void build(const char *_str) {
str = _str;
len=strlen(str);
For(i,len) sa[i]=i,rank[i]=str[i];
for(gap=1;;gap*=2) {
sort(sa, sa+len, cmp);
For(i, len-1) tmp[i+1]=tmp[i]+cmp(sa[i], sa[i+1]);
For(i, len) rank[sa[i]]=tmp[i];
if (tmp[len-1]==len-1) break;
}
}
void oet(Ptr<Int> p)
{
setReadStride(1);
setWriteStride(1);
Int evens = *p;
Int odds = *(p+1);
For (Int count = 0, count < 16, count++)
Int evens2 = min(evens, odds);
Int odds2 = max(evens, odds);
Int evens3 = rotate(evens2, 15);
Int odds3 = odds2;
Where (index() != 15)
odds2 = min(evens3, odds3);
End
Where (index() != 0)
evens2 = rotate(max(evens3, odds3), 1);
End
evens = evens2;
odds = odds2;
End
*p = evens;
*(p+1) = odds;
}
void MachineLinear::save() {
string strict = "";
if (strict_compare) strict = "-strict";
if (strict_compare==SPECIAL_TRAINING) strict = "-special";
ofstream file("regres/lr-train"+strict, fstream::out);
for(auto d : data)
For(i,SIZE(d)) file << d[i] << char((i+1==SIZE(d))?'\n':' ');
file.close();
}
void Make_Tree_4_Pars(arbre *tree, allseq *alldata, int n_site)
{
int i;
tree->site_pars = (int *)mCalloc(tree->n_pattern, sizeof(int));
tree->step_mat = (int *)mCalloc(tree->mod->ns * tree->mod->ns, sizeof(int));
For(i,2*tree->n_otu-3) Make_Edge_Pars(tree->t_edges[i],tree);
Init_Ui_Tips(tree);
Init_P_Pars_Tips(tree); /* Must be called after Init_Ui_Tips is called */
Get_Step_Mat(tree);
}
void PMat_Empirical(phydbl l, t_mod *mod, int pos, phydbl *Pij)
{
int n = mod->ns;
int i, j, k;
phydbl *U,*V,*R;
phydbl *expt;
phydbl *uexpt;
phydbl sum;
expt = mod->eigen->e_val_im;
uexpt = mod->eigen->r_e_vect_im;
U = mod->eigen->r_e_vect;
V = mod->eigen->l_e_vect;
R = mod->eigen->e_val; /* exponential of the eigen value matrix */
//Initialize a rate-specific N*N matrix
For(i,n) For(k,n) Pij[pos+mod->ns*i+k] = .0;
/* compute POW(EXP(D/mr),l) into mat_eDmrl */
For(k,n)
{
expt[k] = (phydbl)POW(R[k],l);
}
void PMat_K80(phydbl l, phydbl kappa, int pos, phydbl *Pij)
{
phydbl Ts,Tv,e1,e2,aux;
int i,j;
/*0 => A*/
/*1 => C*/
/*2 => G*/
/*3 => T*/
/* Ts -> transition*/
/* Tv -> transversion*/
aux = -2*l/(kappa+2);
e1 = (phydbl)EXP(aux *2);
e2 = (phydbl)EXP(aux *(kappa+1));
Tv = .25*(1-e1);
Ts = .25*(1+e1-2*e2);
Pij[pos+ 4*0+0] = Pij[pos+ 4*1+1] =
Pij[pos+ 4*2+2] = Pij[pos+ 4*3+3] = 1.-Ts-2.*Tv;
Pij[pos+ 4*0+1] = Pij[pos+ 4*1+0] = Tv;
Pij[pos+ 4*0+2] = Pij[pos+ 4*2+0] = Ts;
Pij[pos+ 4*0+3] = Pij[pos+ 4*3+0] = Tv;
Pij[pos+ 4*1+2] = Pij[pos+ 4*2+1] = Tv;
Pij[pos+ 4*1+3] = Pij[pos+ 4*3+1] = Ts;
Pij[pos+ 4*2+3] = Pij[pos+ 4*3+2] = Tv;
For(i,4) For(j,4)
if(Pij[pos + 4*i+j] < SMALL_PIJ) Pij[pos + 4*i+j] = SMALL_PIJ;
}
int Dinic()
{
bfs();
For(i,1,n) now[i]=head[i];
int res=0,top=0,u=st;
while (d[st]<n)
{
if (u==ed)
{
int tp=oo,inser=n;
for (int i=0;i!=top;i++)
if (tp>w[stk[i]])
{
tp=w[stk[i]]; inser=i;
}
for (int i=0;i!=top;i++)
{
w[stk[i]]-=tp; w[stk[i]^1]+=tp;
}
res+=tp; top=inser;
u=x[stk[top]];
}
if (u!=ed&&sd[d[u]-1]==0) break;
int go;
for (go=now[u];go;go=Next[go])
if (w[go]!=0&&d[u]==d[y[go]]+1) break;
if (go)
{
now[u]=go; stk[top++]=go; u=y[go];
} else
{
int mi=n;
for (go=head[u];go;go=Next[go])
{
if (w[go]==0) continue;
if (mi>d[y[go]])
{
mi=d[y[go]]; now[u]=go;
}
}
sd[d[u]]--;
sd[d[u]=mi+1]++;
if (u!=st) u=x[stk[--top]];
}
}
return res;
}
///[W, F, errors, times, iters] = NMFSparseKL(V, W0, F0, maxIter, tolerence)
void mexFunction(int nlhs, mxArray *outs[], int nrhs, const mxArray *inps[])
{
srand (9999);
int nz, m, n, k, d1, d2;
unsigned long *x, *ind;
double *values, **W, **F, **Wr, **Fr;
get(inps[0], nz, n, m, x, ind, values);
//mexPrintf(" m = %d, n = %d\n", m, n);
vector<map<int, double>> V, VT;
vector<vector<pair<int, double> > > VV, VVT;
convert(nz, m, n, x, ind, values, V);
transpose(nz, m, n, x, ind, values, VT);
map_vector(V, VV);
map_vector(VT, VVT);
getArray(inps[1], m, k, W);
getArray(inps[2], n, k, F);
int maxIter = (int) getDouble(inps[3]);
double tolerance = getDouble(inps[4]);
int maxThread = (int) getDouble(inps[5]);
double **params;
getArray(inps[6], d1, d2, params);
vector<double> errors, times, iters;
printfFnc(" m = %d, n = %d, k = %d\n", m, n, k);
printfFnc(" %f %f %f %f\n", (*params)[0], (*params)[1], (*params)[2], (*params)[3]);
/// Output arguments
outs[0] = mxCreateDoubleMatrix(m, k, mxREAL);
outs[1] = mxCreateDoubleMatrix(n, k, mxREAL);
outs[2] = mxCreateDoubleMatrix(1, maxIter, mxREAL);
double* derrors = mxGetPr(outs[2]);
outs[3] = mxCreateDoubleMatrix(1, maxIter, mxREAL);
double* dtimes = mxGetPr(outs[3]);
outs[4] = mxCreateDoubleMatrix(1, maxIter, mxREAL);
double* diters = mxGetPr(outs[4]);
getArray(outs[0], m, k, Wr);
getArray(outs[1], n, k, Fr);
MultipleIterativeAlgorithmPar(VV, VVT, W, F, Wr, Fr, m, n, k, maxIter,
tolerance, errors, times, iters, maxThread, *params);
For(i, maxIter)
derrors[i] = errors[i], dtimes[i] = times[i], diters[i] = iters[i];
}
/* Handle any number of states (>1) */
void PMat_JC69(phydbl l, int pos, phydbl *Pij, t_mod *mod)
{
int ns;
int i,j;
ns = mod->ns;
For(i,ns) Pij[pos+ ns*i+i] = 1. - ((ns - 1.)/ns)*(1. - EXP(-ns*l/(ns - 1.)));
For(i,ns-1)
for(j=i+1;j<ns;j++)
{
Pij[pos+ ns*i+j] = (1./ns)*(1. - EXP(-ns*l/(ns - 1.)));
if(Pij[pos+ns*i+j] < SMALL_PIJ) Pij[pos+ns*i+j] = SMALL_PIJ;
Pij[pos+ ns*j+i] = Pij[pos+ ns*i+j];
}
}
void read()
{
int i, j;
For(i, n)
scanf("%lf", &s[i]);
For(i, n)
For(j, n)
scanf("%lf", &P[i][j]);
For(i, n)
For(j, m)
scanf("%lf", &A[i][j]);
For(i, n)
{
s[i] /= 100;
For(j, n)
P[i][j] /= 100, A[i][j] /= 100;
}
// 函数块
