| /dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/hmm2/src/hmmer2/ |
| H A D | plan7.cpp | 33 struct plan7_s *hmm; in AllocPlan7() local
42 struct plan7_s *hmm; in AllocPlan7Shell() local
95 AllocPlan7Body(struct plan7_s *hmm, int M) in AllocPlan7Body()
167 FreePlan7(struct plan7_s *hmm) in FreePlan7()
208 ZeroPlan7(struct plan7_s *hmm) in ZeroPlan7()
239 Plan7SetName(struct plan7_s *hmm, const char *name) in Plan7SetName()
252 Plan7SetAccession(struct plan7_s *hmm, char *acc) in Plan7SetAccession()
282 Plan7SetCtime(struct plan7_s *hmm) in Plan7SetCtime()
501 Plan7Renormalize(struct plan7_s *hmm) in Plan7Renormalize()
557 Plan7RenormalizeExits(struct plan7_s *hmm) in Plan7RenormalizeExits()
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| /dports/biology/wise/wise2.4.1/src/HMMer2/ |
| H A D | plan7.c | 45 struct plan7_s *hmm; in AllocPlan7() local
113 struct plan7_s *hmm; in AllocPlan7Shell() local
150 AllocPlan7Body(struct plan7_s *hmm, int M) in AllocPlan7Body()
203 FreePlan7(struct plan7_s *hmm) in FreePlan7()
238 ZeroPlan7(struct plan7_s *hmm) in ZeroPlan7()
265 Plan7SetName(struct plan7_s *hmm, char *name) in Plan7SetName()
278 Plan7SetDescription(struct plan7_s *hmm, char *desc) in Plan7SetDescription()
329 Plan7SetCtime(struct plan7_s *hmm) in Plan7SetCtime()
398 P7Logoddsify(struct plan7_s *hmm, int viterbi_mode) in P7Logoddsify()
514 Plan7Renormalize(struct plan7_s *hmm) in Plan7Renormalize()
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| H A D | plan9.c | 35 struct plan9_s *hmm; /* RETURN: blank HMM */ in P9AllocHMM() local
52 P9FreeHMM(struct plan9_s *hmm) in P9FreeHMM()
72 P9ZeroHMM(struct plan9_s *hmm) in P9ZeroHMM()
106 P9Renormalize(struct plan9_s *hmm) in P9Renormalize()
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| /dports/science/ghmm/ghmm-0.9-rc3/HMMEd/ |
| H A D | EditingContext.py | 16 hmm = my_new_hmm.finalize() variable
28 hmm = c.finalize() variable
48 hmm = c.finalize() variable
55 hmm = c.finalize() variable
59 hmm = c.finalize() variable
125 hmm = c.finalize() variable
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| /dports/biology/infernal/infernal-1.1.3/hmmer/src/ |
| H A D | p7_hmm.c | 52 P7_HMM *hmm = NULL; in p7_hmm_Create() local
78 P7_HMM *hmm = NULL; in p7_hmm_CreateShell() local
191 p7_hmm_Destroy(P7_HMM *hmm) in p7_hmm_Destroy()
259 p7_hmm_Clone(const P7_HMM *hmm) in p7_hmm_Clone()
313 p7_hmm_Zero(P7_HMM *hmm) in p7_hmm_Zero()
575 p7_hmm_SetCtime(P7_HMM *hmm) in p7_hmm_SetCtime()
946 P7_HMM *hmm = NULL; in p7_hmm_Sample() local
1006 P7_HMM *hmm = NULL; in p7_hmm_SampleUngapped() local
1053 P7_HMM *hmm = NULL; in p7_hmm_SampleEnumerable() local
1128 P7_HMM *hmm = NULL; in p7_hmm_SampleUniform() local
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| H A D | modelstats.c | 34 p7_MeanMatchInfo(const P7_HMM *hmm, const P7_BG *bg) in p7_MeanMatchInfo()
53 p7_MeanMatchEntropy(const P7_HMM *hmm) in p7_MeanMatchEntropy()
80 p7_MeanMatchRelativeEntropy(const P7_HMM *hmm, const P7_BG *bg) in p7_MeanMatchRelativeEntropy()
102 p7_MeanForwardScore(const P7_HMM *hmm, const P7_BG *bg) in p7_MeanForwardScore()
