/*
  
  \input cnoweb
  
  Program: weighbor                             \hfill\break
  File: build.c                                 \hfill\break
  Author: N. D. Socci                           \hfill\break
  Created: 6-Feb-97                             \hfill\break
  
  \title{build.c}
  \job{Weighbor}
  
  \synopsis{\|buildTree| will be a tree given a distance matrix
  \"D". It uses the weighted neighbor joining algorithm of W. Bruno
  (\'refs').}
  
  
*/

/*__*
 *__*
 *__* WEIGHBOR 1.2 [21-Jun-01]
 *__*
 *__* Copyright (c) 1997-2001 
 *__*    Los Alamos National Laboratories
 *__*    The Rockefeller University
 *__*
 *__* This file is part of the WEIGHBOR program that can be used free of
 *__* charge in academic research and teaching. Any commercial use of
 *__* this software requires prior permission and possibly a license. For
 *__* commercial use contact: W. Bruno at billb@t10.lanl.gov Los Alamos
 *__* National Laboratories makes no representations about the
 *__* suitability of this software for any purpose. It is provided 
 *__* "as is" without express or implied warranty
 *__*	
 *__* For those using this program for research please use the following 
 *__* citation for this program:
 *__*
 *__*    Bruno, W. J., Socci, N. D. and Halpern, A. L., ``Weighted 
 *__*        Neighbor Joining: A Fast Approximation to Maximum-Likelihood
 *__*        Phylogeny Reconstruction,'' Molecular Biology and Evolution, 
 *__*        17(1): 189-197, (2000).
 *__*
 *__* 
 *__*/


#include <math.h>
#include <stdlib.h>
#include <assert.h>
#include <float.h>

#include "tree.h"
#include "matrix.h"
#include "weighbor.h"
#include "io.h"

static char version[] __attribute__ ((unused)) = "$Id: build.c,v 1.7 2001/06/22 19:05:45 nds Exp $";

#define NDEBUG 1  /* turn off asserts */
#undef assert
#define assert(expr)           ((void) 0)


RootNodeT *
buildTree(int N, MatrixT Dorig, char **taxon)
{
  
  /* 
     \section{Initialize} 
     Initialize main variables 
  */
  
  int i;
  RootNodeT *root;
  int Nleft, Nnext; /* number of Nodes left to be joined 
		       and the next index to be used */
  
  
  MatrixT b=matrix(N);      /* the $b_{i;j}$ matrix (eq 0.7) */ 
  
  /* $q(i)$ array: value which minimizes $R(i,q(i),j)\,\forall j\ne i,q(i)$ */
  int *q;
  
  int *q2;                  /* Second best value */ 
  VectorT R=vector(N);      /* $R(i,q(i))$ (eq 0.10) */
  VectorT LLR=vector(N);    /* $R(i,q(i),q2(i))$ */
  VectorT Zscore=vector(N); /* $z(i,q(i))$ */
  
  /*
    
    This auxilary matrices are globally defined in \|weighbor.h| we do
    this to make it simplier so we do not always have to pass these
    around. Note that the need to be visible here as we will be
    calling \|calcR| later in this function and \|calcR| needs these
    values
    
  */
  
  s       = matrix(N);      /* $s_{ij}$ eq 0.9 */
  deltaB  = matrix(N);      /* $\Delta b_{ij}$ eq 0.8 */
  delta2B = matrix(N);      /* $\Delta^2 b_{ij}$ */
  if(recalcB)
    oldDeltaB = matrix(N);
  
  /* 
     
     This will hold this orignal $N$ distances plus any distances from
     the $N-3$ internal nodes. Note we do not care about the root node
     so $N-3$ and not $N-2$
     
  */
  
  mD=matrix(2*N-3); 
  
  /*
    
    This is the renormalization vector $c_i$ (eq 0.39) and matrix
    $c_{i;j}$ (eq 0.43 ver0.2.5); again it must
    be large enough to hold both the original and the new joined taxa
    
    N.B. \|vector| sets all elements to zero.
    