void CodeGenerator::Block() {
while(!isNext("}")) {
CodeToken T = getToken();
string value = T.value;
if(value == "if") {
If();
} else if(value == "while") {
While();
} else if(value == "for") {
For();
} else if(value == "read") {
match("("); addQuad("read", getToken().value, "$", "$"); match(")"); match(";");
} else if(value == "write") {
match("("); addQuad("write", getToken().value, "$", "$"); match(")"); match(";");
} else if(value == "return") {
addQuad("return", itos(getToken().num), "$", "$"); match(";");
} else if(CodeToString(T) == "id") {
CurToken--;
Assign();
} else {
puts("函数块错误！！"); printf("in %d", CurLine()); exit(0);
}
}
}
//=========================================================
bool Parser::FreeStatement () {
PrintRule rule("FreeStatement");
return rule.Accept(If() || While() || For());
}
void PMat_TN93(phydbl l, t_mod *mod, int pos, phydbl *Pij)
{
int i,j;
phydbl e1,e2,e3;
phydbl a1t,a2t,bt;
phydbl A,C,G,T,R,Y;
phydbl kappa1,kappa2;
A = mod->e_frq->pi->v[0]; C = mod->e_frq->pi->v[1]; G = mod->e_frq->pi->v[2]; T = mod->e_frq->pi->v[3];
R = A+G; Y = T+C;
if(mod->kappa->v < .0) mod->kappa->v = 1.0e-5;
if((mod->whichmodel != F84) && (mod->whichmodel != TN93)) mod->lambda->v = 1.;
else if(mod->whichmodel == F84)
{
mod->lambda->v = Get_Lambda_F84(mod->e_frq->pi->v,&mod->kappa->v);
}
kappa2 = mod->kappa->v*2./(1.+mod->lambda->v);
kappa1 = kappa2 * mod->lambda->v;
bt = l/(2.*(A*G*kappa1+C*T*kappa2+R*Y));
a1t = kappa1;
a2t = kappa2;
a1t*=bt; a2t*=bt;
e1 = (phydbl)EXP(-a1t*R-bt*Y);
e2 = (phydbl)EXP(-a2t*Y-bt*R);
e3 = (phydbl)EXP(-bt);
/*A->A*/Pij[pos + 4*0+0] = A+Y*A/R*e3+G/R*e1;
/*A->C*/Pij[pos + 4*0+1] = C*(1-e3);
/*A->G*/Pij[pos + 4*0+2] = G+Y*G/R*e3-G/R*e1;
/*A->T*/Pij[pos + 4*0+3] = T*(1-e3);
/*C->A*/Pij[pos + 4*1+0] = A*(1-e3);
/*C->C*/Pij[pos + 4*1+1] = C+R*C/Y*e3+T/Y*e2;
/*C->G*/Pij[pos + 4*1+2] = G*(1-e3);
/*C->T*/Pij[pos + 4*1+3] = T+R*T/Y*e3-T/Y*e2;
/*G->A*/Pij[pos + 4*2+0] = A+Y*A/R*e3-A/R*e1;
/*G->C*/Pij[pos + 4*2+1] = C*(1-e3);
/*G->G*/Pij[pos + 4*2+2] = G+Y*G/R*e3+A/R*e1;
/*G->T*/Pij[pos + 4*2+3] = T*(1-e3);
/*T->A*/Pij[pos + 4*3+0] = A*(1-e3);
/*T->C*/Pij[pos + 4*3+1] = C+R*C/Y*e3-C/Y*e2;
/*T->G*/Pij[pos + 4*3+2] = G*(1-e3);
/*T->T*/Pij[pos + 4*3+3] = T+R*T/Y*e3+C/Y*e2;
For(i,4) For(j,4)
if(Pij[pos + 4*i+j] < SMALL_PIJ) Pij[pos + 4*i+j] = SMALL_PIJ;
/* /\*A->A*\/(*Pij)[0][0] = A+Y*A/R*e3+G/R*e1; */
/* /\*A->C*\/(*Pij)[0][1] = C*(1-e3); */
/* /\*A->G*\/(*Pij)[0][2] = G+Y*G/R*e3-G/R*e1; */
/* /\*A->T*\/(*Pij)[0][3] = T*(1-e3); */
/* /\*C->A*\/(*Pij)[1][0] = A*(1-e3); */
/* /\*C->C*\/(*Pij)[1][1] = C+R*C/Y*e3+T/Y*e2; */
/* /\*C->G*\/(*Pij)[1][2] = G*(1-e3); */
/* /\*C->T*\/(*Pij)[1][3] = T+R*T/Y*e3-T/Y*e2; */
/* /\*G->A*\/(*Pij)[2][0] = A+Y*A/R*e3-A/R*e1; */
/* /\*G->C*\/(*Pij)[2][1] = C*(1-e3); */
/* /\*G->G*\/(*Pij)[2][2] = G+Y*G/R*e3+A/R*e1; */
/* /\*G->T*\/(*Pij)[2][3] = T*(1-e3); */
/* /\*T->A*\/(*Pij)[3][0] = A*(1-e3); */
/* /\*T->C*\/(*Pij)[3][1] = C+R*C/Y*e3-C/Y*e2; */
/* /\*T->G*\/(*Pij)[3][2] = G*(1-e3); */
/* /\*T->T*\/(*Pij)[3][3] = T+R*T/Y*e3+C/Y*e2; */
/* For(i,4) For(j,4) */
/* if((*Pij)[i][j] < SMALL) (*Pij)[i][j] = SMALL; */
}
/**
* Fill the Option fields, with the argc array
*/
int Read_Command_Line(option *io, int argc, char **argv)
{
int c;
int idx;
int i;
int writemode;
PhyML_Printf("\n. command-line: ");
For(i,argc) PhyML_Printf("%s ",argv[i]);
if(argc == 1) Exit("\n. No argument was passed to the program. Please check the documentation. \n");
struct option longopts[] =
{
{"n_rgrft", required_argument,NULL,0},
{"n_globl", required_argument,NULL,1},
{"max_dist", required_argument,NULL,2},
{"n_optim", required_argument,NULL,3},
{"n_best", required_argument,NULL,4},
{"model", required_argument,NULL,5},
{"search", required_argument,NULL,6},
{"datatype", required_argument,NULL,7},
{"multiple", required_argument,NULL,8},
{"input", required_argument,NULL,9},
{"bootstrap", required_argument,NULL,10},
{"ts/tv", required_argument,NULL,11},
{"nclasses", required_argument,NULL,12},
{"pinv", required_argument,NULL,13},
{"alpha", required_argument,NULL,14},
{"inputtree", required_argument,NULL,15},
{"min_diff_lk_local", required_argument,NULL,16},
{"min_diff_lk_global",required_argument,NULL,17},
{"steph_spr", no_argument,NULL,18},
{"brent_it_max", required_argument,NULL,19},
{"rand_start", no_argument,NULL,20},
{"n_rand_starts", required_argument,NULL,21},
{"sequential", no_argument,NULL,22},
{"inside_opt", no_argument,NULL,23},
{"p_moves", required_argument,NULL,24},
{"fast_nni", no_argument,NULL,25},
{"g_pars", no_argument,NULL,26},
{"r_seed", required_argument,NULL,27},
{"collapse_boot", required_argument,NULL,28},
{"random_boot", required_argument,NULL,29},
{"print_trace", no_argument,NULL,30},
{"print_site_lnl", no_argument,NULL,31},
{"print_site_lk", no_argument,NULL,31},
{"cov", no_argument,NULL,32},
{"cov_delta", required_argument,NULL,33},
{"cov_alpha", required_argument,NULL,34},
{"cov_ncats", required_argument,NULL,35},
{"ps", no_argument,NULL,36},
{"cov_free", no_argument,NULL,37},
{"no_gap", no_argument,NULL,38},
{"n_rr_branch", required_argument,NULL,39},
{"append", no_argument,NULL,40},
{"no_five_branch", no_argument,NULL,41},
{"pars_thresh", required_argument,NULL,42},
{"min_diff_lk_move", required_argument,NULL,43},
{"hybrid", no_argument,NULL,44},
{"use_median", no_argument,NULL,45},
{"run_id", required_argument,NULL,46},
{"pars", no_argument,NULL,47},
{"quiet", no_argument,NULL,48},
