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dfib.c

/*
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 <limits.h>
#include <stdlib.h>

#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;
}

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