/* Function: p7_emit_FancyConsensus()
* Synopsis: Emit a fancier consensus with upper/lower case and N/X's.
* Incept: SRE, Fri May 14 09:33:10 2010 [Janelia]
*
* Purpose: Generate a consensus sequence for model <hmm>, consisting
* of the maximum probability residue in each match state;
* store this sequence in text-mode <sq> provided by the caller.
*
* If the probability of the consensus residue is less than
* <min_lower>, show an ``any'' residue (N or X) instead.
* If the probability of the consensus residue is $\geq$
* <min_lower> and less than <min_upper>, show the residue
* as lower case; if it is $\geq$ <min_upper>, show it as
* upper case.
*
* Returns: <eslOK> on success.
*
* Throws: <eslEINVAL> if the <sq> isn't in text mode.
*
* Xref: SRE:J6/59.
*/
int
p7_emit_FancyConsensus(const P7_HMM *hmm, float min_lower, float min_upper, ESL_SQ *sq)
{
int k, x;
float p;
char c;
int status;
if (! esl_sq_IsText(sq)) ESL_EXCEPTION(eslEINVAL, "p7_emit_FancyConsensus() expects a text-mode <sq>");
if ((status = esl_sq_GrowTo(sq, hmm->M)) != eslOK) return status;
for (k = 1; k <= hmm->M; k++)
{
if (hmm->mm && hmm->mm[k] == 'm') { //masked position, spit out the degenerate code
if ((status = esl_sq_CAddResidue(sq, tolower(esl_abc_CGetUnknown(hmm->abc))) ) != eslOK) return status;
} else {
p = esl_vec_FMax( hmm->mat[k], hmm->abc->K);
x = esl_vec_FArgMax(hmm->mat[k], hmm->abc->K);
if (p < min_lower) c = tolower(esl_abc_CGetUnknown(hmm->abc));
else if (p >= min_upper) c = toupper(hmm->abc->sym[x]);
else c = tolower(hmm->abc->sym[x]);
if ((status = esl_sq_CAddResidue(sq, c)) != eslOK) return status;
}
}
if ((status = esl_sq_CAddResidue(sq, '\0')) != eslOK) return status;
return eslOK;
}
/* Fetch in a random sequence of length <L> from the the pre-digitized
* concatenated sequence database, select a random subseq, shuffle it
* by the chosen algorithm; set dsq[1..L] to the resulting randomized
* segment.
*
* If <logfp> is non-NULL, append one or more "<sqname> <from> <to>"
* fields to current line, to record where the random segment was
* selected from. This is useful in cases where we want to track back
* the origin of a high-scoring segment, in case the randomization
* wasn't good enough to obscure the identity of a segment.
*
*/
static int
set_random_segment(ESL_GETOPTS *go, struct cfg_s *cfg, FILE *logfp, ESL_DSQ *dsq, int L)
{
ESL_SQ *sq = esl_sq_CreateDigital(cfg->abc);
int minDPL = esl_opt_GetInteger(go, "--minDPL");
int db_dependent = (esl_opt_GetBoolean(go, "--iid") == TRUE ? FALSE : TRUE);
char *pkey = NULL;
int start, end;
int64_t Lseq;
int status;
if (L==0) return eslOK;
if (L > cfg->db_maxL) esl_fatal("can't fetch a segment of length %d; database max is %d\n", L, cfg->db_maxL);
/* fetch a random subseq from the source database */
esl_sq_GrowTo(sq, L);
if (db_dependent)
{
do {
if (pkey != NULL) free(pkey);
if (esl_ssi_FindNumber(cfg->dbfp->data.ascii.ssi, esl_rnd_Roll(cfg->r, cfg->db_nseq), NULL, NULL, NULL, &Lseq, &pkey) != eslOK)
esl_fatal("failed to look up a random seq");
