File: treesort.c

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/*
 * treesort.c
 *
 *
 * Part of TREE-PUZZLE 5.2 (July 2004)
 *
 * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler
 * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer,
 *                  M. Vingron, and Arndt von Haeseler
 * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler
 *
 * All parts of the source except where indicated are distributed under
 * the GNU public licence.  See http://www.opensource.org for details.
 *
 * ($Id$)
 *
 */


#define EXTERN extern
#include "treesort.h"

int YYY=0;
/* fprintf(stderr, "YYY: %d (%s:%d)\n", YYY++, __FILE__, __LINE__); */


/*******************************************/
/* tree sorting                            */
/*******************************************/

/* compute address of the 4 int (sort key) in the 4 int node */
int ct_sortkeyaddr(int addr)
{
  int a, res;
  a = addr % 4;
  res = addr - a + 3;
  return res;
} /* ct_sortkeyaddr */


/**********/

/* compute address of the next edge pointer in a 4 int node (0->1->2->0) */
int ct_nextedgeaddr(int addr)
{
  int a, res;
  a = addr % 4;
  if ( a == 2 ) { res = addr - 2; }
  else          { res = addr + 1; }
  return res;
} /* ct_nextedgeaddr */


/**********/

/* compute address of 1st edge of a 4 int node from node number */
int ct_1stedge(int node)
{
  int res;
  res = 4 * node;
  return res;
} /* ct_1stedge */


/**********/

/* compute address of 2nd edge of a 4 int node from node number */
int ct_2ndedge(int node)
{
  int res;
  res = 4 * node +1;
  return res;
} /* ct_2ndedge */


/**********/

/* compute address of 3rd edge of a 4 int node from node number */
int ct_3rdedge(int node)
{
  int res;
  res = 4 * node +2;
  return res;
} /* ct_3rdedge */


/**********/

/* check whether node 'node' is a leaf (2nd/3rd edge pointer = -1) */
int ct_isleaf(int node, int *ctree)
{
  return (ctree[ct_3rdedge(node)] < 0);
} /* ct_isleaf */


/**********/

/* compute node number of 4 int node from an edge addr. */
int ct_addr2node(int addr)
{
  int a, res;
  a = addr % 4;
  res = (int) ((addr - a) / 4);
  return res;
} /* ct_addr2node */


/**********/

/* print graph pointers for checking */
void printctree(int *ctree)
{
	int n;
	for (n=0; n < 2*Maxspc; n++) {
		printf("n[%3d] = (%3d.%2d, %3d.%2d, %3d.%2d | %3d)\n", n,
		(int) ctree[ct_1stedge(n)]/4,
		(int) ctree[ct_1stedge(n)]%4,
		(int) ctree[ct_2ndedge(n)]/4,
		(int) ctree[ct_2ndedge(n)]%4,
		(int) ctree[ct_3rdedge(n)]/4,
		(int) ctree[ct_3rdedge(n)]%4,
		ctree[ct_3rdedge(n)+1]);
	}
        printf("\n");
} /* printctree */


/**********/

/* allocate memory for ctree 3 ints pointer plus 1 check byte */
int *initctree(void)
{
  int *snodes;
  int n;

  snodes = (int *) calloc((size_t) (4 * 2 * Maxspc), sizeof(int));
  if (snodes == NULL) maerror("snodes in copytree");

  for (n=0; n<(4 * 2 * Maxspc); n++) {
      snodes[n]=-1;
  }
  return snodes;
} /* initctree */


/**********/

/* free memory of a tree for sorting */
void freectree(int **snodes)
{
	free(*snodes);
	*snodes = NULL;
} /* freectree */


#if 0
/**********/

/* trueID (HAS) */
/* copy subtree recursively */
void copyOTU_trueID(int   *ctree,      /* in/out: tree array struct         */
             int          *ct_nextnode,/* in/out: next free node            */
             int           ct_curredge,/* in: currend edge to add subtree   */
             int          *ct_nextleaf,/* in/out: next free leaf (0-maxspc) */
             int           ed,         /* in: current edge in puzzling tree */
             ONEEDGE      *edge,       /* in: tree topology                 */
             int          *edgeofleaf, /* in: external edge list            */
             int           numleaves,  /* in: number of leaves              */
             int          *trueID)     /* in: permutation vector            */
{
        int i, nextcurredge;

