bio-velvet_underground 0.0.1

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Files changed (286) hide show
  1. checksums.yaml +7 -0
  2. data/.document +5 -0
  3. data/.gitmodules +3 -0
  4. data/.travis.yml +13 -0
  5. data/Gemfile +19 -0
  6. data/LICENSE.txt +20 -0
  7. data/README.md +53 -0
  8. data/Rakefile +51 -0
  9. data/VERSION +1 -0
  10. data/ext/bioruby.patch +60 -0
  11. data/ext/mkrf_conf.rb +50 -0
  12. data/ext/src/Makefile +125 -0
  13. data/ext/src/src/allocArray.c +305 -0
  14. data/ext/src/src/allocArray.h +86 -0
  15. data/ext/src/src/autoOpen.c +107 -0
  16. data/ext/src/src/autoOpen.h +18 -0
  17. data/ext/src/src/binarySequences.c +813 -0
  18. data/ext/src/src/binarySequences.h +125 -0
  19. data/ext/src/src/concatenatedGraph.c +233 -0
  20. data/ext/src/src/concatenatedGraph.h +30 -0
  21. data/ext/src/src/concatenatedPreGraph.c +262 -0
  22. data/ext/src/src/concatenatedPreGraph.h +29 -0
  23. data/ext/src/src/correctedGraph.c +2642 -0
  24. data/ext/src/src/correctedGraph.h +32 -0
  25. data/ext/src/src/dfib.c +509 -0
  26. data/ext/src/src/dfib.h +69 -0
  27. data/ext/src/src/dfibHeap.c +89 -0
  28. data/ext/src/src/dfibHeap.h +39 -0
  29. data/ext/src/src/dfibpriv.h +105 -0
  30. data/ext/src/src/fib.c +628 -0
  31. data/ext/src/src/fib.h +78 -0
  32. data/ext/src/src/fibHeap.c +79 -0
  33. data/ext/src/src/fibHeap.h +41 -0
  34. data/ext/src/src/fibpriv.h +110 -0
  35. data/ext/src/src/globals.h +153 -0
  36. data/ext/src/src/graph.c +3983 -0
  37. data/ext/src/src/graph.h +233 -0
  38. data/ext/src/src/graphReConstruction.c +1472 -0
  39. data/ext/src/src/graphReConstruction.h +30 -0
  40. data/ext/src/src/graphStats.c +2167 -0
  41. data/ext/src/src/graphStats.h +72 -0
  42. data/ext/src/src/kmer.c +652 -0
  43. data/ext/src/src/kmer.h +73 -0
  44. data/ext/src/src/kmerOccurenceTable.c +236 -0
  45. data/ext/src/src/kmerOccurenceTable.h +44 -0
  46. data/ext/src/src/kseq.h +223 -0
  47. data/ext/src/src/locallyCorrectedGraph.c +557 -0
  48. data/ext/src/src/locallyCorrectedGraph.h +40 -0
  49. data/ext/src/src/passageMarker.c +677 -0
  50. data/ext/src/src/passageMarker.h +137 -0
  51. data/ext/src/src/preGraph.c +1717 -0
  52. data/ext/src/src/preGraph.h +106 -0
  53. data/ext/src/src/preGraphConstruction.c +990 -0
  54. data/ext/src/src/preGraphConstruction.h +26 -0
  55. data/ext/src/src/readCoherentGraph.c +557 -0
  56. data/ext/src/src/readCoherentGraph.h +30 -0
  57. data/ext/src/src/readSet.c +1734 -0
  58. data/ext/src/src/readSet.h +67 -0
  59. data/ext/src/src/recycleBin.c +199 -0
  60. data/ext/src/src/recycleBin.h +58 -0
  61. data/ext/src/src/roadMap.c +342 -0
  62. data/ext/src/src/roadMap.h +65 -0
  63. data/ext/src/src/run.c +318 -0
  64. data/ext/src/src/run.h +52 -0
  65. data/ext/src/src/run2.c +712 -0
  66. data/ext/src/src/scaffold.c +1876 -0
  67. data/ext/src/src/scaffold.h +64 -0
  68. data/ext/src/src/shortReadPairs.c +1243 -0
  69. data/ext/src/src/shortReadPairs.h +32 -0
  70. data/ext/src/src/splay.c +259 -0
  71. data/ext/src/src/splay.h +43 -0
  72. data/ext/src/src/splayTable.c +1315 -0
  73. data/ext/src/src/splayTable.h +31 -0
  74. data/ext/src/src/tightString.c +362 -0
  75. data/ext/src/src/tightString.h +82 -0
  76. data/ext/src/src/utility.c +199 -0
  77. data/ext/src/src/utility.h +98 -0
  78. data/ext/src/third-party/zlib-1.2.3/ChangeLog +855 -0
  79. data/ext/src/third-party/zlib-1.2.3/FAQ +339 -0
  80. data/ext/src/third-party/zlib-1.2.3/INDEX +51 -0
  81. data/ext/src/third-party/zlib-1.2.3/Makefile +154 -0
  82. data/ext/src/third-party/zlib-1.2.3/Makefile.in +154 -0
  83. data/ext/src/third-party/zlib-1.2.3/README +125 -0
  84. data/ext/src/third-party/zlib-1.2.3/adler32.c +149 -0
  85. data/ext/src/third-party/zlib-1.2.3/algorithm.txt +209 -0
  86. data/ext/src/third-party/zlib-1.2.3/amiga/Makefile.pup +66 -0
  87. data/ext/src/third-party/zlib-1.2.3/amiga/Makefile.sas +65 -0
  88. data/ext/src/third-party/zlib-1.2.3/as400/bndsrc +132 -0
  89. data/ext/src/third-party/zlib-1.2.3/as400/compile.clp +123 -0
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  92. data/ext/src/third-party/zlib-1.2.3/compress.c +79 -0
  93. data/ext/src/third-party/zlib-1.2.3/configure +459 -0
  94. data/ext/src/third-party/zlib-1.2.3/contrib/README.contrib +71 -0
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  107. data/ext/src/third-party/zlib-1.2.3/contrib/asm586/README.586 +43 -0
  108. data/ext/src/third-party/zlib-1.2.3/contrib/asm586/match.S +364 -0
  109. data/ext/src/third-party/zlib-1.2.3/contrib/asm686/README.686 +34 -0
  110. data/ext/src/third-party/zlib-1.2.3/contrib/asm686/match.S +329 -0
  111. data/ext/src/third-party/zlib-1.2.3/contrib/blast/Makefile +8 -0
  112. data/ext/src/third-party/zlib-1.2.3/contrib/blast/README +4 -0
  113. data/ext/src/third-party/zlib-1.2.3/contrib/blast/blast.c +444 -0
  114. data/ext/src/third-party/zlib-1.2.3/contrib/blast/blast.h +71 -0
  115. data/ext/src/third-party/zlib-1.2.3/contrib/blast/test.pk +0 -0
  116. data/ext/src/third-party/zlib-1.2.3/contrib/blast/test.txt +1 -0
  117. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/ZLib.pas +557 -0
  118. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/ZLibConst.pas +11 -0
  119. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/readme.txt +76 -0
  120. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/zlibd32.mak +93 -0
  121. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.build +33 -0
  122. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.chm +0 -0
  123. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.sln +21 -0
  124. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/AssemblyInfo.cs +58 -0
  125. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/ChecksumImpl.cs +202 -0
  126. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/CircularBuffer.cs +83 -0
  127. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/CodecBase.cs +198 -0
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  129. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/DotZLib.cs +288 -0
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  131. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/GZipStream.cs +301 -0
  132. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/Inflater.cs +105 -0
  133. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/UnitTests.cs +274 -0
  134. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/LICENSE_1_0.txt +23 -0
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  136. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/README +1 -0
  137. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/infback9.c +608 -0
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  141. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inftree9.c +323 -0
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  145. data/ext/src/third-party/zlib-1.2.3/contrib/iostream/test.cpp +24 -0
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  250. data/ext/src/third-party/zlib-1.2.3/old/README +3 -0
  251. data/ext/src/third-party/zlib-1.2.3/old/descrip.mms +48 -0
  252. data/ext/src/third-party/zlib-1.2.3/old/os2/Makefile.os2 +136 -0
  253. data/ext/src/third-party/zlib-1.2.3/old/os2/zlib.def +51 -0
  254. data/ext/src/third-party/zlib-1.2.3/old/visual-basic.txt +160 -0
  255. data/ext/src/third-party/zlib-1.2.3/old/zlib.html +971 -0