} while (Lseq < L);
start = 1 + esl_rnd_Roll(cfg->r, Lseq-L);
end = start + L - 1;
if (esl_sqio_FetchSubseq(cfg->dbfp, pkey, start, end, sq) != eslOK) esl_fatal("failed to fetch subseq");
esl_sq_ConvertDegen2X(sq);
}
/* log sequence source info: <name> <start> <end> */
if (logfp != NULL && db_dependent)
fprintf(logfp, " %-15s %5d %5d", pkey, start, end);
/* Now apply the appropriate randomization algorithm */
if (esl_opt_GetBoolean(go, "--mono")) status = esl_rsq_XShuffle (cfg->r, sq->dsq, L, sq->dsq);
else if (esl_opt_GetBoolean(go, "--di")) {
if (L < minDPL) status = esl_rsq_XShuffle (cfg->r, sq->dsq, L, sq->dsq);
else status = esl_rsq_XShuffleDP(cfg->r, sq->dsq, L, cfg->abc->Kp, sq->dsq);
}
else if (esl_opt_GetBoolean(go, "--markov0")) status = esl_rsq_XMarkov0 (cfg->r, sq->dsq, L, cfg->abc->Kp, sq->dsq);
else if (esl_opt_GetBoolean(go, "--markov1")) status = esl_rsq_XMarkov1 (cfg->r, sq->dsq, L, cfg->abc->Kp, sq->dsq);
else if (esl_opt_GetBoolean(go, "--reverse")) status = esl_rsq_XReverse (sq->dsq, L, sq->dsq);
else if (esl_opt_GetBoolean(go, "--iid")) status = esl_rsq_xIID (cfg->r, cfg->fq, cfg->abc->K, L, sq->dsq);
else status = eslEINCONCEIVABLE;
if (status != eslOK) esl_fatal("esl's shuffling failed");
memcpy(dsq, sq->dsq+1, sizeof(ESL_DSQ) * L);
esl_sq_Destroy(sq);
free(pkey);
return eslOK;
}
/* seq_generation()
*
* Generating sequences.
*/
static int
seq_generation(ESL_GETOPTS *go, ESL_RANDOMNESS *r, FILE *ofp, int outfmt)
{
ESL_ALPHABET *abc = NULL;
ESL_SQ *sq = NULL;
double *fq = NULL;
int alphatype = eslUNKNOWN; // static checkers can't see that 1 of --rna, --dna, --amino must be true
int N = esl_opt_GetInteger(go, "-N");
int L = esl_opt_GetInteger(go, "-L");
int i;
int status;
if (L <= 0) esl_fatal("To generate sequences, set -L option (length of generated seqs) > 0 ");
if (esl_opt_GetBoolean(go, "--rna")) alphatype = eslRNA;
if (esl_opt_GetBoolean(go, "--dna")) alphatype = eslDNA;
if (esl_opt_GetBoolean(go, "--amino")) alphatype = eslAMINO;
abc = esl_alphabet_Create(alphatype);
sq = esl_sq_CreateDigital(abc);
esl_sq_GrowTo(sq, L);
/* Pick the iid frequency distribution to use */
ESL_ALLOC(fq, sizeof(double) * abc->K);
switch (alphatype) {
case eslRNA:
case eslDNA: esl_vec_DSet(fq, 4, 0.25); break;
case eslAMINO: esl_composition_SW34(fq); break;
default: esl_vec_DSet(fq, abc->K, 1.0 / (double) abc->K); break;
}
/* generate */
for (i = 0; i < N; i++)
{
esl_rsq_xIID(r, fq, abc->K, L, sq->dsq);
if (N > 1) esl_sq_FormatName(sq, "random%d", i);
else esl_sq_SetName(sq, "random");
sq->n = L;
esl_sqio_Write(ofp, sq, outfmt, FALSE);
}
free(fq);
esl_alphabet_Destroy(abc);
esl_sq_Destroy(sq);
return eslOK;
ERROR:
if (fq != NULL) free(fq);
esl_alphabet_Destroy(abc);
esl_sq_Destroy(sq);
return status;
}
static int
synthesize_negatives(ESL_GETOPTS *go, struct cfg_s *cfg, int nneg)
{
ESL_SQ *sq = esl_sq_CreateDigital(cfg->abc);
int a;
int i;
int L1,L2,L3,d1n,d2n;
for (i = 0; i < nneg; i++)
{
/* Select a random test seq, to use its same segments */
a = esl_rnd_Roll(cfg->r, cfg->ntest);