{"version", no_argument,NULL,49},
{"calibration_file", required_argument,NULL,50},
{"calibration", required_argument,NULL,50},
{"clade_file", required_argument,NULL,50},
{"boot_progress_every", required_argument,NULL,51},
{"aa_rate_file", required_argument,NULL,52},
{"chain_len", required_argument,NULL,53},
{"sample_freq", required_argument,NULL,54},
{"burnin", required_argument,NULL,55},
{"no_memory_check", no_argument,NULL,56},
{"no_colalias", no_argument,NULL,57},
{"alias_subpatt", no_argument,NULL,58},
{"no_sequences", no_argument,NULL,59},
{"prior", no_argument,NULL,59},
{"fastlk", no_argument,NULL,60},
{"free_rates", no_argument,NULL,61},
{"freerates", no_argument,NULL,61},
{"freerate", no_argument,NULL,61},
{"free_rate", no_argument,NULL,61},
{"is", no_argument,NULL,62},
// no 63 since it corresponds to character '?'
{"rate_model", required_argument,NULL,64},
{"ratemodel", required_argument,NULL,64},
{"log_l", no_argument,NULL,65},
{"gamma_lens", no_argument,NULL,66},
{"il", no_argument,NULL,66},
{"codpos", required_argument,NULL,67},
{"constraint_file", required_argument,NULL,68},
{"constraint_tree", required_argument,NULL,68},
{"help", no_argument,NULL,69},
{"mutmap", no_argument,NULL,70},
{"parvals", required_argument,NULL,71},
{"constrained_lens", no_argument,NULL,72},
{"xml", required_argument,NULL,73},
{"l_var", required_argument,NULL,74},
#ifdef BEAGLE
{"beagle_resource", required_argument,NULL,75},
#endif
{"ancestral", no_argument,NULL,76},
{"anc", no_argument,NULL,76},
{"coord_file", required_argument,NULL,77},
{0,0,0,0}
};
io->datatype = UNDEFINED;
#ifndef PHYML
int open_ps_file = 0;
#endif
idx=-1;
do
{
c = getopt_long(argc,argv,"qi:d:m:b:n:t:f:zk:v:c:a:u:ho:s:x:g:l:ep",longopts,&idx);
switch(c)
{
case 77:
{
char *tmp;
tmp = (char *)mCalloc(T_MAX_FILE, sizeof(char));
if(strlen(optarg) > T_MAX_FILE -11)
{
char choix;
strcpy (tmp, "\n. The file name'");
strcat (tmp, optarg);
strcat (tmp, "' is too long.\n");
PhyML_Printf("%s",tmp);
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
else if (!Filexists (optarg))
{
char choix;
strcpy (tmp, "\n. The file '");
strcat (tmp, optarg);
strcat (tmp, "' doesn't exist.\n");
PhyML_Printf("%s",tmp);
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
else
{
strcpy(io->in_coord_file, optarg);
io->fp_in_coord = Openfile(io->in_coord_file,READ);
}
Free(tmp);
break;
}
case 76:
{
io->ancestral = YES;
break;
}
#ifdef BEAGLE
case 75:
{
io->beagle_resource = (int)atoi(optarg);
break;
}
#endif
case 74:
{
io->mod->l_var_sigma = String_To_Dbl(optarg);
break;
}
case 73:
{
#ifdef INVITEE
Free_Optimiz(io->mod->s_opt);
M4_Free_M4_Model(io->mod->m4mod);
Free_Model_Basic(io->mod);
Free_Input(io);
PhyTime_XML(optarg);
return 0;
#elif defined(PHYML)
Free_Optimiz(io->mod->s_opt);
M4_Free_M4_Model(io->mod->m4mod);
Free_Model_Basic(io->mod);
Free_Input(io);
PhyML_XML(optarg);
return 0;
#elif defined(DATE)
Free_Optimiz(io->mod->s_opt);
M4_Free_M4_Model(io->mod->m4mod);
Free_Model_Basic(io->mod);
Free_Input(io);
DATE_XML(optarg);
return 0;
#endif
break;
}
case 72:
{
io->mod->s_opt->constrained_br_len = YES;
break;
}
case 71:
{
io->mcmc->in_fp_par = fopen(optarg,"r");
io->mcmc->randomize = NO;
break;
}
case 70:
{
io->mutmap = YES;
break;
}
case 68:
{
char *tmp;
tmp = (char *)mCalloc(T_MAX_FILE, sizeof(char));
if(strlen(optarg) > T_MAX_FILE -11)
{
char choix;
strcpy (tmp, "\n. The file name'");
strcat (tmp, optarg);
strcat (tmp, "' is too long.\n");
PhyML_Printf("%s",tmp);
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
else if (!Filexists (optarg))
{
char choix;
strcpy (tmp, "\n. The file '");
strcat (tmp, optarg);
strcat (tmp, "' doesn't exist.\n");
PhyML_Printf("%s",tmp);
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
else
{
strcpy(io->in_constraint_tree_file, optarg);
io->fp_in_constraint_tree = Openfile(io->in_constraint_tree_file,0);
}
Free(tmp);
break;
}
case 67:
{
phydbl pos;
pos = atof(optarg);
io->codpos = (int)pos;
if(io->codpos < 1 || io->codpos > 3)
{
char choix;
PhyML_Printf("\n. Coding position must be set to 1, 2 or 3.\n");
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
break;
break;
}
case 66:
{
io->mod->gamma_mgf_bl = YES;
io->mod->s_opt->opt_gamma_br_len = YES;
break;
}
case 65:
{
io->mod->log_l = YES;
break;
}
case 64:
{
char *s;
int i;
s = (char *)mCalloc(T_MAX_NAME,sizeof(char));
i = 0;
while(optarg[i++]) s[i]=tolower(optarg[i]);
if(!strcmp(optarg,"gbd")) io->rates->model = THORNE;
else if(!strcmp(optarg,"gbs")) io->rates->model = GUINDON;
else if(!strcmp(optarg,"gamma")) io->rates->model = GAMMA;
else if(!strcmp(optarg,"clock")) io->rates->model = STRICTCLOCK;
else if(!strcmp(optarg,"strictclock")) io->rates->model = STRICTCLOCK;
else if(!strcmp(optarg,"strict_clock")) io->rates->model = STRICTCLOCK;
else
{
PhyML_Printf("\n. rate_model should be 'gbs', 'gbd', 'gamma' or 'clock'.");
Exit("\n");
}
Free(s);
break;
}
case 62:
{
io->mcmc->is = YES;
break;
}
case 61:
{
io->mod->ras->free_mixt_rates = YES;
io->mod->s_opt->opt_free_mixt_rates = YES;
break;
}
case 60:
{
io->lk_approx = NORMAL;
break;
}
case 59:
{
io->mcmc->use_data = NO;
break;
}
case 58:
{
io->do_alias_subpatt = YES;
break;
}
case 57:
{
io->colalias = NO;
break;
}
case 56:
{
io->mem_question = NO;
break;
}
case 55:
{
phydbl len;
len = atof(optarg);
io->mcmc->chain_len_burnin = (int)len;
if(io->mcmc->chain_len_burnin < 1)
{
char choix;
PhyML_Printf("\n. chain_len_burnin must be an integer greater than 0.\n");
