finishm 0.0.1

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Files changed (554) hide show
  1. checksums.yaml +7 -0
  2. data/.document +5 -0
  3. data/.gitmodules +3 -0
  4. data/.rspec +1 -0
  5. data/Gemfile +31 -0
  6. data/LICENSE.txt +20 -0
  7. data/README.md +59 -0
  8. data/Rakefile +51 -0
  9. data/VERSION +1 -0
  10. data/bin/assembly_visualiser +106 -0
  11. data/bin/check_primer_combinations.rb +73 -0
  12. data/bin/contig_joiner.rb +244 -0
  13. data/bin/contigs_against_assembly.rb +153 -0
  14. data/bin/finishm +143 -0
  15. data/bin/finishm_assembler +55 -0
  16. data/bin/finishm_gap_closer.rb +241 -0
  17. data/bin/kmer_abundance_file_tool.rb +49 -0
  18. data/bin/kmer_pattern_to_assembly.rb +377 -0
  19. data/bin/kmer_profile_finder.rb +92 -0
  20. data/bin/kmers_count_parse.d +52 -0
  21. data/bin/kmers_count_tabulate.d +123 -0
  22. data/bin/kmers_count_tabulate.rb +84 -0
  23. data/bin/pcr_result_parser.rb +108 -0
  24. data/bin/primer_finder.rb +119 -0
  25. data/bin/read_selection_by_kmer.d +174 -0
  26. data/bin/scaffold_by_pattern.rb +119 -0
  27. data/bin/scaffold_connection_possibilities_to_knowns.rb +193 -0
  28. data/bin/scaffold_end_coverages.rb +69 -0
  29. data/bin/trail_validator.rb +84 -0
  30. data/ext/mkrf_conf.rb +56 -0
  31. data/ext/src/Makefile +140 -0
  32. data/ext/src/src/allocArray.c +305 -0
  33. data/ext/src/src/allocArray.h +86 -0
  34. data/ext/src/src/autoOpen.c +107 -0
  35. data/ext/src/src/autoOpen.h +18 -0
  36. data/ext/src/src/binarySequences.c +813 -0
  37. data/ext/src/src/binarySequences.h +125 -0
  38. data/ext/src/src/concatenatedGraph.c +233 -0
  39. data/ext/src/src/concatenatedGraph.h +30 -0
  40. data/ext/src/src/concatenatedPreGraph.c +262 -0
  41. data/ext/src/src/concatenatedPreGraph.h +29 -0
  42. data/ext/src/src/correctedGraph.c +2643 -0
  43. data/ext/src/src/correctedGraph.h +32 -0
  44. data/ext/src/src/dfib.c +509 -0
  45. data/ext/src/src/dfib.h +69 -0
  46. data/ext/src/src/dfibHeap.c +89 -0
  47. data/ext/src/src/dfibHeap.h +39 -0
  48. data/ext/src/src/dfibpriv.h +105 -0
  49. data/ext/src/src/fib.c +628 -0
  50. data/ext/src/src/fib.h +78 -0
  51. data/ext/src/src/fibHeap.c +79 -0
  52. data/ext/src/src/fibHeap.h +41 -0
  53. data/ext/src/src/fibpriv.h +110 -0
  54. data/ext/src/src/globals.h +154 -0
  55. data/ext/src/src/graph.c +3932 -0
  56. data/ext/src/src/graph.h +233 -0
  57. data/ext/src/src/graphReConstruction.c +1472 -0
  58. data/ext/src/src/graphReConstruction.h +30 -0
  59. data/ext/src/src/graphStats.c +2167 -0
  60. data/ext/src/src/graphStats.h +72 -0
  61. data/ext/src/src/graphStructures.h +52 -0
  62. data/ext/src/src/kmer.c +652 -0
  63. data/ext/src/src/kmer.h +73 -0
  64. data/ext/src/src/kmerOccurenceTable.c +236 -0
  65. data/ext/src/src/kmerOccurenceTable.h +44 -0
  66. data/ext/src/src/kseq.h +223 -0
  67. data/ext/src/src/locallyCorrectedGraph.c +557 -0
  68. data/ext/src/src/locallyCorrectedGraph.h +40 -0
  69. data/ext/src/src/passageMarker.c +677 -0
  70. data/ext/src/src/passageMarker.h +137 -0
  71. data/ext/src/src/preGraph.c +1717 -0
  72. data/ext/src/src/preGraph.h +106 -0
  73. data/ext/src/src/preGraphConstruction.c +990 -0
  74. data/ext/src/src/preGraphConstruction.h +26 -0
  75. data/ext/src/src/probe_node_finder.c +84 -0
  76. data/ext/src/src/probe_node_finder.h +6 -0
  77. data/ext/src/src/readCoherentGraph.c +557 -0
  78. data/ext/src/src/readCoherentGraph.h +30 -0
  79. data/ext/src/src/readSet.c +1734 -0
  80. data/ext/src/src/readSet.h +67 -0
  81. data/ext/src/src/readToNode.c +218 -0
  82. data/ext/src/src/readToNode.h +35 -0
  83. data/ext/src/src/recycleBin.c +199 -0
  84. data/ext/src/src/recycleBin.h +58 -0
