/dports/biology/infernal/infernal-1.1.3/hmmer/src/impl_sse/ |
H A D | ssvfilter.c | 716 calc_band_1(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, int q, __m128i beginv, register __m12… in calc_band_1() 722 calc_band_2(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, int q, __m128i beginv, register __m12… in calc_band_2() 728 calc_band_3(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, int q, __m128i beginv, register __m12… in calc_band_3() 734 calc_band_4(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, int q, __m128i beginv, register __m12… in calc_band_4() 740 calc_band_5(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, int q, __m128i beginv, register __m12… in calc_band_5() 746 calc_band_6(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, int q, __m128i beginv, register __m12… in calc_band_6() 753 calc_band_7(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, int q, __m128i beginv, register __m12… in calc_band_7() 759 calc_band_8(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, int q, __m128i beginv, register __m12… in calc_band_8() 765 calc_band_9(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, int q, __m128i beginv, register __m12… in calc_band_9() 832 get_xE(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om) in get_xE() [all …]
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H A D | fwdback.c | 90 p7_Forward(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, P7_OMX *ox, float *opt_sc) in p7_Forward() 132 p7_ForwardParser(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, P7_OMX *ox, float *opt_sc) in p7_ForwardParser() 190 p7_Backward(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, const P7_OMX *fwd, P7_OMX *bck, float… in p7_Backward() 236 p7_BackwardParser(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, const P7_OMX *fwd, P7_OMX *bck,… in p7_BackwardParser() 256 forward_engine(int do_full, const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, P7_OMX *ox, float *op… in forward_engine() 468 backward_engine(int do_full, const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, const P7_OMX *fwd, P… in backward_engine() 798 ESL_DSQ *dsq = malloc(sizeof(ESL_DSQ) * (L+2)); in main() local 900 ESL_DSQ *dsq = malloc(sizeof(ESL_DSQ) * (L+2)); in utest_fwdback() local
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/dports/biology/hmmer/hmmer-3.3/src/impl_sse/ |
H A D | ssvfilter.c | 716 calc_band_1(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, int q, __m128i beginv, register __m12… in calc_band_1() 722 calc_band_2(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, int q, __m128i beginv, register __m12… in calc_band_2() 728 calc_band_3(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, int q, __m128i beginv, register __m12… in calc_band_3() 734 calc_band_4(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, int q, __m128i beginv, register __m12… in calc_band_4() 740 calc_band_5(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, int q, __m128i beginv, register __m12… in calc_band_5() 746 calc_band_6(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, int q, __m128i beginv, register __m12… in calc_band_6() 753 calc_band_7(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, int q, __m128i beginv, register __m12… in calc_band_7() 759 calc_band_8(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, int q, __m128i beginv, register __m12… in calc_band_8() 765 calc_band_9(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, int q, __m128i beginv, register __m12… in calc_band_9() 832 get_xE(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om) in get_xE() [all …]
