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utilities.c
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utilities.c
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/*
PhyML: a program that computes maximum likelihood phylogenies from
DNA or AA homologous sequences.
Copyright (C) Stephane Guindon. Oct 2003 onward.
All parts of the source except where indicated are distributed under
the GNU public licence. See http://www.opensource.org for details.
*/
#include "spr.h"
#include "utilities.h"
#include "lk.h"
#include "optimiz.h"
#include "models.h"
#include "free.h"
#include "bionj.h"
#include "simu.h"
#include "eigen.h"
#include "pars.h"
#include "alrt.h"
#include "m4.h"
#include "mc.h"
#ifdef MG
#include "mg.h"
#endif
/*********************************************************/
double Uni()
{
double r;
r=rand();
r/=RAND_MAX;
return r;
}
/*********************************************************************/
/********************* random Gamma generator ************************
* Properties:
* (1) X = Gamma(alpha,lambda) = Gamma(alpha,1)/lambda
* (2) X1 = Gamma(alpha1,1), X2 = Gamma(alpha2,1) independent
* then X = X1+X2 = Gamma(alpha1+alpha2,1)
* (3) alpha = k = integer then
* X = Gamma(k,1) = Erlang(k,1) = -sum(log(Ui)) = -log(prod(Ui))
* where U1,...Uk iid uniform(0,1)
*
* Decompose alpha = k+delta with k = [alpha], and 0<delta<1
* Apply (3) for Gamma(k,1)
* Apply Ahrens-Dieter algorithm for Gamma(delta,1)
*/
double Ahrensdietergamma(double alpha)
{
double x = 0.;
if (alpha>0.)
{
double y = 0.;
double b = (alpha+exp(1.))/exp(1.);
double p = 1./alpha;
int go = 0;
while (go==0)
{
double u = Uni();
double w = Uni();
double v = b*u;
if (v<=1.)
{
x = pow(v,p);
y = exp(-x);
}
else
{
x = -log(p*(b-v));
y = pow(x,alpha-1.);
}
go = (w<y); // x is accepted when go=1
}
}
return x;
}
/*********************************************************/
double Rgamma(double shape, double scale)
{
int i;
double x1 = 0.;
double delta = shape;
if (shape>=1.)
{
int k = (int) floor(shape);
delta = shape - k;
double u = 1.;
for (i=0; i<k; i++)
u *= Uni();
x1 = -log(u);
}
double x2 = Ahrensdietergamma(delta);
return (x1 + x2)*scale;
}
double Rexp(double lambda)
{
return -log(Uni()+1.E-30)/lambda;
}
/*********************************************************/
/* NUMERICAL RECIPES ROUTINES FOR COMPUTING C(n,k) */
/*********************************************************/
phydbl bico(int n, int k)
{
return floor(0.5+exp(factln(n)-factln(k)-factln(n-k)));
}
phydbl factln(int n)
{
static phydbl a[101];
if (n < 0){ Warn_And_Exit("Err: negative factorial in routine FACTLN"); }
if (n <= 1) return 0.0;
if (n <= 100) return a[n] ? a[n] : (a[n]=gammln(n+1.0));
else return gammln(n+1.0);
}
/*********************************************************/
phydbl gammln(phydbl xx)
