the original software. If you use this software
15
+ in a product, an acknowledgment in the product documentation would be
16
+ appreciated but is not required.
17
+ 2. Altered source versions must be plainly marked as such, and must not be
18
+ misrepresented as being the original software.
19
+ 3. This notice may not be removed or altered from any source distribution.
20
+
21
+ Mark Adler madler@alumni.caltech.edu
22
+ */
23
+
24
+
25
+ /*
26
+ * blast() decompresses the PKWare Data Compression Library (DCL) compressed
27
+ * format. It provides the same functionality as the explode() function in
28
+ * that library. (Note: PKWare overused the "implode" verb, and the format
29
+ * used by their library implode() function is completely different and
30
+ * incompatible with the implode compression method supported by PKZIP.)
31
+ */
32
+
33
+
34
+ typedef unsigned (*blast_in)(void *how, unsigned char **buf);
35
+ typedef int (*blast_out)(void *how, unsigned char *buf, unsigned len);
36
+ /* Definitions for input/output functions passed to blast(). See below for
37
+ * what the provided functions need to do.
38
+ */
39
+
40
+
41
+ int blast(blast_in infun, void *inhow, blast_out outfun, void *outhow);
42
+ /* Decompress input to output using the provided infun() and outfun() calls.
43
+ * On success, the return value of blast() is zero. If there is an error in
44
+ * the source data, i.e. it is not in the proper format, then a negative value
45
+ * is returned. If there is not enough input available or there is not enough
46
+ * output space, then a positive error is returned.
47
+ *
48
+ * The input function is invoked: len = infun(how, &buf), where buf is set by
49
+ * infun() to point to the input buffer, and infun() returns the number of
50
+ * available bytes there. If infun() returns zero, then blast() returns with
51
+ * an input error. (blast() only asks for input if it needs it.) inhow is for
52
+ * use by the application to pass an input descriptor to infun(), if desired.
53
+ *
54
+ * The output function is invoked: err = outfun(how, buf, len), where the bytes
55
+ * to be written are buf[0..len-1]. If err is not zero, then blast() returns
56
+ * with an output error. outfun() is always called with len <= 4096. outhow
57
+ * is for use by the application to pass an output descriptor to outfun(), if
58
+ * desired.
59
+ *
60
+ * The return codes are:
61
+ *
62
+ * 2: ran out of input before completing decompression
63
+ * 1: output error before completing decompression
64
+ * 0: successful decompression
65
+ * -1: literal flag not zero or one
66
+ * -2: dictionary size not in 4..6
67
+ * -3: distance is too far back
68
+ *
69
+ * At the bottom of blast.c is an example program that uses blast() that can be
70
+ * compiled to produce a command-line decompression filter by defining TEST.
71
+ */
@@ -0,0 +1,557 @@
1
+ {*******************************************************}
2
+ { }
3
+ { Borland Delphi Supplemental Components }
4
+ { ZLIB Data Compression Interface Unit }
5
+ { }
6
+ { Copyright (c) 1997,99 Borland Corporation }
7
+ { }
8
+ {*******************************************************}
9
+
10
+ { Updated for zlib 1.2.x by Cosmin Truta <cosmint@cs.ubbcluj.ro> }
11
+
12
+ unit ZLib;
13
+
14
+ interface
15
+
16
+ uses SysUtils, Classes;
17
+
18
+ type
19
+ TAlloc = function (AppData: Pointer; Items, Size: Integer): Pointer; cdecl;
20
+ TFree = procedure (AppData, Block: Pointer); cdecl;
21
+
22
+ // Internal structure. Ignore.
23
+ TZStreamRec = packed record
24
+ next_in: PChar; // next input byte
25
+ avail_in: Integer; // number of bytes available at next_in
26
+ total_in: Longint; // total nb of input bytes read so far
27
+
28
+ next_out: PChar; // next output byte should be put here
29
+ avail_out: Integer; // remaining free space at next_out
30
+ total_out: Longint; // total nb of bytes output so far
31
+
32
+ msg: PChar; // last error message, NULL if no error
33
+ internal: Pointer; // not visible by applications
34
+
35
+ zalloc: TAlloc; // used to allocate the internal state
36
+ zfree: TFree; // used to free the internal state
37
+ AppData: Pointer; // private data object passed to zalloc and zfree
38
+
39
+ data_type: Integer; // best guess about the data type: ascii or binary
40
+ adler: Longint; // adler32 value of the uncompressed data
41
+ reserved: Longint; // reserved for future use
42
+ end;
43
+
44
+ // Abstract ancestor class
45
+ TCustomZlibStream = class(TStream)
46
+ private
47
+ FStrm: TStream;
48
+ FStrmPos: Integer;
49
+ FOnProgress: TNotifyEvent;
50
+ FZRec: TZStreamRec;
51
+ FBuffer: array [Word] of Char;
52
+ protected
53
+ procedure Progress(Sender: TObject); dynamic;
54
+ property OnProgress: TNotifyEvent read FOnProgress write FOnProgress;
55
+ constructor Create(Strm: TStream);
56
+ end;
57
+
58
+ { TCompressionStream compresses data on the fly as data is written to it, and
59
+ stores the compressed data to another stream.