        /* test whether we are on a leaf */
        if (edge[ed].downright == NULL && edge[ed].downleft == NULL) {
                for (i = 1; i < numleaves; i++) {
                        if (edgeofleaf[i] == ed) { /* i is the leaf of ed */
				nextcurredge          = ct_1stedge(*ct_nextleaf);
				ctree[ct_curredge]    = nextcurredge;
				ctree[nextcurredge]   = ct_curredge;
				/* trueID (HAS) */
                                ctree[ct_sortkeyaddr(nextcurredge)] = trueID[i];
				(*ct_nextleaf)++;
                                return;
                        }
                }
        }

        /* we are NOT on a leaf */
	nextcurredge        = ct_1stedge(*ct_nextnode);
        ctree[ct_curredge]     = nextcurredge;
	ctree[nextcurredge] = ct_curredge;
        (*ct_nextnode)++;
	nextcurredge = ct_nextedgeaddr(nextcurredge);
        copyOTU_trueID(ctree, ct_nextnode, nextcurredge, 
                ct_nextleaf, edge[ed].downleft->numedge,
                edge, edgeofleaf, numleaves, trueID);

	nextcurredge = ct_nextedgeaddr(nextcurredge);
        copyOTU_trueID(ctree, ct_nextnode, nextcurredge, 
                ct_nextleaf, edge[ed].downright->numedge, 
                edge, edgeofleaf, numleaves, trueID);
} /* copyOTU_trueID */

/********/


/* trueID (HAS) */
/* copy treestructure to sorting structure */
void copytree_trueID(int   *ctree,      /* out: copy for effective sorting */
              int          *trueID,     /* in:  permutation vector         */
              ONEEDGE      *edgeset,    /* in: intermediate tree topology  */
              int          *edgeofleaf, /*     dito.                       */
              int           numleaves)  /* in: number of leaves            */
{
        int ct_curredge;
        int ct_nextleaf;
        int ct_nextnode;

        ct_nextnode = Maxspc;
        ct_curredge = ct_1stedge(ct_nextnode);
        ct_nextleaf = 1;

        ctree[ct_1stedge(0)] = ct_curredge;
        ctree[ct_curredge]   = ct_1stedge(0);
	/* trueID (HAS) */
        ctree[ct_sortkeyaddr(0)] = trueID[0];

        ct_nextnode++;
        
        ct_curredge = ct_nextedgeaddr(ct_curredge);

        copyOTU_trueID(ctree, &ct_nextnode, ct_curredge, 
                &ct_nextleaf, edgeset[edgeofleaf[0]].downleft->numedge,
                edgeset, edgeofleaf, numleaves, trueID);

        ct_curredge = ct_nextedgeaddr(ct_curredge);
        copyOTU_trueID(ctree, &ct_nextnode, ct_curredge, 
                &ct_nextleaf, edgeset[edgeofleaf[0]].downright->numedge,
                edgeset, edgeofleaf, numleaves, trueID);
} /* copytree_trueID */
#endif


/**********/

/* copy subtree recursively */
void copyOTU(int          *ctree,      /* in/out: tree array struct         */
             int          *ct_nextnode,/* in/out: next free node            */
             int           ct_curredge,/* in: currend edge to add subtree   */
             int          *ct_nextleaf,/* in/out: next free leaf (0-maxspc) */
             int           ed,         /* in: current edge in puzzling tree */
             ONEEDGE      *edge,       /* in: tree topology                 */
             int          *edgeofleaf, /* in: external edge list            */
             int           numleaves)  /* in: number of leaves              */
{
        int nextcurredge;

        /* test whether we are on a leaf */
        if (edge[ed].downright == NULL && edge[ed].downleft == NULL) {
		nextcurredge          = ct_1stedge(*ct_nextleaf);
		ctree[ct_curredge]    = nextcurredge;
		ctree[nextcurredge]   = ct_curredge;
		ctree[ct_sortkeyaddr(nextcurredge)] = edge[ed].taxon;
		(*ct_nextleaf)++;
		return;
        }

