bio-velvet_underground 0.0.1

data/ext/src/src/dfib.h

@@ -0,0 +1,69 @@
+/*
+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, 1998-2003 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.h,v 1.8 2007/04/24 12:16:41 zerbino Exp $
+ *
+ */
+
+#ifndef _DFIB_H_
+#define _DFIB_H_
+
+#include "globals.h"
+
+/* functions for key heaps */
+DFibHeap *dfh_makekeyheap(void);
+DFibHeapNode *dfh_insertkey(DFibHeap *, Time, void *);
+Time dfh_replacekey(DFibHeap *, DFibHeapNode *, Time);
+void *dfh_replacekeydata(DFibHeap *, DFibHeapNode *, Time, void *);
+
+void *dfh_extractmin(DFibHeap *);
+void *dfh_replacedata(DFibHeapNode *, void *);
+void *dfh_delete(DFibHeap *, DFibHeapNode *);
+void dfh_deleteheap(DFibHeap *);
+
+IDnum dfibheap_getSize(DFibHeap *);
+Time dfibheap_el_getKey(DFibHeapNode *);
+
+#endif				/* _FIB_H_ */

data/ext/src/src/dfibHeap.c

@@ -0,0 +1,89 @@
+/*
+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
+
+*/
+#include <stdlib.h>
+#include <stdio.h>
+
+#include  "globals.h"
+#include "dfib.h"
+#include "utility.h"
+
+
+// Constructor
+// Memory allocated
+DFibHeap *newDFibHeap()
+{
+	DFibHeap* dheap = dfh_makekeyheap();
+	if (dheap == NULL)
+		exitErrorf(EXIT_FAILURE, true, "Can't allocate DFibHeap");
+
+	return dheap;
+}
+
+// Add new node into heap with a key, and a pointer to the specified node
+DFibHeapNode *insertNodeIntoDHeap(DFibHeap * heap, Time key,
+				  struct node_st * node)
+{
+	DFibHeapNode *res;
+	res = dfh_insertkey(heap, key, node);
+
+	return res;
+}
+
+// Replaces the key for a given node
+Time replaceKeyInDHeap(DFibHeap * heap, DFibHeapNode * node, Time newKey)
+{
+	Time res;
+	res = dfh_replacekey(heap, node, newKey);
+
+	return res;
+}
+
+// Removes the node with the shortest key, then returns it.
+Node *removeNextNodeFromDHeap(DFibHeap * heap)
+{
+	Node *node;
+	node = (Node *) dfh_extractmin(heap);
+
+	return node;
+}
+
+// Destructor
+void destroyDHeap(DFibHeap * heap)
+{
+	dfh_deleteheap(heap);
+}
+
+// Replace the node pointed to by a heap node
+void replaceValueInDHeap(DFibHeapNode * node, Node * newValue)
+{
+	dfh_replacedata(node, newValue);
+}
+
+// Remove unwanted node
+void destroyNodeInDHeap(DFibHeapNode * node, DFibHeap * heap)
+{
+	dfh_delete(heap, node);
+}
+
+Time getKey(DFibHeapNode * node)
+{
+	return dfibheap_el_getKey(node);
+}

data/ext/src/src/dfibHeap.h

@@ -0,0 +1,39 @@
+/*
+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
+
+*/
+#ifndef _DFIBHEAP_H_
+#define _DFIBHEAP_H_
+
+DFibHeap *newDFibHeap();
+
+DFibHeapNode *insertNodeIntoDHeap(DFibHeap * heap, Time key, Node * node);
+
+Time replaceKeyInDHeap(DFibHeap * heap, DFibHeapNode * node, Time newKey);
+
+Node *removeNextNodeFromDHeap(DFibHeap * heap);
+
+void destroyDHeap(DFibHeap * heap);
+
+void replaceValueInDHeap(DFibHeapNode * node, Node * newValue);
+
+void *destroyNodeInDHeap(DFibHeapNode * node, DFibHeap * heap);
+
+Time getKey(DFibHeapNode * node);
+#endif