  256. data/ext/src/third-party/zlib-1.2.3/projects/README.projects +41 -0
  257. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/README.txt +73 -0
  258. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/example.dsp +278 -0
  259. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/minigzip.dsp +278 -0
  260. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/zlib.dsp +609 -0
  261. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/zlib.dsw +59 -0
  262. data/ext/src/third-party/zlib-1.2.3/qnx/package.qpg +141 -0
  263. data/ext/src/third-party/zlib-1.2.3/trees.c +1219 -0
  264. data/ext/src/third-party/zlib-1.2.3/trees.h +128 -0
  265. data/ext/src/third-party/zlib-1.2.3/uncompr.c +61 -0
  266. data/ext/src/third-party/zlib-1.2.3/win32/DLL_FAQ.txt +397 -0
  267. data/ext/src/third-party/zlib-1.2.3/win32/Makefile.bor +107 -0
  268. data/ext/src/third-party/zlib-1.2.3/win32/Makefile.emx +69 -0
  269. data/ext/src/third-party/zlib-1.2.3/win32/Makefile.gcc +141 -0
  270. data/ext/src/third-party/zlib-1.2.3/win32/Makefile.msc +126 -0
  271. data/ext/src/third-party/zlib-1.2.3/win32/VisualC.txt +3 -0
  272. data/ext/src/third-party/zlib-1.2.3/win32/zlib.def +60 -0
  273. data/ext/src/third-party/zlib-1.2.3/win32/zlib1.rc +39 -0
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  276. data/ext/src/third-party/zlib-1.2.3/zlib.3 +159 -0
  277. data/ext/src/third-party/zlib-1.2.3/zlib.h +1357 -0
  278. data/ext/src/third-party/zlib-1.2.3/zutil.c +318 -0
  279. data/ext/src/third-party/zlib-1.2.3/zutil.h +269 -0
  280. data/lib/bio-velvet_underground.rb +12 -0
  281. data/lib/bio-velvet_underground/external/VERSION +1 -0
  282. data/lib/bio-velvet_underground/velvet_underground.rb +72 -0
  283. data/spec/binary_sequence_store_spec.rb +27 -0
  284. data/spec/data/1/CnyUnifiedSeq +0 -0
  285. data/spec/spec_helper.rb +31 -0
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+ <QPM:VendorEmbedURL></QPM:VendorEmbedURL>
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+ <QPM:VendorEmail></QPM:VendorEmail>
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+ <QPM:AuthorName>Jean-Loup Gailly,Mark Adler</QPM:AuthorName>
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+ <QPM:AuthorURL>www.gzip.org/zlib</QPM:AuthorURL>
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@@ -0,0 +1,1219 @@
1
+ /* trees.c -- output deflated data using Huffman coding
2
+ * Copyright (C) 1995-2005 Jean-loup Gailly
3
+ * For conditions of distribution and use, see copyright notice in zlib.h
4
+ */
5
+
6
+ /*
7
+ * ALGORITHM
8
+ *
9
+ * The "deflation" process uses several Huffman trees. The more
10
+ * common source values are represented by shorter bit sequences.
11
+ *
12
+ * Each code tree is stored in a compressed form which is itself
13
+ * a Huffman encoding of the lengths of all the code strings (in
14
+ * ascending order by source values). The actual code strings are
15
+ * reconstructed from the lengths in the inflate process, as described
16
+ * in the deflate specification.
17
+ *
18
+ * REFERENCES
19
+ *
20
+ * Deutsch, L.P.,"'Deflate' Compressed Data Format Specification".
21
+ * Available in ftp.uu.net:/pub/archiving/zip/doc/deflate-1.1.doc
22
+ *
23
+ * Storer, James A.
24
+ * Data Compression: Methods and Theory, pp. 49-50.
25
+ * Computer Science Press, 1988. ISBN 0-7167-8156-5.
26
+ *
27
+ * Sedgewick, R.
28
+ * Algorithms, p290.
29
+ * Addison-Wesley, 1983. ISBN 0-201-06672-6.
30
+ */
31
+
32
+ /* @(#) $Id$ */
33
+
34
+ /* #define GEN_TREES_H */
35
+
36
+ #include "deflate.h"
37
+
38
+ #ifdef DEBUG
39
+ # include <ctype.h>
40
+ #endif
41
+
42
+ /* ===========================================================================
43
+ * Constants
44
+ */
45
+
46
+ #define MAX_BL_BITS 7
47
+ /* Bit length codes must not exceed MAX_BL_BITS bits */
48
+
49
+ #define END_BLOCK 256
50
+ /* end of block literal code */
51
+
52
+ #define REP_3_6 16
53
+ /* repeat previous bit length 3-6 times (2 bits of repeat count) */
54
+
55
+ #define REPZ_3_10 17
56
+ /* repeat a zero length 3-10 times (3 bits of repeat count) */
57
+
58
+ #define REPZ_11_138 18
59
+ /* repeat a zero length 11-138 times (7 bits of repeat count) */
60
+
61
+ local const int extra_lbits[LENGTH_CODES] /* extra bits for each length code */
62
+ = {0,0,0,0,0,0,0,0,1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4,5,5,5,5,0};
63
+
64
+ local const int extra_dbits[D_CODES] /* extra bits for each distance code */
65
+ = {0,0,0,0,1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,12,12,13,13};
66
+
67
+ local const int extra_blbits[BL_CODES]/* extra bits for each bit length code */
68
+ = {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,3,7};
69
+
70
+ local const uch bl_order[BL_CODES]
71
+ = {16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15};
72
+ /* The lengths of the bit length codes are sent in order of decreasing
73
+ * probability, to avoid transmitting the lengths for unused bit length codes.
74
+ */
75
+
76
+ #define Buf_size (8 * 2*sizeof(char))
77
+ /* Number of bits used within bi_buf. (bi_buf might be implemented on
78
+ * more than 16 bits on some systems.)
79
+ */
80
+
81
+ /* ===========================================================================
82
+ * Local data. These are initialized only once.
83
+ */
84
+
85
+ #define DIST_CODE_LEN 512 /* see definition of array dist_code below */
86
+
87
+ #if defined(GEN_TREES_H) || !defined(STDC)
88
+ /* non ANSI compilers may not accept trees.h */
89
+
90
+ local ct_data static_ltree[L_CODES+2];
91
+ /* The static literal tree. Since the bit lengths are imposed, there is no
92
+ * need for the L_CODES extra codes used during heap construction. However
93
+ * The codes 286 and 287 are needed to build a canonical tree (see _tr_init
94
+ * below).
95
+ */
96
+
97
+ local ct_data static_dtree[D_CODES];
98
+ /* The static distance tree. (Actually a trivial tree since all codes use
99
+ * 5 bits.)
100
+ */
101
+
102
+ uch _dist_code[DIST_CODE_LEN];
103
+ /* Distance codes. The first 256 values correspond to the distances
104
+ * 3 .. 258, the last 256 values correspond to the top 8 bits of
105
+ * the 15 bit distances.
106
+ */
107
+
108
+ uch _length_code[MAX_MATCH-MIN_MATCH+1];
109
+ /* length code for each normalized match length (0 == MIN_MATCH) */
110
+
111
+ local int base_length[LENGTH_CODES];
112
+ /* First normalized length for each code (0 = MIN_MATCH) */
113
+
114
+ local int base_dist[D_CODES];
115
+ /* First normalized distance for each code (0 = distance of 1) */
116
+
117
+ #else
118
+ # include "trees.h"
119
+ #endif /* GEN_TREES_H */
120
+
121
+ struct static_tree_desc_s {
122
+ const ct_data *static_tree; /* static tree or NULL */
123
+ const intf *extra_bits; /* extra bits for each code or NULL */
124
+ int extra_base; /* base index for extra_bits */
125
+ int elems; /* max number of elements in the tree */
126
+ int max_length; /* max bit length for the codes */
127
+ };
128
+
129
+ local static_tree_desc static_l_desc =
130
+ {static_ltree, extra_lbits, LITERALS+1, L_CODES, MAX_BITS};
131
+
132
+ local static_tree_desc static_d_desc =
133
+ {static_dtree, extra_dbits, 0, D_CODES, MAX_BITS};
134
+
135
+ local static_tree_desc static_bl_desc =
136
+ {(const ct_data *)0, extra_blbits, 0, BL_CODES, MAX_BL_BITS};
137
+
138
+ /* ===========================================================================
139
+ * Local (static) routines in this file.