        /* we are NOT on a leaf */
	nextcurredge        = ct_1stedge(*ct_nextnode);
        ctree[ct_curredge]     = nextcurredge;
	ctree[nextcurredge] = ct_curredge;
        (*ct_nextnode)++;
	nextcurredge = ct_nextedgeaddr(nextcurredge);
        copyOTU(ctree, ct_nextnode, nextcurredge, 
                ct_nextleaf, edge[ed].downleft->numedge,
                edge, edgeofleaf, numleaves);

	nextcurredge = ct_nextedgeaddr(nextcurredge);
        copyOTU(ctree, ct_nextnode, nextcurredge, 
                ct_nextleaf, edge[ed].downright->numedge, 
                edge, edgeofleaf, numleaves);
} /* copyOTU */


/**********/

/* copy treestructure to sorting structure */
void copytree(int          *ctree,      /* out: copy for effective sorting */
              ONEEDGE      *edgeset,    /* in: intermediate tree topology  */
              int          *edgeofleaf, /*     dito.                       */
              int           rootleaf,
              int           numleaves)  /* in: number of leaves            */
{
        int ct_curredge;
        int ct_nextleaf;
        int ct_nextnode;

        ct_nextnode = Maxspc;
        ct_curredge = ct_1stedge(ct_nextnode);
        ct_nextleaf = 1;

        ctree[ct_1stedge(0)]     = ct_curredge;
        ctree[ct_curredge]       = ct_1stedge(0);
        ctree[ct_sortkeyaddr(0)] = rootleaf;

        ct_nextnode++;
        
        ct_curredge = ct_nextedgeaddr(ct_curredge);

        copyOTU(ctree, &ct_nextnode, ct_curredge, 
                &ct_nextleaf, edgeset[edgeofleaf[rootleaf]].downleft->numedge,
                edgeset, edgeofleaf, numleaves);

        ct_curredge = ct_nextedgeaddr(ct_curredge);
        copyOTU(ctree, &ct_nextnode, ct_curredge, 
                &ct_nextleaf, edgeset[edgeofleaf[rootleaf]].downright->numedge,
                edgeset, edgeofleaf, numleaves);
} /* copytree */


/**********/

/* sort subtree from edge recursively by indices */
int sortOTU(int edge, int *ctree)
{
	int key1, key2;
	int edge1, edge2;
	int tempedge;

	/* if leaf, return taxonID */
	if (ctree[ct_2ndedge((int) (edge / 4))] < 0)
		return ctree[ct_sortkeyaddr(edge)];

	edge1 = ctree[ct_nextedgeaddr(edge)];
	edge2 = ctree[ct_nextedgeaddr(ct_nextedgeaddr(edge))];

        /* printf ("visiting [%5d] -> [%5d], [%5d]\n", edge, edge1, edge2); */
        /* printf ("visiting [%2d.%2d] -> [%2d.%2d], [%2d.%2d]\n", 
           (int)(edge/4), edge%4, (int)(edge1/4), edge1%4, 
           (int)(edge2/4), edge2%4); */

	key1  = sortOTU(edge1, ctree); 
	key2  = sortOTU(edge2, ctree); 
	
	if (key2 < key1) {
		tempedge            = ctree[ctree[edge1]];
		ctree[ctree[edge1]] = ctree[ctree[edge2]];
		ctree[ctree[edge2]] = tempedge;
		tempedge            = ctree[edge1];
		ctree[edge1]        = ctree[edge2];
		ctree[edge2]        = tempedge;
	  	ctree[ct_sortkeyaddr(edge)] = key2;
		
	} else {
	  ctree[ct_sortkeyaddr(edge)] = key1;
	}
	return ctree[ct_sortkeyaddr(edge)];
} /* sortOTU */


/**********/

/* sort ctree recursively by indices */
int sortctree(int *ctree)
{
	int n, startnode=-1;

	/* find virtual root node (ID=0) */
	for(n=0; n<Maxspc; n++) {
		if (ctree[ct_sortkeyaddr(n*4)] == 0)
			startnode = n;
	}

	/* sort it starting at virtual root node */
	sortOTU(ctree[startnode * 4], ctree);
	return startnode;
} /* sortctree */


