finishm 0.0.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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
  234. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlibvc.sln +78 -0
  235. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlibvc.vcproj +445 -0
  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
  259. data/ext/src/third-party/zlib-1.2.3/examples/gzlog.h +58 -0
  260. data/ext/src/third-party/zlib-1.2.3/examples/zlib_how.html +523 -0
  261. data/ext/src/third-party/zlib-1.2.3/examples/zpipe.c +191 -0
  262. data/ext/src/third-party/zlib-1.2.3/examples/zran.c +404 -0
  263. data/ext/src/third-party/zlib-1.2.3/gzio.c +1026 -0
  264. data/ext/src/third-party/zlib-1.2.3/gzio.o +0 -0
  265. data/ext/src/third-party/zlib-1.2.3/infback.c +623 -0
  266. data/ext/src/third-party/zlib-1.2.3/infback.o +0 -0
  267. data/ext/src/third-party/zlib-1.2.3/inffast.c +318 -0
  268. data/ext/src/third-party/zlib-1.2.3/inffast.h +11 -0
  269. data/ext/src/third-party/zlib-1.2.3/inffast.o +0 -0
  270. data/ext/src/third-party/zlib-1.2.3/inffixed.h +94 -0
  271. data/ext/src/third-party/zlib-1.2.3/inflate.c +1368 -0
  272. data/ext/src/third-party/zlib-1.2.3/inflate.h +115 -0
  273. data/ext/src/third-party/zlib-1.2.3/inflate.o +0 -0
  274. data/ext/src/third-party/zlib-1.2.3/inftrees.c +329 -0
  275. data/ext/src/third-party/zlib-1.2.3/inftrees.h +55 -0
  276. data/ext/src/third-party/zlib-1.2.3/inftrees.o +0 -0
  277. data/ext/src/third-party/zlib-1.2.3/libz.a +0 -0
  278. data/ext/src/third-party/zlib-1.2.3/make_vms.com +461 -0
  279. data/ext/src/third-party/zlib-1.2.3/minigzip +0 -0
  280. data/ext/src/third-party/zlib-1.2.3/minigzip.c +322 -0
  281. data/ext/src/third-party/zlib-1.2.3/msdos/Makefile.bor +109 -0
  282. data/ext/src/third-party/zlib-1.2.3/msdos/Makefile.dj2 +104 -0
  283. data/ext/src/third-party/zlib-1.2.3/msdos/Makefile.emx +69 -0
  284. data/ext/src/third-party/zlib-1.2.3/msdos/Makefile.msc +106 -0
  285. data/ext/src/third-party/zlib-1.2.3/msdos/Makefile.tc +94 -0
  286. data/ext/src/third-party/zlib-1.2.3/old/Makefile.riscos +151 -0
  287. data/ext/src/third-party/zlib-1.2.3/old/README +3 -0
  288. data/ext/src/third-party/zlib-1.2.3/old/descrip.mms +48 -0
  289. data/ext/src/third-party/zlib-1.2.3/old/os2/Makefile.os2 +136 -0
  290. data/ext/src/third-party/zlib-1.2.3/old/os2/zlib.def +51 -0
  291. data/ext/src/third-party/zlib-1.2.3/old/visual-basic.txt +160 -0
  292. data/ext/src/third-party/zlib-1.2.3/old/zlib.html +971 -0
  293. data/ext/src/third-party/zlib-1.2.3/projects/README.projects +41 -0
  294. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/README.txt +73 -0
  295. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/example.dsp +278 -0
  296. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/minigzip.dsp +278 -0
  297. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/zlib.dsp +609 -0
  298. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/zlib.dsw +59 -0
  299. data/ext/src/third-party/zlib-1.2.3/qnx/package.qpg +141 -0
  300. data/ext/src/third-party/zlib-1.2.3/trees.c +1219 -0
  301. data/ext/src/third-party/zlib-1.2.3/trees.h +128 -0
  302. data/ext/src/third-party/zlib-1.2.3/trees.o +0 -0
  303. data/ext/src/third-party/zlib-1.2.3/uncompr.c +61 -0
  304. data/ext/src/third-party/zlib-1.2.3/uncompr.o +0 -0
  305. data/ext/src/third-party/zlib-1.2.3/win32/DLL_FAQ.txt +397 -0
  306. data/ext/src/third-party/zlib-1.2.3/win32/Makefile.bor +107 -0
  307. data/ext/src/third-party/zlib-1.2.3/win32/Makefile.emx +69 -0
  308. data/ext/src/third-party/zlib-1.2.3/win32/Makefile.gcc +141 -0
  309. data/ext/src/third-party/zlib-1.2.3/win32/Makefile.msc +126 -0
  310. data/ext/src/third-party/zlib-1.2.3/win32/VisualC.txt +3 -0
  311. data/ext/src/third-party/zlib-1.2.3/win32/zlib.def +60 -0
  312. data/ext/src/third-party/zlib-1.2.3/win32/zlib1.rc +39 -0
  313. data/ext/src/third-party/zlib-1.2.3/zconf.h +332 -0
  314. data/ext/src/third-party/zlib-1.2.3/zconf.in.h +332 -0
  315. data/ext/src/third-party/zlib-1.2.3/zlib.3 +159 -0
  316. data/ext/src/third-party/zlib-1.2.3/zlib.h +1357 -0
  317. data/ext/src/third-party/zlib-1.2.3/zutil.c +318 -0
  318. data/ext/src/third-party/zlib-1.2.3/zutil.h +269 -0
  319. data/ext/src/third-party/zlib-1.2.3/zutil.o +0 -0
  320. data/lib/assembly/a_b_visualiser.rb +169 -0
  321. data/lib/assembly/acyclic_connection_finder.rb +81 -0
  322. data/lib/assembly/all_orfs.rb +615 -0
  323. data/lib/assembly/bad_format_writer.rb +46 -0
  324. data/lib/assembly/bam_probe_read_selector.rb +48 -0
  325. data/lib/assembly/bubbly_assembler.rb +842 -0
  326. data/lib/assembly/c_probe_node_finder.rb +38 -0
  327. data/lib/assembly/connection_interpreter.rb +350 -0
  328. data/lib/assembly/contig_printer.rb +400 -0
  329. data/lib/assembly/coverage_based_graph_filter.rb +68 -0
  330. data/lib/assembly/depth_first_search.rb +63 -0
  331. data/lib/assembly/dijkstra.rb +216 -0
  332. data/lib/assembly/fluffer.rb +253 -0
  333. data/lib/assembly/graph_explorer.rb +85 -0
  334. data/lib/assembly/graph_generator.rb +315 -0
  335. data/lib/assembly/height_finder.rb +355 -0
  336. data/lib/assembly/hybrid_velvet_graph.rb +70 -0
  337. data/lib/assembly/input_genome.rb +182 -0
  338. data/lib/assembly/kmer_coverage_based_path_filter.rb +65 -0
  339. data/lib/assembly/node_finder.rb +171 -0
  340. data/lib/assembly/oriented_node_trail.rb +507 -0
  341. data/lib/assembly/paired_end_assembler.rb +53 -0
  342. data/lib/assembly/paired_end_neighbour_finder.rb +176 -0
  343. data/lib/assembly/probed_graph.rb +105 -0
  344. data/lib/assembly/read_input.rb +79 -0
  345. data/lib/assembly/read_to_node.rb +37 -0
  346. data/lib/assembly/scaffold_breaker.rb +126 -0
  347. data/lib/assembly/sequence_hasher.rb +71 -0
  348. data/lib/assembly/single_coherent_paths_between_nodes.rb +533 -0
  349. data/lib/assembly/single_coherent_wanderer.rb +261 -0
  350. data/lib/assembly/single_ended_assembler.rb +441 -0
  351. data/lib/assembly/velvet_c_binding.rb +54 -0
  352. data/lib/assembly/velvet_graph_sequence_extractor.rb +123 -0
  353. data/lib/external/VERSION +1 -0
  354. data/lib/finishm/assemble.rb +224 -0
