str_addelementlen.c

fastDNAml is an attempt to solve the same problem as DNAML, but to do so faster and using less memo

#include  <stdlib.h>
#include  <stdio.h>
#include  <string.h>
#include  <math.h>
#include  "fastDNAml_types.h"
#include  "fastDNAml_funcs.h"

extern FILE *dbgfp;


boolean  str_addElementLen (char **treestrp, tree *tr, nodeptr p)
  { /* str_addElementLen */
    double   z, branch;
    nodeptr  q;
    int      n, ch;

    if ((ch = str_treeGetCh(treestrp)) == '(') { /*  A new internal node */
      n = (tr->nextnode)++;
      if (n > 2*(tr->mxtips) - 2) {
        if (tr->rooted || n > 2*(tr->mxtips) - 1) {
          printf("ERROR: too many internal nodes.  Is tree rooted?\n");
          printf("Deepest splitting should be a trifurcation.\n");
          return  FALSE;
        }
        else {
          tr->rooted = TRUE;
        }
      }
      q = tr->nodep[n];
      if (! str_addElementLen(treestrp, tr, q->next))          return FALSE;
      if (! str_treeNeedCh(treestrp, ',', "in"))               return FALSE;
      if (! str_addElementLen(treestrp, tr, q->next->next))    return FALSE;
      if (! str_treeNeedCh(treestrp, ')', "in"))               return FALSE;
    /*if (! str_treeFlushLabel(treestrp))                      return FALSE;*//*DKB-orig*/
    }

    else {                           /*  A new tip */
    /*n = str_treeFindTipName(treestrp, tr, ch);*/ /*DKB-orig*/
      if(ch=='\'') (*treestrp)--;                  /*DKB-change*/
      n = str_treeFindTipName(treestrp, tr);       /*DKB-change*/
      if (n <= 0) return FALSE;
      q = tr->nodep[n];
      if (tr->start->number > n)  tr->start = q;
      (tr->ntips)++;
    }

    /*  Master and Slave always use lengths */

    if (! str_treeNeedCh(treestrp, ':', "in"))                 return FALSE;
    if (! str_treeProcessLength(treestrp, &branch))            return FALSE;
    z = exp(-branch / tr->rdta->fracchange);
    if (z > zmax)  z = zmax;
    hookup(p, q, z);

    return  TRUE;
  } /* str_addElementLen */