/**********/

/* print recursively subtree of edge of sorted tree ctree */
void fprintfsortOTU(FILE *ofp, int edge, int *ctree)
{
        int edge1, edge2;

        if (ctree[ct_2ndedge((int) (edge / 4))] < 0) {
                fprintf(ofp, "%d", ctree[ct_sortkeyaddr(edge)]);
                return;
        }

        edge1 = ctree[ct_nextedgeaddr(edge)];
        edge2 = ctree[ct_nextedgeaddr(ct_nextedgeaddr(edge))];

        fprintf(ofp, "(");
        fprintfsortOTU(ofp, edge1, ctree); 
        fprintf(ofp, ",");
        fprintfsortOTU(ofp, edge2, ctree); 
        fprintf(ofp, ")");

} /* fprintfsortOTU */


/**********/

/* print recursively sorted tree ctree */
int fprintfsortctree(FILE *ofp, int *ctree)
{
        int n, startnode=-1;
        for(n=0; n<Maxspc; n++) {
                if (ctree[ct_sortkeyaddr(n*4)] == 0)
                        startnode = n;
        }
        fprintf (ofp, "(%d,", ctree[ct_sortkeyaddr(startnode*4)]);
        fprintfsortOTU(ofp, ctree[startnode * 4], ctree);
        fprintf (ofp, ");\n");
        return startnode;
} /* fprintfsortctree */


/**********/

/* print recursively subtree of edge of sorted tree ctree to string */
void sprintfOTU(char *str, int *len, int edge, int *ctree)
{
        int edge1, edge2;

        if (ctree[ct_2ndedge((int) (edge / 4))] < 0) {
                *len+=sprintf(&(str[*len]), "%d", ctree[ct_sortkeyaddr(edge)]);
		return;
	}

        edge1 = ctree[ct_nextedgeaddr(edge)];
        edge2 = ctree[ct_nextedgeaddr(ct_nextedgeaddr(edge))];

	sprintf(&(str[*len]), "(");
	(*len)++;
        sprintfOTU(str, len, edge1, ctree); 
	sprintf(&(str[*len]), ",");
	(*len)++;
        sprintfOTU(str, len, edge2, ctree); 
	sprintf(&(str[*len]), ")");
	(*len)++;
} /* sprintfOTU */

/**********/


/* print recursively sorted tree ctree to string */
char *sprintfctree(int *ctree, int strglen)
{
	char *treestr,
	     *tmpptr;
        int n,
	    len=0,
	    startnode=-1;
	treestr = (char *) calloc((size_t) strglen, sizeof(char));
	tmpptr  = treestr;
        for(n=0; n<Maxspc; n++) {
                if (ctree[ct_sortkeyaddr(n*4)] == 0)
                        startnode = n;
        }
	len+=sprintf (&(tmpptr[len]), "(%d,", ctree[ct_sortkeyaddr(startnode*4)]);
        sprintfOTU(tmpptr, &len, ctree[startnode * 4], ctree);
	len+=sprintf (&(tmpptr[len]), ");");
        return treestr;
} /* sprintfctree */


/**********/


/***********************************************/
/* establish and handle a list of sorted trees */
/***********************************************/

int itemcount;

/* initialize structure */
treelistitemtype *inittreelist(int *treenum)
{
	*treenum = 0;
	return    NULL;
} /* itemcount */


/**********/

/* malloc new tree list item */
treelistitemtype *gettreelistitem()
{
	treelistitemtype *tmpptr;
	tmpptr = (treelistitemtype *)calloc((size_t) 1, sizeof(treelistitemtype));
	if (tmpptr == NULL) maerror("item of intermediate tree stuctures");
	(*tmpptr).pred = NULL;
	(*tmpptr).succ = NULL;
	(*tmpptr).tree = NULL;
	(*tmpptr).count = 0;
	(*tmpptr).idx = itemcount++;
	return tmpptr;
} /* gettreelistitem */

/**********/

/* free whole tree list */
void freetreelist(treelistitemtype **list,
                  int               *numitems,
                  int               *numsum)
{
	treelistitemtype *current; 
	treelistitemtype *next;
	current = *list;
	while (current != NULL) {
		next = (*current).succ;
		if ((*current).tree != NULL) {
			free ((*current).tree);
			(*current).tree = NULL;
		}
		free(current);
		current = next;
	}
	*list = NULL;
	*numitems = 0;
	*numsum = 0;
} /* freetreelist */


