| /dports/biology/hmmer/hmmer-3.3/src/ |
| H A D | p7_hmmfile.c | 563 p7_hmmfile_WriteASCII(FILE *fp, int format, P7_HMM *hmm) in p7_hmmfile_WriteASCII()
1029 p7_hmmfile_WriteBinary(FILE *fp, int format, P7_HMM *hmm) in p7_hmmfile_WriteBinary()
1296 P7_HMM *hmm = NULL; in read_asc30hmm() local
1635 P7_HMM *hmm = NULL; in read_bin30hmm() local
1756 P7_HMM *hmm = NULL; in read_asc20hmm() local
2286 P7_HMM *hmm = NULL; in main() local
2361 utest_io_30(char *tmpfile, int format, P7_HMM *hmm) in utest_io_30()
2413 utest_io_current(char *tmpfile, P7_HMM *hmm) in utest_io_current()
2426 utest_io_3a(char *tmpfile, P7_HMM *hmm) in utest_io_3a()
2476 P7_HMM *hmm = NULL; in main() local
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| H A D | eweight.c | 18 const P7_HMM *hmm; /* ptr to the original count-based HMM, which remains unchanged */ member
61 p7_EntropyWeight(const P7_HMM *hmm, const P7_BG *bg, const P7_PRIOR *pri, double etarget, double *r… in p7_EntropyWeight()
142 p7_EntropyWeight_exp(const P7_HMM *hmm, const P7_BG *bg, const P7_PRIOR *pri, double etarget, doubl… in p7_EntropyWeight_exp()
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| H A D | build.c | 261 P7_HMM *hmm = NULL; /* RETURN: new hmm */ in matassign2hmm() local
339 annotate_model(P7_HMM *hmm, int *matassign, ESL_MSA *msa) in annotate_model()
418 P7_HMM *hmm = NULL; in utest_basic() local
462 P7_HMM *hmm = NULL; in utest_fragments() local
587 P7_HMM *hmm = NULL; in main() local
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| H A D | modelconfig.c | 48 p7_ProfileConfig(const P7_HMM *hmm, const P7_BG *bg, P7_PROFILE *gm, int L, int mode) in p7_ProfileConfig()
294 utest_Config(P7_HMM *hmm, P7_BG *bg) in utest_Config()
312 utest_occupancy(P7_HMM *hmm) in utest_occupancy()
348 P7_HMM *hmm = NULL; in main() local
420 P7_HMM *hmm = NULL; /* sampled HMM to emit from */ in main() local
642 ideal_local_endpoints(ESL_RANDOMNESS *r, P7_HMM *hmm, ESL_SQ *sq, P7_TRACE *tr, int Lbins, in ideal_local_endpoints()
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| H A D | hmmfetch.c | 163 P7_HMM *hmm = NULL; in create_ssi_index() local
238 P7_HMM *hmm = NULL; in multifetch() local
298 P7_HMM *hmm = NULL; in onefetch() local
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| /dports/biology/seqan1/seqan-1.3.1/seqan/graph_algorithms/ |
| H A D | graph_algorithm_hmm.h | 63 viterbiAlgorithm(Graph<Hmm<TAlphabet, TProbability, TSpec> > const& hmm, in viterbiAlgorithm()
226 _forwardAlgorithm(Graph<Hmm<TAlphabet, TProbability, TSpec> > const& hmm, in _forwardAlgorithm()
334 forwardAlgorithm(Graph<Hmm<TAlphabet, TProbability, TSpec> > const& hmm, in forwardAlgorithm()
527 generateSequence(Graph<Hmm<TAlphabet, TProbability, TSpec> > const& hmm, in generateSequence()
623 _parameterEstimator(Graph<Hmm<TAlphabet, TProbability, TSpec> >& hmm, in _parameterEstimator()
660 estimationWithStates(Graph<Hmm<TAlphabet, TProbability, TSpec> >& hmm, in estimationWithStates()
721 _fillHmmUniform(Graph<Hmm<TAlphabet, TProbability, TSpec> >& hmm) in _fillHmmUniform()
750 _fillHmmRandom(Graph<Hmm<TAlphabet, TProbability, TSpec> >& hmm, in _fillHmmRandom()
796 randomizeHmm(Graph<Hmm<TAlphabet, TProbability, TSpec> >& hmm, in randomizeHmm()
807 _baumWelchAlgorithm(Graph<Hmm<TAlphabet, TProbability, TSpec > >& hmm, in _baumWelchAlgorithm()
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| /dports/biology/seqan/seqan-library-2.4.0/include/seqan/graph_algorithms/ |
| H A D | graph_algorithm_hmm.h | 91 viterbiAlgorithm(TPath & path, in viterbiAlgorithm()
254 _forwardAlgorithm(Graph<Hmm<TAlphabet, TProbability, TSpec> > const& hmm, in _forwardAlgorithm()
