finishm 0.0.1

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Files changed (554) hide show
  1. checksums.yaml +7 -0
  2. data/.document +5 -0
  3. data/.gitmodules +3 -0
  4. data/.rspec +1 -0
  5. data/Gemfile +31 -0
  6. data/LICENSE.txt +20 -0
  7. data/README.md +59 -0
  8. data/Rakefile +51 -0
  9. data/VERSION +1 -0
  10. data/bin/assembly_visualiser +106 -0
  11. data/bin/check_primer_combinations.rb +73 -0
  12. data/bin/contig_joiner.rb +244 -0
  13. data/bin/contigs_against_assembly.rb +153 -0
  14. data/bin/finishm +143 -0
  15. data/bin/finishm_assembler +55 -0
  16. data/bin/finishm_gap_closer.rb +241 -0
  17. data/bin/kmer_abundance_file_tool.rb +49 -0
  18. data/bin/kmer_pattern_to_assembly.rb +377 -0
  19. data/bin/kmer_profile_finder.rb +92 -0
  20. data/bin/kmers_count_parse.d +52 -0
  21. data/bin/kmers_count_tabulate.d +123 -0
  22. data/bin/kmers_count_tabulate.rb +84 -0
  23. data/bin/pcr_result_parser.rb +108 -0
  24. data/bin/primer_finder.rb +119 -0
  25. data/bin/read_selection_by_kmer.d +174 -0
  26. data/bin/scaffold_by_pattern.rb +119 -0
  27. data/bin/scaffold_connection_possibilities_to_knowns.rb +193 -0
  28. data/bin/scaffold_end_coverages.rb +69 -0
  29. data/bin/trail_validator.rb +84 -0
  30. data/ext/mkrf_conf.rb +56 -0
  31. data/ext/src/Makefile +140 -0
  32. data/ext/src/src/allocArray.c +305 -0
  33. data/ext/src/src/allocArray.h +86 -0
  34. data/ext/src/src/autoOpen.c +107 -0
  35. data/ext/src/src/autoOpen.h +18 -0
  36. data/ext/src/src/binarySequences.c +813 -0
  37. data/ext/src/src/binarySequences.h +125 -0
  38. data/ext/src/src/concatenatedGraph.c +233 -0
  39. data/ext/src/src/concatenatedGraph.h +30 -0
  40. data/ext/src/src/concatenatedPreGraph.c +262 -0
  41. data/ext/src/src/concatenatedPreGraph.h +29 -0
  42. data/ext/src/src/correctedGraph.c +2643 -0
  43. data/ext/src/src/correctedGraph.h +32 -0
  44. data/ext/src/src/dfib.c +509 -0
  45. data/ext/src/src/dfib.h +69 -0
  46. data/ext/src/src/dfibHeap.c +89 -0
  47. data/ext/src/src/dfibHeap.h +39 -0
  48. data/ext/src/src/dfibpriv.h +105 -0
  49. data/ext/src/src/fib.c +628 -0
  50. data/ext/src/src/fib.h +78 -0
  51. data/ext/src/src/fibHeap.c +79 -0
  52. data/ext/src/src/fibHeap.h +41 -0
  53. data/ext/src/src/fibpriv.h +110 -0
  54. data/ext/src/src/globals.h +154 -0
  55. data/ext/src/src/graph.c +3932 -0
  56. data/ext/src/src/graph.h +233 -0
  57. data/ext/src/src/graphReConstruction.c +1472 -0
  58. data/ext/src/src/graphReConstruction.h +30 -0
  59. data/ext/src/src/graphStats.c +2167 -0
  60. data/ext/src/src/graphStats.h +72 -0
  61. data/ext/src/src/graphStructures.h +52 -0
  62. data/ext/src/src/kmer.c +652 -0
  63. data/ext/src/src/kmer.h +73 -0
  64. data/ext/src/src/kmerOccurenceTable.c +236 -0
  65. data/ext/src/src/kmerOccurenceTable.h +44 -0
  66. data/ext/src/src/kseq.h +223 -0
  67. data/ext/src/src/locallyCorrectedGraph.c +557 -0
  68. data/ext/src/src/locallyCorrectedGraph.h +40 -0
  69. data/ext/src/src/passageMarker.c +677 -0
  70. data/ext/src/src/passageMarker.h +137 -0
  71. data/ext/src/src/preGraph.c +1717 -0
  72. data/ext/src/src/preGraph.h +106 -0
  73. data/ext/src/src/preGraphConstruction.c +990 -0
  74. data/ext/src/src/preGraphConstruction.h +26 -0
  75. data/ext/src/src/probe_node_finder.c +84 -0
  76. data/ext/src/src/probe_node_finder.h +6 -0
  77. data/ext/src/src/readCoherentGraph.c +557 -0
  78. data/ext/src/src/readCoherentGraph.h +30 -0
  79. data/ext/src/src/readSet.c +1734 -0
  80. data/ext/src/src/readSet.h +67 -0
  81. data/ext/src/src/readToNode.c +218 -0
  82. data/ext/src/src/readToNode.h +35 -0
  83. data/ext/src/src/recycleBin.c +199 -0
  84. data/ext/src/src/recycleBin.h +58 -0
  85. data/ext/src/src/roadMap.c +342 -0
  86. data/ext/src/src/roadMap.h +65 -0
  87. data/ext/src/src/run.c +318 -0
  88. data/ext/src/src/run.h +52 -0
  89. data/ext/src/src/run2.c +744 -0
  90. data/ext/src/src/runReadToNode.c +29 -0
  91. data/ext/src/src/scaffold.c +1876 -0
  92. data/ext/src/src/scaffold.h +64 -0
  93. data/ext/src/src/shortReadPairs.c +1243 -0
  94. data/ext/src/src/shortReadPairs.h +32 -0
  95. data/ext/src/src/splay.c +259 -0
  96. data/ext/src/src/splay.h +43 -0
  97. data/ext/src/src/splayTable.c +1315 -0
  98. data/ext/src/src/splayTable.h +31 -0
  99. data/ext/src/src/tightString.c +362 -0
  100. data/ext/src/src/tightString.h +82 -0
  101. data/ext/src/src/utility.c +199 -0
  102. data/ext/src/src/utility.h +98 -0