140
+ */
141
+
142
+ local void tr_static_init OF((void));
143
+ local void init_block OF((deflate_state *s));
144
+ local void pqdownheap OF((deflate_state *s, ct_data *tree, int k));
145
+ local void gen_bitlen OF((deflate_state *s, tree_desc *desc));
146
+ local void gen_codes OF((ct_data *tree, int max_code, ushf *bl_count));
147
+ local void build_tree OF((deflate_state *s, tree_desc *desc));
148
+ local void scan_tree OF((deflate_state *s, ct_data *tree, int max_code));
149
+ local void send_tree OF((deflate_state *s, ct_data *tree, int max_code));
150
+ local int build_bl_tree OF((deflate_state *s));
151
+ local void send_all_trees OF((deflate_state *s, int lcodes, int dcodes,
152
+ int blcodes));
153
+ local void compress_block OF((deflate_state *s, ct_data *ltree,
154
+ ct_data *dtree));
155
+ local void set_data_type OF((deflate_state *s));
156
+ local unsigned bi_reverse OF((unsigned value, int length));
157
+ local void bi_windup OF((deflate_state *s));
158
+ local void bi_flush OF((deflate_state *s));
159
+ local void copy_block OF((deflate_state *s, charf *buf, unsigned len,
160
+ int header));
161
+
162
+ #ifdef GEN_TREES_H
163
+ local void gen_trees_header OF((void));
164
+ #endif
165
+
166
+ #ifndef DEBUG
167
+ # define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
168
+ /* Send a code of the given tree. c and tree must not have side effects */
169
+
170
+ #else /* DEBUG */
171
+ # define send_code(s, c, tree) \
172
+ { if (z_verbose>2) fprintf(stderr,"\ncd %3d ",(c)); \
173
+ send_bits(s, tree[c].Code, tree[c].Len); }
174
+ #endif
175
+
176
+ /* ===========================================================================
177
+ * Output a short LSB first on the stream.
178
+ * IN assertion: there is enough room in pendingBuf.
179
+ */
180
+ #define put_short(s, w) { \
181
+ put_byte(s, (uch)((w) & 0xff)); \
182
+ put_byte(s, (uch)((ush)(w) >> 8)); \
183
+ }
184
+
185
+ /* ===========================================================================
186
+ * Send a value on a given number of bits.
187
+ * IN assertion: length <= 16 and value fits in length bits.
188
+ */
189
+ #ifdef DEBUG
190
+ local void send_bits OF((deflate_state *s, int value, int length));
191
+
192
+ local void send_bits(s, value, length)
193
+ deflate_state *s;
194
+ int value; /* value to send */
195
+ int length; /* number of bits */
196
+ {
197
+ Tracevv((stderr," l %2d v %4x ", length, value));
198
+ Assert(length > 0 && length <= 15, "invalid length");
199
+ s->bits_sent += (ulg)length;
200
+
201
+ /* If not enough room in bi_buf, use (valid) bits from bi_buf and
202
+ * (16 - bi_valid) bits from value, leaving (width - (16-bi_valid))
203
+ * unused bits in value.
204
+ */
205
+ if (s->bi_valid > (int)Buf_size - length) {
206
+ s->bi_buf |= (value << s->bi_valid);
207
+ put_short(s, s->bi_buf);
208
+ s->bi_buf = (ush)value >> (Buf_size - s->bi_valid);
209
+ s->bi_valid += length - Buf_size;
210
+ } else {
211
+ s->bi_buf |= value << s->bi_valid;
212
+ s->bi_valid += length;
213
+ }
214
+ }
215
+ #else /* !DEBUG */
216
+
217
+ #define send_bits(s, value, length) \
218
+ { int len = length;\
219
+ if (s->bi_valid > (int)Buf_size - len) {\
220
+ int val = value;\
221
+ s->bi_buf |= (val << s->bi_valid);\
222
+ put_short(s, s->bi_buf);\
223
+ s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
224
+ s->bi_valid += len - Buf_size;\
225
+ } else {\
226
+ s->bi_buf |= (value) << s->bi_valid;\
227
+ s->bi_valid += len;\
228
+ }\
229
+ }
230
+ #endif /* DEBUG */
231
+
232
+
233
+ /* the arguments must not have side effects */
234
+
235
+ /* ===========================================================================
236
+ * Initialize the various 'constant' tables.
237
+ */
238
+ local void tr_static_init()
239
+ {
240
+ #if defined(GEN_TREES_H) || !defined(STDC)
241
+ static int static_init_done = 0;
242
+ int n; /* iterates over tree elements */
243
+ int bits; /* bit counter */
244
+ int length; /* length value */
245
+ int code; /* code value */
246
+ int dist; /* distance index */
247
+ ush bl_count[MAX_BITS+1];
248
+ /* number of codes at each bit length for an optimal tree */
249
+
250
+ if (static_init_done) return;
251
+
252
+ /* For some embedded targets, global variables are not initialized: */
253
+ static_l_desc.static_tree = static_ltree;
254
+ static_l_desc.extra_bits = extra_lbits;
255
+ static_d_desc.static_tree = static_dtree;
256
+ static_d_desc.extra_bits = extra_dbits;
257
+ static_bl_desc.extra_bits = extra_blbits;
258
+
259
+ /* Initialize the mapping length (0..255) -> length code (0..28) */
260
+ length = 0;
261
+ for (code = 0; code < LENGTH_CODES-1; code++) {
262
+ base_length[code] = length;
263
+ for (n = 0; n < (1<<extra_lbits[code]); n++) {
264
+ _length_code[length++] = (uch)code;
265
+ }
266
+ }
267
+ Assert (length == 256, "tr_static_init: length != 256");
268
+ /* Note that the length 255 (match length 258) can be represented
269
+ * in two different ways: code 284 + 5 bits or code 285, so we
270
+ * overwrite length_code[255] to use the best encoding:
271
+ */
272
+ _length_code[length-1] = (uch)code;
273
+
274
+ /* Initialize the mapping dist (0..32K) -> dist code (0..29) */
275
+ dist = 0;
276
+ for (code = 0 ; code < 16; code++) {
277
+ base_dist[code] = dist;
278
+ for (n = 0; n < (1<<extra_dbits[code]); n++) {
279
+ _dist_code[dist++] = (uch)code;
280
+ }
281
+ }
282
+ Assert (dist == 256, "tr_static_init: dist != 256");
283
+ dist >>= 7; /* from now on, all distances are divided by 128 */
284
+ for ( ; code < D_CODES; code++) {
285
+ base_dist[code] = dist << 7;
286
+ for (n = 0; n < (1<<(extra_dbits[code]-7)); n++) {
287
+ _dist_code[256 + dist++] = (uch)code;
288
+ }
289
+ }
290
+ Assert (dist == 256, "tr_static_init: 256+dist != 512");
291
+
292
+ /* Construct the codes of the static literal tree */
293
+ for (bits = 0; bits <= MAX_BITS; bits++) bl_count[bits] = 0;
294
+ n = 0;
295
+ while (n <= 143) static_ltree[n++].Len = 8, bl_count[8]++;
296
+ while (n <= 255) static_ltree[n++].Len = 9, bl_count[9]++;
297
+ while (n <= 279) static_ltree[n++].Len = 7, bl_count[7]++;
298
+ while (n <= 287) static_ltree[n++].Len = 8, bl_count[8]++;
299
+ /* Codes 286 and 287 do not exist, but we must include them in the
300
+ * tree construction to get a canonical Huffman tree (longest code
301
+ * all ones)
302
+ */
303
+ gen_codes((ct_data *)static_ltree, L_CODES+1, bl_count);
304
+
305
+ /* The static distance tree is trivial: */
306
+ for (n = 0; n < D_CODES; n++) {
307
+ static_dtree[n].Len = 5;
308
+ static_dtree[n].Code = bi_reverse((unsigned)n, 5);
309
+ }
310
+ static_init_done = 1;
311
+
312
+ # ifdef GEN_TREES_H
313
+ gen_trees_header();
314
+ # endif
315
+ #endif /* defined(GEN_TREES_H) || !defined(STDC) */
316
+ }
317
+
318
+ /* ===========================================================================
319
+ * Genererate the file trees.h describing the static trees.