  85. data/ext/src/src/roadMap.c +342 -0
  86. data/ext/src/src/roadMap.h +65 -0
  87. data/ext/src/src/run.c +318 -0
  88. data/ext/src/src/run.h +52 -0
  89. data/ext/src/src/run2.c +744 -0
  90. data/ext/src/src/runReadToNode.c +29 -0
  91. data/ext/src/src/scaffold.c +1876 -0
  92. data/ext/src/src/scaffold.h +64 -0
  93. data/ext/src/src/shortReadPairs.c +1243 -0
  94. data/ext/src/src/shortReadPairs.h +32 -0
  95. data/ext/src/src/splay.c +259 -0
  96. data/ext/src/src/splay.h +43 -0
  97. data/ext/src/src/splayTable.c +1315 -0
  98. data/ext/src/src/splayTable.h +31 -0
  99. data/ext/src/src/tightString.c +362 -0
  100. data/ext/src/src/tightString.h +82 -0
  101. data/ext/src/src/utility.c +199 -0
  102. data/ext/src/src/utility.h +98 -0
  103. data/ext/src/third-party/zlib-1.2.3/ChangeLog +855 -0
  104. data/ext/src/third-party/zlib-1.2.3/FAQ +339 -0
  105. data/ext/src/third-party/zlib-1.2.3/INDEX +51 -0
  106. data/ext/src/third-party/zlib-1.2.3/Makefile +154 -0
  107. data/ext/src/third-party/zlib-1.2.3/Makefile.in +154 -0
  108. data/ext/src/third-party/zlib-1.2.3/README +125 -0
  109. data/ext/src/third-party/zlib-1.2.3/adler32.c +149 -0
  110. data/ext/src/third-party/zlib-1.2.3/adler32.o +0 -0
  111. data/ext/src/third-party/zlib-1.2.3/algorithm.txt +209 -0
  112. data/ext/src/third-party/zlib-1.2.3/amiga/Makefile.pup +66 -0
  113. data/ext/src/third-party/zlib-1.2.3/amiga/Makefile.sas +65 -0
  114. data/ext/src/third-party/zlib-1.2.3/as400/bndsrc +132 -0
  115. data/ext/src/third-party/zlib-1.2.3/as400/compile.clp +123 -0
  116. data/ext/src/third-party/zlib-1.2.3/as400/readme.txt +111 -0
  117. data/ext/src/third-party/zlib-1.2.3/as400/zlib.inc +331 -0
  118. data/ext/src/third-party/zlib-1.2.3/compress.c +79 -0
  119. data/ext/src/third-party/zlib-1.2.3/compress.o +0 -0
  120. data/ext/src/third-party/zlib-1.2.3/configure +459 -0
  121. data/ext/src/third-party/zlib-1.2.3/contrib/README.contrib +71 -0
  122. data/ext/src/third-party/zlib-1.2.3/contrib/ada/buffer_demo.adb +106 -0
  123. data/ext/src/third-party/zlib-1.2.3/contrib/ada/mtest.adb +156 -0
  124. data/ext/src/third-party/zlib-1.2.3/contrib/ada/read.adb +156 -0
  125. data/ext/src/third-party/zlib-1.2.3/contrib/ada/readme.txt +65 -0
  126. data/ext/src/third-party/zlib-1.2.3/contrib/ada/test.adb +463 -0
  127. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-streams.adb +225 -0
  128. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-streams.ads +114 -0
  129. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-thin.adb +141 -0
  130. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-thin.ads +450 -0
  131. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib.adb +701 -0
  132. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib.ads +328 -0
  133. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib.gpr +20 -0
  134. data/ext/src/third-party/zlib-1.2.3/contrib/asm586/README.586 +43 -0
  135. data/ext/src/third-party/zlib-1.2.3/contrib/asm586/match.S +364 -0
  136. data/ext/src/third-party/zlib-1.2.3/contrib/asm686/README.686 +34 -0
  137. data/ext/src/third-party/zlib-1.2.3/contrib/asm686/match.S +329 -0
  138. data/ext/src/third-party/zlib-1.2.3/contrib/blast/Makefile +8 -0
  139. data/ext/src/third-party/zlib-1.2.3/contrib/blast/README +4 -0
  140. data/ext/src/third-party/zlib-1.2.3/contrib/blast/blast.c +444 -0
  141. data/ext/src/third-party/zlib-1.2.3/contrib/blast/blast.h +71 -0
  142. data/ext/src/third-party/zlib-1.2.3/contrib/blast/test.pk +0 -0
  143. data/ext/src/third-party/zlib-1.2.3/contrib/blast/test.txt +1 -0
  144. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/ZLib.pas +557 -0
  145. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/ZLibConst.pas +11 -0