  103. data/ext/src/third-party/zlib-1.2.3/ChangeLog +855 -0
  104. data/ext/src/third-party/zlib-1.2.3/FAQ +339 -0
  105. data/ext/src/third-party/zlib-1.2.3/INDEX +51 -0
  106. data/ext/src/third-party/zlib-1.2.3/Makefile +154 -0
  107. data/ext/src/third-party/zlib-1.2.3/Makefile.in +154 -0
  108. data/ext/src/third-party/zlib-1.2.3/README +125 -0
  109. data/ext/src/third-party/zlib-1.2.3/adler32.c +149 -0
  110. data/ext/src/third-party/zlib-1.2.3/adler32.o +0 -0
  111. data/ext/src/third-party/zlib-1.2.3/algorithm.txt +209 -0
  112. data/ext/src/third-party/zlib-1.2.3/amiga/Makefile.pup +66 -0
  113. data/ext/src/third-party/zlib-1.2.3/amiga/Makefile.sas +65 -0
  114. data/ext/src/third-party/zlib-1.2.3/as400/bndsrc +132 -0
  115. data/ext/src/third-party/zlib-1.2.3/as400/compile.clp +123 -0
  116. data/ext/src/third-party/zlib-1.2.3/as400/readme.txt +111 -0
  117. data/ext/src/third-party/zlib-1.2.3/as400/zlib.inc +331 -0
  118. data/ext/src/third-party/zlib-1.2.3/compress.c +79 -0
  119. data/ext/src/third-party/zlib-1.2.3/compress.o +0 -0
  120. data/ext/src/third-party/zlib-1.2.3/configure +459 -0
  121. data/ext/src/third-party/zlib-1.2.3/contrib/README.contrib +71 -0
  122. data/ext/src/third-party/zlib-1.2.3/contrib/ada/buffer_demo.adb +106 -0
  123. data/ext/src/third-party/zlib-1.2.3/contrib/ada/mtest.adb +156 -0
  124. data/ext/src/third-party/zlib-1.2.3/contrib/ada/read.adb +156 -0
  125. data/ext/src/third-party/zlib-1.2.3/contrib/ada/readme.txt +65 -0
  126. data/ext/src/third-party/zlib-1.2.3/contrib/ada/test.adb +463 -0
  127. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-streams.adb +225 -0
  128. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-streams.ads +114 -0
  129. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-thin.adb +141 -0
  130. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-thin.ads +450 -0
  131. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib.adb +701 -0
  132. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib.ads +328 -0
  133. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib.gpr +20 -0
  134. data/ext/src/third-party/zlib-1.2.3/contrib/asm586/README.586 +43 -0
  135. data/ext/src/third-party/zlib-1.2.3/contrib/asm586/match.S +364 -0
  136. data/ext/src/third-party/zlib-1.2.3/contrib/asm686/README.686 +34 -0
  137. data/ext/src/third-party/zlib-1.2.3/contrib/asm686/match.S +329 -0
  138. data/ext/src/third-party/zlib-1.2.3/contrib/blast/Makefile +8 -0
  139. data/ext/src/third-party/zlib-1.2.3/contrib/blast/README +4 -0
  140. data/ext/src/third-party/zlib-1.2.3/contrib/blast/blast.c +444 -0
  141. data/ext/src/third-party/zlib-1.2.3/contrib/blast/blast.h +71 -0
  142. data/ext/src/third-party/zlib-1.2.3/contrib/blast/test.pk +0 -0
  143. data/ext/src/third-party/zlib-1.2.3/contrib/blast/test.txt +1 -0
  144. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/ZLib.pas +557 -0
  145. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/ZLibConst.pas +11 -0
  146. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/readme.txt +76 -0
  147. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/zlibd32.mak +93 -0
  148. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.build +33 -0
  149. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.chm +0 -0
  150. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.sln +21 -0
  151. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/AssemblyInfo.cs +58 -0
  152. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/ChecksumImpl.cs +202 -0
  153. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/CircularBuffer.cs +83 -0
  154. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/CodecBase.cs +198 -0
  155. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/Deflater.cs +106 -0
  156. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/DotZLib.cs +288 -0
  157. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/DotZLib.csproj +141 -0
  158. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/GZipStream.cs +301 -0
  159. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/Inflater.cs +105 -0
  160. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/UnitTests.cs +274 -0
  161. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/LICENSE_1_0.txt +23 -0
  162. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/readme.txt +58 -0
  163. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/README +1 -0
