int p7_hit_Compare(const P7_HIT *h1, const P7_HIT *h2, float tol) { int d; int status; if ( strcmp(h1->name, h2->name) != 0) return eslFAIL; if (esl_strcmp(h1->acc, h2->acc) != 0) return eslFAIL; if (esl_strcmp(h1->desc, h2->desc) != 0) return eslFAIL; if ( h1->window_length != h2->window_length) return eslFAIL; if ( h1->ndom != h2->ndom) return eslFAIL; if ( h1->noverlaps != h2->noverlaps) return eslFAIL; if ( h1->flags != h2->flags) return eslFAIL; if ( h1->nreported != h2->nreported) return eslFAIL; if ( h1->nincluded != h2->nincluded) return eslFAIL; if ( h1->best_domain != h2->best_domain) return eslFAIL; if ( h1->seqidx != h2->seqidx) return eslFAIL; if ( h1->subseq_start != h2->subseq_start) return eslFAIL; if ( h1->offset != h2->offset) return eslFAIL; if ( esl_DCompare( h1->sortkey, h2->sortkey, tol ) != eslOK) return eslFAIL; if ( esl_FCompare( h1->score, h2->score, tol ) != eslOK) return eslFAIL; if ( esl_FCompare( h1->pre_score, h2->pre_score, tol ) != eslOK) return eslFAIL; if ( esl_FCompare( h1->sum_score, h2->sum_score, tol ) != eslOK) return eslFAIL; if ( esl_DCompare( h1->lnP, h2->lnP, tol ) != eslOK) return eslFAIL; if ( esl_DCompare( h1->pre_lnP, h2->pre_lnP, tol ) != eslOK) return eslFAIL; if ( esl_DCompare( h1->sum_lnP, h2->sum_lnP, tol ) != eslOK) return eslFAIL; if ( esl_DCompare( h1->nexpected, h2->nexpected, tol ) != eslOK) return eslFAIL; for (d = 0; d < h1->ndom; d++) if (( status = p7_domain_Compare(&(h1->dcl[d]), &(h2->dcl[d]), tol)) != eslOK) return status; return eslOK; }
/* tests: * 1. each sampled trace must validate. * 2. each trace must be <= viterbi trace score * 3. in a large # of traces, one is "equal" to the viterbi trace score. * (this of course is stochastic; but it's true for the particular * choice of RNG seed used in tests here.) */ static void utest_stotrace(ESL_GETOPTS *go, ESL_RANDOMNESS *rng, ESL_ALPHABET *abc, P7_PROFILE *gm, P7_OPROFILE *om, ESL_DSQ *dsq, int L, int ntrace) { P7_GMX *gx = NULL; P7_OMX *ox = NULL; P7_TRACE *tr = NULL; char errbuf[eslERRBUFSIZE]; int idx; float maxsc = -eslINFINITY; float vsc, sc; if ((gx = p7_gmx_Create(gm->M, L)) == NULL) esl_fatal("generic DP matrix creation failed"); if ((ox = p7_omx_Create(gm->M, L, L)) == NULL) esl_fatal("optimized DP matrix create failed"); if ((tr = p7_trace_Create()) == NULL) esl_fatal("trace creation failed"); if (p7_GViterbi(dsq, L, gm, gx, &vsc) != eslOK) esl_fatal("viterbi failed"); if (p7_Forward (dsq, L, om, ox, NULL) != eslOK) esl_fatal("forward failed"); for (idx = 0; idx < ntrace; idx++) { if (p7_StochasticTrace(rng, dsq, L, om, ox, tr) != eslOK) esl_fatal("stochastic trace failed"); if (p7_trace_Validate(tr, abc, dsq, errbuf) != eslOK) esl_fatal("trace invalid:\n%s", errbuf); if (p7_trace_Score(tr, dsq, gm, &sc) != eslOK) esl_fatal("trace scoring failed"); maxsc = ESL_MAX(sc, maxsc); if (sc > vsc) esl_fatal("sampled trace has score > optimal Viterbi path; not possible"); p7_trace_Reuse(tr); } if (esl_FCompare(maxsc, vsc, 0.1) != eslOK) esl_fatal("stochastic trace failed to sample the Viterbi path"); p7_trace_Destroy(tr); p7_omx_Destroy(ox); p7_gmx_Destroy(gx); }
