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
  274. data/ext/src/third-party/zlib-1.2.3/zconf.h +332 -0
  275. data/ext/src/third-party/zlib-1.2.3/zconf.in.h +332 -0
  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
  286. metadata +456 -0
@@ -0,0 +1,32 @@
1
+ /*
2
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
3
+
4
+ This file is part of Velvet.
5
+
6
+ Velvet is free software; you can redistribute it and/or modify
7
+ it under the terms of the GNU General Public License as published by
8
+ the Free Software Foundation; either version 2 of the License, or
9
+ (at your option) any later version.
10
+
11
+ Velvet is distributed in the hope that it will be useful,
12
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
13
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14
+ GNU General Public License for more details.
15
+
16
+ You should have received a copy of the GNU General Public License
17
+ along with Velvet; if not, write to the Free Software
18
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
19
+
20
+ */
21
+ #ifndef _CORRECTEDGRAPH_H_
22
+ #define _CORRECTEDGRAPH_H_
23
+
24
+ void clipTipsHard(Graph * graph, boolean conserveLong);
25
+
26
+ void correctGraph(Graph * graph, ShortLength *sequenceLengths, Category * sequenceCategories, boolean conserveLong);
27
+
28
+ // Black arts:
29
+ void setMaxReadLength(int value);
30
+ void setMaxGaps(int value);
31
+ void setMaxDivergence(double value);
32
+ #endif
@@ -0,0 +1,509 @@
1
+ /*
2
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
3
+
4
+ This file is part of Velvet.
5
+
6
+ Velvet is free software; you can redistribute it and/or modify
7
+ it under the terms of the GNU General Public License as published by
8
+ the Free Software Foundation; either version 2 of the License, or
9
+ (at your option) any later version.
10
+
11
+ Velvet is distributed in the hope that it will be useful,
12
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
13
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14
+ GNU General Public License for more details.
15
+
16
+ You should have received a copy of the GNU General Public License
17
+ along with Velvet; if not, write to the Free Software
18
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
19
+
20
+ */
21
+ /*-
22
+ * Copyright 1997-2003 John-Mark Gurney.
23
+ * All rights reserved.
24
+ *
25
+ * Redistribution and use in source and binary forms, with or without
26
+ * modification, are permitted provided that the following conditions
27
+ * are met:
28
+ * 1. Redistributions of source code must retain the above copyright
29
+ * notice, this list of conditions and the following disclaimer.
30
+ * 2. Redistributions in binary form must reproduce the above copyright
31
+ * notice, this list of conditions and the following disclaimer in the
32
+ * documentation and/or other materials provided with the distribution.
33
+ *
34
+ * THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND
35
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
36
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
37
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE
38
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
39
+ * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
40
+ * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
41
+ * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
42
+ * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
43
+ * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
44
+ * SUCH DAMAGE.
45
+ *
46
+ * $Id: dfib.c,v 1.12 2007/10/19 13:09:26 zerbino Exp $
47
+ *
48
+ */
49
+ #include <limits.h>
50
+ #include <stdlib.h>
51
+
52
+ #include "recycleBin.h"
53
+ #include "dfib.h"
54
+
55
+ #include "dfibpriv.h"
56
+
57
+ #define BLOCKSIZE 10000
58
+ static DFibHeapNode *allocateDFibHeapNode(DFibHeap * heap)
59
+ {
60
+ return allocatePointer(heap->nodeMemory);
61
+ }
62
+
63
+ static void deallocateDFibHeapNode(DFibHeapNode * a, DFibHeap * heap)
64
+ {
65
+ deallocatePointer(heap->nodeMemory, a);
66
+ }
67
+
68
+ IDnum dfibheap_getSize(DFibHeap * heap)
69
+ {
70
+ return heap->dfh_n;
71
+ }
72
+
73
+ #define swap(type, a, b) \
74
+ do { \
75
+ type c; \
76
+ c = a; \
77
+ a = b; \
78
+ b = c; \
79
+ } while (0) \
80
+
81
+ #define INT_BITS (sizeof(IDnum) * 8)
82
+
83
+ static inline IDnum ceillog2(IDnum a)
84
+ {
85
+ IDnum oa;
86
+ IDnum i;
87
+ IDnum b;
88
+ IDnum cons;
89
+
90
+ oa = a;
91
+ b = INT_BITS / 2;
92
+ i = 0;
93
+ while (b) {
94
+ i = (i << 1);
95
+ cons = ((IDnum) 1) << b;
96
+ if (a >= cons) {
97
+ a /= cons;
98
+ i = i | 1;
99
+ } else
100
+ a &= cons - 1;
101
+ b /= 2;
102
+ }
103
+ if ((((IDnum) 1 << i)) == oa)
104
+ return i;
105
+ else
106
+ return i + 1;
107
+ }
108
+
109
+ /*
110
+ * Public Heap Functions
111
+ */
112
+ DFibHeap *dfh_makekeyheap()
113
+ {
114
+ DFibHeap *n;
115
+
116
+ if ((n = malloc(sizeof *n)) == NULL)
117
+ return NULL;
118
+
119
+ n->nodeMemory = newRecycleBin(sizeof(DFibHeapNode), BLOCKSIZE);
120
+ n->dfh_n = 0;
121
+ n->dfh_Dl = -1;
122
+ n->dfh_cons = NULL;
123
+ n->dfh_min = NULL;
124
+ n->dfh_root = NULL;
125
+
126
+ return n;
127
+ }
128
+
129
+ void dfh_deleteheap(DFibHeap * h)
130
+ {
131
+ destroyRecycleBin(h->nodeMemory);
132
+ if (h->dfh_cons != NULL)
133
+ free(h->dfh_cons);
134
+ free(h);
135
+ }
136
+
137
+ /*
138
+ * Public Key Heap Functions
139
+ */
140
+ DFibHeapNode *dfh_insertkey(DFibHeap * h, Time key, void *data)
141
+ {
142
+ DFibHeapNode *x;
143
+
144
+ if ((x = dfhe_newelem(h)) == NULL)
145
+ return NULL;
146
+
147
+ /* just insert on root list, and make sure it's not the new min */
148
+ x->dfhe_data = data;
149
+ x->dfhe_key = key;
150
+
151
+ dfh_insertel(h, x);
152
+
153
+ return x;
154
+ }
155
+
156
+ Time dfh_replacekey(DFibHeap * h, DFibHeapNode * x, Time key)
157
+ {
158
+ Time ret;
159
+
160
+ ret = x->dfhe_key;
161
+ (void) dfh_replacekeydata(h, x, key, x->dfhe_data);
162
+
163
+ return ret;
164
+ }
165
+
166
+ void *dfh_replacekeydata(DFibHeap * h, DFibHeapNode * x,
167
+ Time key, void *data)
168
+ {
169
+ void *odata;
170
+ Time okey;
171
+ DFibHeapNode *y;
172
+ int r;
173
+
174
+ odata = x->dfhe_data;
175
+ okey = x->dfhe_key;
176
+
177
+ /*
178
+ * we can increase a key by deleting and reinserting, that
179
+ * requires O(lgn) time.
180
+ */
181
+ if ((r = dfh_comparedata(h, key, data, x)) > 0) {
182
+ /* XXX - bad code! */
183
+ abort();
184
+ }
185
+
186
+ x->dfhe_data = data;
187
+ x->dfhe_key = key;
188
+
189
+ /* because they are equal, we don't have to do anything */
190
+ if (r == 0)
191
+ return odata;
192
+
193
+ y = x->dfhe_p;
194
+
195
+ if (okey == key)
196
+ return odata;
197
+
198
+ if (y != NULL && dfh_compare(h, x, y) <= 0) {
199
+ dfh_cut(h, x, y);
200
+ dfh_cascading_cut(h, y);
201
+ }
202
+
203
+ /*
204
+ * the = is so that the call from dfh_delete will delete the proper
205
+ * element.
206
+ */
207
+ if (dfh_compare(h, x, h->dfh_min) <= 0)