320
+ */
321
+ #ifdef GEN_TREES_H
322
+ # ifndef DEBUG
323
+ # include <stdio.h>
324
+ # endif
325
+
326
+ # define SEPARATOR(i, last, width) \
327
+ ((i) == (last)? "\n};\n\n" : \
328
+ ((i) % (width) == (width)-1 ? ",\n" : ", "))
329
+
330
+ void gen_trees_header()
331
+ {
332
+ FILE *header = fopen("trees.h", "w");
333
+ int i;
334
+
335
+ Assert (header != NULL, "Can't open trees.h");
336
+ fprintf(header,
337
+ "/* header created automatically with -DGEN_TREES_H */\n\n");
338
+
339
+ fprintf(header, "local const ct_data static_ltree[L_CODES+2] = {\n");
340
+ for (i = 0; i < L_CODES+2; i++) {
341
+ fprintf(header, "{{%3u},{%3u}}%s", static_ltree[i].Code,
342
+ static_ltree[i].Len, SEPARATOR(i, L_CODES+1, 5));
343
+ }
344
+
345
+ fprintf(header, "local const ct_data static_dtree[D_CODES] = {\n");
346
+ for (i = 0; i < D_CODES; i++) {
347
+ fprintf(header, "{{%2u},{%2u}}%s", static_dtree[i].Code,
348
+ static_dtree[i].Len, SEPARATOR(i, D_CODES-1, 5));
349
+ }
350
+
351
+ fprintf(header, "const uch _dist_code[DIST_CODE_LEN] = {\n");
352
+ for (i = 0; i < DIST_CODE_LEN; i++) {
353
+ fprintf(header, "%2u%s", _dist_code[i],
354
+ SEPARATOR(i, DIST_CODE_LEN-1, 20));
355
+ }
356
+
357
+ fprintf(header, "const uch _length_code[MAX_MATCH-MIN_MATCH+1]= {\n");
358
+ for (i = 0; i < MAX_MATCH-MIN_MATCH+1; i++) {
359
+ fprintf(header, "%2u%s", _length_code[i],
360
+ SEPARATOR(i, MAX_MATCH-MIN_MATCH, 20));
361
+ }
362
+
363
+ fprintf(header, "local const int base_length[LENGTH_CODES] = {\n");
364
+ for (i = 0; i < LENGTH_CODES; i++) {
365
+ fprintf(header, "%1u%s", base_length[i],
366
+ SEPARATOR(i, LENGTH_CODES-1, 20));
367
+ }
368
+
369
+ fprintf(header, "local const int base_dist[D_CODES] = {\n");
370
+ for (i = 0; i < D_CODES; i++) {
371
+ fprintf(header, "%5u%s", base_dist[i],
372
+ SEPARATOR(i, D_CODES-1, 10));
373
+ }
374
+
375
+ fclose(header);
376
+ }
377
+ #endif /* GEN_TREES_H */
378
+
379
+ /* ===========================================================================
380
+ * Initialize the tree data structures for a new zlib stream.
381
+ */
382
+ void _tr_init(s)
383
+ deflate_state *s;
384
+ {
385
+ tr_static_init();
386
+
387
+ s->l_desc.dyn_tree = s->dyn_ltree;
388
+ s->l_desc.stat_desc = &static_l_desc;
389
+
390
+ s->d_desc.dyn_tree = s->dyn_dtree;
391
+ s->d_desc.stat_desc = &static_d_desc;
392
+
393
+ s->bl_desc.dyn_tree = s->bl_tree;
394
+ s->bl_desc.stat_desc = &static_bl_desc;
395
+
396
+ s->bi_buf = 0;
397
+ s->bi_valid = 0;
398
+ s->last_eob_len = 8; /* enough lookahead for inflate */
399
+ #ifdef DEBUG
400
+ s->compressed_len = 0L;
401
+ s->bits_sent = 0L;
402
+ #endif
403
+
404
+ /* Initialize the first block of the first file: */
405
+ init_block(s);
406
+ }
407
+
408
+ /* ===========================================================================
409
+ * Initialize a new block.
410
+ */
411
+ local void init_block(s)
412
+ deflate_state *s;
413
+ {
414
+ int n; /* iterates over tree elements */
415
+
416
+ /* Initialize the trees. */
417
+ for (n = 0; n < L_CODES; n++) s->dyn_ltree[n].Freq = 0;
418
+ for (n = 0; n < D_CODES; n++) s->dyn_dtree[n].Freq = 0;
419
+ for (n = 0; n < BL_CODES; n++) s->bl_tree[n].Freq = 0;
420
+
421
+ s->dyn_ltree[END_BLOCK].Freq = 1;
422
+ s->opt_len = s->static_len = 0L;
423
+ s->last_lit = s->matches = 0;
424
+ }
425
+
426
+ #define SMALLEST 1
427
+ /* Index within the heap array of least frequent node in the Huffman tree */
428
+
429
+
430
+ /* ===========================================================================
431
+ * Remove the smallest element from the heap and recreate the heap with
432
+ * one less element. Updates heap and heap_len.
433
+ */
434
+ #define pqremove(s, tree, top) \
435
+ {\
436
+ top = s->heap[SMALLEST]; \
437
+ s->heap[SMALLEST] = s->heap[s->heap_len--]; \
438
+ pqdownheap(s, tree, SMALLEST); \
439
+ }
440
+
441
+ /* ===========================================================================
442
+ * Compares to subtrees, using the tree depth as tie breaker when
443
+ * the subtrees have equal frequency. This minimizes the worst case length.
444
+ */
445
+ #define smaller(tree, n, m, depth) \
446
+ (tree[n].Freq < tree[m].Freq || \
447
+ (tree[n].Freq == tree[m].Freq && depth[n] <= depth[m]))
448
+
449
+ /* ===========================================================================
450
+ * Restore the heap property by moving down the tree starting at node k,
451
+ * exchanging a node with the smallest of its two sons if necessary, stopping
452
+ * when the heap property is re-established (each father smaller than its
453
+ * two sons).
454
+ */
455
+ local void pqdownheap(s, tree, k)
456
+ deflate_state *s;
457
+ ct_data *tree; /* the tree to restore */
458
+ int k; /* node to move down */
459
+ {
460
+ int v = s->heap[k];
461
+ int j = k << 1; /* left son of k */
462
+ while (j <= s->heap_len) {
463
+ /* Set j to the smallest of the two sons: */
464
+ if (j < s->heap_len &&
465
+ smaller(tree, s->heap[j+1], s->heap[j], s->depth)) {
466
+ j++;
467
+ }
468
+ /* Exit if v is smaller than both sons */
469
+ if (smaller(tree, v, s->heap[j], s->depth)) break;
470
+
471
+ /* Exchange v with the smallest son */
472
+ s->heap[k] = s->heap[j]; k = j;
473
+
474
+ /* And continue down the tree, setting j to the left son of k */
475
+ j <<= 1;
476
+ }
477
+ s->heap[k] = v;
478
+ }
479
+
480
+ /* ===========================================================================
481
+ * Compute the optimal bit lengths for a tree and update the total bit length
482
+ * for the current block.
483
+ * IN assertion: the fields freq and dad are set, heap[heap_max] and
484
+ * above are the tree nodes sorted by increasing frequency.
485
+ * OUT assertions: the field len is set to the optimal bit length, the
486
+ * array bl_count contains the frequencies for each bit length.
487
+ * The length opt_len is updated; static_len is also updated if stree is
488
+ * not null.
489
+ */
490
+ local void gen_bitlen(s, desc)
491
+ deflate_state *s;
492
+ tree_desc *desc; /* the tree descriptor */
493
+ {
494
+ ct_data *tree = desc->dyn_tree;
495
+ int max_code = desc->max_code;
496
+ const ct_data *stree = desc->stat_desc->static_tree;
497
+ const intf *extra = desc->stat_desc->extra_bits;
498
+ int base = desc->stat_desc->extra_base;
499
+ int max_length = desc->stat_desc->max_length;
500
+ int h; /* heap index */
501
+ int n, m; /* iterate over the tree elements */
502
+ int bits; /* bit length */
503
+ int xbits; /* extra bits */
504
+ ush f; /* frequency */
505
+ int overflow = 0; /* number of elements with bit length too large */
506
+
507
+ for (bits = 0; bits <= MAX_BITS; bits++) s->bl_count[bits] = 0;
508
+
509
+ /* In a first pass, compute the optimal bit lengths (which may
510
+ * overflow in the case of the bit length tree).