{
phydbl x,tmp,ser;
static phydbl cof[6]={76.18009173,-86.50532033,24.01409822,
-1.231739516,0.120858003e-2,-0.536382e-5};
int j;
x=xx-1.0;
tmp=x+5.5;
tmp -= (x+0.5)*(phydbl)log(tmp);
ser=1.0;
for (j=0;j<=5;j++)
{
x += 1.0;
ser += cof[j]/x;
}
return -tmp+(phydbl)log(2.50662827465*ser);
}
/*********************************************************/
/* END OF NUMERICAL RECIPES ROUTINES */
/*********************************************************/
phydbl Pbinom(int N, int ni, phydbl p)
{
return bico(N,ni)*pow(p,ni)*pow(1-p,N-ni);
}
/*********************************************************/
void Plim_Binom(phydbl pH0, int N, phydbl *pinf, phydbl *psup)
{
*pinf = pH0 - 1.64*sqrt(pH0*(1-pH0)/(phydbl)N);
if(*pinf < 0) *pinf = .0;
*psup = pH0 + 1.64*sqrt(pH0*(1-pH0)/(phydbl)N);
}
/*********************************************************/
/*wash. commented out following functions since they also exist in seq-gen gamma.c*/
/* phydbl LnGamma (phydbl alpha) */
/* { */
/* /\* returns ln(gamma(alpha)) for alpha>0, accurate to 10 decimal places. */
/* Stirling's formula is used for the central polynomial part of the procedure. */
/* Pike MC & Hill ID (1966) Algorithm 291: Logarithm of the gamma function. */
/* Communications of the Association for Computing Machinery, 9:684 */
/* *\/ */
/* phydbl x=alpha, f=0, z; */
/* if (x<7) { */
/* f=1; z=x-1; */
/* while (++z<7) f*=z; */
/* x=z; f=-(phydbl)log(f); */
/* } */
/* z = 1/(x*x); */
/* return f + (x-0.5)*(phydbl)log(x) - x + .918938533204673 */
/* + (((-.000595238095238*z+.000793650793651)*z-.002777777777778)*z */
/* +.083333333333333)/x; */
/* } */
/*********************************************************/
/* phydbl IncompleteGamma(phydbl x, phydbl alpha, phydbl ln_gamma_alpha) */
/* { */
/* /\* returns the incomplete gamma ratio I(x,alpha) where x is the upper */
/* limit of the integration and alpha is the shape parameter. */
/* returns (-1) if in error */
/* ln_gamma_alpha = ln(Gamma(alpha)), is almost redundant. */
/* (1) series expansion if (alpha>x || x<=1) */
/* (2) continued fraction otherwise */
/* RATNEST FORTRAN by */
/* Bhattacharjee GP (1970) The incomplete gamma integral. Applied Statistics, */
/* 19: 285-287 (AS32) */
/* *\/ */
/* int i; */
/* phydbl p=alpha, g=ln_gamma_alpha; */
/* phydbl accurate=1e-8, overflow=1e30; */
/* phydbl factor, gin=0, rn=0, a=0,b=0,an=0,dif=0, term=0, pn[6]; */
/* if (x==0) return (0); */
/* if (x<0 || p<=0) return (-1); */
/* factor=(phydbl)exp(p*(phydbl)log(x)-x-g); */
/* if (x>1 && x>=p) goto l30; */
/* /\* (1) series expansion *\/ */
/* gin=1; term=1; rn=p; */
/* l20: */
/* rn++; */
/* term*=x/rn; gin+=term; */
/* if (term > accurate) goto l20; */
/* gin*=factor/p; */
/* goto l50; */
/* l30: */
/* /\* (2) continued fraction *\/ */
/* a=1-p; b=a+x+1; term=0; */