data/ext/src/src/dfibpriv.h

@@ -0,0 +1,105 @@
+/*
+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, 1999-2003 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: dfibpriv.h,v 1.8 2007/10/09 09:56:46 zerbino Exp $
+ *
+ */
+
+#ifndef _DFIBPRIV_H_
+#define _DFIBPRIV_H_
+
+#include "globals.h"
+
+/*
+ * specific node operations
+ */
+struct dfibheap_el {
+	DFibHeapNode *dfhe_p;
+	DFibHeapNode *dfhe_child;
+	DFibHeapNode *dfhe_left;
+	DFibHeapNode *dfhe_right;
+	void *dfhe_data;
+	Time dfhe_key;
+	int dfhe_degree;
+	boolean dfhe_mark;
+}  ATTRIBUTE_PACKED;
+
+static DFibHeapNode *dfhe_newelem(DFibHeap *);
+static void dfhe_insertafter(DFibHeapNode * a, DFibHeapNode * b);
+static inline void dfhe_insertbefore(DFibHeapNode * a, DFibHeapNode * b);
+static DFibHeapNode *dfhe_remove(DFibHeapNode * a);
+
+/*
+ * global heap operations
+ */
+struct dfibheap {
+	RecycleBin *nodeMemory;
+	DFibHeapNode **dfh_cons;
+	DFibHeapNode *dfh_min;
+	DFibHeapNode *dfh_root;
+	IDnum dfh_n;
+	IDnum dfh_Dl;
+}  ATTRIBUTE_PACKED;
+
+static void dfh_insertrootlist(DFibHeap *, DFibHeapNode *);
+static void dfh_removerootlist(DFibHeap *, DFibHeapNode *);
+static void dfh_consolidate(DFibHeap *);
+static void dfh_heaplink(DFibHeap * h, DFibHeapNode * y, DFibHeapNode * x);
+static void dfh_cut(DFibHeap *, DFibHeapNode *, DFibHeapNode *);
+static void dfh_cascading_cut(DFibHeap *, DFibHeapNode *);
+static DFibHeapNode *dfh_extractminel(DFibHeap *);
+static void dfh_checkcons(DFibHeap * h);
+static int dfh_compare(DFibHeap * h, DFibHeapNode * a, DFibHeapNode * b);
+static int dfh_comparedata(DFibHeap * h, Time key,
+			   void *data, DFibHeapNode * b);
+static void dfh_insertel(DFibHeap * h, DFibHeapNode * x);
+
+
+/*
+ * general functions
+ */
+static inline IDnum ceillog2(IDnum a);
+
+#endif				/* _FIBPRIV_H_ */