511
+ */
512
+ tree[s->heap[s->heap_max]].Len = 0; /* root of the heap */
513
+
514
+ for (h = s->heap_max+1; h < HEAP_SIZE; h++) {
515
+ n = s->heap[h];
516
+ bits = tree[tree[n].Dad].Len + 1;
517
+ if (bits > max_length) bits = max_length, overflow++;
518
+ tree[n].Len = (ush)bits;
519
+ /* We overwrite tree[n].Dad which is no longer needed */
520
+
521
+ if (n > max_code) continue; /* not a leaf node */
522
+
523
+ s->bl_count[bits]++;
524
+ xbits = 0;
525
+ if (n >= base) xbits = extra[n-base];
526
+ f = tree[n].Freq;
527
+ s->opt_len += (ulg)f * (bits + xbits);
528
+ if (stree) s->static_len += (ulg)f * (stree[n].Len + xbits);
529
+ }
530
+ if (overflow == 0) return;
531
+
532
+ Trace((stderr,"\nbit length overflow\n"));
533
+ /* This happens for example on obj2 and pic of the Calgary corpus */
534
+
535
+ /* Find the first bit length which could increase: */
536
+ do {
537
+ bits = max_length-1;
538
+ while (s->bl_count[bits] == 0) bits--;
539
+ s->bl_count[bits]--; /* move one leaf down the tree */
540
+ s->bl_count[bits+1] += 2; /* move one overflow item as its brother */
541
+ s->bl_count[max_length]--;
542
+ /* The brother of the overflow item also moves one step up,
543
+ * but this does not affect bl_count[max_length]
544
+ */
545
+ overflow -= 2;
546
+ } while (overflow > 0);
547
+
548
+ /* Now recompute all bit lengths, scanning in increasing frequency.
549
+ * h is still equal to HEAP_SIZE. (It is simpler to reconstruct all
550
+ * lengths instead of fixing only the wrong ones. This idea is taken
551
+ * from 'ar' written by Haruhiko Okumura.)
552
+ */
553
+ for (bits = max_length; bits != 0; bits--) {
554
+ n = s->bl_count[bits];
555
+ while (n != 0) {
556
+ m = s->heap[--h];
557
+ if (m > max_code) continue;
558
+ if ((unsigned) tree[m].Len != (unsigned) bits) {
559
+ Trace((stderr,"code %d bits %d->%d\n", m, tree[m].Len, bits));
560
+ s->opt_len += ((long)bits - (long)tree[m].Len)
561
+ *(long)tree[m].Freq;
562
+ tree[m].Len = (ush)bits;
563
+ }
564
+ n--;
565
+ }
566
+ }
567
+ }
568
+
569
+ /* ===========================================================================
570
+ * Generate the codes for a given tree and bit counts (which need not be
571
+ * optimal).
572
+ * IN assertion: the array bl_count contains the bit length statistics for
573
+ * the given tree and the field len is set for all tree elements.
574
+ * OUT assertion: the field code is set for all tree elements of non
575
+ * zero code length.
576
+ */
577
+ local void gen_codes (tree, max_code, bl_count)
578
+ ct_data *tree; /* the tree to decorate */
579
+ int max_code; /* largest code with non zero frequency */
580
+ ushf *bl_count; /* number of codes at each bit length */
581
+ {
582
+ ush next_code[MAX_BITS+1]; /* next code value for each bit length */
583
+ ush code = 0; /* running code value */
584
+ int bits; /* bit index */
585
+ int n; /* code index */
586
+
587
+ /* The distribution counts are first used to generate the code values
588
+ * without bit reversal.
589
+ */
590
+ for (bits = 1; bits <= MAX_BITS; bits++) {
591
+ next_code[bits] = code = (code + bl_count[bits-1]) << 1;
592
+ }
593
+ /* Check that the bit counts in bl_count are consistent. The last code
594
+ * must be all ones.
595
+ */
596
+ Assert (code + bl_count[MAX_BITS]-1 == (1<<MAX_BITS)-1,
597
+ "inconsistent bit counts");
598
+ Tracev((stderr,"\ngen_codes: max_code %d ", max_code));
599
+
600
+ for (n = 0; n <= max_code; n++) {
601
+ int len = tree[n].Len;
602
+ if (len == 0) continue;
603
+ /* Now reverse the bits */
604
+ tree[n].Code = bi_reverse(next_code[len]++, len);
605
+
606
+ Tracecv(tree != static_ltree, (stderr,"\nn %3d %c l %2d c %4x (%x) ",
607
+ n, (isgraph(n) ? n : ' '), len, tree[n].Code, next_code[len]-1));
608
+ }
609
+ }
610
+
611
+ /* ===========================================================================
612
+ * Construct one Huffman tree and assigns the code bit strings and lengths.
613
+ * Update the total bit length for the current block.
614
+ * IN assertion: the field freq is set for all tree elements.
615
+ * OUT assertions: the fields len and code are set to the optimal bit length
616
+ * and corresponding code. The length opt_len is updated; static_len is
617
+ * also updated if stree is not null. The field max_code is set.
618
+ */
619
+ local void build_tree(s, desc)
620
+ deflate_state *s;
621
+ tree_desc *desc; /* the tree descriptor */
622
+ {
623
+ ct_data *tree = desc->dyn_tree;
624
+ const ct_data *stree = desc->stat_desc->static_tree;
625
+ int elems = desc->stat_desc->elems;
626
+ int n, m; /* iterate over heap elements */
627
+ int max_code = -1; /* largest code with non zero frequency */
628
+ int node; /* new node being created */
629
+
630
+ /* Construct the initial heap, with least frequent element in
631
+ * heap[SMALLEST]. The sons of heap[n] are heap[2*n] and heap[2*n+1].
632
+ * heap[0] is not used.
633
+ */
634
+ s->heap_len = 0, s->heap_max = HEAP_SIZE;
635
+
636
+ for (n = 0; n < elems; n++) {
637
+ if (tree[n].Freq != 0) {
638
+ s->heap[++(s->heap_len)] = max_code = n;
639
+ s->depth[n] = 0;
640
+ } else {
641
+ tree[n].Len = 0;
642
+ }
643
+ }
644
+
645
+ /* The pkzip format requires that at least one distance code exists,
646
+ * and that at least one bit should be sent even if there is only one
647
+ * possible code. So to avoid special checks later on we force at least
648
+ * two codes of non zero frequency.
649
+ */
650
+ while (s->heap_len < 2) {
651
+ node = s->heap[++(s->heap_len)] = (max_code < 2 ? ++max_code : 0);
652
+ tree[node].Freq = 1;
653
+ s->depth[node] = 0;
654
+ s->opt_len--; if (stree) s->static_len -= stree[node].Len;
655
+ /* node is 0 or 1 so it does not have extra bits */
656
+ }
657
+ desc->max_code = max_code;
658
+
659
+ /* The elements heap[heap_len/2+1 .. heap_len] are leaves of the tree,
660
+ * establish sub-heaps of increasing lengths:
661
+ */
662
+ for (n = s->heap_len/2; n >= 1; n--) pqdownheap(s, tree, n);
663
+
664
+ /* Construct the Huffman tree by repeatedly combining the least two
665
+ * frequent nodes.
666
+ */
667
+ node = elems; /* next internal node of the tree */
668
+ do {
669
+ pqremove(s, tree, n); /* n = node of least frequency */
670
+ m = s->heap[SMALLEST]; /* m = node of next least frequency */
671
+
672
+ s->heap[--(s->heap_max)] = n; /* keep the nodes sorted by frequency */
673
+ s->heap[--(s->heap_max)] = m;
674
+
675
+ /* Create a new node father of n and m */
676
+ tree[node].Freq = tree[n].Freq + tree[m].Freq;
677
+ s->depth[node] = (uch)((s->depth[n] >= s->depth[m] ?