L1 = cfg->test_lens[a].L1;
L2 = cfg->test_lens[a].L2;
L3 = cfg->test_lens[a].L3;
d1n = cfg->test_lens[a].d1n;
d2n = cfg->test_lens[a].d2n;
esl_sq_GrowTo(sq, cfg->test_lens[a].L);
esl_sq_FormatName(sq, "decoy%d", i+1);
esl_sq_FormatDesc(sq, "L=%d in segments: %d/%d/%d/%d/%d", cfg->test_lens[a].L, L1, d1n, L2, d2n, L3);
sq->n = cfg->test_lens[a].L;
fprintf(cfg->negsummfp, "%-15s %5d %5d %5d %5d %5d %5d",
sq->name, (int) sq->n,
L1, d1n, L2, d2n, L3);
sq->dsq[0] = sq->dsq[cfg->test_lens[a].L+1] = eslDSQ_SENTINEL;
set_random_segment(go, cfg, cfg->negsummfp, sq->dsq+1, L1);
set_random_segment(go, cfg, cfg->negsummfp, sq->dsq+1+L1, d1n);
set_random_segment(go, cfg, cfg->negsummfp, sq->dsq+1+L1+d1n, L2);
set_random_segment(go, cfg, cfg->negsummfp, sq->dsq+1+L1+d1n+L2, d2n);
set_random_segment(go, cfg, cfg->negsummfp, sq->dsq+1+L1+d1n+L2+d2n, L3);
fprintf(cfg->negsummfp, "\n");
esl_sqio_Write(cfg->out_seqfp, sq, eslSQFILE_FASTA, FALSE);
esl_sq_Reuse(sq);
}
esl_sq_Destroy(sq);
return eslOK;
}
/* Function: p7_emit_SimpleConsensus()
* Synopsis: Generate simple consensus: ML residue in each match state
* Incept: SRE, Mon Sep 1 09:10:47 2008 [Janelia]
*
* Purpose: Generate a simple consensus sequence for model <hmm>
* consisting of the maximum probability residue in each
* match state; store this consensus in digital <sq>.
*
* Returns: <eslOK> on success.
*
* Throws: <eslEINVAL> if the <sq> isn't in digital mode.
*/
int
p7_emit_SimpleConsensus(const P7_HMM *hmm, ESL_SQ *sq)
{
int k;
int x;
int status;
if (! esl_sq_IsDigital(sq)) ESL_EXCEPTION(eslEINVAL, "p7_emit_SimpleConsensus() expects a digital-mode <sq>");
if ((status = esl_sq_GrowTo(sq, hmm->M)) != eslOK) return status;
for (k = 1; k <= hmm->M; k++)
{
if (hmm->mm && hmm->mm[k] == 'm') { //masked position, spit out the degenerate code
if ((status = esl_sq_XAddResidue(sq, hmm->abc->Kp-3)) != eslOK) return status;
} else {
x = esl_vec_FArgMax(hmm->mat[k], hmm->abc->K);
if ((status = esl_sq_XAddResidue(sq, x)) != eslOK) return status;
}
}
if ((status = esl_sq_XAddResidue(sq, eslDSQ_SENTINEL)) != eslOK) return status;
return eslOK;
}
/* Function: p7_alidisplay_Backconvert()
* Synopsis: Convert an alidisplay to a faux trace and subsequence.
* Incept: SRE, Wed Dec 10 09:49:28 2008 [Janelia]
*
* Purpose: Convert alignment display object <ad> to a faux subsequence
* and faux subsequence trace, returning them in <ret_sq> and
* <ret_tr>.
*
* The subsequence <*ret_sq> is digital; ascii residues in
* <ad> are digitized using digital alphabet <abc>.
*
* The subsequence and trace are suitable for passing as
* array elements to <p7_MultipleAlignment>. This is the
* main purpose of backconversion. Results of a profile
* search are stored in a hit list as a processed
* <P7_ALIDISPLAY>, not as a <P7_TRACE> and <ESL_SQ>, to
* reduce space and to reduce communication overhead in
* parallelized search implementations. After reduction
* to a final hit list, a master may want to construct a
* multiple alignment of all the significant hits.