data/ext/src/src/fib.c

@@ -0,0 +1,628 @@
+/*
+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: fib.c,v 1.10 2007/10/19 13:09:26 zerbino Exp $
+ *
+ */
+#include <limits.h>
+#include <stdlib.h>
+
+#include "fib.h"
+#include "recycleBin.h"
+
+#include "fibpriv.h"
+
+#define BLOCKSIZE 10000
+
+static FibHeapNode *allocateFibHeapEl(FibHeap * heap)
+{
+	return allocatePointer(heap->nodeMemory);
+}
+
+static void deallocateFibHeapEl(FibHeapNode * a, FibHeap * heap)
+{
+	deallocatePointer(heap->nodeMemory, a);
+}
+
+#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;
+}
+
+/*
+ * Private Heap Functions
+ */
+static void fh_initheap(FibHeap * new)
+{
+	new->fh_cmp_fnct = NULL;
+	new->nodeMemory = newRecycleBin(sizeof(FibHeapNode), BLOCKSIZE);
+	new->fh_neginf = NULL;
+	new->fh_n = 0;
+	new->fh_Dl = -1;
+	new->fh_cons = NULL;
+	new->fh_min = NULL;
+	new->fh_root = NULL;
+	new->fh_keys = 0;
+}
+
+static void fh_destroyheap(FibHeap * h)
+{
+	h->fh_cmp_fnct = NULL;
+	h->fh_neginf = NULL;
+	if (h->fh_cons != NULL)
+		free(h->fh_cons);
+	h->fh_cons = NULL;
+	free(h);
+}
+
+/*
+ * Public Heap Functions
+ */
+FibHeap *fh_makekeyheap()
+{
+	FibHeap *n;
+
+	if ((n = malloc(sizeof *n)) == NULL)
+		return NULL;
+
+	fh_initheap(n);
+	n->fh_keys = 1;
+
+	return n;
+}
+
+FibHeap *fh_makeheap()
+{
+	FibHeap *n;
+
+	if ((n = malloc(sizeof *n)) == NULL)
+		return NULL;
+
+	fh_initheap(n);
+
+	return n;
+}
+
+voidcmp fh_setcmp(FibHeap * h, voidcmp fnct)
+{
+	voidcmp oldfnct;
+
+	oldfnct = h->fh_cmp_fnct;
+	h->fh_cmp_fnct = fnct;
+
+	return oldfnct;
+}
+
+void *fh_setneginf(FibHeap * h, void *data)
+{
+	void *old;
+
+	old = h->fh_neginf;
+	h->fh_neginf = data;
+
+	return old;
+}
+
+FibHeap *fh_union(FibHeap * ha, FibHeap * hb)
+{
+	FibHeapNode *x;
+
+	if (ha->fh_root == NULL || hb->fh_root == NULL) {
+		/* either one or both are empty */
+		if (ha->fh_root == NULL) {
+			fh_destroyheap(ha);
+			return hb;
+		} else {
+			fh_destroyheap(hb);
+			return ha;
+		}
+	}
+	ha->fh_root->fhe_left->fhe_right = hb->fh_root;
+	hb->fh_root->fhe_left->fhe_right = ha->fh_root;
+	x = ha->fh_root->fhe_left;
+	ha->fh_root->fhe_left = hb->fh_root->fhe_left;
+	hb->fh_root->fhe_left = x;
+	ha->fh_n += hb->fh_n;
+	/*
+	 * we probably should also keep stats on number of unions
+	 */
+
+	/* set fh_min if necessary */
+	if (fh_compare(ha, hb->fh_min, ha->fh_min) < 0)
+		ha->fh_min = hb->fh_min;
+
+	fh_destroyheap(hb);
+	return ha;
+}
+
+void fh_deleteheap(FibHeap * h)
+{
+	destroyRecycleBin(h->nodeMemory);
+	fh_destroyheap(h);
+}
+
+/*
+ * Public Key Heap Functions
+ */
+FibHeapNode *fh_insertkey(FibHeap * h, Coordinate key, void *data)
+{
+	FibHeapNode *x;
+
+	if ((x = fhe_newelem(h)) == NULL)
+		return NULL;
+
+	/* just insert on root list, and make sure it's not the new min */
+	x->fhe_data = data;
+	x->fhe_key = key;
+
+	fh_insertel(h, x);
+
+	return x;
+}
+
+Coordinate fh_minkey(FibHeap * h)
+{
+	if (h->fh_min == NULL)
+		return (Coordinate) INT_MIN;
+	return h->fh_min->fhe_key;
+}
+
+Coordinate fh_replacekey(FibHeap * h, FibHeapNode * x, Coordinate key)
+{
+	Coordinate ret;
+
+	ret = x->fhe_key;
+	(void) fh_replacekeydata(h, x, key, x->fhe_data);
+
+	return ret;
+}
+
+void *fh_replacekeydata(FibHeap * h, FibHeapNode * x,
+			Coordinate key, void *data)
+{
+	void *odata;
+	Coordinate okey;
+	FibHeapNode *y;
+	int r;
+
