| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/align/util/ |
| H A D | score_builder.hpp | 142 void SetEffectiveSearchSpace(Int8 searchsp) // required for blast e-values in SetEffectiveSearchSpace() argument
144 m_EffectiveSearchSpace = searchsp; in SetEffectiveSearchSpace()
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| /dports/biology/ncbi-toolkit/ncbi/tools/ |
| H A D | blastkar.h | 545 …CALL BlastKarlinEtoS_simple PROTO((Nlm_FloatHi E, BLAST_KarlinBlkPtr kbp, Nlm_FloatHi searchsp));
553 …BCALL BlastKarlinStoP_simple PROTO((BLAST_Score S, BLAST_KarlinBlkPtr kbp, Nlm_FloatHi searchsp));
557 …BCALL BlastKarlinStoE_simple PROTO((BLAST_Score S, BLAST_KarlinBlkPtr kbp, Nlm_FloatHi searchsp));
611 Int2 ConvertEtoPseudoS PROTO((Nlm_FloatHi E, Nlm_FloatHi searchsp));
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| H A D | blastkar.c | 4342 Nlm_FloatHi searchsp, /* size of search space. */ in BlastCutoffs() argument
4369 es = BlastKarlinEtoS_simple(e, kbp, searchsp); in BlastCutoffs()
4385 e = BlastKarlinStoE_simple(s, kbp, searchsp); in BlastCutoffs()
4423 Nlm_FloatHi searchsp) /* size of search space */ in BlastKarlinEtoS_simple() argument
4463 Nlm_FloatHi searchsp) /* size of search space. */ in BlastKarlinStoP_simple() argument
4467 x = BlastKarlinStoE_simple(S, kbp, searchsp); in BlastKarlinStoP_simple()
4492 Nlm_FloatHi searchsp) /* size of search space. */ in BlastKarlinStoE_simple() argument
4503 return searchsp * exp((Nlm_FloatHi)(-Lambda * S) + kbp->logK); in BlastKarlinStoE_simple()
4958 ConvertEtoPseudoS(Nlm_FloatHi E, Nlm_FloatHi searchsp) in ConvertEtoPseudoS() argument
4966 if (E > searchsp) in ConvertEtoPseudoS()
[all …]
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| H A D | blastpri.h | 1078 avglen, Nlm_FloatHi searchsp, Int4 window));
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| H A D | rpsutil.c | 648 FloatHi searchsp; in RPSUpdateDbSize() local
663 searchsp = BLASTCalculateSearchSpace(options, options->dbseq_num, dblen, in RPSUpdateDbSize()
671 options->searchsp_eff = searchsp; in RPSUpdateDbSize()
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| /dports/biology/ncbi-toolkit/ncbi/algo/blast/core/ |
| H A D | blast_parameters.c | 909 Int8 searchsp; in BlastHitSavingParametersUpdate() local
920 searchsp = query_info->contexts[context].eff_searchsp; in BlastHitSavingParametersUpdate()
925 searchsp /= NUM_FRAMES; in BlastHitSavingParametersUpdate()
937 BLAST_Cutoffs(&new_cutoff, &evalue, kbp, searchsp, FALSE, 0); in BlastHitSavingParametersUpdate()
952 Int8 searchsp = (Int8)MIN(avg_qlen, avg_subject_length) * in BlastHitSavingParametersUpdate() local
966 BLAST_Cutoffs(&new_cutoff, &evalue_hsp, kbp, searchsp, in BlastHitSavingParametersUpdate()
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| H A D | blast_stat.h | 487 double BLAST_KarlinStoE_simple (Int4 S, Blast_KarlinBlk* kbp, Int8 searchsp);
578 Int8 searchsp, Boolean dodecay, double gap_decay_rate);
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| H A D | blast_stat.c | 4025 Int8 searchsp) /* size of search space */ in BlastKarlinEtoS_simple() argument
4044 S = (Int4) (ceil( log((double)(K * searchsp / E)) / Lambda )); in BlastKarlinEtoS_simple()
4076 Int8 searchsp, /* size of search space. */ in BLAST_Cutoffs() argument
4103 es = BlastKarlinEtoS_simple(e, kbp, searchsp); in BLAST_Cutoffs()
4119 e = BLAST_KarlinStoE_simple(s, kbp, searchsp); in BLAST_Cutoffs()
4142 Int8 searchsp) /* size of search space. */ in BLAST_KarlinStoE_simple() argument
4153 return (double) searchsp * exp((double)(-Lambda * S) + kbp->logK); in BLAST_KarlinStoE_simple()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/core/ |