  355. data/lib/finishm/explore.rb +217 -0
  356. data/lib/finishm/finisher.rb +303 -0
  357. data/lib/finishm/fluff.rb +122 -0
  358. data/lib/finishm/gapfiller.rb +325 -0
  359. data/lib/finishm/orfs_finder.rb +88 -0
  360. data/lib/finishm/path_counter.rb +90 -0
  361. data/lib/finishm/primers.rb +425 -0
  362. data/lib/finishm/primers_check.rb +176 -0
  363. data/lib/finishm/roundup.rb +344 -0
  364. data/lib/finishm/sequence.rb +142 -0
  365. data/lib/finishm/visualise.rb +430 -0
  366. data/lib/finishm/wander.rb +270 -0
  367. data/lib/kmer_abundance_pattern.rb +79 -0
  368. data/lib/kmer_multi_abundance_file.rb +48 -0
  369. data/lib/oligo_designer.rb +88 -0
  370. data/lib/priner.rb +66 -0
  371. data/spec/acyclic_connection_finder_spec.rb +551 -0
  372. data/spec/all_orfs_spec.rb +443 -0
  373. data/spec/assemble_spec.rb +186 -0
  374. data/spec/bubbly_assembler_spec.rb +707 -0
  375. data/spec/c_node_finder_spec.rb +58 -0
  376. data/spec/connection_interpreter_spec.rb +284 -0
  377. data/spec/contig_printer_spec.rb +291 -0
  378. data/spec/coverage_based_graph_filter_spec.rb +102 -0
  379. data/spec/data/6_3e4e5e6e.1vANME.bam +0 -0
  380. data/spec/data/6_3e4e5e6e.1vANME.bam.bai +0 -0
  381. data/spec/data/acyclic_connection_finder/1/probes.fa +5 -0
  382. data/spec/data/acyclic_connection_finder/1/random1.fa +2 -0
  383. data/spec/data/acyclic_connection_finder/1/random1.sammy.fa.gz +0 -0
  384. data/spec/data/acyclic_connection_finder/1/random2.fa +2 -0
  385. data/spec/data/acyclic_connection_finder/1/random2.sammy.fa.gz +0 -0
  386. data/spec/data/assembly/1_simple_bubble_uneven_coverage/random3000.fa +39 -0
  387. data/spec/data/assembly/1_simple_bubble_uneven_coverage/random3000.slightly_changed.fa +39 -0
  388. data/spec/data/assembly/1_simple_bubble_uneven_coverage/reads_combined.fa.gz +0 -0
  389. data/spec/data/assembly_visualiser/Contig_6_1_to_250.fa.kmers31 +220 -0
  390. data/spec/data/assembly_visualiser/Contig_7_1_to_250.fa.kmers31 +220 -0
  391. data/spec/data/assembly_visualiser/Graph +46 -0
  392. data/spec/data/assembly_visualiser/start_kmers1 +2 -0
  393. data/spec/data/bands.csv +1 -0
  394. data/spec/data/c_probe_node_finder/1/CnyUnifiedSeq +0 -0
  395. data/spec/data/c_probe_node_finder/1/CnyUnifiedSeq.names +544 -0
  396. data/spec/data/c_probe_node_finder/1/Graph2 +668 -0
  397. data/spec/data/c_probe_node_finder/1/LastGraph +668 -0
  398. data/spec/data/c_probe_node_finder/1/Log +756 -0
  399. data/spec/data/c_probe_node_finder/1/PreGraph +11 -0
  400. data/spec/data/c_probe_node_finder/1/Roadmaps +2009 -0
  401. data/spec/data/c_probe_node_finder/1/contigs.fa +29 -0
  402. data/spec/data/c_probe_node_finder/1/stats.txt +6 -0
  403. data/spec/data/contig_printer/1/HOWTO_RECREATE +17 -0
  404. data/spec/data/contig_printer/1/contigs.fa +4 -0
  405. data/spec/data/contig_printer/1/seq.fa +2408 -0
  406. data/spec/data/contig_printer/1/seq.fa.svg +153 -0
  407. data/spec/data/contig_printer/1/seq.fa.velvet/Graph2 +2953 -0
  408. data/spec/data/contig_printer/1/seq.fa.velvet/LastGraph +2953 -0
  409. data/spec/data/contig_printer/1/seq.fa.velvet/Log +21 -0
  410. data/spec/data/contig_printer/1/seq.fa.velvet/PreGraph +27 -0
  411. data/spec/data/contig_printer/1/seq.fa.velvet/Roadmaps +5182 -0
  412. data/spec/data/contig_printer/1/seq.fa.velvet/Sequences +3612 -0
  413. data/spec/data/contig_printer/1/seq.fa.velvet/contigs.fa +36 -0
  414. data/spec/data/contig_printer/1/seq.fa.velvet/stats.txt +14 -0
  415. data/spec/data/contig_printer/1/seq.faVseq2_1to550.fa.bam +0 -0
  416. data/spec/data/contig_printer/1/seq.faVseq2_1to550.fa.bam.bai +0 -0
  417. data/spec/data/contig_printer/1/seq.node12.fa +4 -0
  418. data/spec/data/contig_printer/1/seq1_1to550.fa +2 -0
  419. data/spec/data/contig_printer/1/seq2_1to550.fa +2 -0
  420. data/spec/data/contig_printer/1/seq2_1to550.fa.fai +1 -0
  421. data/spec/data/explore/1/2seqs.sammy.fa +12004 -0
  422. data/spec/data/explore/1/HOWTO_RECREATE.txt +6 -0
  423. data/spec/data/explore/1/a.fa +2 -0
  424. data/spec/data/explore/1/seq1_and_a.fa +3 -0
  425. data/spec/data/explore/1/seq2.fa +2 -0
  426. data/spec/data/fluff/1/2seqs.sammy.fa +12004 -0
  427. data/spec/data/fluff/1/HOWTO_RECREATE.txt +5 -0
  428. data/spec/data/fluff/1/seq1.fa +2 -0
  429. data/spec/data/fluff/1/seq2.fa +2 -0
  430. data/spec/data/gapfilling/1/reads.fa +171 -0
  431. data/spec/data/gapfilling/1/trail_with_Ns.fa +5 -0
  432. data/spec/data/gapfilling/1/velvetAssembly/Graph2 +130 -0
  433. data/spec/data/gapfilling/1/velvetAssembly/LastGraph +130 -0
  434. data/spec/data/gapfilling/1/velvetAssembly/Log +199 -0
  435. data/spec/data/gapfilling/1/velvetAssembly/PreGraph +7 -0
  436. data/spec/data/gapfilling/1/velvetAssembly/Roadmaps +239 -0
  437. data/spec/data/gapfilling/1/velvetAssembly/Sequences +281 -0
  438. data/spec/data/gapfilling/1/velvetAssembly/contigs.fa +12 -0
  439. data/spec/data/gapfilling/1/velvetAssembly/stats.txt +4 -0
  440. data/spec/data/gapfilling/2/HOWTO_recreate +17 -0
  441. data/spec/data/gapfilling/2/reference.fa +2 -0
  442. data/spec/data/gapfilling/2/reference_part1.fa +4 -0
  443. data/spec/data/gapfilling/2/reference_part2.fa +4 -0
  444. data/spec/data/gapfilling/2/sammy_reads.fa.gz +0 -0
  445. data/spec/data/gapfilling/2/with_gaps.fa +4 -0
  446. data/spec/data/gapfilling/3/HOWTO_recreate +4 -0
  447. data/spec/data/gapfilling/3/reads.fa.gz +0 -0
  448. data/spec/data/gapfilling/3/reference_part1.fa +4 -0
  449. data/spec/data/gapfilling/3/reference_part2.fa +4 -0
  450. data/spec/data/gapfilling/3/with_gaps.fa +4 -0
  451. data/spec/data/gapfilling/4/HOWTO_recreate +1 -0
  452. data/spec/data/gapfilling/4/reads.fa.gz +0 -0
  453. data/spec/data/gapfilling/5/HOWTO_RECREATE +7 -0
  454. data/spec/data/gapfilling/5/answer.fna +2 -0
  455. data/spec/data/gapfilling/5/gappy.fna +2 -0
  456. data/spec/data/gapfilling/5/reads.fa +17961 -0
  457. data/spec/data/gapfilling/5/velvet51_3.5/LastGraph +8337 -0
  458. data/spec/data/gapfilling/5/velvet51_3.5/Sequences +20921 -0
  459. data/spec/data/gapfilling/6/random1.fa +28 -0
  460. data/spec/data/gapfilling/6/random2.fa +28 -0
  461. data/spec/data/gapfilling/6/random_sequence_length_2000 +0 -0