367 forwardAlgorithm(Graph<Hmm<TAlphabet, TProbability, TSpec> > const & hmm, in forwardAlgorithm()
562 void generateSequence(TSequenceSet & sequences, in generateSequence()
654 _parameterEstimator(Graph<Hmm<TAlphabet, TProbability, TSpec> >& hmm, in _parameterEstimator()
688 estimationWithStates(Graph<Hmm<TAlphabet, TProbability, TSpec> >& hmm, in estimationWithStates()
748 _fillHmmUniform(Graph<Hmm<TAlphabet, TProbability, TSpec> >& hmm) in _fillHmmUniform()
774 _fillHmmRandom(Graph<Hmm<TAlphabet, TProbability, TSpec> >& hmm, in _fillHmmRandom()
817 randomizeHmm(Graph<Hmm<TAlphabet, TProbability, TSpec> >& hmm, in randomizeHmm()
827 _baumWelchAlgorithm(Graph<Hmm<TAlphabet, TProbability, TSpec > >& hmm, in _baumWelchAlgorithm()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/ |
| H A D | graph_algorithm_hmm.h | 91 viterbiAlgorithm(TPath & path, in viterbiAlgorithm()
254 _forwardAlgorithm(Graph<Hmm<TAlphabet, TProbability, TSpec> > const& hmm, in _forwardAlgorithm()
367 forwardAlgorithm(Graph<Hmm<TAlphabet, TProbability, TSpec> > const & hmm, in forwardAlgorithm()
562 void generateSequence(TSequenceSet & sequences, in generateSequence()
654 _parameterEstimator(Graph<Hmm<TAlphabet, TProbability, TSpec> >& hmm, in _parameterEstimator()
688 estimationWithStates(Graph<Hmm<TAlphabet, TProbability, TSpec> >& hmm, in estimationWithStates()
748 _fillHmmUniform(Graph<Hmm<TAlphabet, TProbability, TSpec> >& hmm) in _fillHmmUniform()
774 _fillHmmRandom(Graph<Hmm<TAlphabet, TProbability, TSpec> >& hmm, in _fillHmmRandom()
817 randomizeHmm(Graph<Hmm<TAlphabet, TProbability, TSpec> >& hmm, in randomizeHmm()
827 _baumWelchAlgorithm(Graph<Hmm<TAlphabet, TProbability, TSpec > >& hmm, in _baumWelchAlgorithm()
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| /dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/graph_algorithms/ |
| H A D | graph_algorithm_hmm.h | 91 viterbiAlgorithm(TPath & path, in viterbiAlgorithm()
254 _forwardAlgorithm(Graph<Hmm<TAlphabet, TProbability, TSpec> > const& hmm, in _forwardAlgorithm()
368 forwardAlgorithm(Graph<Hmm<TAlphabet, TProbability, TSpec> > const & hmm, in forwardAlgorithm()
566 void generateSequence(TSequenceSet & sequences, in generateSequence()
660 _parameterEstimator(Graph<Hmm<TAlphabet, TProbability, TSpec> >& hmm, in _parameterEstimator()
694 estimationWithStates(Graph<Hmm<TAlphabet, TProbability, TSpec> >& hmm, in estimationWithStates()
754 _fillHmmUniform(Graph<Hmm<TAlphabet, TProbability, TSpec> >& hmm) in _fillHmmUniform()
781 _fillHmmRandom(Graph<Hmm<TAlphabet, TProbability, TSpec> >& hmm, in _fillHmmRandom()
825 randomizeHmm(Graph<Hmm<TAlphabet, TProbability, TSpec> >& hmm, in randomizeHmm()
835 _baumWelchAlgorithm(Graph<Hmm<TAlphabet, TProbability, TSpec > >& hmm, in _baumWelchAlgorithm()
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| /dports/www/firefox-legacy/firefox-52.8.0esr/media/pocketsphinx/src/ |
| H A D | phone_loop_search.c | 172 hmm_t *hmm = (hmm_t *)&pls->hmms[i]; in phone_loop_search_start() local
210 hmm_t *hmm = (hmm_t *)&pls->hmms[i]; in evaluate_hmms() local
229 hmm_t *hmm = (hmm_t *)&pls->hmms[i]; in store_scores() local
255 hmm_t *hmm = (hmm_t *)&pls->hmms[i]; in prune_hmms() local
278 hmm_t *hmm = (hmm_t *)&pls->hmms[i]; in phone_transition() local
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| H A D | kws_search.c | 53 #define hmm_is_active(hmm) ((hmm)->frame > 0) argument
212 hmm_t *hmm = &kwss->pl_hmms[i]; in kws_search_hmm_eval() local
223 hmm_t *hmm = kws_nth_hmm(keyword, i); in kws_search_hmm_eval() local
251 hmm_t *hmm = kws_nth_hmm(keyword, i); in kws_search_hmm_prune() local
329 hmm_t *hmm = kws_nth_hmm(keyword, i); in kws_search_trans() local
