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Searched refs:gap_extend (Results 1 – 25 of 208) sorted by relevance

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/dports/biology/ncbi-toolkit/ncbi/algo/blast/core/
H A Dblast_setup.c65 scoring_options->gap_open, scoring_options->gap_extend, in Blast_ScoreBlkKbpGappedCalc()
94 scoring_options->gap_open, scoring_options->gap_extend, in Blast_ScoreBlkKbpGappedCalc()
167 if ((11 == options->gap_open) && (1 == options->gap_extend)) { in s_PHIScoreBlkFill()
190 if ((9 == options->gap_open) && (1 == options->gap_extend)) { in s_PHIScoreBlkFill()
213 if ((10 == options->gap_open) && (1 == options->gap_extend)) { in s_PHIScoreBlkFill()
236 if ((10 == options->gap_open) && (1 == options->gap_extend)) { in s_PHIScoreBlkFill()
259 if ((14 == options->gap_open) && (2 == options->gap_extend)) { in s_PHIScoreBlkFill()
305 options->gap_open, options->gap_extend, options->matrix); in s_PHIScoreBlkFill()
801 scoring_options->gap_extend, in BLAST_CalcEffLengths()
809 scoring_options->gap_extend, in BLAST_CalcEffLengths()
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H A Dblast_sw.c73 Int4 gap_open_extend = gap_open + gap_extend; in s_SmithWatermanScoreOnly()
124 best_score = insert_score - gap_extend; in s_SmithWatermanScoreOnly()
179 Int4 gap_open_extend = gap_open + gap_extend; in s_NuclSmithWaterman()
216 best_score = insert_score - gap_extend; in s_NuclSmithWaterman()
341 curr_score -= gap_extend; in s_GetTraceback()
350 curr_score -= gap_extend; in s_GetTraceback()
442 Int4 gap_extend = score_params->gap_extend; in SmithWatermanScoreWithTraceback() local
443 Int4 gap_open_extend = gap_open + gap_extend; in SmithWatermanScoreWithTraceback()
502 best_score = insert_score - gap_extend; in SmithWatermanScoreWithTraceback()
596 gap_open, gap_extend, in SmithWatermanScoreWithTraceback()
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H A Dblast_gapalign.c189 gap_extend = 2*score_params->gap_extend; in s_BlastGreedyAlignMemAlloc()
197 gap_extend = score_params->gap_extend; in s_BlastGreedyAlignMemAlloc()
377 Int4 gap_extend; in ALIGN_EX() local
408 gap_extend = score_params->gap_extend; in ALIGN_EX()
735 Int4 gap_extend; in Blast_SemiGappedAlign() local
765 gap_extend = score_params->gap_extend; in Blast_SemiGappedAlign()
992 Int4 gap_extend; in s_RestrictedGappedAlign() local
1014 gap_extend = score_params->gap_extend; in s_RestrictedGappedAlign()
1368 gap_extend = score_params->gap_extend; in s_OutOfFrameAlignWithTraceback()
1984 gap_extend = score_params->gap_extend; in s_OutOfFrameGappedAlign()
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H A Dgreedy_align.c205 Int4 gap_open_extend = gap_open + gap_extend; in s_GetNextAffineTbackFromIndel()
225 last_d = (*d) - gap_extend; in s_GetNextAffineTbackFromIndel()
256 *d -= gap_extend; in s_GetNextAffineTbackFromIndel()
781 Int4 gap_extend; in BLAST_AffineGreedyAlign() local
837 gap_extend = in_gap_extend + match_score_half; in BLAST_AffineGreedyAlign()
839 gap_open_extend = gap_open + gap_extend; in BLAST_AffineGreedyAlign()
846 scaled_max_dist = max_dist * gap_extend; in BLAST_AffineGreedyAlign()
1001 if (k + 1 <= diag_upper[d - gap_extend] && in BLAST_AffineGreedyAlign()
1002 k + 1 >= diag_lower[d - gap_extend] && in BLAST_AffineGreedyAlign()
1023 if (k - 1 <= diag_upper[d - gap_extend] && in BLAST_AffineGreedyAlign()