163 p7_MeanPositionRelativeEntropy(const P7_HMM *hmm, const P7_BG *bg, double *ret_entropy) in p7_MeanPositionRelativeEntropy()
231 p7_hmm_CompositionKLD(const P7_HMM *hmm, const P7_BG *bg, float *ret_KL, float **opt_avp) in p7_hmm_CompositionKLD()
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| /dports/biology/hmmer/hmmer-3.3/src/ |
| H A D | p7_hmm.c | 52 P7_HMM *hmm = NULL; in p7_hmm_Create() local
78 P7_HMM *hmm = NULL; in p7_hmm_CreateShell() local
191 p7_hmm_Destroy(P7_HMM *hmm) in p7_hmm_Destroy()
259 p7_hmm_Clone(const P7_HMM *hmm) in p7_hmm_Clone()
313 p7_hmm_Zero(P7_HMM *hmm) in p7_hmm_Zero()
575 p7_hmm_SetCtime(P7_HMM *hmm) in p7_hmm_SetCtime()
946 P7_HMM *hmm = NULL; in p7_hmm_Sample() local
1006 P7_HMM *hmm = NULL; in p7_hmm_SampleUngapped() local
1053 P7_HMM *hmm = NULL; in p7_hmm_SampleEnumerable() local
1128 P7_HMM *hmm = NULL; in p7_hmm_SampleUniform() local
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| H A D | modelstats.c | 34 p7_MeanMatchInfo(const P7_HMM *hmm, const P7_BG *bg) in p7_MeanMatchInfo()
53 p7_MeanMatchEntropy(const P7_HMM *hmm) in p7_MeanMatchEntropy()
80 p7_MeanMatchRelativeEntropy(const P7_HMM *hmm, const P7_BG *bg) in p7_MeanMatchRelativeEntropy()
102 p7_MeanForwardScore(const P7_HMM *hmm, const P7_BG *bg) in p7_MeanForwardScore()
163 p7_MeanPositionRelativeEntropy(const P7_HMM *hmm, const P7_BG *bg, double *ret_entropy) in p7_MeanPositionRelativeEntropy()
231 p7_hmm_CompositionKLD(const P7_HMM *hmm, const P7_BG *bg, float *ret_KL, float **opt_avp) in p7_hmm_CompositionKLD()
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| /dports/audio/julius/julius-4.1.2/libsent/src/hmminfo/ |
| H A D | rdhmmdef_var.c | 38 var_new(HTK_HMM_INFO *hmm) in var_new()
59 var_add(HTK_HMM_INFO *hmm, HTK_HMM_Var *new) in var_add()
93 var_lookup(HTK_HMM_INFO *hmm, char *keyname) in var_lookup()
120 var_read(FILE *fp, HTK_HMM_INFO *hmm) in var_read()
163 get_var_data(FILE *fp, HTK_HMM_INFO *hmm) in get_var_data()
198 def_var_macro(char *name, FILE *fp, HTK_HMM_INFO *hmm) in def_var_macro()
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| H A D | rdhmmdef_streamweight.c | 36 sw_new(HTK_HMM_INFO *hmm) in sw_new()
57 sw_add(HTK_HMM_INFO *hmm, HTK_HMM_StreamWeight *new) in sw_add()
91 sw_lookup(HTK_HMM_INFO *hmm, char *keyname) in sw_lookup()
118 sw_read(FILE *fp, HTK_HMM_INFO *hmm) in sw_read()
159 get_streamweight_data(FILE *fp, HTK_HMM_INFO *hmm) in get_streamweight_data()
194 def_streamweight_macro(char *name, FILE *fp, HTK_HMM_INFO *hmm) in def_streamweight_macro()
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| H A D | rdhmmdef_state.c | 36 state_new(HTK_HMM_INFO *hmm) in state_new()
62 state_add(HTK_HMM_INFO *hmm, HTK_HMM_State *new) in state_add()
96 state_lookup(HTK_HMM_INFO *hmm, char *keyname) in state_lookup()
123 state_read(FILE *fp, HTK_HMM_INFO *hmm) in state_read()
187 get_state_data(FILE *fp, HTK_HMM_INFO *hmm) in get_state_data()
224 def_state_macro(char *name, FILE *fp, HTK_HMM_INFO *hmm) in def_state_macro()
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| H A D | rdhmmdef_trans.c | 41 trans_new(HTK_HMM_INFO *hmm) in trans_new()