  146. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/readme.txt +76 -0
  147. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/zlibd32.mak +93 -0
  148. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.build +33 -0
  149. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.chm +0 -0
  150. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.sln +21 -0
  151. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/AssemblyInfo.cs +58 -0
  152. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/ChecksumImpl.cs +202 -0
  153. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/CircularBuffer.cs +83 -0
  154. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/CodecBase.cs +198 -0
  155. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/Deflater.cs +106 -0
  156. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/DotZLib.cs +288 -0
  157. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/DotZLib.csproj +141 -0
  158. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/GZipStream.cs +301 -0
  159. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/Inflater.cs +105 -0
  160. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/UnitTests.cs +274 -0
  161. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/LICENSE_1_0.txt +23 -0
  162. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/readme.txt +58 -0
  163. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/README +1 -0
  164. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/infback9.c +608 -0
  165. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/infback9.h +37 -0
  166. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inffix9.h +107 -0
  167. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inflate9.h +47 -0
  168. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inftree9.c +323 -0
  169. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inftree9.h +55 -0
  170. data/ext/src/third-party/zlib-1.2.3/contrib/inflate86/inffas86.c +1157 -0
  171. data/ext/src/third-party/zlib-1.2.3/contrib/inflate86/inffast.S +1368 -0
  172. data/ext/src/third-party/zlib-1.2.3/contrib/iostream/test.cpp +24 -0
  173. data/ext/src/third-party/zlib-1.2.3/contrib/iostream/zfstream.cpp +329 -0
  174. data/ext/src/third-party/zlib-1.2.3/contrib/iostream/zfstream.h +128 -0
  175. data/ext/src/third-party/zlib-1.2.3/contrib/iostream2/zstream.h +307 -0
  176. data/ext/src/third-party/zlib-1.2.3/contrib/iostream2/zstream_test.cpp +25 -0
  177. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/README +35 -0
  178. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/TODO +17 -0
  179. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/test.cc +50 -0
  180. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/zfstream.cc +479 -0
  181. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/zfstream.h +466 -0
  182. data/ext/src/third-party/zlib-1.2.3/contrib/masm686/match.asm +413 -0
  183. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/bld_ml64.bat +2 -0
  184. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/gvmat64.asm +513 -0
  185. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/gvmat64.obj +0 -0
  186. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/inffas8664.c +186 -0
  187. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/inffasx64.asm +392 -0
  188. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/inffasx64.obj +0 -0
  189. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/readme.txt +28 -0
  190. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/bld_ml32.bat +2 -0
  191. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/gvmat32.asm +972 -0
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  193. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/gvmat32c.c +62 -0