/* The "basic" utest is a minimal driver for making a small DNA profile and a small DNA sequence, * then running Viterbi and Forward. It's useful for dumping DP matrices and profiles for debugging. */ static void utest_basic(ESL_GETOPTS *go) { char *query= "# STOCKHOLM 1.0\n\nseq1 GAATTC\nseq2 GAATTC\n//\n"; int fmt = eslMSAFILE_STOCKHOLM; char *targ = "GAATTC"; ESL_ALPHABET *abc = NULL; ESL_MSA *msa = NULL; P7_HMM *hmm = NULL; P7_PROFILE *gm = NULL; P7_BG *bg = NULL; P7_PRIOR *pri = NULL; ESL_DSQ *dsq = NULL; P7_GMX *gx = NULL; P7_TRACE *tr = NULL; int L = strlen(targ); float vsc, vsc2, fsc; if ((abc = esl_alphabet_Create(eslDNA)) == NULL) esl_fatal("failed to create alphabet"); if ((pri = p7_prior_CreateNucleic()) == NULL) esl_fatal("failed to create prior"); if ((msa = esl_msa_CreateFromString(query, fmt)) == NULL) esl_fatal("failed to create MSA"); if (esl_msa_Digitize(abc, msa, NULL) != eslOK) esl_fatal("failed to digitize MSA"); if (p7_Fastmodelmaker(msa, 0.5, NULL, &hmm, NULL) != eslOK) esl_fatal("failed to create GAATTC model"); if (p7_ParameterEstimation(hmm, pri) != eslOK) esl_fatal("failed to parameterize GAATTC model"); if (p7_hmm_SetConsensus(hmm, NULL) != eslOK) esl_fatal("failed to make consensus"); if ((bg = p7_bg_Create(abc)) == NULL) esl_fatal("failed to create DNA null model"); if ((gm = p7_profile_Create(hmm->M, abc)) == NULL) esl_fatal("failed to create GAATTC profile"); if (p7_ProfileConfig(hmm, bg, gm, L, p7_UNILOCAL)!= eslOK) esl_fatal("failed to config profile"); if (p7_profile_Validate(gm, NULL, 0.0001) != eslOK) esl_fatal("whoops, profile is bad!"); if (esl_abc_CreateDsq(abc, targ, &dsq) != eslOK) esl_fatal("failed to create GAATTC digital sequence"); if ((gx = p7_gmx_Create(gm->M, L)) == NULL) esl_fatal("failed to create DP matrix"); if ((tr = p7_trace_Create()) == NULL) esl_fatal("trace creation failed"); p7_GViterbi (dsq, L, gm, gx, &vsc); if (esl_opt_GetBoolean(go, "-v")) printf("Viterbi score: %.4f\n", vsc); if (esl_opt_GetBoolean(go, "-v")) p7_gmx_Dump(stdout, gx, p7_DEFAULT); p7_GTrace (dsq, L, gm, gx, tr); p7_trace_Score(tr, dsq, gm, &vsc2); if (esl_opt_GetBoolean(go, "-v")) p7_trace_Dump(stdout, tr, gm, dsq); if (esl_FCompare(vsc, vsc2, 1e-5) != eslOK) esl_fatal("trace score and Viterbi score don't agree."); p7_GForward (dsq, L, gm, gx, &fsc); if (esl_opt_GetBoolean(go, "-v")) printf("Forward score: %.4f\n", fsc); if (esl_opt_GetBoolean(go, "-v")) p7_gmx_Dump(stdout, gx, p7_DEFAULT); p7_trace_Destroy(tr); p7_gmx_Destroy(gx); free(dsq); p7_profile_Destroy(gm); p7_bg_Destroy(bg); p7_hmm_Destroy(hmm); esl_msa_Destroy(msa); p7_prior_Destroy(pri); esl_alphabet_Destroy(abc); return; }
/* check_msa_weights * * Given an MSA, check if it has any weight that is * different from 1.0. If yes return TRUE, if not * return FALSE. If it does not have weights return * FALSE. */ static int check_msa_weights(ESL_MSA *msa) { int i; if(msa->wgt == NULL) return FALSE; for(i = 0; i < msa->nseq; i++) { if (esl_FCompare(msa->wgt[i], 1.0, eslSMALLX1) != eslOK) return TRUE; } return FALSE; }
/* Function: p7_gmx_Compare() * Synopsis: Compare two DP matrices for equality within given tolerance. * * Purpose: Compare all the values in DP matrices <gx1> and <gx2> using * <esl_FCompare()> and relative epsilon <tolerance>. If any * value pairs differ by more than the acceptable <tolerance> * return <eslFAIL>. If all value pairs are identical within * tolerance, return <eslOK>. */ int p7_gmx_Compare(P7_GMX *gx1, P7_GMX *gx2, float tolerance) { int i,k,x; if (gx1->M != gx2->M) return eslFAIL; if (gx1->L != gx2->L) return eslFAIL; for (i = 0; i <= gx1->L; i++) { for (k = 1; k <= gx1->M; k++) /* k=0 is a boundary; doesn't need to be checked */ { if (esl_FCompare(gx1->dp[i][k * p7G_NSCELLS + p7G_M], gx2->dp[i][k * p7G_NSCELLS + p7G_M], tolerance) != eslOK) return eslFAIL; if (esl_FCompare(gx1->dp[i][k * p7G_NSCELLS + p7G_I], gx2->dp[i][k * p7G_NSCELLS + p7G_I], tolerance) != eslOK) return eslFAIL; if (esl_FCompare(gx1->dp[i][k * p7G_NSCELLS + p7G_D], gx2->dp[i][k * p7G_NSCELLS + p7G_D], tolerance) != eslOK) return eslFAIL; } for (x = 0; x < p7G_NXCELLS; x++) if (esl_FCompare(gx1->xmx[i * p7G_NXCELLS + x], gx2->xmx[i * p7G_NXCELLS + x], tolerance) != eslOK) return eslFAIL; } return eslOK; }