61 trans_add(HTK_HMM_INFO *hmm, HTK_HMM_Trans *new) in trans_add()
94 trans_lookup(HTK_HMM_INFO *hmm, char *keyname) in trans_lookup()
121 trans_read(FILE *fp, HTK_HMM_INFO *hmm) in trans_read()
173 get_trans_data(FILE *fp, HTK_HMM_INFO *hmm) in get_trans_data()
208 def_trans_macro(char *name, FILE *fp, HTK_HMM_INFO *hmm) in def_trans_macro()
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| H A D | rdhmmdef_dens.c | 57 dens_new(HTK_HMM_INFO *hmm) in dens_new()
80 dens_add(HTK_HMM_INFO *hmm, HTK_HMM_Dens *new) in dens_add()
113 dens_lookup(HTK_HMM_INFO *hmm, char *keyname) in dens_lookup()
140 dens_read( FILE *fp, HTK_HMM_INFO *hmm) in dens_read()
200 get_dens_data(FILE *fp, HTK_HMM_INFO *hmm) in get_dens_data()
234 def_dens_macro(char *name, FILE *fp, HTK_HMM_INFO *hmm) in def_dens_macro()
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| H A D | rdhmmdef_mpdf.c | 36 mpdf_new(HTK_HMM_INFO *hmm) in mpdf_new()
60 mpdf_add(HTK_HMM_INFO *hmm, HTK_HMM_PDF *new) in mpdf_add()
93 mpdf_lookup(HTK_HMM_INFO *hmm, char *keyname) in mpdf_lookup()
121 mpdf_read(FILE *fp, HTK_HMM_INFO *hmm, int mix_num) in mpdf_read()
217 get_mpdf_data(FILE *fp, HTK_HMM_INFO *hmm, int mix_num, short stream_id) in get_mpdf_data()
265 def_mpdf_macro(char *name, FILE *fp, HTK_HMM_INFO *hmm) in def_mpdf_macro()
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| H A D | check_hmmtype.c | 38 check_hmm_options(HTK_HMM_INFO *hmm) in check_hmm_options()
71 check_param_coherence(HTK_HMM_INFO *hmm, HTK_Param *pinfo) in check_param_coherence()
109 check_param_basetype(HTK_HMM_INFO *hmm, HTK_Param *pinfo) in check_param_basetype()
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| H A D | read_binhmm.c | 88 rdn_strfunc(FILE *fp, HTK_HMM_INFO *hmm) in rdn_strfunc()
268 rd_type(FILE *fp, HTK_HMM_INFO *hmm) in rd_type()
291 rd_trans(FILE *fp, HTK_HMM_INFO *hmm) in rd_trans()
340 rd_var(FILE *fp, HTK_HMM_INFO *hmm) in rd_var()
384 rd_dens(FILE *fp, HTK_HMM_INFO *hmm) in rd_dens()
433 rd_streamweight(FILE *fp, HTK_HMM_INFO *hmm) in rd_streamweight()
477 rd_tmix(FILE *fp, HTK_HMM_INFO *hmm) in rd_tmix()
532 rd_pdf_sub(FILE *fp, HTK_HMM_INFO *hmm, HTK_HMM_PDF *m) in rd_pdf_sub()
576 rd_mpdf(FILE *fp, HTK_HMM_INFO *hmm) in rd_mpdf()
621 rd_state(FILE *fp, HTK_HMM_INFO *hmm, boolean mpdf_macro) in rd_state()
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| /dports/biology/infernal/infernal-1.1.3/src/ |
| H A D | cp9.c | 41 CP9_t *hmm; in AllocCPlan9() local
51 CP9_t *hmm; in AllocCPlan9Shell() local
87 AllocCPlan9Body(CP9_t *hmm, int M, const ESL_ALPHABET *abc) in AllocCPlan9Body()
172 FreeCPlan9(CP9_t *hmm) in FreeCPlan9()
219 ZeroCPlan9(CP9_t *hmm) in ZeroCPlan9()
263 CPlan9SetNullModel(CP9_t *hmm, float *null, float p1) in CPlan9SetNullModel()
463 CP9Logoddsify(CP9_t *hmm) in CP9Logoddsify()
571 CPlan9Renormalize(CP9_t *hmm) in CPlan9Renormalize()
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| /dports/biology/infernal/infernal-1.1.3/easel/ |
| H A D | esl_hmm.c | 31 ESL_HMM *hmm = NULL; in esl_hmm_Create() local
