/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/Matrix/IO/ |
H A D | mlagan.pm | 105 my (@matrix, $gap_open, $gap_cont); 112 ($gap_open, $gap_cont) = split; 120 -gap_open => $gap_open, 139 my $gap_open = $matrix->gap_open; 142 unless (defined $gap_open && defined $gap_continue) { 158 $self->_print("\n$gap_open $gap_continue");
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/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() 800 scoring_options->gap_open, in BLAST_CalcEffLengths() 808 scoring_options->gap_open, in BLAST_CalcEffLengths() [all …]
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H A D | blast_sw.c | 59 Int4 gap_open, Int4 gap_extend, in s_SmithWatermanScoreOnly() argument 73 Int4 gap_open_extend = gap_open + gap_extend; in s_SmithWatermanScoreOnly() 179 Int4 gap_open_extend = gap_open + gap_extend; in s_NuclSmithWaterman() 339 curr_score -= gap_open; in s_GetTraceback() 348 curr_score -= gap_open; in s_GetTraceback() 441 Int4 gap_open = score_params->gap_open; in SmithWatermanScoreWithTraceback() local 443 Int4 gap_open_extend = gap_open + gap_extend; in SmithWatermanScoreWithTraceback() 553 gap_open, gap_extend, in SmithWatermanScoreWithTraceback() 596 gap_open, gap_extend, in SmithWatermanScoreWithTraceback() 613 gap_open, gap_extend, in SmithWatermanScoreWithTraceback() [all …]
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H A D | blast_stat.h | 377 Int2 Blast_KarlinBlkGappedCalc (Blast_KarlinBlk* kbp, Int4 gap_open, 397 Blast_KarlinBlkNuclGappedCalc(Blast_KarlinBlk* kbp, Int4 gap_open, 427 Int2 Blast_KarlinBlkGappedLoadFromTables(Blast_KarlinBlk* kbp, Int4 gap_open, Int4 gap_extend, cons… 438 Int2 Blast_GumbelBlkCalc (Blast_GumbelBlk* gbp, Int4 gap_open, 452 Int2 Blast_GumbelBlkLoadFromTables(Blast_GumbelBlk* gbp, Int4 gap_open, 472 char* BLAST_PrintAllowedValues(const char *matrix, Int4 gap_open, Int4 gap_extend); 694 double *beta, Boolean gapped, Int4 gap_open, 712 Int2 Blast_GetNuclAlphaBeta(Int4 reward, Int4 penalty, Int4 gap_open,
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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() 800 scoring_options->gap_open, in BLAST_CalcEffLengths() 808 scoring_options->gap_open, in BLAST_CalcEffLengths() [all …]
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H A D | blast_sw.c | 59 Int4 gap_open, Int4 gap_extend, in s_SmithWatermanScoreOnly() argument 73 Int4 gap_open_extend = gap_open + gap_extend; in s_SmithWatermanScoreOnly() 179 Int4 gap_open_extend = gap_open + gap_extend; in s_NuclSmithWaterman() 339 curr_score -= gap_open; in s_GetTraceback() 348 curr_score -= gap_open; in s_GetTraceback() 441 Int4 gap_open = score_params->gap_open; in SmithWatermanScoreWithTraceback() local 443 Int4 gap_open_extend = gap_open + gap_extend; in SmithWatermanScoreWithTraceback() 553 gap_open, gap_extend, in SmithWatermanScoreWithTraceback() 596 gap_open, gap_extend, in SmithWatermanScoreWithTraceback() 613 gap_open, gap_extend, in SmithWatermanScoreWithTraceback() [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() 800 scoring_options->gap_open, in BLAST_CalcEffLengths() 808 scoring_options->gap_open, in BLAST_CalcEffLengths() [all …]
