/* Step 2. Extract the training set and test set.
*/
static int
separate_sets(struct cfg_s *cfg, ESL_MSA *msa, ESL_MSA **ret_trainmsa, ESL_STACK **ret_teststack)
{
ESL_MSA *trainmsa = NULL;
ESL_MSA *test_msa = NULL;
ESL_STACK *teststack = NULL;
ESL_SQ *sq = NULL;
int *assignment = NULL;
int *nin = NULL;
int *useme = NULL;
int nc = 0;
int c;
int ctrain; /* index of the cluster that becomes the training alignment */
int ntrain; /* number of seqs in the training alignment */
int nskip;
int i;
int status;
if ((teststack = esl_stack_PCreate()) == NULL) { status = eslEMEM; goto ERROR; }
ESL_ALLOC(useme, sizeof(int) * msa->nseq);
if ((status = esl_msacluster_SingleLinkage(msa, cfg->idthresh1, &assignment, &nin, &nc)) != eslOK) goto ERROR;
ctrain = esl_vec_IArgMax(nin, nc);
ntrain = esl_vec_IMax(nin, nc);
for (i = 0; i < msa->nseq; i++) useme[i] = (assignment[i] == ctrain) ? 1 : 0;
if ((status = esl_msa_SequenceSubset(msa, useme, &trainmsa)) != eslOK) goto ERROR;
/* If all the seqs went into the training msa, none are left for testing; we're done here */
if (trainmsa->nseq == msa->nseq) {
free(useme);
free(assignment);
free(nin);
*ret_trainmsa = trainmsa;
*ret_teststack = teststack;
return eslOK;
}
/* Put all the other sequences into an MSA of their own; from these, we'll
* choose test sequences.
*/
for (i = 0; i < msa->nseq; i++) useme[i] = (assignment[i] != ctrain) ? 1 : 0;
if ((status = esl_msa_SequenceSubset(msa, useme, &test_msa)) != eslOK) goto ERROR;
/* Cluster those test sequences. */
free(nin); nin = NULL;
free(assignment); assignment = NULL;
if ((status = esl_msacluster_SingleLinkage(test_msa, cfg->idthresh2, &assignment, &nin, &nc)) != eslOK) goto ERROR;
for (c = 0; c < nc; c++)
{
nskip = esl_rnd_Roll(cfg->r, nin[c]); /* pick a random seq in this cluster to be the test. */
for (i=0; i < test_msa->nseq; i++)
if (assignment[i] == c) {
if (nskip == 0) {
esl_sq_FetchFromMSA(test_msa, i, &sq);
esl_stack_PPush(teststack, (void *) sq);
break;
} else nskip--;
}
}
esl_msa_Destroy(test_msa);
free(useme);
free(nin);
free(assignment);
*ret_trainmsa = trainmsa;
*ret_teststack = teststack;
return eslOK;
ERROR:
if (useme != NULL) free(useme);
if (assignment != NULL) free(assignment);
if (nin != NULL) free(nin);
esl_msa_Destroy(trainmsa);
esl_msa_Destroy(test_msa);
while (esl_stack_PPop(teststack, (void **) &sq) == eslOK) esl_sq_Destroy(sq);
esl_stack_Destroy(teststack);
*ret_trainmsa = NULL;
*ret_teststack = NULL;
return status;
}
static int
map_alignment(const char *msafile, const P7_HMM *hmm, ESL_SQ ***ret_sq, P7_TRACE ***ret_tr, int *ret_ntot)
{
ESL_SQ **sq = NULL;
P7_TRACE **tr = NULL;
ESLX_MSAFILE *afp = NULL;
ESL_MSA *msa = NULL;
ESL_ALPHABET *abc = (ESL_ALPHABET *) hmm->abc; /* removing const'ness to make compiler happy. Safe. */
int *matassign = NULL;
uint32_t chksum = 0;
int i,k;
int status;
status = eslx_msafile_Open(&abc, msafile, NULL, eslMSAFILE_UNKNOWN, NULL, &afp);
if (status != eslOK) eslx_msafile_OpenFailure(afp, status);
status = eslx_msafile_Read(afp, &msa);
if (status != eslOK) eslx_msafile_ReadFailure(afp, status);
if (! (hmm->flags & p7H_CHKSUM) ) esl_fatal("HMM has no checksum. --mapali unreliable without it.");
if (! (hmm->flags & p7H_MAP) ) esl_fatal("HMM has no map. --mapali can't work without it.");
esl_msa_Checksum(msa, &chksum);
if (hmm->checksum != chksum) esl_fatal("--mapali MSA %s isn't same as the one HMM came from (checksum mismatch)", msafile);
ESL_ALLOC(sq, sizeof(ESL_SQ *) * msa->nseq);
ESL_ALLOC(tr, sizeof(P7_TRACE *) * msa->nseq);
ESL_ALLOC(matassign, sizeof(int) * (msa->alen + 1));
esl_vec_ISet(matassign, msa->alen+1, 0);
for (k = 1; k <= hmm->M; k++) matassign[hmm->map[k]] = 1;
p7_trace_FauxFromMSA(msa, matassign, p7_DEFAULT, tr);
/* The 'faux' core traces constructed by FauxFromMSA() may contain
* D->I and I->D transitions. They may *only* now be passed to
* p7_tracealign_Seqs(), which can deal with these 'illegal'
* transitions, in order to exactly reproduce the input --mapali
* alignment.
*/
for (i = 0; i < msa->nseq; i++)
esl_sq_FetchFromMSA(msa, i, &(sq[i]));
*ret_ntot = msa->nseq;
*ret_tr = tr;
*ret_sq = sq;
eslx_msafile_Close(afp);
esl_msa_Destroy(msa);
free(matassign);
return eslOK;
ERROR:
*ret_ntot = 0;
*ret_tr = NULL;
*ret_sq = NULL;
if (afp != NULL) eslx_msafile_Close(afp);
if (msa != NULL) esl_msa_Destroy(msa);
if (matassign != NULL) free(matassign);
return status;
}