  462. data/spec/data/gapfilling/6/reads.random1.fa.gz +0 -0
  463. data/spec/data/gapfilling/6/reads.random2.fa.gz +0 -0
  464. data/spec/data/gapfilling/6/to_gapfill.fa +22 -0
  465. data/spec/data/kmer_profile_to_assembly/multiple_abundance_file1.csv +2 -0
  466. data/spec/data/kmers_count1.csv +2 -0
  467. data/spec/data/kmers_count2.csv +3 -0
  468. data/spec/data/out +3 -0
  469. data/spec/data/positive_latching_pair.fa +2 -0
  470. data/spec/data/primers.csv +4 -0
  471. data/spec/data/read_selection_by_kmer/blacklist1.txt +1 -0
  472. data/spec/data/read_selection_by_kmer/input.fasta +6 -0
  473. data/spec/data/read_selection_by_kmer/whitelist1.txt +1 -0
  474. data/spec/data/read_selection_by_kmer/whitelist2.txt +2 -0
  475. data/spec/data/read_to_node/1_a_graph/HOWTO_RECREATE.txt +2 -0
  476. data/spec/data/read_to_node/1_a_graph/LastGraph +6695 -0
  477. data/spec/data/read_to_node/1_a_graph/ReadToNode.bin +0 -0
  478. data/spec/data/read_to_node/2_no_read256_or_259/HOWTO_RECREATE.txt +3 -0
  479. data/spec/data/read_to_node/2_no_read256_or_259/LastGraph +6693 -0
  480. data/spec/data/read_to_node/2_no_read256_or_259/ReadToNode.bin +0 -0
  481. data/spec/data/read_to_node/3_no_last_read/LastGraph +6694 -0
  482. data/spec/data/read_to_node/3_no_last_read/ReadToNode.bin +0 -0
  483. data/spec/data/t/details.txt +5 -0
  484. data/spec/data/t/details.txt.srt +5 -0
  485. data/spec/data/t/location.txt +3 -0
  486. data/spec/data/t/location.txt.srt +3 -0
  487. data/spec/data/tweak/1_gap_then_unscaffolded/answer.fa +2 -0
  488. data/spec/data/tweak/1_gap_then_unscaffolded/reads.fa.gz +0 -0
  489. data/spec/data/tweak/1_gap_then_unscaffolded/scaffolds.fa +6 -0
  490. data/spec/data/tweak/2_second_genome/answer2.fa +2 -0
  491. data/spec/data/tweak/2_second_genome/reads.fa.gz +0 -0
  492. data/spec/data/tweak/3_variant/answer.fa +2 -0
  493. data/spec/data/tweak/3_variant/lesser_answer.fa +2 -0
  494. data/spec/data/tweak/3_variant/reads.fa.gz +0 -0
  495. data/spec/data/tweak/3_variant/with_gaps.fa +2 -0
  496. data/spec/data/velvet_test_trails/Assem/Graph +17 -0
  497. data/spec/data/velvet_test_trails/Assem/Graph2 +40 -0
  498. data/spec/data/velvet_test_trails/Assem/LastGraph +40 -0
  499. data/spec/data/velvet_test_trails/Assem/Log +35 -0
  500. data/spec/data/velvet_test_trails/Assem/PreGraph +9 -0
  501. data/spec/data/velvet_test_trails/Assem/Roadmaps +89 -0
  502. data/spec/data/velvet_test_trails/Assem/Sequences +50 -0
  503. data/spec/data/velvet_test_trails/Assem/a.svg +53 -0
  504. data/spec/data/velvet_test_trails/Assem/contigs.fa +15 -0
  505. data/spec/data/velvet_test_trails/Assem/stats.txt +5 -0
  506. data/spec/data/velvet_test_trails/node_fwds.fa +8 -0
  507. data/spec/data/velvet_test_trails/node_seqs.fa +9 -0
  508. data/spec/data/velvet_test_trails/nodes_fwd_rev.fa +16 -0
  509. data/spec/data/velvet_test_trails/read1.fa +2 -0
  510. data/spec/data/velvet_test_trails/reads.fa +50 -0
  511. data/spec/data/velvet_test_trails_reverse/Assem/LastGraph +17 -0
  512. data/spec/data/velvet_test_trails_reverse/Assem/a.svg +53 -0
  513. data/spec/data/velvet_test_trails_reverse/reads_reversed.fa +10 -0
  514. data/spec/data/visualise/1/LastGraph +6695 -0
  515. data/spec/data/visualise/2_paired_end/HOWTO_RECREATE.txt +10 -0
  516. data/spec/data/visualise/2_paired_end/rand1.fa +2 -0
  517. data/spec/data/visualise/2_paired_end/rand2.fa +2 -0
  518. data/spec/data/visualise/2_paired_end/with_gaps.fa +8 -0
  519. data/spec/data/visualise/2_paired_end/with_gaps.read_pairs.fa.gz +0 -0
  520. data/spec/data/wander/1/random1.fa +2 -0
  521. data/spec/data/wander/1/random1.sammy.fa +804 -0
  522. data/spec/depth_first_search_spec.rb +190 -0
  523. data/spec/dijkstra_spec.rb +143 -0
  524. data/spec/explore_spec.rb +29 -0
  525. data/spec/fluffer_spec.rb +155 -0
  526. data/spec/gapfiller_spec.rb +107 -0
  527. data/spec/graph_explorer_spec.rb +475 -0
  528. data/spec/graph_generator_spec.rb +99 -0
  529. data/spec/height_finder_spec.rb +306 -0
  530. data/spec/kmer_abundance_pattern_spec.rb +56 -0
  531. data/spec/kmer_coverage_based_path_filter_spec.rb +73 -0
  532. data/spec/kmer_profile_finder_spec.rb +38 -0
  533. data/spec/kmers_count_tabulate_spec.rb +120 -0
  534. data/spec/oriented_node_trail_spec.rb +221 -0
  535. data/spec/paired_end_neighbours_spec.rb +126 -0
  536. data/spec/paths_between_nodes_spec.rb +349 -0
  537. data/spec/priner_spec.rb +7 -0
  538. data/spec/read_input_spec.rb +23 -0
  539. data/spec/read_selection_by_kmer_spec.rb +166 -0
  540. data/spec/read_to_node_spec.rb +35 -0
  541. data/spec/roundup_spec.rb +366 -0
  542. data/spec/scaffold_breaker_spec.rb +144 -0
  543. data/spec/sequence_spec.rb +43 -0
  544. data/spec/single_coherent_paths_between_nodes_spec.rb +492 -0
  545. data/spec/single_coherent_wanderer_spec.rb +120 -0
  546. data/spec/single_ended_assembler_spec.rb +398 -0
  547. data/spec/spec_helper.rb +310 -0
  548. data/spec/velvet_graph_sequence_extractor_spec.rb +80 -0
  549. data/spec/visualise_spec.rb +105 -0
  550. data/spec/wander_spec.rb +119 -0
  551. data/spec/watch_for_changes.sh +16 -0
  552. data/validation/fasta_compare.rb +72 -0
  553. data/validation/gapfill_simulate_perfect.rb +108 -0
  554. metadata +899 -0
@@ -0,0 +1,450 @@
1
+ ----------------------------------------------------------------
2
+ -- ZLib for Ada thick binding. --
3
+ -- --
4
+ -- Copyright (C) 2002-2003 Dmitriy Anisimkov --
5
+ -- --
6
+ -- Open source license information is in the zlib.ads file. --
7
+ ----------------------------------------------------------------
8
+
9
+ -- $Id: zlib-thin.ads,v 1.11 2004/07/23 06:33:11 vagul Exp $
10
+
11
+ with Interfaces.C.Strings;
12
+
13
+ with System;
14
+
15
+ private package ZLib.Thin is
16
+
17
+ -- From zconf.h
18
+
19
+ MAX_MEM_LEVEL : constant := 9; -- zconf.h:105
20
+ -- zconf.h:105
21
+ MAX_WBITS : constant := 15; -- zconf.h:115
22
+ -- 32K LZ77 window
23
+ -- zconf.h:115
24
+ SEEK_SET : constant := 8#0000#; -- zconf.h:244
25
+ -- Seek from beginning of file.
26
+ -- zconf.h:244
27
+ SEEK_CUR : constant := 1; -- zconf.h:245
28
+ -- Seek from current position.