  164. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/infback9.c +608 -0
  165. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/infback9.h +37 -0
  166. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inffix9.h +107 -0
  167. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inflate9.h +47 -0
  168. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inftree9.c +323 -0
  169. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inftree9.h +55 -0
  170. data/ext/src/third-party/zlib-1.2.3/contrib/inflate86/inffas86.c +1157 -0
  171. data/ext/src/third-party/zlib-1.2.3/contrib/inflate86/inffast.S +1368 -0
  172. data/ext/src/third-party/zlib-1.2.3/contrib/iostream/test.cpp +24 -0
  173. data/ext/src/third-party/zlib-1.2.3/contrib/iostream/zfstream.cpp +329 -0
  174. data/ext/src/third-party/zlib-1.2.3/contrib/iostream/zfstream.h +128 -0
  175. data/ext/src/third-party/zlib-1.2.3/contrib/iostream2/zstream.h +307 -0
  176. data/ext/src/third-party/zlib-1.2.3/contrib/iostream2/zstream_test.cpp +25 -0
  177. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/README +35 -0
  178. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/TODO +17 -0
  179. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/test.cc +50 -0
  180. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/zfstream.cc +479 -0
  181. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/zfstream.h +466 -0
  182. data/ext/src/third-party/zlib-1.2.3/contrib/masm686/match.asm +413 -0
  183. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/bld_ml64.bat +2 -0
  184. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/gvmat64.asm +513 -0
  185. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/gvmat64.obj +0 -0
  186. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/inffas8664.c +186 -0
  187. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/inffasx64.asm +392 -0
  188. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/inffasx64.obj +0 -0
  189. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/readme.txt +28 -0
  190. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/bld_ml32.bat +2 -0
  191. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/gvmat32.asm +972 -0
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  193. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/gvmat32c.c +62 -0
  194. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/inffas32.asm +1083 -0
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  196. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/mkasm.bat +3 -0
  197. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/readme.txt +21 -0
  198. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/ChangeLogUnzip +67 -0
  199. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/Makefile +25 -0
  200. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/crypt.h +132 -0
  201. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/ioapi.c +177 -0
  202. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/ioapi.h +75 -0
  203. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/iowin32.c +270 -0
  204. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/iowin32.h +21 -0
  205. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/miniunz.c +585 -0
  206. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/minizip.c +420 -0
  207. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/mztools.c +281 -0
  208. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/mztools.h +31 -0
  209. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/unzip.c +1598 -0
  210. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/unzip.h +354 -0
  211. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/zip.c +1219 -0
  212. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/zip.h +235 -0
  213. data/ext/src/third-party/zlib-1.2.3/contrib/pascal/example.pas +599 -0
  214. data/ext/src/third-party/zlib-1.2.3/contrib/pascal/readme.txt +76 -0
  215. data/ext/src/third-party/zlib-1.2.3/contrib/pascal/zlibd32.mak +93 -0
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  217. data/ext/src/third-party/zlib-1.2.3/contrib/puff/Makefile +8 -0
  218. data/ext/src/third-party/zlib-1.2.3/contrib/puff/README +63 -0
  219. data/ext/src/third-party/zlib-1.2.3/contrib/puff/puff.c +837 -0
  220. data/ext/src/third-party/zlib-1.2.3/contrib/puff/puff.h +31 -0
  221. data/ext/src/third-party/zlib-1.2.3/contrib/puff/zeros.raw +0 -0
  222. data/ext/src/third-party/zlib-1.2.3/contrib/testzlib/testzlib.c +275 -0