/* pn[0]=1; pn[1]=x; pn[2]=x+1; pn[3]=x*b; */
/* gin=pn[2]/pn[3]; */
/* l32: */
/* a++; b+=2; term++; an=a*term; */
/* for (i=0; i<2; i++) pn[i+4]=b*pn[i+2]-an*pn[i]; */
/* if (pn[5] == 0) goto l35; */
/* rn=pn[4]/pn[5]; dif=fabs(gin-rn); */
/* if (dif>accurate) goto l34; */
/* if (dif<=accurate*rn) goto l42; */
/* l34: */
/* gin=rn; */
/* l35: */
/* for (i=0; i<4; i++) pn[i]=pn[i+2]; */
/* if (fabs(pn[4]) < overflow) goto l32; */
/* for (i=0; i<4; i++) pn[i]/=overflow; */
/* goto l32; */
/* l42: */
/* gin=1-factor*gin; */
/* l50: */
/* return (gin); */
/* } */
/*********************************************************/
/* phydbl PointChi2 (phydbl prob, phydbl v) */
/* { */
/* /\* returns z so that Prob{x<z}=prob where x is Chi2 distributed with df=v */
/* returns -1 if in error. 0.000002<prob<0.999998 */
/* RATNEST FORTRAN by */
/* Best DJ & Roberts DE (1975) The percentage points of the */
/* Chi2 distribution. Applied Statistics 24: 385-388. (AS91) */
/* Converted into C by Ziheng Yang, Oct. 1993. */
/* *\/ */
/* phydbl e=.5e-6, aa=.6931471805, p=prob, g; */
/* phydbl xx, c, ch, a=0,q=0,p1=0,p2=0,t=0,x=0,b=0,s1,s2,s3,s4,s5,s6; */
/* if (p<.000002 || p>.999998 || v<=0) return (-1); */
/* g = LnGamma (v/2); */
/* xx=v/2; c=xx-1; */
/* if (v >= -1.24*(phydbl)log(p)) goto l1; */
/* ch=pow((p*xx*(phydbl)exp(g+xx*aa)), 1/xx); */
/* if (ch-e<0) return (ch); */
/* goto l4; */
/* l1: */
/* if (v>.32) goto l3; */
/* ch=0.4; a=(phydbl)log(1-p); */
/* l2: */
/* q=ch; p1=1+ch*(4.67+ch); p2=ch*(6.73+ch*(6.66+ch)); */
/* t=-0.5+(4.67+2*ch)/p1 - (6.73+ch*(13.32+3*ch))/p2; */
/* ch-=(1-(phydbl)exp(a+g+.5*ch+c*aa)*p2/p1)/t; */
/* if (fabs(q/ch-1)-.01 <= 0) goto l4; */
/* else goto l2; */
/* l3: */
/* x=PointNormal (p); */
/* p1=0.222222/v; ch=v*pow((x*sqrt(p1)+1-p1), 3.0); */
/* if (ch>2.2*v+6) ch=-2*((phydbl)log(1-p)-c*(phydbl)log(.5*ch)+g); */
/* l4: */
/* q=ch; p1=.5*ch; */
/* if ((t=IncompleteGamma (p1, xx, g))<0) { */
/* printf ("\nerr IncompleteGamma"); */
/* return (-1); */
/* } */
/* p2=p-t; */
/* t=p2*(phydbl)exp(xx*aa+g+p1-c*(phydbl)log(ch)); */
/* b=t/ch; a=0.5*t-b*c; */
/* s1=(210+a*(140+a*(105+a*(84+a*(70+60*a))))) / 420; */
/* s2=(420+a*(735+a*(966+a*(1141+1278*a))))/2520; */
/* s3=(210+a*(462+a*(707+932*a)))/2520; */
/* s4=(252+a*(672+1182*a)+c*(294+a*(889+1740*a)))/5040; */
/* s5=(84+264*a+c*(175+606*a))/2520; */
/* s6=(120+c*(346+127*c))/5040; */
/* ch+=t*(1+0.5*t*s1-b*c*(s1-b*(s2-b*(s3-b*(s4-b*(s5-b*s6)))))); */
/* if (fabs(q/ch-1) > e) goto l4; */
/* return (ch); */
/* } */
/* /\*********************************************************\/ */
/* phydbl PointNormal (phydbl prob) */
/* { */
/* /\* returns z so that Prob{x<z}=prob where x ~ N(0,1) and (1e-12)<prob<1-(1e-12) */
/* returns (-9999) if in error */
