int* irep(int val, int n)
{
int i;
int *v = new_ivec(n);
for(i=0; i<n; i++) v[i] = val;
return v;
}
int* new_izero(int n)
{
int i;
int *v = new_ivec(n);
for(i=0; i<n; i++) v[i] = 0;
return v;
}
void la_dgesv(int Arow, int Bcol, double **A, double **B)
{
int info;
int *ip = new_ivec(Arow); /* pivot indices which define P;
row i was interchanged with row ip[i]*/
dgesv_(&Arow, &Bcol, *A, &Arow, ip, *B, &Arow, &info);
assert(info==0); // if info = -i, i'th arg is wrong. if info > 0, A is not pos-def.
}
int* new_iseq(int from, int to)
{
int n,i;
assert( from <= to);
n = (to - from) + 1;
int *v = new_ivec(n);
v[0] = from;
for(i=1; i<n; i++) v[i] = v[i-1] + 1;
return v;
}
int genrmt(char *infile, char *outfile)
{
int i,j;
FILE *fp;
double x,t0,t1;
char *cbuf,*fext;
/* open file */
switch(seqmode) {
case SEQ_MOLPHY: fext=fext_molphy; break;
case SEQ_PAML: fext=fext_paml; break;
case SEQ_PAUP: fext=fext_paup; break;
case SEQ_PUZZLE: fext=fext_puzzle; break;
case SEQ_PHYML: fext=fext_phyml; break;
case SEQ_MT:
default: fext=fext_mt; break;
}
if(infile) {
fp=openfp(infile,fext,"r",&cbuf);
printf("\n# reading %s",cbuf);
} else {
fp=STDIN;
printf("\n# reading from stdin");
}
/* read file */
mm=nn=0;
switch(seqmode) {
case SEQ_MOLPHY:
datmat = fread_mat_lls(fp, &mm, &nn); break;
case SEQ_PAML:
datmat = fread_mat_lfh(fp, &mm, &nn); break;
case SEQ_PAUP:
datmat = fread_mat_paup(fp, &mm, &nn); break;
case SEQ_PUZZLE:
datmat = fread_mat_puzzle(fp, &mm, &nn); break;
case SEQ_PHYML:
datmat = fread_mat_phyml(fp, &mm, &nn); break;
case SEQ_MT:
default:
datmat = fread_mat(fp, &mm, &nn); break;
}
if(infile) {fclose(fp); FREE(cbuf);}
printf("\n# M:%d N:%d",mm,nn);
/* allocating buffers */
datvec=new_vec(mm);
bn=new_ivec(kk); rr1=new_vec(kk);
/* calculate the log-likelihoods */
for(i=0;i<mm;i++) {
x=0; for(j=0;j<nn;j++) x+=datmat[i][j];
datvec[i]=x;
}
/* calculate scales */
for(i=0;i<kk;i++) {
bn[i]=(int)(rr[i]*nn); /* sample size for bootstrap */
rr1[i]=(double)bn[i]/nn; /* recalculate rr for integer adjustment */
}
/* open out file */
if(outfile) {
/* vt ascii write to file */
fp=openfp(outfile,fext_vt,"w",&cbuf);
printf("\n# writing %s",cbuf);
fwrite_vec(fp,datvec,mm);
fclose(fp); FREE(cbuf);
/* rmt binary write to file */
fp=openfp(outfile,fext_rmt,"wb",&cbuf);
printf("\n# writing %s",cbuf);
fwrite_bvec(fp,datvec,mm);
fwrite_bvec(fp,rr1,kk);
fwrite_bivec(fp,bb,kk);
fwrite_bi(fp,kk);
} else {
/* rmt ascii write to stdout */
printf("\n# writing to stdout");
printf("\n# OBS:\n"); write_vec(datvec,mm);
printf("\n# R:\n"); write_vec(rr1,kk);
printf("\n# B:\n"); write_ivec(bb,kk);
printf("\n# RMAT:\n");
printf("%d\n",kk);
}
/* generating the replicates by resampling*/