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H A D | fwdback.c | 90 p7_Forward(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, P7_OMX *ox, float *opt_sc) in p7_Forward() 132 p7_ForwardParser(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, P7_OMX *ox, float *opt_sc) in p7_ForwardParser() 190 p7_Backward(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, const P7_OMX *fwd, P7_OMX *bck, float… in p7_Backward() 236 p7_BackwardParser(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, const P7_OMX *fwd, P7_OMX *bck,… in p7_BackwardParser() 256 forward_engine(int do_full, const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, P7_OMX *ox, float *op… in forward_engine() 468 backward_engine(int do_full, const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, const P7_OMX *fwd, P… in backward_engine() 798 ESL_DSQ *dsq = malloc(sizeof(ESL_DSQ) * (L+2)); in main() local 900 ESL_DSQ *dsq = malloc(sizeof(ESL_DSQ) * (L+2)); in utest_fwdback() local
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/dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/hmm2/src/hmmer2/ |
H A D | alphabet.cpp | 143 unsigned char *dsq; in DigitizeSequence() local 161 unsigned char *dsq; in DigitizeSequenceHP() local 184 DedigitizeSequence(unsigned char *dsq, int L) in DedigitizeSequence() 217 unsigned char **dsq; in DigitizeAlignment() local
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H A D | masks.cpp | 84 XNU(unsigned char *dsq, int len) in XNU() 172 TraceScoreCorrection(struct plan7_s *hmm, struct p7trace_s *tr, unsigned char *dsq) in TraceScoreCorrection()
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/dports/biology/hmmer/hmmer-3.3/easel/ |
H A D | esl_alphabet.c | 1847 ESL_DSQ *dsq; in utest_CreateCustom() local 1875 ESL_DSQ *dsq; in utest_SetEquiv() local 1901 ESL_DSQ *dsq; in utest_SetCaseInsensitive() local 1927 ESL_DSQ *dsq; in utest_SetDegeneracy() local 1969 ESL_DSQ *dsq; in utest_SetIgnored() local 2001 ESL_DSQ *dsq; in utest_CreateDsq() local 2028 ESL_DSQ *dsq; in utest_Digitize() local 2058 ESL_DSQ *dsq; in utest_Textize() local 2084 ESL_DSQ *dsq; in utest_TextizeN() local 2143 ESL_DSQ *dsq; in utest_dsqcat() local [all …]
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H A D | esl_randomseq.c | 779 esl_rsq_xIID(ESL_RANDOMNESS *r, const double *p, int K, int L, ESL_DSQ *dsq) in esl_rsq_xIID() 789 esl_rsq_xfIID(ESL_RANDOMNESS *r, const float *p, int K, int L, ESL_DSQ *dsq) in esl_rsq_xfIID() 907 esl_rsq_XShuffle(ESL_RANDOMNESS *r, const ESL_DSQ *dsq, int L, ESL_DSQ *shuffled) in esl_rsq_XShuffle() 944 esl_rsq_XShuffleDP(ESL_RANDOMNESS *r, const ESL_DSQ *dsq, int L, int K, ESL_DSQ *shuffled) in esl_rsq_XShuffleDP() 1121 esl_rsq_XReverse(const ESL_DSQ *dsq, int L, ESL_DSQ *rev) in esl_rsq_XReverse() 1208 esl_rsq_XMarkov0(ESL_RANDOMNESS *r, const ESL_DSQ *dsq, int L, int K, ESL_DSQ *markoved) in esl_rsq_XMarkov0() 1279 esl_rsq_XMarkov1(ESL_RANDOMNESS *r, const ESL_DSQ *dsq, int L, int K, ESL_DSQ *markoved) in esl_rsq_XMarkov1() 1482 xcomposition(ESL_DSQ *dsq, int L, int K, int *mono, int **di) in xcomposition() 1774 ESL_DSQ *dsq = NULL; in utest_XShufflers() local 1883 ESL_DSQ *dsq = NULL; in utest_XMarkovs() local [all …]