  */
  
  vC=vector(2*N-3);
  
  
  /*
    
    This matrices hold the previous iterations values of $s_{ij}$,
    $\Delta b_{ij}$, etc. They are used to speed up the next
    iterations calcultions of these quantities.
    
  */
  
  mS     = matrix(2*N-3);
  mDelB  = matrix(2*N-3);
  mDel2B = matrix(2*N-3);
  
  /*
    
    Init \|mS| to -1 to keep track of which entries have not yet been
    computed.  */
  
  for(i=0;i<2*N-3;++i) {
    int j;
    for(j=0;j<2*N-3;++j)
      mS[i][j] = -1.0;
  }
  
  /*
    
    Make a copy of the original distance matrix; embed it in the
    larger matrix which will hold the new distance from the added
    internal nodes of the tree.
    
  */
  
  setMM(N, Dorig, mD);
  
  /*
    
    Allocate and initialize the \|q|, \|q2| and \|nodes| array. $2N-3$
    nodes to hold both the original and the added nodes.
    
  */
  
  q = (int *)malloc(N*sizeof(int));
  if(!q) printError("build::buildTree:out of memory-q\n");
  q2 = (int *)malloc(N*sizeof(int));
  if(!q2) printError("build::buildTree:out of memory-q2\n");
  
  nodes = (NodeT **)malloc( (2*N-3)*sizeof(NodeT *));
  if(!nodes) printError("build::buildTree:out of memory-nodes");
  
  for(i=0;i<N;++i) {
    nodes[i] = createNode();
    nodes[i]->name = taxon[i];
    nodes[i]->ind  = i;
  }
  
  
  Nleft = N;
  Nnext = N;
  
  /*
    
    \section{Loop until 3 taxa left}
    
    While we have more than 3 nodes left do the neighbor joining algorithm. 
    Each pass of the algorithm will join 2 nodes replacing them with one.
    
  */
  
  while(Nleft>3) {
    
    int j, k, ip, ip2;
    double minR=0.0, min2R=0.0;
    NodeT *newNode, *tmpNode;
    double sigma_inf_i, sigma_inf_ip, sigma_inf_rat;
    double sig_r, sig_l;
    int jj, jjmin;
    double LLRp=0, tR, tmp;
    
    /* \subsection{Calculate Residual} */
    
    calc_q(Nleft, q, R, b, q2, LLR, Zscore);
    
    if(printLevel>2)
      for(k=0;k<Nleft;++k)
	fprintf(outfile, "q[%d]=%d R(%d,%d)=%g\n",
		k, q[k], k, q[k], R[k]); 
    
    /*
      
      Find $i$ than minimizes $R(i,q(i))$. With the constraint that
      $q(q(i))=i$ first if no pair found then find the best $i$
      without this constraint.
      
      Note: the \|checkQQI| flag determines if we will use the
      $q(q(i))=i$ constraint.
      
      Note: j will hold the next best pair
      
    */
    
    i = -1;
    j = -1;
    
    if(checkQQI) { 
      for(k=0;k<Nleft;++k)
	if(q[q[k]]==k) {
	  if(R[k]<minR || i==-1) {
	    if(printLevel>3)
	      fprintf(outfile, 
		      "ij=%d,%d k=%d q[k]=%d minR = %.16g R[k] = %.16g\n",
		      i,j,k, q[k], minR, R[k]);
	    j = i;
	    min2R = minR;
	    i = k;
	    minR = R[k];
	  }
	  else if(R[k]>minR && (R[k]<min2R || j==-1) ) {
	    j = k;
	    min2R = R[k];
	  }
	}
    }
    