29
+ -- zconf.h:245
30
+ SEEK_END : constant := 2; -- zconf.h:246
31
+ -- Set file pointer to EOF plus "offset"
32
+ -- zconf.h:246
33
+
34
+ type Byte is new Interfaces.C.unsigned_char; -- 8 bits
35
+ -- zconf.h:214
36
+ type UInt is new Interfaces.C.unsigned; -- 16 bits or more
37
+ -- zconf.h:216
38
+ type Int is new Interfaces.C.int;
39
+
40
+ type ULong is new Interfaces.C.unsigned_long; -- 32 bits or more
41
+ -- zconf.h:217
42
+ subtype Chars_Ptr is Interfaces.C.Strings.chars_ptr;
43
+
44
+ type ULong_Access is access ULong;
45
+ type Int_Access is access Int;
46
+
47
+ subtype Voidp is System.Address; -- zconf.h:232
48
+
49
+ subtype Byte_Access is Voidp;
50
+
51
+ Nul : constant Voidp := System.Null_Address;
52
+ -- end from zconf
53
+
54
+ Z_NO_FLUSH : constant := 8#0000#; -- zlib.h:125
55
+ -- zlib.h:125
56
+ Z_PARTIAL_FLUSH : constant := 1; -- zlib.h:126
57
+ -- will be removed, use
58
+ -- Z_SYNC_FLUSH instead
59
+ -- zlib.h:126
60
+ Z_SYNC_FLUSH : constant := 2; -- zlib.h:127
61
+ -- zlib.h:127
62
+ Z_FULL_FLUSH : constant := 3; -- zlib.h:128
63
+ -- zlib.h:128
64
+ Z_FINISH : constant := 4; -- zlib.h:129
65
+ -- zlib.h:129
66
+ Z_OK : constant := 8#0000#; -- zlib.h:132
67
+ -- zlib.h:132
68
+ Z_STREAM_END : constant := 1; -- zlib.h:133
69
+ -- zlib.h:133
70
+ Z_NEED_DICT : constant := 2; -- zlib.h:134
71
+ -- zlib.h:134
72
+ Z_ERRNO : constant := -1; -- zlib.h:135
73
+ -- zlib.h:135
74
+ Z_STREAM_ERROR : constant := -2; -- zlib.h:136
75
+ -- zlib.h:136
76
+ Z_DATA_ERROR : constant := -3; -- zlib.h:137
77
+ -- zlib.h:137
78
+ Z_MEM_ERROR : constant := -4; -- zlib.h:138
79
+ -- zlib.h:138
80
+ Z_BUF_ERROR : constant := -5; -- zlib.h:139
81
+ -- zlib.h:139
82
+ Z_VERSION_ERROR : constant := -6; -- zlib.h:140
83
+ -- zlib.h:140
84
+ Z_NO_COMPRESSION : constant := 8#0000#; -- zlib.h:145
85
+ -- zlib.h:145
86
+ Z_BEST_SPEED : constant := 1; -- zlib.h:146
87
+ -- zlib.h:146
88
+ Z_BEST_COMPRESSION : constant := 9; -- zlib.h:147
89
+ -- zlib.h:147
90
+ Z_DEFAULT_COMPRESSION : constant := -1; -- zlib.h:148
91
+ -- zlib.h:148
92
+ Z_FILTERED : constant := 1; -- zlib.h:151
93
+ -- zlib.h:151
94
+ Z_HUFFMAN_ONLY : constant := 2; -- zlib.h:152
95
+ -- zlib.h:152
96
+ Z_DEFAULT_STRATEGY : constant := 8#0000#; -- zlib.h:153
97
+ -- zlib.h:153
98
+ Z_BINARY : constant := 8#0000#; -- zlib.h:156
99
+ -- zlib.h:156
100
+ Z_ASCII : constant := 1; -- zlib.h:157
101
+ -- zlib.h:157
102
+ Z_UNKNOWN : constant := 2; -- zlib.h:158
103
+ -- zlib.h:158
104
+ Z_DEFLATED : constant := 8; -- zlib.h:161
105
+ -- zlib.h:161
106
+ Z_NULL : constant := 8#0000#; -- zlib.h:164
107
+ -- for initializing zalloc, zfree, opaque
108
+ -- zlib.h:164
109
+ type gzFile is new Voidp; -- zlib.h:646
110
+
111
+ type Z_Stream is private;
112
+
113
+ type Z_Streamp is access all Z_Stream; -- zlib.h:89
114
+
115
+ type alloc_func is access function
116
+ (Opaque : Voidp;
117
+ Items : UInt;
118
+ Size : UInt)
119
+ return Voidp; -- zlib.h:63
120
+
121
+ type free_func is access procedure (opaque : Voidp; address : Voidp);
122
+
123
+ function zlibVersion return Chars_Ptr;
124
+
125
+ function Deflate (strm : Z_Streamp; flush : Int) return Int;
126
+
127
+ function DeflateEnd (strm : Z_Streamp) return Int;
128
+
129
+ function Inflate (strm : Z_Streamp; flush : Int) return Int;
130
+
131
+ function InflateEnd (strm : Z_Streamp) return Int;
132
+
133
+ function deflateSetDictionary
134
+ (strm : Z_Streamp;
135
+ dictionary : Byte_Access;
136
+ dictLength : UInt)
137
+ return Int;
138
+
139
+ function deflateCopy (dest : Z_Streamp; source : Z_Streamp) return Int;
140
+ -- zlib.h:478
141
+
142
+ function deflateReset (strm : Z_Streamp) return Int; -- zlib.h:495
143
+
144
+ function deflateParams
145
+ (strm : Z_Streamp;
146
+ level : Int;
147
+ strategy : Int)
148
+ return Int; -- zlib.h:506
149
+
150
+ function inflateSetDictionary
151
+ (strm : Z_Streamp;
152
+ dictionary : Byte_Access;
153
+ dictLength : UInt)
154
+ return Int; -- zlib.h:548
155
+
156
+ function inflateSync (strm : Z_Streamp) return Int; -- zlib.h:565
157
+
158
+ function inflateReset (strm : Z_Streamp) return Int; -- zlib.h:580
159
+
160
+ function compress
161
+ (dest : Byte_Access;
162
+ destLen : ULong_Access;
163
+ source : Byte_Access;
164
+ sourceLen : ULong)
165
+ return Int; -- zlib.h:601
166
+
167
+ function compress2
168
+ (dest : Byte_Access;
169
+ destLen : ULong_Access;
170
+ source : Byte_Access;
171
+ sourceLen : ULong;
172
+ level : Int)
173
+ return Int; -- zlib.h:615
174
+
175
+ function uncompress
176
+ (dest : Byte_Access;
177
+ destLen : ULong_Access;
178
+ source : Byte_Access;
179
+ sourceLen : ULong)
180
+ return Int;
181
+
182
+ function gzopen (path : Chars_Ptr; mode : Chars_Ptr) return gzFile;
183
+
184
+ function gzdopen (fd : Int; mode : Chars_Ptr) return gzFile;
185
+
186
+ function gzsetparams
187
+ (file : gzFile;
188
+ level : Int;
189
+ strategy : Int)
190
+ return Int;
191
+
192
+ function gzread
193
+ (file : gzFile;
194
+ buf : Voidp;
195
+ len : UInt)
196
+ return Int;
197
+
198
+ function gzwrite
199
+ (file : in gzFile;
200
+ buf : in Voidp;
201
+ len : in UInt)
202
+ return Int;
203
+
204
+ function gzprintf (file : in gzFile; format : in Chars_Ptr) return Int;
205
+
206
+ function gzputs (file : in gzFile; s : in Chars_Ptr) return Int;
207
+
208
+ function gzgets
209
+ (file : gzFile;
210
+ buf : Chars_Ptr;
211
+ len : Int)
212
+ return Chars_Ptr;
213
+
214
+ function gzputc (file : gzFile; char : Int) return Int;
215
+
216
+ function gzgetc (file : gzFile) return Int;
217
+
218
+ function gzflush (file : gzFile; flush : Int) return Int;
219
+
220
+ function gzseek
221
+ (file : gzFile;
222
+ offset : Int;
223
+ whence : Int)
224
+ return Int;
225
+
226
+ function gzrewind (file : gzFile) return Int;
227
+
228
+ function gztell (file : gzFile) return Int;
229
+
230
+ function gzeof (file : gzFile) return Int;
231
+
232
+ function gzclose (file : gzFile) return Int;
233
+
234
+ function gzerror (file : gzFile; errnum : Int_Access) return Chars_Ptr;
235
+
236
+ function adler32
237
+ (adler : ULong;
238
+ buf : Byte_Access;
239
+ len : UInt)
240
+ return ULong;
241
+
242
+ function crc32
243
+ (crc : ULong;
244
+ buf : Byte_Access;
245
+ len : UInt)
246
+ return ULong;
247
+
248
+ function deflateInit
249
+ (strm : Z_Streamp;
250
+ level : Int;
251
+ version : Chars_Ptr;
252
+ stream_size : Int)
253
+ return Int;
254
+
255
+ function deflateInit2
256
+ (strm : Z_Streamp;
257
+ level : Int;
258
+ method : Int;
259
+ windowBits : Int;
260
+ memLevel : Int;
261
+ strategy : Int;
262
+ version : Chars_Ptr;
263
+ stream_size : Int)
264
+ return Int;
265
+
266
+ function Deflate_Init
267
+ (strm : Z_Streamp;
268
+ level : Int;
269
+ method : Int;
270
+ windowBits : Int;
271
+ memLevel : Int;
272
+ strategy : Int)
273
+ return Int;
274
+ pragma Inline (Deflate_Init);
275
+
276
+ function inflateInit
277
+ (strm : Z_Streamp;
278
+ version : Chars_Ptr;
279
+ stream_size : Int)
280
+ return Int;
281
+
282
+ function inflateInit2
283
+ (strm : in Z_Streamp;
284
+ windowBits : in Int;
285
+ version : in Chars_Ptr;
286
+ stream_size : in Int)
287
+ return Int;
288
+
289
+ function inflateBackInit
290
+ (strm : in Z_Streamp;
291
+ windowBits : in Int;
292
+ window : in Byte_Access;
293
+ version : in Chars_Ptr;
294
+ stream_size : in Int)
295
+ return Int;
296
+ -- Size of window have to be 2**windowBits.
