bio-velvet_underground 0.0.1

data/ext/src/src/correctedGraph.h

@@ -0,0 +1,32 @@
+/*
+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 _CORRECTEDGRAPH_H_
+#define _CORRECTEDGRAPH_H_
+
+void clipTipsHard(Graph * graph, boolean conserveLong);
+
+void correctGraph(Graph * graph, ShortLength *sequenceLengths, Category * sequenceCategories, boolean conserveLong);
+
+// Black arts:
+void setMaxReadLength(int value);
+void setMaxGaps(int value);
+void setMaxDivergence(double value);
+#endif

data/ext/src/src/dfib.c

@@ -0,0 +1,509 @@
+/*
+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;
+}