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H A D | blast_sw.c | 59 Int4 gap_open, Int4 gap_extend, in s_SmithWatermanScoreOnly() argument 73 Int4 gap_open_extend = gap_open + gap_extend; in s_SmithWatermanScoreOnly() 179 Int4 gap_open_extend = gap_open + gap_extend; in s_NuclSmithWaterman() 339 curr_score -= gap_open; in s_GetTraceback() 348 curr_score -= gap_open; in s_GetTraceback() 441 Int4 gap_open = score_params->gap_open; in SmithWatermanScoreWithTraceback() local 443 Int4 gap_open_extend = gap_open + gap_extend; in SmithWatermanScoreWithTraceback() 553 gap_open, gap_extend, in SmithWatermanScoreWithTraceback() 596 gap_open, gap_extend, in SmithWatermanScoreWithTraceback() 613 gap_open, gap_extend, in SmithWatermanScoreWithTraceback() [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() 234 if (gap_open < 0) in SBlastOptionsSetMatrixAndGapCosts() 235 gap_open = gap_open_priv; in SBlastOptionsSetMatrixAndGapCosts() 240 options->score_options->gap_open = gap_open; in SBlastOptionsSetMatrixAndGapCosts() 248 Int4 gap_open, Int4 gap_extend, in SBlastOptionsSetRewardPenaltyAndGapCosts() argument 265 if (gap_open < 0 || gap_extend < 0) in SBlastOptionsSetRewardPenaltyAndGapCosts() 285 if (gap_open < 0) in SBlastOptionsSetRewardPenaltyAndGapCosts() 286 gap_open = gap_open_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 | 189 scoring_opts->gap_open = kGapOpenBad; in BOOST_AUTO_TEST_CASE() 212 scoring_opts->gap_open = kGapOpenGood; in BOOST_AUTO_TEST_CASE() 370 score_opts->gap_open = 3; in BOOST_AUTO_TEST_CASE() 381 Blast_KarlinBlkNuclGappedCalc(kbp, score_opts->gap_open, in BOOST_AUTO_TEST_CASE() 404 score_opts->gap_open = 4; in BOOST_AUTO_TEST_CASE() 408 Blast_KarlinBlkNuclGappedCalc(kbp, score_opts->gap_open, in BOOST_AUTO_TEST_CASE() 430 score_opts->gap_open = 30; in BOOST_AUTO_TEST_CASE() 434 Blast_KarlinBlkNuclGappedCalc(kbp, score_opts->gap_open, in BOOST_AUTO_TEST_CASE() 449 score_opts->gap_open = 4; in BOOST_AUTO_TEST_CASE() 468 score_opts->gap_open = 3; 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 | 189 scoring_opts->gap_open = kGapOpenBad; in BOOST_AUTO_TEST_CASE() 212 scoring_opts->gap_open = kGapOpenGood; in BOOST_AUTO_TEST_CASE() 370 score_opts->gap_open = 3; in BOOST_AUTO_TEST_CASE() 381 Blast_KarlinBlkNuclGappedCalc(kbp, score_opts->gap_open, in BOOST_AUTO_TEST_CASE() 404 score_opts->gap_open = 4; in BOOST_AUTO_TEST_CASE() 408 Blast_KarlinBlkNuclGappedCalc(kbp, score_opts->gap_open, in BOOST_AUTO_TEST_CASE() 430 score_opts->gap_open = 30; in BOOST_AUTO_TEST_CASE() 434 Blast_KarlinBlkNuclGappedCalc(kbp, score_opts->gap_open, in BOOST_AUTO_TEST_CASE() 449 score_opts->gap_open = 4; in BOOST_AUTO_TEST_CASE() 468 score_opts->gap_open = 3; 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 29 self.gap_open = gap_open 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 216 if isinstance(gap_open, float): 220 …ss = ScoringScheme(gap_open, gap_extend, alphabet1=alphabet1, alphabet2=alphabet2, gap1=gap1, gap2… 276 rval -= scoring_scheme.gap_open 283 rval -= scoring_scheme.gap_open 318 score -= scoring_scheme.gap_open [all …]
