--- /dev/null
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include <stdarg.h>
+
+
+#include "io_lib_header.h"
+#include "util_lib_header.h"
+#include "define_header.h"
+
+HaschT * hcreate ( int n_elements,struct Hasch_data * declare_data(struct Hasch_entry *), struct Hasch_data *free_data(struct Hasch_data *) )
+ {
+ HaschT *T;
+ int a;
+
+ n_elements=n_elements*2+1;
+
+ T=vcalloc ( 1, sizeof (HaschT));
+ T->ne=n_elements;
+ T->p=vcalloc (n_elements,sizeof ( Hasch_entry*));
+ for ( a=0; a<n_elements; a++)
+ {
+ T->p[a]=allocate_hasch_entry(NULL,DECLARE,declare_data, free_data);
+ }
+ return T;
+ }
+HaschT *hdestroy (HaschT *T,struct Hasch_data * declare_data(struct Hasch_entry *), struct Hasch_data *free_data(struct Hasch_data *) )
+
+
+ {
+ int a;
+ Hasch_entry *p, *pp;
+
+ if ( T==NULL)return NULL;
+
+ for (a=0; a< T->ne; a++)
+ {
+ p=T->p[a];
+ while (p)
+ {
+ pp=p;
+ p=p->n;
+ allocate_hasch_entry(pp,FREE, declare_data, free_data);
+ }
+ }
+ vfree (T->p);
+ vfree ( T);
+ return NULL;
+ }
+
+
+Hasch_entry* hsearch (HaschT *T, int k, int action, struct Hasch_data * declare_data(struct Hasch_entry *), struct Hasch_data *free_data(struct Hasch_data *) )
+
+
+ {
+ /*action: FIND,ADD, REMOVE*/
+ Hasch_entry *p, *pi;
+ int h;
+
+
+
+ /* find the key: k->h*/
+
+ h=k%T->ne;
+
+
+ if ( action==ADD || action==FIND)
+ {
+ p=pi=T->p[h];
+ while (p && p->k!=k){p=p->n;}
+ if (action==ADD && !p)
+ {
+ p=insert_hasch_entry_in_list (pi, NULL, NULL, declare_data, free_data);
+ p->k=k;
+ }
+ else if (action==FIND && !p)p=NULL;
+ return p;
+ }
+ else if ( action==REMOVE)
+ {
+ allocate_hasch_entry(hsearch ( T, k, FIND, declare_data, free_data), FREE, declare_data, free_data);
+ return NULL;
+ }
+ return NULL;
+ }
+
+
+Hasch_entry * extract_hasch_entry_from_list (Hasch_entry *e, struct Hasch_data * declare_data(struct Hasch_entry *), struct Hasch_data *free_data(struct Hasch_data *) )
+
+
+ {
+ /*extracts entry e and returns p, or next if is NULL*/
+ Hasch_entry *p=NULL, *n=NULL;
+
+ if (!e);
+ else
+ {
+ p=e->p;
+ n=e->n;
+
+ if (p)p->n=n;
+ if (n)n->p=p;
+ e->p=e->n=NULL;
+ }
+ return e;
+ }
+
+Hasch_entry * insert_hasch_entry_in_list (Hasch_entry *p, Hasch_entry *e, Hasch_entry *n, struct Hasch_data * declare_data(struct Hasch_entry *), struct Hasch_data *free_data(struct Hasch_data *) )
+
+
+{
+ /*inserts entry e between entry p and entry n and returns e*/
+
+ if (!e)e=allocate_hasch_entry (NULL,DECLARE, declare_data, free_data);
+
+
+
+ if (!p && !n);
+ else if ( !p)p=n->p;
+ else if ( !n)n=p->n;
+
+ e->p=p;
+ if (p)p->n=e;
+
+ e->n=n;
+ if (n)n->p=e;
+
+ return e;
+ }
+
+Hasch_entry * allocate_hasch_entry (Hasch_entry *e, int action,struct Hasch_data * declare_data(struct Hasch_entry *), struct Hasch_data *free_data(struct Hasch_data *) )
+
+
+{
+ static Hasch_entry *s;
+ Hasch_entry *ns;
+
+ if ( !s)s=vcalloc ( 1, sizeof (Hasch_entry));
+
+ if ( action==DECLARE)
+ {
+ ns=s->p;
+ e=extract_hasch_entry_from_list (s, declare_data, free_data);
+ if ( e->free_data)(e->free_data)(e->data);
+ e->declare_data=declare_data;
+ e->free_data=free_data;
+ e->declare_data (e);