+	odata = x->fhe_data;
+	okey = x->fhe_key;
+
+	/*
+	 * we can increase a key by deleting and reinserting, that
+	 * requires O(lgn) time.
+	 */
+	if ((r = fh_comparedata(h, key, data, x)) > 0) {
+		/* XXX - bad code! */
+		abort();
+	}
+
+	x->fhe_data = data;
+	x->fhe_key = key;
+
+	/* because they are equal, we don't have to do anything */
+	if (r == 0)
+		return odata;
+
+	y = x->fhe_p;
+
+	if (h->fh_keys && okey == key)
+		return odata;
+
+	if (y != NULL && fh_compare(h, x, y) <= 0) {
+		fh_cut(h, x, y);
+		fh_cascading_cut(h, y);
+	}
+
+	/*
+	 * the = is so that the call from fh_delete will delete the proper
+	 * element.
+	 */
+	if (fh_compare(h, x, h->fh_min) <= 0)
+		h->fh_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
+ */
+FibHeapNode *fh_insert(FibHeap * h, void *data)
+{
+	FibHeapNode *x;
+
+	if ((x = fhe_newelem(h)) == NULL)
+		return NULL;
+
+	/* just insert on root list, and make sure it's not the new min */
+	x->fhe_data = data;
+
+	fh_insertel(h, x);
+
+	return x;
+}
+
+void *fh_min(FibHeap * h)
+{
+	if (h->fh_min == NULL)
+		return NULL;
+	return h->fh_min->fhe_data;
+}
+
+void *fh_extractmin(FibHeap * h)
+{
+	FibHeapNode *z;
+	void *ret;
+
+	ret = NULL;
+
+	if (h->fh_min != NULL) {
+		z = fh_extractminel(h);
+		ret = z->fhe_data;
+#ifndef NO_FREE
+		deallocateFibHeapEl(z, h);
+#endif
+
+	}
+
+	return ret;
+}
+
+void *fh_replacedata(FibHeapNode * x, void *data)
+{
+	void *odata = x->fhe_data;
+	x->fhe_data = data;
+	return odata;
+}
+
+void *fh_delete(FibHeap * h, FibHeapNode * x)
+{
+	void *k;
+
+	k = x->fhe_data;
+	if (!h->fh_keys)
+		fh_replacedata(x, h->fh_neginf);
+	else
+		fh_replacekey(h, x, (Coordinate) INT_MIN);
+	fh_extractmin(h);
+
+	return k;
+}
+
+/*
+ * begin of private element fuctions
+ */
+static FibHeapNode *fh_extractminel(FibHeap * h)
+{
+	FibHeapNode *ret;
+	FibHeapNode *x, *y, *orig;
+
+	ret = h->fh_min;
+
+	orig = NULL;
+	/* put all the children on the root list */
+	/* for true consistancy, we should use fhe_remove */
+	for (x = ret->fhe_child; x != orig && x != NULL;) {
+		if (orig == NULL)
+			orig = x;
+		y = x->fhe_right;
+		x->fhe_p = NULL;
+		fh_insertrootlist(h, x);
+		x = y;
+	}
+	/* remove minimum from root list */
+	fh_removerootlist(h, ret);
+	h->fh_n--;
+
+	/* if we aren't empty, consolidate the heap */
+	if (h->fh_n == 0)
+		h->fh_min = NULL;
+	else {
+		h->fh_min = ret->fhe_right;
+		fh_consolidate(h);
+	}
+
+	return ret;
+}
+
+static void fh_insertrootlist(FibHeap * h, FibHeapNode * x)
+{
+	if (h->fh_root == NULL) {
+		h->fh_root = x;
+		x->fhe_left = x;
+		x->fhe_right = x;
+		return;
+	}
+
+	fhe_insertafter(h->fh_root, x);
+}
+
+static void fh_removerootlist(FibHeap * h, FibHeapNode * x)
+{
+	if (x->fhe_left == x)
+		h->fh_root = NULL;
+	else
+		h->fh_root = fhe_remove(x);
+}
+
+static void fh_consolidate(FibHeap * h)
+{
+	FibHeapNode **a;
+	FibHeapNode *w;
+	FibHeapNode *y;
+	FibHeapNode *x;
+	IDnum i;
+	IDnum d;
+	IDnum D;
+
+	fh_checkcons(h);
+
+	/* assign a the value of h->fh_cons so I don't have to rewrite code */
+	D = h->fh_Dl + 1;
+	a = h->fh_cons;
+
+	for (i = 0; i < D; i++)
+		a[i] = NULL;
+
+	while ((w = h->fh_root) != NULL) {
+		x = w;
+		fh_removerootlist(h, w);
+		d = x->fhe_degree;
+		/* XXX - assert that d < D */
+		while (a[d] != NULL) {
+			y = a[d];
+			if (fh_compare(h, x, y) > 0)
+				swap(FibHeapNode *, x, y);