  223. data/ext/src/third-party/zlib-1.2.3/contrib/testzlib/testzlib.txt +10 -0
  224. data/ext/src/third-party/zlib-1.2.3/contrib/untgz/Makefile +14 -0
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  226. data/ext/src/third-party/zlib-1.2.3/contrib/untgz/untgz.c +674 -0
  227. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/readme.txt +73 -0
  228. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/miniunz.vcproj +126 -0
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  245. data/ext/src/third-party/zlib-1.2.3/crc32.c +423 -0
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  248. data/ext/src/third-party/zlib-1.2.3/deflate.c +1736 -0
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  251. data/ext/src/third-party/zlib-1.2.3/example +0 -0
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  253. data/ext/src/third-party/zlib-1.2.3/examples/README.examples +42 -0
  254. data/ext/src/third-party/zlib-1.2.3/examples/fitblk.c +233 -0
  255. data/ext/src/third-party/zlib-1.2.3/examples/gun.c +693 -0
  256. data/ext/src/third-party/zlib-1.2.3/examples/gzappend.c +500 -0
  257. data/ext/src/third-party/zlib-1.2.3/examples/gzjoin.c +448 -0
  258. data/ext/src/third-party/zlib-1.2.3/examples/gzlog.c +413 -0
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@@ -0,0 +1,83 @@
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+ //
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+ // � Copyright Henrik Ravn 2004
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+ //
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+ // 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
+
11
+ namespace DotZLib
12
+ {
13
+
14
+ /// <summary>
15
+ /// This class implements a circular buffer
16
+ /// </summary>
17
+ internal class CircularBuffer
18
+ {
19
+ #region Private data
20
+ private int _capacity;
21
+ private int _head;
22
+ private int _tail;
23
+ private int _size;
24
+ private byte[] _buffer;
25
+ #endregion
26
+
27
+ public CircularBuffer(int capacity)
28
+ {
29
+ Debug.Assert( capacity > 0 );
30
+ _buffer = new byte[capacity];
31
+ _capacity = capacity;
32
+ _head = 0;
33
+ _tail = 0;
34
+ _size = 0;
35
+ }
36
+
37
+ public int Size { get { return _size; } }
38
+
39
+ public int Put(byte[] source, int offset, int count)
40
+ {
41
+ Debug.Assert( count > 0 );
42
+ int trueCount = Math.Min(count, _capacity - Size);
43
+ for (int i = 0; i < trueCount; ++i)
44
+ _buffer[(_tail+i) % _capacity] = source[offset+i];
45
+ _tail += trueCount;
46
+ _tail %= _capacity;
47
+ _size += trueCount;
48
+ return trueCount;
49
+ }
50
+
51
+ public bool Put(byte b)
52
+ {
53
+ if (Size == _capacity) // no room
54
+ return false;
55
+ _buffer[_tail++] = b;
56
+ _tail %= _capacity;
57
+ ++_size;
58
+ return true;
59
+ }
60
+
61
+ public int Get(byte[] destination, int offset, int count)
62
+ {
63
+ int trueCount = Math.Min(count,Size);
64
+ for (int i = 0; i < trueCount; ++i)
65
+ destination[offset + i] = _buffer[(_head+i) % _capacity];
66
+ _head += trueCount;
67
+ _head %= _capacity;
68
+ _size -= trueCount;
69
+ return trueCount;
70
+ }
71
+
72
+ public int Get()
73
+ {
74
+ if (Size == 0)
75
+ return -1;
76
+
77
+ int result = (int)_buffer[_head++ % _capacity];
78
+ --_size;
79
+ return result;
80
+ }
81
+
82
+ }
83
+ }
@@ -0,0 +1,198 @@
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.Runtime.InteropServices;
10
+
11
+ namespace DotZLib
12
+ {
13
+ /// <summary>
14
+ /// Implements the common functionality needed for all <see cref="Codec"/>s
15
+ /// </summary>
16
+ public abstract class CodecBase : Codec, IDisposable
17
+ {
18
+
19
+ #region Data members
20
+
21
+ /// <summary>
22
+ /// Instance of the internal zlib buffer structure that is
23
+ /// passed to all functions in the zlib dll
24
+ /// </summary>
25
+ internal ZStream _ztream = new ZStream();
26
+
27
+ /// <summary>
28
+ /// True if the object instance has been disposed, false otherwise
29
+ /// </summary>
30
+ protected bool _isDisposed = false;
31
+
32
+ /// <summary>
33
+ /// The size of the internal buffers
34
+ /// </summary>
35
+ protected const int kBufferSize = 16384;
36
+
37
+ private byte[] _outBuffer = new byte[kBufferSize];
38
+ private byte[] _inBuffer = new byte[kBufferSize];
39
+
40
+ private GCHandle _hInput;
41
+ private GCHandle _hOutput;
42
+
43
+ private uint _checksum = 0;
44
+
45
+ #endregion
46
+
47
+ /// <summary>
48
+ /// Initializes a new instance of the <c>CodeBase</c> class.