/* Odeh RE & Evans JO (1974) The percentage points of the normal distribution. */
/* Applied Statistics 22: 96-97 (AS70) */
/* Newer methods: */
/* Wichura MJ (1988) Algorithm AS 241: the percentage points of the */
/* normal distribution. 37: 477-484. */
/* Beasley JD & Springer SG (1977). Algorithm AS 111: the percentage */
/* points of the normal distribution. 26: 118-121. */
/* *\/ */
/* phydbl a0=-.322232431088, a1=-1, a2=-.342242088547, a3=-.0204231210245; */
/* phydbl a4=-.453642210148e-4, b0=.0993484626060, b1=.588581570495; */
/* phydbl b2=.531103462366, b3=.103537752850, b4=.0038560700634; */
/* phydbl y, z=0, p=prob, p1; */
/* p1 = (p<0.5 ? p : 1-p); */
/* if (p1<1e-20) return (-9999); */
/* y = sqrt ((phydbl)log(1/(p1*p1))); */
/* z = y + ((((y*a4+a3)*y+a2)*y+a1)*y+a0) / ((((y*b4+b3)*y+b2)*y+b1)*y+b0); */
/* return (p<0.5 ? -z : z); */
/* } */
/* /\*********************************************************\/ */
/* int DiscreteGamma (phydbl freqK[], phydbl rK[], */
/* phydbl alfa, phydbl beta, int K, int median) */
/* { */
/* /\* discretization of gamma distribution with equal proportions in each */
/* category */
/* *\/ */
/* int i; */
/* phydbl gap05=1.0/(2.0*K), t, factor=alfa/beta*K, lnga1; */
/* if(K==1) */
/* { */
/* rK[0] = 1.0; */
/* return 0; */
/* } */
/* if (median) */
/* { */
/* for (i=0; i<K; i++) rK[i]=PointGamma((i*2.0+1)*gap05, alfa, beta); */
/* for (i=0,t=0; i<K; i++) t+=rK[i]; */
/* for (i=0; i<K; i++) rK[i]*=factor/t; */
/* } */
/* else { */
/* lnga1=LnGamma(alfa+1); */
/* for (i=0; i<K-1; i++) */
/* freqK[i]=PointGamma((i+1.0)/K, alfa, beta); */
/* for (i=0; i<K-1; i++) */
/* freqK[i]=IncompleteGamma(freqK[i]*beta, alfa+1, lnga1); */
/* rK[0] = freqK[0]*factor; */
/* rK[K-1] = (1-freqK[K-2])*factor; */
/* for (i=1; i<K-1; i++) rK[i] = (freqK[i]-freqK[i-1])*factor; */
/* } */
/* for (i=0; i<K; i++) freqK[i]=1.0/K; */
/* return (0); */
/* } */
/*********************************************************/
phydbl CDF_Normal(phydbl x, phydbl mean, phydbl var)
{
const double b1 = 0.319381530;
const double b2 = -0.356563782;
const double b3 = 1.781477937;
const double b4 = -1.821255978;
const double b5 = 1.330274429;
const double p = 0.2316419;
const double c = 0.39894228;
x = (x-mean)/var;
if(x >= 0.0)
{
double t = 1.0 / ( 1.0 + p * x );
return (1.0 - c * exp( -x * x / 2.0 ) * t *
( t *( t * ( t * ( t * b5 + b4 ) + b3 ) + b2 ) + b1 ));
}
else
{
double t = 1.0 / ( 1.0 - p * x );
return ( c * exp( -x * x / 2.0 ) * t *
( t *( t * ( t * ( t * b5 + b4 ) + b3 ) + b2 ) + b1 ));
}
}
/*********************************************************/
phydbl CDF_Gamma(phydbl x, phydbl mean, phydbl var)
{
phydbl scale,shape;
scale = var / mean;
shape = mean * mean / var;
/* scale = mean; */
/* shape = var; */
printf("\n. shape=%f, scale=%f",shape,scale);