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
break;
}
case 54:
{
phydbl len;
len = atof(optarg);
io->mcmc->sample_interval = (int)len;
if(io->mcmc->sample_interval < 1)
{
char choix;
PhyML_Printf("\n. sample_interval must be an integer greater than 0.\n");
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
break;
}
case 53:
{
phydbl len;
len = atof(optarg);
io->mcmc->chain_len = (int)len;
if(io->mcmc->chain_len < 1)
{
char choix;
PhyML_Printf("\n. chain_len must be an integer greater than 0.\n");
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
break;
}
case 52:
{
char *s;
s = (char *)mCalloc(T_MAX_FILE, sizeof(char));
strcpy(s,optarg);
io->mod->fp_aa_rate_mat = Openfile(s,0);
strcpy(io->mod->aa_rate_mat_file->s,s);
Free(s);
break;
}
case 51:
{
io->boot_prog_every = atoi(optarg);
if(io->boot_prog_every < 1)
{
char choix;
PhyML_Printf("\n. boot_progress_every must be an integer greater than 0.\n");
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
break;
}
case 50:
{
strcpy(io->clade_list_file,optarg);
break;
}
case 49:
{
PhyML_Printf("\n. This is PhyML version %s.\n\n",VERSION);
Exit("");
break;
}
case 48 :
{
io->quiet = 1;
break;
}
case 'p' : case 47 :
{
io->in_tree = 1;
break;
}
case 46 :
{
io->append_run_ID = YES;
strcpy(io->run_id_string,optarg);
break;
}
case 45 :
{
io->mod->ras->gamma_median = 1;
break;
}
case 44 :
{
io->mod->s_opt->hybrid_thresh = 0;
break;
}
case 43 :
{
io->mod->s_opt->min_diff_lk_move = atof(optarg);
if(io->mod->s_opt->min_diff_lk_move < 0)
{
char choix;
PhyML_Printf("\n. Min_diff_lk_move must be a double greater than 0.\n");
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
break;
}
case 42 :
{
io->mod->s_opt->pars_thresh = (int)atoi(optarg);
if(io->mod->s_opt->pars_thresh < 0)
{
PhyML_Printf("\n. The parsimony threshold must be an integer greater than 0.\n");
PhyML_Printf("\n. Type any key to exit.\n");
Exit("\n");
}
break;
}
case 41 :
{
io->mod->s_opt->opt_five_branch = 0;
break;
}
case 40 :
{
writemode = 2;
break;
}
case 39 :
{
break;
}
case 38 :
{
io->rm_ambigu = 1;
break;
}
case 37 :
{
io->mod->s_opt->opt_cov_free_rates = YES;
io->mod->m4mod->use_cov_alpha = NO;
io->mod->m4mod->use_cov_free = YES;
break;
}
case 36 :
{
#ifndef PHYML
open_ps_file = 1;
#endif
break;
}
case 35 :
{
io->mod->m4mod->n_h = (int)atoi(optarg);
if(io->mod->m4mod->n_h < 1)
{
char choix;
PhyML_Printf("\n. The number of classes must be greater than 0.\n");
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
break;
}
case 34 :
{
io->mod->m4mod->use_cov_alpha = YES;
io->mod->m4mod->use_cov_free = NO;
if(!strcmp(optarg,"e") || !strcmp(optarg,"E") ||
!strcmp(optarg,"estimated") || !strcmp(optarg,"ESTIMATED"))
{
io->mod->s_opt->opt_cov_alpha = YES;
io->mod->m4mod->alpha = 1.0;
}
else
{
io->mod->m4mod->alpha = (phydbl)atof(optarg);
if(io->mod->m4mod->alpha < 1.E-5)
{
char choix;
PhyML_Printf("\n. The value of alpha must be greater than 1.E-5.\n");
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
}
break;
}
case 33 :
{
if(!strcmp(optarg,"e") || !strcmp(optarg,"E") ||
!strcmp(optarg,"estimated") || !strcmp(optarg,"ESTIMATED"))
{
io->mod->s_opt->opt_cov_delta = YES;
io->mod->m4mod->delta = 1.0;
}
else
{
io->mod->m4mod->delta = (phydbl)atof(optarg);
if(atof(optarg) < 1.E-10)
{
char choix;
PhyML_Printf("\n. The value of delta must be larger than 1.E-10.\n");
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
}
break;
}
case 32 :
{
io->mod->use_m4mod = YES;
break;
}
case 31 :
{
io->print_site_lnl = YES;
break;
}
case 30 :
{
io->print_trace = YES;
break;
}
case 29 :
{
io->random_boot_seq_order = (int)atoi(optarg);
break;
}
case 28 :
{
io->collapse_boot = (int)atoi(optarg);
break;
}
case 27 :
{
io->r_seed = (int)atoi(optarg);
break;
}
case 26 :
{
io->mod->s_opt->general_pars = YES;
break;
}
case 25 :
{
io->mod->s_opt->fast_nni = YES;
break;
}
case 24 :
{
io->mod->s_opt->p_moves_to_examine = (phydbl)atof(optarg);
break;
}
case 23 :
{
io->mod->s_opt->wim_inside_opt = 1;
break;
}
case 0 :
{
io->mod->s_opt->wim_n_rgrft = atoi(optarg);
break;
}
case 1 :
{
io->mod->s_opt->wim_n_globl = atoi(optarg);
break;
}
case 2 :
{
io->mod->s_opt->wim_max_dist = atoi(optarg);
break;
}
case 3 :
{
io->mod->s_opt->wim_n_optim = atoi(optarg);
break;
}
case 4 :
{
io->mod->s_opt->wim_n_best = atoi(optarg);
break;
}
case 16 :
{
io->mod->s_opt->min_diff_lk_local = atof(optarg);
break;
}
case 17 :
{
io->mod->s_opt->min_diff_lk_global = atof(optarg);
break;
}
case 18 :
{
io->mod->s_opt->steph_spr = 0;
io->mod->s_opt->greedy = 1;
break;
}
case 19 :
{
io->mod->s_opt->brent_it_max = atoi(optarg);
break;
}
case 20 :
{
io->mod->s_opt->random_input_tree = 1;
break;
}
case 21 :
{
io->mod->s_opt->random_input_tree = 1;
io->mod->s_opt->n_rand_starts = atoi(optarg);
if(io->mod->s_opt->n_rand_starts < 1) Exit("\n== Number of random starting trees must be > 0.\n\n");
}
case 's':case 6:
{
if((!strcmp(optarg,"spr")) || (!strcmp(optarg,"SPR")))
{
io->mod->s_opt->topo_search = SPR_MOVE;
io->mod->s_opt->greedy = (io->mod->s_opt->steph_spr)?(0):(1);
}
else if((!strcmp(optarg,"nni")) || (!strcmp(optarg,"NNI")))
{
io->mod->s_opt->topo_search = NNI_MOVE;
io->mod->s_opt->random_input_tree = 0;
}
else if((!strcmp(optarg,"best")) || (!strcmp(optarg,"BEST")))
{
io->mod->s_opt->topo_search = BEST_OF_NNI_AND_SPR;
io->mod->s_opt->greedy = (io->mod->s_opt->steph_spr)?(0):(1);
}
break;
}
case 'd':case 7:
{
if(!strcmp(optarg,"nt"))
{
io->datatype = NT;
io->mod->ns = 4;