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H A Dblast_stat.h378 Int4 gap_extend, const char* matrix_name, Blast_Message** error_return);
398 Int4 gap_extend, Int4 reward, Int4 penalty,
427 Int2 Blast_KarlinBlkGappedLoadFromTables(Blast_KarlinBlk* kbp, Int4 gap_open, Int4 gap_extend, cons…
439 Int4 gap_extend, const char* matrix_name, Blast_Message** error_return);
453 Int4 gap_extend, const char* matrix_name);
472 char* BLAST_PrintAllowedValues(const char *matrix, Int4 gap_open, Int4 gap_extend);
695 Int4 gap_extend, const Blast_KarlinBlk* kbp_ungapped);
713 Int4 gap_extend, Blast_KarlinBlk* kbp,
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/core/
H A Dblast_setup.c65 scoring_options->gap_open, scoring_options->gap_extend, in Blast_ScoreBlkKbpGappedCalc()
94 scoring_options->gap_open, scoring_options->gap_extend, in Blast_ScoreBlkKbpGappedCalc()
167 if ((11 == options->gap_open) && (1 == options->gap_extend)) { in s_PHIScoreBlkFill()
190 if ((9 == options->gap_open) && (1 == options->gap_extend)) { in s_PHIScoreBlkFill()
213 if ((10 == options->gap_open) && (1 == options->gap_extend)) { in s_PHIScoreBlkFill()
236 if ((10 == options->gap_open) && (1 == options->gap_extend)) { in s_PHIScoreBlkFill()
259 if ((14 == options->gap_open) && (2 == options->gap_extend)) { in s_PHIScoreBlkFill()
305 options->gap_open, options->gap_extend, options->matrix); in s_PHIScoreBlkFill()
801 scoring_options->gap_extend, in BLAST_CalcEffLengths()
809 scoring_options->gap_extend, in BLAST_CalcEffLengths()
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H A Dblast_sw.c73 Int4 gap_open_extend = gap_open + gap_extend; in s_SmithWatermanScoreOnly()
124 best_score = insert_score - gap_extend; in s_SmithWatermanScoreOnly()
179 Int4 gap_open_extend = gap_open + gap_extend; in s_NuclSmithWaterman()
216 best_score = insert_score - gap_extend; in s_NuclSmithWaterman()
341 curr_score -= gap_extend; in s_GetTraceback()
350 curr_score -= gap_extend; in s_GetTraceback()
442 Int4 gap_extend = score_params->gap_extend; in SmithWatermanScoreWithTraceback() local
443 Int4 gap_open_extend = gap_open + gap_extend; in SmithWatermanScoreWithTraceback()
502 best_score = insert_score - gap_extend; in SmithWatermanScoreWithTraceback()
596 gap_open, gap_extend, in SmithWatermanScoreWithTraceback()
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H A Dblast_gapalign.c190 gap_extend = 2*score_params->gap_extend; in s_BlastGreedyAlignMemAlloc()
198 gap_extend = score_params->gap_extend; in s_BlastGreedyAlignMemAlloc()
385 Int4 gap_extend; in ALIGN_EX() local
416 gap_extend = score_params->gap_extend; in ALIGN_EX()
743 Int4 gap_extend; in Blast_SemiGappedAlign() local
773 gap_extend = score_params->gap_extend; in Blast_SemiGappedAlign()
1000 Int4 gap_extend; in s_RestrictedGappedAlign() local
1022 gap_extend = score_params->gap_extend; in s_RestrictedGappedAlign()
1376 gap_extend = score_params->gap_extend; in s_OutOfFrameAlignWithTraceback()
1992 gap_extend = score_params->gap_extend; in s_OutOfFrameGappedAlign()
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H A Dgreedy_align.c205 Int4 gap_open_extend = gap_open + gap_extend; in s_GetNextAffineTbackFromIndel()
225 last_d = (*d) - gap_extend; in s_GetNextAffineTbackFromIndel()
256 *d -= gap_extend; in s_GetNextAffineTbackFromIndel()
784 Int4 gap_extend; in BLAST_AffineGreedyAlign() local
840 gap_extend = in_gap_extend + match_score_half; in BLAST_AffineGreedyAlign()
