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Searched refs:gap_prob (Results 1 – 16 of 16) sorted by relevance

/dports/biology/ncbi-toolkit/ncbi/algo/blast/core/
H A Dblast_parameters.c605 params->gap_prob = BLAST_GAP_PROB; in BlastLinkHSPParametersNew()
608 params->gap_prob = BLAST_GAP_PROB_GAPPED; in BlastLinkHSPParametersNew()
998 double gap_prob, gap_decay_rate, x_variable, y_variable; in CalculateLinkHSPCutoffs() local
1010 gap_prob = link_hsp_params->gap_prob = BLAST_GAP_PROB; in CalculateLinkHSPCutoffs()
1054 x_variable /= (1.0 - gap_prob + kEpsilon); in CalculateLinkHSPCutoffs()
1058 x_variable /= (gap_prob + kEpsilon); in CalculateLinkHSPCutoffs()
1067 link_hsp_params->gap_prob = 0; in CalculateLinkHSPCutoffs()
H A Dlink_hsps.c427 double gap_decay_rate, gap_prob, prob[2]; in s_BlastEvenGapLinkHSPs() local
468 gap_prob = link_hsp_params->gap_prob; in s_BlastEvenGapLinkHSPs()
919 if( gap_prob == 0 || (prob[0] /= gap_prob) > INT4_MAX ) { in s_BlastEvenGapLinkHSPs()
932 if( 1 - gap_prob == 0 || (prob[1] /= 1 - gap_prob) > INT4_MAX ) { in s_BlastEvenGapLinkHSPs()
H A Dblast_parameters.h138 double gap_prob; /**< Probability of decay for linking HSPs */ member
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/core/
H A Dblast_parameters.c609 params->gap_prob = BLAST_GAP_PROB; in BlastLinkHSPParametersNew()
612 params->gap_prob = BLAST_GAP_PROB_GAPPED; in BlastLinkHSPParametersNew()
1002 double gap_prob, gap_decay_rate, x_variable, y_variable; in CalculateLinkHSPCutoffs() local
1017 gap_prob = link_hsp_params->gap_prob = BLAST_GAP_PROB; in CalculateLinkHSPCutoffs()
1061 x_variable /= (1.0 - gap_prob + kEpsilon); in CalculateLinkHSPCutoffs()
1065 x_variable /= (gap_prob + kEpsilon); in CalculateLinkHSPCutoffs()
1074 link_hsp_params->gap_prob = 0; in CalculateLinkHSPCutoffs()
H A Dlink_hsps.c427 double gap_decay_rate, gap_prob, prob[2]; in s_BlastEvenGapLinkHSPs() local
468 gap_prob = link_hsp_params->gap_prob; in s_BlastEvenGapLinkHSPs()
919 if( gap_prob == 0 || (prob[0] /= gap_prob) > INT4_MAX ) { in s_BlastEvenGapLinkHSPs()
932 if( 1 - gap_prob == 0 || (prob[1] /= 1 - gap_prob) > INT4_MAX ) { in s_BlastEvenGapLinkHSPs()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/core/
H A Dblast_parameters.c609 params->gap_prob = BLAST_GAP_PROB; in BlastLinkHSPParametersNew()
612 params->gap_prob = BLAST_GAP_PROB_GAPPED; in BlastLinkHSPParametersNew()
1002 double gap_prob, gap_decay_rate, x_variable, y_variable; in CalculateLinkHSPCutoffs() local
1017 gap_prob = link_hsp_params->gap_prob = BLAST_GAP_PROB; in CalculateLinkHSPCutoffs()
1061 x_variable /= (1.0 - gap_prob + kEpsilon); in CalculateLinkHSPCutoffs()
1065 x_variable /= (gap_prob + kEpsilon); in CalculateLinkHSPCutoffs()
1074 link_hsp_params->gap_prob = 0; in CalculateLinkHSPCutoffs()
H A Dlink_hsps.c427 double gap_decay_rate, gap_prob, prob[2]; in s_BlastEvenGapLinkHSPs() local
468 gap_prob = link_hsp_params->gap_prob; in s_BlastEvenGapLinkHSPs()
919 if( gap_prob == 0 || (prob[0] /= gap_prob) > INT4_MAX ) { in s_BlastEvenGapLinkHSPs()
932 if( 1 - gap_prob == 0 || (prob[1] /= 1 - gap_prob) > INT4_MAX ) { in s_BlastEvenGapLinkHSPs()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/algo/blast/core/
H A Dblast_parameters.h138 double gap_prob; /**< Probability of decay for linking HSPs */ member
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/core/
H A Dblast_parameters.h138 double gap_prob; /**< Probability of decay for linking HSPs */ member
/dports/biology/ncbi-toolkit/ncbi/tools/
H A Dblastdef.h1087 gap_prob; /* Prob of decay. */ member
1388 Nlm_FloatHi gap_prob; /* prob. of gap of size "gap" (above).*/ member
H A Dblast.c2847 Nlm_FloatHi gap_prob, gap_decay_rate, x_variable, y_variable; in CalculateSecondCutoffScore() local
2855 gap_prob = search->pbp->gap_prob; in CalculateSecondCutoffScore()
2882 x_variable /= (1.0 - gap_prob + MY_EPS); in CalculateSecondCutoffScore()
2885 x_variable /= (gap_prob + MY_EPS); in CalculateSecondCutoffScore()
5312 search->pbp->gap_prob = options->gap_prob; in BLASTSetUpSearchInternalByLoc()
11268 Nlm_FloatHi gap_decay_rate, gap_prob, prob[2]; in link_hsps() local
11331 gap_prob = search->pbp->gap_prob; in link_hsps()
11771 if( best[0]->hsp_link.num[0] > 1 && gap_prob == 0 ) { in link_hsps()
11800 prob[0] /= gap_prob; in link_hsps()
11808 if( 1 - gap_prob == 0.0 && best[1]->hsp_link.num[1] > 1 ) { in link_hsps()
[all …]
H A Dblastool.c1522 options->gap_prob = 0.5; in BLASTOptionNewEx()
1583 options->gap_prob = 0.5; in BLASTOptionNewEx()
1635 options->gap_prob = 1.0; in BLASTOptionNewEx()
H A Dmblast.c1645 search->pbp->gap_prob = options->gap_prob; in MegaBlastSetUpSearchInternalByLoc()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/api/
H A Dblastoptions_unit_test.cpp650 link_hsp_params->gap_prob = 0.0; in BOOST_AUTO_TEST_CASE()
657 BOOST_CHECK_EQUAL(5, (int) (10*link_hsp_params->gap_prob)); in BOOST_AUTO_TEST_CASE()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/api/
H A Dblastoptions_unit_test.cpp650 link_hsp_params->gap_prob = 0.0; in BOOST_AUTO_TEST_CASE()
657 BOOST_CHECK_EQUAL(5, (int) (10*link_hsp_params->gap_prob)); in BOOST_AUTO_TEST_CASE()
/dports/biology/ncbi-toolkit/ncbi/biostruc/cdd/
H A Dcddposutil.c1814 search->pbp->gap_prob = options->gap_prob; in CddSetUpSearchInternalByLoc()