    if(i==-1) { /* No pair had $q(q(i))=i$ */
      
      if(R[0]<R[1]) {
	i = 0;
	minR = R[0];
	j = 1;
	min2R = R[1];
      } else {
	i = 1;
	minR = R[1];
	j = 0;
	min2R = R[0];
      }	    
      for(k=1;k<Nleft;++k)
	if(R[k]<minR) {
	  j = i;
	  min2R = minR;
	  i = k;
	  minR = R[k];
	}
	else if(R[k] < min2R && R[k] > minR) {
	  j = k;
	  min2R = R[k];
	}
      
      if(checkQQI && printLevel>1)
	fprintf(outfile, "No pair with q[q[i]]==i ");
      else
	if(q[q[i]]!=i && printLevel>1)
	  fprintf(outfile, 
		  "The pair does not satisfy q[q[i]]==i (checking is off)"
		  );
    }
    
    ip = q[i];
    ip2 = j;
    
    /*
      
      If the extended tournament option is set (-e) then run two 
      more tournaments for (i,q[i]) to see who really wins. 
      
    */
    
    if(extendedTourn) {
      
      double minR1=0, minR2=0, tmpR, oldR=R[i];
      int jmin=-1, jpmin=-1;
      
      /* 
	 First fine the j the minimizes R(i,j)
      */
      
      for(j=0;j<Nleft;++j) 
	if(j!=i && j!=q[i]) {
	  if(j!=q2[i])
	    tmpR = calcR2(Nleft, i, j, q2[i], b);
	  else
	    tmpR = calcR2(Nleft, i, j, q[i], b);
	  
	  if(tmpR<minR1 || jmin==-1)
	    {
	      minR1=tmpR;
	      jmin = j;
	    }
	}
      
      /* 
	 and now the $j'$ that minimizes $R(j',q[i])$
      */
      
      for(j=0;j<Nleft;++j) 
	if(j!=i && j!=q[i]) {
	  if(j!=q2[i])
	    tmpR = calcR2(Nleft, j, q[i], q2[i], b);
	  else
	    tmpR = calcR2(Nleft, j, q[i], i, b);
	  
	  if(tmpR<minR2 || jpmin==-1) {
	    minR2=tmpR;
	    jpmin = j;
	  }
	}
      
      /*
	Now fnd which of the three is the smallest
      */
      
      if(minR1<minR2 && minR1<R[i]) {
	ip = jmin;
	if(printLevel>1)
	  fprintf(outfile, 
		  "Extended Tournament New Winner(A): (%d, %d) R=%g\n",
		  i, ip, minR1);
      }
      else if(minR2<minR1 && minR2<R[i]) {
	i = jpmin;
	if(printLevel>1)
	  fprintf(outfile, 
		  "Extended Tournament New Winner(B): (%d, %d) R=%g\n",
		  i, ip, minR2);
      }	    
      
      if(printLevel>3)
	fprintf(outfile, "R=%g, R1=%g, R2=%g\n", oldR, minR1, minR2);
      
    }
    
    /*
      
      Find the $jj$ that minimizes $R(q(i),i,jj)$ and then print out 
      the LLR and LLR' values.
      
    */
    
    jjmin=-1;
    
    for(jj=0;jj<Nleft;++jj)
      if(jj!=i && jj!=ip 
	 && (((tR=calcR(Nleft, ip, jj, i))<LLRp) || jjmin==-1)) {
	jjmin = jj;
	LLRp = tR;
      }
    
    LLRp *= 0.5;
    
    if( (LLR[i]<1e-6) && (LLRp<1e-6) ) {
      if(!warnFlag) {
	fprintf(stderr, 
		"warning: tie scores encountered; topology may depend on sequence order!\n");
	warnFlag = True;
      }
      if(printLevel>1) {
	fprintf(outfile, 
		"warning: tie scores encountered; topology may depend on sequence order!\n");
	fprintf(outfile, "taxon %s and taxon %s\n\n",
		nodes[i]->name, nodes[ip]->name);
	