49
+ /// </summary>
50
+ public CodecBase()
51
+ {
52
+ try
53
+ {
54
+ _hInput = GCHandle.Alloc(_inBuffer, GCHandleType.Pinned);
55
+ _hOutput = GCHandle.Alloc(_outBuffer, GCHandleType.Pinned);
56
+ }
57
+ catch (Exception)
58
+ {
59
+ CleanUp(false);
60
+ throw;
61
+ }
62
+ }
63
+
64
+
65
+ #region Codec Members
66
+
67
+ /// <summary>
68
+ /// Occurs when more processed data are available.
69
+ /// </summary>
70
+ public event DataAvailableHandler DataAvailable;
71
+
72
+ /// <summary>
73
+ /// Fires the <see cref="DataAvailable"/> event
74
+ /// </summary>
75
+ protected void OnDataAvailable()
76
+ {
77
+ if (_ztream.total_out > 0)
78
+ {
79
+ if (DataAvailable != null)
80
+ DataAvailable( _outBuffer, 0, (int)_ztream.total_out);
81
+ resetOutput();
82
+ }
83
+ }
84
+
85
+ /// <summary>
86
+ /// Adds more data to the codec to be processed.
87
+ /// </summary>
88
+ /// <param name="data">Byte array containing the data to be added to the codec</param>
89
+ /// <remarks>Adding data may, or may not, raise the <c>DataAvailable</c> event</remarks>
90
+ public void Add(byte[] data)
91
+ {
92
+ Add(data,0,data.Length);
93
+ }
94
+
95
+ /// <summary>
96
+ /// Adds more data to the codec to be processed.
97
+ /// </summary>
98
+ /// <param name="data">Byte array containing the data to be added to the codec</param>
99
+ /// <param name="offset">The index of the first byte to add from <c>data</c></param>
100
+ /// <param name="count">The number of bytes to add</param>
101
+ /// <remarks>Adding data may, or may not, raise the <c>DataAvailable</c> event</remarks>
102
+ /// <remarks>This must be implemented by a derived class</remarks>
103
+ public abstract void Add(byte[] data, int offset, int count);
104
+
105
+ /// <summary>
106
+ /// Finishes up any pending data that needs to be processed and handled.
107
+ /// </summary>
108
+ /// <remarks>This must be implemented by a derived class</remarks>
109
+ public abstract void Finish();
110
+
111
+ /// <summary>
112
+ /// Gets the checksum of the data that has been added so far
113
+ /// </summary>
114
+ public uint Checksum { get { return _checksum; } }
115
+
116
+ #endregion
117
+
118
+ #region Destructor & IDisposable stuff
119
+
120
+ /// <summary>
121
+ /// Destroys this instance
122
+ /// </summary>
123
+ ~CodecBase()
124
+ {
125
+ CleanUp(false);
126
+ }
127
+
128
+ /// <summary>
129
+ /// Releases any unmanaged resources and calls the <see cref="CleanUp()"/> method of the derived class
130
+ /// </summary>
131
+ public void Dispose()
132
+ {
133
+ CleanUp(true);
134
+ }
135
+
136
+ /// <summary>
137
+ /// Performs any codec specific cleanup
138
+ /// </summary>
139
+ /// <remarks>This must be implemented by a derived class</remarks>
140
+ protected abstract void CleanUp();
141
+
142
+ // performs the release of the handles and calls the dereived CleanUp()
143
+ private void CleanUp(bool isDisposing)
144
+ {
145
+ if (!_isDisposed)
146
+ {
147
+ CleanUp();
148
+ if (_hInput.IsAllocated)
149
+ _hInput.Free();
150
+ if (_hOutput.IsAllocated)
151
+ _hOutput.Free();
152
+
153
+ _isDisposed = true;
154
+ }
155
+ }
156
+
157
+
158
+ #endregion
159
+
160
+ #region Helper methods
161
+
162
+ /// <summary>
163
+ /// Copies a number of bytes to the internal codec buffer - ready for proccesing
164
+ /// </summary>
165
+ /// <param name="data">The byte array that contains the data to copy</param>
166
+ /// <param name="startIndex">The index of the first byte to copy</param>
167
+ /// <param name="count">The number of bytes to copy from <c>data</c></param>
168
+ protected void copyInput(byte[] data, int startIndex, int count)
169
+ {
170
+ Array.Copy(data, startIndex, _inBuffer,0, count);
171
+ _ztream.next_in = _hInput.AddrOfPinnedObject();
172
+ _ztream.total_in = 0;
173
+ _ztream.avail_in = (uint)count;
174
+
175
+ }
176
+
177
+ /// <summary>
178
+ /// Resets the internal output buffers to a known state - ready for processing
179
+ /// </summary>
180
+ protected void resetOutput()
181
+ {
182
+ _ztream.total_out = 0;
183
+ _ztream.avail_out = kBufferSize;
184