| H A D | blast_parameters.c | 913 Int8 searchsp; in BlastHitSavingParametersUpdate() local
924 searchsp = query_info->contexts[context].eff_searchsp; in BlastHitSavingParametersUpdate()
929 searchsp /= NUM_FRAMES; in BlastHitSavingParametersUpdate()
941 BLAST_Cutoffs(&new_cutoff, &evalue, kbp, searchsp, FALSE, 0); in BlastHitSavingParametersUpdate()
956 Int8 searchsp = (Int8)MIN(avg_qlen, avg_subject_length) * in BlastHitSavingParametersUpdate() local
970 BLAST_Cutoffs(&new_cutoff, &evalue_hsp, kbp, searchsp, in BlastHitSavingParametersUpdate()
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| H A D | blast_stat.c | 4025 Int8 searchsp) /* size of search space */ in BlastKarlinEtoS_simple() argument
4044 S = (Int4) (ceil( log((double)(K * searchsp / E)) / Lambda )); in BlastKarlinEtoS_simple()
4076 Int8 searchsp, /* size of search space. */ in BLAST_Cutoffs() argument
4103 es = BlastKarlinEtoS_simple(e, kbp, searchsp); in BLAST_Cutoffs()
4119 e = BLAST_KarlinStoE_simple(s, kbp, searchsp); in BLAST_Cutoffs()
4142 Int8 searchsp) /* size of search space. */ in BLAST_KarlinStoE_simple() argument
4153 return (double) searchsp * exp((double)(-Lambda * S) + kbp->logK); in BLAST_KarlinStoE_simple()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/core/ |
| H A D | blast_parameters.c | 913 Int8 searchsp; in BlastHitSavingParametersUpdate() local
924 searchsp = query_info->contexts[context].eff_searchsp; in BlastHitSavingParametersUpdate()
929 searchsp /= NUM_FRAMES; in BlastHitSavingParametersUpdate()
941 BLAST_Cutoffs(&new_cutoff, &evalue, kbp, searchsp, FALSE, 0); in BlastHitSavingParametersUpdate()
956 Int8 searchsp = (Int8)MIN(avg_qlen, avg_subject_length) * in BlastHitSavingParametersUpdate() local
970 BLAST_Cutoffs(&new_cutoff, &evalue_hsp, kbp, searchsp, in BlastHitSavingParametersUpdate()
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| H A D | blast_stat.c | 4025 Int8 searchsp) /* size of search space */ in BlastKarlinEtoS_simple() argument
4044 S = (Int4) (ceil( log((double)(K * searchsp / E)) / Lambda )); in BlastKarlinEtoS_simple()
4076 Int8 searchsp, /* size of search space. */ in BLAST_Cutoffs() argument
4103 es = BlastKarlinEtoS_simple(e, kbp, searchsp); in BLAST_Cutoffs()
4119 e = BLAST_KarlinStoE_simple(s, kbp, searchsp); in BLAST_Cutoffs()
4142 Int8 searchsp) /* size of search space. */ in BLAST_KarlinStoE_simple() argument
4153 return (double) searchsp * exp((double)(-Lambda * S) + kbp->logK); in BLAST_KarlinStoE_simple()
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| /dports/biology/diamond/diamond-2.0.13/src/lib/blast/ |
| H A D | blast_stat.h | 458 double BLAST_KarlinStoE_simple (Int4 S, Blast_KarlinBlk* kbp, Int8 searchsp);
549 Int8 searchsp, bool dodecay, double gap_decay_rate);
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/algo/blast/core/ |
| H A D | blast_stat.h | 487 double BLAST_KarlinStoE_simple (Int4 S, Blast_KarlinBlk* kbp, Int8 searchsp);
578 Int8 searchsp, Boolean dodecay, double gap_decay_rate);
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/core/ |
| H A D | blast_stat.h | 487 double BLAST_KarlinStoE_simple (Int4 S, Blast_KarlinBlk* kbp, Int8 searchsp);
578 Int8 searchsp, Boolean dodecay, double gap_decay_rate);
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| /dports/emulators/mess/mame-mame0226/src/mame/machine/ |
| H A D | fddebug.cpp | 243 static int searchsp;
1058 if (searchsp == 0 || searchstack[searchsp-1] != pc)
1062 searchsp = 0;
1069 searchsp--;
1081 while ((keystatus[pc/2] & SEARCH_MASK) != 0 && searchsp > 0)
1082 pc = searchstack[--searchsp];
1130 searchstack[searchsp++] = targetpc;
1152 searchstack[searchsp++] = targetpc;