*
* Returns: <eslOK> on success.
*
* Throws: <eslEMEM> on allocation failures. <eslECORRUPT> on unexpected internal
* data corruption. On any exception, <*ret_sq> and <*ret_tr> are
* <NULL>.
*
* Xref: J4/29.
*/
int
p7_alidisplay_Backconvert(const P7_ALIDISPLAY *ad, const ESL_ALPHABET *abc, ESL_SQ **ret_sq, P7_TRACE **ret_tr)
{
ESL_SQ *sq = NULL; /* RETURN: faux subsequence */
P7_TRACE *tr = NULL; /* RETURN: faux trace */
int subL = 0; /* subsequence length in the <ad> */
int a, i, k; /* coords for <ad>, <sq->dsq>, model */
char st; /* state type: MDI */
int status;
/* Make a first pass over <ad> just to calculate subseq length */
for (a = 0; a < ad->N; a++)
if (! esl_abc_CIsGap(abc, ad->aseq[a])) subL++;
/* Allocations */
if ((sq = esl_sq_CreateDigital(abc)) == NULL) { status = eslEMEM; goto ERROR; }
if ((status = esl_sq_GrowTo(sq, subL)) != eslOK) goto ERROR;
if ((tr = (ad->ppline == NULL) ? p7_trace_Create() : p7_trace_CreateWithPP()) == NULL) { status = eslEMEM; goto ERROR; }
if ((status = p7_trace_GrowTo(tr, subL+6)) != eslOK) goto ERROR; /* +6 is for SNB/ECT */
/* Construction of dsq, trace */
sq->dsq[0] = eslDSQ_SENTINEL;
if ((status = ((ad->ppline == NULL) ? p7_trace_Append(tr, p7T_S, 0, 0) : p7_trace_AppendWithPP(tr, p7T_S, 0, 0, 0.0))) != eslOK) goto ERROR;
if ((status = ((ad->ppline == NULL) ? p7_trace_Append(tr, p7T_N, 0, 0) : p7_trace_AppendWithPP(tr, p7T_N, 0, 0, 0.0))) != eslOK) goto ERROR;
if ((status = ((ad->ppline == NULL) ? p7_trace_Append(tr, p7T_B, 0, 0) : p7_trace_AppendWithPP(tr, p7T_B, 0, 0, 0.0))) != eslOK) goto ERROR;
k = ad->hmmfrom;
i = 1;
for (a = 0; a < ad->N; a++)
{
if (esl_abc_CIsResidue(abc, ad->model[a])) { st = (esl_abc_CIsResidue(abc, ad->aseq[a]) ? p7T_M : p7T_D); } else st = p7T_I;
if ((status = ((ad->ppline == NULL) ? p7_trace_Append(tr, st, k, i) : p7_trace_AppendWithPP(tr, st, k, i, p7_alidisplay_DecodePostProb(ad->ppline[a])))) != eslOK) goto ERROR;
switch (st) {
case p7T_M: sq->dsq[i] = esl_abc_DigitizeSymbol(abc, ad->aseq[a]); k++; i++; break;
case p7T_I: sq->dsq[i] = esl_abc_DigitizeSymbol(abc, ad->aseq[a]); i++; break;
case p7T_D: k++; break;
}
}
if ((status = ((ad->ppline == NULL) ? p7_trace_Append(tr, p7T_E, 0, 0) : p7_trace_AppendWithPP(tr, p7T_E, 0, 0, 0.0))) != eslOK) goto ERROR;
if ((status = ((ad->ppline == NULL) ? p7_trace_Append(tr, p7T_C, 0, 0) : p7_trace_AppendWithPP(tr, p7T_C, 0, 0, 0.0))) != eslOK) goto ERROR;
if ((status = ((ad->ppline == NULL) ? p7_trace_Append(tr, p7T_T, 0, 0) : p7_trace_AppendWithPP(tr, p7T_T, 0, 0, 0.0))) != eslOK) goto ERROR;
sq->dsq[i] = eslDSQ_SENTINEL;
/* some sanity checks */
if (tr->N != ad->N + 6) ESL_XEXCEPTION(eslECORRUPT, "backconverted trace ended up with unexpected size (%s/%s)", ad->sqname, ad->hmmname);