+ _ztream.next_out = _hOutput.AddrOfPinnedObject();
185
+ }
186
+
187
+ /// <summary>
188
+ /// Updates the running checksum property
189
+ /// </summary>
190
+ /// <param name="newSum">The new checksum value</param>
191
+ protected void setChecksum(uint newSum)
192
+ {
193
+ _checksum = newSum;
194
+ }
195
+ #endregion
196
+
197
+ }
198
+ }
@@ -0,0 +1,106 @@
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 compressor, using the deflate algorithm in the ZLib dll
17
+ /// </summary>
18
+ public sealed class Deflater : CodecBase
19
+ {
20
+ #region Dll imports
21
+ [DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl, CharSet=CharSet.Ansi)]
22
+ private static extern int deflateInit_(ref ZStream sz, int level, string vs, int size);
23
+
24
+ [DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
25
+ private static extern int deflate(ref ZStream sz, int flush);
26
+
27
+ [DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
28
+ private static extern int deflateReset(ref ZStream sz);
29
+
30
+ [DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
31
+ private static extern int deflateEnd(ref ZStream sz);
32
+ #endregion
33
+
34
+ /// <summary>
35
+ /// Constructs an new instance of the <c>Deflater</c>
36
+ /// </summary>
37
+ /// <param name="level">The compression level to use for this <c>Deflater</c></param>
38
+ public Deflater(CompressLevel level) : base()
39
+ {
40
+ int retval = deflateInit_(ref _ztream, (int)level, Info.Version, Marshal.SizeOf(_ztream));
41
+ if (retval != 0)
42
+ throw new ZLibException(retval, "Could not initialize deflater");
43
+
44
+ resetOutput();
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
+ while (err >= 0 && _ztream.avail_in > 0)
68
+ {
69
+ err = deflate(ref _ztream, (int)FlushTypes.None);
70
+ if (err == 0)
71
+ while (_ztream.avail_out == 0)
72
+ {
73
+ OnDataAvailable();
74
+ err = deflate(ref _ztream, (int)FlushTypes.None);
75
+ }
76
+ inputIndex += (int)_ztream.total_in;
77
+ }
78
+ }
79
+ setChecksum( _ztream.adler );
80
+ }
81
+
82
+
83
+ /// <summary>
84
+ /// Finishes up any pending data that needs to be processed and handled.
85
+ /// </summary>
86
+ public override void Finish()
87
+ {
88
+ int err;
89
+ do
90
+ {
91
+ err = deflate(ref _ztream, (int)FlushTypes.Finish);
92
+ OnDataAvailable();
93
+ }
94
+ while (err == 0);
95
+ setChecksum( _ztream.adler );
96
+ deflateReset(ref _ztream);
97
+ resetOutput();
98
+ }
99
+
100
+ /// <summary>
101
+ /// Closes the internal zlib deflate stream
102
+ /// </summary>
103
+ protected override void CleanUp() { deflateEnd(ref _ztream); }
104
+
105
+ }
106
+ }
@@ -0,0 +1,288 @@
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
+ using System.Text;
12
+
13
+
14
+ namespace DotZLib
15
+ {
16
+
17
+ #region Internal types
18
+
19
+ /// <summary>
20
+ /// Defines constants for the various flush types used with zlib
21
+ /// </summary>
22
+ internal enum FlushTypes
23
+ {
24
+ None, Partial, Sync, Full, Finish, Block
25
+ }
26
+
27
+ #region ZStream structure
28
+ // internal mapping of the zlib zstream structure for marshalling
29
+ [StructLayoutAttribute(LayoutKind.Sequential, Pack=4, Size=0, CharSet=CharSet.Ansi)]
30
+ internal struct ZStream
31
+ {
32
+ public IntPtr next_in;
33
+ public uint avail_in;
34
+ public uint total_in;
35
+
36
+ public IntPtr next_out;
37
+ public uint avail_out;
38
+ public uint total_out;
39
+
40
+ [MarshalAs(UnmanagedType.LPStr)]
41
+ string msg;
42
+ uint state;
43
+
44
+ uint zalloc;
45
+ uint zfree;
46
+ uint opaque;
47
+
48
+ int data_type;
49
+ public uint adler;
50
+ uint reserved;
51
+ }
52
+
53
+ #endregion
54
+
55
+ #endregion
56
+
57
+ #region Public enums
58
+ /// <summary>
59
+ /// Defines constants for the available compression levels in zlib
60
+ /// </summary>
61
+ public enum CompressLevel : int
62
+ {
63
+ /// <summary>
64
+ /// The default compression level with a reasonable compromise between compression and speed
65
+ /// </summary>
66
+ Default = -1,
67
+ /// <summary>
68
+ /// No compression at all. The data are passed straight through.
