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 +1,69 @@
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, 1998-2003 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.h,v 1.8 2007/04/24 12:16:41 zerbino Exp $
47
+ *
48
+ */
49
+
50
+ #ifndef _DFIB_H_
51
+ #define _DFIB_H_
52
+
53
+ #include "globals.h"
54
+
55
+ /* functions for key heaps */
56
+ DFibHeap *dfh_makekeyheap(void);
57
+ DFibHeapNode *dfh_insertkey(DFibHeap *, Time, void *);
58
+ Time dfh_replacekey(DFibHeap *, DFibHeapNode *, Time);
59
+ void *dfh_replacekeydata(DFibHeap *, DFibHeapNode *, Time, void *);
60
+
61
+ void *dfh_extractmin(DFibHeap *);
62
+ void *dfh_replacedata(DFibHeapNode *, void *);
63
+ void *dfh_delete(DFibHeap *, DFibHeapNode *);
64
+ void dfh_deleteheap(DFibHeap *);
65
+
66
+ IDnum dfibheap_getSize(DFibHeap *);
67
+ Time dfibheap_el_getKey(DFibHeapNode *);
68
+
69
+ #endif /* _FIB_H_ */
@@ -0,0 +1,89 @@
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
+ #include <stdlib.h>
22
+ #include <stdio.h>
23
+
24
+ #include "globals.h"
25
+ #include "dfib.h"
26
+ #include "utility.h"
27
+
28
+
29
+ // Constructor
30
+ // Memory allocated
31
+ DFibHeap *newDFibHeap()
32
+ {
33
+ DFibHeap* dheap = dfh_makekeyheap();
34
+ if (dheap == NULL)
35
+ exitErrorf(EXIT_FAILURE, true, "Can't allocate DFibHeap");
36
+
37
+ return dheap;
38
+ }
39
+
40
+ // Add new node into heap with a key, and a pointer to the specified node
41
+ DFibHeapNode *insertNodeIntoDHeap(DFibHeap * heap, Time key,
42
+ struct node_st * node)
43
+ {
44
+ DFibHeapNode *res;
45
+ res = dfh_insertkey(heap, key, node);
46
+
47
+ return res;
48
+ }
49
+
50
+ // Replaces the key for a given node
51
+ Time replaceKeyInDHeap(DFibHeap * heap, DFibHeapNode * node, Time newKey)
52
+ {
53
+ Time res;
54
+ res = dfh_replacekey(heap, node, newKey);
55
+
56
+ return res;
57
+ }
58
+
59
+ // Removes the node with the shortest key, then returns it.
60
+ Node *removeNextNodeFromDHeap(DFibHeap * heap)
61
+ {
62
+ Node *node;
63
+ node = (Node *) dfh_extractmin(heap);
64
+
65
+ return node;
66
+ }
67
+
68
+ // Destructor
69
+ void destroyDHeap(DFibHeap * heap)
70
+ {
71
+ dfh_deleteheap(heap);
72
+ }
73
+
74
+ // Replace the node pointed to by a heap node
75
+ void replaceValueInDHeap(DFibHeapNode * node, Node * newValue)
76
+ {
77
+ dfh_replacedata(node, newValue);
78
+ }
79
+
80
+ // Remove unwanted node
81
+ void destroyNodeInDHeap(DFibHeapNode * node, DFibHeap * heap)
82
+ {
83
+ dfh_delete(heap, node);
84
+ }
85
+
86
+ Time getKey(DFibHeapNode * node)
87
+ {
88
+ return dfibheap_el_getKey(node);
89
+ }
@@ -0,0 +1,39 @@
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 _DFIBHEAP_H_
22
+ #define _DFIBHEAP_H_
23
+
24
+ DFibHeap *newDFibHeap();
25
+
26
+ DFibHeapNode *insertNodeIntoDHeap(DFibHeap * heap, Time key, Node * node);
27
+
28
+ Time replaceKeyInDHeap(DFibHeap * heap, DFibHeapNode * node, Time newKey);
29
+
30
+ Node *removeNextNodeFromDHeap(DFibHeap * heap);
31
+
32
+ void destroyDHeap(DFibHeap * heap);
33
+
34
+ void replaceValueInDHeap(DFibHeapNode * node, Node * newValue);
35
+
36
+ void *destroyNodeInDHeap(DFibHeapNode * node, DFibHeap * heap);
37
+
38
+ Time getKey(DFibHeapNode * node);
39
+ #endif
@@ -0,0 +1,105 @@
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, 1999-2003 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: dfibpriv.h,v 1.8 2007/10/09 09:56:46 zerbino Exp $