      }
    }
    
    if(printLevel>0) {
      fprintf(outfile, 
	      "\nJoin taxon %s to taxon %s (%s next best choice)\n",
	      nodes[i]->name, nodes[ip]->name, nodes[q2[i]]->name);
      
      
      fprintf(outfile, "     p-value = %g\n", 
	      DMAX(1.0/(exp(LLR[i])+1.0), 1.0/(exp(LLRp)+1.0)));
      
      if(printLevel>1) {
	fprintf(outfile,"\nJoin taxon %s to taxon %s; R=%g\n", 
		nodes[i]->name, nodes[ip]->name, minR);
	
	if(ip2!=-1 && ip2!=i && ip2!=ip)
	  fprintf(outfile, "Second best pair (%s, %s); R=%g\n",
		  nodes[ip2]->name, nodes[q[ip2]]->name, min2R);
	else
	  fprintf(outfile, "No second best pair\n");
      }
    }
    
    
    /* 
       
       Note due to the way we shuffle around nodes after joining:
       i->Nnext, New->i, ip<->Nleft-1, if ip is less than i and
       i=Nleft-1 then the new node will be in position ip not i!!
       But tc (the global that is suppose to point to the position
       of the new node for calcb) is set to i so this will screw us
       up. The simpliest solution is to make sure i<ip; swap if they
       are not.
       
    */
    
    
    if(ip<i) {
      int tt;
      tt=i;
      i=ip;
      ip=tt;
    }
    
    /*
      
      Need to calculate the new branch lengths $\bar b_{i;i'}$ and
      $\bar b_{i';i}$, eq. 0.19.
      
      Note if the z-score is negative then we calculate $\phi$ eq
      (0.26) and use it to renormalize $d_{i,i'}$ and recompute 
      $b_{i;i'}$ and $b_{i';i}$.
      
    */
    
    if(Zscore[i]<0.0) {
      
      double phi_iip, dBar_iip;
      
      phi_iip = calcPhi(Nleft, i, ip);
      if(printLevel>2)
	fprintf(outfile, "Renormalizing z[%d,%d] = %g\n", i, ip, Zscore[i]);
      if(phi_iip>0) {
	dBar_iip = D(i,ip)-phi_iip;
	if(printLevel>2)
	  fprintf(outfile, "phi=%g dBar_iip=%g\n", phi_iip, dBar_iip);
	
	/* renormalize the b's */
	
	if( dBar_iip >= fabs(deltaB[i][ip]) )
	  b[i][ip] = (deltaB[i][ip] + dBar_iip)/2.0;
	else if( dBar_iip < -deltaB[i][ip] )
	  b[i][ip] = 0.0;
	else
	  b[i][ip] = dBar_iip;
	
	
	if( dBar_iip >= fabs(deltaB[ip][i]) )
	  b[ip][i] = (deltaB[ip][i] + dBar_iip)/2.0;
	else if( dBar_iip < -deltaB[ip][i] )
	  b[ip][i] = 0.0;
	else
	  b[ip][i] = dBar_iip;
      }
    }
    
    nodes[i ]->rho = b[i][ip];
    nodes[ip]->rho = b[ip][i];
    
    if(nodes[i ]->rho < 0.0)  {
      if(printLevel>0)
	fprintf(outfile, 
		"WARNING: Negative branch length %g set to zero\n", 
		nodes[i ]->rho);
      nodes[i ]->rho = 0.0;
      nodes[ip]->rho = D(i,ip);
    }
    else if(nodes[ip]->rho < 0.0) {
      if(printLevel>0)
	fprintf(outfile, 
		"WARNING: Negative branch length %g set to zero\n", 
		nodes[ip]->rho);
      nodes[ip]->rho = 0.0;
      nodes[i ]->rho = D(i,ip);
    }
    
    if(printLevel>3) {
      fprintf(outfile, "\\bar b_[%d%d] = %g b_[%d%d]=%g\n",
	      i, ip, nodes[i]->rho, i, ip, b[i][ip]);
      fprintf(outfile, "\\bar b_[%d%d] = %g b_[%d%d]=%g\n\n",
	      ip, i, nodes[ip]->rho, ip, i, b[ip][i]);
    }
    
    newNode = createNode();
    
    newNode->ind = Nnext;
    newNode->child_r = nodes[i];
    newNode->child_l = nodes[ip];
    newNode->name = nodes[i]->name;
    nodes[Nnext] = newNode;
    