69
+ /// </summary>
70
+ None = 0,
71
+ /// <summary>
72
+ /// The maximum compression rate available.
73
+ /// </summary>
74
+ Best = 9,
75
+ /// <summary>
76
+ /// The fastest available compression level.
77
+ /// </summary>
78
+ Fastest = 1
79
+ }
80
+ #endregion
81
+
82
+ #region Exception classes
83
+ /// <summary>
84
+ /// The exception that is thrown when an error occurs on the zlib dll
85
+ /// </summary>
86
+ public class ZLibException : ApplicationException
87
+ {
88
+ /// <summary>
89
+ /// Initializes a new instance of the <see cref="ZLibException"/> class with a specified
90
+ /// error message and error code
91
+ /// </summary>
92
+ /// <param name="errorCode">The zlib error code that caused the exception</param>
93
+ /// <param name="msg">A message that (hopefully) describes the error</param>
94
+ public ZLibException(int errorCode, string msg) : base(String.Format("ZLib error {0} {1}", errorCode, msg))
95
+ {
96
+ }
97
+
98
+ /// <summary>
99
+ /// Initializes a new instance of the <see cref="ZLibException"/> class with a specified
100
+ /// error code
101
+ /// </summary>
102
+ /// <param name="errorCode">The zlib error code that caused the exception</param>
103
+ public ZLibException(int errorCode) : base(String.Format("ZLib error {0}", errorCode))
104
+ {
105
+ }
106
+ }
107
+ #endregion
108
+
109
+ #region Interfaces
110
+
111
+ /// <summary>
112
+ /// Declares methods and properties that enables a running checksum to be calculated
113
+ /// </summary>
114
+ public interface ChecksumGenerator
115
+ {
116
+ /// <summary>
117
+ /// Gets the current value of the checksum
118
+ /// </summary>
119
+ uint Value { get; }
120
+
121
+ /// <summary>
122
+ /// Clears the current checksum to 0
123
+ /// </summary>
124
+ void Reset();
125
+
126
+ /// <summary>
127
+ /// Updates the current checksum with an array of bytes
128
+ /// </summary>
129
+ /// <param name="data">The data to update the checksum with</param>
130
+ void Update(byte[] data);
131
+
132
+ /// <summary>
133
+ /// Updates the current checksum with part of an array of bytes
134
+ /// </summary>
135
+ /// <param name="data">The data to update the checksum with</param>
136
+ /// <param name="offset">Where in <c>data</c> to start updating</param>
137
+ /// <param name="count">The number of bytes from <c>data</c> to use</param>
138
+ /// <exception cref="ArgumentException">The sum of offset and count is larger than the length of <c>data</c></exception>
139
+ /// <exception cref="ArgumentNullException"><c>data</c> is a null reference</exception>
140
+ /// <exception cref="ArgumentOutOfRangeException">Offset or count is negative.</exception>
141
+ void Update(byte[] data, int offset, int count);
142
+
143
+ /// <summary>
144
+ /// Updates the current checksum with the data from a string
145
+ /// </summary>
146
+ /// <param name="data">The string to update the checksum with</param>
147
+ /// <remarks>The characters in the string are converted by the UTF-8 encoding</remarks>
148
+ void Update(string data);
149
+
150
+ /// <summary>
151
+ /// Updates the current checksum with the data from a string, using a specific encoding
152
+ /// </summary>
153
+ /// <param name="data">The string to update the checksum with</param>
154
+ /// <param name="encoding">The encoding to use</param>
155
+ void Update(string data, Encoding encoding);
156
+ }
157
+
158
+
159
+ /// <summary>
160
+ /// Represents the method that will be called from a codec when new data
161
+ /// are available.