590 hmm_t *hmm = (hmm_t *) & kwss->pl_hmms[i]; in kws_search_start() local
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| /dports/audio/sphinx3/sphinx3-0.8/src/libs3decoder/libsearch/ |
| H A D | fsg_search.c | 430 hmm_sen_active(hmm_t * hmm, ascr_t * a, mdef_t * m) in hmm_sen_active()
455 hmm_t *hmm; in fsg_search_sen_active() local
480 hmm_t *hmm; in fsg_search_hmm_eval() local
520 hmm_t *hmm; in fsg_search_pnode_trans() local
542 hmm_t *hmm; in fsg_search_pnode_exit() local
609 hmm_t *hmm; in fsg_search_hmm_prune_prop() local
777 hmm_t *hmm; in fsg_search_frame_fwd() local
1036 hmm_t *hmm; in fsg_search_utt_end() local
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| /dports/biology/infernal/infernal-1.1.3/hmmer/src/ |
| H A D | eweight.c | 18 const P7_HMM *hmm; /* ptr to the original count-based HMM, which remains unchanged */ member
61 p7_EntropyWeight(const P7_HMM *hmm, const P7_BG *bg, const P7_PRIOR *pri, double etarget, double *r… in p7_EntropyWeight()
142 p7_EntropyWeight_exp(const P7_HMM *hmm, const P7_BG *bg, const P7_PRIOR *pri, double etarget, doubl… in p7_EntropyWeight_exp()
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| H A D | build.c | 261 P7_HMM *hmm = NULL; /* RETURN: new hmm */ in matassign2hmm() local
339 annotate_model(P7_HMM *hmm, int *matassign, ESL_MSA *msa) in annotate_model()
418 P7_HMM *hmm = NULL; in utest_basic() local
462 P7_HMM *hmm = NULL; in utest_fragments() local
587 P7_HMM *hmm = NULL; in main() local
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| H A D | modelconfig.c | 48 p7_ProfileConfig(const P7_HMM *hmm, const P7_BG *bg, P7_PROFILE *gm, int L, int mode) in p7_ProfileConfig()
294 utest_Config(P7_HMM *hmm, P7_BG *bg) in utest_Config()
312 utest_occupancy(P7_HMM *hmm) in utest_occupancy()
348 P7_HMM *hmm = NULL; in main() local
420 P7_HMM *hmm = NULL; /* sampled HMM to emit from */ in main() local
642 ideal_local_endpoints(ESL_RANDOMNESS *r, P7_HMM *hmm, ESL_SQ *sq, P7_TRACE *tr, int Lbins, in ideal_local_endpoints()
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| H A D | hmmfetch.c | 163 P7_HMM *hmm = NULL; in create_ssi_index() local
238 P7_HMM *hmm = NULL; in multifetch() local
298 P7_HMM *hmm = NULL; in onefetch() local
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| /dports/biology/vt/vt-0.57721/ |
| H A D | align.cpp | 177 CHMM hmm(debug); in align() local
216 LFHMM hmm(debug); in align() local
254 RFHMM hmm(debug); in align() local
291 RFHMM_X hmm(debug); in align() local
317 AHMM hmm(debug); in align() local
376 WDP_AHMM hmm(debug); in align() local
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| /dports/biology/wise/wise2.4.1/src/HMMer2/ |
| H A D | hmmbuild.c | 140 struct plan7_s *hmm; /* constructed HMM; written to hmmfile */ in main() local
548 save_model(struct plan7_s *hmm, char *hmmfile, int do_append, int do_binary) in save_model()
614 print_all_scores(FILE *fp, struct plan7_s *hmm, in print_all_scores()
655 save_countvectors(char *cfile, struct plan7_s *hmm) in save_countvectors()
717 position_average_score(struct plan7_s *hmm, in position_average_score()
798 frag_trace_score(struct plan7_s *hmm, char *dsq, struct p7trace_s *tr, in frag_trace_score()
853 maximum_entropy(struct plan7_s *hmm, char **dsq, AINFO *ainfo, int nseq, in maximum_entropy()
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| H A D | core_algorithms.c | 191 P7Forward(char *dsq, int L, struct plan7_s *hmm, struct dpmatrix_s **ret_mx) in P7Forward()
286 P7Viterbi(char *dsq, int L, struct plan7_s *hmm, struct p7trace_s **ret_tr) in P7Viterbi()
413 P7ViterbiTrace(struct plan7_s *hmm, char *dsq, int N, in P7ViterbiTrace()