297
+
298
+ function Inflate_Init (strm : Z_Streamp; windowBits : Int) return Int;
299
+ pragma Inline (Inflate_Init);
300
+
301
+ function zError (err : Int) return Chars_Ptr;
302
+
303
+ function inflateSyncPoint (z : Z_Streamp) return Int;
304
+
305
+ function get_crc_table return ULong_Access;
306
+
307
+ -- Interface to the available fields of the z_stream structure.
308
+ -- The application must update next_in and avail_in when avail_in has
309
+ -- dropped to zero. It must update next_out and avail_out when avail_out
310
+ -- has dropped to zero. The application must initialize zalloc, zfree and
311
+ -- opaque before calling the init function.
312
+
313
+ procedure Set_In
314
+ (Strm : in out Z_Stream;
315
+ Buffer : in Voidp;
316
+ Size : in UInt);
317
+ pragma Inline (Set_In);
318
+
319
+ procedure Set_Out
320
+ (Strm : in out Z_Stream;
321
+ Buffer : in Voidp;
322
+ Size : in UInt);
323
+ pragma Inline (Set_Out);
324
+
325
+ procedure Set_Mem_Func
326
+ (Strm : in out Z_Stream;
327
+ Opaque : in Voidp;
328
+ Alloc : in alloc_func;
329
+ Free : in free_func);
330
+ pragma Inline (Set_Mem_Func);
331
+
332
+ function Last_Error_Message (Strm : in Z_Stream) return String;
333
+ pragma Inline (Last_Error_Message);
334
+
335
+ function Avail_Out (Strm : in Z_Stream) return UInt;
336
+ pragma Inline (Avail_Out);
337
+
338
+ function Avail_In (Strm : in Z_Stream) return UInt;
339
+ pragma Inline (Avail_In);
340
+
341
+ function Total_In (Strm : in Z_Stream) return ULong;
342
+ pragma Inline (Total_In);
343
+
344
+ function Total_Out (Strm : in Z_Stream) return ULong;
345
+ pragma Inline (Total_Out);
346
+
347
+ function inflateCopy
348
+ (dest : in Z_Streamp;
349
+ Source : in Z_Streamp)
350
+ return Int;
351
+
352
+ function compressBound (Source_Len : in ULong) return ULong;
353
+
354
+ function deflateBound
355
+ (Strm : in Z_Streamp;
356
+ Source_Len : in ULong)
357
+ return ULong;
358
+
359
+ function gzungetc (C : in Int; File : in gzFile) return Int;
360
+
361
+ function zlibCompileFlags return ULong;
362
+
363
+ private
364
+
365
+ type Z_Stream is record -- zlib.h:68
366
+ Next_In : Voidp := Nul; -- next input byte
367
+ Avail_In : UInt := 0; -- number of bytes available at next_in
368
+ Total_In : ULong := 0; -- total nb of input bytes read so far
369
+ Next_Out : Voidp := Nul; -- next output byte should be put there
370
+ Avail_Out : UInt := 0; -- remaining free space at next_out
371
+ Total_Out : ULong := 0; -- total nb of bytes output so far
372
+ msg : Chars_Ptr; -- last error message, NULL if no error
373
+ state : Voidp; -- not visible by applications
374
+ zalloc : alloc_func := null; -- used to allocate the internal state
375
+ zfree : free_func := null; -- used to free the internal state
376
+ opaque : Voidp; -- private data object passed to
377
+ -- zalloc and zfree
378
+ data_type : Int; -- best guess about the data type:
379
+ -- ascii or binary
380
+ adler : ULong; -- adler32 value of the uncompressed
381
+ -- data
382
+ reserved : ULong; -- reserved for future use
383
+ end record;
384
+
385
+ pragma Convention (C, Z_Stream);
386
+
387
+ pragma Import (C, zlibVersion, "zlibVersion");
388
+ pragma Import (C, Deflate, "deflate");
389
+ pragma Import (C, DeflateEnd, "deflateEnd");
390
+ pragma Import (C, Inflate, "inflate");
391
+ pragma Import (C, InflateEnd, "inflateEnd");
392
+ pragma Import (C, deflateSetDictionary, "deflateSetDictionary");
393
+ pragma Import (C, deflateCopy, "deflateCopy");
394
+ pragma Import (C, deflateReset, "deflateReset");
395
+ pragma Import (C, deflateParams, "deflateParams");
396
+ pragma Import (C, inflateSetDictionary, "inflateSetDictionary");
397
+ pragma Import (C, inflateSync, "inflateSync");
398
+ pragma Import (C, inflateReset, "inflateReset");
399
+ pragma Import (C, compress, "compress");
400
+ pragma Import (C, compress2, "compress2");
401
+ pragma Import (C, uncompress, "uncompress");
402
+ pragma Import (C, gzopen, "gzopen");
403
+ pragma Import (C, gzdopen, "gzdopen");
404
+ pragma Import (C, gzsetparams, "gzsetparams");
405
+ pragma Import (C, gzread, "gzread");
406
+ pragma Import (C, gzwrite, "gzwrite");
407
+ pragma Import (C, gzprintf, "gzprintf");
408
+ pragma Import (C, gzputs, "gzputs");
409
+ pragma Import (C, gzgets, "gzgets");
410
+ pragma Import (C, gzputc, "gzputc");
411
+ pragma Import (C, gzgetc, "gzgetc");
412
+ pragma Import (C, gzflush, "gzflush");
413
+ pragma Import (C, gzseek, "gzseek");
414
+ pragma Import (C, gzrewind, "gzrewind");
415
+ pragma Import (C, gztell, "gztell");
416
+ pragma Import (C, gzeof, "gzeof");
417
+ pragma Import (C, gzclose, "gzclose");
418
+ pragma Import (C, gzerror, "gzerror");
419
+ pragma Import (C, adler32, "adler32");
420
+ pragma Import (C, crc32, "crc32");
421
+ pragma Import (C, deflateInit, "deflateInit_");
422
+ pragma Import (C, inflateInit, "inflateInit_");
423
+ pragma Import (C, deflateInit2, "deflateInit2_");
424
+ pragma Import (C, inflateInit2, "inflateInit2_");
425
+ pragma Import (C, zError, "zError");
426
+ pragma Import (C, inflateSyncPoint, "inflateSyncPoint");
427
+ pragma Import (C, get_crc_table, "get_crc_table");
428
+
429
+ -- since zlib 1.2.0:
430
+
431
+ pragma Import (C, inflateCopy, "inflateCopy");
432
+ pragma Import (C, compressBound, "compressBound");
433
+ pragma Import (C, deflateBound, "deflateBound");
434
+ pragma Import (C, gzungetc, "gzungetc");
435
+ pragma Import (C, zlibCompileFlags, "zlibCompileFlags");
436
+
437
+ pragma Import (C, inflateBackInit, "inflateBackInit_");
438
+
439
+ -- I stopped binding the inflateBack routines, becouse realize that
440
+ -- it does not support zlib and gzip headers for now, and have no
441
+ -- symmetric deflateBack routines.
442
+ -- ZLib-Ada is symmetric regarding deflate/inflate data transformation
443
+ -- and has a similar generic callback interface for the
444
+ -- deflate/inflate transformation based on the regular Deflate/Inflate
445
+ -- routines.