    /*
      
      Calculate $\sigma^2_\infty(i\bar\imath)$ (eq. 0.27) for each
      of the joined taxa.
      
    */
    
    sigma_inf_i  = 0.0;
    sigma_inf_ip = 0.0;
    
    for(j=0;j<Nleft;++j)  {
      if(j!=i && j!=ip) {
	sigma_inf_i  
	  += sigma_na(DMAX(b[i][ip],MINB)+C(i), 
		      DMAX(D(i,j)-b[i][ip],MINB)+C(j) );
	sigma_inf_ip 
	  += sigma_na(DMAX(b[ip][i],MINB)+C(ip), 
		      DMAX(D(ip,j)-b[ip][i],MINB)+C(j) );
      }
    }
    
    /*
      
      Add \|EPSILON| here to make the following formulae a bit simplier
      
    */
    
    sigma_inf_i  += EPSILON;
    sigma_inf_ip += EPSILON;
    
    
    /*
      
      Calculate the new distances from eq. 0.24
      $$
      d_{\bar\imath k} = {{(d_{ik}-b_{i;i'}+\phi_i)/\sigma^2_\infty(i\bar\imath)+
      (d_{i'j}-b_{i';i}+\phi_{i'})/\sigma^2_\infty(i'\bar\imath)}
      \over{
      {1\over\sigma^2_\infty(i'\bar\imath)} +
      {1\over\sigma^2_\infty(i'\bar\imath)}}}
      $$
      where\hfill\break
      $i=$ \|newNode->child_r->ind|,\hfill\break
      $i'=$ \|newNode->child_l->ind|,\hfill\break
      $b_{i;i'}=$ \|newNode->child_r->rho|,\hfill\break
      $b_{i';i}=$ \|newNode->child_l->rho|
      
      
      Also calcuate the renormalization terms $c_{i;j}$ (eq 0.43 ver0.2.5)
      and $c_i$
      
    */
    
    for(j=0;j<Nleft;++j)  {
      if(j!=i && j!=ip) {
	
	/* $1/\sigma^2_\infty(i\bar\imath)+1/\sigma^2_\infty(i'\bar\imath)$ */
	double norm = 
	  1.0/( 1.0/sigma_inf_i + 1.0/sigma_inf_ip);
	
	/*
	  First calcuate the new distances
	*/
	
	D(Nnext,j) = D(j,Nnext) = 
	  norm *
	  (
	   (D(i,j)-RHO(newNode->child_r))/(sigma_inf_i)
	   + 
	   (D(ip,j)-RHO(newNode->child_l))/(sigma_inf_ip)
	   );
	
	if(D(Nnext,j)<0.0)
	  D(Nnext,j) = D(j,Nnext) = 0.0;
	
      }
    }
    
    D(Nnext,Nnext) = 0.0;
    
    /*
      
      And now the new renormalization quantity $c_{\bar\imath}$
      
      N.B. eq 0.30 has been rewritten from
      $$
      {1\over{{1\over X}+{1\over Y}}}
      $$
      to
      $$
      {XY\over X+Y}
      $$
      which is better behaved numerically when $X$ or $Y$ is
      small (and cheeper since it only has one division).
      