if (k != ad->hmmto + 1) ESL_XEXCEPTION(eslECORRUPT, "backconverted trace didn't end at expected place on model (%s/%s)", ad->sqname, ad->hmmname);
if (i != subL + 1) ESL_XEXCEPTION(eslECORRUPT, "backconverted subseq didn't end at expected length (%s/%s)", ad->sqname, ad->hmmname);
/* Set up <sq> annotation as a subseq of a source sequence */
if ((status = esl_sq_FormatName(sq, "%s/%ld-%ld", ad->sqname, ad->sqfrom, ad->sqto)) != eslOK) goto ERROR;
if ((status = esl_sq_FormatDesc(sq, "[subseq from] %s", ad->sqdesc[0] != '\0' ? ad->sqdesc : ad->sqname)) != eslOK) goto ERROR;
if ((status = esl_sq_SetSource (sq, ad->sqname)) != eslOK) goto ERROR;
if (ad->sqacc[0] != '\0') { if ((status = esl_sq_SetAccession (sq, ad->sqacc)) != eslOK) goto ERROR; }
sq->n = subL;
sq->start = ad->sqfrom;
sq->end = ad->sqto;
sq->C = 0;
sq->W = subL;
sq->L = ad->L;
tr->M = ad->M;
tr->L = ad->L;
*ret_sq = sq;
*ret_tr = tr;
return eslOK;
ERROR:
if (sq != NULL) esl_sq_Destroy(sq);
if (tr != NULL) p7_trace_Destroy(tr);
*ret_sq = NULL;
*ret_tr = NULL;
return status;
}
/* seq_shuffling()
* SRE, Tue Jan 22 08:35:51 2008 [Market Street Cafe, Leesburg]
*
* Shuffling of input sequences.
*
* Fixed-length (L>0) vs. full-length (L=0) modes handled differently.
* In fixed-length mode:
* <shuff->seq> only needs to be allocated once, for L
* <targ> is an allocated copy of a random subseq of length L
* sequences < L residues long can't be shuffled
* In full-length mode:
* <shuff->seq> is grown to length <sq->n> for each input seq
* <targ> just points to <sq->seq>
*/
static int
seq_shuffling(ESL_GETOPTS *go, ESL_RANDOMNESS *r, FILE *ofp, int outfmt)
{
char *seqfile = esl_opt_GetArg(go, 1);
int infmt = eslSQFILE_UNKNOWN;
ESL_SQFILE *sqfp = NULL;
ESL_SQ *sq = esl_sq_Create();
ESL_SQ *shuff = esl_sq_Create();
char *targ = NULL;
int N = esl_opt_GetInteger(go, "-N");
int L = esl_opt_GetInteger(go, "-L"); /* L>0 means select random fixed-len subseqs */
int kmers = 0;
int i;
int status;
if (esl_opt_GetString(go, "--informat") != NULL) {
infmt = esl_sqio_EncodeFormat(esl_opt_GetString(go, "--informat"));
if (infmt == eslSQFILE_UNKNOWN) esl_fatal("%s is not a valid input sequence file format for --informat");
}
if (esl_opt_IsOn(go, "-k")) kmers = esl_opt_GetInteger(go, "-k");
status = esl_sqfile_Open(seqfile, infmt, NULL, &sqfp);
if (status == eslENOTFOUND) esl_fatal("No such file %s", seqfile);
else if (status == eslEFORMAT) esl_fatal("Format of seqfile %s unrecognized.", seqfile);
else if (status == eslEINVAL) esl_fatal("Can't autodetect stdin or .gz.");
else if (status != eslOK) esl_fatal("Open failed, code %d.", status);
if (L>0) {
esl_sq_GrowTo(shuff, L);
shuff->n = L;
ESL_ALLOC(targ, sizeof(char) * (L+1));
}
while ((status = esl_sqio_Read(sqfp, sq)) == eslOK)
{
if (L == 0) { /* shuffling entire sequence */
esl_sq_GrowTo(shuff, sq->n); /* make sure shuff can hold sq */