446
+
447
+ -- pragma Import (C, inflateBack, "inflateBack");
448
+ -- pragma Import (C, inflateBackEnd, "inflateBackEnd");
449
+
450
+ end ZLib.Thin;
@@ -0,0 +1,701 @@
1
+ ----------------------------------------------------------------
2
+ -- ZLib for Ada thick binding. --
3
+ -- --
4
+ -- Copyright (C) 2002-2004 Dmitriy Anisimkov --
5
+ -- --
6
+ -- Open source license information is in the zlib.ads file. --
7
+ ----------------------------------------------------------------
8
+
9
+ -- $Id: zlib.adb,v 1.31 2004/09/06 06:53:19 vagul Exp $
10
+
11
+ with Ada.Exceptions;
12
+ with Ada.Unchecked_Conversion;
13
+ with Ada.Unchecked_Deallocation;
14
+
15
+ with Interfaces.C.Strings;
16
+
17
+ with ZLib.Thin;
18
+
19
+ package body ZLib is
20
+
21
+ use type Thin.Int;
22
+
23
+ type Z_Stream is new Thin.Z_Stream;
24
+
25
+ type Return_Code_Enum is
26
+ (OK,
27
+ STREAM_END,
28
+ NEED_DICT,
29
+ ERRNO,
30
+ STREAM_ERROR,
31
+ DATA_ERROR,
32
+ MEM_ERROR,
33
+ BUF_ERROR,
34
+ VERSION_ERROR);
35
+
36
+ type Flate_Step_Function is access
37
+ function (Strm : in Thin.Z_Streamp; Flush : in Thin.Int) return Thin.Int;
38
+ pragma Convention (C, Flate_Step_Function);
39
+
40
+ type Flate_End_Function is access
41
+ function (Ctrm : in Thin.Z_Streamp) return Thin.Int;
42
+ pragma Convention (C, Flate_End_Function);
43
+
44
+ type Flate_Type is record
45
+ Step : Flate_Step_Function;
46
+ Done : Flate_End_Function;
47
+ end record;
48
+
49
+ subtype Footer_Array is Stream_Element_Array (1 .. 8);
50
+
51
+ Simple_GZip_Header : constant Stream_Element_Array (1 .. 10)
52
+ := (16#1f#, 16#8b#, -- Magic header
53
+ 16#08#, -- Z_DEFLATED
54
+ 16#00#, -- Flags
55
+ 16#00#, 16#00#, 16#00#, 16#00#, -- Time
56
+ 16#00#, -- XFlags
57
+ 16#03# -- OS code
58
+ );
59
+ -- The simplest gzip header is not for informational, but just for
60
+ -- gzip format compatibility.
61
+ -- Note that some code below is using assumption
62
+ -- Simple_GZip_Header'Last > Footer_Array'Last, so do not make
63
+ -- Simple_GZip_Header'Last <= Footer_Array'Last.
64
+
65
+ Return_Code : constant array (Thin.Int range <>) of Return_Code_Enum
66
+ := (0 => OK,
67
+ 1 => STREAM_END,
68
+ 2 => NEED_DICT,
69
+ -1 => ERRNO,
70
+ -2 => STREAM_ERROR,
71
+ -3 => DATA_ERROR,
72
+ -4 => MEM_ERROR,
73
+ -5 => BUF_ERROR,
74
+ -6 => VERSION_ERROR);
75
+
76
+ Flate : constant array (Boolean) of Flate_Type
77
+ := (True => (Step => Thin.Deflate'Access,
78
+ Done => Thin.DeflateEnd'Access),
79
+ False => (Step => Thin.Inflate'Access,
80
+ Done => Thin.InflateEnd'Access));
81
+
82
+ Flush_Finish : constant array (Boolean) of Flush_Mode
83
+ := (True => Finish, False => No_Flush);
84
+
85
+ procedure Raise_Error (Stream : in Z_Stream);
86
+ pragma Inline (Raise_Error);
87
+
88
+ procedure Raise_Error (Message : in String);
89
+ pragma Inline (Raise_Error);
90
+
91
+ procedure Check_Error (Stream : in Z_Stream; Code : in Thin.Int);
92
+
93
+ procedure Free is new Ada.Unchecked_Deallocation
94
+ (Z_Stream, Z_Stream_Access);
95
+
96
+ function To_Thin_Access is new Ada.Unchecked_Conversion
97
+ (Z_Stream_Access, Thin.Z_Streamp);
98
+
99
+ procedure Translate_GZip
100
+ (Filter : in out Filter_Type;
101
+ In_Data : in Ada.Streams.Stream_Element_Array;
102
+ In_Last : out Ada.Streams.Stream_Element_Offset;
103
+ Out_Data : out Ada.Streams.Stream_Element_Array;
104
+ Out_Last : out Ada.Streams.Stream_Element_Offset;
105
+ Flush : in Flush_Mode);
106
+ -- Separate translate routine for make gzip header.
107
+
108
+ procedure Translate_Auto
109
+ (Filter : in out Filter_Type;
110
+ In_Data : in Ada.Streams.Stream_Element_Array;
111
+ In_Last : out Ada.Streams.Stream_Element_Offset;
112
+ Out_Data : out Ada.Streams.Stream_Element_Array;
113
+ Out_Last : out Ada.Streams.Stream_Element_Offset;
114
+ Flush : in Flush_Mode);
115
+ -- translate routine without additional headers.
116
+
117
+ -----------------
118
+ -- Check_Error --
119
+ -----------------
120
+
121
+ procedure Check_Error (Stream : in Z_Stream; Code : in Thin.Int) is
122
+ use type Thin.Int;
123
+ begin
124
+ if Code /= Thin.Z_OK then
125
+ Raise_Error
126
+ (Return_Code_Enum'Image (Return_Code (Code))
127
+ & ": " & Last_Error_Message (Stream));
128
+ end if;
129
+ end Check_Error;
130
+
131
+ -----------
132
+ -- Close --
133
+ -----------
134
+
135
+ procedure Close
136
+ (Filter : in out Filter_Type;
137
+ Ignore_Error : in Boolean := False)
138
+ is
139
+ Code : Thin.Int;
140
+ begin
141
+ if not Ignore_Error and then not Is_Open (Filter) then
142
+ raise Status_Error;
143
+ end if;
144
+
145
+ Code := Flate (Filter.Compression).Done (To_Thin_Access (Filter.Strm));
146
+
147
+ if Ignore_Error or else Code = Thin.Z_OK then
148
+ Free (Filter.Strm);
149
+ else
150
+ declare
151
+ Error_Message : constant String
152
+ := Last_Error_Message (Filter.Strm.all);
153
+ begin
154
+ Free (Filter.Strm);
155
+ Ada.Exceptions.Raise_Exception
156
+ (ZLib_Error'Identity,
157
+ Return_Code_Enum'Image (Return_Code (Code))
158
+ & ": " & Error_Message);
159
+ end;
160
+ end if;
161
+ end Close;
162
+
163
+ -----------
164
+ -- CRC32 --
165
+ -----------
166
+
167
+ function CRC32
168
+ (CRC : in Unsigned_32;
169
+ Data : in Ada.Streams.Stream_Element_Array)
170
+ return Unsigned_32
171
+ is
172
+ use Thin;
173
+ begin
174
+ return Unsigned_32 (crc32 (ULong (CRC),
175
+ Data'Address,
176
+ Data'Length));
177
+ end CRC32;
178
+
179
+ procedure CRC32
180
+ (CRC : in out Unsigned_32;
181
+ Data : in Ada.Streams.Stream_Element_Array) is
182
+ begin
183
+ CRC := CRC32 (CRC, Data);
184
+ end CRC32;
185
+
186
+ ------------------
187
+ -- Deflate_Init --
188
+ ------------------
189
+
190
+ procedure Deflate_Init
191
+ (Filter : in out Filter_Type;
192
+ Level : in Compression_Level := Default_Compression;
193
+ Strategy : in Strategy_Type := Default_Strategy;
194
+ Method : in Compression_Method := Deflated;
195
+ Window_Bits : in Window_Bits_Type := Default_Window_Bits;
196
+ Memory_Level : in Memory_Level_Type := Default_Memory_Level;
197
+ Header : in Header_Type := Default)
198
+ is
199
+ use type Thin.Int;
200
+ Win_Bits : Thin.Int := Thin.Int (Window_Bits);
201
+ begin
202
+ if Is_Open (Filter) then
203
+ raise Status_Error;
204
+ end if;
205
+
206
+ -- We allow ZLib to make header only in case of default header type.
207
+ -- Otherwise we would either do header by ourselfs, or do not do
208
+ -- header at all.
209
+
210
+ if Header = None or else Header = GZip then
211
+ Win_Bits := -Win_Bits;
212
+ end if;
213
+
214
+ -- For the GZip CRC calculation and make headers.