return IncompleteGamma(x/scale,shape,LnGamma(shape));
}
/*********************************************************/
phydbl Rand_Normal_Deviate(phydbl mean, phydbl sd)
{
int i;
phydbl x=.0;
For(i,12) x += (phydbl)rand()/(RAND_MAX);
return sd * (x-6.0) + mean;
}
/*********************************************************/
arbre *Read_Tree(char *s_tree)
{
char **subs;
int i,n_ext,n_int,n_otu;
arbre *tree;
int degree;
n_otu=0;
For(i,(int)strlen(s_tree)) if(s_tree[i] == ',') n_otu++;
n_otu+=1;
tree = (arbre *)Make_Tree(n_otu);
Init_Tree(tree,tree->n_otu);
Make_All_Tree_Nodes(tree);
Make_All_Tree_Edges(tree);
Make_Tree_Path(tree);
Make_List_Of_Reachable_Tips(tree);
tree->noeud[n_otu]->num = n_otu;
tree->noeud[n_otu]->tax = 0;
subs = Sub_Trees(s_tree,°ree);
Clean_Multifurcation(subs,degree,3);
if(degree == 2) Unroot_Tree(subs);
degree = 3;
tree->has_branch_lengths = 0;
tree->num_curr_branch_available = 0;
n_int = n_ext = 0;
For(i,degree) R_rtree(s_tree,subs[i],tree->noeud[n_otu],tree,&n_int,&n_ext);
For(i,NODE_DEG_MAX) Free(subs[i]);
Free(subs);
return tree;
}
/*********************************************************/
/* void Make_All_Edges_Light(node *a, node *d, int *curr_num_edge) */
/* { */
/* int i; */
/* Make_Edge_Light(a,d,*curr_num_edge); */
/* (*curr_num_edge)++; */
/* if(d->tax) return; */
/* else */
/* { */
/* For(i,3) */
/* { */
/* if(d->v[i] != a) */
/* Make_All_Edges_Light(d,d->v[i],curr_num_edge); */
/* } */
/* } */
/* } */
/*********************************************************/
void Make_All_Edges_Lk(node *a, node *d, arbre *tree)
{
int i;
For(i,3) if((a->v[i]) && (a->v[i] == d)) Make_Edge_Lk(a->b[i],tree);
if(d->tax) return;
else
{
For(i,3)
{
if(d->v[i] != a)
Make_All_Edges_Lk(d,d->v[i],tree);
}
}
}
/*********************************************************/
/* 'a' in node a stands for ancestor. 'd' stands for descendant */
void R_rtree(char *s_tree_a, char *s_tree_d, node *a, arbre *tree, int *n_int, int *n_ext)
{
int i;
node *d;
int n_otu = tree->n_otu;
if(strstr(s_tree_a," ")) Warn_And_Exit("\n Err : tree must not contain a ' ' character\n");
if(s_tree_d[0] == '(')
{
char **subs;
int degree;
(*n_int)+=1;
d = tree->noeud[n_otu+*n_int];
d->num = n_otu+*n_int;
d->tax = 0;
Read_Branch_Label(s_tree_d,s_tree_a,tree->t_edges[tree->num_curr_branch_available]);
Read_Branch_Length(s_tree_d,s_tree_a,tree);
For(i,3)
{
if(!a->v[i])
{
a->v[i]=d;
d->l[0]=a->l[i]=tree->t_edges[tree->num_curr_branch_available]->l;
break;
}
}
d->v[0]=a;
Connect_One_Edge_To_Two_Nodes(a,d,tree->t_edges[tree->num_curr_branch_available],tree);
tree->num_curr_branch_available++;
subs=Sub_Trees(s_tree_d,°ree);
Clean_Multifurcation(subs,degree,2);
R_rtree(s_tree_d,subs[0],d,tree,n_int,n_ext);
R_rtree(s_tree_d,subs[1],d,tree,n_int,n_ext);
For(i,NODE_DEG_MAX) Free(subs[i]);
Free(subs);
}