  194. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/inffas32.asm +1083 -0
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  196. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/mkasm.bat +3 -0
  197. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/readme.txt +21 -0
  198. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/ChangeLogUnzip +67 -0
  199. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/Makefile +25 -0
  200. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/crypt.h +132 -0
  201. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/ioapi.c +177 -0
  202. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/ioapi.h +75 -0
  203. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/iowin32.c +270 -0
  204. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/iowin32.h +21 -0
  205. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/miniunz.c +585 -0
  206. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/minizip.c +420 -0
  207. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/mztools.c +281 -0
  208. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/mztools.h +31 -0
  209. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/unzip.c +1598 -0
  210. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/unzip.h +354 -0
  211. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/zip.c +1219 -0
  212. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/zip.h +235 -0
  213. data/ext/src/third-party/zlib-1.2.3/contrib/pascal/example.pas +599 -0
  214. data/ext/src/third-party/zlib-1.2.3/contrib/pascal/readme.txt +76 -0
  215. data/ext/src/third-party/zlib-1.2.3/contrib/pascal/zlibd32.mak +93 -0
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  217. data/ext/src/third-party/zlib-1.2.3/contrib/puff/Makefile +8 -0
  218. data/ext/src/third-party/zlib-1.2.3/contrib/puff/README +63 -0
  219. data/ext/src/third-party/zlib-1.2.3/contrib/puff/puff.c +837 -0
  220. data/ext/src/third-party/zlib-1.2.3/contrib/puff/puff.h +31 -0
  221. data/ext/src/third-party/zlib-1.2.3/contrib/puff/zeros.raw +0 -0
  222. data/ext/src/third-party/zlib-1.2.3/contrib/testzlib/testzlib.c +275 -0
  223. data/ext/src/third-party/zlib-1.2.3/contrib/testzlib/testzlib.txt +10 -0
  224. data/ext/src/third-party/zlib-1.2.3/contrib/untgz/Makefile +14 -0
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  226. data/ext/src/third-party/zlib-1.2.3/contrib/untgz/untgz.c +674 -0
  227. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/readme.txt +73 -0
  228. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/miniunz.vcproj +126 -0
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  245. data/ext/src/third-party/zlib-1.2.3/crc32.c +423 -0
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  248. data/ext/src/third-party/zlib-1.2.3/deflate.c +1736 -0
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  251. data/ext/src/third-party/zlib-1.2.3/example +0 -0
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  253. data/ext/src/third-party/zlib-1.2.3/examples/README.examples +42 -0
  254. data/ext/src/third-party/zlib-1.2.3/examples/fitblk.c +233 -0
  255. data/ext/src/third-party/zlib-1.2.3/examples/gun.c +693 -0
  256. data/ext/src/third-party/zlib-1.2.3/examples/gzappend.c +500 -0
  257. data/ext/src/third-party/zlib-1.2.3/examples/gzjoin.c +448 -0
  258. data/ext/src/third-party/zlib-1.2.3/examples/gzlog.c +413 -0
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6
+ ProjectGuid = "{BB1EE0B1-1808-46CB-B786-949D91117FC5}"
7
+ >
8
+ <Build>
9
+ <Settings
10
+ ApplicationIcon = ""
11
+ AssemblyKeyContainerName = ""
12
+ AssemblyName = "DotZLib"
13
+ AssemblyOriginatorKeyFile = ""