208
+ h->dfh_min = x;
209
+
210
+ return odata;
211
+ }
212
+
213
+ /*
214
+ * Public void * Heap Functions
215
+ */
216
+ /*
217
+ * this will return these values:
218
+ * NULL failed for some reason
219
+ * ptr token to use for manipulation of data
220
+ */
221
+ void *dfh_extractmin(DFibHeap * h)
222
+ {
223
+ DFibHeapNode *z;
224
+ void *ret;
225
+
226
+ ret = NULL;
227
+
228
+ if (h->dfh_min != NULL) {
229
+ z = dfh_extractminel(h);
230
+ ret = z->dfhe_data;
231
+ deallocateDFibHeapNode(z, h);
232
+ }
233
+
234
+ return ret;
235
+ }
236
+
237
+ void *dfh_replacedata(DFibHeapNode * x, void *data)
238
+ {
239
+ void *odata = x->dfhe_data;
240
+ x->dfhe_data = data;
241
+ return odata;
242
+ }
243
+
244
+ void *dfh_delete(DFibHeap * h, DFibHeapNode * x)
245
+ {
246
+ void *k;
247
+
248
+ k = x->dfhe_data;
249
+ dfh_replacekey(h, x, INT_MIN);
250
+ dfh_extractmin(h);
251
+
252
+ return k;
253
+ }
254
+
255
+ /*
256
+ * begin of private element fuctions
257
+ */
258
+ static DFibHeapNode *dfh_extractminel(DFibHeap * h)
259
+ {
260
+ DFibHeapNode *ret;
261
+ DFibHeapNode *x, *y, *orig;
262
+
263
+ ret = h->dfh_min;
264
+
265
+ orig = NULL;
266
+ /* put all the children on the root list */
267
+ /* for true consistancy, we should use dfhe_remove */
268
+ for (x = ret->dfhe_child; x != orig && x != NULL;) {
269
+ if (orig == NULL)
270
+ orig = x;
271
+ y = x->dfhe_right;
272
+ x->dfhe_p = NULL;
273
+ dfh_insertrootlist(h, x);
274
+ x = y;
275
+ }
276
+ /* remove minimum from root list */
277
+ dfh_removerootlist(h, ret);
278
+ h->dfh_n--;
279
+
280
+ /* if we aren't empty, consolidate the heap */
281
+ if (h->dfh_n == 0)
282
+ h->dfh_min = NULL;
283
+ else {
284
+ h->dfh_min = ret->dfhe_right;
285
+ dfh_consolidate(h);
286
+ }
287
+
288
+ return ret;
289
+ }
290
+
291
+ static void dfh_insertrootlist(DFibHeap * h, DFibHeapNode * x)
292
+ {
293
+ if (h->dfh_root == NULL) {
294
+ h->dfh_root = x;
295
+ x->dfhe_left = x;
296
+ x->dfhe_right = x;
297
+ return;
298
+ }
299
+
300
+ dfhe_insertafter(h->dfh_root, x);
301
+ }
302
+
303
+ static void dfh_removerootlist(DFibHeap * h, DFibHeapNode * x)
304
+ {
305
+ if (x->dfhe_left == x)
306
+ h->dfh_root = NULL;
307
+ else
308
+ h->dfh_root = dfhe_remove(x);
309
+ }
310
+
311
+ static void dfh_consolidate(DFibHeap * h)
312
+ {
313
+ DFibHeapNode **a;
314
+ DFibHeapNode *w;
315
+ DFibHeapNode *y;
316
+ DFibHeapNode *x;
317
+ IDnum i;
318
+ IDnum d;
319
+ IDnum D;
320
+
321
+ dfh_checkcons(h);
322
+
323
+ /* assign a the value of h->dfh_cons so I don't have to rewrite code */
324
+ D = h->dfh_Dl + 1;
325
+ a = h->dfh_cons;
326
+
327
+ for (i = 0; i < D; i++)
328
+ a[i] = NULL;
329
+
330
+ while ((w = h->dfh_root) != NULL) {
331
+ x = w;
332
+ dfh_removerootlist(h, w);
333
+ d = x->dfhe_degree;
334
+ /* XXX - assert that d < D */
335
+ while (a[d] != NULL) {
336
+ y = a[d];
337
+ if (dfh_compare(h, x, y) > 0)
338
+ swap(DFibHeapNode *, x, y);
339
+ dfh_heaplink(h, y, x);
340
+ a[d] = NULL;
341
+ d++;
342
+ }
343
+ a[d] = x;
344
+ }
345
+ h->dfh_min = NULL;
346
+ for (i = 0; i < D; i++)
347
+ if (a[i] != NULL) {
348
+ dfh_insertrootlist(h, a[i]);
349
+ if (h->dfh_min == NULL
350
+ || dfh_compare(h, a[i], h->dfh_min) < 0)
351
+ h->dfh_min = a[i];
352
+ }
353
+ }
354
+
355
+ static void dfh_heaplink(DFibHeap * h, DFibHeapNode * y, DFibHeapNode * x)
356
+ {
357
+ /* make y a child of x */
358
+ if (x->dfhe_child == NULL)
359
+ x->dfhe_child = y;
360
+ else
361
