/dports/biology/ncbi-toolkit/ncbi/algo/blast/core/ |
H A D | blast_setup.c | 65 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 …]
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H A D | blast_sw.c | 73 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 …]
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H A D | blast_gapalign.c | 189 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() [all …]
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H A D | greedy_align.c | 205 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() [all …]
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H A D | blast_stat.h | 378 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,
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/core/ |
H A D | blast_setup.c | 65 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 …]
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H A D | blast_sw.c | 73 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 …]
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H A D | blast_gapalign.c | 190 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 …]
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H A D | greedy_align.c | 205 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() [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/core/ |
H A D | blast_setup.c | 65 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 …]
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H A D | blast_sw.c | 73 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 …]
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H A D | blast_gapalign.c | 190 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 …]
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H A D | greedy_align.c | 205 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() [all …]
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/dports/biology/ncbi-toolkit/ncbi/algo/blast/api/ |
H A D | blast_options_api.c | 212 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() [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/api/ |
H A D | scoreblk_unit_test.cpp | 190 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 …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/api/ |
H A D | scoreblk_unit_test.cpp | 190 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 …]
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/dports/biology/py-bx-python/bx-python-0.8.13/lib/bx/align/ |
H A D | score.py | 16 …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 [all …]
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/dports/biology/diamond/diamond-2.0.13/src/lib/blast/ |
H A D | blast_stat.h | 352 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,
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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 | 378 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,
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/core/ |
H A D | blast_stat.h | 378 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,
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/dports/biology/wise/wise2.4.1/src/external/mott/ |
H A D | mott_api.c | 9 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()
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/dports/biology/diamond/diamond-2.0.13/src/stats/ |
H A D | stats.cpp | 42 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()
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/dports/biology/diamond/diamond-2.0.13/src/output/daa/ |
H A D | daa_file.h | 61 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()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/api/ |
H A D | rps_aux.cpp | 72 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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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/api/ |
H A D | rps_aux.cpp | 72 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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