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/dports/biology/samtools/samtools-1.14/misc/ |
H A D | psl2sam.pl | 60 my ($gap_open, $gap_ext) = (0, 0, 0); 65 ++$gap_open; 71 ++$gap_open; 81 my $score = $a * $t[0] - $b * $t[1] - $q * $gap_open - $r * $gap_ext;
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/dports/biology/seqan1/seqan-1.3.1/lib/samtools/misc/ |
H A D | psl2sam.pl | 40 my ($gap_open, $gap_ext) = (0, 0, 0); 45 ++$gap_open; 51 ++$gap_open; 61 my $score = $a * $t[0] - $b * $t[1] - $q * $gap_open - $r * $gap_ext;
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/dports/biology/diamond/diamond-2.0.13/src/lib/blast/ |
H A D | blast_stat.h | 351 Int2 Blast_KarlinBlkGappedCalc (Blast_KarlinBlk* kbp, Int4 gap_open, 371 Blast_KarlinBlkNuclGappedCalc(Blast_KarlinBlk* kbp, Int4 gap_open, 400 Int2 Blast_KarlinBlkGappedLoadFromTables(Blast_KarlinBlk* kbp, Int4 gap_open, Int4 gap_extend, cons… 411 Int2 Blast_GumbelBlkCalc (Blast_GumbelBlk* gbp, Int4 gap_open, 425 Int2 Blast_GumbelBlkLoadFromTables(Blast_GumbelBlk* gbp, Int4 gap_open, 443 char* BLAST_PrintAllowedValues(const char *matrix, Int4 gap_open, Int4 gap_extend); 665 double *beta, bool gapped, Int4 gap_open, 683 Int2 Blast_GetNuclAlphaBeta(Int4 reward, Int4 penalty, Int4 gap_open,
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/Matrix/ |
H A D | Mlagan.pm | 121 sub gap_open { subroutine 123 if (@_) { $self->{gap_open} = shift } 124 return $self->{gap_open} || return;
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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 | 377 Int2 Blast_KarlinBlkGappedCalc (Blast_KarlinBlk* kbp, Int4 gap_open, 397 Blast_KarlinBlkNuclGappedCalc(Blast_KarlinBlk* kbp, Int4 gap_open, 427 Int2 Blast_KarlinBlkGappedLoadFromTables(Blast_KarlinBlk* kbp, Int4 gap_open, Int4 gap_extend, cons… 438 Int2 Blast_GumbelBlkCalc (Blast_GumbelBlk* gbp, Int4 gap_open, 452 Int2 Blast_GumbelBlkLoadFromTables(Blast_GumbelBlk* gbp, Int4 gap_open, 472 char* BLAST_PrintAllowedValues(const char *matrix, Int4 gap_open, Int4 gap_extend); 694 double *beta, Boolean gapped, Int4 gap_open, 712 Int2 Blast_GetNuclAlphaBeta(Int4 reward, Int4 penalty, Int4 gap_open,
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/core/ |
H A D | blast_stat.h | 377 Int2 Blast_KarlinBlkGappedCalc (Blast_KarlinBlk* kbp, Int4 gap_open, 397 Blast_KarlinBlkNuclGappedCalc(Blast_KarlinBlk* kbp, Int4 gap_open, 427 Int2 Blast_KarlinBlkGappedLoadFromTables(Blast_KarlinBlk* kbp, Int4 gap_open, Int4 gap_extend, cons… 438 Int2 Blast_GumbelBlkCalc (Blast_GumbelBlk* gbp, Int4 gap_open, 452 Int2 Blast_GumbelBlkLoadFromTables(Blast_GumbelBlk* gbp, Int4 gap_open, 472 char* BLAST_PrintAllowedValues(const char *matrix, Int4 gap_open, Int4 gap_extend); 694 double *beta, Boolean gapped, Int4 gap_open, 712 Int2 Blast_GetNuclAlphaBeta(Int4 reward, Int4 penalty, Int4 gap_open,
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/dports/biology/wise/wise2.4.1/src/models/ |