60
+
61
+ TCompressionStream is write-only and strictly sequential. Reading from the
62
+ stream will raise an exception. Using Seek to move the stream pointer
63
+ will raise an exception.
64
+
65
+ Output data is cached internally, written to the output stream only when
66
+ the internal output buffer is full. All pending output data is flushed
67
+ when the stream is destroyed.
68
+
69
+ The Position property returns the number of uncompressed bytes of
70
+ data that have been written to the stream so far.
71
+
72
+ CompressionRate returns the on-the-fly percentage by which the original
73
+ data has been compressed: (1 - (CompressedBytes / UncompressedBytes)) * 100
74
+ If raw data size = 100 and compressed data size = 25, the CompressionRate
75
+ is 75%
76
+
77
+ The OnProgress event is called each time the output buffer is filled and
78
+ written to the output stream. This is useful for updating a progress
79
+ indicator when you are writing a large chunk of data to the compression
80
+ stream in a single call.}
81
+
82
+
83
+ TCompressionLevel = (clNone, clFastest, clDefault, clMax);
84
+
85
+ TCompressionStream = class(TCustomZlibStream)
86
+ private
87
+ function GetCompressionRate: Single;
88
+ public
89
+ constructor Create(CompressionLevel: TCompressionLevel; Dest: TStream);
90
+ destructor Destroy; override;
91
+ function Read(var Buffer; Count: Longint): Longint; override;
92
+ function Write(const Buffer; Count: Longint): Longint; override;
93
+ function Seek(Offset: Longint; Origin: Word): Longint; override;
94
+ property CompressionRate: Single read GetCompressionRate;
95
+ property OnProgress;
96
+ end;
97
+
98
+ { TDecompressionStream decompresses data on the fly as data is read from it.
99
+
100
+ Compressed data comes from a separate source stream. TDecompressionStream
101
+ is read-only and unidirectional; you can seek forward in the stream, but not
102
+ backwards. The special case of setting the stream position to zero is
103
+ allowed. Seeking forward decompresses data until the requested position in
104
+ the uncompressed data has been reached. Seeking backwards, seeking relative
105
+ to the end of the stream, requesting the size of the stream, and writing to
106
+ the stream will raise an exception.
107
+
108
+ The Position property returns the number of bytes of uncompressed data that
109
+ have been read from the stream so far.
110
+
111
+ The OnProgress event is called each time the internal input buffer of
112
+ compressed data is exhausted and the next block is read from the input stream.
113
+ This is useful for updating a progress indicator when you are reading a
114
+ large chunk of data from the decompression stream in a single call.}
115
+
116
+ TDecompressionStream = class(TCustomZlibStream)
117
+ public
118
+ constructor Create(Source: TStream);
119
+ destructor Destroy; override;
120
+ function Read(var Buffer; Count: Longint): Longint; override;
121
+ function Write(const Buffer; Count: Longint): Longint; override;
122
+ function Seek(Offset: Longint; Origin: Word): Longint; override;
123
+ property OnProgress;
124
+ end;
125
+
126
+
127
+
128
+ { CompressBuf compresses data, buffer to buffer, in one call.
129
+ In: InBuf = ptr to compressed data
130
+ InBytes = number of bytes in InBuf
131
+ Out: OutBuf = ptr to newly allocated buffer containing decompressed data
132
+ OutBytes = number of bytes in OutBuf }
133
+ procedure CompressBuf(const InBuf: Pointer; InBytes: Integer;
134
+ out OutBuf: Pointer; out OutBytes: Integer);
135
+
136
+
137
+ { DecompressBuf decompresses data, buffer to buffer, in one call.