78 esl_hmm_Clone(const ESL_HMM *hmm) in esl_hmm_Clone()
118 esl_hmm_Configure(ESL_HMM *hmm, float *fq) in esl_hmm_Configure()
164 esl_hmm_Destroy(ESL_HMM *hmm) in esl_hmm_Destroy()
353 esl_hmm_Forward(const ESL_DSQ *dsq, int L, const ESL_HMM *hmm, ESL_HMX *fwd, float *opt_sc) in esl_hmm_Forward()
415 esl_hmm_Backward(const ESL_DSQ *dsq, int L, const ESL_HMM *hmm, ESL_HMX *bck, float *opt_sc) in esl_hmm_Backward()
498 ESL_HMM *hmm = esl_hmm_Create(abc, 2); in make_occasionally_dishonest_casino() local
560 ESL_HMM *hmm = NULL; in main() local
650 ESL_HMM *hmm; in create_test_hmm() local
721 ESL_HMM *hmm; in create_null_hmm() local
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| /dports/biology/hmmer/hmmer-3.3/easel/ |
| H A D | esl_hmm.c | 31 ESL_HMM *hmm = NULL; in esl_hmm_Create() local
78 esl_hmm_Clone(const ESL_HMM *hmm) in esl_hmm_Clone()
118 esl_hmm_Configure(ESL_HMM *hmm, float *fq) in esl_hmm_Configure()
164 esl_hmm_Destroy(ESL_HMM *hmm) in esl_hmm_Destroy()
353 esl_hmm_Forward(const ESL_DSQ *dsq, int L, const ESL_HMM *hmm, ESL_HMX *fwd, float *opt_sc) in esl_hmm_Forward()
415 esl_hmm_Backward(const ESL_DSQ *dsq, int L, const ESL_HMM *hmm, ESL_HMX *bck, float *opt_sc) in esl_hmm_Backward()
498 ESL_HMM *hmm = esl_hmm_Create(abc, 2); in make_occasionally_dishonest_casino() local
560 ESL_HMM *hmm = NULL; in main() local
650 ESL_HMM *hmm; in create_test_hmm() local
721 ESL_HMM *hmm; in create_null_hmm() local
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| /dports/biology/bcftools/bcftools-1.14/ |
| H A D | HMM.c | 69 double *hmm_get_tprob(hmm_t *hmm) { return hmm->tprob_arr; } in hmm_get_tprob()
70 int hmm_get_nstates(hmm_t *hmm) { return hmm->nstates; } in hmm_get_nstates()
71 double *hmm_get_fwd_bwd_prob(hmm_t *hmm) { return hmm->fwd; } in hmm_get_fwd_bwd_prob()
93 void hmm_init_states(hmm_t *hmm, double *probs) in hmm_init_states()
130 hmm_t *hmm = (hmm_t*) calloc(1,sizeof(hmm_t)); in hmm_init() local
139 void *hmm_snapshot(hmm_t *hmm, void *_snapshot, uint32_t pos) in hmm_snapshot()
164 void hmm_restore(hmm_t *hmm, void *_snapshot) in hmm_restore()
180 void hmm_reset(hmm_t *hmm, void *_snapshot) in hmm_reset()
189 void hmm_set_tprob(hmm_t *hmm, double *tprob, int ntprob) in hmm_set_tprob()
210 static void _set_tprob(hmm_t *hmm, int pos_diff) in _set_tprob()
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| /dports/biology/bio-mocha/bcftools-1.14/ |
| H A D | HMM.c | 69 double *hmm_get_tprob(hmm_t *hmm) { return hmm->tprob_arr; } in hmm_get_tprob()
70 int hmm_get_nstates(hmm_t *hmm) { return hmm->nstates; } in hmm_get_nstates()
71 double *hmm_get_fwd_bwd_prob(hmm_t *hmm) { return hmm->fwd; } in hmm_get_fwd_bwd_prob()
93 void hmm_init_states(hmm_t *hmm, double *probs) in hmm_init_states()
130 hmm_t *hmm = (hmm_t*) calloc(1,sizeof(hmm_t)); in hmm_init() local
139 void *hmm_snapshot(hmm_t *hmm, void *_snapshot, uint32_t pos) in hmm_snapshot()
164 void hmm_restore(hmm_t *hmm, void *_snapshot) in hmm_restore()
180 void hmm_reset(hmm_t *hmm, void *_snapshot) in hmm_reset()
189 void hmm_set_tprob(hmm_t *hmm, double *tprob, int ntprob) in hmm_set_tprob()