47
+ *
48
+ */
49
+
50
+ #ifndef _DFIBPRIV_H_
51
+ #define _DFIBPRIV_H_
52
+
53
+ #include "globals.h"
54
+
55
+ /*
56
+ * specific node operations
57
+ */
58
+ struct dfibheap_el {
59
+ DFibHeapNode *dfhe_p;
60
+ DFibHeapNode *dfhe_child;
61
+ DFibHeapNode *dfhe_left;
62
+ DFibHeapNode *dfhe_right;
63
+ void *dfhe_data;
64
+ Time dfhe_key;
65
+ int dfhe_degree;
66
+ boolean dfhe_mark;
67
+ } ATTRIBUTE_PACKED;
68
+
69
+ static DFibHeapNode *dfhe_newelem(DFibHeap *);
70
+ static void dfhe_insertafter(DFibHeapNode * a, DFibHeapNode * b);
71
+ static inline void dfhe_insertbefore(DFibHeapNode * a, DFibHeapNode * b);
72
+ static DFibHeapNode *dfhe_remove(DFibHeapNode * a);
73
+
74
+ /*
75
+ * global heap operations
76
+ */
77
+ struct dfibheap {
78
+ RecycleBin *nodeMemory;
79
+ DFibHeapNode **dfh_cons;
80
+ DFibHeapNode *dfh_min;
81
+ DFibHeapNode *dfh_root;
82
+ IDnum dfh_n;
83
+ IDnum dfh_Dl;
84
+ } ATTRIBUTE_PACKED;
85
+
86
+ static void dfh_insertrootlist(DFibHeap *, DFibHeapNode *);
87
+ static void dfh_removerootlist(DFibHeap *, DFibHeapNode *);
88
+ static void dfh_consolidate(DFibHeap *);
89
+ static void dfh_heaplink(DFibHeap * h, DFibHeapNode * y, DFibHeapNode * x);
90
+ static void dfh_cut(DFibHeap *, DFibHeapNode *, DFibHeapNode *);
91
+ static void dfh_cascading_cut(DFibHeap *, DFibHeapNode *);
92
+ static DFibHeapNode *dfh_extractminel(DFibHeap *);
93
+ static void dfh_checkcons(DFibHeap * h);
94
+ static int dfh_compare(DFibHeap * h, DFibHeapNode * a, DFibHeapNode * b);
95
+ static int dfh_comparedata(DFibHeap * h, Time key,
96
+ void *data, DFibHeapNode * b);
97
+ static void dfh_insertel(DFibHeap * h, DFibHeapNode * x);
98
+
99
+
100
+ /*
101
+ * general functions
102
+ */
103
+ static inline IDnum ceillog2(IDnum a);
104
+
105
+ #endif /* _FIBPRIV_H_ */
data/ext/src/src/fib.c ADDED
@@ -0,0 +1,628 @@
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: fib.c,v 1.10 2007/10/19 13:09:26 zerbino Exp $
47
+ *
48
+ */
49
+ #include <limits.h>
50
+ #include <stdlib.h>
51
+
52
+ #include "fib.h"
53
+ #include "recycleBin.h"
54
+
55
+ #include "fibpriv.h"
56
+
57
+ #define BLOCKSIZE 10000
58
+
59
+ static FibHeapNode *allocateFibHeapEl(FibHeap * heap)
60
+ {
61
+ return allocatePointer(heap->nodeMemory);
62
+ }
63
+
64
+ static void deallocateFibHeapEl(FibHeapNode * a, FibHeap * heap)
65
+ {
66
+ deallocatePointer(heap->nodeMemory, a);
67
+ }
68
+
69
+ #define swap(type, a, b) \
70
+ do { \
71
+ type c; \
72
+ c = a; \
73
+ a = b; \
74
+ b = c; \
75
+ } while (0) \
76
+
77
+ #define INT_BITS (sizeof(IDnum) * 8)
78
+
79
+ static inline IDnum ceillog2(IDnum a)
80
+ {
81
+ IDnum oa;
82
+ IDnum i;
83
+ IDnum b;
84
+ IDnum cons;
85
+
86
+ oa = a;
87
+ b = INT_BITS / 2;
88
+ i = 0;
89
+ while (b) {
90
+ i = (i << 1);
91
+ cons = ((IDnum) 1) << b;
92
+ if (a >= cons) {
93
+ a /= cons;
94
+ i = i | 1;
95
+ } else
96
+ a &= cons - 1;
97
+ b /= 2;
98
+ }
99
+ if ((((IDnum) 1 << i)) == oa)
100
+ return i;
101
+ else
102
+ return i + 1;
103
+ }
104
+
105
+ /*
106
+ * Private Heap Functions
107
+ */
108
+ static void fh_initheap(FibHeap * new)
109
+ {
110
+ new->fh_cmp_fnct = NULL;
111
+ new->nodeMemory = newRecycleBin(sizeof(FibHeapNode), BLOCKSIZE);
112
+ new->fh_neginf = NULL;
113