138
+ In: InBuf = ptr to compressed data
139
+ InBytes = number of bytes in InBuf
140
+ OutEstimate = zero, or est. size of the decompressed data
141
+ Out: OutBuf = ptr to newly allocated buffer containing decompressed data
142
+ OutBytes = number of bytes in OutBuf }
143
+ procedure DecompressBuf(const InBuf: Pointer; InBytes: Integer;
144
+ OutEstimate: Integer; out OutBuf: Pointer; out OutBytes: Integer);
145
+
146
+ { DecompressToUserBuf decompresses data, buffer to buffer, in one call.
147
+ In: InBuf = ptr to compressed data
148
+ InBytes = number of bytes in InBuf
149
+ Out: OutBuf = ptr to user-allocated buffer to contain decompressed data
150
+ BufSize = number of bytes in OutBuf }
151
+ procedure DecompressToUserBuf(const InBuf: Pointer; InBytes: Integer;
152
+ const OutBuf: Pointer; BufSize: Integer);
153
+
154
+ const
155
+ zlib_version = '1.2.3';
156
+
157
+ type
158
+ EZlibError = class(Exception);
159
+ ECompressionError = class(EZlibError);
160
+ EDecompressionError = class(EZlibError);
161
+
162
+ implementation
163
+
164
+ uses ZLibConst;
165
+
166
+ const
167
+ Z_NO_FLUSH = 0;
168
+ Z_PARTIAL_FLUSH = 1;
169
+ Z_SYNC_FLUSH = 2;
170
+ Z_FULL_FLUSH = 3;
171
+ Z_FINISH = 4;
172
+
173
+ Z_OK = 0;
174
+ Z_STREAM_END = 1;
175
+ Z_NEED_DICT = 2;
176
+ Z_ERRNO = (-1);
177
+ Z_STREAM_ERROR = (-2);
178
+ Z_DATA_ERROR = (-3);
179
+ Z_MEM_ERROR = (-4);
180
+ Z_BUF_ERROR = (-5);
181
+ Z_VERSION_ERROR = (-6);
182
+
183
+ Z_NO_COMPRESSION = 0;
184
+ Z_BEST_SPEED = 1;
185
+ Z_BEST_COMPRESSION = 9;
186
+ Z_DEFAULT_COMPRESSION = (-1);
187
+
188
+ Z_FILTERED = 1;
189
+ Z_HUFFMAN_ONLY = 2;
190
+ Z_RLE = 3;
191
+ Z_DEFAULT_STRATEGY = 0;
192
+
193
+ Z_BINARY = 0;
194
+ Z_ASCII = 1;
195
+ Z_UNKNOWN = 2;
196
+
197
+ Z_DEFLATED = 8;
198
+
199
+
200
+ {$L adler32.obj}
201
+ {$L compress.obj}
202
+ {$L crc32.obj}
203
+ {$L deflate.obj}
204
+ {$L infback.obj}
205
+ {$L inffast.obj}
206
+ {$L inflate.obj}
207
+ {$L inftrees.obj}
208
+ {$L trees.obj}
209
+ {$L uncompr.obj}
210
+ {$L zutil.obj}
211
+
212
+ procedure adler32; external;
213
+ procedure compressBound; external;
214
+ procedure crc32; external;
215
+ procedure deflateInit2_; external;
216
+ procedure deflateParams; external;
217
+
218
+ function _malloc(Size: Integer): Pointer; cdecl;
219
+ begin
220
+ Result := AllocMem(Size);
221
+ end;
222
+
223
+ procedure _free(Block: Pointer); cdecl;
224
+ begin
225
+ FreeMem(Block);
226
+ end;
227
+
228
+ procedure _memset(P: Pointer; B: Byte; count: Integer); cdecl;
229
+ begin
230
+ FillChar(P^, count, B);
231
+ end;
232
+
233
+ procedure _memcpy(dest, source: Pointer; count: Integer); cdecl;
234
+ begin
235
+ Move(source^, dest^, count);
236
+ end;
237
+
238
+
239
+
240
+ // deflate compresses data
241
+ function deflateInit_(var strm: TZStreamRec; level: Integer; version: PChar;
242
+ recsize: Integer): Integer; external;
243
+ function deflate(var strm: TZStreamRec; flush: Integer): Integer; external;
244
+ function deflateEnd(var strm: TZStreamRec): Integer; external;
245
+
246
+ // inflate decompresses data
247
+ function inflateInit_(var strm: TZStreamRec; version: PChar;
248
+ recsize: Integer): Integer; external;
249
+ function inflate(var strm: TZStreamRec; flush: Integer): Integer; external;
250
+ function inflateEnd(var strm: TZStreamRec): Integer; external;
251
+ function inflateReset(var strm: TZStreamRec): Integer; external;
252
+
253
+
254
+ function zlibAllocMem(AppData: Pointer; Items, Size: Integer): Pointer; cdecl;
255
+ begin
256
+ // GetMem(Result, Items*Size);
257
+ Result := AllocMem(Items * Size);
258
+ end;
259
+
260
+ procedure zlibFreeMem(AppData, Block: Pointer); cdecl;
261
+ begin
262
+ FreeMem(Block);
263
+ end;
264
+
265
+ {function zlibCheck(code: Integer): Integer;
266
+ begin
267
+ Result := code;
268
+ if code < 0 then
269
+ raise EZlibError.Create('error'); //!!