14
+ DefaultClientScript = "JScript"
15
+ DefaultHTMLPageLayout = "Grid"
16
+ DefaultTargetSchema = "IE50"
17
+ DelaySign = "false"
18
+ OutputType = "Library"
19
+ PreBuildEvent = ""
20
+ PostBuildEvent = ""
21
+ RootNamespace = "DotZLib"
22
+ RunPostBuildEvent = "OnBuildSuccess"
23
+ StartupObject = ""
24
+ >
25
+ <Config
26
+ Name = "Debug"
27
+ AllowUnsafeBlocks = "false"
28
+ BaseAddress = "285212672"
29
+ CheckForOverflowUnderflow = "false"
30
+ ConfigurationOverrideFile = ""
31
+ DefineConstants = "DEBUG;TRACE"
32
+ DocumentationFile = "docs\DotZLib.xml"
33
+ DebugSymbols = "true"
34
+ FileAlignment = "4096"
35
+ IncrementalBuild = "false"
36
+ NoStdLib = "false"
37
+ NoWarn = "1591"
38
+ Optimize = "false"
39
+ OutputPath = "bin\Debug\"
40
+ RegisterForComInterop = "false"
41
+ RemoveIntegerChecks = "false"
42
+ TreatWarningsAsErrors = "false"
43
+ WarningLevel = "4"
44
+ />
45
+ <Config
46
+ Name = "Release"
47
+ AllowUnsafeBlocks = "false"
48
+ BaseAddress = "285212672"
49
+ CheckForOverflowUnderflow = "false"
50
+ ConfigurationOverrideFile = ""
51
+ DefineConstants = "TRACE"
52
+ DocumentationFile = "docs\DotZLib.xml"
53
+ DebugSymbols = "false"
54
+ FileAlignment = "4096"
55
+ IncrementalBuild = "false"
56
+ NoStdLib = "false"
57
+ NoWarn = ""
58
+ Optimize = "true"
59
+ OutputPath = "bin\Release\"
60
+ RegisterForComInterop = "false"
61
+ RemoveIntegerChecks = "false"
62
+ TreatWarningsAsErrors = "false"
63
+ WarningLevel = "4"
64
+ />
65
+ </Settings>
66
+ <References>
67
+ <Reference
68
+ Name = "System"
69
+ AssemblyName = "System"
70
+ HintPath = "C:\WINNT\Microsoft.NET\Framework\v1.1.4322\System.dll"
71
+ />
72
+ <Reference
73
+ Name = "System.Data"
74
+ AssemblyName = "System.Data"
75
+ HintPath = "C:\WINNT\Microsoft.NET\Framework\v1.1.4322\System.Data.dll"
76
+ />
77
+ <Reference
78
+ Name = "System.XML"
79
+ AssemblyName = "System.Xml"
80
+ HintPath = "C:\WINNT\Microsoft.NET\Framework\v1.1.4322\System.XML.dll"
81
+ />
82
+ <Reference
83
+ Name = "nunit.framework"
84
+ AssemblyName = "nunit.framework"
85
+ HintPath = "E:\apps\NUnit V2.1\\bin\nunit.framework.dll"
86
+ AssemblyFolderKey = "hklm\dn\nunit.framework"
87
+ />
88
+ </References>
89
+ </Build>
90
+ <Files>
91
+ <Include>
92
+ <File
93
+ RelPath = "AssemblyInfo.cs"
94
+ SubType = "Code"
95
+ BuildAction = "Compile"
96
+ />
97
+ <File
98
+ RelPath = "ChecksumImpl.cs"
99
+ SubType = "Code"
100
+ BuildAction = "Compile"
101
+ />
102
+ <File
103
+ RelPath = "CircularBuffer.cs"
104
+ SubType = "Code"
105
+ BuildAction = "Compile"
106
+ />
107
+ <File
108
+ RelPath = "CodecBase.cs"
109
+ SubType = "Code"
110
+ BuildAction = "Compile"
111
+ />
112
+ <File
113
+ RelPath = "Deflater.cs"
114
+ SubType = "Code"
115
+ BuildAction = "Compile"
116
+ />
117
+ <File
118
+ RelPath = "DotZLib.cs"
119
+ SubType = "Code"
120
+ BuildAction = "Compile"
121
+ />
122
+ <File
123
+ RelPath = "GZipStream.cs"
124
+ SubType = "Code"
125
+ BuildAction = "Compile"
126
+ />
127
+ <File
128
+ RelPath = "Inflater.cs"
129
+ SubType = "Code"
130
+ BuildAction = "Compile"
131
+ />
132
+ <File
133
+ RelPath = "UnitTests.cs"
134
+ SubType = "Code"
135
+ BuildAction = "Compile"
136
+ />
137
+ </Include>
138
+ </Files>
139
+ </CSHARP>
140
+ </VisualStudioProject>
141
+
@@ -0,0 +1,301 @@
1
+ //
2
+ // � Copyright Henrik Ravn 2004
3
+ //
4
+ // Use, modification and distribution are subject to the Boost Software License, Version 1.0.
5
+ // (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
6
+ //
7
+
8
+ using System;
9
+ using System.IO;
10
+ using System.Runtime.InteropServices;
11
+
12
+ namespace DotZLib
13
+ {
14
+ /// <summary>
15
+ /// Implements a compressed <see cref="Stream"/>, in GZip (.gz) format.