678
+ s->depth[n] : s->depth[m]) + 1);
679
+ tree[n].Dad = tree[m].Dad = (ush)node;
680
+ #ifdef DUMP_BL_TREE
681
+ if (tree == s->bl_tree) {
682
+ fprintf(stderr,"\nnode %d(%d), sons %d(%d) %d(%d)",
683
+ node, tree[node].Freq, n, tree[n].Freq, m, tree[m].Freq);
684
+ }
685
+ #endif
686
+ /* and insert the new node in the heap */
687
+ s->heap[SMALLEST] = node++;
688
+ pqdownheap(s, tree, SMALLEST);
689
+
690
+ } while (s->heap_len >= 2);
691
+
692
+ s->heap[--(s->heap_max)] = s->heap[SMALLEST];
693
+
694
+ /* At this point, the fields freq and dad are set. We can now
695
+ * generate the bit lengths.
696
+ */
697
+ gen_bitlen(s, (tree_desc *)desc);
698
+
699
+ /* The field len is now set, we can generate the bit codes */
700
+ gen_codes ((ct_data *)tree, max_code, s->bl_count);
701
+ }
702
+
703
+ /* ===========================================================================
704
+ * Scan a literal or distance tree to determine the frequencies of the codes
705
+ * in the bit length tree.
706
+ */
707
+ local void scan_tree (s, tree, max_code)
708
+ deflate_state *s;
709
+ ct_data *tree; /* the tree to be scanned */
710
+ int max_code; /* and its largest code of non zero frequency */
711
+ {
712
+ int n; /* iterates over all tree elements */
713
+ int prevlen = -1; /* last emitted length */
714
+ int curlen; /* length of current code */
715
+ int nextlen = tree[0].Len; /* length of next code */
716
+ int count = 0; /* repeat count of the current code */
717
+ int max_count = 7; /* max repeat count */
718
+ int min_count = 4; /* min repeat count */
719
+
720
+ if (nextlen == 0) max_count = 138, min_count = 3;
721
+ tree[max_code+1].Len = (ush)0xffff; /* guard */
722
+
723
+ for (n = 0; n <= max_code; n++) {
724
+ curlen = nextlen; nextlen = tree[n+1].Len;
725
+ if (++count < max_count && curlen == nextlen) {
726
+ continue;
727
+ } else if (count < min_count) {
728
+ s->bl_tree[curlen].Freq += count;
729
+ } else if (curlen != 0) {
730
+ if (curlen != prevlen) s->bl_tree[curlen].Freq++;
731
+ s->bl_tree[REP_3_6].Freq++;
732
+ } else if (count <= 10) {
733
+ s->bl_tree[REPZ_3_10].Freq++;
734
+ } else {
735
+ s->bl_tree[REPZ_11_138].Freq++;
736
+ }
737
+ count = 0; prevlen = curlen;
738
+ if (nextlen == 0) {
739
+ max_count = 138, min_count = 3;
740
+ } else if (curlen == nextlen) {
741
+ max_count = 6, min_count = 3;
742
+ } else {
743
+ max_count = 7, min_count = 4;
744
+ }
745
+ }
746
+ }
747
+
748
+ /* ===========================================================================
749
+ * Send a literal or distance tree in compressed form, using the codes in
750
+ * bl_tree.
751
+ */
752
+ local void send_tree (s, tree, max_code)
753
+ deflate_state *s;
754
+ ct_data *tree; /* the tree to be scanned */
755
+ int max_code; /* and its largest code of non zero frequency */
756
+ {
757
+ int n; /* iterates over all tree elements */
758
+ int prevlen = -1; /* last emitted length */
759
+ int curlen; /* length of current code */
760
+ int nextlen = tree[0].Len; /* length of next code */
761
+ int count = 0; /* repeat count of the current code */
762
+ int max_count = 7; /* max repeat count */
763
+ int min_count = 4; /* min repeat count */
764
+
765
+ /* tree[max_code+1].Len = -1; */ /* guard already set */
766
+ if (nextlen == 0) max_count = 138, min_count = 3;
767
+
768
+ for (n = 0; n <= max_code; n++) {
769
+ curlen = nextlen; nextlen = tree[n+1].Len;
770
+ if (++count < max_count && curlen == nextlen) {
771
+ continue;
772
+ } else if (count < min_count) {
773
+ do { send_code(s, curlen, s->bl_tree); } while (--count != 0);
774
+
775
+ } else if (curlen != 0) {
776
+ if (curlen != prevlen) {
777
+ send_code(s, curlen, s->bl_tree); count--;
778
+ }
779
+ Assert(count >= 3 && count <= 6, " 3_6?");
780
+ send_code(s, REP_3_6, s->bl_tree); send_bits(s, count-3, 2);
781
+
782
+ } else if (count <= 10) {
783
+ send_code(s, REPZ_3_10, s->bl_tree); send_bits(s, count-3, 3);
784
+
785
+ } else {
786
+ send_code(s, REPZ_11_138, s->bl_tree); send_bits(s, count-11, 7);
787
+ }
788
+ count = 0; prevlen = curlen;
789
+ if (nextlen == 0) {
790
+ max_count = 138, min_count = 3;
791
+ } else if (curlen == nextlen) {
792
+ max_count = 6, min_count = 3;
793
+ } else {
794
+ max_count = 7, min_count = 4;
795
+ }
796
+ }
797
+ }
798
+
799
+ /* ===========================================================================
800
+ * Construct the Huffman tree for the bit lengths and return the index in
801
+ * bl_order of the last bit length code to send.
802
+ */
803
+ local int build_bl_tree(s)
804
+ deflate_state *s;
805
+ {
806
+ int max_blindex; /* index of last bit length code of non zero freq */
807
+
808
+ /* Determine the bit length frequencies for literal and distance trees */
809
+ scan_tree(s, (ct_data *)s->dyn_ltree, s->l_desc.max_code);
810
+ scan_tree(s, (ct_data *)s->dyn_dtree, s->d_desc.max_code);
811
+
812
+ /* Build the bit length tree: */
813
+ build_tree(s, (tree_desc *)(&(s->bl_desc)));
814
+ /* opt_len now includes the length of the tree representations, except
815
+ * the lengths of the bit lengths codes and the 5+5+4 bits for the counts.
816
+ */
817
+
818
+ /* Determine the number of bit length codes to send. The pkzip format
819
+ * requires that at least 4 bit length codes be sent. (appnote.txt says
820
+ * 3 but the actual value used is 4.)
821
+ */
822
+ for (max_blindex = BL_CODES-1; max_blindex >= 3; max_blindex--) {
823
+ if (s->bl_tree[bl_order[max_blindex]].Len != 0) break;
824
+ }
825
+ /* Update opt_len to include the bit length tree and counts */
826
+ s->opt_len += 3*(max_blindex+1) + 5+5+4;
827
+ Tracev((stderr, "\ndyn trees: dyn %ld, stat %ld",
828
+ s->opt_len, s->static_len));
829
+
830
+ return max_blindex;
831
+ }
832
+
833
+ /* ===========================================================================
834
+ * Send the header for a block using dynamic Huffman trees: the counts, the
835
+ * lengths of the bit length codes, the literal tree and the distance tree.
836
+ * IN assertion: lcodes >= 257, dcodes >= 1, blcodes >= 4.
837
+ */
838
+ local void send_all_trees(s, lcodes, dcodes, blcodes)
839
+ deflate_state *s;
840
+ int lcodes, dcodes, blcodes; /* number of codes for each tree */
841
+ {
842
+ int rank; /* index in bl_order */
843
+
844
+ Assert (lcodes >= 257 && dcodes >= 1 && blcodes >= 4, "not enough codes");
845
+ Assert (lcodes <= L_CODES && dcodes <= D_CODES && blcodes <= BL_CODES,
846
+ "too many codes");
847
+ Tracev((stderr, "\nbl counts: "));
848
+ send_bits(s, lcodes-257, 5); /* not +255 as stated in appnote.txt */
849
+ send_bits(s, dcodes-1, 5);
850
+ send_bits(s, blcodes-4, 4); /* not -3 as stated in appnote.txt */
851
+ for (rank = 0; rank < blcodes; rank++) {
852
+ Tracev((stderr, "\nbl code %2d ", bl_order[rank]));
853
+ send_bits(s, s->bl_tree[bl_order[rank]].Len, 3);
854
+ }
855
+ Tracev((stderr, "\nbl tree: sent %ld", s->bits_sent));
856
+
857
+ send_tree(s, (ct_data *)s->dyn_ltree, lcodes-1); /* literal tree */
858
+ Tracev((stderr, "\nlit tree: sent %ld", s->bits_sent));
859
+
860
+ send_tree(s, (ct_data *)s->dyn_dtree, dcodes-1); /* distance tree */
861
+ Tracev((stderr, "\ndist tree: sent %ld", s->bits_sent));
862
+ }
863
+
864
+ /* ===========================================================================
865
+ * Send a stored block
866
+ */
867
+ void _tr_stored_block(s, buf, stored_len, eof)
868
+ deflate_state *s;
869
+ charf *buf; /* input block */
870
+ ulg stored_len; /* length of input block */
871
+ int eof; /* true if this is the last block for a file */
872
+ {
873
+ send_bits(s, (STORED_BLOCK<<1)+eof, 3); /* send block type */
874
+ #ifdef DEBUG
875
+ s->compressed_len = (s->compressed_len + 3 + 7) & (ulg)~7L;
876
+ s->compressed_len += (stored_len + 4) << 3;
877
+ #endif
878
+ copy_block(s, buf, (unsigned)stored_len, 1); /* with header */
879
+ }
880
+
881
+ /* ===========================================================================
882
+ * Send one empty static block to give enough lookahead for inflate.