else
{
int i;
d = tree->noeud[*n_ext];
d->tax = 1;
Read_Branch_Label(s_tree_d,s_tree_a,tree->t_edges[tree->num_curr_branch_available]);
Read_Branch_Length(s_tree_d,s_tree_a,tree);
Read_Node_Name(d,s_tree_d,tree);
For(i,3)
{
if(!a->v[i])
{
a->v[i]=d;
d->l[0]=a->l[i]=tree->t_edges[tree->num_curr_branch_available]->l;
break;
}
}
d->v[0]=a;
Connect_One_Edge_To_Two_Nodes(a,d,tree->t_edges[tree->num_curr_branch_available],tree);
tree->num_curr_branch_available++;
d->num=*n_ext;
(*n_ext)+=1;
}
}
/*********************************************************/
void Read_Branch_Label(char *s_d, char *s_a, edge *b)
{
char *sub_tp;
char *p;
int i,pos;
sub_tp = (char *)mCalloc(T_MAX_LINE,sizeof(char));
strcpy(sub_tp,s_d);
strcat(sub_tp,"#");
p = strstr(s_a,sub_tp);
i = 0;
b->n_labels = 0;
if(p)
{
if(!(b->n_labels%BLOCK_LABELS)) Make_New_Edge_Label(b);
b->n_labels++;
pos = 0;
do
{
b->labels[b->n_labels-1][pos] = p[i+strlen(s_d)+1];
i++;
pos++;
if(p[i+strlen(s_d)+1] == '#')
{
b->labels[b->n_labels-1][pos] = '\0';
b->n_labels++;
if(!(b->n_labels%BLOCK_LABELS)) Make_New_Edge_Label(b);
i++;
pos=0;
}
}
while((p[i+strlen(s_d)+1] != ':') &&
(p[i+strlen(s_d)+1] != ',') &&
(p[i+strlen(s_d)+1] != '('));
b->labels[b->n_labels-1][pos] = '\0';
}
if(p)
{
if(b->n_labels == 1)
printf("\n. Found label '%s' on edge %3d.",b->labels[0],b->num);
else
{
printf("\n. Found labels ");
For(i,b->n_labels) printf("'%s' ",b->labels[i]);
printf("on edge %3d.",b->num);
}
}
Free(sub_tp);
}
/*********************************************************/
void Read_Branch_Length(char *s_d, char *s_a, arbre *tree)
{
char *sub_tp;
char *p;
edge *b;
int i;
b = tree->t_edges[tree->num_curr_branch_available];
sub_tp = (char *)mCalloc(T_MAX_LINE,sizeof(char));
For(i,b->n_labels)
{
strcat(s_d,"#");
strcat(s_d,b->labels[i]);
}
strcpy(sub_tp,s_d);
strcat(sub_tp,":");
p = strstr(s_a,sub_tp);
if(p)
{
b->l = atof((char *)p+(int)strlen(sub_tp)+1);
tree->has_branch_lengths = 1;
}
Free(sub_tp);
}
/*********************************************************/
void Read_Node_Name(node *d, char *s_tree_d, arbre *tree)
{
int i;
if(!tree->t_edges[tree->num_curr_branch_available]->n_labels)
{
strcpy(d->name,s_tree_d);
}
else
{
i = 0;
do
{
d->name[i] = s_tree_d[i];
i++;
}
while(s_tree_d[i] != '#');
d->name[i] = '\0';
}
}
/*********************************************************/
void Unroot_Tree(char **subtrees)
{
char **tmp_sub;
int degree,i,j;
printf("\n. Removing the root...\n");
tmp_sub = Sub_Trees(subtrees[0],°ree);
if(degree >= 2)
{
strcpy(subtrees[2],subtrees[1]);
Clean_Multifurcation(tmp_sub,degree,2);
For(j,2) strcpy(subtrees[j],tmp_sub[j]);
}
else
{
tmp_sub = Sub_Trees(subtrees[1],°ree);
strcpy(subtrees[2],subtrees[0]);
Clean_Multifurcation(tmp_sub,degree,2);
For(j,2) strcpy(subtrees[j],tmp_sub[j]);
}