+ new->fh_n = 0;
114
+ new->fh_Dl = -1;
115
+ new->fh_cons = NULL;
116
+ new->fh_min = NULL;
117
+ new->fh_root = NULL;
118
+ new->fh_keys = 0;
119
+ }
120
+
121
+ static void fh_destroyheap(FibHeap * h)
122
+ {
123
+ h->fh_cmp_fnct = NULL;
124
+ h->fh_neginf = NULL;
125
+ if (h->fh_cons != NULL)
126
+ free(h->fh_cons);
127
+ h->fh_cons = NULL;
128
+ free(h);
129
+ }
130
+
131
+ /*
132
+ * Public Heap Functions
133
+ */
134
+ FibHeap *fh_makekeyheap()
135
+ {
136
+ FibHeap *n;
137
+
138
+ if ((n = malloc(sizeof *n)) == NULL)
139
+ return NULL;
140
+
141
+ fh_initheap(n);
142
+ n->fh_keys = 1;
143
+
144
+ return n;
145
+ }
146
+
147
+ FibHeap *fh_makeheap()
148
+ {
149
+ FibHeap *n;
150
+
151
+ if ((n = malloc(sizeof *n)) == NULL)
152
+ return NULL;
153
+
154
+ fh_initheap(n);
155
+
156
+ return n;
157
+ }
158
+
159
+ voidcmp fh_setcmp(FibHeap * h, voidcmp fnct)
160
+ {
161
+ voidcmp oldfnct;
162
+
163
+ oldfnct = h->fh_cmp_fnct;
164
+ h->fh_cmp_fnct = fnct;
165
+
166
+ return oldfnct;
167
+ }
168
+
169
+ void *fh_setneginf(FibHeap * h, void *data)
170
+ {
171
+ void *old;
172
+
173
+ old = h->fh_neginf;
174
+ h->fh_neginf = data;
175
+
176
+ return old;
177
+ }
178
+
179
+ FibHeap *fh_union(FibHeap * ha, FibHeap * hb)
180
+ {
181
+ FibHeapNode *x;
182
+
183
+ if (ha->fh_root == NULL || hb->fh_root == NULL) {
184
+ /* either one or both are empty */
185
+ if (ha->fh_root == NULL) {
186
+ fh_destroyheap(ha);
187
+ return hb;
188
+ } else {
189
+ fh_destroyheap(hb);
190
+ return ha;
191
+ }
192
+ }
193
+ ha->fh_root->fhe_left->fhe_right = hb->fh_root;
194
+ hb->fh_root->fhe_left->fhe_right = ha->fh_root;
195
+ x = ha->fh_root->fhe_left;
196
+ ha->fh_root->fhe_left = hb->fh_root->fhe_left;
197
+ hb->fh_root->fhe_left = x;
198
+ ha->fh_n += hb->fh_n;
199
+ /*
200
+ * we probably should also keep stats on number of unions
201
+ */
202
+
203
+ /* set fh_min if necessary */
204
+ if (fh_compare(ha, hb->fh_min, ha->fh_min) < 0)
205
+ ha->fh_min = hb->fh_min;
206
+
207
+ fh_destroyheap(hb);
208
+ return ha;
209
+ }
210
+
211
+ void fh_deleteheap(FibHeap * h)
212
+ {
213
+ destroyRecycleBin(h->nodeMemory);
214
+ fh_destroyheap(h);
215
+ }
216
+
217
+ /*
218
+ * Public Key Heap Functions
219
+ */
220
+ FibHeapNode *fh_insertkey(FibHeap * h, Coordinate key, void *data)
221
+ {
222
+ FibHeapNode *x;
223
+
224
+ if ((x = fhe_newelem(h)) == NULL)
225
+ return NULL;
226
+
227
+ /* just insert on root list, and make sure it's not the new min */
228
+ x->fhe_data = data;
229
+ x->fhe_key = key;
230
+
231
+ fh_insertel(h, x);
232
+
233
+ return x;
234
+ }
235
+
236
+ Coordinate fh_minkey(FibHeap * h)
237
+ {
238
+ if (h->fh_min == NULL)
239
+ return (Coordinate) INT_MIN;
240
+ return h->fh_min->fhe_key;
241
+ }
242
+
243
+ Coordinate fh_replacekey(FibHeap * h, FibHeapNode * x, Coordinate key)
244
+ {
245
+ Coordinate ret;
246
+
247
+ ret = x->fhe_key;
248
+ (void) fh_replacekeydata(h, x, key, x->fhe_data);
249
+
250
+ return ret;
251
+ }
252
+
253
+ void *fh_replacekeydata(FibHeap * h, FibHeapNode * x,
254
+ Coordinate key, void *data)
255
+ {
256
+ void *odata;
257
+ Coordinate okey;
258
+ FibHeapNode *y;
259
+ int r;
260
+
261
+ odata = x->fhe_data;
262
+ okey = x->fhe_key;
263
+
264
+ /*
265
+ * we can increase a key by deleting and reinserting, that
266
+ * requires O(lgn) time.
