static void
utest_pvectors(void)
{
char *msg = "pvector unit test failed";
double p1[4] = { 0.25, 0.25, 0.25, 0.25 };
double p2[4];
double p3[4];
float p1f[4];
float p2f[4] = { 0.0, 0.5, 0.5, 0.0 };
float p3f[4];
int n = 4;
double result;
esl_vec_D2F(p1, n, p1f);
esl_vec_F2D(p2f, n, p2);
if (esl_vec_DValidate(p1, n, 1e-12, NULL) != eslOK) esl_fatal(msg);
if (esl_vec_FValidate(p1f, n, 1e-7, NULL) != eslOK) esl_fatal(msg);
result = esl_vec_DEntropy(p1, n); if (esl_DCompare(2.0, result, 1e-9) != eslOK) esl_fatal(msg);
result = esl_vec_FEntropy(p1f, n); if (esl_DCompare(2.0, result, 1e-9) != eslOK) esl_fatal(msg);
result = esl_vec_DEntropy(p2, n); if (esl_DCompare(1.0, result, 1e-9) != eslOK) esl_fatal(msg);
result = esl_vec_FEntropy(p2f, n); if (esl_DCompare(1.0, result, 1e-9) != eslOK) esl_fatal(msg);
result = esl_vec_DRelEntropy(p2, p1, n); if (esl_DCompare(1.0, result, 1e-9) != eslOK) esl_fatal(msg);
result = esl_vec_FRelEntropy(p2f, p1f, n); if (esl_DCompare(1.0, result, 1e-9) != eslOK) esl_fatal(msg);
result = esl_vec_DRelEntropy(p1, p2, n); if (result != eslINFINITY) esl_fatal(msg);
result = esl_vec_FRelEntropy(p1f, p2f, n); if (result != eslINFINITY) esl_fatal(msg);
esl_vec_DLog(p2, n);
if (esl_vec_DLogValidate(p2, n, 1e-12, NULL) != eslOK) esl_fatal(msg);
esl_vec_DExp(p2, n);
if (p2[0] != 0.) esl_fatal(msg);
esl_vec_FLog(p2f, n);
if (esl_vec_FLogValidate(p2f, n, 1e-7, NULL) != eslOK) esl_fatal(msg);
esl_vec_FExp(p2f, n);
if (p2f[0] != 0.) esl_fatal(msg);
esl_vec_DCopy(p2, n, p3);
esl_vec_DScale(p3, n, 10.);
esl_vec_DNorm(p3, n);
if (esl_vec_DCompare(p2, p3, n, 1e-12) != eslOK) esl_fatal(msg);
esl_vec_DLog(p3, n);
result = esl_vec_DLogSum(p3, n); if (esl_DCompare(0.0, result, 1e-12) != eslOK) esl_fatal(msg);
esl_vec_DIncrement(p3, n, 2.0);
esl_vec_DLogNorm(p3, n);
if (esl_vec_DCompare(p2, p3, n, 1e-12) != eslOK) esl_fatal(msg);
esl_vec_FCopy(p2f, n, p3f);
esl_vec_FScale(p3f, n, 10.);
esl_vec_FNorm(p3f, n);
if (esl_vec_FCompare(p2f, p3f, n, 1e-7) != eslOK) esl_fatal(msg);
esl_vec_FLog(p3f, n);
result = esl_vec_FLogSum(p3f, n); if (esl_DCompare(0.0, result, 1e-7) != eslOK) esl_fatal(msg);
esl_vec_FIncrement(p3f, n, 2.0);
esl_vec_FLogNorm(p3f, n);
if (esl_vec_FCompare(p2f, p3f, n, 1e-7) != eslOK) esl_fatal(msg);
return;
}
/* dump_infocontent_info
*
* Given an MSA with RF annotation, dump information content per column data to
* an open output file.
*/
static int dump_infocontent_info(FILE *fp, ESL_ALPHABET *abc, double **abc_ct, int use_weights, int nali, int64_t alen, int nseq, int *i_am_rf, char *msa_name, char *alifile, char *errbuf)
{
int status;
int apos, rfpos;
double bg_ent;
double *bg = NULL;
double *abc_freq = NULL;
double nnongap;
ESL_ALLOC(bg, sizeof(double) * abc->K);
esl_vec_DSet(bg, abc->K, 1./(abc->K));
bg_ent = esl_vec_DEntropy(bg, abc->K);
free(bg);
ESL_ALLOC(abc_freq, sizeof(double) * abc->K);
fprintf(fp, "# Information content per column (bits):\n");
fprintf(fp, "# Alignment file: %s\n", alifile);
fprintf(fp, "# Alignment idx: %d\n", nali);
if(msa_name != NULL) { fprintf(fp, "# Alignment name: %s\n", msa_name); }
fprintf(fp, "# Number of sequences: %d\n", nseq);
if(use_weights) { fprintf(fp, "# IMPORTANT: Counts are weighted based on sequence weights in alignment file.\n"); }
else { fprintf(fp, "# Sequence weights from alignment were ignored (if they existed).\n"); }
fprintf(fp, "#\n");
if(i_am_rf != NULL) {
fprintf(fp, "# %7s %7s %10s %10s\n", "rfpos", "alnpos", "freqnongap", "info(bits)");
fprintf(fp, "# %7s %7s %10s %10s\n", "-------", "-------", "----------", "----------");
}
else {
fprintf(fp, "# %7s %10s %10s\n", "alnpos", "freqnongap", "info(bits)");
fprintf(fp, "# %7s %10s %10s\n", "-------", "----------", "----------");
}
rfpos = 0;
for(apos = 0; apos < alen; apos++) {
if(i_am_rf != NULL) {
if(i_am_rf[apos]) {
fprintf(fp, " %7d", rfpos+1);
rfpos++;
}
else {
fprintf(fp, " %7s", "-");
}
}
nnongap = esl_vec_DSum(abc_ct[apos], abc->K);
esl_vec_DCopy(abc_ct[apos], abc->K, abc_freq);
esl_vec_DNorm(abc_freq, abc->K);
fprintf(fp, " %7d %10.8f %10.8f\n", apos+1,
nnongap / (nnongap + abc_ct[apos][abc->K]),
(bg_ent - esl_vec_DEntropy(abc_freq, abc->K)));
}
fprintf(fp, "//\n");
if(abc_freq != NULL) free(abc_freq);
return eslOK;
ERROR:
ESL_FAIL(eslEINVAL, errbuf, "out of memory");
return status; /* NEVERREACHED */
}