210 static void _set_tprob(hmm_t *hmm, int pos_diff) in _set_tprob()
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| /dports/biology/py-pysam/pysam-0.18.0/bcftools/ |
| H A D | HMM.c | 69 double *hmm_get_tprob(hmm_t *hmm) { return hmm->tprob_arr; } in hmm_get_tprob()
70 int hmm_get_nstates(hmm_t *hmm) { return hmm->nstates; } in hmm_get_nstates()
71 double *hmm_get_fwd_bwd_prob(hmm_t *hmm) { return hmm->fwd; } in hmm_get_fwd_bwd_prob()
93 void hmm_init_states(hmm_t *hmm, double *probs) in hmm_init_states()
130 hmm_t *hmm = (hmm_t*) calloc(1,sizeof(hmm_t)); in hmm_init() local
139 void *hmm_snapshot(hmm_t *hmm, void *_snapshot, uint32_t pos) in hmm_snapshot()
164 void hmm_restore(hmm_t *hmm, void *_snapshot) in hmm_restore()
180 void hmm_reset(hmm_t *hmm, void *_snapshot) in hmm_reset()
189 void hmm_set_tprob(hmm_t *hmm, double *tprob, int ntprob) in hmm_set_tprob()
210 static void _set_tprob(hmm_t *hmm, int pos_diff) in _set_tprob()
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| H A D | HMM.c.pysam.c | 71 double *hmm_get_tprob(hmm_t *hmm) { return hmm->tprob_arr; } in hmm_get_tprob()
72 int hmm_get_nstates(hmm_t *hmm) { return hmm->nstates; } in hmm_get_nstates()
73 double *hmm_get_fwd_bwd_prob(hmm_t *hmm) { return hmm->fwd; } in hmm_get_fwd_bwd_prob()
95 void hmm_init_states(hmm_t *hmm, double *probs) in hmm_init_states()
132 hmm_t *hmm = (hmm_t*) calloc(1,sizeof(hmm_t)); in hmm_init() local
141 void *hmm_snapshot(hmm_t *hmm, void *_snapshot, uint32_t pos) in hmm_snapshot()
166 void hmm_restore(hmm_t *hmm, void *_snapshot) in hmm_restore()
182 void hmm_reset(hmm_t *hmm, void *_snapshot) in hmm_reset()
191 void hmm_set_tprob(hmm_t *hmm, double *tprob, int ntprob) in hmm_set_tprob()
212 static void _set_tprob(hmm_t *hmm, int pos_diff) in _set_tprob()
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| /dports/multimedia/v4l_compat/linux-5.13-rc2/tools/testing/selftests/vm/ |
| H A D | hmm-tests.c | 56 FIXTURE(hmm) in FIXTURE() argument
84 FIXTURE_SETUP(hmm) in FIXTURE_SETUP() argument
104 FIXTURE_TEARDOWN(hmm) in FIXTURE_TEARDOWN() argument
217 TEST_F(hmm, open_close) in TEST_F() argument
224 TEST_F(hmm, anon_read) in TEST_F() argument
288 TEST_F(hmm, anon_read_prot) in TEST_F() argument
347 TEST_F(hmm, anon_write) in TEST_F() argument
733 TEST_F(hmm, file_read) in TEST_F() argument
788 TEST_F(hmm, file_write) in TEST_F() argument
846 TEST_F(hmm, migrate) in TEST_F() argument
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| /dports/multimedia/libv4l/linux-5.13-rc2/tools/testing/selftests/vm/ |
| H A D | hmm-tests.c | 56 FIXTURE(hmm) in FIXTURE() argument
84 FIXTURE_SETUP(hmm) in FIXTURE_SETUP() argument
104 FIXTURE_TEARDOWN(hmm) in FIXTURE_TEARDOWN() argument
217 TEST_F(hmm, open_close) in TEST_F() argument
224 TEST_F(hmm, anon_read) in TEST_F() argument
288 TEST_F(hmm, anon_read_prot) in TEST_F() argument
347 TEST_F(hmm, anon_write) in TEST_F() argument
733 TEST_F(hmm, file_read) in TEST_F() argument
788 TEST_F(hmm, file_write) in TEST_F() argument
846 TEST_F(hmm, migrate) in TEST_F() argument
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