/* Note that calculate_occupancy has moved to p7_hmm.c, but * unit tests over there aren't hooked up yet; so leave a copy of the unit test * here for now. */ static void utest_occupancy(P7_HMM *hmm) { char *msg = "modelconfig.c::calculate_occupancy() unit test failed"; float *occ; float x; occ = malloc(sizeof(float) * (hmm->M+1)); p7_hmm_CalculateOccupancy(hmm, occ, NULL); x = esl_vec_FSum(occ+1, hmm->M) / (float) hmm->M; if (esl_FCompare(x, 0.6, 0.1) != eslOK) esl_fatal(msg); free(occ); return; }
/* Viterbi validation is done by comparing the returned score * to the score of the optimal trace. Not foolproof, but catches * many kinds of errors. * * Another check is that the average score should be <= 0, * since the random sequences are drawn from the null model. */ static void utest_viterbi(ESL_GETOPTS *go, ESL_RANDOMNESS *r, ESL_ALPHABET *abc, P7_BG *bg, P7_PROFILE *gm, int nseq, int L) { float avg_sc = 0.; char errbuf[eslERRBUFSIZE]; ESL_DSQ *dsq = NULL; P7_GMX *gx = NULL; P7_TRACE *tr = NULL; int idx; float sc1, sc2; if ((dsq = malloc(sizeof(ESL_DSQ) *(L+2))) == NULL) esl_fatal("malloc failed"); if ((tr = p7_trace_Create()) == NULL) esl_fatal("trace creation failed"); if ((gx = p7_gmx_Create(gm->M, L)) == NULL) esl_fatal("matrix creation failed"); for (idx = 0; idx < nseq; idx++) { if (esl_rsq_xfIID(r, bg->f, abc->K, L, dsq) != eslOK) esl_fatal("seq generation failed"); if (p7_GViterbi(dsq, L, gm, gx, &sc1) != eslOK) esl_fatal("viterbi failed"); if (p7_GTrace (dsq, L, gm, gx, tr) != eslOK) esl_fatal("trace failed"); if (p7_trace_Validate(tr, abc, dsq, errbuf) != eslOK) esl_fatal("trace invalid:\n%s", errbuf); if (p7_trace_Score(tr, dsq, gm, &sc2) != eslOK) esl_fatal("trace score failed"); if (esl_FCompare(sc1, sc2, 1e-6) != eslOK) esl_fatal("Trace score != Viterbi score"); if (p7_bg_NullOne(bg, dsq, L, &sc2) != eslOK) esl_fatal("null score failed"); avg_sc += (sc1 - sc2); if (esl_opt_GetBoolean(go, "--vv")) printf("utest_viterbi: Viterbi score: %.4f (null %.4f) (total so far: %.4f)\n", sc1, sc2, avg_sc); p7_trace_Reuse(tr); } avg_sc /= (float) nseq; if (avg_sc > 0.) esl_fatal("Viterbi scores have positive expectation (%f nats)", avg_sc); p7_gmx_Destroy(gx); p7_trace_Destroy(tr); free(dsq); return; }
/* * 1. Compare accscore to GOptimalAccuracy(). * 2. Compare trace to GOATrace(). * * Note: This test is subject to some expected noise and can fail * for entirely innocent reasons. Generic Forward/Backward calculations with * p7_GForward(), p7_GBackward() use coarse-grain table lookups to sum * log probabilities, and sufficient roundoff error can accumulate to * change the optimal accuracy traceback, causing this test to fail. * So, if optacc_utest fails, before you go looking for bugs, first * go to ../logsum.c, change the #ifdef to activate the slow/accurate * version, recompile and rerun optacc_utest. If the failure goes away, * you can ignore it. - SRE, Wed Dec 17 09:45:31 2008 */ static void utest_optacc(ESL_GETOPTS *go, ESL_RANDOMNESS *r, ESL_ALPHABET *abc, P7_BG *bg, int M, int L, int N) { char *msg = "optimal accuracy unit test failed"; P7_HMM *hmm = NULL; P7_PROFILE *gm = NULL; P7_OPROFILE *om = NULL; ESL_SQ *sq = esl_sq_CreateDigital(abc); P7_OMX *ox1 = p7_omx_Create(M, L, L); P7_OMX *ox2 = p7_omx_Create(M, L, L); P7_GMX *gx1 = p7_gmx_Create(M, L); P7_GMX *gx2 = p7_gmx_Create(M, L); P7_TRACE *tr = p7_trace_CreateWithPP(); P7_TRACE *trg = p7_trace_CreateWithPP(); P7_TRACE *tro = p7_trace_CreateWithPP(); float accscore_o; float fsc, bsc, accscore; float fsc_g, bsc_g, accscore_g, accscore_g2; float pptol = 0.01; float sctol = 0.001; float gtol; p7_FLogsumInit(); gtol = ( (p7_FLogsumError(-0.4, -0.5) > 0.0001) ? 