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/dports/biology/infernal/infernal-1.1.3/easel/ |
H A D | esl_alphabet.c | 1847 ESL_DSQ *dsq; in utest_CreateCustom() local 1875 ESL_DSQ *dsq; in utest_SetEquiv() local 1901 ESL_DSQ *dsq; in utest_SetCaseInsensitive() local 1927 ESL_DSQ *dsq; in utest_SetDegeneracy() local 1969 ESL_DSQ *dsq; in utest_SetIgnored() local 2001 ESL_DSQ *dsq; in utest_CreateDsq() local 2028 ESL_DSQ *dsq; in utest_Digitize() local 2058 ESL_DSQ *dsq; in utest_Textize() local 2084 ESL_DSQ *dsq; in utest_TextizeN() local 2143 ESL_DSQ *dsq; in utest_dsqcat() local [all …]
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H A D | esl_randomseq.c | 779 esl_rsq_xIID(ESL_RANDOMNESS *r, const double *p, int K, int L, ESL_DSQ *dsq) in esl_rsq_xIID() 789 esl_rsq_xfIID(ESL_RANDOMNESS *r, const float *p, int K, int L, ESL_DSQ *dsq) in esl_rsq_xfIID() 907 esl_rsq_XShuffle(ESL_RANDOMNESS *r, const ESL_DSQ *dsq, int L, ESL_DSQ *shuffled) in esl_rsq_XShuffle() 944 esl_rsq_XShuffleDP(ESL_RANDOMNESS *r, const ESL_DSQ *dsq, int L, int K, ESL_DSQ *shuffled) in esl_rsq_XShuffleDP() 1121 esl_rsq_XReverse(const ESL_DSQ *dsq, int L, ESL_DSQ *rev) in esl_rsq_XReverse() 1208 esl_rsq_XMarkov0(ESL_RANDOMNESS *r, const ESL_DSQ *dsq, int L, int K, ESL_DSQ *markoved) in esl_rsq_XMarkov0() 1279 esl_rsq_XMarkov1(ESL_RANDOMNESS *r, const ESL_DSQ *dsq, int L, int K, ESL_DSQ *markoved) in esl_rsq_XMarkov1() 1482 xcomposition(ESL_DSQ *dsq, int L, int K, int *mono, int **di) in xcomposition() 1774 ESL_DSQ *dsq = NULL; in utest_XShufflers() local 1883 ESL_DSQ *dsq = NULL; in utest_XMarkovs() local [all …]
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/dports/biology/wise/wise2.4.1/src/HMMer2/ |
H A D | alphabet.c | 172 char *dsq; in DigitizeSequence() local 190 DedigitizeSequence(char *dsq, int L) in DedigitizeSequence() 220 char **dsq; in DigitizeAlignment() local
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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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H A D | masks.c | 72 XNU(char *dsq, int len) in XNU() 156 TraceScoreCorrection(struct plan7_s *hmm, struct p7trace_s *tr, char *dsq) in TraceScoreCorrection()
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/dports/biology/infernal/infernal-1.1.3/hmmer/src/ |
H A D | p7_null3.c | 60 p7_null3_score(const ESL_ALPHABET *abc, const ESL_DSQ *dsq, P7_TRACE *tr, int start, int stop, P7_B… in p7_null3_score() 178 ESL_DSQ *dsq = malloc(sizeof(ESL_DSQ) * (L+2)); in main() local 232 utest_correct_normalization(ESL_RANDOMNESS *r, P7_PROFILE *gm, P7_BG *bg, ESL_DSQ *dsq, int L, P7_G… in utest_correct_normalization() 302 ESL_DSQ *dsq = NULL; in main() local
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H A D | generic_fwdback_chk.c | 32 forward_row(const ESL_DSQ *dsq, const P7_PROFILE *gm, P7_GMXCHK *gxc, const float *dpp, float *dpc,… in forward_row() 128 p7_GForwardCheckpointed(const ESL_DSQ *dsq, int L, const P7_PROFILE *gm, P7_GMXCHK *gxc, float *opt… in p7_GForwardCheckpointed() 188 backward_row(const ESL_DSQ *dsq, const P7_PROFILE *gm, P7_GMXCHK *gxc, const float *dpp, float *dpc… in backward_row() 229 p7_GBackwardCheckpointed(const ESL_DSQ *dsq, int L, const P7_PROFILE *gm, P7_GMXCHK *gxc, P7_GBANDS… in p7_GBackwardCheckpointed() 482 ESL_DSQ *dsq = malloc(sizeof(ESL_DSQ) * (L+2)); in main() local 549 scoring_comparison(ESL_DSQ *dsq, int L, P7_PROFILE *gm, P7_GMX *gx, P7_GMXCHK *gxc, P7_GBANDS *bnd) in scoring_comparison() 579 ESL_DSQ *dsq = malloc(sizeof(ESL_DSQ) * (L+2)); in utest_randomseq() local