    */
    
    sig_r = sigma2t(C(i)+DMAX(RHO(newNode->child_r), MINB));
    sig_l = sigma2t(C(ip)+DMAX(RHO(newNode->child_l), MINB));
    
    if(sigma_inf_i+sigma_inf_ip>0.0) {
      
      
      if(sigma_inf_i+sigma_inf_ip < .9*sqrt(DBL_MAX) && /* no overflow */
         sigma_inf_i+sigma_inf_ip > .9*sqrt(DBL_MIN))   /* no underflow */
	{
	  tmp=
	    (sig_r*SQR(sigma_inf_ip)+ sig_l*SQR(sigma_inf_i))
	    /
	    SQR(sigma_inf_i+sigma_inf_ip);
	}
      else if(sigma_inf_ip > sigma_inf_i)       /* to avoid over/underflow */
	{
	  sigma_inf_rat = sigma_inf_i / sigma_inf_ip;
	  tmp = 
	    sig_r*1.0+sig_l*SQR(sigma_inf_rat) 
	    /
	    SQR(1.0+sigma_inf_rat);
	}
      else
	{
	  sigma_inf_rat = sigma_inf_ip / sigma_inf_i;
	  tmp = 
	    sig_r*SQR(sigma_inf_rat)+sig_l*1.0 
	    /
	    SQR(1.0+sigma_inf_rat);
	}
      
      C(Nnext) = sigma2tinv( tmp  );
    }
    else
      C(Nnext) = sigma2tinv(0.0);
    
    /*      if(!
	    (C(Nnext)<=DMAX(DMAX(RHO(newNode->child_r),MINB)+C(i)+1e-14,
	    DMAX(RHO(newNode->child_l),MINB)+C(ip)+1e-14)))
	    {
	    printf("C(Nnext=%d)=%g\n"
	    "RHO_R=%g C(i=%d)=%g sig_r=%g\nRHO_L=%g C(ip=%d)=%g sig_l=%g -- %g\n",
	    Nnext, C(Nnext),
	    RHO(newNode->child_r), i, C(i), sig_r,
	    RHO(newNode->child_l), ip, C(ip), sig_l,
	    sig_r*sig_l/(sig_r+sig_l));
	    fflush(stdout);
	    } 
	    
	    assert((C(Nnext)<=DMAX(DMAX(RHO(newNode->child_r),MINB)+C(i)+1e-14,
	    DMAX(RHO(newNode->child_l),MINB)+C(ip)+1e-14)));
	    
    */
    
    /*
      Swap $i$ node to the empty node at the end of the list and
      place the new node in position $i$ */
    
    nodes[Nnext] = nodes[i];
    nodes[i] = newNode;
    
    /*
      Swap the $ip$ node and the last node on the list this moves
      $ip$ to the end. When we decrease \|Nleft| by one there will be
      on less node and the two joined nodes $i$ and $ip$ will now be
      after then end (\|Nleft|) of the list
    */
    
    tmpNode = nodes[ip];
    nodes[ip] = nodes[Nleft-1];
    nodes[Nleft-1] = tmpNode;
    
    /*
      In the new node set the child indecies to the
      new indexes of the the joined nodes. This info
      will be used by \|sigma2_3| in the renormalization
      step
    */
    
    newNode->cind_r=Nnext;
    newNode->cind_l=Nleft-1;
    
    /*
      Set up the \|ta|, \|tb| and \|tc| node array indices.  \|ta|
      and \|tb| point to the two taxa that where just joined, and
      \|tc| points to the newly created taxon.
      
      These globals will be used in the next call to \|calcb|.
    */
    
    ta = Nnext;
    tb = Nleft - 1;
    tc = i;
    
    --Nleft;
    ++Nnext;
    