io->mod->m4mod->n_o = 4;
if((io->mod->whichmodel == LG) ||
(io->mod->whichmodel == WAG) ||
(io->mod->whichmodel == DAYHOFF) ||
(io->mod->whichmodel == JTT) ||
(io->mod->whichmodel == BLOSUM62) ||
(io->mod->whichmodel == MTREV) ||
(io->mod->whichmodel == RTREV) ||
(io->mod->whichmodel == CPREV) ||
(io->mod->whichmodel == DCMUT) ||
(io->mod->whichmodel == VT) ||
(io->mod->whichmodel == MTMAM) ||
(io->mod->whichmodel == MTART) ||
(io->mod->whichmodel == HIVW) ||
(io->mod->whichmodel == HIVB) ||
(io->mod->whichmodel == AB) ||
(io->mod->whichmodel == CUSTOMAA)
)
{
io->mod->whichmodel = HKY85;
strcpy(io->mod->modelname->s, "HKY85\0");
}
}
else if (!strcmp(optarg,"aa"))
{
io->datatype = AA;
io->mod->s_opt->opt_kappa = NO;
io->mod->ns = 20;
io->mod->m4mod->n_o = 20;
if(
(io->mod->whichmodel == JC69) ||
(io->mod->whichmodel == K80) ||
(io->mod->whichmodel == F81) ||
(io->mod->whichmodel == HKY85) ||
(io->mod->whichmodel == F84) ||
(io->mod->whichmodel == TN93) ||
(io->mod->whichmodel == GTR) ||
(io->mod->whichmodel == CUSTOM)
)
{
io->mod->whichmodel = LG;
strcpy(io->mod->modelname->s, "LG\0");
}
}
else if ((!strcmp(optarg,"generic")) || (!strcmp(optarg,"gen")))
{
io->datatype = GENERIC;
}
else
{
char choix;
PhyML_Printf("\n. Unknown argument to -d option: please use `nt' for DNA or `aa' for Amino-Acids\n");
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
break;
}
case 'm': case 5 :
{
int i;
For(i,strlen(optarg)) Uppercase(optarg+i);
if(!isalpha(optarg[0]))
{
strcpy(io->mod->custom_mod_string->s,optarg);
if(strlen(io->mod->custom_mod_string->s) != 6)
{
Warn_And_Exit("\n. The string should be of length 6.\n");
}
else
{
/* Make_Custom_Model(io->mod); */
/* Translate_Custom_Mod_String(io->mod); */
}
io->datatype = NT;
io->mod->whichmodel = CUSTOM;
strcpy(io->mod->modelname->s, "custom");
io->mod->s_opt->opt_kappa = NO;
io->mod->s_opt->opt_rr = YES;
}
else if (strcmp(optarg, "JC69") == 0)
{
io->datatype = NT;
io->mod->whichmodel = JC69;
}
else if(strcmp(optarg, "K80") == 0)
{
io->datatype = NT;
io->mod->whichmodel = K80;
}
else if(strcmp(optarg, "F81") == 0)
{
io->datatype = NT;
io->mod->whichmodel = F81;
}
else if (strcmp(optarg, "HKY85") == 0)
{
io->datatype = NT;
io->mod->whichmodel = HKY85;
}
else if(strcmp(optarg, "F84") == 0)
{
io->datatype = NT;
io->mod->whichmodel = F84;
}
else if (strcmp (optarg,"TN93") == 0)
{
io->datatype = NT;
io->mod->whichmodel = TN93;
}
else if(strcmp (optarg, "GTR") == 0)
{
io->datatype = NT;
io->mod->whichmodel = GTR;
}
else if(strcmp(optarg, "DAYHOFF") == 0)
{
io->datatype = AA;
io->mod->whichmodel = DAYHOFF;
}
else if(strcmp (optarg, "JTT") == 0)
{
io->datatype = AA;
io->mod->whichmodel = JTT;
}
else if(strcmp(optarg, "MTREV") == 0)
{
io->datatype = AA;
io->mod->whichmodel = MTREV;
}
else if(strcmp (optarg, "LG") == 0)
{
io->datatype = AA;
io->mod->whichmodel = LG;
}
else if(strcmp (optarg, "WAG") == 0)
{
io->datatype = AA;
io->mod->whichmodel = WAG;
}
else if(strcmp(optarg, "DCMUT") == 0)
{
io->datatype = AA;
io->mod->whichmodel = DCMUT;
}
else if(strcmp (optarg, "RTREV") == 0)
{
io->datatype = AA;
io->mod->whichmodel = RTREV;
}
else if(strcmp(optarg, "CPREV") == 0)
{
io->datatype = AA;
io->mod->whichmodel = CPREV;
}
else if(strcmp(optarg, "VT") == 0)
{
io->datatype = AA;
io->mod->whichmodel = VT;
}
else if(strcmp(optarg, "BLOSUM62") == 0)
{
io->datatype = AA;
io->mod->whichmodel = BLOSUM62;
}
else if(strcmp(optarg, "MTMAM") == 0)
{
io->datatype = AA;
io->mod->whichmodel = MTMAM;
}
else if (strcmp(optarg,"MTART") == 0)
{
io->datatype = AA;
io->mod->whichmodel = MTART;
}
else if (strcmp(optarg,"HIVW") == 0)
{
io->datatype = AA;
io->mod->whichmodel = HIVW;
}
else if(strcmp(optarg, "HIVB") == 0)
{
io->datatype = AA;
io->mod->whichmodel = HIVB;
}
else if(strcmp(optarg, "AB") == 0)
{
io->datatype = AA;
io->mod->whichmodel = AB;
}
else if (strcmp(optarg, "CUSTOM") == 0)
{
io->datatype = AA;
io->mod->whichmodel = CUSTOMAA;
}
else
{
PhyML_Printf("\n. The model name is incorrect. Please see the documentation.\n");
Exit("\n");
}
Set_Model_Name(io->mod);
break;
}
case 'a':case 14 :
{
if ((strcmp (optarg, "e") == 0) ||
(strcmp (optarg, "E") == 0) ||
(strcmp (optarg, "estimated") == 0) ||
(strcmp (optarg, "ESTIMATED") == 0))
{
io->mod->s_opt->opt_alpha = YES;
}
else if (atof(optarg) < 1.E-10)
{
char choix;
PhyML_Printf("\n. Alpha must be > 1.E-10.\n");
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
else
{
io->mod->ras->alpha->v = (phydbl)atof(optarg);
io->mod->s_opt->opt_alpha = 0;
}
break;
}
case 'b':case 10:
{
if ((int)String_To_Dbl(optarg) < -5)
{
char choix;
PhyML_Printf("\n. Branch test value must be a positive integer for bootstrap, or between -1 and -4 for aLRT branch test\n");
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
else
{
if((int)String_To_Dbl(optarg) > 0)
{
io->ratio_test = 0;
io->mod->bootstrap = (int)atoi(optarg);
io->print_boot_trees = 1;
if(io->n_data_sets > 1)
{
char choix;
PhyML_Printf("\n. Bootstrap option is not allowed with multiple data sets\n");
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
}
else if (atoi(optarg)==0)
{
io->mod->bootstrap = 0;
io->ratio_test = 0;
}
else
{
io->mod->bootstrap = 0;
io->ratio_test = -(int)atoi(optarg);
}
}
break;
}
case 'c':case 12:
{
if ((!atoi(optarg)) || (atoi(optarg) < 0))
{
char choix;
PhyML_Printf("\n. Unknown argument to -c option: the number of rate categories must be a positive integer\n");
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