267
+ */
268
+ if ((r = fh_comparedata(h, key, data, x)) > 0) {
269
+ /* XXX - bad code! */
270
+ abort();
271
+ }
272
+
273
+ x->fhe_data = data;
274
+ x->fhe_key = key;
275
+
276
+ /* because they are equal, we don't have to do anything */
277
+ if (r == 0)
278
+ return odata;
279
+
280
+ y = x->fhe_p;
281
+
282
+ if (h->fh_keys && okey == key)
283
+ return odata;
284
+
285
+ if (y != NULL && fh_compare(h, x, y) <= 0) {
286
+ fh_cut(h, x, y);
287
+ fh_cascading_cut(h, y);
288
+ }
289
+
290
+ /*
291
+ * the = is so that the call from fh_delete will delete the proper
292
+ * element.
293
+ */
294
+ if (fh_compare(h, x, h->fh_min) <= 0)
295
+ h->fh_min = x;
296
+
297
+ return odata;
298
+ }
299
+
300
+ /*
301
+ * Public void * Heap Functions
302
+ */
303
+ /*
304
+ * this will return these values:
305
+ * NULL failed for some reason
306
+ * ptr token to use for manipulation of data
307
+ */
308
+ FibHeapNode *fh_insert(FibHeap * h, void *data)
309
+ {
310
+ FibHeapNode *x;
311
+
312
+ if ((x = fhe_newelem(h)) == NULL)
313
+ return NULL;
314
+
315
+ /* just insert on root list, and make sure it's not the new min */
316
+ x->fhe_data = data;
317
+
318
+ fh_insertel(h, x);
319
+
320
+ return x;
321
+ }
322
+
323
+ void *fh_min(FibHeap * h)
324
+ {
325
+ if (h->fh_min == NULL)
326
+ return NULL;
327
+ return h->fh_min->fhe_data;
328
+ }
329
+
330
+ void *fh_extractmin(FibHeap * h)
331
+ {
332
+ FibHeapNode *z;
333
+ void *ret;
334
+
335
+ ret = NULL;
336
+
337
+ if (h->fh_min != NULL) {
338
+ z = fh_extractminel(h);
339
+ ret = z->fhe_data;
340
+ #ifndef NO_FREE
341
+ deallocateFibHeapEl(z, h);
342
+ #endif
343
+
344
+ }
345
+
346
+ return ret;
347
+ }
348
+
349
+ void *fh_replacedata(FibHeapNode * x, void *data)
350
+ {
351
+ void *odata = x->fhe_data;
352
+ x->fhe_data = data;
353
+ return odata;
354
+ }
355
+
356
+ void *fh_delete(FibHeap * h, FibHeapNode * x)
357
+ {
358
+ void *k;
359
+
360
+ k = x->fhe_data;
361
+ if (!h->fh_keys)
362
+ fh_replacedata(x, h->fh_neginf);
363
+ else
364
+ fh_replacekey(h, x, (Coordinate) INT_MIN);
365
+ fh_extractmin(h);
366
+
367
+ return k;
368
+ }
369
+
370
+ /*
371
+ * begin of private element fuctions
372
+ */
373
+ static FibHeapNode *fh_extractminel(FibHeap * h)
374
+ {
375
+ FibHeapNode *ret;
376
+ FibHeapNode *x, *y, *orig;
377
+
378
+ ret = h->fh_min;
379
+
380
+ orig = NULL;
381
+ /* put all the children on the root list */
382
+ /* for true consistancy, we should use fhe_remove */
383
+ for (x = ret->fhe_child; x != orig && x != NULL;) {
384
+ if (orig == NULL)
385
+ orig = x;
386
+ y = x->fhe_right;
387
+ x->fhe_p = NULL;
388
+ fh_insertrootlist(h, x);
389
+ x = y;
390
+ }
391