215
+
216
+ if Header = GZip then
217
+ Filter.CRC := 0;
218
+ Filter.Offset := Simple_GZip_Header'First;
219
+ else
220
+ Filter.Offset := Simple_GZip_Header'Last + 1;
221
+ end if;
222
+
223
+ Filter.Strm := new Z_Stream;
224
+ Filter.Compression := True;
225
+ Filter.Stream_End := False;
226
+ Filter.Header := Header;
227
+
228
+ if Thin.Deflate_Init
229
+ (To_Thin_Access (Filter.Strm),
230
+ Level => Thin.Int (Level),
231
+ method => Thin.Int (Method),
232
+ windowBits => Win_Bits,
233
+ memLevel => Thin.Int (Memory_Level),
234
+ strategy => Thin.Int (Strategy)) /= Thin.Z_OK
235
+ then
236
+ Raise_Error (Filter.Strm.all);
237
+ end if;
238
+ end Deflate_Init;
239
+
240
+ -----------
241
+ -- Flush --
242
+ -----------
243
+
244
+ procedure Flush
245
+ (Filter : in out Filter_Type;
246
+ Out_Data : out Ada.Streams.Stream_Element_Array;
247
+ Out_Last : out Ada.Streams.Stream_Element_Offset;
248
+ Flush : in Flush_Mode)
249
+ is
250
+ No_Data : Stream_Element_Array := (1 .. 0 => 0);
251
+ Last : Stream_Element_Offset;
252
+ begin
253
+ Translate (Filter, No_Data, Last, Out_Data, Out_Last, Flush);
254
+ end Flush;
255
+
256
+ -----------------------
257
+ -- Generic_Translate --
258
+ -----------------------
259
+
260
+ procedure Generic_Translate
261
+ (Filter : in out ZLib.Filter_Type;
262
+ In_Buffer_Size : in Integer := Default_Buffer_Size;
263
+ Out_Buffer_Size : in Integer := Default_Buffer_Size)
264
+ is
265
+ In_Buffer : Stream_Element_Array
266
+ (1 .. Stream_Element_Offset (In_Buffer_Size));
267
+ Out_Buffer : Stream_Element_Array
268
+ (1 .. Stream_Element_Offset (Out_Buffer_Size));
269
+ Last : Stream_Element_Offset;
270
+ In_Last : Stream_Element_Offset;
271
+ In_First : Stream_Element_Offset;
272
+ Out_Last : Stream_Element_Offset;
273
+ begin
274
+ Main : loop
275
+ Data_In (In_Buffer, Last);
276
+
277
+ In_First := In_Buffer'First;
278
+
279
+ loop
280
+ Translate
281
+ (Filter => Filter,
282
+ In_Data => In_Buffer (In_First .. Last),
283
+ In_Last => In_Last,
284
+ Out_Data => Out_Buffer,
285
+ Out_Last => Out_Last,
286
+ Flush => Flush_Finish (Last < In_Buffer'First));
287
+
288
+ if Out_Buffer'First <= Out_Last then
289
+ Data_Out (Out_Buffer (Out_Buffer'First .. Out_Last));
290
+ end if;
291
+
292
+ exit Main when Stream_End (Filter);
293
+
294
+ -- The end of in buffer.
295
+
296
+ exit when In_Last = Last;
297
+
298
+ In_First := In_Last + 1;
299
+ end loop;
300
+ end loop Main;
301
+
302
+ end Generic_Translate;
303
+
304
+ ------------------
305
+ -- Inflate_Init --
306
+ ------------------
307
+
308
+ procedure Inflate_Init
309
+ (Filter : in out Filter_Type;
310
+ Window_Bits : in Window_Bits_Type := Default_Window_Bits;
311
+ Header : in Header_Type := Default)
312
+ is
313
+ use type Thin.Int;
314
+ Win_Bits : Thin.Int := Thin.Int (Window_Bits);
315
+
316
+ procedure Check_Version;
317
+ -- Check the latest header types compatibility.
318
+
319
+ procedure Check_Version is
320
+ begin
321
+ if Version <= "1.1.4" then
322
+ Raise_Error
323
+ ("Inflate header type " & Header_Type'Image (Header)
324
+ & " incompatible with ZLib version " & Version);
325
+ end if;
326
+ end Check_Version;
327
+
328
+ begin
329
+ if Is_Open (Filter) then
330
+ raise Status_Error;
331
+ end if;
332
+
333
+ case Header is
334
+ when None =>
335
+ Check_Version;
336
+
337
+ -- Inflate data without headers determined
338
+ -- by negative Win_Bits.
339
+
340
+ Win_Bits := -Win_Bits;
341
+ when GZip =>
342
+ Check_Version;
343
+
344
+ -- Inflate gzip data defined by flag 16.
345
+
346
+ Win_Bits := Win_Bits + 16;
347
+ when Auto =>
348
+ Check_Version;
349
+
350
+ -- Inflate with automatic detection
351
+ -- of gzip or native header defined by flag 32.
352
+
353
+ Win_Bits := Win_Bits + 32;
354
+ when Default => null;
355
+ end case;
356
+
357
+ Filter.Strm := new Z_Stream;
358
+ Filter.Compression := False;
359
+ Filter.Stream_End := False;
360
+ Filter.Header := Header;
361
+
362
+ if Thin.Inflate_Init
363
+ (To_Thin_Access (Filter.Strm), Win_Bits) /= Thin.Z_OK
364
+ then
365
+ Raise_Error (Filter.Strm.all);
366
+ end if;
367
+ end Inflate_Init;
368
+
369
+ -------------
370
+ -- Is_Open --
371
+ -------------
372
+
373
+ function Is_Open (Filter : in Filter_Type) return Boolean is
374
+ begin
375
+ return Filter.Strm /= null;
376
+ end Is_Open;
377
+
378
+ -----------------
379
+ -- Raise_Error --
380
+ -----------------
381
+
382
+ procedure Raise_Error (Message : in String) is
383
+ begin
384
+ Ada.Exceptions.Raise_Exception (ZLib_Error'Identity, Message);
385
+ end Raise_Error;
386
+
387
+ procedure Raise_Error (Stream : in Z_Stream) is
388
+ begin
389
+ Raise_Error (Last_Error_Message (Stream));
390
+ end Raise_Error;
391
+
392
+ ----------
393
+ -- Read --
394
+ ----------
395
+
396
+ procedure Read
397
+ (Filter : in out Filter_Type;
398
+ Item : out Ada.Streams.Stream_Element_Array;
399
+ Last : out Ada.Streams.Stream_Element_Offset;
400
+ Flush : in Flush_Mode := No_Flush)
401
+ is
402
+ In_Last : Stream_Element_Offset;
403
+ Item_First : Ada.Streams.Stream_Element_Offset := Item'First;
404
+ V_Flush : Flush_Mode := Flush;
405
+
406
+ begin
407
+ pragma Assert (Rest_First in Buffer'First .. Buffer'Last + 1);
408
+ pragma Assert (Rest_Last in Buffer'First - 1 .. Buffer'Last);
409
+
410
+ loop
411
+ if Rest_Last = Buffer'First - 1 then
412
+ V_Flush := Finish;
413
+
414
+ elsif Rest_First > Rest_Last then
415
+ Read (Buffer, Rest_Last);
416
+ Rest_First := Buffer'First;
417
+
418
+ if Rest_Last < Buffer'First then
419
+ V_Flush := Finish;
420
+ end if;
421
+ end if;
422
+
423
+ Translate
424
+ (Filter => Filter,
425
+ In_Data => Buffer (Rest_First .. Rest_Last),
426
+ In_Last => In_Last,
427
+ Out_Data => Item (Item_First .. Item'Last),
428
+ Out_Last => Last,
429
+ Flush => V_Flush);
430
+
431
+ Rest_First := In_Last + 1;
432
+
433
+ exit when Stream_End (Filter)
434
+ or else Last = Item'Last
435
+ or else (Last >= Item'First and then Allow_Read_Some);
436
+
437
+ Item_First := Last + 1;
438
+ end loop;
439
+ end Read;
440
+
441
+ ----------------
442
+ -- Stream_End --
443
+ ----------------
444
+
445
+ function Stream_End (Filter : in Filter_Type) return Boolean is
446
+ begin
447
+ if Filter.Header = GZip and Filter.Compression then
448
+ return Filter.Stream_End
449
+ and then Filter.Offset = Footer_Array'Last + 1;
450
+ else
451
+ return Filter.Stream_End;
452
+ end if;
453
+ end Stream_End;
454
+
455
+ --------------
456
+ -- Total_In --
457
+ --------------
458
+
459
+ function Total_In (Filter : in Filter_Type) return Count is
460
+ begin
461
+ return Count (Thin.Total_In (To_Thin_Access (Filter.Strm).all));