842 gap_open_extend = gap_open + gap_extend; in BLAST_AffineGreedyAlign()
849 scaled_max_dist = max_dist * gap_extend; in BLAST_AffineGreedyAlign()
1009 if (k + 1 <= diag_upper[d - gap_extend] && in BLAST_AffineGreedyAlign()
1010 k + 1 >= diag_lower[d - gap_extend] && in BLAST_AffineGreedyAlign()
1031 if (k - 1 <= diag_upper[d - gap_extend] && in BLAST_AffineGreedyAlign()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/core/
H A Dblast_setup.c65 scoring_options->gap_open, scoring_options->gap_extend, in Blast_ScoreBlkKbpGappedCalc()
94 scoring_options->gap_open, scoring_options->gap_extend, in Blast_ScoreBlkKbpGappedCalc()
167 if ((11 == options->gap_open) && (1 == options->gap_extend)) { in s_PHIScoreBlkFill()
190 if ((9 == options->gap_open) && (1 == options->gap_extend)) { in s_PHIScoreBlkFill()
213 if ((10 == options->gap_open) && (1 == options->gap_extend)) { in s_PHIScoreBlkFill()
236 if ((10 == options->gap_open) && (1 == options->gap_extend)) { in s_PHIScoreBlkFill()
259 if ((14 == options->gap_open) && (2 == options->gap_extend)) { in s_PHIScoreBlkFill()
305 options->gap_open, options->gap_extend, options->matrix); in s_PHIScoreBlkFill()
801 scoring_options->gap_extend, in BLAST_CalcEffLengths()
809 scoring_options->gap_extend, in BLAST_CalcEffLengths()
[all …]
H A Dblast_sw.c73 Int4 gap_open_extend = gap_open + gap_extend; in s_SmithWatermanScoreOnly()
124 best_score = insert_score - gap_extend; in s_SmithWatermanScoreOnly()
179 Int4 gap_open_extend = gap_open + gap_extend; in s_NuclSmithWaterman()
216 best_score = insert_score - gap_extend; in s_NuclSmithWaterman()
341 curr_score -= gap_extend; in s_GetTraceback()
350 curr_score -= gap_extend; in s_GetTraceback()
442 Int4 gap_extend = score_params->gap_extend; in SmithWatermanScoreWithTraceback() local
443 Int4 gap_open_extend = gap_open + gap_extend; in SmithWatermanScoreWithTraceback()
502 best_score = insert_score - gap_extend; in SmithWatermanScoreWithTraceback()
596 gap_open, gap_extend, in SmithWatermanScoreWithTraceback()
[all …]
H A Dblast_gapalign.c190 gap_extend = 2*score_params->gap_extend; in s_BlastGreedyAlignMemAlloc()
198 gap_extend = score_params->gap_extend; in s_BlastGreedyAlignMemAlloc()
385 Int4 gap_extend; in ALIGN_EX() local
416 gap_extend = score_params->gap_extend; in ALIGN_EX()
743 Int4 gap_extend; in Blast_SemiGappedAlign() local
773 gap_extend = score_params->gap_extend; in Blast_SemiGappedAlign()
1000 Int4 gap_extend; in s_RestrictedGappedAlign() local
1022 gap_extend = score_params->gap_extend; in s_RestrictedGappedAlign()
1376 gap_extend = score_params->gap_extend; in s_OutOfFrameAlignWithTraceback()
1992 gap_extend = score_params->gap_extend; in s_OutOfFrameGappedAlign()
[all …]
H A Dgreedy_align.c205 Int4 gap_open_extend = gap_open + gap_extend; in s_GetNextAffineTbackFromIndel()
225 last_d = (*d) - gap_extend; in s_GetNextAffineTbackFromIndel()
256 *d -= gap_extend; in s_GetNextAffineTbackFromIndel()
784 Int4 gap_extend; in BLAST_AffineGreedyAlign() local
840 gap_extend = in_gap_extend + match_score_half; in BLAST_AffineGreedyAlign()
842 gap_open_extend = gap_open + gap_extend; in BLAST_AffineGreedyAlign()
849 scaled_max_dist = max_dist * gap_extend; in BLAST_AffineGreedyAlign()
1009 if (k + 1 <= diag_upper[d - gap_extend] && in BLAST_AffineGreedyAlign()
1010 k + 1 >= diag_lower[d - gap_extend] && in BLAST_AffineGreedyAlign()
1031 if (k - 1 <= diag_upper[d - gap_extend] && in BLAST_AffineGreedyAlign()