+			fh_heaplink(h, y, x);
+			a[d] = NULL;
+			d++;
+		}
+		a[d] = x;
+	}
+	h->fh_min = NULL;
+	for (i = 0; i < D; i++)
+		if (a[i] != NULL) {
+			fh_insertrootlist(h, a[i]);
+			if (h->fh_min == NULL
+			    || fh_compare(h, a[i], h->fh_min) < 0)
+				h->fh_min = a[i];
+		}
+}
+
+static void fh_heaplink(FibHeap * h, FibHeapNode * y, FibHeapNode * x)
+{
+	/* make y a child of x */
+	if (x->fhe_child == NULL)
+		x->fhe_child = y;
+	else
+		fhe_insertbefore(x->fhe_child, y);
+	y->fhe_p = x;
+	x->fhe_degree++;
+	y->fhe_mark = 0;
+}
+
+static void fh_cut(FibHeap * h, FibHeapNode * x, FibHeapNode * y)
+{
+	fhe_remove(x);
+	y->fhe_degree--;
+	fh_insertrootlist(h, x);
+	x->fhe_p = NULL;
+	x->fhe_mark = 0;
+}
+
+static void fh_cascading_cut(FibHeap * h, FibHeapNode * y)
+{
+	FibHeapNode *z;
+
+	while ((z = y->fhe_p) != NULL) {
+		if (y->fhe_mark == 0) {
+			y->fhe_mark = 1;
+			return;
+		} else {
+			fh_cut(h, y, z);
+			y = z;
+		}
+	}
+}
+
+/*
+ * begining of handling elements of fibheap
+ */
+static FibHeapNode *fhe_newelem(FibHeap * h)
+{
+	FibHeapNode *e;
+
+	if ((e = allocateFibHeapEl(h)) == NULL)
+		return NULL;
+
+	fhe_initelem(e);
+
+	return e;
+}
+
+static void fhe_initelem(FibHeapNode * e)
+{
+	e->fhe_degree = 0;
+	e->fhe_mark = 0;
+	e->fhe_p = NULL;
+	e->fhe_child = NULL;
+	e->fhe_left = e;
+	e->fhe_right = e;
+	e->fhe_data = NULL;
+}
+
+static void fhe_insertafter(FibHeapNode * a, FibHeapNode * b)
+{
+	if (a == a->fhe_right) {
+		a->fhe_right = b;
+		a->fhe_left = b;
+		b->fhe_right = a;
+		b->fhe_left = a;
+	} else {
+		b->fhe_right = a->fhe_right;
+		a->fhe_right->fhe_left = b;
+		a->fhe_right = b;
+		b->fhe_left = a;
+	}
+}
+
+static inline void fhe_insertbefore(FibHeapNode * a, FibHeapNode * b)
+{
+	fhe_insertafter(a->fhe_left, b);
+}
+
+static FibHeapNode *fhe_remove(FibHeapNode * x)
+{
+	FibHeapNode *ret;
+
+	if (x == x->fhe_left)
+		ret = NULL;
+	else
+		ret = x->fhe_left;
+
+	/* fix the parent pointer */
+	if (x->fhe_p != NULL && x->fhe_p->fhe_child == x)
+		x->fhe_p->fhe_child = ret;
+
+	x->fhe_right->fhe_left = x->fhe_left;
+	x->fhe_left->fhe_right = x->fhe_right;
+
+	/* clear out hanging pointers */
+	x->fhe_p = NULL;
+	x->fhe_left = x;
+	x->fhe_right = x;
+
+	return ret;
+}
+
+static void fh_checkcons(FibHeap * h)
+{
+	IDnum oDl;
+
+	/* make sure we have enough memory allocated to "reorganize" */
+	if (h->fh_Dl == -1 || h->fh_n > (1 << h->fh_Dl)) {
+		oDl = h->fh_Dl;
+		if ((h->fh_Dl = ceillog2(h->fh_n) + 1) < 8)
+			h->fh_Dl = 8;
+		if (oDl != h->fh_Dl)
+			h->fh_cons =
+			    (FibHeapNode **) realloc(h->fh_cons,
+						     sizeof *h->
+						     fh_cons *
+						     (h->fh_Dl + 1));
+		if (h->fh_cons == NULL)
+			abort();
+	}
+}
+
+static int fh_compare(FibHeap * h, FibHeapNode * a, FibHeapNode * b)
+{
+	if (a->fhe_key < b->fhe_key)
+		return -1;
+	if (a->fhe_key == b->fhe_key)
+		return 0;
+	return 1;
+}
+
+static int
+fh_comparedata(FibHeap * h, Coordinate key, void *data, FibHeapNode * b)
+{
+	FibHeapNode a;
+
+	a.fhe_key = key;
+	a.fhe_data = data;
+
+	return fh_compare(h, &a, b);
+}
+
+static void fh_insertel(FibHeap * h, FibHeapNode * x)
+{
+	fh_insertrootlist(h, x);
+
+	if (h->fh_min == NULL
+	    || (h->fh_keys ? x->fhe_key <
+		h->fh_min->fhe_key : h->fh_cmp_fnct(x->fhe_data,
+						    h->fh_min->fhe_data) <
+		0))
+		h->fh_min = x;
+
+	h->fh_n++;
+}