shuff->n = sq->n;
targ = sq->seq;
} else {
if (sq->n < L) continue; /* reject seqs < L long */
}
for (i = 0; i < N; i++)
{
if (L > 0) { /* fixed-len mode: copy a random subseq */
int pos = esl_rnd_Roll(r, sq->n - L + 1);
strncpy(targ, sq->seq + pos, L);
targ[L] = '\0';
}
/* Do the requested kind of shuffling */
if (esl_opt_GetBoolean(go, "-m")) esl_rsq_CShuffle (r, targ, shuff->seq); /* monoresidue shuffling */
else if (esl_opt_GetBoolean(go, "-d")) esl_rsq_CShuffleDP (r, targ, shuff->seq); /* diresidue shuffling */
else if (esl_opt_IsOn (go, "-k")) esl_rsq_CShuffleKmers(r, targ, kmers, shuff->seq); /* diresidue shuffling */
else if (esl_opt_GetBoolean(go, "-0")) esl_rsq_CMarkov0 (r, targ, shuff->seq); /* 0th order Markov */
else if (esl_opt_GetBoolean(go, "-1")) esl_rsq_CMarkov1 (r, targ, shuff->seq); /* 1st order Markov */
else if (esl_opt_GetBoolean(go, "-r")) esl_rsq_CReverse ( targ, shuff->seq); /* reverse */
else if (esl_opt_IsOn (go, "-w")) { /* regionally shuffle */
int W= esl_opt_GetInteger(go, "-w"); esl_rsq_CShuffleWindows(r, targ, W, shuff->seq);
}
/* Set the name of the shuffled sequence */
if (N > 1) esl_sq_FormatName(shuff, "%s-shuffled-%d", sq->name, i);
else esl_sq_FormatName(shuff, "%s-shuffled", sq->name);
/* Output the resulting sequence */
esl_sqio_Write(ofp, shuff, outfmt, FALSE);
/* don't need to reuse the shuffled sequence: we will use exactly the same memory */
}
esl_sq_Reuse(sq);
}
if (status == eslEFORMAT) esl_fatal("Parse failed (sequence file %s):\n%s\n",
sqfp->filename, esl_sqfile_GetErrorBuf(sqfp));
else if (status != eslEOF) esl_fatal("Unexpected error %d reading sequence file %s",
status, sqfp->filename);
if (L>0) free(targ);
esl_sq_Destroy(shuff);
esl_sq_Destroy(sq);
esl_sqfile_Close(sqfp);
return eslOK;
ERROR:
if (targ != NULL) free(targ);
esl_sq_Destroy(shuff);
esl_sq_Destroy(sq);
esl_sqfile_Close(sqfp);
return status;
}
/* Each test sequence will contain one or two domains, depending on whether --single is set.
*/
static int
synthesize_positives(ESL_GETOPTS *go, struct cfg_s *cfg, char *testname, ESL_STACK *teststack, int *ret_ntest)
{
ESL_SQ *domain1, *domain2;
ESL_SQ *sq;
void *p;
int64_t L; /* total length of synthetic test seq */
int d1n, d2n; /* lengths of two domains */
int L1,L2,L3; /* lengths of three random regions */
int i,j;
int ntest = 0;
int ndomains = ( (esl_opt_GetBoolean(go, "--single") == TRUE) ? 1 : 2);
int status;
while (esl_stack_ObjectCount(teststack) >= ndomains)
{
ESL_RALLOC(cfg->test_lens, p, (cfg->ntest+1) * sizeof(struct testseq_s));
/* Pop our one or two test domains off the stack */
esl_stack_PPop(teststack, &p);
domain1 = p;
d1n = domain1->n;
if (ndomains == 2)
{
esl_stack_PPop(teststack, &p);
domain2 = p;
d2n = domain2->n;
}
else
{
domain2 = NULL;
d2n = 0;
}
/* Select a random total sequence length */