270
+ end;}
271
+
272
+ function CCheck(code: Integer): Integer;
273
+ begin
274
+ Result := code;
275
+ if code < 0 then
276
+ raise ECompressionError.Create('error'); //!!
277
+ end;
278
+
279
+ function DCheck(code: Integer): Integer;
280
+ begin
281
+ Result := code;
282
+ if code < 0 then
283
+ raise EDecompressionError.Create('error'); //!!
284
+ end;
285
+
286
+ procedure CompressBuf(const InBuf: Pointer; InBytes: Integer;
287
+ out OutBuf: Pointer; out OutBytes: Integer);
288
+ var
289
+ strm: TZStreamRec;
290
+ P: Pointer;
291
+ begin
292
+ FillChar(strm, sizeof(strm), 0);
293
+ strm.zalloc := zlibAllocMem;
294
+ strm.zfree := zlibFreeMem;
295
+ OutBytes := ((InBytes + (InBytes div 10) + 12) + 255) and not 255;
296
+ GetMem(OutBuf, OutBytes);
297
+ try
298
+ strm.next_in := InBuf;
299
+ strm.avail_in := InBytes;
300
+ strm.next_out := OutBuf;
301
+ strm.avail_out := OutBytes;
302
+ CCheck(deflateInit_(strm, Z_BEST_COMPRESSION, zlib_version, sizeof(strm)));
303
+ try
304
+ while CCheck(deflate(strm, Z_FINISH)) <> Z_STREAM_END do
305
+ begin
306
+ P := OutBuf;
307
+ Inc(OutBytes, 256);
308
+ ReallocMem(OutBuf, OutBytes);
309
+ strm.next_out := PChar(Integer(OutBuf) + (Integer(strm.next_out) - Integer(P)));
310
+ strm.avail_out := 256;
311
+ end;
312
+ finally
313
+ CCheck(deflateEnd(strm));
314
+ end;
315
+ ReallocMem(OutBuf, strm.total_out);
316
+ OutBytes := strm.total_out;
317
+ except
318
+ FreeMem(OutBuf);
319
+ raise
320
+ end;
321
+ end;
322
+
323
+
324
+ procedure DecompressBuf(const InBuf: Pointer; InBytes: Integer;
325
+ OutEstimate: Integer; out OutBuf: Pointer; out OutBytes: Integer);
326
+ var
327
+ strm: TZStreamRec;
328
+ P: Pointer;
329
+ BufInc: Integer;
330
+ begin
331
+ FillChar(strm, sizeof(strm), 0);
332
+ strm.zalloc := zlibAllocMem;
333
+ strm.zfree := zlibFreeMem;
334
+ BufInc := (InBytes + 255) and not 255;
335
+ if OutEstimate = 0 then
336
+ OutBytes := BufInc
337
+ else
338
+ OutBytes := OutEstimate;
339
+ GetMem(OutBuf, OutBytes);
340
+ try
341
+ strm.next_in := InBuf;
342
+ strm.avail_in := InBytes;
343
+ strm.next_out := OutBuf;
344
+ strm.avail_out := OutBytes;
345
+ DCheck(inflateInit_(strm, zlib_version, sizeof(strm)));
346
+ try
347
+ while DCheck(inflate(strm, Z_NO_FLUSH)) <> Z_STREAM_END do
348
+ begin
349
+ P := OutBuf;
350
+ Inc(OutBytes, BufInc);
351
+ ReallocMem(OutBuf, OutBytes);
352
+ strm.next_out := PChar(Integer(OutBuf) + (Integer(strm.next_out) - Integer(P)));
353
+ strm.avail_out := BufInc;
354
+ end;
355
+ finally
356
+ DCheck(inflateEnd(strm));
357
+ end;
358
+ ReallocMem(OutBuf, strm.total_out);
359
+ OutBytes := strm.total_out;
360
+ except
361
+ FreeMem(OutBuf);
362
+ raise
363
+ end;
364
+ end;
365
+
366
+ procedure DecompressToUserBuf(const InBuf: Pointer; InBytes: Integer;
367
+ const OutBuf: Pointer; BufSize: Integer);