16
+ /// </summary>
17
+ public class GZipStream : Stream, IDisposable
18
+ {
19
+ #region Dll Imports
20
+ [DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl, CharSet=CharSet.Ansi)]
21
+ private static extern IntPtr gzopen(string name, string mode);
22
+
23
+ [DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
24
+ private static extern int gzclose(IntPtr gzFile);
25
+
26
+ [DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
27
+ private static extern int gzwrite(IntPtr gzFile, int data, int length);
28
+
29
+ [DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
30
+ private static extern int gzread(IntPtr gzFile, int data, int length);
31
+
32
+ [DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
33
+ private static extern int gzgetc(IntPtr gzFile);
34
+
35
+ [DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
36
+ private static extern int gzputc(IntPtr gzFile, int c);
37
+
38
+ #endregion
39
+
40
+ #region Private data
41
+ private IntPtr _gzFile;
42
+ private bool _isDisposed = false;
43
+ private bool _isWriting;
44
+ #endregion
45
+
46
+ #region Constructors
47
+ /// <summary>
48
+ /// Creates a new file as a writeable GZipStream
49
+ /// </summary>
50
+ /// <param name="fileName">The name of the compressed file to create</param>
51
+ /// <param name="level">The compression level to use when adding data</param>
52
+ /// <exception cref="ZLibException">If an error occurred in the internal zlib function</exception>
53
+ public GZipStream(string fileName, CompressLevel level)
54
+ {
55
+ _isWriting = true;
56
+ _gzFile = gzopen(fileName, String.Format("wb{0}", (int)level));
57
+ if (_gzFile == IntPtr.Zero)
58
+ throw new ZLibException(-1, "Could not open " + fileName);
59
+ }
60
+
61
+ /// <summary>
62
+ /// Opens an existing file as a readable GZipStream
63
+ /// </summary>
64
+ /// <param name="fileName">The name of the file to open</param>
65
+ /// <exception cref="ZLibException">If an error occurred in the internal zlib function</exception>
66
+ public GZipStream(string fileName)
67
+ {
68
+ _isWriting = false;
69
+ _gzFile = gzopen(fileName, "rb");
70
+ if (_gzFile == IntPtr.Zero)
71
+ throw new ZLibException(-1, "Could not open " + fileName);
72
+
73
+ }
74
+ #endregion
75
+
76
+ #region Access properties
77
+ /// <summary>
78
+ /// Returns true of this stream can be read from, false otherwise
79
+ /// </summary>
80
+ public override bool CanRead
81
+ {
82
+ get
83
+ {
84
+ return !_isWriting;
85
+ }
86
+ }
87
+
88
+
89
+ /// <summary>
90
+ /// Returns false.
91
+ /// </summary>
92
+ public override bool CanSeek
93
+ {
94
+ get
95
+ {
96
+ return false;
97
+ }
98
+ }
99
+
100
+ /// <summary>
101
+ /// Returns true if this tsream is writeable, false otherwise
102
+ /// </summary>
103
+ public override bool CanWrite
104
+ {
105
+ get
106
+ {
107
+ return _isWriting;
108
+ }
109
+ }
110
+ #endregion
111
+
112
+ #region Destructor & IDispose stuff
113
+
114
+ /// <summary>
115
+ /// Destroys this instance
116
+ /// </summary>
117
+ ~GZipStream()
118
+ {
119
+ cleanUp(false);
120
+ }
121
+
122
+ /// <summary>
123
+ /// Closes the external file handle
124
+ /// </summary>
125
+ public void Dispose()
126
+ {
127
+ cleanUp(true);
128
+ }
129
+
130
+ // Does the actual closing of the file handle.
131
+ private void cleanUp(bool isDisposing)
132
+ {
133
+ if (!_isDisposed)
134
+ {
135
+ gzclose(_gzFile);
136
+ _isDisposed = true;
137
+ }
138
+ }
139
+ #endregion
140
+
141
+ #region Basic reading and writing
142
+ /// <summary>
143
+ /// Attempts to read a number of bytes from the stream.
144
+ /// </summary>
145
+ /// <param name="buffer">The destination data buffer</param>
146
+ /// <param name="offset">The index of the first destination byte in <c>buffer</c></param>
147
+ /// <param name="count">The number of bytes requested</param>
148
+ /// <returns>The number of bytes read</returns>
149
+ /// <exception cref="ArgumentNullException">If <c>buffer</c> is null</exception>
150
+ /// <exception cref="ArgumentOutOfRangeException">If <c>count</c> or <c>offset</c> are negative</exception>
151
+ /// <exception cref="ArgumentException">If <c>offset</c> + <c>count</c> is &gt; buffer.Length</exception>
152
+ /// <exception cref="NotSupportedException">If this stream is not readable.</exception>
153
+ /// <exception cref="ObjectDisposedException">If this stream has been disposed.</exception>
154
+ public override int Read(byte[] buffer, int offset, int count)
155
+ {
156
+ if (!CanRead) throw new NotSupportedException();
157
+ if (buffer == null) throw new ArgumentNullException();
158
+ if (offset < 0 || count < 0) throw new ArgumentOutOfRangeException();
159
+ if ((offset+count) > buffer.Length) throw new ArgumentException();
160
+ if (_isDisposed) throw new ObjectDisposedException("GZipStream");
161
+
162
+ GCHandle h = GCHandle.Alloc(buffer, GCHandleType.Pinned);
163
+ int result;
164
+ try
165
+ {
166
+ result = gzread(_gzFile, h.AddrOfPinnedObject().ToInt32() + offset, count);
167
+ if (result < 0)
168
+ throw new IOException();
169
+ }
170
+ finally
171
+ {
172
+ h.Free();
173
+ }
174
+ return result;
175
+ }
176
+
177
+ /// <summary>
178
+ /// Attempts to read a single byte from the stream.