for(i=j=0;i<kk;i++) j+=bb[i];
printf("\n# start generating total %d replicates for %d items",j,mm);
fflush(STDOUT);
t0=get_time();
for(i=0;i<kk;i++) {
repmat=new_lmat(mm,bb[i]);
scaleboot(datmat,repmat,mm,nn,bn[i],bb[i]);
if(outfile) {
fwrite_bmat(fp,repmat,mm,bb[i]);
putdot();
} else {
printf("\n## RMAT[%d]:\n",i); write_mat(repmat,mm,bb[i]);
}
free_lmat(repmat,mm);
}
t1=get_time();
printf("\n# time elapsed for bootstrap t=%g sec",t1-t0);
if(outfile) {
fclose(fp); FREE(cbuf);
}
/* freeing buffers */
free_vec(bn); free_vec(rr1); free_vec(datvec); free_mat(datmat);
return 0;
}
int* new_dup_ivec(int *v, int n)
{
int* iv_new = new_ivec(n);
copy_ivec(iv_new, v, n);
return iv_new;
}
int main() {
int i;
ivec_t* vec = new_ivec(100);
for (i = 0; i < 10000; ++i) {
assert(ivec_push_back(vec, i));
}
printf("size = %u, empty = %d, capacity = %u\n", ivec_size(vec), ivec_empty(vec), ivec_capacity(vec));
printf("popback = %d\n", ivec_pop_back(vec));
printf("size = %u, empty = %d, capacity = %u\n", ivec_size(vec), ivec_empty(vec), ivec_capacity(vec));
int* d = ivec_data(vec);
for (i = 0; i < 9999; ++i) {
assert(*(d+i) == i && i == ivec_at(vec, i));
}
printf("resize to 10, and shrink_to_fit\n");
ivec_resize_default(vec, 10);
ivec_shrink_to_fit(vec);
printf("size = %u, empty = %d, capacity = %u\n", ivec_size(vec), ivec_empty(vec), ivec_capacity(vec));
char buf[1000];
ivec_dump(buf, 1000, vec);
printf("%s\n", buf);
printf("resize to 15\n", ivec_resize_default(vec, 15));
printf("size = %u, empty = %d, capacity = %u\n", ivec_size(vec), ivec_empty(vec), ivec_capacity(vec));
ivec_dump(buf, 1000, vec);
printf("%s\n", buf);
ivec_destroy(vec);
svec_t* svec = new_svec(100);
for (i = 0; i < 100; ++i) {
snprintf(buf, 1000, "%d", i);
assert(svec_push_back(svec, buf));
}
printf("size = %u, empty = %d, capacity = %u\n", svec_size(svec), svec_empty(svec), svec_capacity(svec));
char* ret = svec_pop_back(svec);
printf("popback = %s\n", ret);
free(ret);
printf("size = %u, empty = %d, capacity = %u\n", svec_size(svec), svec_empty(svec), svec_capacity(svec));
char** s = svec_data(svec);
for (i = 0; i < 99; ++i) {
snprintf(buf, 1000, "%d", i);
assert(!strcmp(*(s+i), buf) && !strcmp(buf, svec_at(svec, i)));
}
printf("resize to 10, and shrink to fit\n");
svec_resize_default(svec, 10);
svec_shrink_to_fit(svec);
printf("size = %u, empty = %d, capacity = %u\n", svec_size(svec), svec_empty(svec), svec_capacity(svec));
svec_dump(buf, 1000, svec);
printf("%s\n", buf);
printf("resize to 15\n", svec_resize_default(svec, 15));
printf("size = %u, empty = %d, capacity = %u\n", svec_size(svec), svec_empty(svec), svec_capacity(svec));
svec_dump(buf, 1000, svec);
printf("%s\n", buf);
svec_destroy(svec);
return 0;
}