368
+ var
369
+ strm: TZStreamRec;
370
+ begin
371
+ FillChar(strm, sizeof(strm), 0);
372
+ strm.zalloc := zlibAllocMem;
373
+ strm.zfree := zlibFreeMem;
374
+ strm.next_in := InBuf;
375
+ strm.avail_in := InBytes;
376
+ strm.next_out := OutBuf;
377
+ strm.avail_out := BufSize;
378
+ DCheck(inflateInit_(strm, zlib_version, sizeof(strm)));
379
+ try
380
+ if DCheck(inflate(strm, Z_FINISH)) <> Z_STREAM_END then
381
+ raise EZlibError.CreateRes(@sTargetBufferTooSmall);
382
+ finally
383
+ DCheck(inflateEnd(strm));
384
+ end;
385
+ end;
386
+
387
+ // TCustomZlibStream
388
+
389
+ constructor TCustomZLibStream.Create(Strm: TStream);
390
+ begin
391
+ inherited Create;
392
+ FStrm := Strm;
393
+ FStrmPos := Strm.Position;
394
+ FZRec.zalloc := zlibAllocMem;
395
+ FZRec.zfree := zlibFreeMem;
396
+ end;
397
+
398
+ procedure TCustomZLibStream.Progress(Sender: TObject);
399
+ begin
400
+ if Assigned(FOnProgress) then FOnProgress(Sender);
401
+ end;
402
+
403
+
404
+ // TCompressionStream
405
+
406
+ constructor TCompressionStream.Create(CompressionLevel: TCompressionLevel;
407
+ Dest: TStream);
408
+ const
409
+ Levels: array [TCompressionLevel] of ShortInt =
410
+ (Z_NO_COMPRESSION, Z_BEST_SPEED, Z_DEFAULT_COMPRESSION, Z_BEST_COMPRESSION);
411
+ begin
412
+ inherited Create(Dest);
413
+ FZRec.next_out := FBuffer;
414
+ FZRec.avail_out := sizeof(FBuffer);
415
+ CCheck(deflateInit_(FZRec, Levels[CompressionLevel], zlib_version, sizeof(FZRec)));
416
+ end;
417
+
418
+ destructor TCompressionStream.Destroy;
419
+ begin
420
+ FZRec.next_in := nil;
421
+ FZRec.avail_in := 0;
422
+ try
423
+ if FStrm.Position <> FStrmPos then FStrm.Position := FStrmPos;
424
+ while (CCheck(deflate(FZRec, Z_FINISH)) <> Z_STREAM_END)
425
+ and (FZRec.avail_out = 0) do
426
+ begin
427
+ FStrm.WriteBuffer(FBuffer, sizeof(FBuffer));
428
+ FZRec.next_out := FBuffer;
429
+ FZRec.avail_out := sizeof(FBuffer);
430
+ end;
431
+ if FZRec.avail_out < sizeof(FBuffer) then
432
+ FStrm.WriteBuffer(FBuffer, sizeof(FBuffer) - FZRec.avail_out);
433
+ finally
434
+ deflateEnd(FZRec);
435
+ end;
436
+ inherited Destroy;
437
+ end;
438
+
439
+ function TCompressionStream.Read(var Buffer; Count: Longint): Longint;
440
+ begin
441
+ raise ECompressionError.CreateRes(@sInvalidStreamOp);
442
+ end;
443
+
444
+ function TCompressionStream.Write(const Buffer; Count: Longint): Longint;
445
+ begin
446
+ FZRec.next_in := @Buffer;
447
+ FZRec.avail_in := Count;
448
+ if FStrm.Position <> FStrmPos then FStrm.Position := FStrmPos;
449
+ while (FZRec.avail_in > 0) do
450
+ begin
451
+ CCheck(deflate(FZRec, 0));
452
+ if FZRec.avail_out = 0 then
453
+ begin
454
+ FStrm.WriteBuffer(FBuffer, sizeof(FBuffer));
455
+ FZRec.next_out := FBuffer;
456
+ FZRec.avail_out := sizeof(FBuffer);
457
+ FStrmPos := FStrm.Position;