if (d1n+d2n > cfg->db_maxL) esl_fatal("can't construct test seq; no db seq >= %d residues\n", d1n+d2n);
do {
if (esl_ssi_FindNumber(cfg->dbfp->data.ascii.ssi, esl_rnd_Roll(cfg->r, cfg->db_nseq), NULL, NULL, NULL, &L, NULL) != eslOK)
esl_fatal("failed to look up a random seq");
} while (L < d1n+d2n);
/* Now figure out the embedding */
if (ndomains == 2)
{
/* Select random lengths of three flanking domains;
* Imagine picking two "insert after" points i,j in sequence 1..L', for
* L' = L-d1n-d2n (the total length of nonhomologous test seq)
*/
do {
i = esl_rnd_Roll(cfg->r, L - d1n - d2n + 1 ); /* i = 0..L' */
j = esl_rnd_Roll(cfg->r, L - d1n - d2n + 1 ); /* j = 0..L' */
} while (i > j);
/* now 1 .. i = random region 1 (if i==0, there's none);
* i+1 .. i+d1n = domain 1
* i+d1n+1 .. j+d1n = random region 2 (if i==j, there's none);
* j+d1n+1 .. j+d1n+d2n = domain 2
* j+d1n+d2n+1 .. L = random region 3 (if j == L-d1n-d2n, there's none);
*/
L1 = i;
L2 = j-i;
L3 = L - d1n - d2n - j;
}
else
{ /* embedding one domain */
i = esl_rnd_Roll(cfg->r, L - d1n + 1 ); /* i = 0..L' */
/* now 1 .. i = random region 1 (if i==0, there's none);
* i+1 .. i+d1n = domain 1
* i+d1n+1 .. L = random region 2 (if i==j, there's none);
*/
L1 = i;
L2 = L - d1n - L1;
L3 = 0;
}
sq = esl_sq_CreateDigital(cfg->abc);
esl_sq_GrowTo(sq, L);
sq->n = L;
if (ndomains == 2)
{
esl_sq_FormatName(sq, "%s/%d/%d-%d/%d-%d", testname, cfg->ntest, i+1, i+d1n, j+d1n+1, j+d1n+d2n);
esl_sq_FormatDesc(sq, "domains: %s %s", domain1->name, domain2->name);
}
else
{
esl_sq_FormatName(sq, "%s/%d/%d-%d", testname, cfg->ntest, i+1, i+d1n);
esl_sq_FormatDesc(sq, "domain: %s", domain1->name);
}
fprintf(cfg->possummfp, "%-35s %5d %5d %5d %5d %5d %5d", sq->name, (int) sq->n, L1, d1n, L2, d2n, L3);
sq->dsq[0] = sq->dsq[L+1] = eslDSQ_SENTINEL;
set_random_segment(go, cfg, cfg->possummfp, sq->dsq+1, L1);
memcpy(sq->dsq+i+1, domain1->dsq+1, sizeof(ESL_DSQ) * d1n);
fprintf(cfg->possummfp, " %-24s %5d %5d", domain1->name, 1, d1n);
set_random_segment(go, cfg, cfg->possummfp, sq->dsq+i+d1n+1, L2);
if (ndomains == 2)
{
memcpy(sq->dsq+j+d1n+1, domain2->dsq+1, sizeof(ESL_DSQ) * d2n);
fprintf(cfg->possummfp, " %-24s %5d %5d", domain2->name, 1, d2n);
set_random_segment(go, cfg, cfg->possummfp, sq->dsq+j+d1n+d2n+1, L3);
}
fprintf(cfg->possummfp, "\n");
cfg->test_lens[cfg->ntest].L = L;
cfg->test_lens[cfg->ntest].L1 = L1;
cfg->test_lens[cfg->ntest].d1n = d1n;
cfg->test_lens[cfg->ntest].L2 = L2;
cfg->test_lens[cfg->ntest].d2n = d2n;
cfg->test_lens[cfg->ntest].L3 = L3;
cfg->ntest++;
ntest++;
esl_sqio_Write(cfg->out_seqfp, sq, eslSQFILE_FASTA, FALSE);
esl_sq_Destroy(domain1);
if (ndomains == 2) esl_sq_Destroy(domain2);
esl_sq_Destroy(sq);
}
*ret_ntest = ntest;
return eslOK;
ERROR:
esl_fatal("Failure in synthesize_positives");
return status;
}