+ e->k=UNDEFINED;
+ s=ns;
+ }
+ else if ( action==FREE)
+ {
+ extract_hasch_entry_from_list (e,declare_data, free_data );
+ e->k=UNDEFINED;
+ if ( e->free_data)e->data=(e->free_data)(e->data);
+ e->free_data=NULL;
+ e->declare_data=NULL;
+ s=insert_hasch_entry_in_list (s, e, NULL, declare_data, free_data);
+
+ }
+ else if ( action==FREE_STACK)
+ {
+ while (s)
+ {
+ e=s->p;
+ allocate_hasch_entry (s, FREE, declare_data,free_data);
+ vfree (s);
+ s=e;
+ }
+ }
+ else crash ("Unknown MODE for allocate_hasch_entry\n");
+ return e;
+ }
+
+/*********************************************************************/
+/* */
+/* Get string key */
+/* */
+/* */
+/*********************************************************************/
+
+
+int string2key (char *s, Char_node *n)
+{
+ static Char_node *root;
+
+ if ( !root)root=declare_char_node (DECLARE);
+
+ if ( n==NULL && s==NULL)
+ {
+ declare_char_node (FREE_STACK);
+ }
+ else if (n==NULL)
+ {
+ return string2key(s, root);
+ }
+ else if ( s[0]=='\0')
+ {
+ return n->key;
+ }
+ else
+ {
+ return string2key(s+1, (n->c[(int)s[0]])?(n->c[(int)s[0]]):(n->c[(int)s[0]]=declare_char_node (DECLARE)));
+ }
+ return 0;
+}
+
+Char_node * declare_char_node (int action)
+{
+static struct Char_node **heap;
+static int heap_size, free_heap, a;
+static int key;
+ if ( action==DECLARE)
+ {
+ if ( free_heap==0)
+ {
+ free_heap=100;
+
+ heap=vrealloc (heap,(heap_size+free_heap)*sizeof (struct Char_node *));
+ for ( a=heap_size; a<heap_size+free_heap; a++)
+ {
+ (heap[a])=vcalloc ( 1, sizeof ( struct Char_node));
+ (heap[a])->c=vcalloc ( 256, sizeof (Char_node*));
+ (heap[a])->key=key++;
+ }
+ heap_size+=free_heap;
+ }
+ return heap[heap_size-(free_heap--)];
+ }
+ else if ( action==FREE_STACK)
+ {
+ for (a=0; a< heap_size; a++)
+ {
+ heap[a]->key=key++;
+ vfree ( heap[a]->c);
+ (heap[a])->c=vcalloc ( 256, sizeof (Char_node*));
+ }
+ free_heap=heap_size;
+ return NULL;
+ }
+ return NULL;
+}
+
+/* old declare_char_node (too hungry)
+Char_node * declare_char_node (int action)
+{
+ static int key;
+ Char_node *cn;
+ static Char_node *root;
+
+ if ( action==DECLARE)
+ {
+ cn=vcalloc (1, sizeof (Char_node));
+ cn->key=++key;
+ cn->c=vcalloc (256, sizeof (Char_node *));
+
+ }
+ return cn;
+}
+*/
+/******************************COPYRIGHT NOTICE*******************************/
+/*© Centro de Regulacio Genomica */
+/*and */
+/*Cedric Notredame */
+/*Fri Feb 18 08:27:45 CET 2011 - Revision 596. */
+/*All rights reserved.*/
+/*This file is part of T-COFFEE.*/
+/**/
+/* T-COFFEE 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.*/
+/**/
+/* T-COFFEE 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 Foobar; if not, write to the Free Software*/
+/* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA*/
+/*............................................... |*/
+/* If you need some more information*/
+/* cedric.notredame@europe.com*/
+/*............................................... |*/
+/**/
+/**/
+/* */
+/******************************COPYRIGHT NOTICE*******************************/
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