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/dports/biology/ncbi-toolkit/ncbi/algo/blast/api/
H A Dblast_options_api.c212 Int4 gap_open, Int4 gap_extend) in SBlastOptionsSetMatrixAndGapCosts() argument
224 FALSE, -1, -1, matrix_name, gap_open, gap_extend); in SBlastOptionsSetMatrixAndGapCosts()
228 if (gap_open < 0 || gap_extend < 0) in SBlastOptionsSetMatrixAndGapCosts()
236 if (gap_extend < 0) in SBlastOptionsSetMatrixAndGapCosts()
237 gap_extend = gap_extend_priv; in SBlastOptionsSetMatrixAndGapCosts()
241 options->score_options->gap_extend = gap_extend; in SBlastOptionsSetMatrixAndGapCosts()
248 Int4 gap_open, Int4 gap_extend, in SBlastOptionsSetRewardPenaltyAndGapCosts() argument
265 if (gap_open < 0 || gap_extend < 0) in SBlastOptionsSetRewardPenaltyAndGapCosts()
287 if (gap_extend < 0) in SBlastOptionsSetRewardPenaltyAndGapCosts()
288 gap_extend = gap_extend_priv; in SBlastOptionsSetRewardPenaltyAndGapCosts()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/api/
H A Dscoreblk_unit_test.cpp190 scoring_opts->gap_extend = kGapExtend; in BOOST_AUTO_TEST_CASE()
371 score_opts->gap_extend = 1; in BOOST_AUTO_TEST_CASE()
382 score_opts->gap_extend, score_opts->reward, in BOOST_AUTO_TEST_CASE()
405 score_opts->gap_extend = 2; in BOOST_AUTO_TEST_CASE()
409 score_opts->gap_extend, score_opts->reward, in BOOST_AUTO_TEST_CASE()
431 score_opts->gap_extend = 10; in BOOST_AUTO_TEST_CASE()
435 score_opts->gap_extend, score_opts->reward, in BOOST_AUTO_TEST_CASE()
450 score_opts->gap_extend = 2; in BOOST_AUTO_TEST_CASE()
454 score_opts->gap_extend, score_opts->reward, in BOOST_AUTO_TEST_CASE()
469 score_opts->gap_extend = 2; in BOOST_AUTO_TEST_CASE()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/api/
H A Dscoreblk_unit_test.cpp190 scoring_opts->gap_extend = kGapExtend; in BOOST_AUTO_TEST_CASE()
371 score_opts->gap_extend = 1; in BOOST_AUTO_TEST_CASE()
382 score_opts->gap_extend, score_opts->reward, in BOOST_AUTO_TEST_CASE()
405 score_opts->gap_extend = 2; in BOOST_AUTO_TEST_CASE()
409 score_opts->gap_extend, score_opts->reward, in BOOST_AUTO_TEST_CASE()
431 score_opts->gap_extend = 10; in BOOST_AUTO_TEST_CASE()
435 score_opts->gap_extend, score_opts->reward, in BOOST_AUTO_TEST_CASE()
450 score_opts->gap_extend = 2; in BOOST_AUTO_TEST_CASE()
454 score_opts->gap_extend, score_opts->reward, in BOOST_AUTO_TEST_CASE()
469 score_opts->gap_extend = 2; in BOOST_AUTO_TEST_CASE()
[all …]
/dports/biology/py-bx-python/bx-python-0.8.13/lib/bx/align/
H A Dscore.py16 …def __init__(self, gap_open, gap_extend, default=-100, alphabet1="ACGT", alphabet2=None, gap1="-",… argument
30 self.gap_extend = gap_extend
125 def read_scoring_scheme(f, gap_open, gap_extend, gap1="-", gap2=None, **kwargs): argument
134 …ss = build_scoring_scheme("".join([line for line in f]), gap_open, gap_extend, gap1=gap1, gap2=gap…
140 def build_scoring_scheme(s, gap_open, gap_extend, gap1="-", gap2=None, **kwargs): argument
218 if isinstance(gap_extend, float):
220 …ss = ScoringScheme(gap_open, gap_extend, alphabet1=alphabet1, alphabet2=alphabet2, gap1=gap1, gap2…
274 rval -= scoring_scheme.gap_extend
281 rval -= scoring_scheme.gap_extend
316 score -= scoring_scheme.gap_extend
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/dports/biology/diamond/diamond-2.0.13/src/lib/blast/
H A Dblast_stat.h352 Int4 gap_extend, const char* matrix_name, Blast_Message** error_return);