+ /* remove minimum from root list */
392
+ fh_removerootlist(h, ret);
393
+ h->fh_n--;
394
+
395
+ /* if we aren't empty, consolidate the heap */
396
+ if (h->fh_n == 0)
397
+ h->fh_min = NULL;
398
+ else {
399
+ h->fh_min = ret->fhe_right;
400
+ fh_consolidate(h);
401
+ }
402
+
403
+ return ret;
404
+ }
405
+
406
+ static void fh_insertrootlist(FibHeap * h, FibHeapNode * x)
407
+ {
408
+ if (h->fh_root == NULL) {
409
+ h->fh_root = x;
410
+ x->fhe_left = x;
411
+ x->fhe_right = x;
412
+ return;
413
+ }
414
+
415
+ fhe_insertafter(h->fh_root, x);
416
+ }
417
+
418
+ static void fh_removerootlist(FibHeap * h, FibHeapNode * x)
419
+ {
420
+ if (x->fhe_left == x)
421
+ h->fh_root = NULL;
422
+ else
423
+ h->fh_root = fhe_remove(x);
424
+ }
425
+
426
+ static void fh_consolidate(FibHeap * h)
427
+ {
428
+ FibHeapNode **a;
429
+ FibHeapNode *w;
430
+ FibHeapNode *y;
431
+ FibHeapNode *x;
432
+ IDnum i;
433
+ IDnum d;
434
+ IDnum D;
435
+
436
+ fh_checkcons(h);
437
+
438
+ /* assign a the value of h->fh_cons so I don't have to rewrite code */
439
+ D = h->fh_Dl + 1;
440
+ a = h->fh_cons;
441
+
442
+ for (i = 0; i < D; i++)
443
+ a[i] = NULL;
444
+
445
+ while ((w = h->fh_root) != NULL) {
446
+ x = w;
447
+ fh_removerootlist(h, w);
448
+ d = x->fhe_degree;
449
+ /* XXX - assert that d < D */
450
+ while (a[d] != NULL) {
451
+ y = a[d];
452
+ if (fh_compare(h, x, y) > 0)
453
+ swap(FibHeapNode *, x, y);
454
+ fh_heaplink(h, y, x);
455
+ a[d] = NULL;
456
+ d++;
457
+ }
458
+ a[d] = x;
459
+ }
460
+ h->fh_min = NULL;
461
+ for (i = 0; i < D; i++)
462
+ if (a[i] != NULL) {
463
+ fh_insertrootlist(h, a[i]);
464
+ if (h->fh_min == NULL
465
+ || fh_compare(h, a[i], h->fh_min) < 0)
466
+ h->fh_min = a[i];
467
+ }
468
+ }
469
+
470
+ static void fh_heaplink(FibHeap * h, FibHeapNode * y, FibHeapNode * x)
471
+ {
472
+ /* make y a child of x */
473
+ if (x->fhe_child == NULL)
474
+ x->fhe_child = y;
475
+ else
476
+ fhe_insertbefore(x->fhe_child, y);
477
+ y->fhe_p = x;
478
+ x->fhe_degree++;
479
+ y->fhe_mark = 0;
480
+ }
481
+
482
+ static void fh_cut(FibHeap * h, FibHeapNode * x, FibHeapNode * y)
483
+ {
484
+ fhe_remove(x);
485
+ y->fhe_degree--;
486
+ fh_insertrootlist(h, x);
487
+ x->fhe_p = NULL;
488
+ x->fhe_mark = 0;
489
+ }
490
+
491
+ static void fh_cascading_cut(FibHeap * h, FibHeapNode * y)
492
+ {
493
+ FibHeapNode *z;
494
+
495
+ while ((z = y->fhe_p) != NULL) {
496
+ if (y->fhe_mark == 0) {
497
+ y->fhe_mark = 1;
498
+ return;
499
+ } else {
500
+ fh_cut(h, y, z);
501
+ y = z;
502
+ }
503
+ }
504
+ }
505
+
506
+ /*
507
+ * begining of handling elements of fibheap
508
+ */
509
+ static FibHeapNode *fhe_newelem(FibHeap * h)
510
+ {
511
+ FibHeapNode *e;
512
+