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H A D | generic_fwdback.c | 48 p7_GForward(const ESL_DSQ *dsq, int L, const P7_PROFILE *gm, P7_GMX *gx, float *opt_sc) in p7_GForward() 164 p7_GBackward(const ESL_DSQ *dsq, int L, const P7_PROFILE *gm, P7_GMX *gx, float *opt_sc) in p7_GBackward() 290 p7_GHybrid(const ESL_DSQ *dsq, int L, const P7_PROFILE *gm, P7_GMX *gx, float *opt_fwdscore, float … in p7_GHybrid() 375 ESL_DSQ *dsq = malloc(sizeof(ESL_DSQ) * (L+2)); in main() local 453 ESL_DSQ *dsq = NULL; in utest_forward() local 555 ESL_DSQ *dsq = NULL; in utest_enumeration() local
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H A D | generic_stotrace.c | 47 p7_GStochasticTrace(ESL_RANDOMNESS *r, const ESL_DSQ *dsq, int L, const P7_PROFILE *gm, const P7_GM… in p7_GStochasticTrace() 243 ESL_DSQ *dsq = malloc(sizeof(ESL_DSQ) * (L+2)); in main() local 303 utest_stotrace(ESL_GETOPTS *go, ESL_RANDOMNESS *r, ESL_ALPHABET *abc, P7_PROFILE *gm, ESL_DSQ *dsq,… in utest_stotrace() 373 ESL_DSQ *dsq = NULL; in main() local
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H A D | generic_viterbi.c | 64 p7_GViterbi(const ESL_DSQ *dsq, int L, const P7_PROFILE *gm, P7_GMX *gx, float *opt_sc) in p7_GViterbi() 186 p7_GViterbi_longtarget(const ESL_DSQ *dsq, int L, const P7_PROFILE *gm, P7_GMX *gx, in p7_GViterbi_longtarget() 370 ESL_DSQ *dsq = malloc(sizeof(ESL_DSQ) * (L+2)); in main() local 448 ESL_DSQ *dsq = NULL; in utest_basic() local 507 ESL_DSQ *dsq = NULL; in utest_viterbi() local
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/dports/biology/hmmer/hmmer-3.3/src/ |
H A D | p7_null3.c | 60 p7_null3_score(const ESL_ALPHABET *abc, const ESL_DSQ *dsq, P7_TRACE *tr, int start, int stop, P7_B… in p7_null3_score() 178 ESL_DSQ *dsq = malloc(sizeof(ESL_DSQ) * (L+2)); in main() local 232 utest_correct_normalization(ESL_RANDOMNESS *r, P7_PROFILE *gm, P7_BG *bg, ESL_DSQ *dsq, int L, P7_G… in utest_correct_normalization() 302 ESL_DSQ *dsq = NULL; in main() local
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H A D | generic_fwdback_chk.c | 32 forward_row(const ESL_DSQ *dsq, const P7_PROFILE *gm, P7_GMXCHK *gxc, const float *dpp, float *dpc,… in forward_row() 128 p7_GForwardCheckpointed(const ESL_DSQ *dsq, int L, const P7_PROFILE *gm, P7_GMXCHK *gxc, float *opt… in p7_GForwardCheckpointed() 188 backward_row(const ESL_DSQ *dsq, const P7_PROFILE *gm, P7_GMXCHK *gxc, const float *dpp, float *dpc… in backward_row() 229 p7_GBackwardCheckpointed(const ESL_DSQ *dsq, int L, const P7_PROFILE *gm, P7_GMXCHK *gxc, P7_GBANDS… in p7_GBackwardCheckpointed() 482 ESL_DSQ *dsq = malloc(sizeof(ESL_DSQ) * (L+2)); in main() local 549 scoring_comparison(ESL_DSQ *dsq, int L, P7_PROFILE *gm, P7_GMX *gx, P7_GMXCHK *gxc, P7_GBANDS *bnd) in scoring_comparison() 579 ESL_DSQ *dsq = malloc(sizeof(ESL_DSQ) * (L+2)); in utest_randomseq() local
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H A D | generic_fwdback.c | 48 p7_GForward(const ESL_DSQ *dsq, int L, const P7_PROFILE *gm, P7_GMX *gx, float *opt_sc) in p7_GForward() 164 p7_GBackward(const ESL_DSQ *dsq, int L, const P7_PROFILE *gm, P7_GMX *gx, float *opt_sc) in p7_GBackward() 290 p7_GHybrid(const ESL_DSQ *dsq, int L, const P7_PROFILE *gm, P7_GMX *gx, float *opt_fwdscore, float … in p7_GHybrid() 375 ESL_DSQ *dsq = malloc(sizeof(ESL_DSQ) * (L+2)); in main() local 453 ESL_DSQ *dsq = NULL; in utest_forward() local 555 ESL_DSQ *dsq = NULL; in utest_enumeration() local