883
+ * This takes 10 bits, of which 7 may remain in the bit buffer.
884
+ * The current inflate code requires 9 bits of lookahead. If the
885
+ * last two codes for the previous block (real code plus EOB) were coded
886
+ * on 5 bits or less, inflate may have only 5+3 bits of lookahead to decode
887
+ * the last real code. In this case we send two empty static blocks instead
888
+ * of one. (There are no problems if the previous block is stored or fixed.)
889
+ * To simplify the code, we assume the worst case of last real code encoded
890
+ * on one bit only.
891
+ */
892
+ void _tr_align(s)
893
+ deflate_state *s;
894
+ {
895
+ send_bits(s, STATIC_TREES<<1, 3);
896
+ send_code(s, END_BLOCK, static_ltree);
897
+ #ifdef DEBUG
898
+ s->compressed_len += 10L; /* 3 for block type, 7 for EOB */
899
+ #endif
900
+ bi_flush(s);
901
+ /* Of the 10 bits for the empty block, we have already sent
902
+ * (10 - bi_valid) bits. The lookahead for the last real code (before
903
+ * the EOB of the previous block) was thus at least one plus the length
904
+ * of the EOB plus what we have just sent of the empty static block.
905
+ */
906
+ if (1 + s->last_eob_len + 10 - s->bi_valid < 9) {
907
+ send_bits(s, STATIC_TREES<<1, 3);
908
+ send_code(s, END_BLOCK, static_ltree);
909
+ #ifdef DEBUG
910
+ s->compressed_len += 10L;
911
+ #endif
912
+ bi_flush(s);
913
+ }
914
+ s->last_eob_len = 7;
915
+ }
916
+
917
+ /* ===========================================================================
918
+ * Determine the best encoding for the current block: dynamic trees, static
919
+ * trees or store, and output the encoded block to the zip file.
920
+ */
921
+ void _tr_flush_block(s, buf, stored_len, eof)
922
+ deflate_state *s;
923
+ charf *buf; /* input block, or NULL if too old */
924
+ ulg stored_len; /* length of input block */
925
+ int eof; /* true if this is the last block for a file */
926
+ {
927
+ ulg opt_lenb, static_lenb; /* opt_len and static_len in bytes */
928
+ int max_blindex = 0; /* index of last bit length code of non zero freq */
929
+
930
+ /* Build the Huffman trees unless a stored block is forced */
931
+ if (s->level > 0) {
932
+
933
+ /* Check if the file is binary or text */
934
+ if (stored_len > 0 && s->strm->data_type == Z_UNKNOWN)
935
+ set_data_type(s);
936
+
937
+ /* Construct the literal and distance trees */
938
+ build_tree(s, (tree_desc *)(&(s->l_desc)));
939
+ Tracev((stderr, "\nlit data: dyn %ld, stat %ld", s->opt_len,
940
+ s->static_len));
941
+
942
+ build_tree(s, (tree_desc *)(&(s->d_desc)));
943
+ Tracev((stderr, "\ndist data: dyn %ld, stat %ld", s->opt_len,
944
+ s->static_len));
945
+ /* At this point, opt_len and static_len are the total bit lengths of
946
+ * the compressed block data, excluding the tree representations.
947
+ */
948
+
949
+ /* Build the bit length tree for the above two trees, and get the index
950
+ * in bl_order of the last bit length code to send.
951
+ */
952
+ max_blindex = build_bl_tree(s);
953
+
954
+ /* Determine the best encoding. Compute the block lengths in bytes. */
955
+ opt_lenb = (s->opt_len+3+7)>>3;
956
+ static_lenb = (s->static_len+3+7)>>3;
957
+
958
+ Tracev((stderr, "\nopt %lu(%lu) stat %lu(%lu) stored %lu lit %u ",
959
+ opt_lenb, s->opt_len, static_lenb, s->static_len, stored_len,
960
+ s->last_lit));
961
+
962
+ if (static_lenb <= opt_lenb) opt_lenb = static_lenb;
963
+
964
+ } else {
965
+ Assert(buf != (char*)0, "lost buf");
966
+ opt_lenb = static_lenb = stored_len + 5; /* force a stored block */
967
+ }
968
+
969
+ #ifdef FORCE_STORED
970
+ if (buf != (char*)0) { /* force stored block */
971
+ #else
972
+ if (stored_len+4 <= opt_lenb && buf != (char*)0) {
973
+ /* 4: two words for the lengths */
974
+ #endif
975
+ /* The test buf != NULL is only necessary if LIT_BUFSIZE > WSIZE.
976
+ * Otherwise we can't have processed more than WSIZE input bytes since
977
+ * the last block flush, because compression would have been
978
+ * successful. If LIT_BUFSIZE <= WSIZE, it is never too late to
979
+ * transform a block into a stored block.
980
+ */
981
+ _tr_stored_block(s, buf, stored_len, eof);
982
+
983
+ #ifdef FORCE_STATIC
984
+ } else if (static_lenb >= 0) { /* force static trees */
985
+ #else
986
+ } else if (s->strategy == Z_FIXED || static_lenb == opt_lenb) {
987
+ #endif
988
+ send_bits(s, (STATIC_TREES<<1)+eof, 3);
989
+ compress_block(s, (ct_data *)static_ltree, (ct_data *)static_dtree);
990
+ #ifdef DEBUG
991
+ s->compressed_len += 3 + s->static_len;
992
+ #endif
993
+ } else {
994
+ send_bits(s, (DYN_TREES<<1)+eof, 3);
995
+ send_all_trees(s, s->l_desc.max_code+1, s->d_desc.max_code+1,
996
+ max_blindex+1);
997
+ compress_block(s, (ct_data *)s->dyn_ltree, (ct_data *)s->dyn_dtree);
998
+ #ifdef DEBUG
999
+ s->compressed_len += 3 + s->opt_len;
1000
+ #endif
1001
+ }
1002
+ Assert (s->compressed_len == s->bits_sent, "bad compressed size");
1003
+ /* The above check is made mod 2^32, for files larger than 512 MB
1004
+ * and uLong implemented on 32 bits.
1005
+ */
1006
+ init_block(s);
1007
+
1008
+ if (eof) {
1009
+ bi_windup(s);
1010
+ #ifdef DEBUG
1011
+ s->compressed_len += 7; /* align on byte boundary */
1012
+ #endif
1013
+ }
1014
+ Tracev((stderr,"\ncomprlen %lu(%lu) ", s->compressed_len>>3,
1015
+ s->compressed_len-7*eof));
1016
+ }
1017
+
1018
+ /* ===========================================================================
1019
+ * Save the match info and tally the frequency counts. Return true if
1020
+ * the current block must be flushed.