else
{
io->mod->ras->n_catg = atoi(optarg);
if(io->mod->ras->n_catg < 1)
{
PhyML_Printf("\n. The number of rate categories must be a positive integer\n");
Exit("\n");
}
}
break;
}
case 'f':
{
if(!strcmp(optarg,"e"))
{
if(io->datatype == NT)
io->mod->s_opt->opt_state_freq = NO;
else if (io->datatype == AA)
io->mod->s_opt->opt_state_freq = YES;
else
{
PhyML_Printf("\n. Please define the data type (nt or aa) before setting the -f option\n");
Exit("\n");
}
}
else if(!strcmp(optarg,"m"))
{
if (io->datatype == NT)
io->mod->s_opt->opt_state_freq = YES;
else if (io->datatype == AA)
io->mod->s_opt->opt_state_freq = NO;
else
{
PhyML_Printf("\n. Please define the data type (nt or aa) before setting the -f option\n");
Exit("\n");
}
}
else if(!isalpha(optarg[0]))
{
phydbl sum;
double val1,val2,val3,val4;
io->mod->s_opt->opt_state_freq = 0;
io->mod->s_opt->user_state_freq = 1;
/* sscanf(optarg,"%lf,%lf,%lf,%lf", */
/* io->mod->user_b_freq, */
/* io->mod->user_b_freq+1, */
/* io->mod->user_b_freq+2, */
/* io->mod->user_b_freq+3); */
sscanf(optarg,"%lf,%lf,%lf,%lf",&val1,&val2,&val3,&val4);
io->mod->user_b_freq->v[0] = (phydbl)val1;
io->mod->user_b_freq->v[1] = (phydbl)val2;
io->mod->user_b_freq->v[2] = (phydbl)val3;
io->mod->user_b_freq->v[3] = (phydbl)val4;
sum =
(io->mod->user_b_freq->v[0] +
io->mod->user_b_freq->v[1] +
io->mod->user_b_freq->v[2] +
io->mod->user_b_freq->v[3]);
io->mod->user_b_freq->v[0] /= sum;
io->mod->user_b_freq->v[1] /= sum;
io->mod->user_b_freq->v[2] /= sum;
io->mod->user_b_freq->v[3] /= sum;
if(io->mod->user_b_freq->v[0] < .0 ||
io->mod->user_b_freq->v[1] < .0 ||
io->mod->user_b_freq->v[2] < .0 ||
io->mod->user_b_freq->v[3] < .0 ||
io->mod->user_b_freq->v[0] > 1. ||
io->mod->user_b_freq->v[1] > 1. ||
io->mod->user_b_freq->v[2] > 1. ||
io->mod->user_b_freq->v[3] > 1.)
{
Warn_And_Exit("\n. Invalid base frequencies.\n");
}
}
break;
}
case 'h':case 69:
{
Usage();
break;
}
case 'i':case 9:
{
char *tmp;
tmp = (char *) mCalloc (T_MAX_FILE, sizeof(char));
if (strlen (optarg) > T_MAX_FILE -16)
{
char choix;
strcpy (tmp, "\n. The file name'");
strcat (tmp, optarg);
strcat (tmp, "' is too long.\n");
PhyML_Printf("%s",tmp);
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
else if (!Filexists (optarg))
{
char choix;
strcpy (tmp, "\n. The file '");
strcat (tmp, optarg);
strcat (tmp, "' does not exist.\n");
PhyML_Printf("%s",tmp);
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
else
{
strcpy(io->in_align_file, optarg);
io->fp_in_align = Openfile(io->in_align_file,0);
strcpy(io->out_file, optarg);
strcpy(io->out_tree_file,optarg);
#ifdef PHYML
strcat(io->out_tree_file,"_phyml_tree");
#elif M4
strcat(io->out_tree_file,"_m4_tree");
#elif PHYREX
strcat(io->out_tree_file,"_phyrex_tree");
#endif
strcpy(io->out_stats_file,optarg);
#ifdef PHYML
strcat(io->out_stats_file,"_phyml_stats");
#elif M4
strcat(io->out_stats_file,"_m4_stats");
#elif PHYREX
strcat(io->out_stats_file,"_phyrex_stats");
#endif
#ifdef PHYREX
strcpy(io->out_summary_file,optarg);
strcat(io->out_summary_file,"_phyrex_summary");
#endif
}
Free (tmp);
break;
}
case 't':case 11:
{
if ((io->mod->whichmodel != JC69) &&
(io->mod->whichmodel != F81) &&
(io->mod->whichmodel != GTR))
{
if ((strcmp(optarg, "e") == 0) ||
(strcmp(optarg, "E") == 0) ||
(strcmp(optarg, "estimated") == 0) ||
(strcmp(optarg, "ESTIMATED") == 0))
{
io->mod->kappa->v = 4.0;
io->mod->s_opt->opt_kappa = YES;
if (io->mod->whichmodel == TN93)
io->mod->s_opt->opt_lambda = YES;
}
else
{
if (atof(optarg) < .0)
{
char choix;
PhyML_Printf("\n. The ts/tv ratio must be a positive number\n");
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
else
{
io->mod->kappa->v = (phydbl)atof(optarg);
io->mod->s_opt->opt_kappa = 0;
io->mod->s_opt->opt_lambda = 0;
}
}
}
break;
}
case 'n':case 8:
{
if ((!atoi(optarg)) || (atoi(optarg) < 0))
{
char choix;
PhyML_Printf("\n. The number of alignments must be a positive integer\n");
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
else io->n_data_sets = atoi (optarg);
break;
}
case 'q':case 22:
{
io->interleaved = NO;
break;
}
case 'u':case 15:
{
char *tmp;
tmp = (char *)mCalloc(T_MAX_FILE, sizeof(char));
if(strlen(optarg) > T_MAX_FILE -11)
{
char choix;
strcpy (tmp, "\n. The file name'");
strcat (tmp, optarg);
strcat (tmp, "' is too long.\n");
PhyML_Printf("%s",tmp);
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
else if (! Filexists (optarg))
{
char choix;
strcpy (tmp, "\n. The file '");
strcat (tmp, optarg);
strcat (tmp, "' doesn't exist.\n");
PhyML_Printf("%s",tmp);
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
else
{
strcpy(io->in_tree_file, optarg);
io->in_tree = 2;
io->fp_in_tree = Openfile(io->in_tree_file,READ);
}
Free(tmp);
break;
}
case 'v':case 13:
{
if ((strcmp (optarg, "e") == 0) ||
(strcmp (optarg, "E") == 0) ||
(strcmp (optarg, "estimated") == 0) ||
(strcmp (optarg, "ESTIMATED") == 0))
{
io->mod->s_opt->opt_pinvar = YES;
io->mod->ras->invar = YES;
}
else if ((atof(optarg) < 0.0) || (atof(optarg) > 1.0))
{
char choix;
PhyML_Printf("\n. The proportion of invariable site must be a number between 0.0 and 1.0\n");
PhyML_Printf("\n. Type any key to exit.");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
else
{
io->mod->ras->pinvar->v = (phydbl)atof(optarg);
if (io->mod->ras->pinvar->v > 0.0+SMALL)
io->mod->ras->invar = 1;
else
io->mod->ras->invar = 0;
io->mod->s_opt->opt_pinvar = 0;
}
break;
}
case 'o':
{
if(!strcmp(optarg,"tlr"))
{
io->mod->s_opt->opt_topo = YES;