+ dfhe_insertbefore(x->dfhe_child, y);
362
+ y->dfhe_p = x;
363
+ x->dfhe_degree++;
364
+ y->dfhe_mark = 0;
365
+ }
366
+
367
+ static void dfh_cut(DFibHeap * h, DFibHeapNode * x, DFibHeapNode * y)
368
+ {
369
+ dfhe_remove(x);
370
+ y->dfhe_degree--;
371
+ dfh_insertrootlist(h, x);
372
+ x->dfhe_p = NULL;
373
+ x->dfhe_mark = 0;
374
+ }
375
+
376
+ static void dfh_cascading_cut(DFibHeap * h, DFibHeapNode * y)
377
+ {
378
+ DFibHeapNode *z;
379
+
380
+ while ((z = y->dfhe_p) != NULL) {
381
+ if (y->dfhe_mark == 0) {
382
+ y->dfhe_mark = 1;
383
+ return;
384
+ } else {
385
+ dfh_cut(h, y, z);
386
+ y = z;
387
+ }
388
+ }
389
+ }
390
+
391
+ /*
392
+ * begining of handling elements of dfibheap
393
+ */
394
+ static DFibHeapNode *dfhe_newelem(DFibHeap * h)
395
+ {
396
+ DFibHeapNode *e;
397
+
398
+ if ((e = allocateDFibHeapNode(h)) == NULL)
399
+ return NULL;
400
+
401
+ e->dfhe_degree = 0;
402
+ e->dfhe_mark = 0;
403
+ e->dfhe_p = NULL;
404
+ e->dfhe_child = NULL;
405
+ e->dfhe_left = e;
406
+ e->dfhe_right = e;
407
+ e->dfhe_data = NULL;
408
+
409
+ return e;
410
+ }
411
+
412
+ static void dfhe_insertafter(DFibHeapNode * a, DFibHeapNode * b)
413
+ {
414
+ if (a == a->dfhe_right) {
415
+ a->dfhe_right = b;
416
+ a->dfhe_left = b;
417
+ b->dfhe_right = a;
418
+ b->dfhe_left = a;
419
+ } else {
420
+ b->dfhe_right = a->dfhe_right;
421
+ a->dfhe_right->dfhe_left = b;
422
+ a->dfhe_right = b;
423
+ b->dfhe_left = a;
424
+ }
425
+ }
426
+
427
+ static inline void dfhe_insertbefore(DFibHeapNode * a, DFibHeapNode * b)
428
+ {
429
+ dfhe_insertafter(a->dfhe_left, b);
430
+ }
431
+
432
+ static DFibHeapNode *dfhe_remove(DFibHeapNode * x)
433
+ {
434
+ DFibHeapNode *ret;
435
+
436
+ if (x == x->dfhe_left)
437
+ ret = NULL;
438
+ else
439
+ ret = x->dfhe_left;
440
+
441
+ /* fix the parent pointer */
442
+ if (x->dfhe_p != NULL && x->dfhe_p->dfhe_child == x)
443
+ x->dfhe_p->dfhe_child = ret;
444
+
445
+ x->dfhe_right->dfhe_left = x->dfhe_left;
446
+ x->dfhe_left->dfhe_right = x->dfhe_right;
447
+
448
+ /* clear out hanging pointers */
449
+ x->dfhe_p = NULL;
450
+ x->dfhe_left = x;
451
+ x->dfhe_right = x;
452
+
453
+ return ret;
454
+ }
455
+
456
+ static void dfh_checkcons(DFibHeap * h)
457
+ {
458
+ IDnum oDl;
459
+
460
+ /* make sure we have enough memory allocated to "reorganize" */
461
+ if (h->dfh_Dl == -1 || h->dfh_n > (1 << h->dfh_Dl)) {
462
+ oDl = h->dfh_Dl;
463
+ if ((h->dfh_Dl = ceillog2(h->dfh_n) + 1) < 8)
464
+ h->dfh_Dl = 8;
465
+ if (oDl != h->dfh_Dl)
466
+ h->dfh_cons =
467
+ (DFibHeapNode **) realloc(h->dfh_cons,
468
+ sizeof *h->
469
+ dfh_cons *
470
+ (h->dfh_Dl + 1));
471
+ if (h->dfh_cons == NULL)
472
+ abort();
473
+ }
474
+ }
475
+
476
+ static int dfh_compare(DFibHeap * h, DFibHeapNode * a, DFibHeapNode * b)
477
+ {
478
+ if (a->dfhe_key < b->dfhe_key)
479
+ return -1;
480
+ if (a->dfhe_key == b->dfhe_key)
481
+ return 0;
482
+ return 1;
483
+ }
484
+
485
+ static int
486
+ dfh_comparedata(DFibHeap * h, Time key, void *data, DFibHeapNode * b)
487
+ {
488
+ DFibHeapNode a;
489
+
490
+ a.dfhe_key = key;
491
+ a.dfhe_data = data;
492
+
493
+ return dfh_compare(h, &a, b);
494
+ }
495
+
496
+ static void dfh_insertel(DFibHeap * h, DFibHeapNode * x)
497
+ {
498
+ dfh_insertrootlist(h, x);
499
+
500
+ if (h->dfh_min == NULL || x->dfhe_key < h->dfh_min->dfhe_key)
501
+ h->dfh_min = x;
502
+
503
+ h->dfh_n++;
504
+ }
505
+
506
+ Time dfibheap_el_getKey(DFibHeapNode * node)
507
+ {
508
+ return node->dfhe_key;
509
+ }