/**********/

/* add tree to the tree list */
treelistitemtype *addtree2list(char             **tree,         /* sorted tree string */
                               int                numtrees,     /* how many occurred, e.g. in parallel */
                               treelistitemtype **list,         /* addr. of tree list */
                               int               *numitems,     
                               int               *numsum)
{
	treelistitemtype *tmpptr = NULL;
	treelistitemtype *newptr = NULL;
	int               result;
	int               done = 0;

	if ((*list == NULL) || (numitems == 0)) {
		newptr = gettreelistitem();
		(*newptr).tree = *tree; 
		*tree = NULL;
		(*newptr).id    = *numitems;
		(*newptr).count = numtrees;
		*numitems = 1;
		*numsum   = numtrees;
		*list = newptr;
	} else {
		tmpptr = *list;
		while(done == 0) {
			result = strcmp( (*tmpptr).tree, *tree);
			if (result==0) {
				free(*tree); *tree = NULL;
				(*tmpptr).count += numtrees;
				*numsum += numtrees;
				done = 1;
				newptr = tmpptr;
			} else { if (result < 0) {
					if ((*tmpptr).succ != NULL)
						tmpptr = (*tmpptr).succ;
					else {
						newptr = gettreelistitem();
						(*newptr).tree = *tree; 
						*tree = NULL;
						(*newptr).id    = *numitems;
						(*newptr).count = numtrees;
						(*newptr).pred  = tmpptr;
						(*tmpptr).succ  = newptr;
						(*numitems)++;
						*numsum += numtrees;
						done = 1;
					}
			} else { /* result < 0 */
				newptr = gettreelistitem();
				(*newptr).tree = *tree; 
				*tree = NULL;
				(*newptr).id    = *numitems;
				(*newptr).count = numtrees;
				(*newptr).succ  = tmpptr;
				(*newptr).pred  = (*tmpptr).pred;
				(*tmpptr).pred  = newptr;
				*numsum += numtrees;

				if ((*newptr).pred != NULL) {
				   (*(*newptr).pred).succ = newptr;
				} else {
				   *list = newptr;
				}
				(*numitems)++;
				done = 1;
			} /* end if result < 0 */
			} /* end if result != 0 */
		} /* while  searching in list */
	} /* if list empty, else */
	return (newptr);
} /* addtree2list */


/**********/

/* resort list of trees by number of occurrences for output */
void sortbynum(treelistitemtype *list, treelistitemtype **sortlist)
{
	treelistitemtype *tmpptr = NULL;
	treelistitemtype *curr = NULL;
	treelistitemtype *next = NULL;
	int xchange = 1;

	if (list == NULL) fprintf(stderr, "Grrrrrrrrr>>>>\n");
	tmpptr = list;
	*sortlist = list;
	while (tmpptr != NULL) {
		(*tmpptr).sortnext = (*tmpptr).succ;
		(*tmpptr).sortlast = (*tmpptr).pred;
		tmpptr = (*tmpptr).succ;
	}

	while (xchange > 0) {
		curr = *sortlist;
		xchange = 0;
		if (curr == NULL) fprintf(stderr, "Grrrrrrrrr>>>>\n");
		while((*curr).sortnext != NULL) {
			next = (*curr).sortnext;
			if ((*curr).count >= (*next).count)
				curr = (*curr).sortnext;
			else {
				if ((*curr).sortlast != NULL)
					(*((*curr).sortlast)).sortnext = next;
				if (*sortlist == curr)
					*sortlist = next;
				(*next).sortlast = (*curr).sortlast;

				if ((*next).sortnext != NULL)
					(*((*next).sortnext)).sortlast = curr;
				(*curr).sortnext = (*next).sortnext;