513
+ if ((e = allocateFibHeapEl(h)) == NULL)
514
+ return NULL;
515
+
516
+ fhe_initelem(e);
517
+
518
+ return e;
519
+ }
520
+
521
+ static void fhe_initelem(FibHeapNode * e)
522
+ {
523
+ e->fhe_degree = 0;
524
+ e->fhe_mark = 0;
525
+ e->fhe_p = NULL;
526
+ e->fhe_child = NULL;
527
+ e->fhe_left = e;
528
+ e->fhe_right = e;
529
+ e->fhe_data = NULL;
530
+ }
531
+
532
+ static void fhe_insertafter(FibHeapNode * a, FibHeapNode * b)
533
+ {
534
+ if (a == a->fhe_right) {
535
+ a->fhe_right = b;
536
+ a->fhe_left = b;
537
+ b->fhe_right = a;
538
+ b->fhe_left = a;
539
+ } else {
540
+ b->fhe_right = a->fhe_right;
541
+ a->fhe_right->fhe_left = b;
542
+ a->fhe_right = b;
543
+ b->fhe_left = a;
544
+ }
545
+ }
546
+
547
+ static inline void fhe_insertbefore(FibHeapNode * a, FibHeapNode * b)
548
+ {
549
+ fhe_insertafter(a->fhe_left, b);
550
+ }
551
+
552
+ static FibHeapNode *fhe_remove(FibHeapNode * x)
553
+ {
554
+ FibHeapNode *ret;
555
+
556
+ if (x == x->fhe_left)
557
+ ret = NULL;
558
+ else
559
+ ret = x->fhe_left;
560
+
561
+ /* fix the parent pointer */
562
+ if (x->fhe_p != NULL && x->fhe_p->fhe_child == x)
563
+ x->fhe_p->fhe_child = ret;
564
+
565
+ x->fhe_right->fhe_left = x->fhe_left;
566
+ x->fhe_left->fhe_right = x->fhe_right;
567
+
568
+ /* clear out hanging pointers */
569
+ x->fhe_p = NULL;
570
+ x->fhe_left = x;
571
+ x->fhe_right = x;
572
+
573
+ return ret;
574
+ }
575
+
576
+ static void fh_checkcons(FibHeap * h)
577
+ {
578
+ IDnum oDl;
579
+
580
+ /* make sure we have enough memory allocated to "reorganize" */
581
+ if (h->fh_Dl == -1 || h->fh_n > (1 << h->fh_Dl)) {
582
+ oDl = h->fh_Dl;
583
+ if ((h->fh_Dl = ceillog2(h->fh_n) + 1) < 8)
584
+ h->fh_Dl = 8;
585
+ if (oDl != h->fh_Dl)
586
+ h->fh_cons =
587
+ (FibHeapNode **) realloc(h->fh_cons,
588
+ sizeof *h->
589
+ fh_cons *
590
+ (h->fh_Dl + 1));
591
+ if (h->fh_cons == NULL)
592
+ abort();
593
+ }
594
+ }
595
+
596
+ static int fh_compare(FibHeap * h, FibHeapNode * a, FibHeapNode * b)
597
+ {
598
+ if (a->fhe_key < b->fhe_key)
599
+ return -1;
600
+ if (a->fhe_key == b->fhe_key)
601
+ return 0;
602
+ return 1;
603
+ }
604
+
605
+ static int
606
+ fh_comparedata(FibHeap * h, Coordinate key, void *data, FibHeapNode * b)
607
+ {
608
+ FibHeapNode a;
609
+
610
+ a.fhe_key = key;
611
+ a.fhe_data = data;
612
+
613
+ return fh_compare(h, &a, b);
614
+ }
615
+
616
+ static void fh_insertel(FibHeap * h, FibHeapNode * x)
617
+ {
618
+ fh_insertrootlist(h, x);
619
+
620
+ if (h->fh_min == NULL
621
+ || (h->fh_keys ? x->fhe_key <
622
+ h->fh_min->fhe_key : h->fh_cmp_fnct(x->fhe_data,
623
+ h->fh_min->fhe_data) <
624
+ 0))
625
+ h->fh_min = x;
626
+
627
+ h->fh_n++;
628
+ }