io->mod->s_opt->opt_bl = YES;
io->mod->s_opt->opt_subst_param = YES;
}
else if(!strcmp(optarg,"tl"))
{
io->mod->s_opt->opt_topo = YES;
io->mod->s_opt->opt_bl = YES;
io->mod->s_opt->opt_subst_param = NO;
}
else if(!strcmp(optarg,"t"))
{
Warn_And_Exit("\n. You can't optimize the topology without adjusting branch length too...\n");
}
else if(!strcmp(optarg,"lr"))
{
io->mod->s_opt->opt_topo = NO;
io->mod->s_opt->opt_bl = YES;
io->mod->s_opt->opt_subst_param = YES;
}
else if(!strcmp(optarg,"l"))
{
io->mod->s_opt->opt_topo = NO;
io->mod->s_opt->opt_bl = YES;
io->mod->s_opt->opt_subst_param = NO;
}
else if(!strcmp(optarg,"r"))
{
io->mod->s_opt->opt_topo = NO;
io->mod->s_opt->opt_bl = NO;
io->mod->s_opt->opt_subst_param = YES;
}
else if(!strcmp(optarg,"none") || !strcmp(optarg,"n"))
{
io->mod->s_opt->opt_topo = NO;
io->mod->s_opt->opt_bl = NO;
io->mod->s_opt->opt_subst_param = NO;
}
else
{
char choix;
PhyML_Printf ("\n. The optimization parameter must be 'tlr' or 'tl' or 'lr' or 'l' or 'r' or ''.");
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
break;
}
case '?':
{
Exit("\n");
break;
}
case -1:
{
break;
}
default:
{
Usage();
break;
}
}
}while(c != -1);
/* if((io->mod->whichmodel == K80) || (io->mod->whichmodel == JC69)) */
/* { */
/* if(io->mod->s_opt->opt_state_freq) */
/* { */
/* char c; */
/* PhyML_Printf("\n. WARNING: nucleotide frequencies must be set to 1/4 with this model.\n"); */
/* PhyML_Printf("\n. Type the enter key to resume the analysis.\n"); */
/* scanf("%c",&c); */
/* } */
/* io->mod->s_opt->opt_state_freq = 0; */
/* } */
if(io->mod->s_opt->constrained_br_len == YES)
{
io->mod->s_opt->opt_topo = NO;
/* io->mod->s_opt->opt_bl = NO; */
}
#ifndef PHYML
if((open_ps_file) || (io->m4_model == YES))
{
strcpy(io->out_ps_file,io->in_align_file);
strcat(io->out_ps_file, "_mc_tree.ps");
io->fp_out_ps = Openfile(io->out_ps_file,WRITE);
}
#endif
if(io->datatype == UNDEFINED) io->datatype = NT;
if((io->mod->s_opt->n_rand_starts) &&
(io->mod->s_opt->topo_search == NNI_MOVE) &&
(io->mod->s_opt->random_input_tree))
{
Warn_And_Exit("\n== The random starting tree option is only compatible with SPR based search options.\n");
}
if ((io->datatype == NT) && (io->mod->whichmodel > 10))
{
char choix;
PhyML_Printf("\n== Err.: model incompatible with the data type. Please use JC69, K80, F81, HKY, F84, TN93 or GTR\n");
PhyML_Printf("\n== Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Warn_And_Exit("\n");
}
else if ((io->datatype == AA) && (io->mod->whichmodel < 11))
{
char choix;
PhyML_Printf("\n== Err.: model incompatible with the data type. Please use LG, Dayhoff, JTT, MtREV, WAG, DCMut, RtREV, CpREV, VT, Blosum62, MtMam, MtArt, HIVw, HIVb or AB.\n");
PhyML_Printf("\n== Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
if(io->mod->use_m4mod == NO)
{
io->mod->s_opt->opt_cov_delta = 0;
io->mod->s_opt->opt_cov_alpha = 0;
io->mod->s_opt->opt_cov_free_rates = 0;
}
if((io->mod->s_opt->opt_cov_free_rates) && (io->mod->s_opt->opt_cov_alpha))
{
io->mod->s_opt->opt_cov_free_rates = 1;
io->mod->m4mod->use_cov_alpha = 0;
io->mod->m4mod->use_cov_free = 1;
}
if(io->print_site_lnl)
{
strcpy(io->out_lk_file,io->in_align_file);
strcat(io->out_lk_file, "_phyml_lk");
if(io->append_run_ID) { strcat(io->out_lk_file,"_"); strcat(io->out_lk_file,io->run_id_string); }
io->fp_out_lk = Openfile(io->out_lk_file,1);
}
if(io->print_trace)
{
strcpy(io->out_trace_file,io->in_align_file);
strcat(io->out_trace_file,"_phyml_trace");
if(io->append_run_ID) { strcat(io->out_trace_file,"_"); strcat(io->out_trace_file,io->run_id_string); }
io->fp_out_trace = Openfile(io->out_trace_file,1);
}
if(io->mod->s_opt->random_input_tree)
{
strcpy(io->out_trees_file,io->in_align_file);
strcat(io->out_trees_file,"_phyml_rand_trees");
if(io->append_run_ID) { strcat(io->out_trees_file,"_"); strcat(io->out_trees_file,io->run_id_string); }
io->fp_out_trees = Openfile(io->out_trees_file,1);
}
if((io->print_boot_trees) && (io->mod->bootstrap > 0))
{
strcpy(io->out_boot_tree_file,io->in_align_file);
strcat(io->out_boot_tree_file,"_phyml_boot_trees");
if(io->append_run_ID) { strcat(io->out_boot_tree_file,"_"); strcat(io->out_boot_tree_file,io->run_id_string); }
io->fp_out_boot_tree = Openfile(io->out_boot_tree_file,1);
strcpy(io->out_boot_stats_file,io->in_align_file);
strcat(io->out_boot_stats_file,"_phyml_boot_stats");
if(io->append_run_ID) { strcat(io->out_boot_stats_file,"_"); strcat(io->out_boot_stats_file,io->run_id_string); }
io->fp_out_boot_stats = Openfile(io->out_boot_stats_file,1);
}
if(io->append_run_ID)
{
strcat(io->out_tree_file,"_");
strcat(io->out_stats_file,"_");
strcat(io->out_tree_file,io->run_id_string);
strcat(io->out_stats_file,io->run_id_string);
}
if(io->mod->ras->n_catg == 1) io->mod->s_opt->opt_alpha = 0;
if(!io->mod->s_opt->opt_subst_param)
{
io->mod->s_opt->opt_alpha = 0;
io->mod->s_opt->opt_kappa = 0;
io->mod->s_opt->opt_lambda = 0;
io->mod->s_opt->opt_pinvar = 0;
io->mod->s_opt->opt_rr = 0;
}
if(io->mod->whichmodel != K80 &&
io->mod->whichmodel != HKY85 &&
io->mod->whichmodel != F84 &&
io->mod->whichmodel != TN93)
{
io->mod->s_opt->opt_kappa = 0;
}
if(io->datatype == AA && io->mod->whichmodel == CUSTOMAA && !io->mod->fp_aa_rate_mat)
{
PhyML_Printf("\n== Custom model option with amino-acid requires you to specify a rate matrix file through the '--aa_rate_file' option.\n");
Exit("\n");
}
#if !defined(PHYTIME)
// Make sure you don't erase the input file...