372 Int4 gap_extend, Int4 reward, Int4 penalty,
400 Int2 Blast_KarlinBlkGappedLoadFromTables(Blast_KarlinBlk* kbp, Int4 gap_open, Int4 gap_extend, cons…
412 Int4 gap_extend, const char* matrix_name, Blast_Message** error_return);
426 Int4 gap_extend, const char* matrix_name);
443 char* BLAST_PrintAllowedValues(const char *matrix, Int4 gap_open, Int4 gap_extend);
666 Int4 gap_extend, const Blast_KarlinBlk* kbp_ungapped);
684 Int4 gap_extend, Blast_KarlinBlk* kbp,
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/algo/blast/core/
H A Dblast_stat.h378 Int4 gap_extend, const char* matrix_name, Blast_Message** error_return);
398 Int4 gap_extend, Int4 reward, Int4 penalty,
427 Int2 Blast_KarlinBlkGappedLoadFromTables(Blast_KarlinBlk* kbp, Int4 gap_open, Int4 gap_extend, cons…
439 Int4 gap_extend, const char* matrix_name, Blast_Message** error_return);
453 Int4 gap_extend, const char* matrix_name);
472 char* BLAST_PrintAllowedValues(const char *matrix, Int4 gap_open, Int4 gap_extend);
695 Int4 gap_extend, const Blast_KarlinBlk* kbp_ungapped);
713 Int4 gap_extend, Blast_KarlinBlk* kbp,
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/core/
H A Dblast_stat.h378 Int4 gap_extend, const char* matrix_name, Blast_Message** error_return);
398 Int4 gap_extend, Int4 reward, Int4 penalty,
427 Int2 Blast_KarlinBlkGappedLoadFromTables(Blast_KarlinBlk* kbp, Int4 gap_open, Int4 gap_extend, cons…
439 Int4 gap_extend, const char* matrix_name, Blast_Message** error_return);
453 Int4 gap_extend, const char* matrix_name);
472 char* BLAST_PrintAllowedValues(const char *matrix, Int4 gap_open, Int4 gap_extend);
695 Int4 gap_extend, const Blast_KarlinBlk* kbp_ungapped);
713 Int4 gap_extend, Blast_KarlinBlk* kbp,
/dports/biology/wise/wise2.4.1/src/external/mott/
H A Dmott_api.c9 int gap_extend=0; variable
55 gap_extend = Gap_extend; in InitPvaluesMott()
59 …t_alpha = 2*default_s*exp(-default_lambda0*(gap_init+gap_extend))/(1-exp(-default_lambda0*gap_exte… in InitPvaluesMott()
93 alpha = 2*s*exp(-lambda0*(gap_init+gap_extend))/(1-exp(-lambda0*gap_extend)); in SW_PValueMott()
/dports/biology/diamond/diamond-2.0.13/src/stats/
H A Dstats.cpp42 const StandardMatrix::Parameters& StandardMatrix::constants(int gap_exist, int gap_extend) const { in constants()
43 const double g = gap_exist, e = gap_extend; in constants()
45 if (i.gap_exist == g && i.gap_extend == e) in constants()
/dports/biology/diamond/diamond-2.0.13/src/output/daa/
H A Ddaa_file.h61 int32_t gap_extend, in DAA_header2()
77 gap_extend (gap_extend), in DAA_header2()
95 int32_t mode, gap_open, gap_extend, reward, penalty, reserved1, reserved2, reserved3; member
159 { return h2_.gap_extend; } in gap_extension_penalty()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/api/
H A Drps_aux.cpp72 int gap_extend,
97 int gap_extend, in CBlastRPSAuxInfo() argument
110 m_Data->gap_extend_penalty = gap_extend; in CBlastRPSAuxInfo()
200 int gap_extend; in x_ReadFromFile() local
209 input >> gap_extend; in x_ReadFromFile()
225 gap_extend, in x_ReadFromFile()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/api/
H A Drps_aux.cpp72 int gap_extend,
97 int gap_extend, in CBlastRPSAuxInfo() argument
110 m_Data->gap_extend_penalty = gap_extend; in CBlastRPSAuxInfo()
200 int gap_extend; in x_ReadFromFile() local
209 input >> gap_extend; in x_ReadFromFile()
225 gap_extend, in x_ReadFromFile()

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