0.1 : 0.001); if (p7_oprofile_Sample(r, abc, bg, M, L, &hmm, &gm, &om)!= eslOK) esl_fatal(msg); while (N--) { if (p7_ProfileEmit(r, hmm, gm, bg, sq, tro) != eslOK) esl_fatal(msg); if (p7_omx_GrowTo(ox1, M, sq->n, sq->n) != eslOK) esl_fatal(msg); if (p7_omx_GrowTo(ox2, M, sq->n, sq->n) != eslOK) esl_fatal(msg); if (p7_gmx_GrowTo(gx1, M, sq->n) != eslOK) esl_fatal(msg); if (p7_gmx_GrowTo(gx2, M, sq->n) != eslOK) esl_fatal(msg); if (p7_Forward (sq->dsq, sq->n, om, ox1, &fsc) != eslOK) esl_fatal(msg); if (p7_Backward(sq->dsq, sq->n, om, ox1, ox2, &bsc) != eslOK) esl_fatal(msg); if (p7_Decoding(om, ox1, ox2, ox2) != eslOK) esl_fatal(msg); if (p7_OptimalAccuracy(om, ox2, ox1, &accscore) != eslOK) esl_fatal(msg); #if 0 p7_omx_FDeconvert(ox1, gx1); p7_gmx_Dump(stdout, gx1, p7_DEFAULT); p7_omx_FDeconvert(ox2, gx1); p7_gmx_Dump(stdout, gx1, p7_DEFAULT); #endif if (p7_OATrace(om, ox2, ox1, tr) != eslOK) esl_fatal(msg); if (p7_GForward (sq->dsq, sq->n, gm, gx1, &fsc_g) != eslOK) esl_fatal(msg); if (p7_GBackward(sq->dsq, sq->n, gm, gx2, &bsc_g) != eslOK) esl_fatal(msg); #if 0 p7_gmx_Dump(stdout, gx1, p7_DEFAULT); /* fwd */ p7_gmx_Dump(stdout, gx2, p7_DEFAULT); /* bck */ #endif if (p7_GDecoding(gm, gx1, gx2, gx2) != eslOK) esl_fatal(msg); if (p7_GOptimalAccuracy(gm, gx2, gx1, &accscore_g) != eslOK) esl_fatal(msg); #if 0 p7_gmx_Dump(stdout, gx1, p7_DEFAULT); /* oa */ p7_gmx_Dump(stdout, gx2, p7_DEFAULT); /* pp */ #endif if (p7_GOATrace(gm, gx2, gx1, trg) != eslOK) esl_fatal(msg); if (p7_trace_SetPP(tro, gx2) != eslOK) esl_fatal(msg); if (esl_opt_GetBoolean(go, "--traces")) { p7_trace_Dump(stdout, tro, gm, sq->dsq); p7_trace_Dump(stdout, tr, gm, sq->dsq); p7_trace_Dump(stdout, trg, gm, sq->dsq); } if (p7_trace_Validate(tr, abc, sq->dsq, NULL) != eslOK) esl_fatal(msg); if (p7_trace_Validate(trg, abc, sq->dsq, NULL) != eslOK) esl_fatal(msg); if (p7_trace_Compare(tr, trg, pptol) != eslOK) esl_fatal(msg); accscore_o = p7_trace_GetExpectedAccuracy(tro); /* according to gx2; see p7_trace_SetPP() call above */ accscore_g2 = p7_trace_GetExpectedAccuracy(trg); #if 0 printf("%f %f %f %f\n", accscore, accscore_g, accscore_g2, accscore_o); #endif if (esl_FCompare(fsc, bsc, sctol) != eslOK) esl_fatal(msg); if (esl_FCompare(fsc_g, bsc_g, gtol) != eslOK) esl_fatal(msg); if (esl_FCompare(fsc, fsc_g, gtol) != eslOK) esl_fatal(msg); if (esl_FCompare(accscore, accscore_g, gtol) != eslOK) esl_fatal(msg); if (esl_FCompare(accscore_g, accscore_g2, gtol) != eslOK) esl_fatal(msg); if (accscore_g2 < accscore_o) esl_fatal(msg); /* the above deserves explanation: * - accscore_o is the accuracy of the originally emitted trace, according * to the generic posterior decoding matrix <gx2>. This is a lower bound * on the expected # of accurately aligned residues found by a DP * optimization. * - accscore is the accuracy found by the fast (vector) code DP implementation. * - accscore_g is the accuracy found by the generic DP implementation. * accscore and accscore_g should be nearly identical, * within tolerance of roundoff error accumulation and * the imprecision of Logsum() tables. * - accscore_g2 is the accuracy of the traceback