if(!strcmp(io->out_tree_file,io->in_align_file) ||
!strcmp(io->out_stats_file,io->in_align_file)) Generic_Exit(__FILE__,__LINE__,__FUNCTION__);
writemode = WRITE;
io->fp_out_tree = Openfile(io->out_tree_file,writemode);
io->fp_out_stats = Openfile(io->out_stats_file,writemode);
#endif
#if defined(PHYREX)
io->fp_out_summary = Openfile(io->out_summary_file,writemode);
#endif
writemode++; // just to silence a warning message at compilation
if(io->mod->whichmodel == GTR)
{
/* Make_Custom_Model(io->mod); */
io->mod->s_opt->opt_rr = 1;
}
return 1;
}
int parserCrear (TDA_Parser *Tda_Parser, char *Archivo, char Separador)
{
int I, Contador;
FILE *P_Archivo;
P_Archivo = fopen(Archivo,"r");
if (P_Archivo)
{
rewind(P_Archivo);
if (!EOF)
{
Contador= 1;
do
{
if (Contador == 1)
For (I= 0, I< 20, I++)
(*Tda_Parser).Nombre[I]= '\0';
if (Contador == 2)
For (I= 0, I< 2, I++)
(*Tda_Parser).Jugada01[I]= '\0';
if (Contador == 3)
For (I= 0, I< 2, I++)
(*Tda_Parser).Jugada02[I]= '\0';
if (Contador == 4)
For (I= 0, I< 2, I++)
(*Tda_Parser).Jugada03[I]= '\0';
if (Contador == 5)
For (I= 0, I< 2, I++)
(*Tda_Parser).Jugada04[I]= '\0';
if (Contador == 6)
For (I= 0, I< 2, I++)
(*Tda_Parser).Jugada05[I]= '\0';
if (Contador == 7)
For (I= 0, I< 2, I++)
(*Tda_Parser).Jugada06[I]= '\0';
if (Contador == 8)
For (I= 0, I< 2, I++)
(*Tda_Parser).Jugada07[I]= '\0';
if (Contador == 9)
For (I= 0, I< 2, I++)
(*Tda_Parser).Jugada08[I]= '\0';
if (Contador == 10)
For (I= 0, I< 2, I++)
(*Tda_Parser).Jugada09[I]= '\0';
if (Contador == 11)
For (I= 0, I< 2, I++)
(*Tda_Parser).Jugada10[I]= '\0';
++Contador;
}
while (Contador < 12);
(*Tda_Parser).NumLinea = 0;
(*Tda_Parser).Archivo = P_Archivo;
(*Tda_Parser).Separador = Separador;
}
else
{
printf("El Archivo: -> %s"," ESTA VACIO!!!!!!\n", Archivo);
return 0;
}
}
else
{
printf("El Archivo: -> %s"," NO EXISTE y NO FUE ABIERTO\n", Archivo);
return 0;
}
return 0;
}
TreeNode* Parser::Statement()
{
kdDebug(0)<<"Parser::Statement()"<<endl;
while (currentToken.type == tokEOL) getToken(); // statements can allways start on newlines
switch (currentToken.type)
{
case tokLearn : return Learn(); break;
case tokIf : return If(); break;
case tokFor : return For(); break;
case tokForEach : return ForEach(); break;
case tokWhile : return While(); break;
case tokRun : return ExternalRun(); break;
case tokReturn : return Return(); break;
case tokBreak : return Break(); break;
case tokUnknown : return Other(); break; //assignment or function call
case tokClear : return Clear(); break;
case tokGo : return Go(); break;
case tokGoX : return GoX(); break;
case tokGoY : return GoY(); break;
case tokForward : return Forward(); break;
case tokBackward : return Backward(); break;
case tokDirection : return Direction(); break;
case tokTurnLeft : return TurnLeft(); break;
case tokTurnRight : return TurnRight(); break;
case tokCenter : return Center(); break;
case tokSetPenWidth : return SetPenWidth(); break;
case tokPenUp : return PenUp(); break;
case tokPenDown : return PenDown(); break;
case tokSetFgColor : return SetFgColor(); break;
case tokSetBgColor : return SetBgColor(); break;
case tokResizeCanvas : return ResizeCanvas(); break;
case tokSpriteShow : return SpriteShow(); break;
case tokSpriteHide : return SpriteHide(); break;
case tokSpritePress : return SpritePress(); break;
case tokSpriteChange : return SpriteChange(); break;
case tokPrint : return Print(); break;
case tokInputWindow : return InputWindow(); break;
case tokMessage : return Message(); break;
case tokFontType : return FontType(); break;
case tokFontSize : return FontSize(); break;
case tokRepeat : return Repeat(); break;
case tokRandom : return Random(); break;
case tokWait : return Wait(); break;
case tokWrapOn : return WrapOn(); break;
case tokWrapOff : return WrapOff(); break;
case tokReset : return Reset(); break;
case tokEOF : return EndOfFile(); break;
case tokEnd : Error(currentToken, i18n("Cannot understand ']'"), 1050);
getToken();
return new TreeNode(currentToken, Unknown);
break;
case tokBegin : Error(currentToken, i18n("Cannot understand '['"), 1050);
getToken();
return new TreeNode(currentToken, Unknown);
break;
default : break;
}
if (currentToken.type != tokEnd)
{
Error(currentToken, i18n("Cannot understand '%1'").arg(currentToken.look), 1060);
}
getToken();
return new TreeNode(currentToken, Unknown); // fall-though for unknowns
}
void det(double **a, int n, double *d)
{
int j;
ludcmp(a,n,d);
For(j,n) *d *= a[j][j];
}