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H A D | generic_stotrace.c | 47 p7_GStochasticTrace(ESL_RANDOMNESS *r, const ESL_DSQ *dsq, int L, const P7_PROFILE *gm, const P7_GM… in p7_GStochasticTrace() 243 ESL_DSQ *dsq = malloc(sizeof(ESL_DSQ) * (L+2)); in main() local 303 utest_stotrace(ESL_GETOPTS *go, ESL_RANDOMNESS *r, ESL_ALPHABET *abc, P7_PROFILE *gm, ESL_DSQ *dsq,… in utest_stotrace() 373 ESL_DSQ *dsq = NULL; in main() local
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/dports/biology/infernal/infernal-1.1.3/hmmer/src/impl_vmx/ |
H A D | fwdback.c | 91 p7_Forward(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, P7_OMX *ox, float *opt_sc) in p7_Forward() 133 p7_ForwardParser(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, P7_OMX *ox, float *opt_sc) in p7_ForwardParser() 191 p7_Backward(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, const P7_OMX *fwd, P7_OMX *bck, float… in p7_Backward() 237 p7_BackwardParser(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, const P7_OMX *fwd, P7_OMX *bck,… in p7_BackwardParser() 257 forward_engine(int do_full, const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, P7_OMX *ox, float *op… in forward_engine() 469 backward_engine(int do_full, const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, const P7_OMX *fwd, P… in backward_engine() 797 ESL_DSQ *dsq = malloc(sizeof(ESL_DSQ) * (L+2)); in main() local 899 ESL_DSQ *dsq = malloc(sizeof(ESL_DSQ) * (L+2)); in utest_fwdback() local
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/dports/biology/hmmer/hmmer-3.3/src/impl_vmx/ |
H A D | fwdback.c | 91 p7_Forward(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, P7_OMX *ox, float *opt_sc) in p7_Forward() 133 p7_ForwardParser(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, P7_OMX *ox, float *opt_sc) in p7_ForwardParser() 191 p7_Backward(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, const P7_OMX *fwd, P7_OMX *bck, float… in p7_Backward() 237 p7_BackwardParser(const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, const P7_OMX *fwd, P7_OMX *bck,… in p7_BackwardParser() 257 forward_engine(int do_full, const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, P7_OMX *ox, float *op… in forward_engine() 469 backward_engine(int do_full, const ESL_DSQ *dsq, int L, const P7_OPROFILE *om, const P7_OMX *fwd, P… in backward_engine() 797 ESL_DSQ *dsq = malloc(sizeof(ESL_DSQ) * (L+2)); in main() local 899 ESL_DSQ *dsq = malloc(sizeof(ESL_DSQ) * (L+2)); in utest_fwdback() local
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/dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/hmm2/src/u_build/ |
H A D | uhmmbuild.cpp | 58 unsigned char **dsq; // digitized unaligned aseq's in build() local 235 static void position_average_score(struct plan7_s *hmm, unsigned char **dsq, float *wgt, int nseq, … in position_average_score() 300 static float frag_trace_score(struct plan7_s *hmm, unsigned char *dsq, struct p7trace_s *tr, float … in frag_trace_score() 353 static void maximum_entropy(struct alphabet_s * /*al*/, struct plan7_s *hmm, unsigned char **dsq, M… in maximum_entropy()
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