For(i,degree) Free(tmp_sub[i]);
Free(tmp_sub);
}
/*********************************************************/
void Clean_Multifurcation(char **subtrees, int current_deg, int end_deg)
{
if(current_deg <= end_deg) return;
else
{
char *s_tmp;
int i;
s_tmp = (char *)mCalloc(T_MAX_LINE,sizeof(char));
strcat(s_tmp,"(\0");
strcat(s_tmp,subtrees[0]);
strcat(s_tmp,",\0");
strcat(s_tmp,subtrees[1]);
strcat(s_tmp,")\0");
Free(subtrees[0]);
subtrees[0] = s_tmp;
for(i=1;i<current_deg-1;i++) strcpy(subtrees[i],subtrees[i+1]);
Clean_Multifurcation(subtrees,current_deg-1,end_deg);
}
}
/*********************************************************/
char **Sub_Trees(char *tree, int *degree)
{
char **subs;
int posbeg,posend;
int i;
if(tree[0] != '(') {*degree = 1; return NULL;}
subs=(char **)mCalloc(NODE_DEG_MAX,sizeof(char *));
For(i,NODE_DEG_MAX) subs[i]=(char *)mCalloc(strlen(tree)+1,sizeof(char));
posbeg=posend=1;
(*degree)=0;
do
{
posbeg = posend;
if(tree[posend] != '(')
{
while((tree[posend] != ',' ) &&
(tree[posend] != ':' ) &&
(tree[posend] != '#' ) &&
(tree[posend] != ')' ))
{
posend++ ;
}
posend -= 1;
}
else posend=Next_Par(tree,posend);
while((tree[posend+1] != ',') &&
(tree[posend+1] != ':') &&
(tree[posend+1] != '#') &&
(tree[posend+1] != ')')) {posend++;}
strncpy(subs[(*degree)],tree+posbeg,posend-posbeg+1);
strcat(subs[(*degree)],"\0");
posend += 1;
while((tree[posend] != ',') &&
(tree[posend] != ')')) {posend++;}
posend+=1;
(*degree)++;
if((*degree) == NODE_DEG_MAX)
{
For(i,(*degree))
printf("\n. Subtree %d : %s\n",i+1,subs[i]);
printf("\n. The degree of a node cannot be greater than %d\n",NODE_DEG_MAX);
Warn_And_Exit("\n");
}
}
while(tree[posend-1] != ')');
return subs;
}
/*********************************************************/
int Next_Par(char *s, int pos)
{
int curr;
curr=pos+1;
while(*(s+curr) != ')')
{
if(*(s+curr) == '(') curr=Next_Par(s,curr);
curr++;
}
return curr;
}
/*********************************************************/
void Print_Tree(FILE *fp, arbre *tree)
{
char *s_tree;
int i;
s_tree = (char *)Write_Tree(tree);
if(OUTPUT_TREE_FORMAT == 0)
fprintf(fp,"%s\n",s_tree);
else if(OUTPUT_TREE_FORMAT == 1)
{
fprintf(fp,"#NEXUS\n");
fprintf(fp,"BEGIN TREES;\n");
fprintf(fp,"\tTRANSLATE\n");
For(i,tree->n_otu) fprintf(fp,"\t%3d\t%s,\n",i+1,tree->noeud[i]->name);
fprintf(fp,"\tUTREE PAUP_1=\n");
fprintf(fp,"%s\n",s_tree);
fprintf(fp,"ENDBLOCK;");
}
Free(s_tree);
}
/*********************************************************/
char *Write_Tree(arbre *tree)
{
char *s;
int i;
s=(char *)mCalloc(T_MAX_LINE,sizeof(char));
s[0]='(';
#ifdef PHYML
tree->n_root = NULL;
tree->e_root = NULL;
#endif
/* if(!tree->n_root) */
/* { */
i = 0;
while((!tree->noeud[tree->n_otu+i]->v[0]) ||
(!tree->noeud[tree->n_otu+i]->v[1]) ||
(!tree->noeud[tree->n_otu+i]->v[2])) i++;