identified by the generic * DP implementation. It should be identical (within order-of-evaluation * roundoff error) to accscore_g. * * the "accscore_g2 < accscore_o" test is carefully contrived. * accscore_o is a theoretical lower bound but because of fp error, * accscore and (much more rarely) even accscore_g can exceed accscore_o. * accscore_g2, however, is calculated with identical order of evaluation * as accscore_o if the optimal trace does turn out to be identical to * the originally emitted trace. It should be extremely unlikely (though * not impossible) for accscore_o to exceed accscore_g2. (The DP algorithm * would have to identify a trace that was different than the original trace, * which the DP algorithm, by order-of-evaluation, assigned higher accuracy, * but order-of-evaluation in traceback dependent code assigned lower accuracy. * [xref J5/29] */ esl_sq_Reuse(sq); p7_trace_Reuse(tr); p7_trace_Reuse(trg); p7_trace_Reuse(tro); } p7_trace_Destroy(tro); p7_trace_Destroy(trg); p7_trace_Destroy(tr); p7_gmx_Destroy(gx2); p7_gmx_Destroy(gx1); p7_omx_Destroy(ox2); p7_omx_Destroy(ox1); esl_sq_Destroy(sq); p7_oprofile_Destroy(om); p7_profile_Destroy(gm); p7_hmm_Destroy(hmm); }
/* Function: p7_bg_Read() * Synopsis: Read background frequencies from a file. * * Purpose: Read new background frequencies from file <bgfile>, * overwriting the frequencies previously in the * <P7_BG> object <bg>. * * Note that <bg> is already created by the caller, not * created here. Also note that <p7_bg_Read()> only reads * residue background frequencies used for the "null * model", whereas a <P7_BG> object contains additional * information for the bias filter and for the biased * composition correction. * * Args: bgfile - file to read. * bg - existing <P7_BG> object provided by the caller. * errbuf - OPTIONAL: space for an error message, upon parse errors; or NULL. * * Returns: <eslOK> on success, and background frequencies in <bg> * are overwritten. * * <eslENOTFOUND> if <bgfile> can't be opened for reading. * <eslEFORMAT> if parsing of <bgfile> fails for some * reason. In both cases, <errbuf> contains a * user-directed error message upon return, including (if * relevant) the file name <bgfile> and the line number on * which an error was detected. <bg> is unmodified. * * Throws: <eslEMEM> on allocation failure; <bg> is unmodified, * and <errbuf> is empty. */ int p7_bg_Read(char *bgfile, P7_BG *bg, char *errbuf) { ESL_FILEPARSER *efp = NULL; float *fq = NULL; int n = 0; char *tok; int toklen; int alphatype; ESL_DSQ x; int status; if (errbuf) errbuf[0] = '\0'; status = esl_fileparser_Open(bgfile, NULL, &efp); if (status == eslENOTFOUND) ESL_XFAIL(eslENOTFOUND, errbuf, "couldn't open bg file %s for reading", bgfile); else if (status != eslOK) goto ERROR; esl_fileparser_SetCommentChar(efp, '#'); /* First token is alphabet type: amino | DNA | RNA */ status = esl_fileparser_GetToken(efp, &tok, &toklen); if (status == eslEOF) ESL_XFAIL(eslEFORMAT, errbuf, "premature end of file [line %d of bgfile %s]", efp->linenumber, bgfile); else if (status != eslOK) goto ERROR; alphatype = esl_abc_EncodeType(tok); if (alphatype == eslUNKNOWN) ESL_XFAIL(eslEFORMAT, errbuf, "expected alphabet type but saw \"%s\" [line %d of bgfile %s]", tok, efp->linenumber, bgfile); else if (alphatype != bg->abc->type) ESL_XFAIL(eslEFORMAT, errbuf, "bg file's alphabet is %s; expected %s [line %d, %s]", tok, esl_abc_DecodeType(bg->abc->type), efp->linenumber, bgfile); ESL_ALLOC(fq, sizeof(float) * bg->abc->K); esl_vec_FSet(fq, bg->abc->K, -1.0); while ((status = esl_fileparser_NextLine(efp)) == eslOK) { status = esl_fileparser_GetTokenOnLine(efp, &tok, &toklen); if (status == eslEOL) ESL_XFAIL(eslEFORMAT, errbuf, "premature end of file [line %d of bgfile %s", efp->linenumber, bgfile); else if (status != eslOK) goto ERROR; if (toklen != 1 || ! esl_abc_CIsCanonical(bg->abc, *tok)) ESL_XFAIL(eslEFORMAT, errbuf, "expected to parse a residue letter; saw %s [line %d of bgfile %s]", tok, efp->linenumber, bgfile); x = esl_abc_DigitizeSymbol(bg->abc, *tok); if (fq[x] != -1.0) ESL_XFAIL(eslEFORMAT, errbuf, "already parsed probability of %c [line %d of bgfile %s]", bg->abc->sym[x], efp->linenumber, bgfile); n++; status = esl_fileparser_GetTokenOnLine(efp, &tok, &toklen); if (status == eslEOL) ESL_XFAIL(eslEFORMAT, errbuf, "premature end of file, expected a probability [line %d of bgfile %s]", efp->linenumber, bgfile); else if (status != eslOK) goto ERROR; if (! esl_str_IsReal(tok)) ESL_XFAIL(eslEFORMAT, errbuf, "expected a probability, saw %s [line %d of bgfile %s]", tok, efp->linenumber, bgfile); fq[x] = atof(tok); status = esl_fileparser_GetTokenOnLine(efp, &tok, &toklen); if (status == eslOK) ESL_XFAIL(eslEFORMAT, errbuf, "extra unexpected data found [line %d of bgfile %s]", efp->linenumber, bgfile); else if (status != eslEOL) goto ERROR; } if (status != eslEOF) goto ERROR; if ( n != bg->abc->K) ESL_XFAIL(eslEFORMAT, errbuf, "expected %d residue frequencies, but found %d in bgfile %s", bg->abc->K, n, bgfile); if ( esl_FCompare(esl_vec_FSum(fq, bg->abc->K), 1.0, 0.001) != eslOK) ESL_XFAIL(eslEFORMAT, errbuf, "residue frequencies do not sum to 1.0 in bgfile %s", bgfile); /* all checking complete. no more error cases. overwrite bg with the new frequencies */ esl_vec_FNorm(fq, bg->abc->K); esl_vec_FCopy(fq, bg->abc->K, bg->f); free(fq); esl_fileparser_Close(efp); return eslOK; ERROR: if (fq) free(fq); if (efp) esl_fileparser_Close(efp); return status; }
/* "singlemulti" test. * * Use p7_modelsample_SinglePathedASC() to create a * profile/sequence/anchorset comparison that has only a single * possible path when anchor set constrained. Now the expected true * envelope(s) are known, from that single path, and we can compare. * * In order to guarantee only one possible path, while allowing * multiple domains, the profile is limited to glocal-only. * * We test: * 1. Trace and envelopes agree on number of domains. * 2. For each domain, oa==ia, ob==ib, and these coords * agree with the trace. * 3. In the case of a single domain (D=1), the envelope * score == the trace score. */ static void utest_singlemulti(ESL_RANDOMNESS *rng, int M, const ESL_ALPHABET *abc, int N) { char msg[] = "reference_envelopes singlemulti unit test failed"; P7_BG *bg = p7_bg_Create(abc); P7_HMM *hmm = NULL; P7_PROFILE *gm = NULL; ESL_DSQ *dsq = NULL; int L; P7_TRACE *gtr = NULL; P7_ANCHOR *anch = NULL; int D; P7_REFMX *afu = p7_refmx_Create(M, 20); P7_REFMX *afd = p7_refmx_Create(M, 20); P7_REFMX *apu = p7_refmx_Create(M, 20); P7_REFMX *apd = p7_refmx_Create(M, 20); P7_ENVELOPES *env = p7_envelopes_Create(); float gsc; float tol = 0.001; int idx; int d; for (idx = 0; idx < N; idx++) { if ( p7_modelsample_SinglePathedASC(rng, M, bg, &hmm, &gm, &dsq, &L, >r, &anch, &D, &gsc) != eslOK) esl_fatal(msg); if ( p7_ReferenceASCForward (dsq, L, gm, anch, D, afu, afd, NULL) != eslOK) esl_fatal(msg); if ( p7_ReferenceASCBackward(dsq, L, gm, anch, D, apu, apd, NULL) != eslOK) esl_fatal(msg); if ( p7_ReferenceASCDecoding(dsq, L, gm, anch, D, afu, afd, apu, apd, apu, apd) != eslOK) esl_fatal(msg); if ( p7_reference_Envelopes (dsq, L, gm, anch, D, apu, apd, afu, afd, env) != eslOK) esl_fatal(msg); /* Test 1. Domain #'s agree */ if (! (gtr->ndom == D && env->D == D)) esl_fatal(msg); /* Test 2. Envelope coords (and outer env coords) match trace. * (Beware, trace domains are numbered 0..D-1, env domains are 1..D ) */ for (d = 1; d <= D; d++) { if (! (env->arr[d].ia == gtr->sqfrom[d-1] && env->arr[d].ia == env->arr[d].oa)) esl_fatal(msg); if (! (env->arr[d].ib == gtr->sqto[d-1] && env->arr[d].ib == env->arr[d].ob)) esl_fatal(msg); } /* Test 3. If D == 1, envelope score == trace score. */ if (D == 1 && esl_FCompare(env->arr[1].env_sc, gsc, tol) != eslOK) esl_fatal(msg); p7_envelopes_Reuse(env); p7_refmx_Reuse(afu); p7_refmx_Reuse(afd); p7_refmx_Reuse(apu); p7_refmx_Reuse(apd); free(dsq); free(anch); p7_trace_Destroy(gtr); p7_hmm_Destroy(hmm); p7_profile_Destroy(gm); } p7_envelopes_Destroy(env); p7_refmx_Destroy(afu); p7_refmx_Destroy(afd); p7_refmx_Destroy(apu); p7_refmx_Destroy(apd); p7_bg_Destroy(bg); }
/* Function: p7_GTrace() * Incept: SRE, Thu Feb 1 10:25:56 2007 [UA 8018 St. Louis to Dulles] * * Purpose: Traceback of a Viterbi matrix: retrieval * of optimum alignment. * * This function is currently implemented as a * reconstruction traceback, rather than using a shadow * matrix. Because H3 uses floating point scores, and we * can't compare floats for equality, we have to compare * floats for near-equality and therefore, formally, we can * only guarantee a near-optimal traceback. However, even in * the unlikely event that a suboptimal is returned, the * score difference from true optimal will be negligible. * * Args: dsq - digital sequence aligned to, 1..L * L - length of <dsq> * gm - profile * mx - Viterbi matrix to trace, L x M * tr - storage for the recovered traceback. * * Return: <eslOK> on success. * <eslFAIL> if even the optimal path has zero probability; * in this case, the trace is set blank (<tr->N = 0>). * * Note: Care is taken to evaluate the prev+tsc+emission * calculations in exactly the same order that Viterbi did * them, lest you get numerical problems with * a+b+c = d; d-c != a+b because d,c are nearly equal. * (This bug appeared in dev: xref J1/121.) */ int p7_GTrace(const ESL_DSQ *dsq, int L, const P7_PROFILE *gm, const P7_GMX *gx, P7_TRACE *tr) { int i = L; /* position in seq (1..L) */ int k = 0; /* position in model (1..M) */ int M = gm->M; float **dp = gx->dp; /* so {MDI}MX() macros work */ float *xmx = gx->xmx; /* so XMX() macro works */ float tol = 1e-5; /* floating point "equality" test */ float const *tsc = gm->tsc; int sprv, scur; /* previous, current state in trace */ int status; #ifdef p7_DEBUGGING if (tr->N != 0) ESL_EXCEPTION(eslEINVAL, "trace isn't empty: forgot to Reuse()?"); #endif if ((status = p7_trace_Append(tr, p7T_T, k, i)) != eslOK) return status; if ((status = p7_trace_Append(tr, p7T_C, k, i)) != eslOK) return status; sprv = p7T_C; while (sprv != p7T_S) { float const *rsc = (i>0 ? gm->rsc[dsq[i]] : NULL); switch (sprv) { case p7T_C: /* C(i) comes from C(i-1) or E(i) */ if (XMX(i,p7G_C) == -eslINFINITY) ESL_EXCEPTION(eslFAIL, "impossible C reached at i=%d", i); if (esl_FCompare(XMX(i, p7G_C), XMX(i-1, p7G_C) + gm->xsc[p7P_C][p7P_LOOP], tol) == eslOK) scur = p7T_C; else if (esl_FCompare(XMX(i, p7G_C), XMX(i, p7G_E) + gm->xsc[p7P_E][p7P_MOVE], tol) == eslOK) scur = p7T_E; else ESL_EXCEPTION(eslFAIL, "C at i=%d couldn't be traced", i); break; case p7T_E: /* E connects from any M state. k set here */ if (XMX(i, p7G_E) == -eslINFINITY) ESL_EXCEPTION(eslFAIL, "impossible