/* Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk) This file is part of Velvet. Velvet is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. Velvet is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with Velvet; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA */ /*- * Copyright 1997-2003 John-Mark Gurney. * All rights reserved. * * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions * are met: * 1. Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * 2. Redistributions in binary form must reproduce the above copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the distribution. * * THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE * ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF * SUCH DAMAGE. * * $Id: dfib.c,v 1.12 2007/10/19 13:09:26 zerbino Exp $ * */ #include #include #include "recycleBin.h" #include "dfib.h" #include "dfibpriv.h" #define BLOCKSIZE 10000 static DFibHeapNode *allocateDFibHeapNode(DFibHeap * heap) { return allocatePointer(heap->nodeMemory); } static void deallocateDFibHeapNode(DFibHeapNode * a, DFibHeap * heap) { deallocatePointer(heap->nodeMemory, a); } IDnum dfibheap_getSize(DFibHeap * heap) { return heap->dfh_n; } #define swap(type, a, b) \ do { \ type c; \ c = a; \ a = b; \ b = c; \ } while (0) \ #define INT_BITS (sizeof(IDnum) * 8) static inline IDnum ceillog2(IDnum a) { IDnum oa; IDnum i; IDnum b; IDnum cons; oa = a; b = INT_BITS / 2; i = 0; while (b) { i = (i << 1); cons = ((IDnum) 1) << b; if (a >= cons) { a /= cons; i = i | 1; } else a &= cons - 1; b /= 2; } if ((((IDnum) 1 << i)) == oa) return i; else return i + 1; } /* * Public Heap Functions */ DFibHeap *dfh_makekeyheap() { DFibHeap *n; if ((n = malloc(sizeof *n)) == NULL) return NULL; n->nodeMemory = newRecycleBin(sizeof(DFibHeapNode), BLOCKSIZE); n->dfh_n = 0; n->dfh_Dl = -1; n->dfh_cons = NULL; n->dfh_min = NULL; n->dfh_root = NULL; return n; } void dfh_deleteheap(DFibHeap * h) { destroyRecycleBin(h->nodeMemory); if (h->dfh_cons != NULL) free(h->dfh_cons); free(h); } /* * Public Key Heap Functions */ DFibHeapNode *dfh_insertkey(DFibHeap * h, Time key, void *data) { DFibHeapNode *x; if ((x = dfhe_newelem(h)) == NULL) return NULL; /* just insert on root list, and make sure it's not the new min */ x->dfhe_data = data; x->dfhe_key = key; dfh_insertel(h, x); return x; } Time dfh_replacekey(DFibHeap * h, DFibHeapNode * x, Time key) { Time ret; ret = x->dfhe_key; (void) dfh_replacekeydata(h, x, key, x->dfhe_data); return ret; } void *dfh_replacekeydata(DFibHeap * h, DFibHeapNode * x, Time key, void *data) { void *odata; Time okey; DFibHeapNode *y; int r; odata = x->dfhe_data; okey = x->dfhe_key; /* * we can increase a key by deleting and reinserting, that * requires O(lgn) time. */ if ((r = dfh_comparedata(h, key, data, x)) > 0) { /* XXX - bad code! */ abort(); } x->dfhe_data = data; x->dfhe_key = key; /* because they are equal, we don't have to do anything */ if (r == 0) return odata; y = x->dfhe_p; if (okey == key) return odata; if (y != NULL && dfh_compare(h, x, y) <= 0) { dfh_cut(h, x, y); dfh_cascading_cut(h, y); } /* * the = is so that the call from dfh_delete will delete the proper * element. */ if (dfh_compare(h, x, h->dfh_min) <= 0) h->dfh_min = x; return odata; } /* * Public void * Heap Functions */ /* * this will return these values: * NULL failed for some reason * ptr token to use for manipulation of data */ void *dfh_extractmin(DFibHeap * h) { DFibHeapNode *z; void *ret; ret = NULL; if (h->dfh_min != NULL) { z = dfh_extractminel(h); ret = z->dfhe_data; deallocateDFibHeapNode(z, h); } return ret; } void *dfh_replacedata(DFibHeapNode * x, void *data) { void *odata = x->dfhe_data; x->dfhe_data = data; return odata; } void *dfh_delete(DFibHeap * h, DFibHeapNode * x) { void *k; k = x->dfhe_data; dfh_replacekey(h, x, INT_MIN); dfh_extractmin(h); return k; } /* * begin of private element fuctions */ static DFibHeapNode *dfh_extractminel(DFibHeap * h) { DFibHeapNode *ret; DFibHeapNode *x, *y, *orig; ret = h->dfh_min; orig = NULL; /* put all the children on the root list */ /* for true consistancy, we should use dfhe_remove */ for (x = ret->dfhe_child; x != orig && x != NULL;) { if (orig == NULL) orig = x; y = x->dfhe_right; x->dfhe_p = NULL; dfh_insertrootlist(h, x); x = y; } /* remove minimum from root list */ dfh_removerootlist(h, ret); h->dfh_n--; /* if we aren't empty, consolidate the heap */ if (h->dfh_n == 0) h->dfh_min = NULL; else { h->dfh_min = ret->dfhe_right; dfh_consolidate(h); } return ret; } static void dfh_insertrootlist(DFibHeap * h, DFibHeapNode * x) { if (h->dfh_root == NULL) { h->dfh_root = x; x->dfhe_left = x; x->dfhe_right = x; return; } dfhe_insertafter(h->dfh_root, x); } static void dfh_removerootlist(DFibHeap * h, DFibHeapNode * x) { if (x->dfhe_left == x) h->dfh_root = NULL; else h->dfh_root = dfhe_remove(x); } static void dfh_consolidate(DFibHeap * h) { DFibHeapNode **a; DFibHeapNode *w; DFibHeapNode *y; DFibHeapNode *x; IDnum i; IDnum d; IDnum D; dfh_checkcons(h); /* assign a the value of h->dfh_cons so I don't have to rewrite code */ D = h->dfh_Dl + 1; a = h->dfh_cons; for (i = 0; i < D; i++) a[i] = NULL; while ((w = h->dfh_root) != NULL) { x = w; dfh_removerootlist(h, w); d = x->dfhe_degree; /* XXX - assert that d < D */ while (a[d] != NULL) { y = a[d]; if (dfh_compare(h, x, y) > 0) swap(DFibHeapNode *, x, y); dfh_heaplink(h, y, x); a[d] = NULL; d++; } a[d] = x; } h->dfh_min = NULL; for (i = 0; i < D; i++) if (a[i] != NULL) { dfh_insertrootlist(h, a[i]); if (h->dfh_min == NULL || dfh_compare(h, a[i], h->dfh_min) < 0) h->dfh_min = a[i]; } } static void dfh_heaplink(DFibHeap * h, DFibHeapNode * y, DFibHeapNode * x) { /* make y a child of x */ if (x->dfhe_child == NULL) x->dfhe_child = y; else dfhe_insertbefore(x->dfhe_child, y); y->dfhe_p = x; x->dfhe_degree++; y->dfhe_mark = 0; } static void dfh_cut(DFibHeap * h, DFibHeapNode * x, DFibHeapNode * y) { dfhe_remove(x); y->dfhe_degree--; dfh_insertrootlist(h, x); x->dfhe_p = NULL; x->dfhe_mark = 0; } static void dfh_cascading_cut(DFibHeap * h, DFibHeapNode * y) { DFibHeapNode *z; while ((z = y->dfhe_p) != NULL) { if (y->dfhe_mark == 0) { y->dfhe_mark = 1; return; } else { dfh_cut(h, y, z); y = z; } } } /* * begining of handling elements of dfibheap */ static DFibHeapNode *dfhe_newelem(DFibHeap * h) { DFibHeapNode *e; if ((e = allocateDFibHeapNode(h)) == NULL) return NULL; e->dfhe_degree = 0; e->dfhe_mark = 0; e->dfhe_p = NULL; e->dfhe_child = NULL; e->dfhe_left = e; e->dfhe_right = e; e->dfhe_data = NULL; return e; } static void dfhe_insertafter(DFibHeapNode * a, DFibHeapNode * b) { if (a == a->dfhe_right) { a->dfhe_right = b; a->dfhe_left = b; b->dfhe_right = a; b->dfhe_left = a; } else { b->dfhe_right = a->dfhe_right; a->dfhe_right->dfhe_left = b; a->dfhe_right = b; b->dfhe_left = a; } } static inline void dfhe_insertbefore(DFibHeapNode * a, DFibHeapNode * b) { dfhe_insertafter(a->dfhe_left, b); } static DFibHeapNode *dfhe_remove(DFibHeapNode * x) { DFibHeapNode *ret; if (x == x->dfhe_left) ret = NULL; else ret = x->dfhe_left; /* fix the parent pointer */ if (x->dfhe_p != NULL && x->dfhe_p->dfhe_child == x) x->dfhe_p->dfhe_child = ret; x->dfhe_right->dfhe_left = x->dfhe_left; x->dfhe_left->dfhe_right = x->dfhe_right; /* clear out hanging pointers */ x->dfhe_p = NULL; x->dfhe_left = x; x->dfhe_right = x; return ret; } static void dfh_checkcons(DFibHeap * h) { IDnum oDl; /* make sure we have enough memory allocated to "reorganize" */ if (h->dfh_Dl == -1 || h->dfh_n > (1 << h->dfh_Dl)) { oDl = h->dfh_Dl; if ((h->dfh_Dl = ceillog2(h->dfh_n) + 1) < 8) h->dfh_Dl = 8; if (oDl != h->dfh_Dl) h->dfh_cons = (DFibHeapNode **) realloc(h->dfh_cons, sizeof *h-> dfh_cons * (h->dfh_Dl + 1)); if (h->dfh_cons == NULL) abort(); } } static int dfh_compare(DFibHeap * h, DFibHeapNode * a, DFibHeapNode * b) { if (a->dfhe_key < b->dfhe_key) return -1; if (a->dfhe_key == b->dfhe_key) return 0; return 1; } static int dfh_comparedata(DFibHeap * h, Time key, void *data, DFibHeapNode * b) { DFibHeapNode a; a.dfhe_key = key; a.dfhe_data = data; return dfh_compare(h, &a, b); } static void dfh_insertel(DFibHeap * h, DFibHeapNode * x) { dfh_insertrootlist(h, x); if (h->dfh_min == NULL || x->dfhe_key < h->dfh_min->dfhe_key) h->dfh_min = x; h->dfh_n++; } Time dfibheap_el_getKey(DFibHeapNode * node) { return node->dfhe_key; }