1166 searchstack[searchsp++] = pc;
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| /dports/emulators/mame/mame-mame0226/src/mame/machine/ |
| H A D | fddebug.cpp | 243 static int searchsp;
1058 if (searchsp == 0 || searchstack[searchsp-1] != pc)
1062 searchsp = 0;
1069 searchsp--;
1081 while ((keystatus[pc/2] & SEARCH_MASK) != 0 && searchsp > 0)
1082 pc = searchstack[--searchsp];
1130 searchstack[searchsp++] = targetpc;
1152 searchstack[searchsp++] = targetpc;
1166 searchstack[searchsp++] = pc;
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| /dports/biology/ncbi-toolkit/ncbi/demo/ |
| H A D | rpsblast.c | 511 Int8 searchsp = (Int8) myargs[OPT_SEARCHSP].floatvalue; in s_FillOptions() local
514 dblength, &searchsp, 1); in s_FillOptions()
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| H A D | blast_driver.c | 350 Int8 searchsp = (Int8) myargs[ARG_SEARCHSP].floatvalue; in s_FillOptions() local
351 BLAST_FillEffectiveLengthsOptions(eff_len_options, 0, 0, &searchsp, 1); in s_FillOptions()
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| H A D | megablast.c | 1980 Int8 searchsp = (Int8)myargs[ARG_SEARCHSP].floatvalue; in BLAST_FillOptions() local
1982 BLAST_FillEffectiveLengthsOptions(eff_len_options, 0, dbsize, &searchsp, 1); in BLAST_FillOptions()
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| /dports/biology/ncbi-toolkit/ncbi/algo/blast/composition_adjustment/ |
| H A D | redo_alignment.c | 944 s_EvalueFromScore(int score, double Lambda, double logK, double searchsp) in s_EvalueFromScore() argument
946 return searchsp * exp(-(Lambda * score) + logK); in s_EvalueFromScore()
1368 double searchsp; /* effective search space */ in Blast_RedoOneMatchSmithWaterman() local
1406 searchsp = query_info[query_index].eff_search_space; in Blast_RedoOneMatchSmithWaterman()
1462 s_EvalueFromScore(aSwScore, Lambda, logK, searchsp); in Blast_RedoOneMatchSmithWaterman()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/composition_adjustment/ |
| H A D | redo_alignment.c | 944 s_EvalueFromScore(int score, double Lambda, double logK, double searchsp) in s_EvalueFromScore() argument
946 return searchsp * exp(-(Lambda * score) + logK); in s_EvalueFromScore()
1368 double searchsp; /* effective search space */ in Blast_RedoOneMatchSmithWaterman() local
1406 searchsp = query_info[query_index].eff_search_space; in Blast_RedoOneMatchSmithWaterman()
1462 s_EvalueFromScore(aSwScore, Lambda, logK, searchsp); in Blast_RedoOneMatchSmithWaterman()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/composition_adjustment/ |
| H A D | redo_alignment.c | 944 s_EvalueFromScore(int score, double Lambda, double logK, double searchsp) in s_EvalueFromScore() argument
946 return searchsp * exp(-(Lambda * score) + logK); in s_EvalueFromScore()
1368 double searchsp; /* effective search space */ in Blast_RedoOneMatchSmithWaterman() local
1406 searchsp = query_info[query_index].eff_search_space; in Blast_RedoOneMatchSmithWaterman()
1462 s_EvalueFromScore(aSwScore, Lambda, logK, searchsp); in Blast_RedoOneMatchSmithWaterman()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/api/ |
| H A D | blastoptions_unit_test.cpp | 283 s_FillSearchSpace(BlastQueryInfo *query_info, Int8 searchsp) in s_FillSearchSpace() argument
288 query_info->contexts[i].eff_searchsp = searchsp; in s_FillSearchSpace()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/api/ |
| H A D | blastoptions_unit_test.cpp | 283 s_FillSearchSpace(BlastQueryInfo *query_info, Int8 searchsp) in s_FillSearchSpace() argument
288 query_info->contexts[i].eff_searchsp = searchsp; in s_FillSearchSpace()
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