1021
+ */
1022
+ int _tr_tally (s, dist, lc)
1023
+ deflate_state *s;
1024
+ unsigned dist; /* distance of matched string */
1025
+ unsigned lc; /* match length-MIN_MATCH or unmatched char (if dist==0) */
1026
+ {
1027
+ s->d_buf[s->last_lit] = (ush)dist;
1028
+ s->l_buf[s->last_lit++] = (uch)lc;
1029
+ if (dist == 0) {
1030
+ /* lc is the unmatched char */
1031
+ s->dyn_ltree[lc].Freq++;
1032
+ } else {
1033
+ s->matches++;
1034
+ /* Here, lc is the match length - MIN_MATCH */
1035
+ dist--; /* dist = match distance - 1 */
1036
+ Assert((ush)dist < (ush)MAX_DIST(s) &&
1037
+ (ush)lc <= (ush)(MAX_MATCH-MIN_MATCH) &&
1038
+ (ush)d_code(dist) < (ush)D_CODES, "_tr_tally: bad match");
1039
+
1040
+ s->dyn_ltree[_length_code[lc]+LITERALS+1].Freq++;
1041
+ s->dyn_dtree[d_code(dist)].Freq++;
1042
+ }
1043
+
1044
+ #ifdef TRUNCATE_BLOCK
1045
+ /* Try to guess if it is profitable to stop the current block here */
1046
+ if ((s->last_lit & 0x1fff) == 0 && s->level > 2) {
1047
+ /* Compute an upper bound for the compressed length */
1048
+ ulg out_length = (ulg)s->last_lit*8L;
1049
+ ulg in_length = (ulg)((long)s->strstart - s->block_start);
1050
+ int dcode;
1051
+ for (dcode = 0; dcode < D_CODES; dcode++) {
1052
+ out_length += (ulg)s->dyn_dtree[dcode].Freq *
1053
+ (5L+extra_dbits[dcode]);
1054
+ }
1055
+ out_length >>= 3;
1056
+ Tracev((stderr,"\nlast_lit %u, in %ld, out ~%ld(%ld%%) ",
1057
+ s->last_lit, in_length, out_length,
1058
+ 100L - out_length*100L/in_length));
1059
+ if (s->matches < s->last_lit/2 && out_length < in_length/2) return 1;
1060
+ }
1061
+ #endif
1062
+ return (s->last_lit == s->lit_bufsize-1);
1063
+ /* We avoid equality with lit_bufsize because of wraparound at 64K
1064
+ * on 16 bit machines and because stored blocks are restricted to
1065
+ * 64K-1 bytes.
1066
+ */
1067
+ }
1068
+
1069
+ /* ===========================================================================
1070
+ * Send the block data compressed using the given Huffman trees
1071
+ */
1072
+ local void compress_block(s, ltree, dtree)
1073
+ deflate_state *s;
1074
+ ct_data *ltree; /* literal tree */
1075
+ ct_data *dtree; /* distance tree */
1076
+ {
1077
+ unsigned dist; /* distance of matched string */
1078
+ int lc; /* match length or unmatched char (if dist == 0) */
1079
+ unsigned lx = 0; /* running index in l_buf */
1080
+ unsigned code; /* the code to send */
1081
+ int extra; /* number of extra bits to send */
1082
+
1083
+ if (s->last_lit != 0) do {
1084
+ dist = s->d_buf[lx];
1085
+ lc = s->l_buf[lx++];
1086
+ if (dist == 0) {
1087
+ send_code(s, lc, ltree); /* send a literal byte */
1088
+ Tracecv(isgraph(lc), (stderr," '%c' ", lc));
1089
+ } else {
1090
+ /* Here, lc is the match length - MIN_MATCH */
1091
+ code = _length_code[lc];
1092
+ send_code(s, code+LITERALS+1, ltree); /* send the length code */
1093
+ extra = extra_lbits[code];
1094
+ if (extra != 0) {
1095
+ lc -= base_length[code];
1096
+ send_bits(s, lc, extra); /* send the extra length bits */
1097
+ }
1098
+ dist--; /* dist is now the match distance - 1 */
1099
+ code = d_code(dist);
1100
+ Assert (code < D_CODES, "bad d_code");
1101
+
1102
+ send_code(s, code, dtree); /* send the distance code */
1103
+ extra = extra_dbits[code];
1104
+ if (extra != 0) {
1105
+ dist -= base_dist[code];
1106
+ send_bits(s, dist, extra); /* send the extra distance bits */
1107
+ }
1108
+ } /* literal or match pair ? */
1109
+
1110
+ /* Check that the overlay between pending_buf and d_buf+l_buf is ok: */
1111
+ Assert((uInt)(s->pending) < s->lit_bufsize + 2*lx,
1112
+ "pendingBuf overflow");
1113
+
1114
+ } while (lx < s->last_lit);
1115
+
1116
+ send_code(s, END_BLOCK, ltree);
1117
+ s->last_eob_len = ltree[END_BLOCK].Len;
1118
+ }
1119
+
1120
+ /* ===========================================================================
1121
+ * Set the data type to BINARY or TEXT, using a crude approximation:
1122
+ * set it to Z_TEXT if all symbols are either printable characters (33 to 255)
1123
+ * or white spaces (9 to 13, or 32); or set it to Z_BINARY otherwise.
1124
+ * IN assertion: the fields Freq of dyn_ltree are set.
1125
+ */
1126
+ local void set_data_type(s)
1127
+ deflate_state *s;
1128
+ {
1129
+ int n;
1130
+
1131
+ for (n = 0; n < 9; n++)
1132
+ if (s->dyn_ltree[n].Freq != 0)
1133
+ break;
1134
+ if (n == 9)
1135
+ for (n = 14; n < 32; n++)
1136
+ if (s->dyn_ltree[n].Freq != 0)
1137
+ break;
1138
+ s->strm->data_type = (n == 32) ? Z_TEXT : Z_BINARY;
1139
+ }
1140
+
1141
+ /* ===========================================================================
1142
+ * Reverse the first len bits of a code, using straightforward code (a faster
1143
+ * method would use a table)
1144
+ * IN assertion: 1 <= len <= 15
1145
+ */
1146
+ local unsigned bi_reverse(code, len)
1147
+ unsigned code; /* the value to invert */
1148
+ int len; /* its bit length */
1149
+ {
1150
+ register unsigned res = 0;
1151
+ do {
1152
+ res |= code & 1;
1153
+ code >>= 1, res <<= 1;
1154
+ } while (--len > 0);
1155
+ return res >> 1;
1156
+ }
1157
+
1158
+ /* ===========================================================================
1159
+ * Flush the bit buffer, keeping at most 7 bits in it.
1160
+ */
1161
+ local void bi_flush(s)
1162
+ deflate_state *s;
1163
+ {
1164
+ if (s->bi_valid == 16) {
1165
+ put_short(s, s->bi_buf);
1166
+ s->bi_buf = 0;
1167
+ s->bi_valid = 0;
1168
+ } else if (s->bi_valid >= 8) {
1169
+ put_byte(s, (Byte)s->bi_buf);
1170
+ s->bi_buf >>= 8;
1171
+ s->bi_valid -= 8;
1172
+ }
1173
+ }
1174
+
1175
+ /* ===========================================================================
1176
+ * Flush the bit buffer and align the output on a byte boundary
1177
+ */
1178
+ local void bi_windup(s)
1179
+ deflate_state *s;
1180
+ {
1181
+ if (s->bi_valid > 8) {
1182
+ put_short(s, s->bi_buf);
1183
+ } else if (s->bi_valid > 0) {
1184
+ put_byte(s, (Byte)s->bi_buf);
1185
+ }
1186
+ s->bi_buf = 0;
1187
+ s->bi_valid = 0;
1188
+ #ifdef DEBUG
1189
+ s->bits_sent = (s->bits_sent+7) & ~7;
1190
+ #endif
1191
+ }
1192
+
1193
+ /* ===========================================================================
1194
+ * Copy a stored block, storing first the length and its
1195
+ * one's complement if requested.
1196
+ */
1197
+ local void copy_block(s, buf, len, header)
1198
+ deflate_state *s;
1199
+ charf *buf; /* the input data */
1200
+ unsigned len; /* its length */
1201
+ int header; /* true if block header must be written */
1202
+ {
1203
+ bi_windup(s); /* align on byte boundary */
1204
+ s->last_eob_len = 8; /* enough lookahead for inflate */
1205
+
1206
+ if (header) {
1207
+ put_short(s, (ush)len);
1208
+ put_short(s, (ush)~len);
1209
+ #ifdef DEBUG
1210
+ s->bits_sent += 2*16;
1211
+ #endif
1212
+ }
1213
+ #ifdef DEBUG
1214
+ s->bits_sent += (ulg)len<<3;
1215
+ #endif
1216
+ while (len--) {
1217
+ put_byte(s, *buf++);
1218
+ }
1219
+ }