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"



boolean  addElementLen (FILE *fp, tree *tr, nodeptr p)
  { /* addElementLen */
    double   z, branch;
    nodeptr  q;
    int      n, ch;

    if ((ch = treeGetCh(fp)) == '(') {     /*  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 (! addElementLen(fp, tr, q->next))        return FALSE;
      if (! treeNeedCh(fp, ',', "in"))             return FALSE;
      if (! addElementLen(fp, tr, q->next->next))  return FALSE;
      if (! treeNeedCh(fp, ')', "in"))             return FALSE;
      (void) treeFlushLabel(fp);
      }

    else {                               /*  A new tip */
      ungetc(ch, fp);
      if ((n = treeFindTipName(fp, tr)) <= 0)          return FALSE;
      q = tr->nodep[n];
      if (tr->start->number > n)  tr->start = q;
      (tr->ntips)++;
      }                                  /* End of tip processing */

    if (tr->userlen) {
      if (! treeNeedCh(fp, ':', "in"))             return FALSE;
      if (! treeProcessLength(fp, & branch))       return FALSE;
      z = exp(-branch / tr->rdta->fracchange);
      if (z > zmax)  z = zmax;
      hookup(p, q, z);
      }
    else {
      if (! treeFlushLen(fp))                       return FALSE;
      hookup(p, q, defaultz);
      }

    return TRUE;
  } /* addElementLen */