179
+ /// </summary>
180
+ /// <returns>The byte that was read, or -1 in case of error or End-Of-File</returns>
181
+ public override int ReadByte()
182
+ {
183
+ if (!CanRead) throw new NotSupportedException();
184
+ if (_isDisposed) throw new ObjectDisposedException("GZipStream");
185
+ return gzgetc(_gzFile);
186
+ }
187
+
188
+ /// <summary>
189
+ /// Writes a number of bytes to the stream
190
+ /// </summary>
191
+ /// <param name="buffer"></param>
192
+ /// <param name="offset"></param>
193
+ /// <param name="count"></param>
194
+ /// <exception cref="ArgumentNullException">If <c>buffer</c> is null</exception>
195
+ /// <exception cref="ArgumentOutOfRangeException">If <c>count</c> or <c>offset</c> are negative</exception>
196
+ /// <exception cref="ArgumentException">If <c>offset</c> + <c>count</c> is &gt; buffer.Length</exception>
197
+ /// <exception cref="NotSupportedException">If this stream is not writeable.</exception>
198
+ /// <exception cref="ObjectDisposedException">If this stream has been disposed.</exception>
199
+ public override void Write(byte[] buffer, int offset, int count)
200
+ {
201
+ if (!CanWrite) throw new NotSupportedException();
202
+ if (buffer == null) throw new ArgumentNullException();
203
+ if (offset < 0 || count < 0) throw new ArgumentOutOfRangeException();
204
+ if ((offset+count) > buffer.Length) throw new ArgumentException();
205
+ if (_isDisposed) throw new ObjectDisposedException("GZipStream");
206
+
207
+ GCHandle h = GCHandle.Alloc(buffer, GCHandleType.Pinned);
208
+ try
209
+ {
210
+ int result = gzwrite(_gzFile, h.AddrOfPinnedObject().ToInt32() + offset, count);
211
+ if (result < 0)
212
+ throw new IOException();
213
+ }
214
+ finally
215
+ {
216
+ h.Free();
217
+ }
218
+ }
219
+
220
+ /// <summary>
221
+ /// Writes a single byte to the stream
222
+ /// </summary>
223
+ /// <param name="value">The byte to add to the stream.</param>
224
+ /// <exception cref="NotSupportedException">If this stream is not writeable.</exception>
225
+ /// <exception cref="ObjectDisposedException">If this stream has been disposed.</exception>
226
+ public override void WriteByte(byte value)
227
+ {
228
+ if (!CanWrite) throw new NotSupportedException();
229
+ if (_isDisposed) throw new ObjectDisposedException("GZipStream");
230
+
231
+ int result = gzputc(_gzFile, (int)value);
232
+ if (result < 0)
233
+ throw new IOException();
234
+ }
235
+ #endregion
236
+
237
+ #region Position & length stuff
238
+ /// <summary>
239
+ /// Not supported.
240
+ /// </summary>
241
+ /// <param name="value"></param>
242
+ /// <exception cref="NotSupportedException">Always thrown</exception>
243
+ public override void SetLength(long value)
244
+ {
245
+ throw new NotSupportedException();
246
+ }
247
+
248
+ /// <summary>
249
+ /// Not suppported.
250
+ /// </summary>
251
+ /// <param name="offset"></param>
252
+ /// <param name="origin"></param>
253
+ /// <returns></returns>
254
+ /// <exception cref="NotSupportedException">Always thrown</exception>
255
+ public override long Seek(long offset, SeekOrigin origin)
256
+ {
257
+ throw new NotSupportedException();
258
+ }
259
+
260
+ /// <summary>
261
+ /// Flushes the <c>GZipStream</c>.
262
+ /// </summary>
263
+ /// <remarks>In this implementation, this method does nothing. This is because excessive
264
+ /// flushing may degrade the achievable compression rates.</remarks>
265
+ public override void Flush()
266
+ {
267
+ // left empty on purpose
268
+ }
269
+
270
+ /// <summary>
271
+ /// Gets/sets the current position in the <c>GZipStream</c>. Not suppported.