462
+ end Total_In;
463
+
464
+ ---------------
465
+ -- Total_Out --
466
+ ---------------
467
+
468
+ function Total_Out (Filter : in Filter_Type) return Count is
469
+ begin
470
+ return Count (Thin.Total_Out (To_Thin_Access (Filter.Strm).all));
471
+ end Total_Out;
472
+
473
+ ---------------
474
+ -- Translate --
475
+ ---------------
476
+
477
+ procedure Translate
478
+ (Filter : in out Filter_Type;
479
+ In_Data : in Ada.Streams.Stream_Element_Array;
480
+ In_Last : out Ada.Streams.Stream_Element_Offset;
481
+ Out_Data : out Ada.Streams.Stream_Element_Array;
482
+ Out_Last : out Ada.Streams.Stream_Element_Offset;
483
+ Flush : in Flush_Mode) is
484
+ begin
485
+ if Filter.Header = GZip and then Filter.Compression then
486
+ Translate_GZip
487
+ (Filter => Filter,
488
+ In_Data => In_Data,
489
+ In_Last => In_Last,
490
+ Out_Data => Out_Data,
491
+ Out_Last => Out_Last,
492
+ Flush => Flush);
493
+ else
494
+ Translate_Auto
495
+ (Filter => Filter,
496
+ In_Data => In_Data,
497
+ In_Last => In_Last,
498
+ Out_Data => Out_Data,
499
+ Out_Last => Out_Last,
500
+ Flush => Flush);
501
+ end if;
502
+ end Translate;
503
+
504
+ --------------------
505
+ -- Translate_Auto --
506
+ --------------------
507
+
508
+ procedure Translate_Auto
509
+ (Filter : in out Filter_Type;
510
+ In_Data : in Ada.Streams.Stream_Element_Array;
511
+ In_Last : out Ada.Streams.Stream_Element_Offset;
512
+ Out_Data : out Ada.Streams.Stream_Element_Array;
513
+ Out_Last : out Ada.Streams.Stream_Element_Offset;
514
+ Flush : in Flush_Mode)
515
+ is
516
+ use type Thin.Int;
517
+ Code : Thin.Int;
518
+
519
+ begin
520
+ if not Is_Open (Filter) then
521
+ raise Status_Error;
522
+ end if;
523
+
524
+ if Out_Data'Length = 0 and then In_Data'Length = 0 then
525
+ raise Constraint_Error;
526
+ end if;
527
+
528
+ Set_Out (Filter.Strm.all, Out_Data'Address, Out_Data'Length);
529
+ Set_In (Filter.Strm.all, In_Data'Address, In_Data'Length);
530
+
531
+ Code := Flate (Filter.Compression).Step
532
+ (To_Thin_Access (Filter.Strm),
533
+ Thin.Int (Flush));
534
+
535
+ if Code = Thin.Z_STREAM_END then
536
+ Filter.Stream_End := True;
537
+ else
538
+ Check_Error (Filter.Strm.all, Code);
539
+ end if;
540
+
541
+ In_Last := In_Data'Last
542
+ - Stream_Element_Offset (Avail_In (Filter.Strm.all));
543
+ Out_Last := Out_Data'Last
544
+ - Stream_Element_Offset (Avail_Out (Filter.Strm.all));
545
+ end Translate_Auto;
546
+
547
+ --------------------
548
+ -- Translate_GZip --
549
+ --------------------
550
+
551
+ procedure Translate_GZip
552
+ (Filter : in out Filter_Type;
553
+ In_Data : in Ada.Streams.Stream_Element_Array;
554
+ In_Last : out Ada.Streams.Stream_Element_Offset;
555
+ Out_Data : out Ada.Streams.Stream_Element_Array;
556
+ Out_Last : out Ada.Streams.Stream_Element_Offset;
557
+ Flush : in Flush_Mode)
558
+ is
559
+ Out_First : Stream_Element_Offset;
560
+
561
+ procedure Add_Data (Data : in Stream_Element_Array);
562
+ -- Add data to stream from the Filter.Offset till necessary,
563
+ -- used for add gzip headr/footer.
564
+
565
+ procedure Put_32
566
+ (Item : in out Stream_Element_Array;
567
+ Data : in Unsigned_32);
568
+ pragma Inline (Put_32);
569
+
570
+ --------------
571
+ -- Add_Data --
572
+ --------------
573
+
574
+ procedure Add_Data (Data : in Stream_Element_Array) is
575
+ Data_First : Stream_Element_Offset renames Filter.Offset;
576
+ Data_Last : Stream_Element_Offset;
577
+ Data_Len : Stream_Element_Offset; -- -1
578
+ Out_Len : Stream_Element_Offset; -- -1
579
+ begin
580
+ Out_First := Out_Last + 1;
581
+
582
+ if Data_First > Data'Last then
583
+ return;
584
+ end if;
585
+
586
+ Data_Len := Data'Last - Data_First;
587
+ Out_Len := Out_Data'Last - Out_First;
588
+
589
+ if Data_Len <= Out_Len then
590
+ Out_Last := Out_First + Data_Len;
591
+ Data_Last := Data'Last;
592
+ else
593
+ Out_Last := Out_Data'Last;
594
+ Data_Last := Data_First + Out_Len;
595
+ end if;
596
+
597
+ Out_Data (Out_First .. Out_Last) := Data (Data_First .. Data_Last);
598
+
599
+ Data_First := Data_Last + 1;
600
+ Out_First := Out_Last + 1;
601
+ end Add_Data;
602
+
603
+ ------------
604
+ -- Put_32 --
605
+ ------------
606
+
607
+ procedure Put_32
608
+ (Item : in out Stream_Element_Array;
609
+ Data : in Unsigned_32)
610
+ is
611
+ D : Unsigned_32 := Data;
612
+ begin
613
+ for J in Item'First .. Item'First + 3 loop
614
+ Item (J) := Stream_Element (D and 16#FF#);
615
+ D := Shift_Right (D, 8);
616
+ end loop;
617
+ end Put_32;
618
+
619
+ begin
620
+ Out_Last := Out_Data'First - 1;
621
+
622
+ if not Filter.Stream_End then
623
+ Add_Data (Simple_GZip_Header);
624
+
625
+ Translate_Auto
626
+ (Filter => Filter,
627
+ In_Data => In_Data,
628
+ In_Last => In_Last,
629
+ Out_Data => Out_Data (Out_First .. Out_Data'Last),
630
+ Out_Last => Out_Last,
631
+ Flush => Flush);
632
+
633
+ CRC32 (Filter.CRC, In_Data (In_Data'First .. In_Last));
634
+ end if;
635
+
636
+ if Filter.Stream_End and then Out_Last <= Out_Data'Last then
637
+ -- This detection method would work only when
638
+ -- Simple_GZip_Header'Last > Footer_Array'Last
639
+
640
+ if Filter.Offset = Simple_GZip_Header'Last + 1 then
641
+ Filter.Offset := Footer_Array'First;
642
+ end if;
643
+
644
+ declare
645
+ Footer : Footer_Array;
646
+ begin
647
+ Put_32 (Footer, Filter.CRC);
648
+ Put_32 (Footer (Footer'First + 4 .. Footer'Last),
649
+ Unsigned_32 (Total_In (Filter)));
650
+ Add_Data (Footer);
651
+ end;
652
+ end if;
653
+ end Translate_GZip;
654
+
655
+ -------------
656
+ -- Version --
657
+ -------------
658
+
659
+ function Version return String is
660
+ begin
661
+ return Interfaces.C.Strings.Value (Thin.zlibVersion);
662
+ end Version;
663
+
664
+ -----------
665
+ -- Write --
666
+ -----------
667
+
668
+ procedure Write
669
+ (Filter : in out Filter_Type;
670
+ Item : in Ada.Streams.Stream_Element_Array;
671
+ Flush : in Flush_Mode := No_Flush)
672
+ is
673
+ Buffer : Stream_Element_Array (1 .. Buffer_Size);
674
+ In_Last : Stream_Element_Offset;
675
+ Out_Last : Stream_Element_Offset;
676
+ In_First : Stream_Element_Offset := Item'First;
677
+ begin
678
+ if Item'Length = 0 and Flush = No_Flush then
679
+ return;
680
+ end if;
681
+
682
+ loop
683
+ Translate
684
+ (Filter => Filter,
685
+ In_Data => Item (In_First .. Item'Last),
686
+ In_Last => In_Last,
687
+ Out_Data => Buffer,
688
+ Out_Last => Out_Last,
689
+ Flush => Flush);
690
+
691
+ if Out_Last >= Buffer'First then
692
+ Write (Buffer (1 .. Out_Last));
693
+ end if;
694
+
695
+ exit when In_Last = Item'Last or Stream_End (Filter);
696
+
697
+ In_First := In_Last + 1;
698
+ end loop;
699
+ end Write;
700
+
701
+ end ZLib;