				(*curr).sortlast = next;
				(*next).sortnext = curr;

				xchange++;
			}
		}
	}
}  /* sortbynum */


/**********/

/* print puzzling step tree stuctures for checking */
void printfpstrees(treelistitemtype *list)
{
	char ch;
	treelistitemtype *tmpptr = NULL;
	tmpptr = list;
        ch = '-';
	while (tmpptr != NULL) {
		printf ("%c[%2d]  %5d     %s\n", ch, (*tmpptr).idx, (*tmpptr).count, (*tmpptr).tree);
		tmpptr = (*tmpptr).succ;
		ch = ' ';
	}
} /* printfpstrees */

/**********/

/* print sorted puzzling step tree stucture with names */
void fprintffullpstree(FILE *outf, char *treestr)
{
	int count = 0;
	int idnum = 0;
	int n;
	for(n=0; treestr[n] != '\0'; n++){
		while(isdigit((int)treestr[n])){
			idnum = (10 * idnum) + ((int)treestr[n]-48);
			n++;
			count++;
		}
		if (count > 0){
#			ifdef USEQUOTES
				fprintf(outf, "'");
#			endif
			(void)fputid(outf, idnum);
#			ifdef USEQUOTES
				fprintf(outf, "'");
#			endif
			count = 0;
			idnum = 0;
		}
		fprintf(outf, "%c", treestr[n]);
	}
} /* fprintffullpstree */


/**********/

/* print sorted puzzling step tree stuctures with names */
void fprintfsortedpstrees(FILE *output, 
                          treelistitemtype *list,  /* tree list */
                          int itemnum,             /* order number */
                          int itemsum,             /* number of trees */
                          int comment,             /* with statistics, or puzzle report ? */
                          float cutoff)            /* cutoff percentage */
{
	treelistitemtype *tmpptr = NULL;
	treelistitemtype *slist = NULL;
	int num = 1;
        float percent;

	if (list == NULL) fprintf(stderr, "Grrrrrrrrr>>>>\n");
	sortbynum(list, &slist); 

	tmpptr = slist;
	while (tmpptr != NULL) {
		percent = (float)(100.0 * (*tmpptr).count / itemsum);
		if ((cutoff == 0.0) || (cutoff <= percent)) {
			if (comment)
				fprintf (output, "[ %d. %d %.2f %d %d %d ]", num++, (*tmpptr).count, percent, (*tmpptr).id, itemnum, itemsum);
			else {
				if (num == 1){
					fprintf (output, "\n");
					fprintf (output, "The following tree(s) occured in more than %.2f%% of the %d puzzling steps.\n", cutoff, itemsum);
					fprintf (output, "The trees are orderd descending by the number of occurrences.\n");
					fprintf (output, "\n");
					fprintf (output, "\n       occurrences    ID  Phylip tree\n");
				}
				fprintf (output, "%2d. %5d %6.2f%% %5d  ", num++, (*tmpptr).count, percent, (*tmpptr).id);
			}
			fprintffullpstree(output, (*tmpptr).tree);
			fprintf (output, "\n");
		}
		tmpptr = (*tmpptr).sortnext;
	}

	if (!comment) {
		fprintf (output, "\n");
		switch(num) {
			case 1: fprintf (output, "There were no tree topologies (out of %d) occuring with a percentage \n>= %.2f%% of the %d puzzling steps.\n", itemnum, cutoff, itemsum); break;
			case 2: fprintf (output, "There was one tree topology (out of %d) occuring with a percentage \n>= %.2f%%.\n", itemnum, cutoff); break;
			default: fprintf (output, "There were %d tree topologies (out of %d) occuring with a percentage \n>= %.2f%%.\n", num-1, itemnum, cutoff); break;
		}
		fprintf (output, "\n");
		fprintf (output, "\n");
	}
	
}  /* fprintfsortedpstrees */

/**********/


/* print sorted tree topologies for checking */
void printfsortedpstrees(treelistitemtype *list)
{
	treelistitemtype *tmpptr = NULL;
	treelistitemtype *slist = NULL;

	sortbynum(list, &slist); 

	tmpptr = slist;
	while (tmpptr != NULL) {
		printf ("[%2d]  %5d     %s\n", (*tmpptr).idx, (*tmpptr).count, (*tmpptr).tree);
		tmpptr = (*tmpptr).sortnext;
	}
}  /* printfsortedpstrees */


/*******************************************/
/* end of tree sorting                     */
/*******************************************/