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/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/Matrix/IO/
H A Dmlagan.pm105 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");
/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()
800 scoring_options->gap_open, in BLAST_CalcEffLengths()
808 scoring_options->gap_open, in BLAST_CalcEffLengths()
[all …]
H A Dblast_sw.c59 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 …]
H A Dblast_stat.h377 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,
/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()
800 scoring_options->gap_open, in BLAST_CalcEffLengths()
808 scoring_options->gap_open, in BLAST_CalcEffLengths()
[all …]
H A Dblast_sw.c59 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 …]
/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()
800 scoring_options->gap_open, in BLAST_CalcEffLengths()
808 scoring_options->gap_open, in BLAST_CalcEffLengths()
[all …]
H A Dblast_sw.c59 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 …]
/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()
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 …]
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/api/
H A Dscoreblk_unit_test.cpp189 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 …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/api/
H A Dscoreblk_unit_test.cpp189 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 …]
/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
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 …]
/dports/biology/samtools/samtools-1.14/misc/
H A Dpsl2sam.pl60 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 * $gap_ext;
/dports/biology/seqan1/seqan-1.3.1/lib/samtools/misc/
H A Dpsl2sam.pl40 my ($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;
/dports/biology/diamond/diamond-2.0.13/src/lib/blast/
H A Dblast_stat.h351 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,
/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/Matrix/
H A DMlagan.pm121 sub gap_open { subroutine
123 if (@_) { $self->{gap_open} = shift }
124 return $self->{gap_open} || return;
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/algo/blast/core/
H A Dblast_stat.h377 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,
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/core/
H A Dblast_stat.h377 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,
/dports/biology/wise/wise2.4.1/src/models/
H A Dcdnawise10.h25 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…
H A Dlargeblockdp.h25 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);
/dports/biology/diamond/diamond-2.0.13/src/output/daa/
H A Ddaa_file.h60 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()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/api/
H A Drps_aux.cpp71 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()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/api/
H A Drps_aux.cpp71 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()
/dports/biology/exonerate/exonerate-2.4.0/src/model/
H A Daffine.c26 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()
/dports/biology/mmseqs2/MMseqs2-13-45111/src/alignment/
H A DStripedSmithWaterman.h135 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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