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/dports/biology/infernal/infernal-1.1.3/hmmer/src/impl_sse/
H A Dssvfilter.c716 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 …]
H A Dfwdback.c90 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
/dports/biology/hmmer/hmmer-3.3/src/impl_sse/
H A Dssvfilter.c716 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 …]
H A Dfwdback.c90 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
/dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/hmm2/src/hmmer2/
H A Dalphabet.cpp143 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
H A Dmasks.cpp84 XNU(unsigned char *dsq, int len) in XNU()
172 TraceScoreCorrection(struct plan7_s *hmm, struct p7trace_s *tr, unsigned char *dsq) in TraceScoreCorrection()
/dports/biology/hmmer/hmmer-3.3/easel/
H A Desl_alphabet.c1847 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
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H A Desl_randomseq.c779 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 …]
/dports/biology/infernal/infernal-1.1.3/easel/
H A Desl_alphabet.c1847 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 …]
H A Desl_randomseq.c779 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 …]
/dports/biology/wise/wise2.4.1/src/HMMer2/
H A Dalphabet.c172 char *dsq; in DigitizeSequence() local
190 DedigitizeSequence(char *dsq, int L) in DedigitizeSequence()
220 char **dsq; in DigitizeAlignment() local
H A Dcore_algorithms.c191 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()
H A Dmasks.c72 XNU(char *dsq, int len) in XNU()
156 TraceScoreCorrection(struct plan7_s *hmm, struct p7trace_s *tr, char *dsq) in TraceScoreCorrection()
/dports/biology/infernal/infernal-1.1.3/hmmer/src/
H A Dp7_null3.c60 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
H A Dgeneric_fwdback_chk.c32 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
H A Dgeneric_fwdback.c48 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
H A Dgeneric_stotrace.c47 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
H A Dgeneric_viterbi.c64 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
/dports/biology/hmmer/hmmer-3.3/src/
H A Dp7_null3.c60 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
H A Dgeneric_fwdback_chk.c32 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
H A Dgeneric_fwdback.c48 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
H A Dgeneric_stotrace.c47 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
/dports/biology/infernal/infernal-1.1.3/hmmer/src/impl_vmx/
H A Dfwdback.c91 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
/dports/biology/hmmer/hmmer-3.3/src/impl_vmx/
H A Dfwdback.c91 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
/dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/hmm2/src/u_build/
H A Duhmmbuild.cpp58 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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