272
+ /// </summary>
273
+ /// <remarks>In this implementation this property is not supported</remarks>
274
+ /// <exception cref="NotSupportedException">Always thrown</exception>
275
+ public override long Position
276
+ {
277
+ get
278
+ {
279
+ throw new NotSupportedException();
280
+ }
281
+ set
282
+ {
283
+ throw new NotSupportedException();
284
+ }
285
+ }
286
+
287
+ /// <summary>
288
+ /// Gets the size of the stream. Not suppported.
289
+ /// </summary>
290
+ /// <remarks>In this implementation this property is not supported</remarks>
291
+ /// <exception cref="NotSupportedException">Always thrown</exception>
292
+ public override long Length
293
+ {
294
+ get
295
+ {
296
+ throw new NotSupportedException();
297
+ }
298
+ }
299
+ #endregion
300
+ }
301
+ }
@@ -0,0 +1,105 @@
1
+ //
2
+ // � Copyright Henrik Ravn 2004
3
+ //
4
+ // Use, modification and distribution are subject to the Boost Software License, Version 1.0.
5
+ // (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
6
+ //
7
+
8
+ using System;
9
+ using System.Diagnostics;
10
+ using System.Runtime.InteropServices;
11
+
12
+ namespace DotZLib
13
+ {
14
+
15
+ /// <summary>
16
+ /// Implements a data decompressor, using the inflate algorithm in the ZLib dll
17
+ /// </summary>
18
+ public class Inflater : CodecBase
19
+ {
20
+ #region Dll imports
21
+ [DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl, CharSet=CharSet.Ansi)]
22
+ private static extern int inflateInit_(ref ZStream sz, string vs, int size);
23
+
24
+ [DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
25
+ private static extern int inflate(ref ZStream sz, int flush);
26
+
27
+ [DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
28
+ private static extern int inflateReset(ref ZStream sz);
29
+
30
+ [DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
31
+ private static extern int inflateEnd(ref ZStream sz);
32
+ #endregion
33
+
34
+ /// <summary>
35
+ /// Constructs an new instance of the <c>Inflater</c>
36
+ /// </summary>
37
+ public Inflater() : base()
38
+ {
39
+ int retval = inflateInit_(ref _ztream, Info.Version, Marshal.SizeOf(_ztream));
40
+ if (retval != 0)
41
+ throw new ZLibException(retval, "Could not initialize inflater");
42
+
43
+ resetOutput();
44
+ }
45
+
46
+
47
+ /// <summary>
48
+ /// Adds more data to the codec to be processed.
49
+ /// </summary>
50
+ /// <param name="data">Byte array containing the data to be added to the codec</param>
51
+ /// <param name="offset">The index of the first byte to add from <c>data</c></param>
52
+ /// <param name="count">The number of bytes to add</param>
53
+ /// <remarks>Adding data may, or may not, raise the <c>DataAvailable</c> event</remarks>
54
+ public override void Add(byte[] data, int offset, int count)
55
+ {
56
+ if (data == null) throw new ArgumentNullException();
57
+ if (offset < 0 || count < 0) throw new ArgumentOutOfRangeException();
58
+ if ((offset+count) > data.Length) throw new ArgumentException();
59
+
60
+ int total = count;
61
+ int inputIndex = offset;
62
+ int err = 0;
63
+
64
+ while (err >= 0 && inputIndex < total)
65
+ {
66
+ copyInput(data, inputIndex, Math.Min(total - inputIndex, kBufferSize));
67
+ err = inflate(ref _ztream, (int)FlushTypes.None);
68
+ if (err == 0)
69
+ while (_ztream.avail_out == 0)
70
+ {
71
+ OnDataAvailable();
72
+ err = inflate(ref _ztream, (int)FlushTypes.None);
73
+ }
74
+
75
+ inputIndex += (int)_ztream.total_in;
76
+ }
77
+ setChecksum( _ztream.adler );
78
+ }
79
+
80
+
81
+ /// <summary>
82
+ /// Finishes up any pending data that needs to be processed and handled.
83
+ /// </summary>
84
+ public override void Finish()
85
+ {
86
+ int err;
87
+ do
88
+ {
89
+ err = inflate(ref _ztream, (int)FlushTypes.Finish);
90
+ OnDataAvailable();
91
+ }
92
+ while (err == 0);
93
+ setChecksum( _ztream.adler );
94
+ inflateReset(ref _ztream);
95
+ resetOutput();
96
+ }
97
+
98
+ /// <summary>
99
+ /// Closes the internal zlib inflate stream
100
+ /// </summary>
101
+ protected override void CleanUp() { inflateEnd(ref _ztream); }
102
+
103
+
104
+ }
105
+ }