H A D | cdnawise10.h | 25 Score gap_open; member 50 Score gap_open; member 141 …,CodonMatrixScore * sc,RandomCodonScore * rndcodon,DnaMatrix* utr,Score gap_open,Score gap_ext,Sco… 166 …,CodonMatrixScore * sc,RandomCodonScore * rndcodon,DnaMatrix* utr,Score gap_open,Score gap_ext,Sco… 198 …,CodonMatrixScore * sc,RandomCodonScore * rndcodon,DnaMatrix* utr,Score gap_open,Score gap_ext,Sco… 224 …,CodonMatrixScore * sc,RandomCodonScore * rndcodon,DnaMatrix* utr,Score gap_open,Score gap_ext,Sco… 263 …,CodonMatrixScore * sc,RandomCodonScore * rndcodon,DnaMatrix* utr,Score gap_open,Score gap_ext,Sco… 441 …,CodonMatrixScore * sc,RandomCodonScore * rndcodon,DnaMatrix* utr,Score gap_open,Score gap_ext,Sco… 443 …,CodonMatrixScore * sc,RandomCodonScore * rndcodon,DnaMatrix* utr,Score gap_open,Score gap_ext,Sco…
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H A D | largeblockdp.h | 25 Score gap_open; member 113 …ix* dm,Score real_ext,Score block_open,Score un_dual,Score un_single,Score gap_open,Score gap_ext); 137 …ix* dm,Score real_ext,Score block_open,Score un_dual,Score un_single,Score gap_open,Score gap_ext); 168 … dm,Score real_ext,Score block_open,Score un_dual,Score un_single,Score gap_open,Score gap_ext,DPE… 193 … dm,Score real_ext,Score block_open,Score un_dual,Score un_single,Score gap_open,Score gap_ext,DPR… 231 …ix* dm,Score real_ext,Score block_open,Score un_dual,Score un_single,Score gap_open,Score gap_ext); 407 …ix* dm,Score real_ext,Score block_open,Score un_dual,Score un_single,Score gap_open,Score gap_ext); 409 …ix* dm,Score real_ext,Score block_open,Score un_dual,Score un_single,Score gap_open,Score gap_ext);
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/dports/biology/diamond/diamond-2.0.13/src/output/daa/ |
H A D | daa_file.h | 60 int32_t gap_open, in DAA_header2() 76 gap_open (gap_open), in DAA_header2() 95 int32_t mode, gap_open, gap_extend, reward, penalty, reserved1, reserved2, reserved3; member 156 { return h2_.gap_open; } in gap_open_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 | 71 int gap_open, 96 int gap_open, in CBlastRPSAuxInfo() argument 109 m_Data->gap_open_penalty = gap_open; in CBlastRPSAuxInfo() 199 int gap_open; in x_ReadFromFile() local 208 input >> gap_open; in x_ReadFromFile() 224 gap_open, 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 | 71 int gap_open, 96 int gap_open, in CBlastRPSAuxInfo() argument 109 m_Data->gap_open_penalty = gap_open; in CBlastRPSAuxInfo() 199 int gap_open; in x_ReadFromFile() local 208 input >> gap_open; in x_ReadFromFile() 224 gap_open, in x_ReadFromFile()
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/dports/biology/exonerate/exonerate-2.4.0/src/model/ |
H A D | affine.c | 26 Argument_parse_int, &aas.gap_open); in Affine_ArgumentSet_create() 37 if(aas.gap_open > 0) in Affine_ArgumentSet_create() 39 aas.gap_open); in Affine_ArgumentSet_create() 92 return ad->aas->gap_open; in affine_gap_open_calc_func() 211 aas->gap_open, in Affine_create()
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/dports/biology/mmseqs2/MMseqs2-13-45111/src/alignment/ |
H A D | StripedSmithWaterman.h | 135 const uint8_t gap_open, 257 const uint8_t gap_open, /* will be used as - */ 271 const uint8_t gap_open, /* will be used as - */ 278 …int32_t query_length, int32_t queryStart, int32_t score, const uint32_t gap_open, const uint32_t g…
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