162
+ /// </summary>
163
+ /// <paramref name="data">The byte array containing the processed data</paramref>
164
+ /// <paramref name="startIndex">The index of the first processed byte in <c>data</c></paramref>
165
+ /// <paramref name="count">The number of processed bytes available</paramref>
166
+ /// <remarks>On return from this method, the data may be overwritten, so grab it while you can.
167
+ /// You cannot assume that startIndex will be zero.
168
+ /// </remarks>
169
+ public delegate void DataAvailableHandler(byte[] data, int startIndex, int count);
170
+
171
+ /// <summary>
172
+ /// Declares methods and events for implementing compressors/decompressors
173
+ /// </summary>
174
+ public interface Codec
175
+ {
176
+ /// <summary>
177
+ /// Occurs when more processed data are available.
178
+ /// </summary>
179
+ event DataAvailableHandler DataAvailable;
180
+
181
+ /// <summary>
182
+ /// Adds more data to the codec to be processed.
183
+ /// </summary>
184
+ /// <param name="data">Byte array containing the data to be added to the codec</param>
185
+ /// <remarks>Adding data may, or may not, raise the <c>DataAvailable</c> event</remarks>
186
+ void Add(byte[] data);
187
+
188
+ /// <summary>
189
+ /// Adds more data to the codec to be processed.
190
+ /// </summary>
191
+ /// <param name="data">Byte array containing the data to be added to the codec</param>
192
+ /// <param name="offset">The index of the first byte to add from <c>data</c></param>
193
+ /// <param name="count">The number of bytes to add</param>
194
+ /// <remarks>Adding data may, or may not, raise the <c>DataAvailable</c> event</remarks>
195
+ void Add(byte[] data, int offset, int count);
196
+
197
+ /// <summary>
198
+ /// Finishes up any pending data that needs to be processed and handled.
199
+ /// </summary>
200
+ void Finish();
201
+
202
+ /// <summary>
203
+ /// Gets the checksum of the data that has been added so far
204
+ /// </summary>
205
+ uint Checksum { get; }
206
+
207
+
208
+ }
209
+
210
+ #endregion
211
+
212
+ #region Classes
213
+ /// <summary>
214
+ /// Encapsulates general information about the ZLib library
215
+ /// </summary>
216
+ public class Info
217
+ {
218
+ #region DLL imports
219
+ [DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
220
+ private static extern uint zlibCompileFlags();
221
+
222
+ [DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
223
+ private static extern string zlibVersion();
224
+ #endregion
225
+
226
+ #region Private stuff
227
+ private uint _flags;
228
+
229
+ // helper function that unpacks a bitsize mask
230
+ private static int bitSize(uint bits)
231
+ {
232
+ switch (bits)
233
+ {
234
+ case 0: return 16;
235
+ case 1: return 32;
236
+ case 2: return 64;
237
+ }
238
+ return -1;
239
+ }
240
+ #endregion
241
+
242
+ /// <summary>
243
+ /// Constructs an instance of the <c>Info</c> class.
244
+ /// </summary>
245
+ public Info()
246
+ {
247
+ _flags = zlibCompileFlags();
248
+ }
249
+
250
+ /// <summary>
251
+ /// True if the library is compiled with debug info
252
+ /// </summary>
253
+ public bool HasDebugInfo { get { return 0 != (_flags & 0x100); } }
254
+
255
+ /// <summary>
256
+ /// True if the library is compiled with assembly optimizations
257
+ /// </summary>
258
+ public bool UsesAssemblyCode { get { return 0 != (_flags & 0x200); } }
259
+
260
+ /// <summary>
261
+ /// Gets the size of the unsigned int that was compiled into Zlib
262
+ /// </summary>
263
+ public int SizeOfUInt { get { return bitSize(_flags & 3); } }
264
+
265
+ /// <summary>
266
+ /// Gets the size of the unsigned long that was compiled into Zlib
267
+ /// </summary>
268
+ public int SizeOfULong { get { return bitSize((_flags >> 2) & 3); } }
269
+
270
+ /// <summary>
271
+ /// Gets the size of the pointers that were compiled into Zlib
272
+ /// </summary>
273
+ public int SizeOfPointer { get { return bitSize((_flags >> 4) & 3); } }
274
+
275
+ /// <summary>
276
+ /// Gets the size of the z_off_t type that was compiled into Zlib
277
+ /// </summary>
278
+ public int SizeOfOffset { get { return bitSize((_flags >> 6) & 3); } }
279
+
280
+ /// <summary>
281
+ /// Gets the version of ZLib as a string, e.g. "1.2.1"
282
+ /// </summary>
283
+ public static string Version { get { return zlibVersion(); } }
284
+ }
285
+
286
+ #endregion
287
+
288
+ }