E reached at i=%d", i); if (p7_profile_IsLocal(gm)) { scur = p7T_M; /* can't come from D, in a *local* Viterbi trace. */ for (k = M; k >= 1; k--) if (esl_FCompare(XMX(i, p7G_E), MMX(i,k), tol) == eslOK) break; if (k == 0) ESL_EXCEPTION(eslFAIL, "E at i=%d couldn't be traced", i); } else /* glocal mode: we either come from D_M or M_M */ { if (esl_FCompare(XMX(i, p7G_E), MMX(i,M), tol) == eslOK) { scur = p7T_M; k = M; } else if (esl_FCompare(XMX(i, p7G_E), DMX(i,M), tol) == eslOK) { scur = p7T_D; k = M; } else ESL_EXCEPTION(eslFAIL, "E at i=%d couldn't be traced", i); } break; case p7T_M: /* M connects from i-1,k-1, or B */ if (MMX(i,k) == -eslINFINITY) ESL_EXCEPTION(eslFAIL, "impossible M reached at k=%d,i=%d", k,i); if (esl_FCompare(MMX(i,k), XMX(i-1,p7G_B) + TSC(p7P_BM, k-1) + MSC(k), tol) == eslOK) scur = p7T_B; else if (esl_FCompare(MMX(i,k), MMX(i-1,k-1) + TSC(p7P_MM, k-1) + MSC(k), tol) == eslOK) scur = p7T_M; else if (esl_FCompare(MMX(i,k), IMX(i-1,k-1) + TSC(p7P_IM, k-1) + MSC(k), tol) == eslOK) scur = p7T_I; else if (esl_FCompare(MMX(i,k), DMX(i-1,k-1) + TSC(p7P_DM, k-1) + MSC(k), tol) == eslOK) scur = p7T_D; else ESL_EXCEPTION(eslFAIL, "M at k=%d,i=%d couldn't be traced", k,i); k--; i--; break; case p7T_D: /* D connects from M,D at i,k-1 */ if (DMX(i, k) == -eslINFINITY) ESL_EXCEPTION(eslFAIL, "impossible D reached at k=%d,i=%d", k,i); if (esl_FCompare(DMX(i,k), MMX(i, k-1) + TSC(p7P_MD, k-1), tol) == eslOK) scur = p7T_M; else if (esl_FCompare(DMX(i,k), DMX(i, k-1) + TSC(p7P_DD, k-1), tol) == eslOK) scur = p7T_D; else ESL_EXCEPTION(eslFAIL, "D at k=%d,i=%d couldn't be traced", k,i); k--; break; case p7T_I: /* I connects from M,I at i-1,k*/ if (IMX(i,k) == -eslINFINITY) ESL_EXCEPTION(eslFAIL, "impossible I reached at k=%d,i=%d", k,i); if (esl_FCompare(IMX(i,k), MMX(i-1,k) + TSC(p7P_MI, k) + ISC(k), tol) == eslOK) scur = p7T_M; else if (esl_FCompare(IMX(i,k), IMX(i-1,k) + TSC(p7P_II, k) + ISC(k), tol) == eslOK) scur = p7T_I; else ESL_EXCEPTION(eslFAIL, "I at k=%d,i=%d couldn't be traced", k,i); i--; break; case p7T_N: /* N connects from S, N */ if (XMX(i, p7G_N) == -eslINFINITY) ESL_EXCEPTION(eslFAIL, "impossible N reached at i=%d", i); scur = ( (i == 0) ? p7T_S : p7T_N); break; case p7T_B: /* B connects from N, J */ if (XMX(i,p7G_B) == -eslINFINITY) ESL_EXCEPTION(eslFAIL, "impossible B reached at i=%d", i); if (esl_FCompare(XMX(i,p7G_B), XMX(i, p7G_N) + gm->xsc[p7P_N][p7P_MOVE], tol) == eslOK) scur = p7T_N; else if (esl_FCompare(XMX(i,p7G_B), XMX(i, p7G_J) + gm->xsc[p7P_J][p7P_MOVE], tol) == eslOK) scur = p7T_J; else ESL_EXCEPTION(eslFAIL, "B at i=%d couldn't be traced", i); break; case p7T_J: /* J connects from E(i) or J(i-1) */ if (XMX(i,p7G_J) == -eslINFINITY) ESL_EXCEPTION(eslFAIL, "impossible J reached at i=%d", i); if (esl_FCompare(XMX(i,p7G_J), XMX(i-1,p7G_J) + gm->xsc[p7P_J][p7P_LOOP], tol) == eslOK) scur = p7T_J; else if (esl_FCompare(XMX(i,p7G_J), XMX(i, p7G_E) + gm->xsc[p7P_E][p7P_LOOP], tol) == eslOK) scur = p7T_E; else ESL_EXCEPTION(eslFAIL, "J at i=%d couldn't be traced", i); break; default: ESL_EXCEPTION(eslFAIL, "bogus state in traceback"); } /* end switch over statetype[tpos-1] */ /* Append this state and the current i,k to be explained to the growing trace */ if ((status = p7_trace_Append(tr, scur, k, i)) != eslOK) return status; /* For NCJ, we had to defer i decrement. */ if ( (scur == p7T_N || scur == p7T_J || scur == p7T_C) && scur == sprv) i--; sprv = scur; } /* end traceback, at S state */ tr->M = gm->M; tr->L = L; return p7_trace_Reverse(tr); }