669 P7SmallViterbi(char *dsq, int L, struct plan7_s *hmm, struct p7trace_s **ret_tr) in P7SmallViterbi()
836 P7ParsingViterbi(char *dsq, int L, struct plan7_s *hmm, struct p7trace_s **ret_tr) in P7ParsingViterbi()
1035 P7WeeViterbi(char *dsq, int L, struct plan7_s *hmm, struct p7trace_s **ret_tr) in P7WeeViterbi()
1251 Plan7ESTViterbi(char *dsq, int L, struct plan7_s *hmm, struct dpmatrix_s **ret_mx) in Plan7ESTViterbi()
1421 get_wee_midpt(struct plan7_s *hmm, char *dsq, int L, in get_wee_midpt()
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| /dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/hmm2/src/u_calibrate/ |
| H A D | uhmmcalibrate.cpp | 27 void UHMMCalibrate::calibrate(plan7_s* hmm, const UHMMCalibrateSettings& s, TaskStateInfo& si) { in calibrate()
70 static void main_loop_serial(struct plan7_s *hmm, int seed, int nsample, in main_loop_serial()
144 struct plan7_s *hmm = wpool->hmm; in calibrateParallel() local
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| /dports/databases/postgresql11-server/postgresql-11.14/src/include/access/ |
| H A D | brin_page.h | 72 #define BRIN_CURRENT_VERSION 1
93 #define REVMAP_PAGE_MAXITEMS \
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| /dports/audio/pocketsphinx/pocketsphinx-0.8/src/libpocketsphinx/ |
| H A D | phone_loop_search.c | 161 hmm_t *hmm = (hmm_t *)&pls->phones[i]; in phone_loop_search_start() local
195 hmm_t *hmm = (hmm_t *)&pls->phones[i]; in evaluate_hmms() local
218 hmm_t *hmm = (hmm_t *)&pls->phones[i]; in prune_hmms() local
241 hmm_t *hmm = (hmm_t *)&pls->phones[i]; in phone_transition() local
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| /dports/biology/infernal/infernal-1.1.3/src/ |
| H A D | cp9_trace.c | 205 CP9TraceCount(CP9_t *hmm, ESL_DSQ *dsq, float wt, CP9trace_t *tr) in CP9TraceCount()
315 CP9TraceScore(CP9_t *hmm, ESL_DSQ *dsq, CP9trace_t *tr) in CP9TraceScore()
379 CP9PrintTrace(FILE *fp, CP9trace_t *tr, CP9_t *hmm, ESL_DSQ *dsq) in CP9PrintTrace()
471 CP9TransitionScoreLookup(CP9_t *hmm, char st1, int k1, in CP9TransitionScoreLookup()
548 CP9ViterbiTrace(CP9_t *hmm, ESL_DSQ *dsq, int i0, int j0, in CP9ViterbiTrace()
1379 CP9TraceScoreCorrectionNull2(CP9_t *hmm, char *errbuf, CP9trace_t *tr, ESL_DSQ *dsq, int start, flo… in CP9TraceScoreCorrectionNull2()
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| /dports/lang/nwcc/nwcc_0.8.3/ |
| H A D | Makefile | 1 hmm: target
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| /dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/hmm2/src/hmmer2/ |
| H A D | core_algorithms.cpp | 454 P7Forward(unsigned char *dsq, int L, struct plan7_s *hmm, struct dpmatrix_s **ret_mx) in P7Forward()
559 P7Viterbi(unsigned char *dsq, int L, struct plan7_s *hmm, struct dpmatrix_s *mx, struct p7trace_s *… in P7Viterbi()
684 P7ViterbiTrace(struct plan7_s *hmm, unsigned char *dsq, int N, in P7ViterbiTrace()
952 P7SmallViterbi(unsigned char *dsq, int L, struct plan7_s *hmm, struct dpmatrix_s *mx, struct p7trac… in P7SmallViterbi()
1128 P7ParsingViterbi(unsigned char *dsq, int L, struct plan7_s *hmm, struct p7trace_s **ret_tr, int& pr… in P7ParsingViterbi()
1329 P7WeeViterbi(unsigned char *dsq, int L, struct plan7_s *hmm, struct p7trace_s **ret_tr) in P7WeeViterbi()
1550 Plan7ESTViterbi(unsigned char *dsq, int L, struct plan7_s *hmm, struct dpmatrix_s **ret_mx) in Plan7ESTViterbi()
1720 get_wee_midpt(struct plan7_s *hmm, unsigned char *dsq, int L, in get_wee_midpt()
2089 P7ViterbiAlignAlignment(MSA *msa, struct plan7_s *hmm) in P7ViterbiAlignAlignment()
2284 ShadowTrace(struct dpshadow_s *tb, struct plan7_s *hmm, int L) in ShadowTrace()
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