double mrand()
#endif
{
long lval;
static Real factor = 1.0 / ((Real) MODULUS);
if (!started)
smrand(3127);
inext = (inext >= 54) ? 0 : inext + 1;
inextp = (inextp >= 54) ? 0 : inextp + 1;
lval = mrand_list[inext] - mrand_list[inextp];
if (lval < 0L)
lval += MODULUS;
mrand_list[inext] = lval;
return (double) lval * factor;
}
void mrandlist(Real a[], int len)
#endif
{
int i;
long lval;
static Real factor = 1.0 / ((Real) MODULUS);
if (!started)
smrand(3127);
for (i = 0; i < len; i++) {
inext = (inext >= 54) ? 0 : inext + 1;
inextp = (inextp >= 54) ? 0 : inextp + 1;
lval = mrand_list[inext] - mrand_list[inextp];
if (lval < 0L)
lval += MODULUS;
mrand_list[inext] = lval;
a[i] = (Real) lval * factor;
}
}
int main(int argc, char** argv)
{
/* working variables */
int i,j,mf;
FILE *fp;
char *cbuf,**infiles,**outfiles;
printf("# %s",rcsid);
/* args */
for(i=j=1;i<argc;i++) {
if(argv[i][0] != '-') {
switch(j) {
case 1: fname_mt=argv[i]; break;
case 2: fname_rmt=argv[i]; break;
default: byebye();
}
j++;
} else if(streq(argv[i],"-s")) {
if(i+1>=argc ||
sscanf(argv[i+1],"%lu",&seed) != 1)
byebye();
i+=1;
} else if(streq(argv[i],"-p")) {
if(i+1>=argc) byebye();
fname_pa=argv[i+1];
i+=1;
} else if(streq(argv[i],"-b")) {
if(i+1>=argc ||
sscanf(argv[i+1],"%lf",&bbfact) != 1)
byebye();
i+=1;
} else if(streq(argv[i],"-f")) {
sw_fastrep=1;
} else if(streq(argv[i],"-g")) {
sw_multi=1;
} else if(streq(argv[i],"--molphy")) {
seqmode=SEQ_MOLPHY;
} else if(streq(argv[i],"--paml")) {
seqmode=SEQ_PAML;
} else if(streq(argv[i],"--paup")) {
seqmode=SEQ_PAUP;
} else if(streq(argv[i],"--puzzle")) {
seqmode=SEQ_PUZZLE;
} else if(streq(argv[i],"--phyml")) {
seqmode=SEQ_PHYML;
} else if(streq(argv[i],"-d")) {
if(i+1>=argc ||
sscanf(argv[i+1],"%d",&debugmode) != 1)
byebye();
i+=1;
} else byebye();
}
/* random seed */
smrand(seed);
/* reading parameters */
if(fname_pa!=NULL) {
fp=openfp(fname_pa,fext_pa,"r",&cbuf);
printf("\n# reading %s",cbuf);
kk=0;
rr=fread_vec(fp,&kk);
bb=fread_ivec(fp,&kk);
fclose(fp); FREE(cbuf);
} else {
if(sw_fastrep) {kk=kk00; rr=rr00; bb=bb00;}
else {kk=kk0; rr=rr0; bb=bb0;}
}
for(i=0;i<kk;i++) bb[i] *= bbfact;
printf("\n# seed:%lu (MT19937 generator)",seed);
printf("\n# K:%d",kk);
printf("\n# R:"); for(i=0;i<kk;i++) printf("%g ",rr[i]);
printf("\n# B:"); for(i=0;i<kk;i++) printf("%d ",bb[i]);
if(sw_multi) {
if(fname_mt) fp=openfp(fname_mt,fext_svt,"r",&cbuf); else fp=STDIN;
mf=0; infiles=fread_svec(fp,&mf);
if(fname_mt) {fclose(fp); FREE(cbuf);}
if(fname_rmt) {
fp=openfp(fname_rmt,fext_svt,"r",&cbuf);
outfiles=fread_svec(fp,&mf);
fclose(fp); FREE(cbuf);
} else {
outfiles=NEW_A(mf,char*);
for(i=0;i<mf;i++) outfiles[i]=rmvaxt(infiles[i]);
}
for(i=0;i<mf;i++) {
printf("\n# %d/%d %s %s",i+1,mf,infiles[i],outfiles[i]);
genrmt(infiles[i],outfiles[i]);
}
} else {
if(fname_mt && !fname_rmt) fname_rmt=rmvaxt(fname_mt);