R_wtree(tree->noeud[tree->n_otu+i],tree->noeud[tree->n_otu+i]->v[0],s,tree);
R_wtree(tree->noeud[tree->n_otu+i],tree->noeud[tree->n_otu+i]->v[1],s,tree);
R_wtree(tree->noeud[tree->n_otu+i],tree->noeud[tree->n_otu+i]->v[2],s,tree);
/* } */
/* else */
/* { */
/* R_wtree(tree->n_root,tree->n_root->v[0],s,tree); */
/* R_wtree(tree->n_root,tree->n_root->v[1],s,tree); */
/* } */
s[(int)strlen(s)-1]=')';
s[(int)strlen(s)]=';';
return s;
}
/*********************************************************/
void R_wtree(node *pere, node *fils, char *s_tree, arbre *tree)
{
int i,p;
p = -1;
if(fils->tax)
{
if(OUTPUT_TREE_FORMAT == 0)
strcat(s_tree,fils->name);
else
sprintf(s_tree+(int)strlen(s_tree),"%d",fils->num+1);
if((fils->b[0]) && (fils->b[0]->l != -1))
{
if(tree->print_labels)
{
if(fils->b[0]->n_labels < 10)
For(i,fils->b[0]->n_labels) sprintf(s_tree+(int)strlen(s_tree),"#%s",fils->b[0]->labels[i]);
else
sprintf(s_tree+(int)strlen(s_tree),"#%d_labels",fils->b[0]->n_labels);
}
strcat(s_tree,":");
/* sprintf(s_tree+(int)strlen(s_tree),"%.10f",fils->b[0]->l); */
sprintf(s_tree+(int)strlen(s_tree),"%f",fils->b[0]->l);
}
sprintf(s_tree+(int)strlen(s_tree),",");
}
else
{
s_tree[(int)strlen(s_tree)]='(';
For(i,3)
{
/* if((fils->v[i] != pere) && (fils->b[i] != tree->e_root)) */
if(fils->v[i] != pere)
R_wtree(fils,fils->v[i],s_tree,tree);
else p=i;
}
s_tree[(int)strlen(s_tree)-1]=')';
if(fils->b[0]->l != -1)
{
if(tree->print_boot_val)
sprintf(s_tree+(int)strlen(s_tree),"%d",fils->b[p]->bip_score);
else if(tree->print_alrt_val)
sprintf(s_tree+(int)strlen(s_tree),"%f",fils->b[p]->ratio_test);
if(tree->print_labels)
{
if(fils->b[p]->n_labels < 10)
For(i,fils->b[p]->n_labels) sprintf(s_tree+(int)strlen(s_tree),"#%s",fils->b[p]->labels[i]);
else
sprintf(s_tree+(int)strlen(s_tree),"#%d_labels",fils->b[p]->n_labels);
}
strcat(s_tree,":");
sprintf(s_tree+(int)strlen(s_tree),"%f",fils->b[p]->l);
strcat(s_tree,",");
}
}
}
/*********************************************************/
void Init_Tree(arbre *tree, int n_otu)
{
tree->n_otu = n_otu;
tree->best_tree = NULL;
tree->old_tree = NULL;
tree->mat = NULL;
tree->n_root = NULL;
tree->e_root = NULL;
tree->ps_tree = NULL;
tree->depth_curr_path = 0;
tree->has_bip = 0;
tree->n_moves = 0;
tree->n_improvements = 0;
tree->number_of_lk_calls = 0;
tree->number_of_branch_lk_calls = 0;
tree->bl_from_node_stamps = 0;
tree->lock_topo = 0;
tree->ps_page_number = 0;
tree->init_lnL = UNLIKELY;
tree->best_lnL = UNLIKELY;
tree->c_lnL = UNLIKELY;
tree->n_swap = 0;
tree->n_pattern = -1;
tree->prop_of_sites_to_consider = 1.;
tree->n_root_pos = -1.;
tree->print_labels = 1;
tree->print_boot_val = 0;
tree->print_alrt_val = 0;
tree->num_curr_branch_available = 0;
}
/*********************************************************/
void Make_New_Edge_Label(edge *b)
{
int i;