    /* 
       Print out the values of the various variables
    */
    
    if(printLevel>2) {
      int a, b;
      fprintf(outfile, "\nReduced d_ij=\n");
      for(a=0;a<Nleft;++a)
	{
	  for(b=0;b<Nleft;++b)
	    fprintf(outfile,"%7.4g ", D(a,b));
	  fprintf(outfile,"\n");
	}
      fprintf(outfile,"\n");
    }
    
    
    if(printLevel>3) {
      int a, b;
      
      for(a=0;a<Nnext;++a) {
	for(b=0;b<Nnext;++b)
	  fprintf(outfile,"%7.4g ", mD[a][b]);
	fprintf(outfile,"\n");
      }
      fprintf(outfile,"\n");
      
      fprintf(outfile, "c_i = ");
      for(a=0;a<Nleft;++a) {
	fprintf(outfile,"%7.4g ", C(a));
      }
      fprintf(outfile,"\n");
      
      for(a=0;a<Nnext;++a) {
	fprintf(outfile,"%7.4g ", vC[a]);
      }
      fprintf(outfile,"\n");
      
      
      fprintf(outfile, "\n");
    }
  }	    
  
  /*
    
    \section{Final three taxa}
    
    Now there are just three taxa left. They will join to the root
    node of our tree. Find their branch lengths (which we can do
    exactly) and set up the root node to be passed back on return from
    this functin.
    
  */
  
  root = createRootNode();
  if(!root) printError("build::buildTree:out of memory-root");
  
  root->child_l = nodes[0];
  root->child_m = nodes[1];
  root->child_r = nodes[2];
  
  /*
    
    Now get the root branch lengths. We can solve this exactly since
    we have three equations and three unknows. The equations to solve
    are:
    $$
    \rho_0+\rho_1 = d_{01},
    \rho_0+\rho_2 = d_{02},
    \rho_1+\rho_2 = d_{12}
    $$
    And the solution is:
    $$
    \rho_0={1 \over 2}\left(d_{01}+d_{02}-d_{12}\right),
    \rho_1={1 \over 2}\left(d_{01}-d_{02}+d_{12}\right),
    \rho_2={1 \over 2}\left(-d_{01}+d_{02}+d_{12}\right)
    $$
    
  */
  
  root->child_l->rho = 0.5*( D(0,1)+D(0,2)-D(1,2));
  root->child_m->rho = 0.5*( D(0,1)-D(0,2)+D(1,2));
  root->child_r->rho = 0.5*(-D(0,1)+D(0,2)+D(1,2));
  
  /* check for negative lengths and set to zero if found and decrease
     the other each by half the the negative length (note + a neg
     number is a decrease) */
  
  if(root->child_l->rho < 0.0) {
    root->child_m->rho += 0.5*root->child_l->rho;
    root->child_r->rho += 0.5*root->child_l->rho;
    root->child_l->rho=0.0;
  }
  
  if(root->child_m->rho < 0.0) { 
    root->child_l->rho += 0.5*root->child_m->rho;
    root->child_r->rho += 0.5*root->child_m->rho;
    root->child_m->rho=0.0;
  }
  if(root->child_r->rho < 0.0) {
    root->child_l->rho += 0.5*root->child_r->rho;
    root->child_m->rho += 0.5*root->child_r->rho;
    root->child_r->rho=0.0;
  }
  
  /*
    Clean up
  */
  
  freeMatrix(mD);
  
  freeMatrix(b);
  freeMatrix(delta2B);
  freeMatrix(deltaB);
  if(recalcB)
    freeMatrix(oldDeltaB);
  freeMatrix(s);
  
  freeVector(R);
  freeVector(LLR);
  freeVector(Zscore);
  
  freeVector(vC);
  
  freeMatrix(mS);
  freeMatrix(mDelB);
  freeMatrix(mDel2B);
  
  free(nodes);
  free(q);
  free(q2);
  
  return(root);
  
}




/*
  
  \section{maxVector}
  
  Return the index of the maximum element of a \|VectorT|
  
*/

int
maxVector(int num, VectorT v)
{
  
  int i, maxind = 0;
  double max = v[maxind];
  
  for(i=1;i<num;++i)
    if(v[i]>max)
      {
	maxind = i;
	max = v[i];
      }
  
  return(maxind);
  
}


/* \endc */