458
+ Progress(Self);
459
+ end;
460
+ end;
461
+ Result := Count;
462
+ end;
463
+
464
+ function TCompressionStream.Seek(Offset: Longint; Origin: Word): Longint;
465
+ begin
466
+ if (Offset = 0) and (Origin = soFromCurrent) then
467
+ Result := FZRec.total_in
468
+ else
469
+ raise ECompressionError.CreateRes(@sInvalidStreamOp);
470
+ end;
471
+
472
+ function TCompressionStream.GetCompressionRate: Single;
473
+ begin
474
+ if FZRec.total_in = 0 then
475
+ Result := 0
476
+ else
477
+ Result := (1.0 - (FZRec.total_out / FZRec.total_in)) * 100.0;
478
+ end;
479
+
480
+
481
+ // TDecompressionStream
482
+
483
+ constructor TDecompressionStream.Create(Source: TStream);
484
+ begin
485
+ inherited Create(Source);
486
+ FZRec.next_in := FBuffer;
487
+ FZRec.avail_in := 0;
488
+ DCheck(inflateInit_(FZRec, zlib_version, sizeof(FZRec)));
489
+ end;
490
+
491
+ destructor TDecompressionStream.Destroy;
492
+ begin
493
+ FStrm.Seek(-FZRec.avail_in, 1);
494
+ inflateEnd(FZRec);
495
+ inherited Destroy;
496
+ end;
497
+
498
+ function TDecompressionStream.Read(var Buffer; Count: Longint): Longint;
499
+ begin
500
+ FZRec.next_out := @Buffer;
501
+ FZRec.avail_out := Count;
502
+ if FStrm.Position <> FStrmPos then FStrm.Position := FStrmPos;
503
+ while (FZRec.avail_out > 0) do
504
+ begin
505
+ if FZRec.avail_in = 0 then
506
+ begin
507
+ FZRec.avail_in := FStrm.Read(FBuffer, sizeof(FBuffer));
508
+ if FZRec.avail_in = 0 then
509
+ begin
510
+ Result := Count - FZRec.avail_out;
511
+ Exit;
512
+ end;
513
+ FZRec.next_in := FBuffer;
514
+ FStrmPos := FStrm.Position;
515
+ Progress(Self);
516
+ end;
517
+ CCheck(inflate(FZRec, 0));
518
+ end;
519
+ Result := Count;
520
+ end;
521
+
522
+ function TDecompressionStream.Write(const Buffer; Count: Longint): Longint;
523
+ begin
524
+ raise EDecompressionError.CreateRes(@sInvalidStreamOp);
525
+ end;
526
+
527
+ function TDecompressionStream.Seek(Offset: Longint; Origin: Word): Longint;
528
+ var
529
+ I: Integer;
530
+ Buf: array [0..4095] of Char;
531
+ begin
532
+ if (Offset = 0) and (Origin = soFromBeginning) then
533
+ begin
534
+ DCheck(inflateReset(FZRec));
535
+ FZRec.next_in := FBuffer;
536
+ FZRec.avail_in := 0;
537
+ FStrm.Position := 0;
538
+ FStrmPos := 0;
539
+ end
540
+ else if ( (Offset >= 0) and (Origin = soFromCurrent)) or
541
+ ( ((Offset - FZRec.total_out) > 0) and (Origin = soFromBeginning)) then
542
+ begin
543
+ if Origin = soFromBeginning then Dec(Offset, FZRec.total_out);
544
+ if Offset > 0 then
545
+ begin
546
+ for I := 1 to Offset div sizeof(Buf) do
547
+ ReadBuffer(Buf, sizeof(Buf));
548
+ ReadBuffer(Buf, Offset mod sizeof(Buf));
549
+ end;
550
+ end
551
+ else
552
+ raise EDecompressionError.CreateRes(@sInvalidStreamOp);
553
+ Result := FZRec.total_out;
554
+ end;
555
+
556
+
557
+ end.